A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

A

AboutDialog - Class in edu.jhu.tmaj.client.shared

A Dialog that displays the version number, credits, and copyright information about TMAJ.

ABSTRACT_FIELD - Static variable in class edu.jhu.tmaj.beans.PaperBean

AbstractConnectionFactory - Class in edu.jhu.tmaj.database.conn

Base Class for ConnectionFactories.

AbstractConnectionFactory(DatabaseParameters) - Constructor for class edu.jhu.tmaj.database.conn.AbstractConnectionFactory

AbstractDrawable - Class in edu.jhu.tmaj.client.image.draw

All shapes drawn onto a DrawableLabel extend this class

AbstractDrawable(DrawableLabel) - Constructor for class edu.jhu.tmaj.client.image.draw.AbstractDrawable

AbstractMask - Class in edu.jhu.tmaj.beans.masks

An Abstract Mask where we know the mask name and the mask type.

AbstractMask(String, MaskType) - Constructor for class edu.jhu.tmaj.beans.masks.AbstractMask

AbstractModifySQL - Class in edu.jhu.tmaj.database.sql

The superclass of InsertSQL and updateSQL.

AbstractModifySQL(String) - Constructor for class edu.jhu.tmaj.database.sql.AbstractModifySQL

AbstractSessionsPanel - Class in edu.jhu.tmaj.client.image

A Panel containing a List of sessions.

AbstractSessionsPanel(String) - Constructor for class edu.jhu.tmaj.client.image.AbstractSessionsPanel

AbstractTableCellRenderer - Class in edu.jhu.tmaj.util.swing

A TableCellRenderer that renders images.

AbstractTableCellRenderer() - Constructor for class edu.jhu.tmaj.util.swing.AbstractTableCellRenderer

accept(File) - Method in class edu.jhu.tmaj.util.swing.DefaultFileFilter

Returns true if the File is a directory or ends with the specified extention, otherwise false.

acceptCheckBox - Variable in class edu.jhu.tmaj.client.image.ArrayImageFrame

acceptChoice() - Method in class edu.jhu.tmaj.client.image.ArrayImageFrame

ACCESS_IMAGES_APP_FIELD - Static variable in class edu.jhu.tmaj.beans.UserBean

ACCESS_IMPORT_APP_FIELD - Static variable in class edu.jhu.tmaj.beans.UserBean

ACCESS_SAMPLES_APP_FIELD - Static variable in class edu.jhu.tmaj.beans.UserBean

accessAdminApp() - Method in class edu.jhu.tmaj.beans.UserBean

accessArrayBuilderApplication() - Method in class edu.jhu.tmaj.beans.UserBean

Returns true if the user may access the Array Builder application.

accessArrayManagerApplication() - Method in class edu.jhu.tmaj.beans.UserBean

Returns true if the user may access the ArrayManager application.

accessDetailedPatientData() - Method in class edu.jhu.tmaj.beans.UserBean

Returns true if the user can access detailed patient data like the history number and date of birth.

accessImagesApplication() - Method in class edu.jhu.tmaj.beans.UserBean

Returns true if the user may access the Image Analysis application.

accessImportApplication() - Method in class edu.jhu.tmaj.beans.UserBean

Returns true if the user may access the Import application.

ACCESSION_DATE_FIELD - Static variable in class edu.jhu.tmaj.beans.dynamic.SpecimenBean

accessMetaDataApplication() - Method in class edu.jhu.tmaj.beans.UserBean

Returns true if the user may access the Meta Data application.

accessSamplesApplication() - Method in class edu.jhu.tmaj.beans.UserBean

Returns true if the user may access the Samples application.

accessSpecimensApp() - Method in class edu.jhu.tmaj.beans.UserBean

Returns true if the user may access the Specimenss application.

accessSurgPathNumber() - Method in enum edu.jhu.tmaj.beans.data.PatientDataPermission

accessSurgPathNumber() - Method in class edu.jhu.tmaj.beans.UserBean

AcisImageOutputParser - Class in edu.jhu.tmaj.client.importer.data

Implements an ImageOutputParser for the Chromavision ACIS system

AcisImageOutputParser() - Constructor for class edu.jhu.tmaj.client.importer.data.AcisImageOutputParser

AcisMachineScoresParser - Class in edu.jhu.tmaj.servlet.request.impl

A MachineScoresParser for the Chromavision ACIS machine.

AcisMachineScoresParser() - Constructor for class edu.jhu.tmaj.servlet.request.impl.AcisMachineScoresParser

ActionList<E> - Class in edu.jhu.tmaj.beans.masks.color

Represents a data structure of ACTIONS that the user might want to undo or redo.

ActionList() - Constructor for class edu.jhu.tmaj.beans.masks.color.ActionList

ActionMaskInfo - Class in edu.jhu.tmaj.beans.masks.meta

Represents a Mask Action.

ActionMaskInfo(Mask, boolean, boolean, int) - Constructor for class edu.jhu.tmaj.beans.masks.meta.ActionMaskInfo

actionPerformed(ActionEvent) - Method in class edu.jhu.tmaj.client.admin.AddKeysDialog

actionPerformed(ActionEvent) - Method in class edu.jhu.tmaj.client.arraybuilder.ExpressEntryDialog

actionPerformed(ActionEvent) - Method in class edu.jhu.tmaj.client.image.draw.ShapesFrame

Indicates user has finished drawing current shape by removing it from the ShapeListener

actionPerformed(ActionEvent) - Method in class edu.jhu.tmaj.client.image.ThumbnailsMenuHelper

actionPerformed(ActionEvent) - Method in class edu.jhu.tmaj.client.shared.ButtonClickActionListener

actionPerformed(ActionEvent) - Method in class edu.jhu.tmaj.client.shared.LoginDialog

actionPerformed(ActionEvent) - Method in class edu.jhu.tmaj.client.tables.InputPanel4

activate() - Method in class edu.jhu.tmaj.client.image.draw.ShapesFrame

Adds the shape listeners to the JLabel, enabling user to draw shapes

add(ArrayImageCell, int, int) - Method in class edu.jhu.tmaj.beans.misc.ArrayImageCollectionBean

add(E) - Method in class edu.jhu.tmaj.client.image.data.FastCollection

add(int) - Method in class edu.jhu.tmaj.client.importer.images.data.ArrayImageU

Puts this ArrayImage in the Database, either with an INSERT or UPDATE.

add(Component) - Method in class edu.jhu.tmaj.client.tables.GridBagPanelMaker

add(Component, int, int) - Method in class edu.jhu.tmaj.client.tables.GridBagPanelMaker

ADD_TO_MANAGER - Static variable in class edu.jhu.tmaj.beans.masks.results.ParticleAnalyzer2

Add particles to ROI Manager.

addAction(E) - Method in class edu.jhu.tmaj.beans.masks.color.ActionList

Adds a ACTION (like a selected pixel) to this class.

addActionListener(ActionListener) - Method in class edu.jhu.tmaj.client.image.SpecialTree

addActionMaskInfo(ActionMaskInfo) - Method in class edu.jhu.tmaj.beans.masks.meta.MetaMask

addArrayImageDynamicField(ArrayImageDynamicField) - Method in class edu.jhu.tmaj.beans.dynamic.data.ArrayImageDynamicMetaData

Adds a DynamicField from the ArrayImageFieldNames table.

addBean(JBean) - Method in class edu.jhu.tmaj.beans.ArrayCoreReferenceBean

Add either a SpecimenBean,BlockBean, or TissueDiagnosisBean.

addBoolean(String, Boolean) - Method in class edu.jhu.tmaj.database.sql.AbstractModifySQL

Add/Change the value(s) in columnName to value for a bit column.

addBoolean(String, Boolean) - Method in class edu.jhu.tmaj.database.sql.SQLValues

addButtonPanel(JPanel) - Method in class edu.jhu.tmaj.client.image.AbstractSessionsPanel

addColorMaskInfo(Map<Integer, Mask>, int) - Static method in class edu.jhu.tmaj.beans.masks.color.ColorMaskDatabaseUtil.Reader

addColumn(C) - Method in interface edu.jhu.tmaj.util.file.TableArray

addColumn(C) - Method in class edu.jhu.tmaj.util.file.TableArrayImpl

addColumnValue(String, String) - Method in class edu.jhu.tmaj.client.importer.specimens.data.TranslatedTable

addComponent(JComponent) - Method in class edu.jhu.tmaj.client.tables.InputPanel4

addCondition(String, long) - Method in class edu.jhu.tmaj.database.sql.DeleteSQL

Adds a condition onto which record(s) will be deleted.

addConditionLong(String, long) - Method in class edu.jhu.tmaj.database.sql.UpdateSQL

addConditionString(String, String) - Method in class edu.jhu.tmaj.database.sql.UpdateSQL

addCoordinate(Coordinate, int) - Method in class edu.jhu.tmaj.servlet.response.impl.ArrayImageCoresResponse

addData(String, Destination) - Method in class edu.jhu.tmaj.client.importer.specimens.data.TranslatedRow

addDate(String, Date) - Method in class edu.jhu.tmaj.database.sql.AbstractModifySQL

Add/Change the values in columnName to value for an date/time column.

addDate(String, Date) - Method in class edu.jhu.tmaj.database.sql.SQLValues

addDateTime(String, Date) - Method in class edu.jhu.tmaj.database.sql.AbstractModifySQL

addDateTime(String, Date) - Method in class edu.jhu.tmaj.database.sql.SQLValues

addDefaultValue(DatabaseField, Object) - Method in class edu.jhu.tmaj.client.tables.data.TableData4

Sets the default value to be assigned for a column when the user adds a new row

addDeletedRow(int) - Method in class edu.jhu.tmaj.client.tables.data.ChangedCells

addDisposableFrame(JFrame...) - Method in class edu.jhu.tmaj.client.image.data.SessionGuis

addDisposeRelatedWindowsListener(JFrame, JFrame...) - Static method in class edu.jhu.tmaj.client.image.data.DisposeRelatedWindowsListener

addDouble(String, Double) - Method in class edu.jhu.tmaj.database.sql.AbstractModifySQL

Add/Change the value(s) in columnName to value for a double column.

addDouble(String, Double) - Method in class edu.jhu.tmaj.database.sql.SQLValues

addDynamicEnumeration(DynamicEnumeration) - Method in class edu.jhu.tmaj.beans.dynamic.data.DynamicMetaData

Adds a record from the XXXEnumerations table.

addDynamicField(DynamicTField) - Method in class edu.jhu.tmaj.beans.dynamic.data.DynamicMetaData

Adds a record from the XXXFieldNames table.

addDynamicValue(int, DynamicValue) - Method in class edu.jhu.tmaj.beans.dynamic.DynamicJBean

Adds dynamic data to this Bean from a record in a Dynamic-Data table, such as TissueDiagnosisData

addDynamicValue(int, DynamicValue) - Method in class edu.jhu.tmaj.client.importer.specimens.data.DynamicTranslatedTable

addErrorMessage(String) - Method in class edu.jhu.tmaj.util.data.LevelMessages

addField(MainTableSection, DatabaseField) - Method in class edu.jhu.tmaj.client.image.data.StaticFields

addFileStats(ExternalFile, FileStats) - Method in class edu.jhu.tmaj.beans.masks.results.AllFileStats

addFilterMaskInfo(Map<Integer, Mask>, int) - Static method in class edu.jhu.tmaj.beans.masks.filter.FilterMaskDatabaseUtil.Reader

addFloat(String, Float) - Method in class edu.jhu.tmaj.database.sql.AbstractModifySQL

addFloat(String, Float) - Method in class edu.jhu.tmaj.database.sql.SQLValues

addFolder(ImageSize, ExternalFolder) - Method in class edu.jhu.tmaj.client.importer.images.data.VariedSizeFolders

addFrame(JFrame) - Method in class edu.jhu.tmaj.client.image.data.FramesHolder

addIASessionBean(IASessionBean) - Method in class edu.jhu.tmaj.client.image.AbstractSessionsPanel

addIASessionBeanToTop(IASessionBean) - Method in class edu.jhu.tmaj.client.image.AbstractSessionsPanel

Adds a SessionBean to the top of the JList.

addImagePlusInfo(ImagePlusInfo) - Method in class edu.jhu.tmaj.client.frida.data.ImagePlusHolder

addInfoMessage(String) - Method in class edu.jhu.tmaj.util.data.LevelMessages

addInputLog(int, String) - Method in class edu.jhu.tmaj.database.sql.AbstractModifySQL

addInputLog(InputLog) - Method in class edu.jhu.tmaj.database.sql.SQLValues

addInteger(String, Integer) - Method in class edu.jhu.tmaj.database.sql.AbstractModifySQL

addInteger(String, Integer) - Method in class edu.jhu.tmaj.database.sql.SQLValues

addKey(int, int) - Method in class edu.jhu.tmaj.beans.manytomany.LinkGroup

Adds a key mapping.

addKeyListener(KeyListener) - Method in class edu.jhu.tmaj.client.frida.gui.masks.color.FullSlider

addKeyListener(KeyListener) - Method in class edu.jhu.tmaj.client.frida.gui.masks.color.HsbRangeComponent

addKeyListener(KeyListener) - Method in class edu.jhu.tmaj.client.frida.gui.masks.lasso.LassoMaskGui

addKeyListener(KeyListener) - Method in class edu.jhu.tmaj.client.frida.gui.shared.LimitedToolBar

addKeyListener(Container, KeyListener) - Static method in class edu.jhu.tmaj.util.swing.KeyListenerUtils

Adds a KeyListener to every Component in a Container.

addKeyListenerToJList(KeyListener) - Method in class edu.jhu.tmaj.client.image.AbstractSessionsPanel

Add a keyListener to respond to KeyEvents when typed in the JList.

AddKeysDialog - Class in edu.jhu.tmaj.client.admin

A Dialog that displays a JList where users may select items from the list and then click the OKAY button.

AddKeysDialog(GeneralListModel, List, Frame) - Constructor for class edu.jhu.tmaj.client.admin.AddKeysDialog

addLasso(ExternalFile, Lasso) - Method in class edu.jhu.tmaj.beans.masks.lasso.LassoMask

addLassoedFile(LassoedFile) - Method in class edu.jhu.tmaj.beans.masks.lasso.LassoMask

addLassoMaskInfo(Map<Integer, Mask>, int) - Static method in class edu.jhu.tmaj.beans.masks.lasso.LassoMaskDatabaseUtil.Reader

addListDataListener(ListDataListener) - Method in class edu.jhu.tmaj.util.swing.GeneralListModel

addListener(JTable, GeneralTableModel) - Static method in class edu.jhu.tmaj.client.tables.data.InputPanelClipBoard

addLiteralValue(String, LiteralValue) - Method in class edu.jhu.tmaj.database.sql.AbstractModifySQL

addLiteralValue(String, LiteralValue) - Method in class edu.jhu.tmaj.database.sql.SQLValues

addLong(String, Long) - Method in class edu.jhu.tmaj.database.sql.AbstractModifySQL

Add/Change the value(s) in columnName to value for an integer column.

addLong(String, Long) - Method in class edu.jhu.tmaj.database.sql.SQLValues

addMap(Map) - Method in class edu.jhu.tmaj.beans.data.ExpandingMap

addMask(Mask) - Method in class edu.jhu.tmaj.client.frida.gui.DefinedMasksGui

addMaskChangeListener(MaskChangeListener) - Method in class edu.jhu.tmaj.client.frida.gui.DefinedMasksGui

Adds a maskChangeListener to this class; this class will notify the listener whenever a mask is added, has its name changed, or deleted.

AddMaskDialog - Class in edu.jhu.tmaj.client.frida.gui

A dialog that prompts the user for a mask name and a mask type (color, lasso, or meta).

AddMaskDialog.BasicMaskInfo - Class in edu.jhu.tmaj.client.frida.gui

Represents 2 major components of a mask: its name and its type.

AddMaskDialog.BasicMaskInfo(String, MaskType) - Constructor for class edu.jhu.tmaj.client.frida.gui.AddMaskDialog.BasicMaskInfo

addMaskStats(Mask, MaskStats) - Method in class edu.jhu.tmaj.beans.masks.results.FileStats

addMeans(String, int) - Method in class edu.jhu.tmaj.beans.masks.results.ParticleAnalyzer2

addMessage(String) - Method in class edu.jhu.tmaj.util.data.Messages

addMessages(Messages) - Method in class edu.jhu.tmaj.util.data.Messages

addMessageSection(String) - Method in class edu.jhu.tmaj.util.data.Messages

addMetaMaskInfo(Map<Integer, Mask>, int) - Static method in class edu.jhu.tmaj.beans.masks.meta.MetaMaskDatabaseUtil.Reader

addMouseListenerToJList(MouseListener) - Method in class edu.jhu.tmaj.client.image.AbstractSessionsPanel

Add a MouseListener that will response to MouseEvents generated in the JList.

addNode(DefaultMutableTreeNode, DefaultMutableTreeNode, DefaultTreeModel) - Static method in class edu.jhu.tmaj.client.admin.data.TreeUtils

addObject(Object, Object) - Method in class edu.jhu.tmaj.client.image.SpecialTree

addObject(Object) - Method in class edu.jhu.tmaj.util.ObjectPool

Adds an element to the pool.

addPartialFolder(PartialFolder) - Method in class edu.jhu.tmaj.beans.exfile.data.PartialFolderCollection

addRadioButtonsToMenu(JMenu) - Method in class edu.jhu.tmaj.client.image.ThumbnailsMenuHelper

addRow(List) - Method in class edu.jhu.tmaj.client.tables.data.GeneralTableModel

addRow() - Method in class edu.jhu.tmaj.client.tables.data.TableData4

addRow(boolean) - Method in class edu.jhu.tmaj.client.tables.data.TableData4

Adds a row to the table.

addRow() - Method in interface edu.jhu.tmaj.util.file.TableArray

addRow(List<T>) - Method in interface edu.jhu.tmaj.util.file.TableArray

addRow() - Method in class edu.jhu.tmaj.util.file.TableArrayImpl

addRow(List<T>) - Method in class edu.jhu.tmaj.util.file.TableArrayImpl

addSearchTerm(SearchTerm) - Method in class edu.jhu.tmaj.client.tables.data.TableData4

Add a SearchTerm to the list of fields the user can search.

addSessionBean(SessionBean) - Method in class edu.jhu.tmaj.client.image.AbstractSessionsPanel

Adds a SessionBean to the bottom of the JList.

addSessionBeanToTop(SessionBean) - Method in class edu.jhu.tmaj.client.image.AbstractSessionsPanel

Adds a SessionBean to the top of the JList.

addString(String, String) - Method in class edu.jhu.tmaj.database.sql.AbstractModifySQL

Add/Change the value(s) in columnName to value for a varchar column.

addString(String, String) - Method in class edu.jhu.tmaj.database.sql.SQLValues

addSubFolders(List<ExternalFolder>) - Method in class edu.jhu.tmaj.client.importer.images.data.VariedSizeFolders

addSubMapValue(Object, int, Object, Object) - Method in class edu.jhu.tmaj.beans.data.ExpandingMap

addTableCellEditor(int, TableCellEditor) - Method in class edu.jhu.tmaj.client.tables.data.HorizontalTable

addToArraySlide(ArraySlideFrame, SessionBean, OpenSessionsPanel, ImageAppGuis) - Static method in class edu.jhu.tmaj.client.image.data.SessionWindowListener

addToFridaGui(IASessionBean, OpenSessionsPanel, ImageAppGuis) - Static method in class edu.jhu.tmaj.client.image.data.IASessionWindowListener

addToManager - Variable in class edu.jhu.tmaj.beans.masks.results.ParticleAnalyzer2

addToOpenedList(ArrayBlockFrame) - Method in class edu.jhu.tmaj.client.arraybuilder.OpenedArrayBlocksPanel

addToTextField(JTextField, JButton) - Static method in class edu.jhu.tmaj.client.shared.ButtonClickActionListener

addUpdatedCell(int, int) - Method in class edu.jhu.tmaj.client.tables.data.ChangedCells

AddUserDialog - Class in edu.jhu.tmaj.client.image

A dialog that displays a list of all the Users in TMAJ.

AddUserDialog(ShareSessionDialog) - Constructor for class edu.jhu.tmaj.client.image.AddUserDialog

addValue(int, Object, Object) - Method in class edu.jhu.tmaj.beans.data.SubMap

addWarning(String) - Method in class edu.jhu.tmaj.servlet.response.impl.MachineScoresImportResponse

addWarningMessage(String) - Method in class edu.jhu.tmaj.util.data.LevelMessages

ADMIN_APP_FIELD - Static variable in class edu.jhu.tmaj.beans.UserBean

AdminAppPermission - Enum in edu.jhu.tmaj.beans.data

Represents the 2 types of administrators: Group Admin and Full-Admin.

AdminGUI - Class in edu.jhu.tmaj.client.admin

The main gui class for the Admin application

AGE_FIELD - Static variable in class edu.jhu.tmaj.beans.CellLineBean

AGE_FIELD - Static variable in class edu.jhu.tmaj.beans.dynamic.SpecimenBean

ALGORITHM_NAME - Static variable in class edu.jhu.tmaj.util.crypt.KeyManagementUtil

AllFileStats - Class in edu.jhu.tmaj.beans.masks.results

AllFileStats() - Constructor for class edu.jhu.tmaj.beans.masks.results.AllFileStats

AllFileStatsUtil - Class in edu.jhu.tmaj.beans.masks.results

allowMoving() - Method in class edu.jhu.tmaj.client.image.draw.AbstractDrawable

Returns true if user has completed drawing the shape

allowMoving() - Method in class edu.jhu.tmaj.client.image.draw.TextDrawable

AlphabeticalComparator - Class in edu.jhu.tmaj.util.data

A Comparator that compares objects in case insensitive alphabetical order using their toString() method.

AnalysisFrame - Class in edu.jhu.tmaj.client.image

A Frame that displays a table of a user's scored-sessions; The user may highlight one or more sessions and download the data for those sessions to a tab-delimited file

AnalysisFrame(ProjectsGUI) - Constructor for class edu.jhu.tmaj.client.image.AnalysisFrame

analyze(ImagePlus) - Method in class edu.jhu.tmaj.beans.masks.results.ParticleAnalyzer2

Performs particle analysis on the specified image.

analyze(ImagePlus, ImageProcessor) - Method in class edu.jhu.tmaj.beans.masks.results.ParticleAnalyzer2

Performs particle analysis on the specified ImagePlus and ImageProcessor.

analyzeParticle(int, int, ImagePlus, ImageProcessor) - Method in class edu.jhu.tmaj.beans.masks.results.ParticleAnalyzer2

analyzer - Variable in class edu.jhu.tmaj.beans.masks.results.ParticleAnalyzer2

Analyzer2 - Class in edu.jhu.tmaj.beans.masks.results

This plugin implements ImageJ's Analyze/Measure and Analyze/Set Measurements commands.

Analyzer2() - Constructor for class edu.jhu.tmaj.beans.masks.results.Analyzer2

Analyzer2(ImagePlus) - Constructor for class edu.jhu.tmaj.beans.masks.results.Analyzer2

Constructs a new Analyzer using the specified ImagePlus object and the current measurement options and default results table.

Analyzer2(ImagePlus, int, ResultsTable) - Constructor for class edu.jhu.tmaj.beans.masks.results.Analyzer2

Construct a new Analyzer using an ImagePlus object and private measurement options and results table.

ANIMAL_EXPERIMENT_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.dynamic.SpecimenBean

ANIMAL_TYPE_1_FIELD - Static variable in class edu.jhu.tmaj.beans.AnimalExperimentBean

ANIMAL_TYPE_2_FIELD - Static variable in class edu.jhu.tmaj.beans.AnimalExperimentBean

AnimalExperimentBean - Class in edu.jhu.tmaj.beans

Represents a record from the AnimalExperiments table.

AnimalExperimentBean(StaticMetaData) - Constructor for class edu.jhu.tmaj.beans.AnimalExperimentBean

AnimalExperimentsFrame - Class in edu.jhu.tmaj.client.specimens

Represents the AnimalExperiments Table.

AnotherArrayImageRenderer - Class in edu.jhu.tmaj.client.image

A Renderer for the Images Lineup Frame.

AnotherArrayImageRenderer() - Constructor for class edu.jhu.tmaj.client.image.AnotherArrayImageRenderer

AperioImageOutputParser - Class in edu.jhu.tmaj.client.importer.data

Implements an ImageOutputParser for the Aperio ScanScope System

AperioImageOutputParser() - Constructor for class edu.jhu.tmaj.client.importer.data.AperioImageOutputParser

applyButtonClicked() - Method in class edu.jhu.tmaj.client.arraybuilder.TissueDiagnosisIDPanel

Called when user clicks the apply button.

applyColumnWidths(TableColumnModel) - Method in class edu.jhu.tmaj.client.tables.data.ColumnWidthData

Sets the widths in the specified tableColumnModel to a previously saved one.

applyFilter() - Method in class edu.jhu.tmaj.client.frida.gui.shared.MaskRepresentationPanel

Sets all pixels to red that are IN the filter.

applyTo(TableColumnModel) - Method in class edu.jhu.tmaj.client.tables.data.ColumnSet

Changes the widths in tableColumnModel to match this object

ARE_TISSUE_TYPES_RESTRICTED_FIELD - Static variable in class edu.jhu.tmaj.beans.ProjectBean

AREA_FIELD - Static variable in class edu.jhu.tmaj.beans.BlockBean

AREA_FIELD - Static variable in class edu.jhu.tmaj.beans.dynamic.TissueDiagnosisBean

areMessages() - Method in class edu.jhu.tmaj.util.data.Messages

areTissueTypesRestricted() - Method in class edu.jhu.tmaj.beans.ProjectBean

Returns true if users may only use TissueTypes for ScoredImages that were used on the original diagnosis.

areTissueTypesRestrictedForProject(SessionBean) - Static method in class edu.jhu.tmaj.client.image.TopMenu

areWarningsGenerated() - Method in class edu.jhu.tmaj.servlet.response.impl.MachineScoresImportResponse

argTypes - Variable in class edu.jhu.tmaj.client.tables.data.StandardizedCellEditor

AriolFileRenamerHelper - Class in edu.jhu.tmaj.client.importer

Renames the jpeg files generated by the ARIOL machine to include an x and y coordinate at the front.

ariolHelpButton - Variable in class edu.jhu.tmaj.client.importer.images.ArrayImagesImportGui2

ariolHelpButtonPressed() - Method in class edu.jhu.tmaj.client.importer.images.ArrayImagesImportHelper

ariolRenamerButton - Variable in class edu.jhu.tmaj.client.importer.images.ArrayImagesImportGui2

ariolRenamerButtonPressed(boolean) - Method in class edu.jhu.tmaj.client.importer.images.ArrayImagesImportHelper

arrangeWindowsButtonPressed() - Method in class edu.jhu.tmaj.client.image.OpenSessionsPanel

Arranges all Windows of the open sessions is a easy-to-read, standard format.

ARRAY_BLOCK_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.ArrayCoreBean

ARRAY_BLOCK_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.ArraySlideBean

ARRAY_BUILDER_APP_FIELD - Static variable in class edu.jhu.tmaj.beans.UserBean

ARRAY_CORE_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.ArrayImageBean

ARRAY_CORES_PANEL_NAME - Static variable in class edu.jhu.tmaj.client.specimens.SpecimensAppGUI

ARRAY_IMAGE_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.dynamic.ScoredImageBean

ARRAY_IMAGE_ID_POSITION - Static variable in class edu.jhu.tmaj.beans.dynamic.ScoredImageBean

ARRAY_MANAGER_APP_FIELD - Static variable in class edu.jhu.tmaj.beans.UserBean

ARRAY_SLIDE_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.ScanBean

ArrayBlockBean - Class in edu.jhu.tmaj.beans

Represents an ArrayBlock, which is a block created from many donor-blocks.

ArrayBlockBean() - Constructor for class edu.jhu.tmaj.beans.ArrayBlockBean

arrayBlockBean - Variable in class edu.jhu.tmaj.client.importer.images.data.SelectedScan

ArrayBlockExporter - Class in edu.jhu.tmaj.client.arraybuilder.data

Class provides functions that export the design of an ArrayBlock to a file.

ArrayBlockExporter(ArrayBlockBean, ArrayBuilderTable, ArrayCoreReferenceBean, CellLinesReferenceBean, Component) - Constructor for class edu.jhu.tmaj.client.arraybuilder.data.ArrayBlockExporter

ArrayBlockExporter.ArrayExportFormat - Enum in edu.jhu.tmaj.client.arraybuilder.data

Represents different formats for exporting ArrayBuilder data in an Array-like text file.

ArrayBlockExporterFull - Class in edu.jhu.tmaj.client.arraybuilder.data

ArrayBlockExporterFull(Component) - Constructor for class edu.jhu.tmaj.client.arraybuilder.data.ArrayBlockExporterFull

ArrayBlockFrame - Class in edu.jhu.tmaj.client.arraybuilder

The gui that holds an ArrayBlock in the ArrayBuilder application.

arrayBlockID - Variable in class edu.jhu.tmaj.client.importer.images.data.FilenameData

ARRAYBLOCKID_FIELD - Static variable in class edu.jhu.tmaj.servlet.request.impl.ScoredImageDetailsRequest

arrayBlockTextField - Variable in class edu.jhu.tmaj.client.importer.images.ArrayImagesImportGui2

ArrayBuilderGUI - Class in edu.jhu.tmaj.client.arraybuilder

The main gui class for the ArrayBuilder application

ArrayBuilderPermission - Enum in edu.jhu.tmaj.beans.data

Represents the level of permission a user has for the ArrayBuilder Application.

ArrayBuilderTable - Class in edu.jhu.tmaj.client.arraybuilder

Represents the JTable-related classes in the ArrayBuilder application.

ArrayBuilderTable(ArrayBlockBean, CoreDataPanel, ArrayCoreReferenceBean, CellLinesReferenceBean) - Constructor for class edu.jhu.tmaj.client.arraybuilder.ArrayBuilderTable

Constructs this object.

ArrayCoreBean - Class in edu.jhu.tmaj.beans

Represents the ArrayCores Table.

ArrayCoreBean(StaticMetaData) - Constructor for class edu.jhu.tmaj.beans.ArrayCoreBean

ArrayCoreC - Class in edu.jhu.tmaj.servlet.request.impl

Represents an ArrayCore.

ArrayCoreC(int, int, int, String, String) - Constructor for class edu.jhu.tmaj.servlet.request.impl.ArrayCoreC

ArrayCoreCell - Class in edu.jhu.tmaj.client.arraybuilder.data

A cell in the JTable.

ArrayCoreCell(ArrayCoreRep, ArrayCoreReferenceBean, CellLinesReferenceBean) - Constructor for class edu.jhu.tmaj.client.arraybuilder.data.ArrayCoreCell

ArrayCoreData - Class in edu.jhu.tmaj.client.arraybuilder.data

Represents data assigned to each ArrayCore, namely a TissueDiagnosisID or ControlName.

ArrayCoreDetailsRequest - Class in edu.jhu.tmaj.servlet.request.impl

Returns the detailed design of an ArrayBlock to be printed to a tab-delimited file.

ArrayCoreDetailsRequest(Set<Integer>, DynamicMetaData, DynamicMetaData, Map<Integer, LookupRecord>, Map<Integer, LookupRecord>) - Constructor for class edu.jhu.tmaj.servlet.request.impl.ArrayCoreDetailsRequest

Since this is executed on the server side, the request must pass in the cached MetaData from MyBeans

ArrayCoreReferenceBean - Class in edu.jhu.tmaj.beans

This bean queries the Specimen, Block, and TissueDiagnosis tables so that ArrayBuilder can quickly lookup background information on any TissueDiagnosisID, which every ArrayCore contains.

ArrayCoreReferenceBean() - Constructor for class edu.jhu.tmaj.beans.ArrayCoreReferenceBean

ArrayCoreReferenceRequest - Class in edu.jhu.tmaj.servlet.request.impl

Used to get information about Specimens,Blocks, and TissueDiagnosis in the ArrayBuilder application.

ArrayCoreReferenceRequest(int, ArrayCoreReferenceRequest.ReferenceRequestType) - Constructor for class edu.jhu.tmaj.servlet.request.impl.ArrayCoreReferenceRequest

Initializes the Request.

ArrayCoreReferenceRequest.ReferenceRequestType - Enum in edu.jhu.tmaj.servlet.request.impl

How an ArrayCoreReferenceBean may be initialized, either by the entire ArrayBlock, or just one TissueDiagnosisID.

ArrayCoreReferenceResponse - Class in edu.jhu.tmaj.servlet.response.impl

Contains an ArrayCoreReferenceBean

ArrayCoreReferenceResponse(ArrayCoreReferenceBean) - Constructor for class edu.jhu.tmaj.servlet.response.impl.ArrayCoreReferenceResponse

ArrayCoreRenderer - Class in edu.jhu.tmaj.client.arraybuilder.data

The renderer for the JTable.

ArrayCoreRenderer(ArrayCoreReferenceBean, CellLinesReferenceBean) - Constructor for class edu.jhu.tmaj.client.arraybuilder.data.ArrayCoreRenderer

ArrayCoreRep - Class in edu.jhu.tmaj.beans.misc

Represents the table ArrayCores.

ArrayCoreRep(int, Coordinate, int, String) - Constructor for class edu.jhu.tmaj.beans.misc.ArrayCoreRep

ArrayCoresGetResponse - Class in edu.jhu.tmaj.servlet.response.impl

Contains a List of ArrayCoreBeans

ArrayCoresGetResponse(List<ArrayCoreRep>) - Constructor for class edu.jhu.tmaj.servlet.response.impl.ArrayCoresGetResponse

ArrayCoresOpenRequest - Class in edu.jhu.tmaj.servlet.request.impl

Gets the arraycores for a specified ArrayBlock.

ArrayCoresOpenRequest(int) - Constructor for class edu.jhu.tmaj.servlet.request.impl.ArrayCoresOpenRequest

ArrayCoresSaveRequest - Class in edu.jhu.tmaj.servlet.request.impl

Writes a List of ArrayCores to the database.

ArrayCoresSaveRequest(int, List<ArrayCoreRep>) - Constructor for class edu.jhu.tmaj.servlet.request.impl.ArrayCoresSaveRequest

arrayImage - Variable in class edu.jhu.tmaj.client.image.ArrayImageFrame

ArrayImage2 - Class in edu.jhu.tmaj.client.importer.images.data

ArrayImage2(int, ScanBean, ExternalFile, ExternalFile, ExternalFile, ExternalFile) - Constructor for class edu.jhu.tmaj.client.importer.images.data.ArrayImage2

ArrayImageAddRequest - Class in edu.jhu.tmaj.servlet.request.impl

Used for importing scanned arrayImages into the database.

ArrayImageAddRequest(ArrayImage2) - Constructor for class edu.jhu.tmaj.servlet.request.impl.ArrayImageAddRequest

ArrayImageBean - Class in edu.jhu.tmaj.beans

ArrayImageBean() - Constructor for class edu.jhu.tmaj.beans.ArrayImageBean

ArrayImageCell - Class in edu.jhu.tmaj.client.image.data

This class represents an ArrayImage in the ArraySlideFrame,ArrayImageFrame, and DotDataFrame.

ArrayImageCollectionBean - Class in edu.jhu.tmaj.beans.misc

A Collection of ArrayImages from the same session.

ArrayImageCollectionBean(Pair, int) - Constructor for class edu.jhu.tmaj.beans.misc.ArrayImageCollectionBean

ArrayImageCollectionRequest - Class in edu.jhu.tmaj.servlet.request.impl

Class is responsible for initialing the ArraySlideFrame in the Images Application.

ArrayImageCollectionRequest(int) - Constructor for class edu.jhu.tmaj.servlet.request.impl.ArrayImageCollectionRequest

ArrayImageCollectionResponse - Class in edu.jhu.tmaj.servlet.response.impl

Contains an ArrayImageCollectionBean

ArrayImageCollectionResponse(ArrayImageCollectionBean) - Constructor for class edu.jhu.tmaj.servlet.response.impl.ArrayImageCollectionResponse

ArrayImageCoresRequest - Class in edu.jhu.tmaj.servlet.request.impl

ArrayImageCoresRequest(ArrayBlockBean) - Constructor for class edu.jhu.tmaj.servlet.request.impl.ArrayImageCoresRequest

ArrayImageCoresResponse - Class in edu.jhu.tmaj.servlet.response.impl

ArrayImageCoresResponse() - Constructor for class edu.jhu.tmaj.servlet.response.impl.ArrayImageCoresResponse

ArrayImageDynamicField - Class in edu.jhu.tmaj.beans.dynamic.data

Represents a record in the ArrayImageFieldsNames Table.

ArrayImageDynamicField(int, int, int, String) - Constructor for class edu.jhu.tmaj.beans.dynamic.data.ArrayImageDynamicField

Initializes this class.

ArrayImageDynamicField.AIDynamicFieldType - Enum in edu.jhu.tmaj.beans.dynamic.data

Either a REGULAR_DYNAMIC_FIELD or a SCORING_STRATEGY_FIELD

ArrayImageDynamicMetaData - Class in edu.jhu.tmaj.beans.dynamic.data

The DynamicMetaData class for the ArrayImages section, this contains support for dynamic Scoring Strategies.

ArrayImageDynamicMetaData() - Constructor for class edu.jhu.tmaj.beans.dynamic.data.ArrayImageDynamicMetaData

ArrayImageFrame - Class in edu.jhu.tmaj.client.image

A Frame that displays an ArrayImage and data fields for scoring.

ArrayImageFrame(SessionBean, ImageAppGuis, InfoFrame) - Constructor for class edu.jhu.tmaj.client.image.ArrayImageFrame

ArrayImageFrameTable - Class in edu.jhu.tmaj.client.image

Contains jtable-related objects on the ArrayImageFrame.

ArrayImageFrameTable(ArrayImageFrame) - Constructor for class edu.jhu.tmaj.client.image.ArrayImageFrameTable

ARRAYIMAGEID_FIELD - Static variable in class edu.jhu.tmaj.servlet.request.impl.ScoredImageDetailsRequest

arrayImagePanel - Variable in class edu.jhu.tmaj.client.image.ArrayImageFrame

ArrayImagePanel - Class in edu.jhu.tmaj.client.image

A panel in ArrayImageFrame that displays the actual Image

ArrayImagePanel() - Constructor for class edu.jhu.tmaj.client.image.ArrayImagePanel

ArrayImageRenderer - Class in edu.jhu.tmaj.client.image.data

A TableCellRenderer and a JLabel that properly renders an ArrayImage in the ArraySlideFrame.

ArrayImageRenderer() - Constructor for class edu.jhu.tmaj.client.image.data.ArrayImageRenderer

ArrayImageRendererCache - Class in edu.jhu.tmaj.client.image.data

ArrayImageRendererCache() - Constructor for class edu.jhu.tmaj.client.image.data.ArrayImageRendererCache

arrayImagesClipBoard - Variable in class edu.jhu.tmaj.client.image.ArrayImageFrameTable

ArrayImagesClipBoard - Class in edu.jhu.tmaj.client.image.data

A class that enables coping and pasting of scoring data in the Images application.

ArrayImagesClipBoard(TableModel, JComboBox) - Constructor for class edu.jhu.tmaj.client.image.data.ArrayImagesClipBoard

ArrayImageSettable - Interface in edu.jhu.tmaj.client.image.data

An frame that can be set to a certain state or value calling a setArrayImageData(ArrayImageData) method.

ArrayImagesImportGui2 - Class in edu.jhu.tmaj.client.importer.images

ArrayImagesImportGui2(JComponent) - Constructor for class edu.jhu.tmaj.client.importer.images.ArrayImagesImportGui2

ArrayImagesImportHelper - Class in edu.jhu.tmaj.client.importer.images

ArrayImagesImportHelper(Component, ArrayImagesImportGui2) - Constructor for class edu.jhu.tmaj.client.importer.images.ArrayImagesImportHelper

ArrayImageU - Class in edu.jhu.tmaj.client.importer.images.data

Represents an ArrayImage that is going to be updated or inserted into the database.

ArrayImageU(String, String, int, int) - Constructor for class edu.jhu.tmaj.client.importer.images.data.ArrayImageU

ArrayManagerAppGUI - Class in edu.jhu.tmaj.client.arrays

The main gui class for the ArrayManager Application.

ArrayManagerPanel - Class in edu.jhu.tmaj.client.arrays

ArrayManagerPanel() - Constructor for class edu.jhu.tmaj.client.arrays.ArrayManagerPanel

ArraySlideAdderFrame - Class in edu.jhu.tmaj.client.admin

A Frame that allows the user to add multiple ArraySlides at once.

ArraySlideAdderFrame() - Constructor for class edu.jhu.tmaj.client.admin.ArraySlideAdderFrame

ArraySlideBean - Class in edu.jhu.tmaj.beans

Represents a cut of an ArrayBlock.

ArraySlideBean(StaticMetaData) - Constructor for class edu.jhu.tmaj.beans.ArraySlideBean

arraySlideBean - Variable in class edu.jhu.tmaj.client.importer.images.data.SelectedScan

ArraySlideFrame - Class in edu.jhu.tmaj.client.image

A frame that displays a representation of an ArraySlide

ArraySlideFrame(SessionBean, ImageAppGuis) - Constructor for class edu.jhu.tmaj.client.image.ArraySlideFrame

arraySlideTextField - Variable in class edu.jhu.tmaj.client.importer.images.ArrayImagesImportGui2

arrayTo2dList(Object[][]) - Static method in class edu.jhu.tmaj.util.ListConvertUtil

arrayToList(Object[]) - Static method in class edu.jhu.tmaj.util.ListConvertUtil

Converts an Array of Objects to a List of Objects.

arrayToSet(Object[]) - Static method in class edu.jhu.tmaj.util.ListConvertUtil

Converts an array into a Set.

arrayToString(Object[]) - Static method in class edu.jhu.tmaj.util.ListConvertUtil

Returns a description of every object in the provided Array.

ArrowDrawable - Class in edu.jhu.tmaj.client.image.draw

An arrow

ArrowDrawable(DrawableLabel) - Constructor for class edu.jhu.tmaj.client.image.draw.ArrowDrawable

AssignPasswordDialog - Class in edu.jhu.tmaj.client.admin

A JFrame that allows administrators to assign "good" passwords (random, 6+ characters) to new users.

AssignSpecimensDialog - Class in edu.jhu.tmaj.client.specimens

A GUI admins use to assign users to specimens.

ATCC_NUMBER_FIELD - Static variable in class edu.jhu.tmaj.beans.CellLineBean

AUTHORS_FIELD - Static variable in class edu.jhu.tmaj.beans.PaperBean

autoLogIn(String, String) - Static method in class edu.jhu.tmaj.client.shared.LoginDialog

Used to automatically log someone into the GUI.

autoLoginWithoutChecking() - Static method in class edu.jhu.tmaj.client.shared.LoginDialog

Used to automatically log in for a text-based application.

B

b - Variable in class edu.jhu.tmaj.beans.masks.data.HsbPixel

backButton - Variable in class edu.jhu.tmaj.client.image.NavigationGUI

BadImagesUpdateRequest - Class in edu.jhu.tmaj.servlet.request.impl

Updates the isBad status of an ArrayImage if it is inconsistent from the value in provided ArrayImageCollectionBean.

BadImagesUpdateRequest(ArrayImageCollectionBean) - Constructor for class edu.jhu.tmaj.servlet.request.impl.BadImagesUpdateRequest

BAR_CODE_FIELD - Static variable in class edu.jhu.tmaj.beans.ScanBean

barCode - Variable in class edu.jhu.tmaj.client.importer.images.data.FilenameData

Base64Coder - Class in edu.jhu.tmaj.util

A Base64 Encoder/Decoder.

BaseRequest - Class in edu.jhu.tmaj.servlet.request

All Requests extend this class.

BaseRequest(String, String) - Constructor for class edu.jhu.tmaj.servlet.request.BaseRequest

Construct this request with a specified username and password.

BaseRequest() - Constructor for class edu.jhu.tmaj.servlet.request.BaseRequest

Construct this request with the currently logged on user.

BeanLogger - Class in edu.jhu.tmaj.client.tables.logs

Provides utility classes for logging changes to any of the JBean classes in TMAJ.

BeanTableModel - Class in edu.jhu.tmaj.client.tables.data

A TableModel that overrides isCellEditable() to ensure that deleted rows and the first column are not editable

BeanTableModel() - Constructor for class edu.jhu.tmaj.client.tables.data.BeanTableModel

beanToStaticEnumeration(JBean, String) - Static method in class edu.jhu.tmaj.beans.data.StaticMetaData

BIRTH_DATE_FIELD - Static variable in class edu.jhu.tmaj.beans.PatientBean

BLACK_SQUARE_SIZE - Static variable in class edu.jhu.tmaj.client.image.draw.AbstractDrawable

The size of the black squares that are drawn around an image when it's selected

BLACK_VALUE - Static variable in class edu.jhu.tmaj.client.frida.data.CalibrationCalculator

BlissImageOutputParser - Class in edu.jhu.tmaj.client.importer.data

Implements an ImageOutputParser for the Bacus labs BLISS system

BlissImageOutputParser() - Constructor for class edu.jhu.tmaj.client.importer.data.BlissImageOutputParser

BlissMachineScoresParser - Class in edu.jhu.tmaj.servlet.request.impl

A MachineScoresParser for the Bacus Labs BLISS machine.

BlissMachineScoresParser() - Constructor for class edu.jhu.tmaj.servlet.request.impl.BlissMachineScoresParser

BLOCK_DESIGNATION_FIELD - Static variable in class edu.jhu.tmaj.beans.BlockBean

BLOCK_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.BlockUsageAltBean

BLOCK_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.BlockUsageBean

BLOCK_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.dynamic.TissueDiagnosisBean

BLOCK_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.MolecularSampleBean

BLOCK_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.SlideBean

BLOCK_PANEL_NAME - Static variable in class edu.jhu.tmaj.client.samples.SamplesAppGUI

BLOCK_PANEL_NAME - Static variable in class edu.jhu.tmaj.client.specimens.SpecimensAppGUI

BLOCK_STATUS_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.BlockBean

BLOCK_USAGES_PANEL_NAME - Static variable in class edu.jhu.tmaj.client.samples.SamplesAppGUI

BLOCK_USAGES_PANEL_NAME - Static variable in class edu.jhu.tmaj.client.specimens.SpecimensAppGUI

BlockBean - Class in edu.jhu.tmaj.beans

Represents a donor (regular,non-array) block cut from a Specimen.

BlockBean(StaticMetaData) - Constructor for class edu.jhu.tmaj.beans.BlockBean

blockInputPanel - Variable in class edu.jhu.tmaj.client.specimens.SpecimensAppGUI

BlockOrSlideExchangeBean - Class in edu.jhu.tmaj.beans

Represents a record from the AnimalExperiments table.

BlockOrSlideExchangeBean(StaticMetaData) - Constructor for class edu.jhu.tmaj.beans.BlockOrSlideExchangeBean

BlockOrSlideExchangesFrame - Class in edu.jhu.tmaj.client.specimens

Represents the AnimalExperiments Table.

BlockUsageAltBean - Class in edu.jhu.tmaj.beans

Represent a Usage (such as a Slide or Tube) of a regular block.

BlockUsageAltBean(StaticMetaData) - Constructor for class edu.jhu.tmaj.beans.BlockUsageAltBean

BlockUsageBean - Class in edu.jhu.tmaj.beans

Represents tha BlockUsages Table.

BlockUsageBean() - Constructor for class edu.jhu.tmaj.beans.BlockUsageBean

BLOOD_PANEL_NAME - Static variable in class edu.jhu.tmaj.client.samples.SamplesAppGUI

BLOOD_SAMPLE_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.BloodUsageBean

BLOOD_SAMPLE_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.MolecularSampleBean

BLOOD_TYPE_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.BloodSampleBean

BLOOD_USAGES_PANEL_NAME - Static variable in class edu.jhu.tmaj.client.samples.SamplesAppGUI

BloodSampleBean - Class in edu.jhu.tmaj.beans

Represents a Blood Sample.

BloodSampleBean(StaticMetaData) - Constructor for class edu.jhu.tmaj.beans.BloodSampleBean

BloodUsageBean - Class in edu.jhu.tmaj.beans

Represents usages of the Blood Samples Table.

BloodUsageBean(StaticMetaData) - Constructor for class edu.jhu.tmaj.beans.BloodUsageBean

BOLD_FONT - Static variable in class edu.jhu.tmaj.client.tables.data.HeaderTableCellRenderer

booleanArrayPrimitiveAsList(boolean[]) - Static method in class edu.jhu.tmaj.util.ListConvertUtil

bringToFront(SessionBean) - Method in class edu.jhu.tmaj.client.image.OpenSessionsPanel

bringToFront(IASessionBean) - Method in class edu.jhu.tmaj.client.image.OpenSessionsPanel

browseDirectoryButton - Variable in class edu.jhu.tmaj.client.importer.images.ArrayImagesImportGui2

browseDirectoryButtonPressed() - Method in class edu.jhu.tmaj.client.importer.images.ArrayImagesImportHelper

ButtonClickActionListener - Class in edu.jhu.tmaj.client.shared

An ActionListener that pressing a button when a user hits the return button in a text field.

ButtonEditor - Class in edu.jhu.tmaj.client.image.data

A TableCellEditor that displays a JButton.

ButtonEditor(JButton) - Constructor for class edu.jhu.tmaj.client.image.data.ButtonEditor

BYTE - Static variable in class edu.jhu.tmaj.beans.masks.results.ParticleAnalyzer2

byteToUnsignedInt(byte) - Static method in class edu.jhu.tmaj.beans.masks.data.PixelUtil

Converts a byte (-128 to 127) to an unsigned int, which ranges from 0 - 255.

ByteUtil - Class in edu.jhu.tmaj.util

Provides methods for converting byte arrays to objects, and objects to byte arrays

ByteUtil() - Constructor for class edu.jhu.tmaj.util.ByteUtil

C

CacheableBean - Enum in edu.jhu.tmaj.beans.cache

Any JBean whose records may be cached in CachedBeans.

CacheableDynamicMetaData - Enum in edu.jhu.tmaj.beans.cache

Represents the 3 tables which have DynamicMetaData.

CacheableStaticMetaData - Enum in edu.jhu.tmaj.beans.cache

Represents JBeans who StaticMetaData is cached.

CacheableStaticMetaData.AnimalExperimentsHolder - Class in edu.jhu.tmaj.beans.cache

The StaticMetaData for the Animal Experiments Table.

CacheableStaticMetaData.AnimalExperimentsHolder() - Constructor for class edu.jhu.tmaj.beans.cache.CacheableStaticMetaData.AnimalExperimentsHolder

CacheableStaticMetaData.ArraySlidesHolder - Class in edu.jhu.tmaj.beans.cache

The StaticMetaData for the ArraySlides Table.

CacheableStaticMetaData.ArraySlidesHolder() - Constructor for class edu.jhu.tmaj.beans.cache.CacheableStaticMetaData.ArraySlidesHolder

CacheableStaticMetaData.BlockOrSlideExchangesHolder - Class in edu.jhu.tmaj.beans.cache

The StaticMetaData for the BlockOrSlideExchanges Table.

CacheableStaticMetaData.BlockOrSlideExchangesHolder() - Constructor for class edu.jhu.tmaj.beans.cache.CacheableStaticMetaData.BlockOrSlideExchangesHolder

CacheableStaticMetaData.BlocksHolder - Class in edu.jhu.tmaj.beans.cache

The StaticMetaData for the Blocks Table.

CacheableStaticMetaData.BlocksHolder() - Constructor for class edu.jhu.tmaj.beans.cache.CacheableStaticMetaData.BlocksHolder

CacheableStaticMetaData.BlockUsagesAltHolder - Class in edu.jhu.tmaj.beans.cache

The StaticMetaData for the BlockUsagesAlt Table.

CacheableStaticMetaData.BlockUsagesAltHolder() - Constructor for class edu.jhu.tmaj.beans.cache.CacheableStaticMetaData.BlockUsagesAltHolder

CacheableStaticMetaData.BloodHolder - Class in edu.jhu.tmaj.beans.cache

The StaticMetaData for the BloodSamples Table.

CacheableStaticMetaData.BloodHolder() - Constructor for class edu.jhu.tmaj.beans.cache.CacheableStaticMetaData.BloodHolder

CacheableStaticMetaData.CellLineExperimentsHolder - Class in edu.jhu.tmaj.beans.cache

The StaticMetaData for the CellLineExperiments Table.

CacheableStaticMetaData.CellLineExperimentsHolder() - Constructor for class edu.jhu.tmaj.beans.cache.CacheableStaticMetaData.CellLineExperimentsHolder

CacheableStaticMetaData.CellLinesHolder - Class in edu.jhu.tmaj.beans.cache

The StaticMetaData for the CellLines Table.

CacheableStaticMetaData.CellLinesHolder() - Constructor for class edu.jhu.tmaj.beans.cache.CacheableStaticMetaData.CellLinesHolder

CacheableStaticMetaData.EnumsGetter - Class in edu.jhu.tmaj.beans.cache

A Utility class for getting the enumerations for a particular choice.

CacheableStaticMetaData.EnumsGetter() - Constructor for class edu.jhu.tmaj.beans.cache.CacheableStaticMetaData.EnumsGetter

CacheableStaticMetaData.MachineSessionsHolder - Class in edu.jhu.tmaj.beans.cache

The StaticMetaData for the MachineSessions Table.

CacheableStaticMetaData.MachineSessionsHolder() - Constructor for class edu.jhu.tmaj.beans.cache.CacheableStaticMetaData.MachineSessionsHolder

CacheableStaticMetaData.MolecularSamplesHolder - Class in edu.jhu.tmaj.beans.cache

The StaticMetaData for the MolecularSamples Table.

CacheableStaticMetaData.MolecularSamplesHolder() - Constructor for class edu.jhu.tmaj.beans.cache.CacheableStaticMetaData.MolecularSamplesHolder

CacheableStaticMetaData.PaperHolder - Class in edu.jhu.tmaj.beans.cache

The StaticMetaData for the Papers Table.

CacheableStaticMetaData.PaperHolder() - Constructor for class edu.jhu.tmaj.beans.cache.CacheableStaticMetaData.PaperHolder

CacheableStaticMetaData.PatientsHolder - Class in edu.jhu.tmaj.beans.cache

The StaticMetaData for the Patients Table.

CacheableStaticMetaData.PatientsHolder() - Constructor for class edu.jhu.tmaj.beans.cache.CacheableStaticMetaData.PatientsHolder

CacheableStaticMetaData.SampleUsagesHolder - Class in edu.jhu.tmaj.beans.cache

The StaticMetaData for the SampleUsagess Table.

CacheableStaticMetaData.SampleUsagesHolder() - Constructor for class edu.jhu.tmaj.beans.cache.CacheableStaticMetaData.SampleUsagesHolder

CacheableStaticMetaData.ScanHolder - Class in edu.jhu.tmaj.beans.cache

The StaticMetaData for the Scans Table.

CacheableStaticMetaData.ScanHolder() - Constructor for class edu.jhu.tmaj.beans.cache.CacheableStaticMetaData.ScanHolder

CacheableStaticMetaData.SlidesHolder - Class in edu.jhu.tmaj.beans.cache

The StaticMetaData for the Slides Table.

CacheableStaticMetaData.SlidesHolder() - Constructor for class edu.jhu.tmaj.beans.cache.CacheableStaticMetaData.SlidesHolder

CacheableStaticMetaData.SpecimensHolder - Class in edu.jhu.tmaj.beans.cache

The StaticMetaData for the Specimens Table.

CacheableStaticMetaData.SpecimensHolder() - Constructor for class edu.jhu.tmaj.beans.cache.CacheableStaticMetaData.SpecimensHolder

CacheableStaticMetaData.StaticMetaDataHolder - Interface in edu.jhu.tmaj.beans.cache

Holds the StaticMetaData for a table in TMAJ.

CacheableStaticMetaData.TissueDiagnosisHolder - Class in edu.jhu.tmaj.beans.cache

The StaticMetaData for the TissueDiagnosisH Table.

CacheableStaticMetaData.TissueDiagnosisHolder() - Constructor for class edu.jhu.tmaj.beans.cache.CacheableStaticMetaData.TissueDiagnosisHolder

CacheableStaticMetaData.TissueHolder - Class in edu.jhu.tmaj.beans.cache

The StaticMetaData for the TissueSamples Table.

CacheableStaticMetaData.TissueHolder() - Constructor for class edu.jhu.tmaj.beans.cache.CacheableStaticMetaData.TissueHolder

CacheableStaticMetaData.UrineHolder - Class in edu.jhu.tmaj.beans.cache

The StaticMetaData for the UrineSamples Table.

CacheableStaticMetaData.UrineHolder() - Constructor for class edu.jhu.tmaj.beans.cache.CacheableStaticMetaData.UrineHolder

CacheableStaticMetaData.UsersHolder - Class in edu.jhu.tmaj.beans.cache

The StaticMetaData for the Users Table.

CacheableStaticMetaData.UsersHolder() - Constructor for class edu.jhu.tmaj.beans.cache.CacheableStaticMetaData.UsersHolder

CachedBeans - Class in edu.jhu.tmaj.beans.cache

Represents a holding class for commonly used Beans.

CachedDynamicMetaData - Class in edu.jhu.tmaj.beans.cache

A holder for DynamicMetaData on the client's side.

CachedLookupTables - Class in edu.jhu.tmaj.beans.cache

Represents all cached lookup tables in TMAJ.

CachedManyToManyBeans - Class in edu.jhu.tmaj.beans.cache

Contains initialized ManyToManyBeans on the client Side of TMAJ.

CachedStaticMetaData - Class in edu.jhu.tmaj.beans.cache

A holder for ALL StaticMetaData used in TMAJ.

cacheThumbnailForCell(ArrayImageCell) - Method in class edu.jhu.tmaj.client.image.data.ArrayImageRenderer

CacheUtils - Class in edu.jhu.tmaj.beans.cache

Utility functions for the cache TMAJ clients use.

CALCULATED_PARTICLE_SIZE_MAXIMUM - Static variable in class edu.jhu.tmaj.beans.masks.results.ParticleStatsUtil

CALCULATED_PARTICLE_SIZE_MINIMUM - Static variable in class edu.jhu.tmaj.beans.masks.results.ParticleStatsUtil

Calibration - Class in edu.jhu.tmaj.client.frida.data

Calibration() - Constructor for class edu.jhu.tmaj.client.frida.data.Calibration

CALIBRATION_COEFFICIENT_1_FIELD - Static variable in class edu.jhu.tmaj.beans.IASessionBean

CALIBRATION_COEFFICIENT_2_FIELD - Static variable in class edu.jhu.tmaj.beans.IASessionBean

CALIBRATION_COEFFICIENT_3_FIELD - Static variable in class edu.jhu.tmaj.beans.IASessionBean

CALIBRATION_COEFFICIENT_4_FIELD - Static variable in class edu.jhu.tmaj.beans.IASessionBean

CALIBRATION_COEFFICIENT_5_FIELD - Static variable in class edu.jhu.tmaj.beans.IASessionBean

CALIBRATION_FUNCTION_FIELD - Static variable in class edu.jhu.tmaj.beans.IASessionBean

CalibrationCalculator - Class in edu.jhu.tmaj.client.frida.data

CalibrationCalculator() - Constructor for class edu.jhu.tmaj.client.frida.data.CalibrationCalculator

CalibrationDialog - Class in edu.jhu.tmaj.beans

CalibrationDialog(JDialog, IASessionBean) - Constructor for class edu.jhu.tmaj.beans.CalibrationDialog

CalibrationFunction - Enum in edu.jhu.tmaj.client.frida.data

callSuperDotDraw(Graphics) - Method in class edu.jhu.tmaj.client.image.draw.RectangleDrawable

cancelGracefully() - Method in class edu.jhu.tmaj.util.swing.PublicSwingWorker

cancelUploadButton - Variable in class edu.jhu.tmaj.client.importer.images.ArrayImagesImportGui2

cancelUploadButtonPressed() - Method in class edu.jhu.tmaj.client.importer.images.ArrayImagesImportHelper

CELL_LINE_EXPERIMENT_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.dynamic.TissueDiagnosisBean

CELL_LINE_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.CellLineExperimentBean

CELL_LINE_MAKER_FIELD - Static variable in class edu.jhu.tmaj.beans.CellLineBean

CELL_LINE_NAME_FIELD - Static variable in class edu.jhu.tmaj.beans.CellLineBean

CellLineBean - Class in edu.jhu.tmaj.beans

Represents the CellLines table.

CellLineBean(StaticMetaData) - Constructor for class edu.jhu.tmaj.beans.CellLineBean

CellLineExperimentBean - Class in edu.jhu.tmaj.beans

Represents the CellLineExperiments table.

CellLineExperimentBean(StaticMetaData) - Constructor for class edu.jhu.tmaj.beans.CellLineExperimentBean

CellLinesFrame - Class in edu.jhu.tmaj.client.specimens

Represents the AnimalExperiments Table.

CellLinesReferenceBean - Class in edu.jhu.tmaj.beans

CellLinesReferenceBean() - Constructor for class edu.jhu.tmaj.beans.CellLinesReferenceBean

CellLinesReferenceRequest - Class in edu.jhu.tmaj.servlet.request.impl

CellLinesReferenceRequest(int, CellLinesReferenceRequest.ReferenceRequestType) - Constructor for class edu.jhu.tmaj.servlet.request.impl.CellLinesReferenceRequest

Initializes the Request.

CellLinesReferenceRequest.ReferenceRequestType - Enum in edu.jhu.tmaj.servlet.request.impl

CellLinesReferenceResponse - Class in edu.jhu.tmaj.servlet.response.impl

CellLinesReferenceResponse(CellLinesReferenceBean) - Constructor for class edu.jhu.tmaj.servlet.response.impl.CellLinesReferenceResponse

CellView - Enum in edu.jhu.tmaj.client.arraybuilder.data

ChangedCells - Class in edu.jhu.tmaj.client.tables.data

Represents cells (coordinates) in a JTable that the user has updated.

ChangedCells() - Constructor for class edu.jhu.tmaj.client.tables.data.ChangedCells

ChangeLog - Interface in edu.jhu.tmaj.client.tables.logs

Represents a single unit of change to the database.

ChangeLogsSaveRequest - Class in edu.jhu.tmaj.servlet.request.impl

Inserts a List of ChangeLogs into the database.

ChangeLogsSaveRequest(List<ChangeLog>) - Constructor for class edu.jhu.tmaj.servlet.request.impl.ChangeLogsSaveRequest

changeNormalStatusToModified() - Method in class edu.jhu.tmaj.client.image.draw.AbstractDrawable

Indicate user has modified an existing shape in the database

changePassword(int, String, boolean, Component) - Static method in class edu.jhu.tmaj.client.shared.ChangePasswordDialog

Sends a request to the database to change the password of a specified user.

ChangePasswordDialog - Class in edu.jhu.tmaj.client.shared

A frame that allows users to change their password

ChangePasswordRequest - Class in edu.jhu.tmaj.servlet.request.impl

Used to change the password of a user.

ChangePasswordRequest(int, String) - Constructor for class edu.jhu.tmaj.servlet.request.impl.ChangePasswordRequest

Constructs a request to change a user's password.

CheckableObject - Class in edu.jhu.tmaj.client.image

CheckableObject(Object, boolean) - Constructor for class edu.jhu.tmaj.client.image.CheckableObject

checkBox - Variable in class edu.jhu.tmaj.client.tables.CheckBoxField

CheckBoxField - Class in edu.jhu.tmaj.client.tables

A CheckBox representing a field in a bean.

CheckBoxField(DatabaseField) - Constructor for class edu.jhu.tmaj.client.tables.CheckBoxField

checkButtonPressed() - Method in class edu.jhu.tmaj.client.importer.images.ArrayImagesImportHelper

checkFolderButton - Variable in class edu.jhu.tmaj.client.importer.images.ArrayImagesImportGui2

checkForUnassignedArraySlide(ArraySlideBean, Component) - Static method in class edu.jhu.tmaj.client.importer.images.ProjectSelectDialog

CheckIfSpecimenExistsRequest - Class in edu.jhu.tmaj.servlet.request.impl

Checks to see if a specimen with the same SurgPathNumber and HospitalID exists.

CheckIfSpecimenExistsRequest(String, int, String, String, String) - Constructor for class edu.jhu.tmaj.servlet.request.impl.CheckIfSpecimenExistsRequest

CheckIfSpecimenExistsResponse - Class in edu.jhu.tmaj.servlet.response.impl

Contains booleans representing if a Specimen and TissueDiagonsis exist in the database.

CheckIfSpecimenExistsResponse(boolean, boolean) - Constructor for class edu.jhu.tmaj.servlet.response.impl.CheckIfSpecimenExistsResponse

checkMaskForCircularReference(Mask) - Static method in class edu.jhu.tmaj.beans.masks.data.CircularReferenceUtil

checkPolygonLength(Polygon, Component) - Static method in class edu.jhu.tmaj.client.image.draw.PolygonDrawable

checksumsAgree(ExternalFile) - Static method in class edu.jhu.tmaj.servlet.request.impl.FileDeleteRequest

ChecksumUtil - Interface in edu.jhu.tmaj.util.file

ChecksumUtilImpl - Class in edu.jhu.tmaj.util.file

ChecksumUtilImpl() - Constructor for class edu.jhu.tmaj.util.file.ChecksumUtilImpl

choiceChanged() - Method in class edu.jhu.tmaj.client.image.data.DividedComboBox

choiceChanged() - Method in class edu.jhu.tmaj.client.image.data.RecentComboBox

Adds the newly selected item to the "top" of the ComboBox in the "recently chosen" section

CircleRange - Class in edu.jhu.tmaj.beans.masks.color

Represents a range on a circle.

CircularReferenceUtil - Class in edu.jhu.tmaj.beans.masks.data

CircularReferenceUtil() - Constructor for class edu.jhu.tmaj.beans.masks.data.CircularReferenceUtil

clear() - Static method in class edu.jhu.tmaj.beans.cache.CachedBeans

clear() - Static method in class edu.jhu.tmaj.beans.cache.CachedDynamicMetaData

clear() - Static method in class edu.jhu.tmaj.beans.cache.CachedLookupTables

clear() - Static method in class edu.jhu.tmaj.beans.cache.CachedManyToManyBeans

clear() - Static method in class edu.jhu.tmaj.beans.cache.CachedStaticMetaData

clear() - Method in class edu.jhu.tmaj.beans.masks.color.ActionList

clear() - Method in class edu.jhu.tmaj.client.image.data.FramesHolder

clear() - Method in class edu.jhu.tmaj.client.tables.data.HorizontalTable

clear() - Method in class edu.jhu.tmaj.util.swing.GeneralListModel

CLEAR_WORKSHEET - Static variable in class edu.jhu.tmaj.beans.masks.results.ParticleAnalyzer2

Clear ImageJ console before starting.

clearActionMaskInfo() - Method in class edu.jhu.tmaj.beans.masks.meta.MetaMask

clearAll() - Method in class edu.jhu.tmaj.client.tables.data.ChangedCells

clearAll() - Method in interface edu.jhu.tmaj.util.file.TableArray

clearAll() - Method in class edu.jhu.tmaj.util.file.TableArrayImpl

clearAllCache() - Static method in class edu.jhu.tmaj.beans.cache.CacheUtils

Clear out all cached data, forcing new requests to hit the database.

clearDefaultValues() - Method in class edu.jhu.tmaj.client.tables.data.TableData4

clearDirtyRows() - Method in class edu.jhu.tmaj.client.tables.data.TableData4

Indicates that no rows have been modified, and thus no rows need to be saved.

clearHistory() - Method in class edu.jhu.tmaj.client.image.data.ArrayImageCell

Indicate the user has not yet visited this image.

ClearingListSelectionListener - Class in edu.jhu.tmaj.client.image

Added to 2 JLists, this ListSelectionListener clears the currently highlighted value in one JList if a value in the other JList is selected.

ClearingListSelectionListener(JList, JList) - Constructor for class edu.jhu.tmaj.client.image.ClearingListSelectionListener

clearList() - Method in class edu.jhu.tmaj.client.image.AbstractSessionsPanel

Clears the JList

clearRows() - Method in class edu.jhu.tmaj.client.tables.data.GeneralTableModel

clearRows() - Method in interface edu.jhu.tmaj.util.file.TableArray

clearRows() - Method in class edu.jhu.tmaj.util.file.TableArrayImpl

clearShapesFromDrawableLabel() - Method in class edu.jhu.tmaj.client.image.ArrayImagePanel

clearTableData() - Method in class edu.jhu.tmaj.client.tables.data.TableData4

Clears all data in this class.

ClientConstants - Class in edu.jhu.tmaj.config

Represents the constants found in the client config file.

ClientConstants.ClientConfigKey - Enum in edu.jhu.tmaj.config

The options in the client config file.

clone() - Method in interface edu.jhu.tmaj.util.file.TableArray

clone() - Method in class edu.jhu.tmaj.util.file.TableArrayImpl

closeAll() - Method in class edu.jhu.tmaj.client.frida.gui.shared.GeneralMaskPanel

closeAllArrayBlockFrames() - Method in class edu.jhu.tmaj.client.arraybuilder.OpenedArrayBlocksPanel

closeAllImagePluses() - Method in class edu.jhu.tmaj.client.frida.data.ImagePlusHolder

closed() - Method in class edu.jhu.tmaj.client.tables.SingleInputPanel

ClosingWindowListener - Class in edu.jhu.tmaj.client.shared

This class calls the abstract method handleWindowClosed whenever a window is closed, either programmatically or by the user.

ClosingWindowListener() - Constructor for class edu.jhu.tmaj.client.shared.ClosingWindowListener

COLLECTION_DATE_FIELD - Static variable in class edu.jhu.tmaj.beans.BlockBean

COLLECTION_DATE_FIELD - Static variable in class edu.jhu.tmaj.beans.BloodSampleBean

COLLECTION_DATE_FIELD - Static variable in class edu.jhu.tmaj.beans.TissueSampleBean

ColorCoded - Interface in edu.jhu.tmaj.client.image.data

ColorCodedObject - Enum in edu.jhu.tmaj.beans

ColorCodedString - Class in edu.jhu.tmaj.client.arraybuilder.data

ColorCodedString(String, Color) - Constructor for class edu.jhu.tmaj.client.arraybuilder.data.ColorCodedString

ColorContrastUtil - Class in edu.jhu.tmaj.util.swing

ColorContrastUtil() - Constructor for class edu.jhu.tmaj.util.swing.ColorContrastUtil

ColorDelegate - Class in edu.jhu.tmaj.client.arraybuilder.data

ColorDelegate(KeyValueGetRequest.KeyName) - Constructor for class edu.jhu.tmaj.client.arraybuilder.data.ColorDelegate

ColorLegend - Class in edu.jhu.tmaj.client.arraybuilder.data

ColorLegend() - Constructor for class edu.jhu.tmaj.client.arraybuilder.data.ColorLegend

ColorMask - Class in edu.jhu.tmaj.beans.masks.color

Represents a mask that selects pixels based upon whether or not they are in a given color range.

ColorMask(String) - Constructor for class edu.jhu.tmaj.beans.masks.color.ColorMask

ColorMaskDatabaseUtil - Class in edu.jhu.tmaj.beans.masks.color

ColorMaskDatabaseUtil() - Constructor for class edu.jhu.tmaj.beans.masks.color.ColorMaskDatabaseUtil

ColorMaskDatabaseUtil.Reader - Class in edu.jhu.tmaj.beans.masks.color

ColorMaskDatabaseUtil.Reader() - Constructor for class edu.jhu.tmaj.beans.masks.color.ColorMaskDatabaseUtil.Reader

ColorMaskDatabaseUtil.Writer - Class in edu.jhu.tmaj.beans.masks.color

ColorMaskDatabaseUtil.Writer() - Constructor for class edu.jhu.tmaj.beans.masks.color.ColorMaskDatabaseUtil.Writer

ColorMaskGui - Class in edu.jhu.tmaj.client.frida.gui.masks.color

The GUI component that gets a Color Mask.

ColorMaskGui(ColorMask, List<ExternalFileCoordinate>, IASessionBean, ImageAppGuis) - Constructor for class edu.jhu.tmaj.client.frida.gui.masks.color.ColorMaskGui

ColorTableCellRenderer - Class in edu.jhu.tmaj.client.tables.data

This class relies on the CellEditor to determine the Color of the cell Renderer.

ColorTableCellRenderer() - Constructor for class edu.jhu.tmaj.client.tables.data.ColorTableCellRenderer

colorToPixel(Color) - Static method in class edu.jhu.tmaj.beans.masks.data.PixelUtil

Converts a java.awt.Color into a int pixel.

columnAdded(TableColumnModelEvent) - Method in class edu.jhu.tmaj.client.tables.data.TableColumnModelAdapter

ColumnExpanderMouseListener - Class in edu.jhu.tmaj.client.tables.data

Added to a TableHeader, this MouseListener sets the column to the natural size when double clicked.

ColumnExpanderMouseListener(JTable) - Constructor for class edu.jhu.tmaj.client.tables.data.ColumnExpanderMouseListener

columnMarginChanged(ChangeEvent) - Method in class edu.jhu.tmaj.client.tables.data.TableColumnModelAdapter

columnMoved(TableColumnModelEvent) - Method in class edu.jhu.tmaj.client.tables.data.TableColumnModelAdapter

columnName - Variable in enum edu.jhu.tmaj.servlet.request.impl.SurgPathNumberRequest.TableType

columnRemoved(TableColumnModelEvent) - Method in class edu.jhu.tmaj.client.tables.data.TableColumnModelAdapter

columnSelectionChanged(ListSelectionEvent) - Method in class edu.jhu.tmaj.client.tables.data.TableColumnModelAdapter

ColumnSet - Class in edu.jhu.tmaj.client.tables.data

Used for one set of a ColumnModel.

ColumnSet(TableColumnModel) - Constructor for class edu.jhu.tmaj.client.tables.data.ColumnSet

Initializes this object with the columnnames and widths in tableColumnModel

ColumnWidthData - Class in edu.jhu.tmaj.client.tables.data

This class stores the user-assigned width and order to columns in a table.

ColumnWidthData() - Constructor for class edu.jhu.tmaj.client.tables.data.ColumnWidthData

CommandRequest - Interface in edu.jhu.tmaj.servlet.request

All Requests must implement this interface.

CommandResponse - Interface in edu.jhu.tmaj.servlet.response

All ServerResponses implement this class; it contains two methods, one that returns whether the operation was successful and another that returns a String describing the error if the ServerRequest was not successful.

CommandServlet - Class in edu.jhu.tmaj.servlet

This class handles all Requests made to the server on Apache Tomcat, and returns a Response.

CommandServlet() - Constructor for class edu.jhu.tmaj.servlet.CommandServlet

CommandServletClient - Class in edu.jhu.tmaj.servlet

This class is responsible for sending all Request objects from the client to the server.

CommandServletClient() - Constructor for class edu.jhu.tmaj.servlet.CommandServletClient

CommandServletClient(URL) - Constructor for class edu.jhu.tmaj.servlet.CommandServletClient

compare(JBean, JBean) - Method in class edu.jhu.tmaj.beans.data.PrimaryKeyComparator

compare(ActionMaskInfo, ActionMaskInfo) - Method in class edu.jhu.tmaj.beans.masks.meta.MetaMask.ActionMaskInfoComparable

compare(Object, Object) - Method in class edu.jhu.tmaj.client.image.data.TableFieldComparator

compare(TableSection, TableSection) - Method in class edu.jhu.tmaj.client.image.data.TableSectionComparator

compare(Object, Object) - Method in class edu.jhu.tmaj.client.tables.data.TableComparator

compare(Object, Object) - Method in class edu.jhu.tmaj.util.data.AlphabeticalComparator

compare(Object, Object) - Method in class edu.jhu.tmaj.util.data.DefaultComparator

compareTo(Object) - Method in class edu.jhu.tmaj.beans.ArrayBlockBean

compareTo(Object) - Method in class edu.jhu.tmaj.beans.ArraySlideBean

compareTo(LookupRecord) - Method in class edu.jhu.tmaj.beans.data.datatypes.LookupRecord

compareTo(Object) - Method in class edu.jhu.tmaj.beans.data.StaticEnumeration

compareTo(Object) - Method in class edu.jhu.tmaj.beans.exfile.ExternalFile

compareTo(Object) - Method in class edu.jhu.tmaj.beans.exfile.ExternalFolder

compareTo(Object) - Method in class edu.jhu.tmaj.beans.JBean

Compares this Bean to another Bean by doing a case-insensitive compare using toString()

compareTo(Mask) - Method in class edu.jhu.tmaj.beans.masks.AbstractMask

compareTo(Object) - Method in class edu.jhu.tmaj.beans.ScanBean

compareTo(Object) - Method in class edu.jhu.tmaj.beans.SessionBean

compareTo(Object) - Method in class edu.jhu.tmaj.client.arraybuilder.data.ColorCodedString

compareTo(SubTableSection) - Method in class edu.jhu.tmaj.client.image.data.SubTableSection

compareTo(Object) - Method in class edu.jhu.tmaj.util.data.Pair

Compares by Y, then by X.

compareTo(Object) - Method in class edu.jhu.tmaj.util.data.Triplet

Returns 1 if this object is greater than the specified object, and -1 if the reverse is true.

componentResized(ComponentEvent) - Method in class edu.jhu.tmaj.client.image.data.ResizableTableComponentListener

Updates the table and scrollpane's row size if isOn() is set to true.

compressionParametersButton - Variable in class edu.jhu.tmaj.client.importer.images.ArrayImagesImportGui2

compressionParametersButtonPressed() - Method in class edu.jhu.tmaj.client.importer.images.ArrayImagesImportHelper

computeMask(ImagePlus, ExternalFile) - Method in class edu.jhu.tmaj.beans.masks.lasso.LassoMask

concatStringArrays(String[], String[]) - Static method in class edu.jhu.tmaj.util.ListConvertUtil

Merges Two String arrays into one big array.

CONCENTRATION_FIELD - Static variable in class edu.jhu.tmaj.beans.MolecularSampleBean

ConfigKey - Interface in edu.jhu.tmaj.util.config.data

Represents a key found in a config file.

ConfigKeyType - Enum in edu.jhu.tmaj.util.config.data

The types of ConfigKeys (found in a config file).

CONFLUENCE_FIELD - Static variable in class edu.jhu.tmaj.beans.CellLineExperimentBean

ConnectionFactory - Interface in edu.jhu.tmaj.database.conn

A ConnectionFactory is used to generate new Connections to the database.

ConnectionFactoryGetter - Class in edu.jhu.tmaj.database.conn

A utility class that gets a proper ConnectionFactory given the proper database type and database parameters.

ConnectionManager - Interface in edu.jhu.tmaj.database.conn

Interface for managing connections to the database.

ConnectionManagerGetter - Class in edu.jhu.tmaj.database.conn

A Utility class that gets a ConnectionManager given the proper database type and database parameters.

ConstantsHolder - Class in edu.jhu.tmaj.util.config.data

A Helper class for reading config files.

ConstantsHolder(Properties, String, List<? extends ConfigKey>) - Constructor for class edu.jhu.tmaj.util.config.data.ConstantsHolder

Constructs this object.

constructor - Variable in class edu.jhu.tmaj.client.tables.data.StandardizedCellEditor

CONTACT_USER_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.ArraySlideBean

CONTACT_USER_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.BlockBean

contains(String) - Method in class edu.jhu.tmaj.client.image.data.StringSet

containsKey(Object) - Method in class edu.jhu.tmaj.client.image.SpecialTree

containsPosition(int) - Method in class edu.jhu.tmaj.beans.masks.color.CircleRange

Returns true if the current range contains the given position.

control - Variable in class edu.jhu.tmaj.servlet.request.impl.ArrayCoreC

CONTROL_FIELD - Static variable in class edu.jhu.tmaj.beans.ArrayCoreBean

CONTROL_TISSUE_DIAGNOSIS_ID - Static variable in class edu.jhu.tmaj.beans.misc.ArrayCoreRep

The TissueDiagnosisID for Controls.

convertBytesToObject(byte[]) - Static method in class edu.jhu.tmaj.util.ByteUtil

convertBytesToObject(byte[], boolean) - Static method in class edu.jhu.tmaj.util.ByteUtil

convertCollectionToVector(Collection<T>) - Static method in class edu.jhu.tmaj.util.ListConvertUtil

convertListOfLists_TO_ListOfMaps(List<List>, List) - Static method in class edu.jhu.tmaj.util.ListConvertUtil

Convert List-of-List (spreadsheet) to a List-of-Maps.

convertListOfLists_TO_ListOfTabDelimitedStrings(List<List>) - Static method in class edu.jhu.tmaj.util.ListConvertUtil

convertListOfMaps_TO_ListOfLists(List<Map>, List) - Static method in class edu.jhu.tmaj.util.ListConvertUtil

Convert a List of Maps into a SpreadSheet-like List-Of-Lists.

convertListOfMaps_TO_ListOfTabDelimitedStrings(List<Map>, List) - Static method in class edu.jhu.tmaj.client.tables.data.GeneralTableModel

convertListOfStringsToListOfMaps(List<String>) - Static method in class edu.jhu.tmaj.util.ListConvertUtil

Converts a List of tab-delimited Strings into a List of Maps.

convertObjectToBytes(Object) - Static method in class edu.jhu.tmaj.util.ByteUtil

convertObjectToBytes(Object, boolean) - Static method in class edu.jhu.tmaj.util.ByteUtil

convertToListOfTabDelimitedStrings(GeneralTableModel) - Static method in class edu.jhu.tmaj.client.tables.data.GeneralTableModel

Converts a TableModel to a list of tab-delimited Strings.

coordinate - Variable in class edu.jhu.tmaj.beans.exfile.data.ExternalFileCoordinate

Coordinate - Class in edu.jhu.tmaj.util.data

Represents a position on an Array, where both x and y are greater than zero.

Coordinate(int, int) - Constructor for class edu.jhu.tmaj.util.data.Coordinate

CopyArrayBlockDialog - Class in edu.jhu.tmaj.client.arraybuilder

A Dialog used for copying the design of one ArrayBlock to another.

CopyArrayBlockRequest - Class in edu.jhu.tmaj.servlet.request.impl

Copies the design of one arrayBlock to another.

CopyArrayBlockRequest(int, int) - Constructor for class edu.jhu.tmaj.servlet.request.impl.CopyArrayBlockRequest

copyColumns() - Method in class edu.jhu.tmaj.client.tables.InputPanel4

copyFile(File, File) - Method in interface edu.jhu.tmaj.util.file.FileUtil

copyFile(File, File) - Method in class edu.jhu.tmaj.util.file.FileUtilImpl

copyInfo() - Method in class edu.jhu.tmaj.client.image.data.ArrayImagesClipBoard

Pastes the current information from the Table and ComboBox.

CopySessionDialog - Class in edu.jhu.tmaj.client.image

A Dialog that allows the user to copy the data from one session to another.

CopySessionRequest - Class in edu.jhu.tmaj.servlet.request.impl

Copies the scored data from one Session to another.

CopySessionRequest(int, int) - Constructor for class edu.jhu.tmaj.servlet.request.impl.CopySessionRequest

CORE_SIZE_FIELD - Static variable in class edu.jhu.tmaj.beans.ArrayBlockBean

CoreDataPanel - Class in edu.jhu.tmaj.client.arraybuilder

Represents the bottom panel in the ArrayBuilder application that displays the Specimen and Donor-Block information when a user clicks on an individual ArrayCore coordinate.

CoreDataPanel(ArrayCoreReferenceBean, CellLinesReferenceBean, ArrayBlockFrame) - Constructor for class edu.jhu.tmaj.client.arraybuilder.CoreDataPanel

Constructs this object.

counter - Variable in class edu.jhu.tmaj.beans.masks.results.ParticleAnalyzer2

CREATE_DATE_FIELD - Static variable in class edu.jhu.tmaj.beans.ArrayBlockBean

createAllDownloadFrame(ArrayImageCollectionBean) - Static method in class edu.jhu.tmaj.client.image.DownloadImagesPanel

createAndWriteKeyAndIV() - Static method in class edu.jhu.tmaj.util.crypt.KeyManagementUtil

creates a new key and initialation list and writes them to disk.

createCompressedJpeg(File, File, double, int) - Static method in class edu.jhu.tmaj.util.JpegCompressionUtil

createDrawable(ShapeRecord, DrawableLabel) - Static method in class edu.jhu.tmaj.client.image.draw.ShapeRecord

createExternalFileInDB(ExternalFolder, String, byte[]) - Static method in class edu.jhu.tmaj.beans.exfile.data.FilePutUtil

createExternalFolderInDB(String, ExternalFolder) - Static method in class edu.jhu.tmaj.beans.exfile.data.FolderPutUtil

createFolder(String, ExternalFolder) - Method in class edu.jhu.tmaj.beans.exfile.data.ExternalFileClient

createFrame(ArrayImageCollectionBean, ImageSize) - Static method in class edu.jhu.tmaj.client.image.DownloadImagesPanel

createFromResultSet(ResultSet, Set<String>) - Method in class edu.jhu.tmaj.beans.JBean

Creates this Bean from a row in the database.

createFromResultSet(ResultSet) - Method in class edu.jhu.tmaj.client.image.draw.ShapeRecord

Creates this Object from a ResultSet of a single row in the Shapes table

createFromShapeRecord(ShapeRecord) - Method in class edu.jhu.tmaj.client.image.draw.AbstractDrawable

Called from subclasses that override this method, this class only sets the shapeID variable

createFromShapeRecord(ShapeRecord) - Method in interface edu.jhu.tmaj.client.image.draw.Drawable

Creates a shape from a single record in the Shapes table

createFromShapeRecord(ShapeRecord) - Method in class edu.jhu.tmaj.client.image.draw.FreeHandDrawable

createFromShapeRecord(ShapeRecord) - Method in class edu.jhu.tmaj.client.image.draw.LineDrawable

createFromShapeRecord(ShapeRecord) - Method in class edu.jhu.tmaj.client.image.draw.PolygonDrawable

createFromShapeRecord(ShapeRecord) - Method in class edu.jhu.tmaj.client.image.draw.RectangleDrawable

createFromShapeRecord(ShapeRecord) - Method in class edu.jhu.tmaj.client.image.draw.TextDrawable

createFromSwingMap(Map<DatabaseField, Object>) - Method in class edu.jhu.tmaj.beans.dynamic.DynamicJBean

Creates this Bean, both the static and dynamic part, from a Map obtained from a JTable.

createFromSwingMap(Map<DatabaseField, Object>) - Method in class edu.jhu.tmaj.beans.JBean

Creates this Bean from a row in a swing JTable.

createNewShapeOnMousePress() - Method in class edu.jhu.tmaj.client.image.draw.AbstractDrawable

Returns true

createNewShapeOnMousePress() - Method in interface edu.jhu.tmaj.client.image.draw.Drawable

createNewShapeOnMousePress() - Method in class edu.jhu.tmaj.client.image.draw.FreeHandDrawable

createNewShapeOnMousePress() - Method in class edu.jhu.tmaj.client.image.draw.PolygonDrawable

createNewShapeOnMousePress() - Method in class edu.jhu.tmaj.client.image.draw.TextDrawable

createPopup() - Method in class edu.jhu.tmaj.client.image.data.SteppedComboBoxUI

CREATION_DATE_FIELD - Static variable in class edu.jhu.tmaj.beans.IASessionBean

CREATION_DATE_FIELD - Static variable in class edu.jhu.tmaj.beans.MachineSessionBean

CREATION_DATE_FIELD - Static variable in class edu.jhu.tmaj.beans.SessionBean

CREATOR_FIELD - Static variable in class edu.jhu.tmaj.beans.ArrayBlockBean

CryptUtil - Class in edu.jhu.tmaj.util.crypt

A utility class encryption and decryption of data (2-way).

CryptUtil() - Constructor for class edu.jhu.tmaj.util.crypt.CryptUtil

CurrentUser - Class in edu.jhu.tmaj.client.shared

Stores information about the user who is currently using the application.

CUT_DATE_FIELD - Static variable in class edu.jhu.tmaj.beans.SlideBean

CUT_NUMBER_FIELD - Static variable in class edu.jhu.tmaj.beans.SlideBean

cutNumber - Variable in class edu.jhu.tmaj.client.importer.images.data.FilenameData

D

DARK_ORANGE - Static variable in class edu.jhu.tmaj.util.swing.MoreColors

darkBlue - Static variable in class edu.jhu.tmaj.beans.masks.results.Analyzer2

DatabaseConstants - Class in edu.jhu.tmaj.database.config

Represents the values found in database.properties file.

databaseField - Variable in class edu.jhu.tmaj.client.image.data.TableField

DatabaseField - Class in edu.jhu.tmaj.database.data

This class makes up the ColumnIdentifiers for the Bean-JTables.

DatabaseField(String, DatabaseFieldType, boolean) - Constructor for class edu.jhu.tmaj.database.data.DatabaseField

DatabaseField(String, DatabaseFieldType) - Constructor for class edu.jhu.tmaj.database.data.DatabaseField

DatabaseFieldType - Enum in edu.jhu.tmaj.database.data

The data-types of a Database Field

DatabaseLink - Class in edu.jhu.tmaj.database.data

databaseParameters - Variable in class edu.jhu.tmaj.database.conn.AbstractConnectionFactory

DatabaseParameters - Class in edu.jhu.tmaj.database.conn

Represents parameters used to connect to a database, such as IP address and login information.

DatabaseParameters(InetSocketAddress, String, UserCredentials, DatabaseType, String) - Constructor for class edu.jhu.tmaj.database.conn.DatabaseParameters

DatabasePropertiesFile - Class in edu.jhu.tmaj.database.config

DatabasePropertiesFile() - Constructor for class edu.jhu.tmaj.database.config.DatabasePropertiesFile

DatabaseQuery - Class in edu.jhu.tmaj.database

A class for executing SELECT statement.

DatabaseQuery(String, DatabaseLink) - Constructor for class edu.jhu.tmaj.database.DatabaseQuery

Creates this object.

DatabaseQuery(String) - Constructor for class edu.jhu.tmaj.database.DatabaseQuery

DatabaseTable - Enum in edu.jhu.tmaj.beans.data

DatabaseType - Enum in edu.jhu.tmaj.database.data

Represents the types of databases that JAnyDatabase supports.

DatabaseUtil - Class in edu.jhu.tmaj.database

Contains various functions used to modify the database (UPDATE, INSERT, and DELETE statements) and to query the database (very simple SELECT statements).

DatabaseUtil(DatabaseLink) - Constructor for class edu.jhu.tmaj.database.DatabaseUtil

Constructs this object.

DatabaseUtil() - Constructor for class edu.jhu.tmaj.database.DatabaseUtil

DATE_CELLS_ISOLATED_FIELD - Static variable in class edu.jhu.tmaj.beans.CellLineExperimentBean

DATE_CUT_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.BlockUsageAltBean

DATE_OF_EXCHANGE_FIELD - Static variable in class edu.jhu.tmaj.beans.BlockOrSlideExchangeBean

DATE_ONLY_DATE_FORMAT - Static variable in class edu.jhu.tmaj.database.data.DateTimeFormats

DATE_RECEIVED_FIELD - Static variable in class edu.jhu.tmaj.beans.CellLineBean

DATE_SPECIMEN_TAKEN_FIELD - Static variable in class edu.jhu.tmaj.beans.dynamic.SpecimenBean

DATE_TIME_DATE_FORMAT - Static variable in class edu.jhu.tmaj.database.data.DateTimeFormats

DatedProjectSession - Class in edu.jhu.tmaj.beans.data

DatedProjectSession(int, ProjectSessionType, Date) - Constructor for class edu.jhu.tmaj.beans.data.DatedProjectSession

DateTimeFormats - Class in edu.jhu.tmaj.database.data

DateTimeFormats() - Constructor for class edu.jhu.tmaj.database.data.DateTimeFormats

dbFieldName - Variable in enum edu.jhu.tmaj.client.importer.machscores.MachineScoreField

decode(String) - Static method in class edu.jhu.tmaj.util.Base64Coder

Decodes a byte array from Base64 format.

decode(char[]) - Static method in class edu.jhu.tmaj.util.Base64Coder

Decodes a byte array from Base64 format.

decodeBase64(String) - Static method in class edu.jhu.tmaj.util.StringFormatUtils

Gets the byte array for base64 encoded string

decodeString(String) - Static method in class edu.jhu.tmaj.util.Base64Coder

Decodes a string from Base64 format.

decrypt(String) - Method in class edu.jhu.tmaj.util.crypt.CryptUtil

Decrypts a string.

DEFAULT_MAX_SIZE - Static variable in class edu.jhu.tmaj.beans.masks.results.ParticleAnalyzer2

DEFAULT_MIN_SIZE - Static variable in class edu.jhu.tmaj.beans.masks.results.ParticleAnalyzer2

DEFAULT_NORMAL_WIDTH - Static variable in class edu.jhu.tmaj.client.image.data.JTableUtil

DefaultComparator - Class in edu.jhu.tmaj.util.data

This class should be unnecessary.

DefaultComparator() - Constructor for class edu.jhu.tmaj.util.data.DefaultComparator

DefaultFileFilter - Class in edu.jhu.tmaj.util.swing

A file filter that display only directories and files that end with a specified extention

DefaultFileFilter(String) - Constructor for class edu.jhu.tmaj.util.swing.DefaultFileFilter

DefinedMasksGui - Class in edu.jhu.tmaj.client.frida.gui

All the masks that the user defines.

DefinedMasksGui(List<ExternalFileCoordinate>, MessageLabel, IASessionBean, ImageAppGuis) - Constructor for class edu.jhu.tmaj.client.frida.gui.DefinedMasksGui

delete() - Method in class edu.jhu.tmaj.beans.JBean

Deletes this Bean from the database.

delete() - Method in class edu.jhu.tmaj.beans.MachineSessionBean

delete() - Method in class edu.jhu.tmaj.beans.ScanBean

delete() - Method in class edu.jhu.tmaj.beans.SessionBean

delete() - Method in class edu.jhu.tmaj.client.tables.InputPanel4

deleteAllScanDataButtonPressed() - Method in class edu.jhu.tmaj.client.importer.images.ArrayImagesImportHelper

deleteDirtyRows() - Method in class edu.jhu.tmaj.client.tables.data.TableData4

Deletes rows in the table that have been marked by the user.

deleteFolderAndSubFolders(ExternalFolder) - Method in class edu.jhu.tmaj.beans.exfile.data.ExternalFileClient

deleteNode(DefaultMutableTreeNode, DefaultTreeModel) - Static method in class edu.jhu.tmaj.client.admin.data.TreeUtils

deleteRow() - Method in class edu.jhu.tmaj.client.tables.data.TableData4

Marks a row for deletion.

deleteScanDataButton - Variable in class edu.jhu.tmaj.client.importer.images.ArrayImagesImportGui2

deleteSingleRecord(DeleteSQL) - Method in class edu.jhu.tmaj.database.DatabaseUtil

DeleteSQL - Class in edu.jhu.tmaj.database.sql

Represents a DELETE SQL statement.

DeletionLog - Class in edu.jhu.tmaj.client.tables.logs

A ChangeLog indicating a record was deleted.

DeletionLog(RecordModify) - Constructor for class edu.jhu.tmaj.client.tables.logs.DeletionLog

DEPARTMENT_FIELD - Static variable in class edu.jhu.tmaj.beans.UserBean

DESCRIPTION_FIELD - Static variable in class edu.jhu.tmaj.beans.ProjectBean

deSelect() - Method in class edu.jhu.tmaj.client.image.data.ArrayImageCell

Indicate user has de-selected this image.

Destination - Interface in edu.jhu.tmaj.client.importer.specimens.data

Represents a place to where the import is going, for example a tableName and a fieldname, or if the table is dynamic, a tablename and a FieldID.

DestinationUtils - Class in edu.jhu.tmaj.client.importer.specimens.data

Utilities for the specimens import app that convert columnnames from a tab-delimited file into columnnames in the database.

DetachableIndicesDialog - Class in edu.jhu.tmaj.client.tables

A Dialog that displays a List of TabGroups as a list of JCheckBoxes.

Detacher - Class in edu.jhu.tmaj.client.tables

Contains functionality that allows a JTabbedPane to be split up into several windows, with each window represents one tab.

Detacher(List<TabGroup>, JTabbedPane) - Constructor for class edu.jhu.tmaj.client.tables.Detacher

DETAILS_SAMPLE_TEXT - Static variable in class edu.jhu.tmaj.client.arraybuilder.data.ArrayCoreCell

DetailsRequest - Class in edu.jhu.tmaj.servlet.request.impl

A Details request generally returns a response that is put into a table format.

DetailsRequest() - Constructor for class edu.jhu.tmaj.servlet.request.impl.DetailsRequest

DetailsResponse - Class in edu.jhu.tmaj.servlet.response.impl

Contains information to create a table describing each X and Y position.

DetailsResponse(List, List<List>, Messages) - Constructor for class edu.jhu.tmaj.servlet.response.impl.DetailsResponse

determineColumnIdentifiers() - Method in class edu.jhu.tmaj.client.tables.data.DynamicTableData

Calls the parent method, but if there are no rows, a dialog is displayed asking the user to pick a type.

determineColumnIdentifiers() - Method in class edu.jhu.tmaj.client.tables.data.TableData4

Returns a List containing the Column Identifiers for the Bean.

DIAGNOSIS_PRIMARY_FIELD - Static variable in class edu.jhu.tmaj.beans.TissueSampleBean

DIAGNOSIS_SECONDARY_FIELD - Static variable in class edu.jhu.tmaj.beans.TissueSampleBean

DiagnosisLookupRequest - Class in edu.jhu.tmaj.servlet.request.impl

Enables use of the "Automatic Lookup Feature" to lookup a Diagnosis (not a type) in ArrayImages.

DiagnosisLookupRequest(int) - Constructor for class edu.jhu.tmaj.servlet.request.impl.DiagnosisLookupRequest

DiagnosisLookupResponse - Class in edu.jhu.tmaj.servlet.response.impl

Contains the FieldID and EnumID of the looked-up diagnosis the ArrayImages table.

DiagnosisLookupResponse() - Constructor for class edu.jhu.tmaj.servlet.response.impl.DiagnosisLookupResponse

DialogUtil - Class in edu.jhu.tmaj.util.swing

This class contains methods that display information, warning, and error messages on the client side

digest(String) - Static method in class edu.jhu.tmaj.util.crypt.StringDigest

Returns a one-way hash digest of the specified string.

Dimension - Class in edu.jhu.tmaj.client.image.draw

Represents width and height.

Dimension(int, int) - Constructor for class edu.jhu.tmaj.client.image.draw.Dimension

directoryTextField - Variable in class edu.jhu.tmaj.client.importer.images.ArrayImagesImportGui2

disableAddingNewRows() - Method in class edu.jhu.tmaj.client.tables.InputPanel4

disableEditing() - Method in class edu.jhu.tmaj.client.tables.data.TableData4

Sets the tableModel such that the user can not edit the table cells.

disableEditing() - Method in class edu.jhu.tmaj.client.tables.InputPanel4

DISEASE_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.CellLineBean

display() - Method in class edu.jhu.tmaj.client.admin.AddKeysDialog

display() - Method in class edu.jhu.tmaj.client.arraybuilder.ArrayBlockFrame

display() - Method in class edu.jhu.tmaj.client.frida.gui.masks.color.ExternalFilesChooserDialog

display() - Method in class edu.jhu.tmaj.client.image.AnalysisFrame

display(IASessionBean, ProjectsGUI, DefaultMutableTreeNode, DefaultTreeModel, Frame) - Static method in class edu.jhu.tmaj.client.image.IASessionDialog

display(Point) - Method in class edu.jhu.tmaj.client.image.SaveFrame

display(SessionBean, ProjectsGUI, DefaultMutableTreeNode, DefaultTreeModel, Frame) - Static method in class edu.jhu.tmaj.client.image.SessionDialog

Displays a dialog to edit a session and returns true if a published or shared sesssion status was updated.

display(JDialog, SessionBean) - Static method in class edu.jhu.tmaj.client.image.ShareSessionDialog

display() - Method in class edu.jhu.tmaj.client.importer.images.SizeParametersGui

display(ScanBean, Component) - Static method in class edu.jhu.tmaj.client.shared.ScanScopeDialog

display() - Method in class edu.jhu.tmaj.client.tables.FindFrame

Display this frame, initialized for the specified column number.

display(int, Component) - Method in class edu.jhu.tmaj.client.tables.FindFrame

DISPLAY_SUMMARY - Static variable in class edu.jhu.tmaj.beans.masks.results.ParticleAnalyzer2

Display a summary.

displayColorLegend(boolean, JTable) - Method in class edu.jhu.tmaj.client.arraybuilder.data.ArrayCoreRenderer

displayDialog() - Method in class edu.jhu.tmaj.beans.CalibrationDialog

displayDialog(UserBean, Component) - Static method in class edu.jhu.tmaj.client.admin.AssignPasswordDialog

displayDialog(Frame) - Static method in class edu.jhu.tmaj.client.arraybuilder.CopyArrayBlockDialog

Displays a CopyArrayBlockDialog.

displayDialog(ScanBean, ProjectBean, ProjectsGUI, DefaultMutableTreeNode, DefaultTreeModel, JTree, Frame) - Static method in class edu.jhu.tmaj.client.image.SessionCreateDialog

displayDialog() - Method in class edu.jhu.tmaj.client.importer.images.ScanSelectDialog

displayDialog(UserBean, Component) - Static method in class edu.jhu.tmaj.client.shared.ChangePasswordDialog

displayDialog(Component, String, String) - Static method in class edu.jhu.tmaj.client.shared.PasswordDialog

Display a dialog prompting the user for a password.

displayDialog(Frame) - Method in class edu.jhu.tmaj.client.tables.SearchDialog

displayDialog(Component, Point) - Method in class edu.jhu.tmaj.client.tables.SortFilterDialog

displayDialogIfMessage(Component) - Method in class edu.jhu.tmaj.util.data.LevelMessages

displayFrame(List<ArrayImageCell>, DotTableFrame, ImageAppGuis, SessionBean) - Static method in class edu.jhu.tmaj.client.image.LineupFrame

displayGPL(Component) - Static method in class edu.jhu.tmaj.client.shared.GplPanel

displayGUI() - Static method in class edu.jhu.tmaj.client.shared.MainApplicationGUI

displayGUI() - Static method in class edu.jhu.tmaj.client.shared.OptionsGUI

displayHistory() - Method in class edu.jhu.tmaj.client.tables.data.TableData4

displayHistory(int) - Method in class edu.jhu.tmaj.client.tables.data.TableData4

displayHistory(String, int, int, Component) - Static method in class edu.jhu.tmaj.client.tables.logs.HistoryDialog

Displays the History Dialog, showing all the changes to the given record.

displayLegend(List<ColorCodedString>, Component) - Method in class edu.jhu.tmaj.client.arraybuilder.data.ColorLegend

Displays a frame that contains a legend indicating which colors go to which tissueTypes.

displayResults() - Method in class edu.jhu.tmaj.beans.masks.results.Analyzer2

Writes the last row in the system results table to the Results window.

displaySummary - Variable in class edu.jhu.tmaj.beans.masks.results.ParticleAnalyzer2

displayTissueDiagnoses(List<Integer>) - Static method in class edu.jhu.tmaj.client.specimens.CellLinesFrame

dispose() - Method in class edu.jhu.tmaj.client.arraybuilder.ArrayBlockFrame

dispose() - Method in class edu.jhu.tmaj.client.image.AnalysisFrame

disposeAll() - Method in class edu.jhu.tmaj.client.image.data.FramesHolder

disposeAll() - Method in class edu.jhu.tmaj.client.image.data.IASessionGuis

disposeAll() - Method in class edu.jhu.tmaj.client.image.data.SessionGuis

disposeAllWindows() - Method in class edu.jhu.tmaj.client.frida.gui.DefinedMasksGui

disposeFrame() - Static method in class edu.jhu.tmaj.client.admin.AdminGUI

disposeFrame() - Static method in class edu.jhu.tmaj.client.admin.MetaDataAppGUI

disposeFrame() - Static method in class edu.jhu.tmaj.client.arraybuilder.ArrayBuilderGUI

Dispose the ArrayBuilder application.

disposeFrame() - Static method in class edu.jhu.tmaj.client.arrays.ArrayManagerAppGUI

disposeFrame() - Static method in class edu.jhu.tmaj.client.image.ProjectsGUI

disposeFrame() - Static method in class edu.jhu.tmaj.client.importer.ImportAppGUI

Destroy the Import Application.

disposeFrame() - Static method in class edu.jhu.tmaj.client.samples.SamplesAppGUI

disposeFrame() - Static method in class edu.jhu.tmaj.client.shared.OptionsGUI

disposeFrame() - Static method in class edu.jhu.tmaj.client.specimens.SpecimensAppGUI

DisposeRelatedWindowsListener - Class in edu.jhu.tmaj.client.image.data

Added to a major window such that when the window is closed, all related windows are also closed.

DividedComboBox - Class in edu.jhu.tmaj.client.image.data

A ComboBox that divides its elements into groups.

DividedComboBox(List) - Constructor for class edu.jhu.tmaj.client.image.data.DividedComboBox

Initialize the ComboBox with the elements of a non-empty list.

doDelete(DeleteSQL) - Method in class edu.jhu.tmaj.database.DatabaseUtil

Handles a single update SQL statement, and returns the number of rows updated

doesGroupAdminControlUser(int, int) - Method in class edu.jhu.tmaj.beans.manytomany.UsersUsersBean

doGet(HttpServletRequest, HttpServletResponse) - Method in class edu.jhu.tmaj.servlet.CommandServlet

Handles a GET request to the servlet.

doInsert(InsertSQL) - Method in class edu.jhu.tmaj.database.DatabaseUtil

Inserts a row into the database given a SQL statement and returns the ID assigned.

doLogin(JFrame, boolean) - Static method in class edu.jhu.tmaj.client.shared.LoginDialog

Displays this dialog where a user enters a username and password and clicks the okay button to verify the entered values on the server.

doMetaDataQueries() - Method in class edu.jhu.tmaj.servlet.request.impl.ArrayCoreDetailsRequest

Add meta data to the rows from the Specimens and TissueDiagnosis meta data

doMetaDataQueries() - Method in class edu.jhu.tmaj.servlet.request.impl.DetailsRequest

Queries the Dynamic tables to add data obtained from the "Main" query.

doMetaDataQueries() - Method in class edu.jhu.tmaj.servlet.request.impl.ScoredImageDetailsRequest

Add Dynamic data from the Specimens,TissueDiagnosis, and ArrayImage sections

doMetaDataQuery(String, TableField, TableField, MainTableSection, DynamicMetaData) - Method in class edu.jhu.tmaj.servlet.request.impl.DetailsRequest

Adds MetaData (for example from the Specimens table) to the data obtained from the Main query

doModifies(List<? extends ModifySQL>, String) - Method in class edu.jhu.tmaj.database.DatabaseUtil

Executes a List of Modifying SQL statements.

doModifies(List<? extends ModifySQL>) - Method in class edu.jhu.tmaj.database.DatabaseUtil

doPost(HttpServletRequest, HttpServletResponse) - Method in class edu.jhu.tmaj.servlet.CommandServlet

Handles a POST Request to the servlet.

doRowsNeedUpdating() - Method in class edu.jhu.tmaj.client.tables.data.ChangedCells

doSearch(Search) - Method in class edu.jhu.tmaj.client.tables.data.TableData4

doSetDialog() - Method in class edu.jhu.tmaj.beans.masks.results.Analyzer2

DotTableFrame - Class in edu.jhu.tmaj.client.image

The window with the table showing all the scores the user has made.

DotTableFrame(ImageAppGuis, SessionBean) - Constructor for class edu.jhu.tmaj.client.image.DotTableFrame

doubleArrayToList(double[]) - Static method in class edu.jhu.tmaj.util.ListConvertUtil

Converts an doubles array to a List of Doubles.

DoubleTabbedPane - Class in edu.jhu.tmaj.client.tables

A TabbedPane that can have sub-tabs for each tab.

DoubleTabbedPane(List<TabGroup>) - Constructor for class edu.jhu.tmaj.client.tables.DoubleTabbedPane

Constructs this object.

DoubleTabbedPaneHolder - Interface in edu.jhu.tmaj.client.tables.data

Represents a component that contains a DoubleTabbedPane.

doUpdate(UpdateSQL) - Method in class edu.jhu.tmaj.database.DatabaseUtil

Handles a single update SQL statement, and returns the number of rows updated

downButton - Variable in class edu.jhu.tmaj.client.image.NavigationGUI

downloadFile(ExternalFile) - Method in class edu.jhu.tmaj.beans.exfile.data.ExternalFileClient

DownloadImagesPanel - Class in edu.jhu.tmaj.client.image

A frame that allows the user to download images to their local harddrive.

DownloadImagesPanel(ArrayImageCollectionBean, ImageSize) - Constructor for class edu.jhu.tmaj.client.image.DownloadImagesPanel

draw(Graphics) - Method in class edu.jhu.tmaj.client.image.draw.AbstractDrawable

Sets the color and draws the black squares aroudn the Drawable

draw(Graphics) - Method in class edu.jhu.tmaj.client.image.draw.ArrowDrawable

draw(Graphics) - Method in interface edu.jhu.tmaj.client.image.draw.Drawable

Draws the shape

draw(Graphics) - Method in class edu.jhu.tmaj.client.image.draw.FreeHandDrawable

draw(Graphics) - Method in class edu.jhu.tmaj.client.image.draw.LineDrawable

draw(Graphics) - Method in class edu.jhu.tmaj.client.image.draw.OvalDrawable

draw(Graphics) - Method in class edu.jhu.tmaj.client.image.draw.PolygonDrawable

draw(Graphics) - Method in class edu.jhu.tmaj.client.image.draw.RectangleDrawable

draw(Graphics) - Method in class edu.jhu.tmaj.client.image.draw.TextDrawable

Drawable - Interface in edu.jhu.tmaj.client.image.draw

All shapes that are drawn onto a DrawableLabel implement this interface

drawableLabel - Variable in class edu.jhu.tmaj.client.image.draw.AbstractDrawable

DrawableLabel - Class in edu.jhu.tmaj.client.image.draw

A JLabel that contains a List of Drawables that are painted if isActive is true.

DrawableLabel(String, int) - Constructor for class edu.jhu.tmaj.client.image.draw.DrawableLabel

DrawableStatus - Enum in edu.jhu.tmaj.client.image.draw

Status of the Shape indicating the to-do database action.

drawBlackSquare(Graphics, int, int) - Static method in class edu.jhu.tmaj.client.image.draw.AbstractDrawable

Draws a black square of size BLACK_SQUARE_SIZE at position (x,y)

drawBlackSquares(Graphics, Point[]) - Method in class edu.jhu.tmaj.client.image.draw.AbstractDrawable

Draws black squares around the shape (indicates the shape has been selected)

drawEllipse(ImageProcessor, ImageStatistics, int) - Method in class edu.jhu.tmaj.beans.masks.results.ParticleAnalyzer2

drawFilledParticle(ImageProcessor, Roi, ImageProcessor) - Method in class edu.jhu.tmaj.beans.masks.results.ParticleAnalyzer2

drawOutline(ImageProcessor, Roi, int) - Method in class edu.jhu.tmaj.beans.masks.results.ParticleAnalyzer2

drawParticle(ImageProcessor, Roi, ImageStatistics, ImageProcessor) - Method in class edu.jhu.tmaj.beans.masks.results.ParticleAnalyzer2

Draws a selected particle in a separate image.

drawRoiFilledParticle(ImageProcessor, Roi, ImageProcessor, int) - Method in class edu.jhu.tmaj.beans.masks.results.ParticleAnalyzer2

DUMMY_ENUMERATION_OBJECT - Static variable in class edu.jhu.tmaj.client.tables.data.TableData4

DUMMY_EXTERNAL_FOLDER - Static variable in class edu.jhu.tmaj.beans.exfile.ExternalFolder

DUMMY_EXTERNAL_FOLDER - Static variable in class edu.jhu.tmaj.client.importer.images.ArrayImagesImportHelper

DUMMY_TISSUE_DIAGNOSIS_ID - Static variable in class edu.jhu.tmaj.beans.misc.ArrayCoreRep

The tissueDiagnosisID assigned to ArrayCores that are null.

DURATION_FIELD - Static variable in class edu.jhu.tmaj.beans.AnimalExperimentBean

DynamicDataPrinter - Class in edu.jhu.tmaj.client.tables.data

Class provides functions for exporting data from a dynamic table to a tab-delimited file.

DynamicDataRecord - Class in edu.jhu.tmaj.beans.dynamic.data

Represents data that would be found in one record of a dynamic data table (for example, SpecimenData)

DynamicDataRecord(int, int, DynamicValue) - Constructor for class edu.jhu.tmaj.beans.dynamic.data.DynamicDataRecord

Initializes this class from a single record found in a dynamic data table (XXXData).

DynamicDestination - Class in edu.jhu.tmaj.client.importer.specimens.data

A FieldID that represents a field in SpecimenFields.

DynamicDestination(int) - Constructor for class edu.jhu.tmaj.client.importer.specimens.data.DynamicDestination

DynamicEnumeration - Class in edu.jhu.tmaj.beans.dynamic.data

Represents a record found in the Dynamic Enumerations Tables (such as TissueDiagnosisEnums)

DynamicEnumeration(int, int, String) - Constructor for class edu.jhu.tmaj.beans.dynamic.data.DynamicEnumeration

Initializes this class.

DynamicEnumsTable - Enum in edu.jhu.tmaj.beans.data.datatypes

Represents the 3 Dynamic enumeration tables in TMAJ.

DynamicJBean - Class in edu.jhu.tmaj.beans.dynamic

A JBean that represents a DynamicTable, such as Specimens.

DynamicJBean(StaticMetaData, DynamicMetaData) - Constructor for class edu.jhu.tmaj.beans.dynamic.DynamicJBean

DynamicMetaData - Class in edu.jhu.tmaj.beans.dynamic.data

Represents the MetaData for a Dynamic table.

DynamicMetaData() - Constructor for class edu.jhu.tmaj.beans.dynamic.data.DynamicMetaData

dynamicMetaData - Variable in class edu.jhu.tmaj.beans.dynamic.DynamicJBean

The DynamicMetaData tells which types have which dynamic fields, and which fields are enumerated.

DynamicMetaDataRequest - Class in edu.jhu.tmaj.servlet.request.impl

This Request is used to initialize DyanmicMetaData .

DynamicMetaDataRequest(FieldsTable, DynamicEnumsTable) - Constructor for class edu.jhu.tmaj.servlet.request.impl.DynamicMetaDataRequest

DynamicMetaDataResponse - Class in edu.jhu.tmaj.servlet.response.impl

Contains an initialized MetaDataBean

DynamicMetaDataResponse(DynamicMetaData) - Constructor for class edu.jhu.tmaj.servlet.response.impl.DynamicMetaDataResponse

DynamicSection - Enum in edu.jhu.tmaj.beans.data.datatypes

Represents the 3 areas of TMAJ that may have dynamic fields.

DynamicTableData - Class in edu.jhu.tmaj.client.tables.data

A class to manage the data in an InputPanel for a dynamic table.

DynamicTableData(DynamicJBean, Map<Integer, LookupRecord>, Component, boolean, boolean) - Constructor for class edu.jhu.tmaj.client.tables.data.DynamicTableData

DynamicTableData(DynamicJBean, Map<Integer, LookupRecord>, Component, boolean, boolean, BeanTableModel) - Constructor for class edu.jhu.tmaj.client.tables.data.DynamicTableData

Constructs this object.

DynamicTableModel - Class in edu.jhu.tmaj.client.tables.data

A TableModel that overrides isCellEditable() to ensure that irrelevant dynamic columns are not editable

DynamicTableModel(String) - Constructor for class edu.jhu.tmaj.client.tables.data.DynamicTableModel

DynamicTField - Class in edu.jhu.tmaj.beans.dynamic.data

The TField for a Dynamic table.

DynamicTField(int, int, String) - Constructor for class edu.jhu.tmaj.beans.dynamic.data.DynamicTField

DynamicTranslatedTable - Class in edu.jhu.tmaj.client.importer.specimens.data

A TranslatedTable that includes dynamic fieldnames.

DynamicTranslatedTable(String, String) - Constructor for class edu.jhu.tmaj.client.importer.specimens.data.DynamicTranslatedTable

DynamicTreeHelper - Class in edu.jhu.tmaj.client.admin.data

A helper class for the MetaData application.

DynamicTreeHelper() - Constructor for class edu.jhu.tmaj.client.admin.data.DynamicTreeHelper

dynamicTypeID - Variable in class edu.jhu.tmaj.beans.dynamic.data.DynamicTField

DynamicValue - Class in edu.jhu.tmaj.beans.dynamic.data

Represents a combination of the EnumerationID and FieldValue columns in a dynamic data table (xxxData).

E

editNode(Object, DefaultMutableTreeNode, DefaultTreeModel) - Static method in class edu.jhu.tmaj.client.admin.data.TreeUtils

edu.jhu.tmaj.beans - package edu.jhu.tmaj.beans

Provides the bean classes, which generally represent a single table in the database.

edu.jhu.tmaj.beans.cache - package edu.jhu.tmaj.beans.cache

Contains classes that cache JBeans,Lookup Tables,ManyToManyBeans,StaticMetaData, and DynamicMetaData.

edu.jhu.tmaj.beans.data - package edu.jhu.tmaj.beans.data

Provides data structure and helper classes for classes in the beans package.

edu.jhu.tmaj.beans.data.datatypes - package edu.jhu.tmaj.beans.data.datatypes

edu.jhu.tmaj.beans.dynamic - package edu.jhu.tmaj.beans.dynamic

edu.jhu.tmaj.beans.dynamic.data - package edu.jhu.tmaj.beans.dynamic.data

edu.jhu.tmaj.beans.exfile - package edu.jhu.tmaj.beans.exfile

edu.jhu.tmaj.beans.exfile.data - package edu.jhu.tmaj.beans.exfile.data

edu.jhu.tmaj.beans.manytomany - package edu.jhu.tmaj.beans.manytomany

The manyToMany beans represent the ManyToMany tables in the database.

edu.jhu.tmaj.beans.masks - package edu.jhu.tmaj.beans.masks

edu.jhu.tmaj.beans.masks.color - package edu.jhu.tmaj.beans.masks.color

edu.jhu.tmaj.beans.masks.data - package edu.jhu.tmaj.beans.masks.data

edu.jhu.tmaj.beans.masks.filter - package edu.jhu.tmaj.beans.masks.filter

edu.jhu.tmaj.beans.masks.lasso - package edu.jhu.tmaj.beans.masks.lasso

edu.jhu.tmaj.beans.masks.meta - package edu.jhu.tmaj.beans.masks.meta

edu.jhu.tmaj.beans.masks.results - package edu.jhu.tmaj.beans.masks.results

edu.jhu.tmaj.beans.misc - package edu.jhu.tmaj.beans.misc

edu.jhu.tmaj.beans2 - package edu.jhu.tmaj.beans2

edu.jhu.tmaj.client.admin - package edu.jhu.tmaj.client.admin

Provides the gui classes for running the Admin application on the client.

edu.jhu.tmaj.client.admin.data - package edu.jhu.tmaj.client.admin.data

Provides data structures and helper classes for running the Admin application.

edu.jhu.tmaj.client.arraybuilder - package edu.jhu.tmaj.client.arraybuilder

Provides the gui classes for running the ArrayBuilder application on the client.

edu.jhu.tmaj.client.arraybuilder.data - package edu.jhu.tmaj.client.arraybuilder.data

Provides data structures and helper classes for running the ArrayBuilder application.

edu.jhu.tmaj.client.arrays - package edu.jhu.tmaj.client.arrays

Provides the gui classes for running the ArrayManager application on the client.

edu.jhu.tmaj.client.frida.data - package edu.jhu.tmaj.client.frida.data

edu.jhu.tmaj.client.frida.gui - package edu.jhu.tmaj.client.frida.gui

edu.jhu.tmaj.client.frida.gui.masks - package edu.jhu.tmaj.client.frida.gui.masks

edu.jhu.tmaj.client.frida.gui.masks.color - package edu.jhu.tmaj.client.frida.gui.masks.color

edu.jhu.tmaj.client.frida.gui.masks.filter - package edu.jhu.tmaj.client.frida.gui.masks.filter

edu.jhu.tmaj.client.frida.gui.masks.lasso - package edu.jhu.tmaj.client.frida.gui.masks.lasso

edu.jhu.tmaj.client.frida.gui.masks.meta - package edu.jhu.tmaj.client.frida.gui.masks.meta

edu.jhu.tmaj.client.frida.gui.shared - package edu.jhu.tmaj.client.frida.gui.shared

edu.jhu.tmaj.client.image - package edu.jhu.tmaj.client.image

Provides the gui classes for running the Image Analysis application on the client.

edu.jhu.tmaj.client.image.data - package edu.jhu.tmaj.client.image.data

Provides data structures and helper classes for running the Image Analysis application.

edu.jhu.tmaj.client.image.draw - package edu.jhu.tmaj.client.image.draw

Provides classes that allow the user to draw shapes or text on a JLabel.

edu.jhu.tmaj.client.importer - package edu.jhu.tmaj.client.importer

Provides classes that import data into the database from other sources, such as images from a TMA scanning system, or a tab-delimited file containing data on specimens and patients.

edu.jhu.tmaj.client.importer.data - package edu.jhu.tmaj.client.importer.data

Provides data structures and helper classes for running the Import application.

edu.jhu.tmaj.client.importer.images - package edu.jhu.tmaj.client.importer.images

edu.jhu.tmaj.client.importer.images.data - package edu.jhu.tmaj.client.importer.images.data

edu.jhu.tmaj.client.importer.machscores - package edu.jhu.tmaj.client.importer.machscores

edu.jhu.tmaj.client.importer.specimens - package edu.jhu.tmaj.client.importer.specimens

edu.jhu.tmaj.client.importer.specimens.data - package edu.jhu.tmaj.client.importer.specimens.data

edu.jhu.tmaj.client.samples - package edu.jhu.tmaj.client.samples

Contains GUI classes for the Cleveland Clinic Samples Application.

edu.jhu.tmaj.client.shared - package edu.jhu.tmaj.client.shared

Contains GUI components shared by client applications.

edu.jhu.tmaj.client.specimens - package edu.jhu.tmaj.client.specimens

Provides classes that allow for detailed input and modification of Specimens,Donor-Blocks, and TissueDiagonsis.

edu.jhu.tmaj.client.tables - package edu.jhu.tmaj.client.tables

Contain classes that lets a database table be displayed as a JTable.

edu.jhu.tmaj.client.tables.data - package edu.jhu.tmaj.client.tables.data

Provides data classes that support the InputPanel Table Guis.

edu.jhu.tmaj.client.tables.logs - package edu.jhu.tmaj.client.tables.logs

Provide classes that enabled database logging of any changes.

edu.jhu.tmaj.config - package edu.jhu.tmaj.config

edu.jhu.tmaj.database - package edu.jhu.tmaj.database

A stand-alone package called JAnyDatabase.

edu.jhu.tmaj.database.config - package edu.jhu.tmaj.database.config

edu.jhu.tmaj.database.conn - package edu.jhu.tmaj.database.conn

Contains classes for generating and managing database connections.

edu.jhu.tmaj.database.data - package edu.jhu.tmaj.database.data

edu.jhu.tmaj.database.sql - package edu.jhu.tmaj.database.sql

Provides the classes that convert SQL objects into raw-sql by using database-specific SQLManagers.

edu.jhu.tmaj.database.test - package edu.jhu.tmaj.database.test

edu.jhu.tmaj.servlet - package edu.jhu.tmaj.servlet

Provides the classes that allow communication between the client and server.

edu.jhu.tmaj.servlet.request - package edu.jhu.tmaj.servlet.request

edu.jhu.tmaj.servlet.request.impl - package edu.jhu.tmaj.servlet.request.impl

Contains all the Requests that can be sent to the server from the client.

edu.jhu.tmaj.servlet.response - package edu.jhu.tmaj.servlet.response

Contains all the Responses that the server can send to the client after a Request.

edu.jhu.tmaj.servlet.response.impl - package edu.jhu.tmaj.servlet.response.impl

edu.jhu.tmaj.util - package edu.jhu.tmaj.util

Provides utility classes such as string-formatting and reading/writing files.

edu.jhu.tmaj.util.config.data - package edu.jhu.tmaj.util.config.data

edu.jhu.tmaj.util.crypt - package edu.jhu.tmaj.util.crypt

Provides classes that encrypt data.

edu.jhu.tmaj.util.data - package edu.jhu.tmaj.util.data

Contains mostly data structure packages, that are all shared among the all of the tmaj packages.

edu.jhu.tmaj.util.file - package edu.jhu.tmaj.util.file

edu.jhu.tmaj.util.swing - package edu.jhu.tmaj.util.swing

ELLIPSES - Static variable in class edu.jhu.tmaj.beans.masks.results.ParticleAnalyzer2

EMAIL_FIELD - Static variable in class edu.jhu.tmaj.beans.UserBean

encode(byte[]) - Static method in class edu.jhu.tmaj.util.Base64Coder

Encodes a byte array into Base64 format.

encode(byte[], int) - Static method in class edu.jhu.tmaj.util.Base64Coder

Encodes a byte array into Base64 format.

encodeBase64(byte[]) - Static method in class edu.jhu.tmaj.util.StringFormatUtils

Gets the String representation of a byte array using base64 encoding.

encodeString(String) - Static method in class edu.jhu.tmaj.util.Base64Coder

Encodes a string into Base64 format.

encrypt(String) - Method in class edu.jhu.tmaj.util.crypt.CryptUtil

Encrypts a string.

END_DATE_FIELD - Static variable in class edu.jhu.tmaj.beans.AnimalExperimentBean

END_USER_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.BlockUsageAltBean

ENDING_NUMBER_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.BlockUsageAltBean

ensureRangeContains(int) - Method in class edu.jhu.tmaj.beans.masks.color.CircleRange

Ensures that the given position is in current given range; if necessary, the range is expanded.

ensureRangeContains(HsbPixel) - Method in class edu.jhu.tmaj.beans.masks.color.HsbRange

Updates the range to the smallest amount that will encompass the prevoius range, plus the supplied pixel.

ensureRangeContains(int) - Method in class edu.jhu.tmaj.beans.masks.color.SimpleRange

Expands this range if necessary to include the supplied value.

ensureRangeContains(HsbPixel) - Method in class edu.jhu.tmaj.client.frida.gui.masks.color.HsbRangeComponent

Ensures this GUI component contains the hsbPixel supplied by expanding the JSliders if necessary.

ensureRangeContains(List<HsbPixel>) - Method in class edu.jhu.tmaj.client.frida.gui.masks.color.HsbRangeComponent

Same as ensureRangeContains(), except a List is processed instead of just 1 pixel.

ensureUserWillSeeSpecimenInSpecimensApp(UserBean, int, boolean) - Static method in class edu.jhu.tmaj.beans.manytomany.UsersSpecimens

Guarantee that the given user will be able to access to given specimen.

EnumerationGroup - Enum in edu.jhu.tmaj.beans.data.datatypes

Represents the group types that appear in the Enumerations table.

EnumerationsRequest - Class in edu.jhu.tmaj.servlet.request.impl

Gets the Enumerations for given an EnumerationsGroup.

EnumerationsRequest(EnumerationGroup) - Constructor for class edu.jhu.tmaj.servlet.request.impl.EnumerationsRequest

EnumerationsResponse - Class in edu.jhu.tmaj.servlet.response.impl

Contains a list of StaticEnumerations obtained from an EnumerationsRequest.

EnumerationsResponse(List<StaticEnumeration>) - Constructor for class edu.jhu.tmaj.servlet.response.impl.EnumerationsResponse

EnvironmentUtils - Class in edu.jhu.tmaj.util.config.data

Contains a method that determines if the user is running Windows.

equals(Object) - Method in class edu.jhu.tmaj.beans.data.datatypes.LookupRecord

equals(Object) - Method in class edu.jhu.tmaj.beans.data.StaticEnumeration

equals(Object) - Method in class edu.jhu.tmaj.beans.dynamic.data.DynamicEnumeration

equals(Object) - Method in class edu.jhu.tmaj.beans.dynamic.data.DynamicTField

equals(Object) - Method in class edu.jhu.tmaj.beans.exfile.ExternalFile

equals(Object) - Method in class edu.jhu.tmaj.beans.exfile.ExternalFolder

equals(Object) - Method in class edu.jhu.tmaj.beans.JBean

Returns true if this bean is equal to obj, that is, if the bean's classes and ids are the same.

equals(Object) - Method in class edu.jhu.tmaj.beans.masks.color.HsbRange

equals(Object) - Method in class edu.jhu.tmaj.beans.masks.color.SimpleRange

equals(Object) - Method in class edu.jhu.tmaj.beans.masks.data.HsbPixel

equals(ArrayCoreData, ArrayCoreRep) - Static method in class edu.jhu.tmaj.client.arraybuilder.data.ArrayCoreData

equals(Object) - Method in class edu.jhu.tmaj.client.image.data.ArrayImageCell

Returns true if object is an ArrayImage with the same x and y coordinates.

equals(Object) - Method in class edu.jhu.tmaj.client.image.data.SubTableSection

equals(Object) - Method in class edu.jhu.tmaj.client.image.data.TableField

Returns true if tableName and fieldName are equal

equals(Object) - Method in class edu.jhu.tmaj.client.image.data.UserPermission

equals(Object) - Method in class edu.jhu.tmaj.client.importer.specimens.data.RecordIdentifier

equals(Object) - Method in class edu.jhu.tmaj.client.tables.data.SearchTerm

Returns true if the tableName and fieldName are equal

equals(Object) - Method in class edu.jhu.tmaj.database.data.DatabaseField

equals(Object) - Method in class edu.jhu.tmaj.util.data.Pair

equals(Object) - Method in class edu.jhu.tmaj.util.data.Triplet

equals(Object) - Method in interface edu.jhu.tmaj.util.file.TableArray

equals(Object) - Method in class edu.jhu.tmaj.util.file.TableArrayImpl

eraseOutsideRoi(ImageProcessor, Rectangle, ImageProcessor) - Method in class edu.jhu.tmaj.beans.masks.results.ParticleAnalyzer2

ErrorResponse - Class in edu.jhu.tmaj.servlet.response

A ServerResponse for a ServerRequest that failed, along with the reason the ServerRequest failed.

ErrorResponse(String) - Constructor for class edu.jhu.tmaj.servlet.response.ErrorResponse

ErrorUtil - Class in edu.jhu.tmaj.util

ETHNICITY_FIELD - Static variable in class edu.jhu.tmaj.beans.CellLineBean

ExcelUtil - Class in edu.jhu.tmaj.util

Contains utilities for opening Microsoft Excel from our program.

EXCLUDE_EDGE_PARTICLES - Static variable in class edu.jhu.tmaj.beans.masks.results.ParticleAnalyzer2

Do not measure particles touching edge of image.

excludeEdgeParticles - Variable in class edu.jhu.tmaj.beans.masks.results.ParticleAnalyzer2

execute() - Method in class edu.jhu.tmaj.database.DatabaseQuery

executeCommand() - Method in class edu.jhu.tmaj.servlet.request.BaseRequest

executeCommand() - Method in interface edu.jhu.tmaj.servlet.request.CommandRequest

Executes code on the server side that queries the database, and returns a ServerResponse.

executeCommand() - Method in class edu.jhu.tmaj.servlet.request.impl.InitDatabaseRequest

exists() - Method in class edu.jhu.tmaj.client.importer.images.data.ArrayImage2

expand(Map<Object, Object>) - Method in class edu.jhu.tmaj.beans.data.SubMap

expandColumn(JTable, int) - Static method in class edu.jhu.tmaj.client.tables.data.ColumnExpanderMouseListener

expandColumnWidth(TableColumnModel, String, int) - Static method in class edu.jhu.tmaj.client.tables.data.ColumnWidthData

ExpandingMap - Class in edu.jhu.tmaj.beans.data

Here is how an expanding map works: An expanding map actually keeps track of a LIST of maps.

ExpandingMap(Object[]) - Constructor for class edu.jhu.tmaj.beans.data.ExpandingMap

expandMaps() - Method in class edu.jhu.tmaj.beans.data.ExpandingMap

expandTree() - Method in class edu.jhu.tmaj.client.image.ProjectsGUI

Expands the first row of the tree to save the user a mouse click.

EXPERIMENT_NUMBER_FIELD - Static variable in class edu.jhu.tmaj.beans.AnimalExperimentBean

EXPERIMENT_NUMBER_FIELD - Static variable in class edu.jhu.tmaj.beans.ArraySlideBean

EXPERIMENT_NUMBER_FIELD - Static variable in class edu.jhu.tmaj.beans.CellLineBean

EXPERIMENT_NUMBER_FIELD - Static variable in class edu.jhu.tmaj.beans.CellLineExperimentBean

EXPERIMENT_NUMBER_FIELD - Static variable in class edu.jhu.tmaj.beans.SlideBean

EXPERIMENTER_FIELD - Static variable in class edu.jhu.tmaj.beans.ArraySlideBean

EXPERIMENTER_FIELD - Static variable in class edu.jhu.tmaj.beans.SlideBean

EXPERIMENTER_USER_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.AnimalExperimentBean

exportCellLine(boolean) - Method in class edu.jhu.tmaj.client.arraybuilder.data.ArrayBlockExporter

exportFull(Set<Integer>, boolean) - Method in class edu.jhu.tmaj.client.arraybuilder.data.ArrayBlockExporterFull

Exports full detail on each of the ArrayCores in the ArrayBlock to a file.

exportStandard(ArrayBlockExporter.ArrayExportFormat, boolean) - Method in class edu.jhu.tmaj.client.arraybuilder.data.ArrayBlockExporter

Exports the arrayBlock design to a tab-delimited file in a grid format, where each grid location corresponds to an ArrayCore position.

ExpressEntryDialog - Class in edu.jhu.tmaj.client.arraybuilder

A dialog in the ArrayBuilder App that allows the user to quickly obtain a TissueDiagnosisID by entering specimen and and donor-block information.

ExpressEntryRequest - Class in edu.jhu.tmaj.servlet.request.impl

Inserts a new specimen, block, and tissueDiagnosis in the ExpressEntryDialog in the ArrayBuilder application.

ExpressEntryRequest(String, int, String, int, int, String, String, String, int, boolean) - Constructor for class edu.jhu.tmaj.servlet.request.impl.ExpressEntryRequest

ExpressEntryResponse - Class in edu.jhu.tmaj.servlet.response.impl

Contains a patientID,SpecimenID,BlockID, tissueDiagnosisID.

ExpressEntryResponse(int, int, int, int) - Constructor for class edu.jhu.tmaj.servlet.response.impl.ExpressEntryResponse

externalFile - Variable in class edu.jhu.tmaj.beans.exfile.data.ExternalFileCoordinate

ExternalFile - Class in edu.jhu.tmaj.beans.exfile

ExternalFile(int, ExternalFolder, String, long) - Constructor for class edu.jhu.tmaj.beans.exfile.ExternalFile

ExternalFileClient - Class in edu.jhu.tmaj.beans.exfile.data

ExternalFileCoordinate - Class in edu.jhu.tmaj.beans.exfile.data

ExternalFileCoordinate(ExternalFile, Coordinate) - Constructor for class edu.jhu.tmaj.beans.exfile.data.ExternalFileCoordinate

ExternalFileCoordinateResponse - Class in edu.jhu.tmaj.servlet.response.impl

ExternalFileCoordinateResponse(List<ExternalFileCoordinate>) - Constructor for class edu.jhu.tmaj.servlet.response.impl.ExternalFileCoordinateResponse

externalFileExistsOnFileServer(String, ExternalFolder) - Static method in class edu.jhu.tmaj.beans.exfile.data.FolderGetUtil

ExternalFilesChooserDialog - Class in edu.jhu.tmaj.client.frida.gui.masks.color

ExternalFilesChooserDialog(List<ExternalFileCoordinate>, Component) - Constructor for class edu.jhu.tmaj.client.frida.gui.masks.color.ExternalFilesChooserDialog

ExternalFolder - Class in edu.jhu.tmaj.beans.exfile

ExternalFolder(int, String, ExternalFolder) - Constructor for class edu.jhu.tmaj.beans.exfile.ExternalFolder

externalFolderComboBox - Variable in class edu.jhu.tmaj.client.importer.images.ArrayImagesImportGui2

externalFolderExistsInDatabase(String, ExternalFolder) - Static method in class edu.jhu.tmaj.beans.exfile.data.FolderGetUtil

extraInformation - Variable in class edu.jhu.tmaj.client.importer.images.data.FilenameData

F

failed() - Method in class edu.jhu.tmaj.servlet.response.impl.DiagnosisLookupResponse

FastCollection<E> - Class in edu.jhu.tmaj.client.image.data

Similar to a List, this class provides a fastIndexOf(object) method that is quicker.

FastCollection() - Constructor for class edu.jhu.tmaj.client.image.data.FastCollection

fastIndexOf(E) - Method in class edu.jhu.tmaj.client.image.data.FastCollection

field - Variable in class edu.jhu.tmaj.client.tables.CheckBoxField

fieldID - Variable in class edu.jhu.tmaj.beans.dynamic.data.DynamicTField

fieldID - Variable in class edu.jhu.tmaj.client.importer.specimens.data.DynamicDestination

fieldName - Variable in class edu.jhu.tmaj.client.importer.specimens.data.StaticDestination

FieldsTable - Enum in edu.jhu.tmaj.beans.data.datatypes

Any of the 3 Dynamic field tables in the TMAJ database.

FieldUpdateLog - Class in edu.jhu.tmaj.client.tables.logs

A ChangeLog indicating a field of a record was updated.

FieldUpdateLog(RecordModify, String, String, String) - Constructor for class edu.jhu.tmaj.client.tables.logs.FieldUpdateLog

Constructs this object.

file - Variable in class edu.jhu.tmaj.client.frida.data.ImagePlusInfo

The file of the ImagePlus

FileChecksumRequest - Class in edu.jhu.tmaj.servlet.request.impl

FileChecksumRequest(ExternalFile) - Constructor for class edu.jhu.tmaj.servlet.request.impl.FileChecksumRequest

FileChecksumResponse - Class in edu.jhu.tmaj.servlet.response.impl

fileChooser - Variable in class edu.jhu.tmaj.client.importer.images.ArrayImagesImportGui2

FileCoordinate - Class in edu.jhu.tmaj.client.importer.images.data

Represents a file name and a coordinate.

FileCoordinate(File, Coordinate) - Constructor for class edu.jhu.tmaj.client.importer.images.data.FileCoordinate

FileData - Class in edu.jhu.tmaj.util.data

Represents the data found in a tab-delimited file.

FileData() - Constructor for class edu.jhu.tmaj.util.data.FileData

FileDataUtilsOld - Class in edu.jhu.tmaj.util

FileDeleteRequest - Class in edu.jhu.tmaj.servlet.request.impl

FileDeleteRequest(ExternalFile) - Constructor for class edu.jhu.tmaj.servlet.request.impl.FileDeleteRequest

FileDownloadRequest - Class in edu.jhu.tmaj.servlet.request.impl

FileDownloadRequest(ExternalFile) - Constructor for class edu.jhu.tmaj.servlet.request.impl.FileDownloadRequest

FileDownloadResponse - Class in edu.jhu.tmaj.servlet.response.impl

FileDownloadResponse(byte[]) - Constructor for class edu.jhu.tmaj.servlet.response.impl.FileDownloadResponse

fileExists(String, ExternalFolder) - Static method in class edu.jhu.tmaj.beans.exfile.data.FileGetUtil

fileExists() - Method in class edu.jhu.tmaj.servlet.response.impl.FileChecksumResponse

fileFieldName - Variable in enum edu.jhu.tmaj.client.importer.machscores.MachineScoreField

FileGetAllUtil - Class in edu.jhu.tmaj.beans.exfile.data

FileGetUtil - Class in edu.jhu.tmaj.beans.exfile.data

FileManager - Class in edu.jhu.tmaj.util

Utilities for reading and writing files.

filename - Variable in class edu.jhu.tmaj.client.importer.images.data.FilenameData

FilenameData - Class in edu.jhu.tmaj.client.importer.images.data

A way of writing files that uniquely identifies a scan in TMAJ, while still conveying infomration that is useful to the end-user such as stain and bar code.

FilePathUtils - Class in edu.jhu.tmaj.util

FilePathUtils() - Constructor for class edu.jhu.tmaj.util.FilePathUtils

FilePutUtil - Class in edu.jhu.tmaj.beans.exfile.data

FileResponse - Class in edu.jhu.tmaj.servlet.response.impl

FileResponse(ExternalFile) - Constructor for class edu.jhu.tmaj.servlet.response.impl.FileResponse

FileSelectorPanel - Class in edu.jhu.tmaj.client.importer.data

A Panel that lets the user select multiple files.

FileSelectorPanel(JFileChooser) - Constructor for class edu.jhu.tmaj.client.importer.data.FileSelectorPanel

FilesGetRequest - Class in edu.jhu.tmaj.servlet.request.impl

FilesGetRequest(ExternalFolder) - Constructor for class edu.jhu.tmaj.servlet.request.impl.FilesGetRequest

FilesLargeGetRequest - Class in edu.jhu.tmaj.servlet.request.impl

FilesLargeGetRequest(int) - Constructor for class edu.jhu.tmaj.servlet.request.impl.FilesLargeGetRequest

FilesResponse - Class in edu.jhu.tmaj.servlet.response.impl

FilesResponse(List<ExternalFile>) - Constructor for class edu.jhu.tmaj.servlet.response.impl.FilesResponse

FileStats - Class in edu.jhu.tmaj.beans.masks.results

FileStats(int) - Constructor for class edu.jhu.tmaj.beans.masks.results.FileStats

FileUploadRequest - Class in edu.jhu.tmaj.servlet.request.impl

FileUploadRequest(ExternalFolder, String, byte[]) - Constructor for class edu.jhu.tmaj.servlet.request.impl.FileUploadRequest

FileUtil - Interface in edu.jhu.tmaj.util.file

FileUtilImpl - Class in edu.jhu.tmaj.util.file

FileUtilImpl() - Constructor for class edu.jhu.tmaj.util.file.FileUtilImpl

FileUtilOld - Class in edu.jhu.tmaj.util

FileUtilOld() - Constructor for class edu.jhu.tmaj.util.FileUtilOld

FilterMask - Class in edu.jhu.tmaj.beans.masks.filter

FilterMask(String) - Constructor for class edu.jhu.tmaj.beans.masks.filter.FilterMask

FilterMaskDatabaseUtil - Class in edu.jhu.tmaj.beans.masks.filter

FilterMaskDatabaseUtil() - Constructor for class edu.jhu.tmaj.beans.masks.filter.FilterMaskDatabaseUtil

FilterMaskDatabaseUtil.Reader - Class in edu.jhu.tmaj.beans.masks.filter

FilterMaskDatabaseUtil.Reader() - Constructor for class edu.jhu.tmaj.beans.masks.filter.FilterMaskDatabaseUtil.Reader

FilterMaskDatabaseUtil.Writer - Class in edu.jhu.tmaj.beans.masks.filter

FilterMaskDatabaseUtil.Writer() - Constructor for class edu.jhu.tmaj.beans.masks.filter.FilterMaskDatabaseUtil.Writer

FilterMaskGui - Class in edu.jhu.tmaj.client.frida.gui.masks.filter

FilterMaskGui(FilterMask, List<ExternalFileCoordinate>, IASessionBean, ImageAppGuis) - Constructor for class edu.jhu.tmaj.client.frida.gui.masks.filter.FilterMaskGui

FilterMaskType - Enum in edu.jhu.tmaj.beans.masks.filter

FINAL_DATE_FIELD - Static variable in class edu.jhu.tmaj.beans.ArrayBlockBean

findColumn(String) - Method in class edu.jhu.tmaj.client.tables.data.GeneralTableModel

FindFrame - Class in edu.jhu.tmaj.client.tables

A Frame displayed in an InputPanel to search for values and optionally replace them.

FindFrame(JScrollPane, JTable, GeneralTableModel) - Constructor for class edu.jhu.tmaj.client.tables.FindFrame

Creates this object.

finish() - Method in class edu.jhu.tmaj.util.TextProgressMonitor

Indicate to user task has finished.

firePropertyChange(String, Object, Object) - Method in class edu.jhu.tmaj.util.swing.AbstractTableCellRenderer

Overridden for performance reasons

firePropertyChange(String, boolean, boolean) - Method in class edu.jhu.tmaj.util.swing.AbstractTableCellRenderer

Overridden for performance reasons

fireUpdateEvent() - Method in class edu.jhu.tmaj.client.image.ArrayImageFrameTable

ensures that tableData will save even if the user doesn't changed the tableData

firstParticle - Static variable in class edu.jhu.tmaj.beans.masks.results.Analyzer2

FIXATION_FIELD - Static variable in class edu.jhu.tmaj.beans.BlockBean

FIXATION_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.dynamic.SpecimenBean

FIXATION_TIME_IN_HOURS_FIELD - Static variable in class edu.jhu.tmaj.beans.CellLineExperimentBean

FIXATION_TYPE_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.CellLineExperimentBean

FlatFileSyncer - Interface in edu.jhu.tmaj.util.file

Provides a way to read and write a tableArray object to a delimited file.

FlatFileSyncerImpl - Class in edu.jhu.tmaj.util.file

FlatFileSyncerImpl() - Constructor for class edu.jhu.tmaj.util.file.FlatFileSyncerImpl

FLOAT - Static variable in class edu.jhu.tmaj.beans.masks.results.ParticleAnalyzer2

floatArrayToString(float[]) - Static method in class edu.jhu.tmaj.beans.masks.lasso.Lasso

floodFill - Variable in class edu.jhu.tmaj.beans.masks.results.ParticleAnalyzer2

FolderCheckRequest - Class in edu.jhu.tmaj.servlet.request.impl

FolderCheckRequest(ExternalFolder) - Constructor for class edu.jhu.tmaj.servlet.request.impl.FolderCheckRequest

FolderCreateRequest - Class in edu.jhu.tmaj.servlet.request.impl

FolderCreateRequest(String, ExternalFolder) - Constructor for class edu.jhu.tmaj.servlet.request.impl.FolderCreateRequest

FolderDeleteRequest - Class in edu.jhu.tmaj.servlet.request.impl

FolderDeleteRequest(ExternalFolder) - Constructor for class edu.jhu.tmaj.servlet.request.impl.FolderDeleteRequest

FolderGetAllUtil - Class in edu.jhu.tmaj.beans.exfile.data

FolderGetRequest - Class in edu.jhu.tmaj.servlet.request.impl

FolderGetRequest(ExternalFolder) - Constructor for class edu.jhu.tmaj.servlet.request.impl.FolderGetRequest

FolderGetUtil - Class in edu.jhu.tmaj.beans.exfile.data

FolderGetUtil() - Constructor for class edu.jhu.tmaj.beans.exfile.data.FolderGetUtil

folderName - Variable in class edu.jhu.tmaj.beans.exfile.data.PartialFolder

FolderNameUtil - Class in edu.jhu.tmaj.client.importer.images.data

FolderPutUtil - Class in edu.jhu.tmaj.beans.exfile.data

FolderResponse - Class in edu.jhu.tmaj.servlet.response.impl

FolderResponse(ExternalFolder) - Constructor for class edu.jhu.tmaj.servlet.response.impl.FolderResponse

FoldersResponse - Class in edu.jhu.tmaj.servlet.response.impl

FoldersResponse(List<ExternalFolder>) - Constructor for class edu.jhu.tmaj.servlet.response.impl.FoldersResponse

foreignSearch(SearchTerm, String, List) - Method in class edu.jhu.tmaj.client.tables.InputPanel4

Sets the search fields in the gui and then does a search.

Form - Class in edu.jhu.tmaj.util.swing

An example of using SpringLayout to create a forms-type layout.

formatKey(String) - Static method in class edu.jhu.tmaj.util.StringFormatUtils

Converts a string into lower case and removes any underscores or hypens.

formatStat(Number) - Static method in class edu.jhu.tmaj.beans.masks.data.MaskIntensityStatUtil

FOUR_CONNECTED - Static variable in class edu.jhu.tmaj.beans.masks.results.ParticleAnalyzer2

Use 4-connected particle tracing.

FramesHolder - Class in edu.jhu.tmaj.client.image.data

FramesHolder() - Constructor for class edu.jhu.tmaj.client.image.data.FramesHolder

FreeHandDrawable - Class in edu.jhu.tmaj.client.image.draw

A polygon

FreeHandDrawable(DrawableLabel) - Constructor for class edu.jhu.tmaj.client.image.draw.FreeHandDrawable

FridaGui - Class in edu.jhu.tmaj.client.frida.gui

FridaGui(IASessionBean, ImageAppGuis) - Constructor for class edu.jhu.tmaj.client.frida.gui.FridaGui

FullSlider - Class in edu.jhu.tmaj.client.frida.gui.masks.color

A JSlider that has arrows on the end and a text box that shows the current value.

FullSlider(int, int, ActionListener) - Constructor for class edu.jhu.tmaj.client.frida.gui.masks.color.FullSlider

Constructs this object

FullSlider.HeldMouseListener - Class in edu.jhu.tmaj.client.frida.gui.masks.color

A MouseListener that fires off a Timer when the mouse is pressed and stops the timer when the Mouse is released.

FullSlider.HeldMouseListener(Timer) - Constructor for class edu.jhu.tmaj.client.frida.gui.masks.color.FullSlider.HeldMouseListener

G

GENDER_FIELD - Static variable in class edu.jhu.tmaj.beans.CellLineBean

GeneralListModel - Class in edu.jhu.tmaj.util.swing

A ListModel for general use.

GeneralListModel() - Constructor for class edu.jhu.tmaj.util.swing.GeneralListModel

GeneralListModel(List) - Constructor for class edu.jhu.tmaj.util.swing.GeneralListModel

GeneralMaskPanel - Class in edu.jhu.tmaj.client.frida.gui.shared

GeneralMaskPanel(Mask, List<ExternalFileCoordinate>, IASessionBean, ImageAppGuis, JFrame, MaskPanelListener, boolean) - Constructor for class edu.jhu.tmaj.client.frida.gui.shared.GeneralMaskPanel

GeneralSQLMaker - Class in edu.jhu.tmaj.database.sql

A SQLMaker that provides the typical functionality for most databases.

GeneralSQLMaker() - Constructor for class edu.jhu.tmaj.database.sql.GeneralSQLMaker

GeneralTableModel - Class in edu.jhu.tmaj.client.tables.data

The TableModel used for JTables in TMAJ.

GeneralTableModel() - Constructor for class edu.jhu.tmaj.client.tables.data.GeneralTableModel

GeneralTableModel(List, List) - Constructor for class edu.jhu.tmaj.client.tables.data.GeneralTableModel

GenericBeans - Class in edu.jhu.tmaj.beans.cache

A holder class for generic JBeans, with their StaticMetaData initialized.

GENETIC_MODIFICATIONS_FIELD - Static variable in class edu.jhu.tmaj.beans.CellLineBean

get(int, int) - Method in class edu.jhu.tmaj.beans.misc.ArrayImageCollectionBean

Returns the ArrayImage as the specified position.

get(int) - Method in class edu.jhu.tmaj.client.image.data.FastCollection

getAbsoluteDirectoryOnClient(ExternalFolder) - Static method in class edu.jhu.tmaj.beans.exfile.ExternalFolder

getAbsoluteDirectoryOnClient() - Method in class edu.jhu.tmaj.beans.exfile.ExternalFolder

getAbsoluteDirectoryOnServer(ExternalFolder) - Static method in class edu.jhu.tmaj.beans.exfile.ExternalFolder

getAbsoluteDirectoryOnServer() - Method in class edu.jhu.tmaj.beans.exfile.ExternalFolder

getAbsoluteFileOnClient() - Method in class edu.jhu.tmaj.beans.exfile.ExternalFile

getAbsoluteFileOnServer() - Method in class edu.jhu.tmaj.beans.exfile.ExternalFile

getAbsoluteFileOnServer(ExternalFolder, String) - Static method in class edu.jhu.tmaj.beans.exfile.ExternalFile

getAbsolutePath(File, File) - Static method in class edu.jhu.tmaj.util.FilePathUtils

getAbstract() - Method in class edu.jhu.tmaj.beans.PaperBean

getActionMaskInfoList() - Method in class edu.jhu.tmaj.beans.masks.meta.MetaMask

Returns the ActionMaskInfos Objects in order.

getActionMaskInfoSet() - Method in class edu.jhu.tmaj.beans.masks.meta.MetaMask

Gets a list of all the masks in order that are to be added and subtracted in this meta-mask.

getActionsList() - Method in class edu.jhu.tmaj.beans.masks.color.ActionList

getAdminAppPermission() - Method in class edu.jhu.tmaj.beans.UserBean

Returns the Permission Object related to the Array Builder App

getAll() - Method in class edu.jhu.tmaj.beans.misc.ArrayImageCollectionBean

Returns a List of all ArrayImages in this class.

getAll() - Method in class edu.jhu.tmaj.client.frida.data.ImagePlusHolder

getAllExclusiveMask(int) - Static method in class edu.jhu.tmaj.beans.masks.data.MaskUtil

Gets an all-exclusive mask of the supplied size

getAllFiles() - Method in class edu.jhu.tmaj.beans.masks.lasso.LassoMask

getAllFileStats(List<ExternalFileCoordinate>, List<Mask>, Calibration, PublicSwingWorker) - Static method in class edu.jhu.tmaj.beans.masks.results.AllFileStatsUtil

getAllIASessionBeans() - Method in class edu.jhu.tmaj.client.image.AbstractSessionsPanel

Returns a list of IASessionBeans in the JList.

getAllInclusiveMask(int) - Static method in class edu.jhu.tmaj.beans.masks.data.MaskUtil

Gets a boolean[] mask where all elements are included.

getAllIndices() - Method in class edu.jhu.tmaj.client.tables.DoubleTabbedPane

getAllKey1s() - Method in class edu.jhu.tmaj.beans.manytomany.ManyToManyBean

getAllKey2s() - Method in class edu.jhu.tmaj.beans.manytomany.ManyToManyBean

getAllKeys(List<Map>) - Static method in class edu.jhu.tmaj.util.ListConvertUtil

Gets a Map containing the union of all keys found in many Maps

getAllSessionBeans() - Method in class edu.jhu.tmaj.client.image.AbstractSessionsPanel

Returns a list of SessionBeans in the JList.

getAllStaticColumnIdentifiers() - Method in class edu.jhu.tmaj.beans.JBean

Returns a List of all regular columnIdentifiers for this Bean.

getAllTissueDiagnosisBeans() - Method in class edu.jhu.tmaj.beans.ArrayCoreReferenceBean

getAltToString() - Method in class edu.jhu.tmaj.client.importer.specimens.data.PatientTranslatedTable

getAltToString() - Method in class edu.jhu.tmaj.client.importer.specimens.data.SpecimenTranslatedTable

getAltToString() - Method in class edu.jhu.tmaj.client.importer.specimens.data.TranslatedTable

getAnimalExperimentBean() - Static method in class edu.jhu.tmaj.beans.cache.GenericBeans

getApplication() - Method in class edu.jhu.tmaj.database.sql.InputLog

getArea(Polygon) - Method in class edu.jhu.tmaj.beans.masks.results.Analyzer2

getArrayBlockBean() - Static method in class edu.jhu.tmaj.beans.cache.GenericBeans

getArrayBlockBean() - Method in class edu.jhu.tmaj.client.arraybuilder.ArrayBlockFrame

getArrayBlockID() - Method in class edu.jhu.tmaj.beans.ArraySlideBean

Returns the id of the ArrayBlock from which this slide was cut.

getArrayBlockID() - Method in class edu.jhu.tmaj.beans.misc.ArrayCoreRep

Returns the ArrayBlock of which this ArrayCore is part.

getArrayBlockID() - Method in class edu.jhu.tmaj.servlet.response.impl.ImagesDirectoryResponse

getArrayBuilderPermission() - Method in class edu.jhu.tmaj.beans.UserBean

Returns the Permission Object related to the Array Builder App

getArrayBuilderTable() - Method in class edu.jhu.tmaj.client.arraybuilder.ArrayBlockFrame

getArrayCoreBean() - Static method in class edu.jhu.tmaj.beans.cache.GenericBeans

getArrayCoreBean() - Method in class edu.jhu.tmaj.client.arraybuilder.data.ArrayCoreCell

getArrayCoreCell(Coordinate) - Method in class edu.jhu.tmaj.client.arraybuilder.ArrayBuilderTable

Returns the tableModel's ArrayCoreCell for the given coordinate.

getArrayCoreData() - Method in class edu.jhu.tmaj.client.arraybuilder.TissueDiagnosisIDPanel

Returns an ArrayCoreData object representing the data the user filled in on this panel.

getArrayCoreID(Coordinate) - Method in class edu.jhu.tmaj.servlet.response.impl.ArrayImageCoresResponse

getArrayCoreReferenceBean() - Method in class edu.jhu.tmaj.servlet.response.impl.ArrayCoreReferenceResponse

getArrayImage(int, int) - Method in class edu.jhu.tmaj.client.image.ArraySlideFrame

getArrayImage() - Method in class edu.jhu.tmaj.client.image.SelectableImage

getArrayImageCollectionBean() - Method in class edu.jhu.tmaj.client.image.ArraySlideFrame

getArrayImageCollectionBean() - Method in class edu.jhu.tmaj.servlet.response.impl.ArrayImageCollectionResponse

getArrayImageEnumID() - Method in class edu.jhu.tmaj.servlet.response.impl.DiagnosisLookupResponse

getArrayImageFieldID() - Method in class edu.jhu.tmaj.servlet.response.impl.DiagnosisLookupResponse

getArrayImageFrame() - Method in class edu.jhu.tmaj.client.image.ArraySlideFrame

getArrayImageFrame() - Method in class edu.jhu.tmaj.client.image.data.SessionGuis

getArrayImageFrameTable() - Method in class edu.jhu.tmaj.client.image.ArrayImageFrame

getArrayImageID() - Method in class edu.jhu.tmaj.client.image.data.ArrayImageCell

Returns this ArrayImage's unique id in the ArrayImages table.

getArrayImagesBeanList() - Method in class edu.jhu.tmaj.servlet.response.impl.ImagesDirectoryResponse

getArraySlideBean() - Static method in class edu.jhu.tmaj.beans.cache.GenericBeans

getArraySlideDirectory(ImageSize) - Method in class edu.jhu.tmaj.beans.misc.ArrayImageCollectionBean

getArraySlideFrame() - Method in class edu.jhu.tmaj.client.image.data.SessionGuis

getArraySlideID() - Method in class edu.jhu.tmaj.beans.ScanBean

Returns the ArraySlideID that was scanned.

getArraySlideID() - Method in class edu.jhu.tmaj.servlet.response.impl.ImagesDirectoryResponse

Gets the ArraySlideID of the directory the user is importing.

getArraySlidesForProject(int) - Method in class edu.jhu.tmaj.beans.manytomany.ProjectsArraySlidesBean

Returns a Set of ArraySlideIDs of ArraySlides that are in the given project.

getAssignedID() - Method in class edu.jhu.tmaj.servlet.response.impl.MetaDataAddResponse

getAuthors() - Method in class edu.jhu.tmaj.beans.PaperBean

getAvailableCount() - Method in class edu.jhu.tmaj.util.ObjectPool

Gets the number of unused objects in the pool.

getBack(ArrayImageCell, boolean) - Method in class edu.jhu.tmaj.client.image.data.Navigator

Returns the last ArrayImage in this navigation sequence.

getBarcode() - Method in class edu.jhu.tmaj.beans.ScanBean

getBaseSQL(Search) - Method in class edu.jhu.tmaj.beans.JBean

Returns the SQL for a Search without the WHERE Clause.

getBean() - Method in enum edu.jhu.tmaj.beans.cache.CacheableBean

getBean(CacheableBean, Integer) - Static method in class edu.jhu.tmaj.beans.cache.CachedBeans

getBean(int) - Method in class edu.jhu.tmaj.client.tables.data.TableData4

Converts a row in the JTable to a JBean.

getBean() - Method in class edu.jhu.tmaj.servlet.response.impl.UpdateResponse

getBeanInDatabase() - Method in class edu.jhu.tmaj.beans.JBean

getBeanList(Search) - Method in class edu.jhu.tmaj.beans.dynamic.DynamicJBean

getBeanList(String) - Method in class edu.jhu.tmaj.beans.JBean

Returns a List of Beans from a SQL statement.

getBeanList(Search) - Method in class edu.jhu.tmaj.beans.JBean

Returns a List of Beans from a Search.

getBeanMap(CacheableBean) - Static method in class edu.jhu.tmaj.beans.cache.CachedBeans

getBeansList() - Method in class edu.jhu.tmaj.servlet.response.impl.ArrayCoresGetResponse

getBeansList() - Method in class edu.jhu.tmaj.servlet.response.impl.SelectResponse

getBlackSquares() - Method in class edu.jhu.tmaj.client.image.draw.AbstractDrawable

Returns an empty array; This method is overwritten in subclasses

getBlackSquares() - Method in class edu.jhu.tmaj.client.image.draw.FreeHandDrawable

getBlackSquares() - Method in class edu.jhu.tmaj.client.image.draw.LineDrawable

getBlackSquares() - Method in class edu.jhu.tmaj.client.image.draw.PolygonDrawable

getBlackSquares() - Method in class edu.jhu.tmaj.client.image.draw.RectangleDrawable

getBlackSquares() - Method in class edu.jhu.tmaj.client.image.draw.TextDrawable

getBlockBean(int) - Method in class edu.jhu.tmaj.beans.ArrayCoreReferenceBean

getBlockBean() - Static method in class edu.jhu.tmaj.beans.cache.GenericBeans

getBlockDesignation() - Method in class edu.jhu.tmaj.beans.BlockBean

Returns the block Designation, a letter and number written on the physical block.

getBlockID() - Method in class edu.jhu.tmaj.beans.dynamic.TissueDiagnosisBean

Returns the BlockID on which this TissueDiagnosis has been circled.

getBlockID() - Method in class edu.jhu.tmaj.beans.SlideBean

Returns the id of the Block from which this slide was cut.

getBlockID() - Method in class edu.jhu.tmaj.servlet.response.impl.ExpressEntryResponse

getBlockOrSlideExchangeBean() - Static method in class edu.jhu.tmaj.beans.cache.GenericBeans

getBlockUsageAltBean() - Static method in class edu.jhu.tmaj.beans.cache.GenericBeans

getBlockUsageBean() - Static method in class edu.jhu.tmaj.beans.cache.GenericBeans

getBloodSampleBean() - Static method in class edu.jhu.tmaj.beans.cache.GenericBeans

getBloodUsageBean() - Static method in class edu.jhu.tmaj.beans.cache.GenericBeans

getBoolean(ConfigKey) - Method in class edu.jhu.tmaj.util.config.data.ConstantsHolder

Gets the boolean value for a config key that has a boolean type.

getBooleanField(DatabaseField) - Method in class edu.jhu.tmaj.beans.JBean

Gets the boolean value of a field whose type is TFieldType.BOOLEAN

getBytes() - Method in class edu.jhu.tmaj.servlet.response.impl.FileDownloadResponse

getCalibrationCoefficient1() - Method in class edu.jhu.tmaj.beans.IASessionBean

getCalibrationCoefficient2() - Method in class edu.jhu.tmaj.beans.IASessionBean

getCalibrationCoefficient3() - Method in class edu.jhu.tmaj.beans.IASessionBean

getCalibrationCoefficient4() - Method in class edu.jhu.tmaj.beans.IASessionBean

getCalibrationCoefficient5() - Method in class edu.jhu.tmaj.beans.IASessionBean

getCalibrationFunction() - Method in class edu.jhu.tmaj.beans.IASessionBean

getCalibrationFunction() - Method in class edu.jhu.tmaj.client.frida.data.Calibration

getCell(int, int) - Method in interface edu.jhu.tmaj.util.file.TableArray

getCell(int, C) - Method in interface edu.jhu.tmaj.util.file.TableArray

getCell(int, int) - Method in class edu.jhu.tmaj.util.file.TableArrayImpl

getCell(int, C) - Method in class edu.jhu.tmaj.util.file.TableArrayImpl

getCellEditor(int, int) - Method in class edu.jhu.tmaj.client.tables.data.HorizontalTable

Returns a ComboBox CellEditor for second column if one is registered for that row number

getCellEditorValue() - Method in class edu.jhu.tmaj.client.image.data.ButtonEditor

Returns the Object in the tableModel that was last selected for editing.

getCellEditorValue() - Method in class edu.jhu.tmaj.client.image.MyTreeCellEditor

getCellLineBean() - Static method in class edu.jhu.tmaj.beans.cache.GenericBeans

getCellLineBean(int) - Method in class edu.jhu.tmaj.beans.CellLinesReferenceBean

getCellLineExperimentBean() - Static method in class edu.jhu.tmaj.beans.cache.GenericBeans

getCellLineExperimentBean(Integer) - Method in class edu.jhu.tmaj.beans.CellLinesReferenceBean

getCellLineExperimentID() - Method in class edu.jhu.tmaj.beans.dynamic.TissueDiagnosisBean

getCellLineID() - Method in class edu.jhu.tmaj.beans.CellLineExperimentBean

getCellLineName() - Method in class edu.jhu.tmaj.beans.CellLineBean

getCellLinesReferenceBean() - Method in class edu.jhu.tmaj.servlet.response.impl.CellLinesReferenceResponse

getCellValue(int, DatabaseField) - Method in class edu.jhu.tmaj.client.tables.data.TableData4

getChar() - Method in class edu.jhu.tmaj.client.image.data.ScoreData

Gets the character that will be displayed in the scoredimages position in the ArraySlide Frame.

getCheckboxText(Object) - Static method in class edu.jhu.tmaj.client.image.SpecialTree

getCheckedObjects() - Method in class edu.jhu.tmaj.client.image.SpecialTree

getChecksum() - Method in class edu.jhu.tmaj.beans.exfile.ExternalFile

getChecksum() - Method in class edu.jhu.tmaj.servlet.response.impl.FileChecksumResponse

getChecksum(byte[]) - Method in interface edu.jhu.tmaj.util.file.ChecksumUtil

getChecksum(byte[]) - Method in class edu.jhu.tmaj.util.file.ChecksumUtilImpl

getCipher() - Static method in class edu.jhu.tmaj.util.crypt.KeyManagementUtil

getClassFormat(Object) - Static method in class edu.jhu.tmaj.util.StringFormatUtils

Returns the classname of an object in parenthesis without the package information.

getClassForType(DatabaseFieldType) - Static method in class edu.jhu.tmaj.beans.JBean

getClassificationID() - Method in class edu.jhu.tmaj.beans.dynamic.data.ArrayImageDynamicField

Returns whether this dynamic fieldname is a regular dynamic field or a scoring stategy field.

getCoefficient1() - Method in class edu.jhu.tmaj.client.frida.data.Calibration

getCoefficient2() - Method in class edu.jhu.tmaj.client.frida.data.Calibration

getCoefficient3() - Method in class edu.jhu.tmaj.client.frida.data.Calibration

getCoefficient4() - Method in class edu.jhu.tmaj.client.frida.data.Calibration

getCoefficient5() - Method in class edu.jhu.tmaj.client.frida.data.Calibration

getColor() - Method in class edu.jhu.tmaj.client.arraybuilder.data.ColorCodedString

getColor(Integer) - Method in class edu.jhu.tmaj.client.arraybuilder.data.ColorDelegate

Gets a color for the supplied TissueTypeID.

getColor(ArrayImageCell, boolean) - Static method in class edu.jhu.tmaj.client.image.data.ArrayImageRenderer

Returns a proper Color for an ArrayImage based on factors such as being enabled or being visited.

getColor() - Method in interface edu.jhu.tmaj.client.image.data.ColorCoded

getColor() - Method in enum edu.jhu.tmaj.client.image.data.MainTableSection

getColor() - Method in class edu.jhu.tmaj.client.image.data.SubTableSection

getColor() - Method in class edu.jhu.tmaj.client.image.data.TableField

getColor() - Method in class edu.jhu.tmaj.client.image.draw.AbstractDrawable

Returns the color in which the drawable will be painted

getColorMaskID() - Method in class edu.jhu.tmaj.beans.masks.color.ColorMask

getColumn(int) - Method in interface edu.jhu.tmaj.util.file.TableArray

getColumn(int) - Method in class edu.jhu.tmaj.util.file.TableArrayImpl

getColumnClass(int) - Method in class edu.jhu.tmaj.client.tables.data.BeanTableModel

getColumnCount() - Method in class edu.jhu.tmaj.client.tables.data.GeneralTableModel

getColumnEnumerations - Variable in class edu.jhu.tmaj.beans2.SwingBean

getColumnID(String) - Method in class edu.jhu.tmaj.beans.masks.results.ParticleAnalyzer2

getColumnIdentifiers(Search, List<JBean>) - Method in class edu.jhu.tmaj.beans.dynamic.DynamicJBean

getColumnIdentifiers(Search, List<JBean>) - Method in class edu.jhu.tmaj.beans.JBean

Returns a List of ColumnIdentifiers based on a Search and the list of Beans generated.

getColumnIdentifiers() - Method in class edu.jhu.tmaj.client.tables.data.GeneralTableModel

getColumnIdentifiers() - Method in class edu.jhu.tmaj.servlet.response.impl.SelectResponse

getColumnName() - Method in enum edu.jhu.tmaj.client.image.data.ImageSize

getColumnName(int) - Method in class edu.jhu.tmaj.client.tables.data.GeneralTableModel

getColumnNames(MainTableSection) - Method in class edu.jhu.tmaj.client.image.data.StaticFields

getColumnNamesSet(ResultSet) - Static method in class edu.jhu.tmaj.beans.JBean

Returns a Set of lowercase column names contained in the ResultSet

getColumns - Variable in class edu.jhu.tmaj.beans2.SwingBean

getColumns() - Method in interface edu.jhu.tmaj.util.file.TableArray

getColumns() - Method in class edu.jhu.tmaj.util.file.TableArrayImpl

getColumnValue(String) - Method in class edu.jhu.tmaj.client.importer.specimens.data.TranslatedTable

getColumnValueMap() - Method in class edu.jhu.tmaj.client.importer.specimens.data.TranslatedTable

getCompletionMessage() - Method in class edu.jhu.tmaj.servlet.response.impl.MachineScoresImportResponse

getComponent() - Method in class edu.jhu.tmaj.client.frida.gui.DefinedMasksGui

getComponent() - Method in class edu.jhu.tmaj.client.frida.gui.masks.color.HsbRangeComponent

Gets the GUI object that this class represents.

getComponent() - Method in class edu.jhu.tmaj.client.frida.gui.shared.LimitedToolBar

Gets the Swing Component that this class represents.

getComponent() - Method in class edu.jhu.tmaj.client.frida.gui.shared.ProgressLabel

getComponent() - Method in class edu.jhu.tmaj.client.specimens.SpecimenInfoDisplay

getComponent(String) - Method in class edu.jhu.tmaj.client.tables.DoubleTabbedPane

Returns the Component which will be found in the one the Sub-TabbedPanes.

getComponent() - Method in class edu.jhu.tmaj.client.tables.Tab

getComponent() - Method in class edu.jhu.tmaj.client.tables.TabGroup

getComponent(String) - Method in class edu.jhu.tmaj.client.tables.TabGroup

getCompressedObjectSize(Object) - Static method in class edu.jhu.tmaj.util.ByteUtil

getConnection() - Method in interface edu.jhu.tmaj.database.conn.ConnectionManager

Returns a valid connection to the database.

getConnection() - Method in class edu.jhu.tmaj.database.conn.PooledConnectionManager

Returns a shared connection from the connection pool.

getConnectionFactory(DatabaseParameters) - Static method in class edu.jhu.tmaj.database.conn.ConnectionFactoryGetter

getConnectionManager(DatabaseParameters) - Static method in class edu.jhu.tmaj.database.conn.ConnectionManagerGetter

getConnectionManager() - Method in class edu.jhu.tmaj.database.data.DatabaseLink

getConnectionString() - Method in class edu.jhu.tmaj.database.conn.AbstractConnectionFactory

getConnectionString() - Method in class edu.jhu.tmaj.database.conn.MySqlConnectionFactory

getConnectionString() - Method in class edu.jhu.tmaj.database.conn.OracleConnectionFactory

getConnectionString() - Method in class edu.jhu.tmaj.database.conn.SQLServerConnectionFactory

getConnectionString() - Method in class edu.jhu.tmaj.database.conn.SybaseConnectionFactory

getControlInstance(String) - Static method in class edu.jhu.tmaj.client.arraybuilder.data.ArrayCoreData

Returns ArrayCoreData that has been designated a control.

getControlName() - Method in class edu.jhu.tmaj.beans.misc.ArrayCoreRep

Returns the Control name of the ArrayCoreBean.

getControlName() - Method in class edu.jhu.tmaj.client.arraybuilder.data.ArrayCoreCell

getControlName() - Method in class edu.jhu.tmaj.client.arraybuilder.data.ArrayCoreData

getCoordinate() - Method in class edu.jhu.tmaj.beans.misc.ArrayCoreRep

Returns the position of this ArrayCore in the ArrayBlock, for example, x=5,y=10.

getCoordinate() - Method in class edu.jhu.tmaj.client.arraybuilder.data.ArrayCoreCell

getCoordinate(String) - Method in class edu.jhu.tmaj.client.importer.data.AcisImageOutputParser

getCoordinate(String) - Method in class edu.jhu.tmaj.client.importer.data.AperioImageOutputParser

getCoordinate(String) - Method in class edu.jhu.tmaj.client.importer.data.BlissImageOutputParser

getCoordinate(String) - Method in class edu.jhu.tmaj.client.importer.data.StandardImageOutputParser

getCoordinate() - Method in class edu.jhu.tmaj.client.importer.images.data.FileCoordinate

getCoordinate(String) - Method in interface edu.jhu.tmaj.client.importer.images.data.ImageOutputParser

Gets the Coordinate (x and y position) by parsing the fileName

getCoordinate(Map<String, String>) - Method in class edu.jhu.tmaj.servlet.request.impl.AcisMachineScoresParser

getCoordinate(Map<String, String>) - Method in class edu.jhu.tmaj.servlet.request.impl.BlissMachineScoresParser

getCoordinate(Map<String, String>) - Method in interface edu.jhu.tmaj.servlet.request.impl.MachineScoresParser

Gets the X,Y Coordinate from a Map representing one row in the file.

getCoordinateArrayImageIDHash(int) - Static method in class edu.jhu.tmaj.client.importer.machscores.MachineSessionUtils

getCoordinates() - Method in class edu.jhu.tmaj.servlet.response.impl.ArrayImageCoresResponse

getCounter() - Static method in class edu.jhu.tmaj.beans.masks.results.Analyzer2

Returns the current measurement count.

getCreationDate() - Method in class edu.jhu.tmaj.beans.IASessionBean

getCreationDate() - Method in class edu.jhu.tmaj.beans.SessionBean

Returns the data this session was created.

getCurrentSize() - Method in class edu.jhu.tmaj.client.image.ArrayImagePanel

getDatabaseColumnName() - Method in enum edu.jhu.tmaj.beans.masks.results.MaskStats.StatName

getDatabaseFieldsList() - Method in class edu.jhu.tmaj.database.sql.SQLValues

getDatabaseLink() - Static method in class edu.jhu.tmaj.database.config.DatabaseConstants

getDatabaseType() - Method in class edu.jhu.tmaj.database.conn.DatabaseParameters

getDatabaseValue() - Method in enum edu.jhu.tmaj.beans.masks.filter.FilterMaskType

getDataList() - Method in class edu.jhu.tmaj.client.tables.data.GeneralTableModel

Returns a List of Lists that represents the objects in the table's cells.

getDataList() - Method in class edu.jhu.tmaj.servlet.response.impl.HistoryResponse

getDataList() - Method in class edu.jhu.tmaj.util.swing.GeneralListModel

getDataPanel() - Method in class edu.jhu.tmaj.client.admin.ManyDataPanel

getDataString() - Method in class edu.jhu.tmaj.servlet.response.impl.ImageInfoResponse

getDataString() - Method in class edu.jhu.tmaj.servlet.response.impl.MachineScoresInfoResponse

getDataType() - Method in class edu.jhu.tmaj.database.data.DatabaseField

getDateAccessed() - Method in class edu.jhu.tmaj.beans.data.DatedProjectSession

getDatedProjectSessionsList() - Method in class edu.jhu.tmaj.servlet.response.impl.RecentSessionGetResponse

getDateField(DatabaseField) - Method in class edu.jhu.tmaj.beans.JBean

Gets a Date value of a field who type is TField.DATE

getDbName() - Method in class edu.jhu.tmaj.database.conn.DatabaseParameters

Returns the name of the database.

getDBValue() - Method in enum edu.jhu.tmaj.beans.data.AdminAppPermission

Returns the integer that is stored in the database representing this permission.

getDBValue() - Method in enum edu.jhu.tmaj.beans.data.ArrayBuilderPermission

getDBValue() - Method in enum edu.jhu.tmaj.beans.data.MetaDataAppPermission

getDBValue() - Method in enum edu.jhu.tmaj.beans.data.PatientDataPermission

Returns the integer that is stored in the database representing this permission.

getDBValue() - Method in enum edu.jhu.tmaj.beans.data.SpecimensAppPermission

getDefaultBeanObjectForType(DatabaseFieldType) - Static method in class edu.jhu.tmaj.beans.JBean

getDefaultSwingObjectForType(DatabaseFieldType) - Static method in class edu.jhu.tmaj.beans.JBean

getDefinedMaskGui() - Method in class edu.jhu.tmaj.client.frida.gui.FridaGui

getDefinedRange(int, int) - Static method in class edu.jhu.tmaj.beans.masks.color.CircleRange

getDefinedRange(int, int) - Static method in class edu.jhu.tmaj.beans.masks.color.SimpleRange

Gets a defined (non-reset) range.

getDeletedRows() - Method in class edu.jhu.tmaj.client.tables.data.ChangedCells

getDeleteSQL(DeleteSQL) - Method in class edu.jhu.tmaj.database.sql.GeneralSQLMaker

getDeleteSQL(DeleteSQL) - Method in interface edu.jhu.tmaj.database.sql.SQLMaker

Returns a DELETE SQL string that is ready to be run on the database.

getDescription() - Method in enum edu.jhu.tmaj.client.frida.data.CalibrationFunction

getDescription() - Method in enum edu.jhu.tmaj.client.image.data.ImageSize

getDescription() - Method in class edu.jhu.tmaj.util.swing.DefaultFileFilter

Returns the extention

getDescriptionColumnName() - Method in enum edu.jhu.tmaj.beans.data.datatypes.DynamicEnumsTable

getDescriptionColumnName() - Method in enum edu.jhu.tmaj.beans.data.datatypes.FieldsTable

getDescriptionColumnName() - Method in enum edu.jhu.tmaj.beans.data.datatypes.LookupTable

getDescriptionColumnName() - Method in interface edu.jhu.tmaj.beans.data.datatypes.NameTable

Returns the name of the column that describes the record.

getDescriptionColumnName() - Method in enum edu.jhu.tmaj.beans.data.datatypes.TypesTable

getDiagnosis() - Method in class edu.jhu.tmaj.servlet.response.impl.GrossDescriptionResponse

getDialogForComponent(Component) - Static method in class edu.jhu.tmaj.util.swing.DialogUtil

getDisabledInstance(Pair) - Static method in class edu.jhu.tmaj.client.image.data.ArrayImageCell

Returns a disabled ArrayImage with null for filename and directory path.

getDotTableFrame() - Method in class edu.jhu.tmaj.client.image.data.SessionGuis

getDoubleField(DatabaseField) - Method in class edu.jhu.tmaj.beans.JBean

Gets the int value of a field whose type is TFieldType.DOUBLE

getDoubleSpecifiedSearch(SearchTerm, String, SearchTerm, String, List<DatabaseField>, int) - Static method in class edu.jhu.tmaj.client.tables.data.Search

A SpecifiedSearch where two columns and their respective values are selected instead of one.

getDoubleTabbedPane() - Method in class edu.jhu.tmaj.client.admin.AdminGUI

getDoubleTabbedPane() - Method in class edu.jhu.tmaj.client.arrays.ArrayManagerPanel

getDoubleTabbedPane() - Method in class edu.jhu.tmaj.client.samples.SamplesAppGUI

getDoubleTabbedPane() - Method in class edu.jhu.tmaj.client.specimens.CellLinesFrame

getDoubleTabbedPane() - Method in class edu.jhu.tmaj.client.specimens.SpecimensAppGUI

getDoubleTabbedPane() - Method in interface edu.jhu.tmaj.client.tables.data.DoubleTabbedPaneHolder

getDown(ArrayImageCell) - Method in class edu.jhu.tmaj.client.image.data.Navigator

Returns the ArrayImage that is directory below currentArrayImage in the ArraySlide.

getDrawableRectangle(Rectangle) - Static method in class edu.jhu.tmaj.client.image.draw.RectangleDrawable

getDrawablesList() - Method in class edu.jhu.tmaj.client.image.draw.DrawableLabel

getDrawablesList() - Method in class edu.jhu.tmaj.servlet.response.impl.ShapesSaveResponse

getDrawingX(int) - Method in class edu.jhu.tmaj.client.image.draw.AbstractDrawable

Gets the X that should be drawn onto the label using the g.drawXXX, given the X in the database

getDrawingX(int, JLabel, ImageIcon) - Static method in class edu.jhu.tmaj.client.image.GridLabel

Returns the X or Y that will be drawn to a screen

getDrawingY(int) - Method in class edu.jhu.tmaj.client.image.draw.AbstractDrawable

getDrawingY(int, JLabel, ImageIcon) - Static method in class edu.jhu.tmaj.client.image.GridLabel

getDriverName() - Method in class edu.jhu.tmaj.database.conn.AbstractConnectionFactory

getDriverName() - Method in class edu.jhu.tmaj.database.conn.MySqlConnectionFactory

getDriverName() - Method in class edu.jhu.tmaj.database.conn.OracleConnectionFactory

getDriverName() - Method in class edu.jhu.tmaj.database.conn.SQLServerConnectionFactory

getDriverName() - Method in class edu.jhu.tmaj.database.conn.SybaseConnectionFactory

getDummyInstance() - Static method in class edu.jhu.tmaj.client.arraybuilder.data.ArrayCoreData

Returns ArrayCoreData for a coordinate with empty data.

getDummyList() - Static method in class edu.jhu.tmaj.client.arraybuilder.CoreDataPanel

getDynamicBaseSQL() - Method in class edu.jhu.tmaj.beans.dynamic.DynamicJBean

Returns a SQL statement that will pull records from the DynamicData table (e.g.

getDynamicColumnIdentifiers(Set<Integer>) - Method in class edu.jhu.tmaj.beans.dynamic.DynamicJBean

Returns the DynamicFields given the types.

getDynamicColumnIdentifiers(Set<Integer>) - Method in class edu.jhu.tmaj.beans.dynamic.ScoredImageBean

Gets the DynamicColumns for the Types supplied, and in addition get the DynamicFields for the session based on the Scoring Strategy.

getDynamicEnumeration(Integer) - Method in class edu.jhu.tmaj.beans.dynamic.data.DynamicMetaData

Returns the DynamicEnumeration in the XXXEnumerations table with a primary key fieldID

getDynamicEnumerationsByField(int) - Method in class edu.jhu.tmaj.beans.dynamic.data.DynamicMetaData

Returns the DynamicEnumerations for the DynamicField with the specified fieldID.

getDynamicField(int) - Method in class edu.jhu.tmaj.beans.dynamic.data.DynamicMetaData

Returns the DynamicField in the XXXFieldNames table with a primary key fieldID

getDynamicFieldsByScoringStrategyID(Integer) - Method in class edu.jhu.tmaj.beans.dynamic.data.ArrayImageDynamicMetaData

Return all the DynamicFields which belong to the specified ScoringStrategyID

getDynamicFieldsByType(Integer) - Method in class edu.jhu.tmaj.beans.dynamic.data.DynamicMetaData

Returns a List of all the DynamicFields whose type is typeID.

getDynamicMetaData(CacheableDynamicMetaData) - Static method in class edu.jhu.tmaj.beans.cache.CachedDynamicMetaData

getDynamicMetaData() - Method in class edu.jhu.tmaj.beans.dynamic.DynamicJBean

Returns the DynamicMetaData for this bean, which determines what the dynamic fields are, and what enumerations they have.

getDynamicMetaData() - Method in class edu.jhu.tmaj.client.importer.specimens.data.MetaDataConverter

getDynamicMetaData() - Method in class edu.jhu.tmaj.servlet.response.impl.DynamicMetaDataResponse

getDynamicSectionForNode(DefaultMutableTreeNode) - Static method in class edu.jhu.tmaj.client.admin.data.DynamicTreeHelper

Returns the DynamicSection of any the given node.

getDynamicSpecifiedSearch(SearchTerm, String, List, int) - Static method in class edu.jhu.tmaj.client.tables.data.Search

getDynamicSQL(Search) - Method in class edu.jhu.tmaj.beans.dynamic.DynamicJBean

Returns a SQL statement that will pull records from the DynamicData table (e.g.

getDynamicSQL(Search) - Method in class edu.jhu.tmaj.beans.dynamic.SpecimenBean

getDynamicSQL(Search) - Method in class edu.jhu.tmaj.beans.dynamic.TissueDiagnosisBean

getDynamicTableName() - Method in class edu.jhu.tmaj.beans.dynamic.DynamicJBean

Returns the name of the Table that contains the DynamicData for this Bean, for example, SpecimenData.

getDynamicTableName() - Method in class edu.jhu.tmaj.beans.dynamic.ScoredImageBean

getDynamicTableName() - Method in class edu.jhu.tmaj.beans.dynamic.SpecimenBean

getDynamicTableName() - Method in class edu.jhu.tmaj.beans.dynamic.TissueDiagnosisBean

getDynamicTypeID() - Method in class edu.jhu.tmaj.beans.dynamic.data.DynamicTField

Returns the type (for example, prostate) to which this DynamicField belongs

getDynamicTypeID() - Method in class edu.jhu.tmaj.client.tables.data.Search

getDynamicValue() - Method in class edu.jhu.tmaj.beans.dynamic.data.DynamicDataRecord

Returns the DynamicValue of this record,a combination of the EnumID and FieldValue fields in the database.

getDynamicValue(int, String) - Method in class edu.jhu.tmaj.client.importer.specimens.data.MetaDataConverter

Returns a DynamicValue (either an EnumID or String) given a fieldID and a text-value.

getElementAt(int) - Method in class edu.jhu.tmaj.util.swing.GeneralListModel

getEndPosition() - Method in class edu.jhu.tmaj.beans.masks.color.CircleRange

Gets the position of where the range ends.

getEntry(int, String) - Static method in class edu.jhu.tmaj.database.sql.InputLog

Returns a String used for logging the user,date, and time of a changed record.

getEnumeratedInstance(int) - Static method in class edu.jhu.tmaj.beans.dynamic.data.DynamicValue

getEnumeratedNullInstance() - Static method in class edu.jhu.tmaj.beans.dynamic.data.DynamicValue

getEnumeration(String, Integer) - Method in class edu.jhu.tmaj.beans.data.StaticMetaData

Translates an id retrieved from the database into a StaticEnumeration.

getEnumerations(String) - Method in class edu.jhu.tmaj.beans.data.StaticMetaData

Returns a List of StaticEnumerations for the column

getEnumerations(DatabaseField) - Method in class edu.jhu.tmaj.beans.dynamic.DynamicJBean

Gets a list of enumerations for a given column.

getEnumerations(DatabaseField) - Method in class edu.jhu.tmaj.beans.JBean

Returns a List of Enumerations for a given field (column).

getEnumID() - Method in class edu.jhu.tmaj.beans.dynamic.data.DynamicValue

Returns the enumID of the dynamic data field

getEnumsTable() - Method in enum edu.jhu.tmaj.beans.cache.CacheableDynamicMetaData

getEnumsTable() - Method in enum edu.jhu.tmaj.beans.data.datatypes.DynamicSection

Gets the Enumerations table for the Dynamic Section.

getError() - Method in interface edu.jhu.tmaj.servlet.response.CommandResponse

Returns an error message if the request could not complete successfully.

getError() - Method in class edu.jhu.tmaj.servlet.response.ErrorResponse

getError() - Method in class edu.jhu.tmaj.servlet.response.SuccessResponse

This method should not be called, as there was no error since this is a Successful Response.

getError() - Method in class edu.jhu.tmaj.util.data.Status

getErrorStatus(String) - Static method in class edu.jhu.tmaj.util.data.Status

getExcelDirectory() - Static method in class edu.jhu.tmaj.config.ClientConstants

getExistingInstance(long) - Static method in class edu.jhu.tmaj.servlet.response.impl.FileChecksumResponse

getExpandingMap() - Method in class edu.jhu.tmaj.servlet.request.impl.DetailsRequest

getExperimentNumber() - Method in class edu.jhu.tmaj.beans.CellLineExperimentBean

getExportList() - Method in class edu.jhu.tmaj.client.tables.data.TableData4

Returns a list of tab-delimited strings that will be written to a file

getExtension(File) - Static method in class edu.jhu.tmaj.util.StringFormatUtils

getExternalFile() - Method in class edu.jhu.tmaj.beans.masks.lasso.LassoedFile

getExternalFile(ImageSize) - Method in class edu.jhu.tmaj.client.image.data.ArrayImageCell

getExternalFile(ImageSize) - Method in class edu.jhu.tmaj.client.image.data.VariedSizeImages

getExternalFile() - Method in class edu.jhu.tmaj.servlet.response.impl.FileResponse

getExternalFileIDs() - Method in class edu.jhu.tmaj.beans.exfile.data.PartialFolderCollection

getExternalFileList() - Method in class edu.jhu.tmaj.servlet.response.impl.FilesResponse

getExternalFiles(ExternalFolder) - Method in class edu.jhu.tmaj.beans.exfile.data.ExternalFileClient

getExternalFiles(Set<Integer>) - Static method in class edu.jhu.tmaj.beans.exfile.data.FileGetAllUtil

getExternalFiles() - Method in class edu.jhu.tmaj.beans.masks.results.AllFileStats

getExternalFiles(ExternalFolder) - Static method in class edu.jhu.tmaj.servlet.request.impl.FilesGetRequest

getExternalFilesList() - Method in class edu.jhu.tmaj.servlet.response.impl.ExternalFileCoordinateResponse

getExternalFolder(int) - Static method in class edu.jhu.tmaj.beans.exfile.data.FolderGetUtil

getExternalFolder() - Method in class edu.jhu.tmaj.servlet.response.impl.FolderResponse

getExternalFolderList() - Method in class edu.jhu.tmaj.servlet.response.impl.FoldersResponse

getExternalFolders(ExternalFolder) - Static method in class edu.jhu.tmaj.servlet.request.impl.FolderGetRequest

getExternalFoldersMap(Set<Integer>) - Static method in class edu.jhu.tmaj.beans.exfile.data.FolderGetAllUtil

getExternalFoldersMapAll() - Static method in class edu.jhu.tmaj.beans.exfile.data.FolderGetAllUtil

getExternalPropertiesFile(File) - Static method in class edu.jhu.tmaj.util.config.data.PropertiesReaderUtil

getExtraPanel() - Method in class edu.jhu.tmaj.client.specimens.SpecimenSingleInputPanel

getExtraPanel() - Method in class edu.jhu.tmaj.client.tables.SingleInputPanel

getFailureMessage() - Method in class edu.jhu.tmaj.servlet.response.impl.DiagnosisLookupResponse

getField() - Method in class edu.jhu.tmaj.client.tables.data.SearchTerm

getFieldID() - Method in class edu.jhu.tmaj.beans.dynamic.data.DynamicDataRecord

Returns the FieldID record.

getFieldID() - Method in class edu.jhu.tmaj.beans.dynamic.data.DynamicEnumeration

Returns the FieldID of the field to which this enumeration belongs

getFieldID_DynamicValue_Map() - Method in class edu.jhu.tmaj.client.importer.specimens.data.DynamicTranslatedTable

getFieldIDs() - Method in class edu.jhu.tmaj.beans.dynamic.data.DynamicMetaData

Returns a List of Integers representing all FieldIDs.

getFieldList() - Method in class edu.jhu.tmaj.servlet.request.impl.AcisMachineScoresParser

getFieldList() - Method in class edu.jhu.tmaj.servlet.request.impl.BlissMachineScoresParser

getFieldList() - Method in interface edu.jhu.tmaj.servlet.request.impl.MachineScoresParser

Returns a List of all the ScoredFields the Machine outputs that TMAJ can import.

getFieldName() - Method in class edu.jhu.tmaj.client.tables.data.SearchTerm

getFieldName() - Method in class edu.jhu.tmaj.database.data.DatabaseField

getFieldNames() - Method in class edu.jhu.tmaj.servlet.response.impl.DetailsResponse

getFieldNamesList() - Method in class edu.jhu.tmaj.servlet.response.impl.HistoryResponse

getFieldNameValue() - Method in class edu.jhu.tmaj.beans.dynamic.data.DynamicValue

Returns the "typed-in" value of the dynamic data field

getFieldsArray() - Method in class edu.jhu.tmaj.beans.AnimalExperimentBean

getFieldsArray() - Method in class edu.jhu.tmaj.beans.ArrayBlockBean

getFieldsArray() - Method in class edu.jhu.tmaj.beans.ArrayCoreBean

getFieldsArray() - Method in class edu.jhu.tmaj.beans.ArrayImageBean

getFieldsArray() - Method in class edu.jhu.tmaj.beans.ArraySlideBean

getFieldsArray() - Method in class edu.jhu.tmaj.beans.BlockBean

getFieldsArray() - Method in class edu.jhu.tmaj.beans.BlockOrSlideExchangeBean

getFieldsArray() - Method in class edu.jhu.tmaj.beans.BlockUsageAltBean

getFieldsArray() - Method in class edu.jhu.tmaj.beans.BlockUsageBean

getFieldsArray() - Method in class edu.jhu.tmaj.beans.BloodSampleBean

getFieldsArray() - Method in class edu.jhu.tmaj.beans.BloodUsageBean

getFieldsArray() - Method in class edu.jhu.tmaj.beans.CellLineBean

getFieldsArray() - Method in class edu.jhu.tmaj.beans.CellLineExperimentBean

getFieldsArray() - Method in class edu.jhu.tmaj.beans.dynamic.ScoredImageBean

getFieldsArray() - Method in class edu.jhu.tmaj.beans.dynamic.SpecimenBean

getFieldsArray() - Method in class edu.jhu.tmaj.beans.dynamic.TissueDiagnosisBean

getFieldsArray() - Method in class edu.jhu.tmaj.beans.IASessionBean

getFieldsArray() - Method in class edu.jhu.tmaj.beans.JBean

Returns an Array of TFields representing the columnnames of this bean.

getFieldsArray() - Method in class edu.jhu.tmaj.beans.MachineSessionBean

getFieldsArray() - Method in class edu.jhu.tmaj.beans.MolecularSampleBean

getFieldsArray() - Method in class edu.jhu.tmaj.beans.MolecularUsageBean

getFieldsArray() - Method in class edu.jhu.tmaj.beans.NullBean

getFieldsArray() - Method in class edu.jhu.tmaj.beans.PaperBean

getFieldsArray() - Method in class edu.jhu.tmaj.beans.PatientBean

getFieldsArray() - Method in class edu.jhu.tmaj.beans.ProjectBean

getFieldsArray() - Method in class edu.jhu.tmaj.beans.ProtocolBean

getFieldsArray() - Method in class edu.jhu.tmaj.beans.ScanBean

getFieldsArray() - Method in class edu.jhu.tmaj.beans.SessionBean

getFieldsArray() - Method in class edu.jhu.tmaj.beans.SlideBean

getFieldsArray() - Method in class edu.jhu.tmaj.beans.TissueSampleBean

getFieldsArray() - Method in class edu.jhu.tmaj.beans.TissueUsageBean

getFieldsArray() - Method in class edu.jhu.tmaj.beans.UrineSampleBean

getFieldsArray() - Method in class edu.jhu.tmaj.beans.UrineUsageBean

getFieldsArray() - Method in class edu.jhu.tmaj.beans.UserBean

getFieldsForSource(ScanningMachine) - Static method in enum edu.jhu.tmaj.client.importer.machscores.MachineScoreField

getFieldsTable() - Method in enum edu.jhu.tmaj.beans.cache.CacheableDynamicMetaData

getFieldsTable() - Method in enum edu.jhu.tmaj.beans.data.datatypes.DynamicSection

Gets the Fields table for the Dynamic Section.

getFieldTypeName() - Method in enum edu.jhu.tmaj.beans.data.datatypes.FieldsTable

Gets the name of the field that refers to the primary key of the Types Table.

getFieldValue(DatabaseField) - Method in class edu.jhu.tmaj.beans.JBean

Gets the value of a field.

getFile() - Method in class edu.jhu.tmaj.client.importer.data.ShortenedFile

getFile() - Method in class edu.jhu.tmaj.client.importer.images.data.FileCoordinate

getFilename() - Method in class edu.jhu.tmaj.beans.exfile.ExternalFile

getFileName() - Method in class edu.jhu.tmaj.beans.masks.results.Analyzer2

getFileName() - Method in class edu.jhu.tmaj.client.importer.images.data.ArrayImageU

getFilenameData(String, String) - Static method in class edu.jhu.tmaj.client.importer.images.data.FilenameData

Gets a DirectoryNameInfo object out of a directory name by parsing useful information out of it.

getFiles() - Method in class edu.jhu.tmaj.client.importer.data.FileSelectorPanel

getFileStats(ExternalFile) - Method in class edu.jhu.tmaj.beans.masks.results.AllFileStats

getFilterMaskID() - Method in class edu.jhu.tmaj.beans.masks.filter.FilterMask

getFilterMaskType() - Method in class edu.jhu.tmaj.beans.masks.filter.FilterMask

getFixationTypeID() - Method in class edu.jhu.tmaj.beans.CellLineExperimentBean

getFolderName(SelectedScan) - Static method in class edu.jhu.tmaj.client.importer.images.data.FolderNameUtil

EXAMPLE: TMA_0612_CUT_001_SCAN_01_ARandNKX31_0_STANDARD_40X

getFormattedProperties(Properties) - Static method in class edu.jhu.tmaj.util.config.data.PropertiesReaderUtil

Returns a Properties file where the keys are all in a standard format.

getFormulaDescription() - Method in enum edu.jhu.tmaj.client.frida.data.CalibrationFunction

getForwardingButton(TableData4, JBean, DoubleTabbedPaneHolder, String, InputPanel4, boolean) - Static method in class edu.jhu.tmaj.client.shared.PanelForwarder

Returns a JButton that when clicked will change the current InputPanel to the Foreign Input Panel.

getFrame() - Method in class edu.jhu.tmaj.client.arraybuilder.ArrayBlockFrame

getFrame() - Method in class edu.jhu.tmaj.client.frida.gui.masks.color.ColorMaskGui

getFrame() - Method in class edu.jhu.tmaj.client.frida.gui.masks.filter.FilterMaskGui

getFrame() - Method in class edu.jhu.tmaj.client.frida.gui.masks.lasso.LassoMaskGui

getFrame() - Method in interface edu.jhu.tmaj.client.frida.gui.masks.MaskGui

getFrame() - Method in class edu.jhu.tmaj.client.frida.gui.masks.meta.MetaMaskGui

getFrame() - Method in class edu.jhu.tmaj.client.image.ArrayImageFrame

getFrame() - Method in class edu.jhu.tmaj.client.image.DotTableFrame

getFrame() - Method in class edu.jhu.tmaj.client.image.InfoFrame

getFrame() - Method in class edu.jhu.tmaj.client.image.MarkBadImagesFrame

getFrame() - Method in class edu.jhu.tmaj.client.image.ProjectsGUI

getFrame(int) - Method in class edu.jhu.tmaj.client.tables.Detacher

getFreshBeansList(JBean) - Static method in class edu.jhu.tmaj.beans.cache.CachedBeans

Returns a FRESH List of Beans of type bean based on the request type.

getFridaGui() - Method in class edu.jhu.tmaj.client.image.data.IASessionGuis

getGeneralSearch() - Static method in class edu.jhu.tmaj.client.tables.data.Search

Returns a Search that indicates all columns should be selected.

getGenericArraySlideBean() - Static method in class edu.jhu.tmaj.beans.cache.GenericBeans

getGenericBean() - Method in class edu.jhu.tmaj.client.tables.data.TableData4

getGenericShapeLasso(float[]) - Static method in class edu.jhu.tmaj.beans.masks.lasso.Lasso

getGoodPassword(int) - Static method in class edu.jhu.tmaj.util.crypt.RandomString

Returns a random password almost guaranteed to have both letters and numbers, but no special characters.

getGridSpacing() - Method in class edu.jhu.tmaj.client.image.GridLabel

getGridSpacing() - Method in class edu.jhu.tmaj.client.image.TopMenu

getGrossDescription() - Method in class edu.jhu.tmaj.servlet.response.impl.GrossDescriptionResponse

getGroupName() - Method in class edu.jhu.tmaj.client.tables.TabGroup

getHashID() - Method in class edu.jhu.tmaj.client.tables.data.ColumnSet

Returns a Hash value for the data contained within this object

getHeight() - Method in class edu.jhu.tmaj.beans.misc.ArrayImageCollectionBean

Returns the number of rows for this session's ArrayBlock.

getHelpMenu() - Method in class edu.jhu.tmaj.client.shared.MenuHelper

getHospitalID() - Method in class edu.jhu.tmaj.beans.dynamic.SpecimenBean

Returns the Hospital where the surgery was performed to obtain this specimen.

getHsbRange() - Method in class edu.jhu.tmaj.beans.masks.color.ColorMask

getIASessionBean() - Static method in class edu.jhu.tmaj.beans.cache.GenericBeans

getIASessionBeansList() - Static method in class edu.jhu.tmaj.client.image.data.IASessionBeanHolder

getIaSessionGui(IASessionBean) - Method in class edu.jhu.tmaj.client.image.data.ImageAppGuis

getIASessionID() - Method in class edu.jhu.tmaj.beans.SessionBean

getID() - Method in class edu.jhu.tmaj.beans.data.datatypes.LookupRecord

Returns the primary key of the record.

getID() - Method in interface edu.jhu.tmaj.beans.data.MetaObject

Returns the primary key in the database.

getID() - Method in class edu.jhu.tmaj.beans.data.StaticEnumeration

Returns the ID of the enumeration

getID() - Method in class edu.jhu.tmaj.beans.dynamic.data.DynamicEnumeration

Returns the primary key of this record

getID() - Method in class edu.jhu.tmaj.beans.dynamic.data.DynamicTField

Returns the primary key of this class

getID() - Method in class edu.jhu.tmaj.beans.exfile.ExternalFile

getID() - Method in class edu.jhu.tmaj.beans.exfile.ExternalFolder

getID() - Method in class edu.jhu.tmaj.beans.JBean

Gets the id of this bean

getID() - Method in class edu.jhu.tmaj.beans.masks.AbstractMask

getID() - Method in class edu.jhu.tmaj.beans.masks.lasso.LassoedFile

getID() - Method in interface edu.jhu.tmaj.beans.masks.Mask

getID() - Method in class edu.jhu.tmaj.beans.masks.meta.ActionMaskInfo

getID_Bean_Map(List<JBean>) - Static method in class edu.jhu.tmaj.beans.JBean

Returns a Map with an Integer representing the JBean's primary key ID and the value representing the Bean record itself.

getIDColumnName() - Method in enum edu.jhu.tmaj.beans.data.datatypes.DynamicEnumsTable

getIDColumnName() - Method in enum edu.jhu.tmaj.beans.data.datatypes.FieldsTable

getIDColumnName() - Method in enum edu.jhu.tmaj.beans.data.datatypes.LookupTable

getIDColumnName() - Method in interface edu.jhu.tmaj.beans.data.datatypes.NameTable

Returns the primary key name.

getIDColumnName() - Method in enum edu.jhu.tmaj.beans.data.datatypes.TypesTable

getIDSetForKey(int) - Method in class edu.jhu.tmaj.beans.manytomany.LinkGroup

Returns a Set of Integers for a specified key in the ManyToManyTable.

getImage(ArrayImageCell) - Method in class edu.jhu.tmaj.client.image.data.ArrayImageRendererCache

getImage(String) - Static method in class edu.jhu.tmaj.util.swing.IconsHelper

getImageIcon(String) - Static method in class edu.jhu.tmaj.util.swing.IconsHelper

getImageJFunction(ImagePlus, boolean[], String) - Static method in class edu.jhu.tmaj.beans.masks.results.ParticleStatsUtil

getImageJFunction(ImagePlus, boolean[], String, int) - Static method in class edu.jhu.tmaj.beans.masks.results.ParticleStatsUtil

getImageJFunctionNumber() - Method in enum edu.jhu.tmaj.client.frida.data.CalibrationFunction

getImagejToolbarNumber() - Method in enum edu.jhu.tmaj.client.frida.gui.shared.LimitedToolBar.ImageTool

getImageLabel() - Method in class edu.jhu.tmaj.client.image.ArrayImagePanel

getImageOutputParser() - Method in enum edu.jhu.tmaj.client.importer.data.ScanningMachine

Gets the custom ImageOutputParser for the scanning machine.

getImagePlus() - Method in class edu.jhu.tmaj.client.frida.gui.shared.NavigationPanel

getImagesDirectory() - Static method in class edu.jhu.tmaj.config.ClientConstants

getImagesFiles(File) - Static method in class edu.jhu.tmaj.client.importer.images.data.ImageFilesUtil

getImagesRootDirectory() - Static method in class edu.jhu.tmaj.config.ServerConstants

Gets the images root directory.

getImportedDataStringForScan(SelectedScan) - Static method in class edu.jhu.tmaj.servlet.request.impl.ScanDeleteRequest

getIndexNameSet() - Method in class edu.jhu.tmaj.client.tables.TabGroup

getInfoFrame() - Method in class edu.jhu.tmaj.client.image.ArraySlideFrame

getInputMask() - Method in class edu.jhu.tmaj.beans.masks.filter.FilterMask

getInputPanel(int) - Method in interface edu.jhu.tmaj.client.shared.IndexablePanel

getInsertSQL(int) - Method in class edu.jhu.tmaj.client.image.draw.AbstractDrawable

Returns a SQL statement to update an existing shape in the database.

getInsertSQL(int) - Method in class edu.jhu.tmaj.client.image.draw.ArrowDrawable

getInsertSQL(int) - Method in interface edu.jhu.tmaj.client.image.draw.Drawable

Returns a SQL statement to insert this shape into the database

getInsertSQL(int) - Method in class edu.jhu.tmaj.client.image.draw.FreeHandDrawable

getInsertSQL(int) - Method in class edu.jhu.tmaj.client.image.draw.LineDrawable

getInsertSQL(int, String) - Method in class edu.jhu.tmaj.client.image.draw.LineDrawable

getInsertSQL(int) - Method in class edu.jhu.tmaj.client.image.draw.OvalDrawable

getInsertSQL(int) - Method in class edu.jhu.tmaj.client.image.draw.PolygonDrawable

getInsertSQL(int) - Method in class edu.jhu.tmaj.client.image.draw.RectangleDrawable

getInsertSQL(String, int) - Method in class edu.jhu.tmaj.client.image.draw.RectangleDrawable

getInsertSQL(int) - Method in class edu.jhu.tmaj.client.image.draw.TextDrawable

getInsertSQL(InsertSQL) - Method in class edu.jhu.tmaj.database.sql.GeneralSQLMaker

getInsertSQL(InsertSQL) - Method in class edu.jhu.tmaj.database.sql.OracleSQLMaker

getInsertSQL(InsertSQL) - Method in interface edu.jhu.tmaj.database.sql.SQLMaker

Returns a INSERT SQL string that is ready to be run on the database.

getInsertSQL() - Method in class edu.jhu.tmaj.database.sql.TwoSQLStatements

Returns the INSERT SQL statement.

getInstance(JBean) - Static method in enum edu.jhu.tmaj.beans.cache.CacheableBean

getInstance(Integer) - Static method in enum edu.jhu.tmaj.beans.data.AdminAppPermission

getInstance(Integer) - Static method in enum edu.jhu.tmaj.beans.data.ArrayBuilderPermission

Get an Instance of this class.

getInstance(Integer) - Static method in enum edu.jhu.tmaj.beans.data.MetaDataAppPermission

getInstance(Integer) - Static method in enum edu.jhu.tmaj.beans.data.PatientDataPermission

getInstance(Integer) - Static method in enum edu.jhu.tmaj.beans.data.SpecimensAppPermission

getInstance() - Static method in class edu.jhu.tmaj.beans.exfile.data.ExternalFileClient

getInstance(String, ExternalFolder) - Static method in class edu.jhu.tmaj.beans.exfile.ExternalFolder

getInstance(ArrayBlockBean, ArrayCoreReferenceBean, CellLinesReferenceBean) - Static method in class edu.jhu.tmaj.client.arraybuilder.ArrayBlockFrame

getInstance(ArrayCoreRep) - Static method in class edu.jhu.tmaj.client.arraybuilder.data.ArrayCoreData

Converts an ArrayCoreRep to ArrayCoreData.

getInstance(Pair, int, VariedSizeImages, boolean) - Static method in class edu.jhu.tmaj.client.image.data.ArrayImageCell

getInstance() - Static method in class edu.jhu.tmaj.client.image.data.TableFieldComparator

getInstance() - Static method in class edu.jhu.tmaj.client.image.data.TableSectionComparator

getInstance() - Static method in class edu.jhu.tmaj.client.specimens.CellLinesFrame

getInstance() - Static method in class edu.jhu.tmaj.client.specimens.SpecimensAppGUI

getInstance(List<TabGroup>, Component) - Static method in class edu.jhu.tmaj.client.tables.DetachableIndicesDialog

Get an instance of this object.

getInstance(JBean, TableData4) - Static method in class edu.jhu.tmaj.client.tables.SearchDialog

Gets an instance of this Dialog.

getInstance(DatabaseParameters) - Static method in class edu.jhu.tmaj.database.data.DatabaseLink

getInstance(String) - Static method in enum edu.jhu.tmaj.database.data.DatabaseType

getInstance() - Static method in class edu.jhu.tmaj.database.DatabaseUtil

getInstance(String) - Static method in class edu.jhu.tmaj.database.sql.DeleteSQL

Returns a instance of a DeleteSQL.

getInstance(String, String, long) - Static method in class edu.jhu.tmaj.database.sql.DeleteSQL

getInstance() - Static method in class edu.jhu.tmaj.database.sql.GeneralSQLMaker

Returns a SQLMaker suitable for most databases (except Oracle.)

getInstance(String, String) - Static method in class edu.jhu.tmaj.database.sql.InsertSQL

getInstance(String) - Static method in class edu.jhu.tmaj.database.sql.InsertSQL

Gets an InsertSQL statement for a table whose primary key name is ID.

getInstance() - Static method in class edu.jhu.tmaj.database.sql.OracleSQLMaker

getInstance(String) - Static method in class edu.jhu.tmaj.database.sql.SelectSQL

getInstance(String) - Static method in class edu.jhu.tmaj.database.sql.UpdateSQL

getInstance(String, String, long) - Static method in class edu.jhu.tmaj.database.sql.UpdateSQL

getInstance() - Static method in class edu.jhu.tmaj.servlet.CommandServletClient

getInstance(String) - Static method in enum edu.jhu.tmaj.servlet.request.impl.SurgPathNumberRequest.TableType

getInstance() - Static method in class edu.jhu.tmaj.util.data.AlphabeticalComparator

getInstanceByDatabaseValue(String) - Static method in enum edu.jhu.tmaj.beans.masks.filter.FilterMaskType

getInstanceBySubDirectory(String) - Static method in enum edu.jhu.tmaj.client.image.data.ImageSize

getInstanceFromDatabase(String) - Static method in enum edu.jhu.tmaj.client.frida.data.CalibrationFunction

getInstanceFromExternalFile(File) - Static method in class edu.jhu.tmaj.database.config.DatabasePropertiesFile

getInstanceFromExternalFile(File) - Static method in class edu.jhu.tmaj.database.data.DatabaseLink

getInstanceFromExternalProperties(File, List<? extends ConfigKey>) - Static method in class edu.jhu.tmaj.util.config.data.ConstantsHolder

getInstanceFromIaSessionBean(IASessionBean) - Static method in class edu.jhu.tmaj.client.frida.data.Calibration

getInstanceFromInternalFile(String) - Static method in class edu.jhu.tmaj.database.config.DatabasePropertiesFile

getInstanceFromInternalFile(String) - Static method in class edu.jhu.tmaj.database.data.DatabaseLink

getInstanceFromInternalProperties(String, List<? extends ConfigKey>) - Static method in class edu.jhu.tmaj.util.config.data.ConstantsHolder

getInstanceFromRoi(Roi) - Static method in class edu.jhu.tmaj.beans.masks.lasso.Lasso

getInt(ConfigKey) - Method in class edu.jhu.tmaj.util.config.data.ConstantsHolder

Gets the int value for a config key that is an int type.

getIntegerField(DatabaseField) - Method in class edu.jhu.tmaj.beans.JBean

Gets the int value of a field whose type is TFieldType.INTEGER

getIntegerList(String, String) - Method in class edu.jhu.tmaj.database.DatabaseUtil

Returns a List of Integers generated by a SQL statement.

getInternalPropertiesFile(String) - Static method in class edu.jhu.tmaj.util.config.data.PropertiesReaderUtil

getIpAddress() - Method in class edu.jhu.tmaj.database.conn.DatabaseParameters

getIterationCount() - Method in class edu.jhu.tmaj.beans.masks.filter.FilterMask

getJNLPLink() - Method in class edu.jhu.tmaj.beans.PaperBean

Returns an http address of a jnlp file that launches TMAJ so that only this paper can be viewed.

getJournalReference() - Method in class edu.jhu.tmaj.beans.PaperBean

getKey(Preference) - Static method in class edu.jhu.tmaj.util.config.data.PreferencesUtil

getKey1List() - Method in class edu.jhu.tmaj.client.admin.ManyToManyPanel

getKey2List() - Method in class edu.jhu.tmaj.client.admin.ManyToManyPanel

getKeySetForKey(int, boolean) - Method in class edu.jhu.tmaj.beans.manytomany.ManyToManyBean

Gets the Set of IDs that are linked to the given key.

getKeyValue(KeyValueGetRequest.KeyName) - Static method in class edu.jhu.tmaj.servlet.request.impl.KeyValueGetRequest

getLabel() - Method in class edu.jhu.tmaj.client.frida.gui.shared.MessageLabel

getLasso() - Method in class edu.jhu.tmaj.beans.masks.lasso.LassoedFile

getLasso(ExternalFile) - Method in class edu.jhu.tmaj.beans.masks.lasso.LassoMask

getLassoedFile(ExternalFile) - Method in class edu.jhu.tmaj.beans.masks.lasso.LassoMask

getLassoForFileName(ExternalFile) - Method in class edu.jhu.tmaj.beans.masks.lasso.LassoMask

getLassoMaskID() - Method in class edu.jhu.tmaj.beans.masks.lasso.LassoMask

getLeftGrayPixels(JLabel, ImageIcon) - Static method in class edu.jhu.tmaj.client.image.GridLabel

getLesionLetter() - Method in class edu.jhu.tmaj.beans.dynamic.TissueDiagnosisBean

Returns the letter assigned to the circle.

getLevelMessages() - Method in class edu.jhu.tmaj.client.shared.SimpleProgressDialog

getListCellRendererComponent(JList, Object, int, boolean, boolean) - Method in class edu.jhu.tmaj.client.image.data.RowHeaderListRenderer

getListCellRendererComponent(JList, Object, int, boolean, boolean) - Method in class edu.jhu.tmaj.client.image.data.SeparatedComboBoxRenderer

getListCopy() - Method in class edu.jhu.tmaj.client.image.data.FastCollection

getListDescription(List) - Static method in class edu.jhu.tmaj.util.ListConvertUtil

Returns a description of every object in the provided List.

getListModel(boolean) - Method in class edu.jhu.tmaj.client.image.ShareSessionDialog

getListOfLists() - Method in class edu.jhu.tmaj.servlet.response.impl.DetailsResponse

getListOfMaps() - Method in class edu.jhu.tmaj.servlet.response.impl.SessionDescriptionsResponse

getListString(boolean) - Method in class edu.jhu.tmaj.client.image.ShareSessionDialog

getLongestValue(String) - Static method in class edu.jhu.tmaj.beans.data.SqlFormatter

Determines the delimiter used in the value string, then gets the length of the longest single token within it.

getLongestValueDelimit(String, String) - Static method in class edu.jhu.tmaj.beans.data.SqlFormatter

Gets the length of the longest token that appears in the value string based on the supplied delimiter.

getLookupRecord(LookupTable, Integer) - Static method in class edu.jhu.tmaj.beans.cache.CachedLookupTables

getLookupTable() - Method in enum edu.jhu.tmaj.beans.data.datatypes.TypesTable

getLookupTableMap(LookupTable) - Static method in class edu.jhu.tmaj.beans.cache.CachedLookupTables

getLookupTableMap() - Method in class edu.jhu.tmaj.servlet.response.impl.LookupTableResponse

getLookupValue(LookupTable, Integer) - Static method in class edu.jhu.tmaj.beans.cache.CachedLookupTables

getMachine(String) - Static method in enum edu.jhu.tmaj.client.importer.data.ScanningMachine

getMachineScoreFieldsAsArray() - Static method in class edu.jhu.tmaj.servlet.request.impl.MachineScoresInfoRequest

getMachineSessionBean() - Static method in class edu.jhu.tmaj.beans.cache.GenericBeans

getMachineSessionID(int, String, FilenameData, int) - Static method in class edu.jhu.tmaj.client.importer.machscores.MachineSessionUtils

getMainComponent() - Method in class edu.jhu.tmaj.client.image.ArrayImageFrameTable

getMainComponent() - Method in class edu.jhu.tmaj.client.image.ProjectsGUI

getMainComponent() - Method in class edu.jhu.tmaj.client.image.SpecialTree

getMainFrame() - Method in class edu.jhu.tmaj.client.frida.gui.FridaGui

getMainFrame() - Method in class edu.jhu.tmaj.client.image.ArraySlideFrame

getMainPanel() - Method in class edu.jhu.tmaj.client.admin.MetaDataAdminPanel

getMainPanel() - Method in class edu.jhu.tmaj.client.arraybuilder.OpenedArrayBlocksPanel

getMainPanel() - Method in class edu.jhu.tmaj.client.arraybuilder.TissueDiagnosisIDPanel

getMainPanel() - Method in class edu.jhu.tmaj.client.arrays.ArrayManagerPanel

getMainPanel() - Method in class edu.jhu.tmaj.client.frida.gui.shared.GeneralMaskPanel

getMainPanel() - Method in class edu.jhu.tmaj.client.image.AbstractSessionsPanel

Returns the JComponent representing this class.

getMainPanel() - Method in class edu.jhu.tmaj.client.image.DownloadImagesPanel

getMainPanel() - Method in class edu.jhu.tmaj.client.importer.data.FileSelectorPanel

getMainPanel() - Method in class edu.jhu.tmaj.client.importer.images.ArrayImagesImportGui2

getMainPanel() - Method in class edu.jhu.tmaj.client.importer.machscores.MachineScoresImportPanel

getMainPanel() - Method in class edu.jhu.tmaj.client.importer.specimens.ImportSpecimensPanel

getMainQuerySQL() - Method in class edu.jhu.tmaj.servlet.request.impl.ArrayCoreDetailsRequest

getMainQuerySQL() - Method in class edu.jhu.tmaj.servlet.request.impl.DetailsRequest

Returns the non-dynamic SQL.

getMainQuerySQL() - Method in class edu.jhu.tmaj.servlet.request.impl.ScoredImageDetailsRequest

The ScoredImages table can not be included in this query, since some of the spots on the ArraySlide may have not been scored yet, and thus not record in the ScoredImages table would exist.

getMainTableSection() - Method in class edu.jhu.tmaj.client.image.data.SubTableSection

getManyToManyBean() - Method in class edu.jhu.tmaj.servlet.response.impl.ManyToManyResponse

getMap() - Method in interface edu.jhu.tmaj.beans2.SwingMap

getMapList() - Method in class edu.jhu.tmaj.beans.data.ExpandingMap

getMappedKeys() - Method in class edu.jhu.tmaj.beans.manytomany.LinkGroup

Returns a set of keys that are mapped to at least one value.

getMask(ImagePlus, ExternalFile) - Method in class edu.jhu.tmaj.beans.masks.color.ColorMask

getMask(ImagePlus, ExternalFile) - Method in class edu.jhu.tmaj.beans.masks.filter.FilterMask

getMask(ImagePlus, ExternalFile) - Method in class edu.jhu.tmaj.beans.masks.lasso.LassoMask

getMask(ImagePlus, ExternalFile) - Method in interface edu.jhu.tmaj.beans.masks.Mask

getMask(ImagePlus, ExternalFile) - Method in class edu.jhu.tmaj.beans.masks.meta.MetaMask

getMask() - Method in class edu.jhu.tmaj.client.frida.data.MaskChangeEvent

getMask(String) - Method in class edu.jhu.tmaj.client.frida.gui.DefinedMasksGui

Gets the Mask object for the supplied mask name.

getMaskFromType(MaskType) - Static method in enum edu.jhu.tmaj.beans.masks.MaskType

getMaskHisto(boolean[]) - Static method in class edu.jhu.tmaj.beans.masks.data.MaskUtil

getMaskList() - Method in class edu.jhu.tmaj.servlet.response.impl.MasksResponse

getMasks() - Method in class edu.jhu.tmaj.beans.masks.results.FileStats

getMasks() - Method in class edu.jhu.tmaj.client.frida.gui.DefinedMasksGui

Gets a list of all defined masks.

getMaskStats(Mask) - Method in class edu.jhu.tmaj.beans.masks.results.FileStats

getMax() - Method in class edu.jhu.tmaj.beans.masks.color.SimpleRange

getMaxBri() - Method in class edu.jhu.tmaj.beans.masks.color.HsbRange

getMaxHue() - Method in class edu.jhu.tmaj.beans.masks.color.HsbRange

getMaximumParticleSize() - Method in class edu.jhu.tmaj.beans.masks.filter.FilterMask

getMaxParticleSizeForCalc() - Method in class edu.jhu.tmaj.beans.masks.filter.FilterMask

getMaxSat() - Method in class edu.jhu.tmaj.beans.masks.color.HsbRange

getMeasurements() - Static method in class edu.jhu.tmaj.beans.masks.results.Analyzer2

getMenuBar() - Method in class edu.jhu.tmaj.client.image.TopMenu

getMessage() - Method in class edu.jhu.tmaj.servlet.response.impl.InitDatabaseResponse

getMessageLabel() - Method in class edu.jhu.tmaj.client.frida.gui.shared.ProgressLabel

getMessages() - Method in class edu.jhu.tmaj.servlet.response.impl.MessagesResponse

getMessagesString() - Method in class edu.jhu.tmaj.util.data.Messages

getMetaDataAppPermission() - Method in class edu.jhu.tmaj.beans.UserBean

Returns the Permission Object related to the MetaData App

getMin() - Method in class edu.jhu.tmaj.beans.masks.color.SimpleRange

getMinBri() - Method in class edu.jhu.tmaj.beans.masks.color.HsbRange

getMinHue() - Method in class edu.jhu.tmaj.beans.masks.color.HsbRange

getMinimumParticleSize() - Method in class edu.jhu.tmaj.beans.masks.filter.FilterMask

getMinParticleSizeForCalc() - Method in class edu.jhu.tmaj.beans.masks.filter.FilterMask

getMinSat() - Method in class edu.jhu.tmaj.beans.masks.color.HsbRange

getMolecularSampleBean() - Static method in class edu.jhu.tmaj.beans.cache.GenericBeans

getMolecularUsageBean() - Static method in class edu.jhu.tmaj.beans.cache.GenericBeans

getName() - Method in class edu.jhu.tmaj.beans.data.datatypes.LookupRecord

Returns the value the record has for the description field.

getName() - Method in class edu.jhu.tmaj.beans.exfile.ExternalFolder

getName() - Method in class edu.jhu.tmaj.beans.masks.AbstractMask

Gets the user-defined name of this mask

getName() - Method in interface edu.jhu.tmaj.beans.masks.Mask

getName() - Method in class edu.jhu.tmaj.client.arraybuilder.data.ColorCodedString

getName() - Method in enum edu.jhu.tmaj.client.importer.data.ScanningMachine

Gets the model name of the scanning machine.

getName() - Method in class edu.jhu.tmaj.client.tables.Tab

getNameFirst() - Method in class edu.jhu.tmaj.beans.UserBean

Returns the User's first name.

getNameLast() - Method in class edu.jhu.tmaj.beans.UserBean

Returns the User's last name.

getNavigator() - Method in class edu.jhu.tmaj.client.image.data.SessionGuis

getNewConnection() - Method in class edu.jhu.tmaj.database.conn.AbstractConnectionFactory

Creates, tests, and returns a new database connection.

getNewConnection() - Method in interface edu.jhu.tmaj.database.conn.ConnectionFactory

Returns a NEW connection to the database

getNewDrawable() - Method in class edu.jhu.tmaj.client.image.draw.ShapesFrame

Returns a new Drawable depending on which shape radioButton the user has selected

getNewExpandingMap() - Method in class edu.jhu.tmaj.servlet.request.impl.ArrayCoreDetailsRequest

getNewExpandingMap() - Method in class edu.jhu.tmaj.servlet.request.impl.DetailsRequest

getNewExpandingMap() - Method in class edu.jhu.tmaj.servlet.request.impl.ScoredImageDetailsRequest

getNewInstance() - Method in class edu.jhu.tmaj.beans.AnimalExperimentBean

getNewInstance() - Method in class edu.jhu.tmaj.beans.ArrayBlockBean

getNewInstance() - Method in class edu.jhu.tmaj.beans.ArrayCoreBean

getNewInstance() - Method in class edu.jhu.tmaj.beans.ArrayImageBean

getNewInstance() - Method in class edu.jhu.tmaj.beans.ArraySlideBean

getNewInstance() - Method in class edu.jhu.tmaj.beans.BlockBean

getNewInstance() - Method in class edu.jhu.tmaj.beans.BlockOrSlideExchangeBean

getNewInstance() - Method in class edu.jhu.tmaj.beans.BlockUsageAltBean

getNewInstance() - Method in class edu.jhu.tmaj.beans.BlockUsageBean

getNewInstance() - Method in class edu.jhu.tmaj.beans.BloodSampleBean

getNewInstance() - Method in class edu.jhu.tmaj.beans.BloodUsageBean

getNewInstance() - Method in class edu.jhu.tmaj.beans.CellLineBean

getNewInstance() - Method in class edu.jhu.tmaj.beans.CellLineExperimentBean

getNewInstance() - Method in class edu.jhu.tmaj.beans.dynamic.ScoredImageBean

getNewInstance() - Method in class edu.jhu.tmaj.beans.dynamic.SpecimenBean

getNewInstance() - Method in class edu.jhu.tmaj.beans.dynamic.TissueDiagnosisBean

getNewInstance() - Method in class edu.jhu.tmaj.beans.IASessionBean

getNewInstance() - Method in class edu.jhu.tmaj.beans.JBean

Returns a new instance of this bean.

getNewInstance() - Method in class edu.jhu.tmaj.beans.MachineSessionBean

getNewInstance() - Method in class edu.jhu.tmaj.beans.MolecularSampleBean

getNewInstance() - Method in class edu.jhu.tmaj.beans.MolecularUsageBean

getNewInstance() - Method in class edu.jhu.tmaj.beans.NullBean

getNewInstance() - Method in class edu.jhu.tmaj.beans.PaperBean

getNewInstance() - Method in class edu.jhu.tmaj.beans.PatientBean

getNewInstance() - Method in class edu.jhu.tmaj.beans.ProjectBean

getNewInstance() - Method in class edu.jhu.tmaj.beans.ProtocolBean

getNewInstance() - Method in class edu.jhu.tmaj.beans.ScanBean

getNewInstance() - Method in class edu.jhu.tmaj.beans.SessionBean

getNewInstance() - Method in class edu.jhu.tmaj.beans.SlideBean

getNewInstance() - Method in class edu.jhu.tmaj.beans.TissueSampleBean

getNewInstance() - Method in class edu.jhu.tmaj.beans.TissueUsageBean

getNewInstance() - Method in class edu.jhu.tmaj.beans.UrineSampleBean

getNewInstance() - Method in class edu.jhu.tmaj.beans.UrineUsageBean

getNewInstance() - Method in class edu.jhu.tmaj.beans.UserBean

getNext(ArrayImageCell, boolean) - Method in class edu.jhu.tmaj.client.image.data.Navigator

Returns the next ArrayImage in this navigation sequence.

getNonEnumeratedInstance(String) - Static method in class edu.jhu.tmaj.beans.dynamic.data.DynamicValue

getNonExistingInstance() - Static method in class edu.jhu.tmaj.servlet.response.impl.FileChecksumResponse

getNonNullString(ResultSet, String) - Static method in class edu.jhu.tmaj.beans.JBean

Returns the value of fieldName in rs, or "" if the value is null.

getNormalInstance(int) - Static method in class edu.jhu.tmaj.client.arraybuilder.data.ArrayCoreData

Returns a typical ArrayCoreData, where a tissueDiagnosisID is assigned.

getNormalX(int) - Method in class edu.jhu.tmaj.client.image.draw.AbstractDrawable

Gets the X that should be stored into the database, given the X that has been generated by a mouseEvent

getNormalX(int, JLabel, ImageIcon) - Static method in class edu.jhu.tmaj.client.image.GridLabel

Returns the X and Y which doesn't include grey to the left, and is stored in the database

getNormalY(int) - Method in class edu.jhu.tmaj.client.image.draw.AbstractDrawable

getNormalY(int, JLabel, ImageIcon) - Static method in class edu.jhu.tmaj.client.image.GridLabel

getNotes() - Method in class edu.jhu.tmaj.beans.IASessionBean

getNotes() - Method in class edu.jhu.tmaj.beans.SessionBean

getNumber() - Method in enum edu.jhu.tmaj.client.importer.data.ScanningMachine

Gets the number of the scanning machine used in the database.

getNumberedList(int, int) - Static method in class edu.jhu.tmaj.client.tables.data.GeneralTableModel

Returns a String array starting with the startNumber.

getNumberOfArrayCores(int) - Static method in class edu.jhu.tmaj.servlet.request.impl.IsArrayBlockBlankRequest

Returns the number of ArrayCores for which a user has put in information (assigned a TissueDiagnosis)

getNumberOfCoefficients() - Method in enum edu.jhu.tmaj.client.frida.data.CalibrationFunction

getNumberOfColumns() - Method in class edu.jhu.tmaj.beans.ArrayBlockBean

Returns the number of columns for this ArrayBlock.

getNumberOfCores() - Method in class edu.jhu.tmaj.servlet.response.impl.ArrayImageCoresResponse

getNumberOfCoresMade() - Method in class edu.jhu.tmaj.servlet.response.impl.IsArrayBlockBlankResponse

getNumberOfImagesAlreadyInserted() - Method in class edu.jhu.tmaj.servlet.response.impl.ImagesDirectoryResponse

Gets the number of ArrayImages that the user has already imported for the directory.

getNumberOfImagesWithNoArrayCore() - Method in class edu.jhu.tmaj.servlet.response.impl.ImagesDirectoryResponse

Gets the number of images that do not have a valid ArrayCore.

getNumberOfLassoMasks(List<Mask>) - Static method in class edu.jhu.tmaj.beans.masks.data.MaskUtil

getNumberOfOpenArrayBlocks() - Method in class edu.jhu.tmaj.client.arraybuilder.OpenedArrayBlocksPanel

getNumberOfRows() - Method in class edu.jhu.tmaj.beans.ArrayBlockBean

Returns the number of rows for this ArrayBlock.

getObject(ObjectPool.WaitTime) - Method in class edu.jhu.tmaj.util.ObjectPool

Acquires an object from the pool.

getObjectDescription(Object) - Static method in class edu.jhu.tmaj.util.ListConvertUtil

Returns a description of an Object including its toString() value and its class name.

getObjectFrequencyHash(List) - Static method in class edu.jhu.tmaj.util.ListConvertUtil

getObjectWaitTime(long) - Method in enum edu.jhu.tmaj.util.ObjectPool.WaitTime

Gets the wait time to put into the object.wait(...) method.

getOkayStatus() - Static method in class edu.jhu.tmaj.util.data.Status

getOneSizeParameters(ImageSize) - Method in class edu.jhu.tmaj.client.importer.images.data.SizeParameters

getOnlyValuesInMask(int[], boolean[]) - Static method in class edu.jhu.tmaj.beans.masks.data.MaskUtil

Returns an int array of pixels where only pixels inside the mask are included.

getOrganID() - Method in class edu.jhu.tmaj.beans.CellLineBean

getOriginalImagePlus(ImagePlus) - Method in class edu.jhu.tmaj.client.frida.data.ImagePlusHolder

getOriginalTissueTypes(int) - Static method in class edu.jhu.tmaj.servlet.request.impl.UsedTissueTypesRequest

Called on the client side, this returns a list of original and used TissueTypes for a particular session.

getOrignalTypeResponse(int) - Static method in class edu.jhu.tmaj.servlet.request.impl.OriginalTypeRequest

getOutputImage() - Method in class edu.jhu.tmaj.beans.masks.results.ParticleAnalyzer2

Returns the "Outlines", "Masks", "Elipses" or "Count Masks" image, or null if "Nothing" is selected in the "Show:" menu.

getOutsideBlockNumber() - Method in class edu.jhu.tmaj.beans.BlockBean

getOutsideTDNumber() - Method in class edu.jhu.tmaj.beans.dynamic.TissueDiagnosisBean

getOwnerUserID() - Method in class edu.jhu.tmaj.beans.SessionBean

getPanel() - Method in class edu.jhu.tmaj.client.frida.gui.masks.color.FullSlider

Gets a Panel that represents this entire component

getPanel() - Method in class edu.jhu.tmaj.client.frida.gui.shared.MaskRepresentationPanel

getPanel() - Method in class edu.jhu.tmaj.client.frida.gui.shared.NavigationPanel

getPanel() - Method in class edu.jhu.tmaj.client.tables.GridBagPanelMaker

getPanel() - Method in class edu.jhu.tmaj.client.tables.InputPanel4

getPaperBean() - Static method in class edu.jhu.tmaj.beans.cache.GenericBeans

getPapersSessionsBean() - Static method in class edu.jhu.tmaj.beans.cache.CachedManyToManyBeans

getParent() - Method in class edu.jhu.tmaj.beans.exfile.ExternalFolder

getParentExternalFolders() - Method in class edu.jhu.tmaj.beans.exfile.data.ExternalFileClient

getPart() - Method in class edu.jhu.tmaj.beans.BlockBean

Returns the part number (written on the physical block.)

getPartialFolder(int) - Method in class edu.jhu.tmaj.beans.exfile.data.PartialFolderCollection

getParticleFilteredMask(ImagePlus, boolean[], double, double) - Static method in class edu.jhu.tmaj.beans.masks.results.ParticleStatsUtil

getParticleStats(ImagePlus, boolean[]) - Static method in class edu.jhu.tmaj.beans.masks.results.ParticleStatsUtil

getPassword() - Method in class edu.jhu.tmaj.beans.UserBean

Returns the digested password of the user.

getPassword() - Static method in class edu.jhu.tmaj.client.shared.CurrentUser

Returns the digested password of the person using this application.

getPassword() - Method in class edu.jhu.tmaj.database.conn.DatabaseParameters

Gets the Password used to connect to the database, e.g.

getPassword() - Method in class edu.jhu.tmaj.servlet.request.BaseRequest

getPassword() - Method in interface edu.jhu.tmaj.servlet.request.CommandRequest

Gets the password of the user making this Request

getPassword() - Method in class edu.jhu.tmaj.servlet.request.impl.InitDatabaseRequest

This method should not be needed for this request.

getPassword() - Method in class edu.jhu.tmaj.util.data.UserCredentials

getPath() - Method in class edu.jhu.tmaj.beans.exfile.ExternalFile

getPatientBean() - Static method in class edu.jhu.tmaj.beans.cache.GenericBeans

getPatientDataPermission() - Method in class edu.jhu.tmaj.beans.UserBean

getPatientID() - Method in class edu.jhu.tmaj.servlet.response.impl.ExpressEntryResponse

getPatientNumber() - Method in class edu.jhu.tmaj.client.importer.specimens.data.PatientTranslatedTable

getPDFLink() - Method in class edu.jhu.tmaj.beans.PaperBean

Returns the URL of the PDF file for the published paper.

getPercentMemoryFreeString() - Static method in class edu.jhu.tmaj.util.MemoryUtil

getPermissionChar() - Method in class edu.jhu.tmaj.client.image.data.UserPermission

getPermissionsArray() - Static method in enum edu.jhu.tmaj.beans.data.AdminAppPermission

getPermissionsArray() - Static method in enum edu.jhu.tmaj.beans.data.ArrayBuilderPermission

getPermissionsArray() - Static method in enum edu.jhu.tmaj.beans.data.MetaDataAppPermission

getPermissionsArray() - Static method in enum edu.jhu.tmaj.beans.data.PatientDataPermission

getPermissionsArray() - Static method in enum edu.jhu.tmaj.beans.data.SpecimensAppPermission

getPermissionType() - Method in class edu.jhu.tmaj.client.image.data.UserPermission

getPolygon() - Method in class edu.jhu.tmaj.beans.masks.lasso.Lasso

getPolygonLasso(Polygon) - Static method in class edu.jhu.tmaj.beans.masks.lasso.Lasso

getPoolSize() - Method in class edu.jhu.tmaj.util.ObjectPool

Gets the total number of objects in the pool.

getPopupSize() - Method in class edu.jhu.tmaj.client.image.data.SteppedComboBox

getPort() - Method in class edu.jhu.tmaj.database.conn.DatabaseParameters

getPosition() - Method in class edu.jhu.tmaj.client.tables.NumberedCheckBox

getPrecision() - Static method in class edu.jhu.tmaj.beans.masks.results.Analyzer2

Returns the number of digits displayed to the right of decimal point.

getPreferredWidth() - Static method in class edu.jhu.tmaj.client.image.ArrayImageFrame

getPrefix() - Method in enum edu.jhu.tmaj.client.image.data.ImageSize

getPrimaryKeyField() - Method in class edu.jhu.tmaj.beans.JBean

Returns the TField that is the Primary Key for the bean's table.

getPrimaryKeyID() - Method in class edu.jhu.tmaj.beans.dynamic.data.DynamicDataRecord

Returns the primary key of the record to which this dynamic data REFERS

getPrimaryKeyID() - Method in class edu.jhu.tmaj.client.importer.specimens.data.TranslatedTable

getPrimaryKeyName() - Method in class edu.jhu.tmaj.beans.JBean

Gets the primary key name of the bean's table.

getPrimaryKeyName() - Method in class edu.jhu.tmaj.client.importer.specimens.data.TranslatedTable

getPrimaryKeyName() - Method in class edu.jhu.tmaj.database.sql.InsertSQL

getPrintableString(String, String) - Method in class edu.jhu.tmaj.util.StopWatch

getProjectID() - Method in class edu.jhu.tmaj.beans.IASessionBean

getProjectID() - Method in class edu.jhu.tmaj.beans.SessionBean

getProjectsArraySlidesBean() - Static method in class edu.jhu.tmaj.beans.cache.CachedManyToManyBeans

getProjectSessionType() - Method in class edu.jhu.tmaj.beans.data.DatedProjectSession

getPublishedPapersNode() - Static method in class edu.jhu.tmaj.client.image.data.PublishedSessionsNodes

Gets the Published Papers Node with all proper sub nodes (papers) attached.

getPubMedLink() - Method in class edu.jhu.tmaj.beans.PaperBean

getQuantityLeft() - Method in class edu.jhu.tmaj.servlet.response.impl.QuantityLeftResponse

getQuantityLeftButton(Component, JBean, JBean, JTable, GeneralTableModel) - Static method in class edu.jhu.tmaj.client.samples.QuantityLeftHelper

getRandomColor() - Method in class edu.jhu.tmaj.client.arraybuilder.data.ColorDelegate

getRandomString(int) - Static method in class edu.jhu.tmaj.util.crypt.RandomString

Returns a random string of a specified length.

getRange() - Method in class edu.jhu.tmaj.client.frida.gui.masks.color.HsbRangeComponent

getRecentSessionsPanel() - Method in class edu.jhu.tmaj.client.image.ProjectsGUI

getRecord_patientID() - Method in class edu.jhu.tmaj.servlet.response.impl.SpecimenIdentifiersResponse

getRecord_specimenID() - Method in class edu.jhu.tmaj.servlet.response.impl.SpecimenIdentifiersResponse

getRedirectImage(ImagePlus) - Static method in class edu.jhu.tmaj.beans.masks.results.Analyzer2

getRedirectStats(int, Roi) - Method in class edu.jhu.tmaj.beans.masks.results.Analyzer2

getReferencedMasks() - Method in class edu.jhu.tmaj.beans.masks.meta.MetaMask

getReferringKey() - Method in class edu.jhu.tmaj.beans.data.SubMap

getRelativeFile() - Method in class edu.jhu.tmaj.beans.exfile.ExternalFile

getRelativePath(ExternalFolder) - Static method in class edu.jhu.tmaj.beans.exfile.ExternalFolder

getRelativePath(File, File) - Static method in class edu.jhu.tmaj.util.FilePathUtils

getRenamedCopy(String) - Method in class edu.jhu.tmaj.beans.data.datatypes.LookupRecord

getRenamedCopy(String) - Method in interface edu.jhu.tmaj.beans.data.MetaObject

Returns the same MetaObject, except with a different name.

getRenamedCopy(String) - Method in class edu.jhu.tmaj.beans.dynamic.data.DynamicEnumeration

getRenamedCopy(String) - Method in class edu.jhu.tmaj.beans.dynamic.data.DynamicTField

getRepresentation(DefaultMutableTreeNode) - Static method in class edu.jhu.tmaj.client.admin.data.TreeDataPrinter

getRequestedColumnIdentifiers() - Method in class edu.jhu.tmaj.client.tables.data.Search

getResetRange() - Static method in class edu.jhu.tmaj.beans.masks.color.CircleRange

getResetRange() - Static method in class edu.jhu.tmaj.beans.masks.color.HsbRange

getResetRange() - Static method in class edu.jhu.tmaj.beans.masks.color.SimpleRange

Gets a reset range.

getResponse(KeyValueGetRequest.KeyName) - Static method in class edu.jhu.tmaj.servlet.request.impl.KeyValueGetRequest

getResultsTable() - Static method in class edu.jhu.tmaj.beans.masks.results.Analyzer2

Returns the default results table.

getRoi() - Method in class edu.jhu.tmaj.beans.masks.lasso.Lasso

getRootNode() - Method in class edu.jhu.tmaj.client.image.data.NodeMaker

Gets the root node of the JTree.

getRow(int) - Method in interface edu.jhu.tmaj.util.file.TableArray

getRow(int) - Method in class edu.jhu.tmaj.util.file.TableArrayImpl

getRowArrayImage(int) - Method in class edu.jhu.tmaj.client.image.DotTableFrame

Constructs and return an ArrayImage from the specified row in the table.

getRowCount() - Method in class edu.jhu.tmaj.client.tables.data.GeneralTableModel

getRowMap(int, GeneralTableModel) - Static method in class edu.jhu.tmaj.client.tables.data.TableData4

Returns a Map containing ColumnIdentifiers as the key and the Object in the JTable's cell as the value

getRows() - Method in interface edu.jhu.tmaj.util.file.TableArray

getRows() - Method in class edu.jhu.tmaj.util.file.TableArrayImpl

getScanBean() - Static method in class edu.jhu.tmaj.beans.cache.GenericBeans

getScanID() - Method in class edu.jhu.tmaj.beans.IASessionBean

Returns the ScanID of the Scan this session was created on.

getScanID() - Method in class edu.jhu.tmaj.beans.SessionBean

Returns the ScanID of the Scan this session was created on.

getScanID(FilenameData) - Static method in class edu.jhu.tmaj.client.importer.machscores.MachineSessionUtils

getScaningMachine() - Method in class edu.jhu.tmaj.beans.ScanBean

getScanningMachine(int) - Static method in enum edu.jhu.tmaj.client.importer.data.ScanningMachine

getScanNumber() - Method in class edu.jhu.tmaj.beans.ScanBean

getScanScopeImageID() - Method in class edu.jhu.tmaj.beans.ScanBean

getScanScopeURL(int) - Static method in class edu.jhu.tmaj.client.arrays.ScanScopeUtil

http://10.113.240.14:82/@59265/is.sis?chost=10.113.240.14:82

getScoreData() - Method in class edu.jhu.tmaj.client.image.ArrayImageFrameTable

getScoreData() - Method in class edu.jhu.tmaj.client.image.data.ArrayImageCell

getScoredImageBean() - Static method in class edu.jhu.tmaj.beans.cache.GenericBeans

getScoredImageDetailsRequest(int[]) - Static method in class edu.jhu.tmaj.client.image.DotTableFrame

getScoredImageID() - Method in class edu.jhu.tmaj.client.image.ArrayImageFrameTable

getScoringStrategyID() - Method in class edu.jhu.tmaj.beans.dynamic.data.ArrayImageDynamicField

Returns the ScoringStrategyID to this DynamicField belongs.

getScoringStrategyID() - Method in class edu.jhu.tmaj.beans.SessionBean

Returns the scoringStrategyID of this session if the user has assigned one.

getScrollPane() - Method in class edu.jhu.tmaj.client.arraybuilder.ArrayBuilderTable

Returns the grapical Component representing this object.

getScrollPane() - Method in class edu.jhu.tmaj.client.tables.data.TableData4

getScrollPaneComponent() - Method in class edu.jhu.tmaj.client.image.ArrayImagePanel

getSearchTerm() - Method in class edu.jhu.tmaj.client.tables.data.Search

getSearchTerm2() - Method in class edu.jhu.tmaj.client.tables.data.Search

getSearchTerms() - Method in class edu.jhu.tmaj.client.tables.data.TableData4

A Convenience method for getSearchTermsForBean(bean)

getSelectedArrayCoreCellSet() - Method in class edu.jhu.tmaj.client.arraybuilder.ArrayBuilderTable

getSelectedColumnIDs(Object) - Method in class edu.jhu.tmaj.client.tables.data.TableData4

getSelectedColumnIDs(Object, JTable, GeneralTableModel) - Static method in class edu.jhu.tmaj.client.tables.data.TableData4

getSelectedCoordinateSet() - Method in class edu.jhu.tmaj.client.arraybuilder.ArrayBuilderTable

getSelectedIASessionBeans() - Method in class edu.jhu.tmaj.client.image.AbstractSessionsPanel

getSelectedKeysString(Object) - Method in class edu.jhu.tmaj.client.tables.data.TableData4

Returns a comma-delimited String of the integers found in a specified ColumnIdentifier

getSelectedMask() - Method in class edu.jhu.tmaj.client.frida.gui.DefinedMasksGui

getSelectedScan() - Method in class edu.jhu.tmaj.client.arrays.ArrayManagerPanel

getSelectedSessionBeans() - Method in class edu.jhu.tmaj.client.image.AbstractSessionsPanel

Gets the currently selected SessionBean, or returns null if nothing is selected.

getSelectedTool() - Method in class edu.jhu.tmaj.client.frida.gui.shared.LimitedToolBar

Gets the currently selected ImageTool.

getSelectResponse(Search) - Method in class edu.jhu.tmaj.beans.JBean

Returns a SelectResponse containing a beanList and columnIdentifiers from a Search.

getSelectSQL(SelectSQL) - Method in class edu.jhu.tmaj.database.sql.GeneralSQLMaker

getSelectSQL(SelectSQL) - Method in interface edu.jhu.tmaj.database.sql.SQLMaker

Returns a SELECT SQL string that is ready to be run on the database.

getSelectSQL() - Method in class edu.jhu.tmaj.database.sql.TwoSQLStatements

Returns the SELECT SQL statement that will get the auto-incremented value in the INSERT statement.

getServletUrl() - Static method in class edu.jhu.tmaj.config.ClientConstants

getSessionBean() - Method in class edu.jhu.tmaj.client.image.ArrayImageFrame

getSessionBeansList() - Static method in class edu.jhu.tmaj.client.image.data.SessionBeansHolder

getSessionDescription() - Method in class edu.jhu.tmaj.beans.IASessionBean

getSessionDescription() - Method in class edu.jhu.tmaj.beans.SessionBean

getSessionGui(SessionBean) - Method in class edu.jhu.tmaj.client.image.data.ImageAppGuis

getSessionID() - Method in class edu.jhu.tmaj.beans.data.DatedProjectSession

getSessionID() - Method in class edu.jhu.tmaj.beans.misc.ArrayImageCollectionBean

getSessionIDsForPaper(int) - Method in class edu.jhu.tmaj.beans.manytomany.PapersSessionsBean

Returns the sessionIDs that are in the given Paper

getSetSQLValues() - Method in class edu.jhu.tmaj.database.sql.AbstractModifySQL

getShapeArray() - Method in class edu.jhu.tmaj.beans.masks.lasso.Lasso

getShapeID() - Method in class edu.jhu.tmaj.client.image.draw.AbstractDrawable

Gets the unique ShapeID of this shape in the database table Shapes

getShapeID() - Method in interface edu.jhu.tmaj.client.image.draw.Drawable

Returns the ShapeID of the shape in the database

getShapeRecordsList() - Method in class edu.jhu.tmaj.servlet.response.impl.ShapesLoadResponse

getSharedSessionsNode() - Static method in class edu.jhu.tmaj.client.image.data.SharedNodes

Gets the main Shared Session Node, with all proper sub nodes attached.

getShortDescription() - Method in class edu.jhu.tmaj.beans.ScanBean

getShortTitle() - Method in class edu.jhu.tmaj.beans.PaperBean

Returns the name (or title) of the paper

getSingleInputPanel() - Method in class edu.jhu.tmaj.client.specimens.SpecimenInputPanel

getSingleInputPanel() - Method in class edu.jhu.tmaj.client.tables.InputPanel4

getSite() - Static method in class edu.jhu.tmaj.config.ClientConstants

getSize() - Method in class edu.jhu.tmaj.util.swing.GeneralListModel

getSizeOfMask(boolean[]) - Static method in class edu.jhu.tmaj.beans.masks.data.MaskUtil

Returns the number of pixels that are INSIDE the mask.

getSizeParameters() - Method in class edu.jhu.tmaj.client.importer.images.SizeParametersGui

getSlideBean() - Static method in class edu.jhu.tmaj.beans.cache.GenericBeans

getSlider() - Method in class edu.jhu.tmaj.client.frida.gui.masks.color.FullSlider

getSocketAddress() - Method in class edu.jhu.tmaj.database.conn.DatabaseParameters

Returns the IP Address and port on which the database runs.

getSpecifiedSearch(SearchTerm, String, List<DatabaseField>) - Static method in class edu.jhu.tmaj.client.tables.data.Search

Returns a Search in which the columnnames are specified, as well as a field and value for which to search.

getSpecimenBean(int) - Method in class edu.jhu.tmaj.beans.ArrayCoreReferenceBean

getSpecimenBean() - Static method in class edu.jhu.tmaj.beans.cache.GenericBeans

getSpecimenID() - Method in class edu.jhu.tmaj.beans.BlockBean

Returns the SpecimenID from which this block was cut.

getSpecimenID() - Method in class edu.jhu.tmaj.servlet.response.impl.ExpressEntryResponse

getSpecimensAppPermission() - Method in class edu.jhu.tmaj.beans.UserBean

Returns the Permission Object related to the Specimens App

getSQL(Search) - Method in class edu.jhu.tmaj.beans.ArrayBlockBean

getSQL(Search) - Method in class edu.jhu.tmaj.beans.ArraySlideBean

getSQL(Search) - Method in class edu.jhu.tmaj.beans.BlockBean

getSQL(Search) - Method in class edu.jhu.tmaj.beans.dynamic.SpecimenBean

getSQL(Search) - Method in class edu.jhu.tmaj.beans.dynamic.TissueDiagnosisBean

getSQL(Search) - Method in class edu.jhu.tmaj.beans.JBean

Returns a SELECT SQL statement given a Search.

getSQL() - Method in class edu.jhu.tmaj.beans.manytomany.ManyToManyBean

Returns a SQL statement that will initialize the bean with every record in the ManyToMany table

getSQL(int) - Method in class edu.jhu.tmaj.beans.manytomany.ManyToManyBean

Returns a SQL statement that will initialize the bean with limited records for which the user needs access

getSQL(int) - Method in class edu.jhu.tmaj.beans.manytomany.PapersSessionsBean

getSQL() - Method in class edu.jhu.tmaj.beans.manytomany.PapersSessionsBean

getSQL(int) - Method in class edu.jhu.tmaj.beans.manytomany.ProjectsArraySlidesBean

getSQL() - Method in class edu.jhu.tmaj.beans.manytomany.ProjectsArraySlidesBean

getSQL(int) - Method in class edu.jhu.tmaj.beans.manytomany.UsersArrayBlocksBean

getSQL() - Method in class edu.jhu.tmaj.beans.manytomany.UsersArrayBlocksBean

getSQL(int) - Method in class edu.jhu.tmaj.beans.manytomany.UsersProjectsBean

getSQL() - Method in class edu.jhu.tmaj.beans.manytomany.UsersProjectsBean

getSQL(int) - Method in class edu.jhu.tmaj.beans.manytomany.UsersUsersBean

getSQL() - Method in class edu.jhu.tmaj.beans.manytomany.UsersUsersBean

getSQL(Search) - Method in class edu.jhu.tmaj.beans.ProjectBean

getSQL(Search) - Method in class edu.jhu.tmaj.beans.ScanBean

getSQL(Search) - Method in class edu.jhu.tmaj.beans.SessionBean

The sql statement sets some extra columns like SharedCount and HasForeignWritePermission.

getSQL(Search) - Method in class edu.jhu.tmaj.beans.UserBeanLimited

getSql() - Method in class edu.jhu.tmaj.database.sql.SelectSQL

getSQLInteger(String, String) - Method in class edu.jhu.tmaj.database.DatabaseUtil

Queries the database for the Integer of the first row in the specified column, given a SQL query.

getSqlMaker() - Method in class edu.jhu.tmaj.database.data.DatabaseLink

getSQLMaker(DatabaseType) - Static method in class edu.jhu.tmaj.database.sql.SQLMakerGetter

getSqlSelectString() - Method in class edu.jhu.tmaj.client.image.data.StaticFields

Returns a comma-delimited list of the static fields for use in the "main" query.

getSQLString(String, String) - Method in class edu.jhu.tmaj.database.DatabaseUtil

getSQLValue(DatabaseField, Object) - Method in class edu.jhu.tmaj.database.sql.GeneralSQLMaker

Get a sql-ready string given a java object.

getSQLValue(DatabaseField, Object) - Method in class edu.jhu.tmaj.database.sql.OracleSQLMaker

getStain() - Method in class edu.jhu.tmaj.beans.ArraySlideBean

Returns the stain of this ArraySlide; for example, H&E

getStartPosition() - Method in class edu.jhu.tmaj.beans.masks.color.CircleRange

Gets the position of where the range starts.

getStat(MaskStats.StatName) - Method in class edu.jhu.tmaj.beans.masks.results.MaskStats

getStaticEnumeration(JBean, DatabaseField, Integer) - Static method in class edu.jhu.tmaj.beans.cache.CachedStaticMetaData

getStaticEnumerationList() - Method in class edu.jhu.tmaj.servlet.response.impl.EnumerationsResponse

getStaticEnumerations(EnumerationGroup) - Static method in class edu.jhu.tmaj.beans.cache.CacheableStaticMetaData.EnumsGetter

getStaticEnumerationString(JBean, DatabaseField, Integer) - Static method in class edu.jhu.tmaj.beans.cache.CachedStaticMetaData

getStaticFields() - Method in class edu.jhu.tmaj.servlet.request.impl.ArrayCoreDetailsRequest

Returns fields from the non-dynamic tables Specimens,Blocks,TissueDiagnosis, and ArrayCores tables

getStaticFields() - Method in class edu.jhu.tmaj.servlet.request.impl.DetailsRequest

Returns fields and their table-names from non-dynamic tables.

getStaticFields() - Method in class edu.jhu.tmaj.servlet.request.impl.ScoredImageDetailsRequest

getStaticMetaData() - Method in class edu.jhu.tmaj.beans.cache.CacheableStaticMetaData.AnimalExperimentsHolder

getStaticMetaData() - Method in class edu.jhu.tmaj.beans.cache.CacheableStaticMetaData.ArraySlidesHolder

getStaticMetaData() - Method in class edu.jhu.tmaj.beans.cache.CacheableStaticMetaData.BlockOrSlideExchangesHolder

getStaticMetaData() - Method in class edu.jhu.tmaj.beans.cache.CacheableStaticMetaData.BlocksHolder

getStaticMetaData() - Method in class edu.jhu.tmaj.beans.cache.CacheableStaticMetaData.BlockUsagesAltHolder

getStaticMetaData() - Method in class edu.jhu.tmaj.beans.cache.CacheableStaticMetaData.BloodHolder

getStaticMetaData() - Method in class edu.jhu.tmaj.beans.cache.CacheableStaticMetaData.CellLineExperimentsHolder

getStaticMetaData() - Method in class edu.jhu.tmaj.beans.cache.CacheableStaticMetaData.CellLinesHolder

getStaticMetaData() - Method in class edu.jhu.tmaj.beans.cache.CacheableStaticMetaData.MachineSessionsHolder

getStaticMetaData() - Method in class edu.jhu.tmaj.beans.cache.CacheableStaticMetaData.MolecularSamplesHolder

getStaticMetaData() - Method in class edu.jhu.tmaj.beans.cache.CacheableStaticMetaData.PaperHolder

getStaticMetaData() - Method in class edu.jhu.tmaj.beans.cache.CacheableStaticMetaData.PatientsHolder

getStaticMetaData() - Method in class edu.jhu.tmaj.beans.cache.CacheableStaticMetaData.SampleUsagesHolder

getStaticMetaData() - Method in class edu.jhu.tmaj.beans.cache.CacheableStaticMetaData.ScanHolder

getStaticMetaData() - Method in class edu.jhu.tmaj.beans.cache.CacheableStaticMetaData.SlidesHolder

getStaticMetaData() - Method in class edu.jhu.tmaj.beans.cache.CacheableStaticMetaData.SpecimensHolder

getStaticMetaData() - Method in interface edu.jhu.tmaj.beans.cache.CacheableStaticMetaData.StaticMetaDataHolder

getStaticMetaData() - Method in class edu.jhu.tmaj.beans.cache.CacheableStaticMetaData.TissueDiagnosisHolder

getStaticMetaData() - Method in class edu.jhu.tmaj.beans.cache.CacheableStaticMetaData.TissueHolder

getStaticMetaData() - Method in class edu.jhu.tmaj.beans.cache.CacheableStaticMetaData.UrineHolder

getStaticMetaData() - Method in class edu.jhu.tmaj.beans.cache.CacheableStaticMetaData.UsersHolder

getStaticMetaData(CacheableStaticMetaData) - Static method in class edu.jhu.tmaj.beans.cache.CachedStaticMetaData

getStaticMetaData() - Method in class edu.jhu.tmaj.beans.JBean

Gets the StaticMetaData of this bean.

getStaticMetaDataHolder() - Method in enum edu.jhu.tmaj.beans.cache.CacheableStaticMetaData

getStatistics(ImageProcessor, int, Calibration) - Method in class edu.jhu.tmaj.beans.masks.results.ParticleAnalyzer2

getStats(int[], Calibration) - Static method in class edu.jhu.tmaj.beans.masks.data.MaskIntensityStatUtil

Gets a stat object for the given pixels.

getStatus() - Method in class edu.jhu.tmaj.client.image.draw.AbstractDrawable

Returns the status of this shape, e.g.

getStatus() - Method in interface edu.jhu.tmaj.client.image.draw.Drawable

getString(ConfigKey) - Method in class edu.jhu.tmaj.util.config.data.ConstantsHolder

Gets the string value for a config key that is an string type.

getStringField(DatabaseField) - Method in class edu.jhu.tmaj.beans.JBean

Gets the String value of a field whose type is TFieldType.STRING

getStringList(String, String) - Method in class edu.jhu.tmaj.database.DatabaseUtil

Returns a List of Strings generated by a SQL statement.

getStringListAsFormattedString(List<String>) - Static method in class edu.jhu.tmaj.beans.data.SqlFormatter

getStringRepresentation(Integer, Integer, String) - Static method in class edu.jhu.tmaj.beans.ArraySlideBean

getStringRepresentation(CellView) - Method in class edu.jhu.tmaj.client.arraybuilder.data.ArrayCoreCell

Returns the Control-Name is isControl(), and the TissueDiagnosisID if it is a regular ArrayCore.

getSubDirectory() - Method in enum edu.jhu.tmaj.client.image.data.ImageSize

getSubFolder(ImageSize) - Method in class edu.jhu.tmaj.client.importer.images.data.VariedSizeFolders

getSubFolders(ExternalFolder) - Method in class edu.jhu.tmaj.beans.exfile.data.ExternalFileClient

getSubSectionName() - Method in class edu.jhu.tmaj.client.image.data.SubTableSection

getSuitableForegroundColor(Color) - Static method in class edu.jhu.tmaj.util.swing.ColorContrastUtil

getSummaryString() - Method in class edu.jhu.tmaj.client.importer.specimens.UpdateTracker

getSurgPathNumber() - Method in class edu.jhu.tmaj.beans.dynamic.SpecimenBean

Returns the unique identifier the hospital assigned to this specimen.

getSurgPathNumber() - Method in class edu.jhu.tmaj.client.importer.specimens.data.SpecimenTranslatedTable

getSurgPathNumber() - Method in class edu.jhu.tmaj.servlet.response.impl.SurgPathNumberResponse

getSwingHash() - Method in class edu.jhu.tmaj.beans.dynamic.DynamicJBean

Converts this Bean to a Map that makes it ready to be converted into a row into a JTable.

getSwingHash() - Method in class edu.jhu.tmaj.beans.JBean

Gets a Map with the fields as the keys, and the swing-ready values as the Map's values.

getSwingToBeanObject(DatabaseField, Object) - Method in class edu.jhu.tmaj.beans.dynamic.DynamicJBean

Converts a value that would be found in a swing JTable into a value that is suitable for this JBean.

getSwingToBeanObject(DatabaseField, Object) - Method in class edu.jhu.tmaj.beans.JBean

Gets the value for this bean from a Swing JTable cell.

getTabbedPane() - Method in class edu.jhu.tmaj.client.tables.DoubleTabbedPane

Returns the JTabbedPane this object has created.

getTabbedPane() - Method in class edu.jhu.tmaj.client.tables.TabGroup

getTabGroup(int) - Method in class edu.jhu.tmaj.client.tables.DoubleTabbedPane

Returns the TabGroup giving the main-index number.

getTable() - Method in class edu.jhu.tmaj.beans.AnimalExperimentBean

getTable() - Method in class edu.jhu.tmaj.beans.ArrayBlockBean

getTable() - Method in class edu.jhu.tmaj.beans.ArrayCoreBean

getTable() - Method in class edu.jhu.tmaj.beans.ArrayImageBean

getTable() - Method in class edu.jhu.tmaj.beans.ArraySlideBean

getTable() - Method in class edu.jhu.tmaj.beans.BlockBean

getTable() - Method in class edu.jhu.tmaj.beans.BlockOrSlideExchangeBean

getTable() - Method in class edu.jhu.tmaj.beans.BlockUsageAltBean

getTable() - Method in class edu.jhu.tmaj.beans.BlockUsageBean

getTable() - Method in class edu.jhu.tmaj.beans.BloodSampleBean

getTable() - Method in class edu.jhu.tmaj.beans.BloodUsageBean

getTable() - Method in class edu.jhu.tmaj.beans.CellLineBean

getTable() - Method in class edu.jhu.tmaj.beans.CellLineExperimentBean

getTable() - Method in class edu.jhu.tmaj.beans.dynamic.ScoredImageBean

getTable() - Method in class edu.jhu.tmaj.beans.dynamic.SpecimenBean

getTable() - Method in class edu.jhu.tmaj.beans.dynamic.TissueDiagnosisBean

getTable() - Method in class edu.jhu.tmaj.beans.IASessionBean

getTable() - Method in class edu.jhu.tmaj.beans.JBean

getTable() - Method in class edu.jhu.tmaj.beans.MachineSessionBean

getTable() - Method in class edu.jhu.tmaj.beans.MolecularSampleBean

getTable() - Method in class edu.jhu.tmaj.beans.MolecularUsageBean

getTable() - Method in class edu.jhu.tmaj.beans.NullBean

getTable() - Method in class edu.jhu.tmaj.beans.PaperBean

getTable() - Method in class edu.jhu.tmaj.beans.PatientBean

getTable() - Method in class edu.jhu.tmaj.beans.ProjectBean

getTable() - Method in class edu.jhu.tmaj.beans.ProtocolBean

getTable() - Method in class edu.jhu.tmaj.beans.ScanBean

getTable() - Method in class edu.jhu.tmaj.beans.SessionBean

getTable() - Method in class edu.jhu.tmaj.beans.SlideBean

getTable() - Method in class edu.jhu.tmaj.beans.TissueSampleBean

getTable() - Method in class edu.jhu.tmaj.beans.TissueUsageBean

getTable() - Method in class edu.jhu.tmaj.beans.UrineSampleBean

getTable() - Method in class edu.jhu.tmaj.beans.UrineUsageBean

getTable() - Method in class edu.jhu.tmaj.beans.UserBean

getTable() - Method in class edu.jhu.tmaj.client.tables.data.TableData4

getTable() - Method in class edu.jhu.tmaj.client.tables.SingleInputPanel

getTableCellEditorComponent(JTable, Object, boolean, int, int) - Method in class edu.jhu.tmaj.client.image.data.ButtonEditor

Sets the current Object to value and returns the JButton.

getTableCellEditorComponent(JTable, Object, boolean, int, int) - Method in class edu.jhu.tmaj.client.tables.data.StandardizedCellEditor

getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class edu.jhu.tmaj.client.arraybuilder.data.ArrayCoreRenderer

Returns this after casting object to an ArrayImage, then setting the icon,background,text,and borders

getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class edu.jhu.tmaj.client.image.AnotherArrayImageRenderer

getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class edu.jhu.tmaj.client.image.data.ArrayImageRenderer

Returns this after casting object to an ArrayImage, then setting the icon,background,text,and borders

getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class edu.jhu.tmaj.client.image.data.LookedUpTableCellRenderer

Returns a yellow table cell renderer component if value is an instance of LookedUpDynamicEnumeration

getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class edu.jhu.tmaj.client.image.data.TableFieldRenderer

getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class edu.jhu.tmaj.client.tables.data.ColorTableCellRenderer

getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class edu.jhu.tmaj.client.tables.data.HeaderTableCellRenderer

getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class edu.jhu.tmaj.client.tables.data.IntegerCellRenderer

getTableData() - Method in class edu.jhu.tmaj.client.image.ArrayImageFrameTable

getTableData() - Method in class edu.jhu.tmaj.client.tables.InputPanel4

getTableFields() - Method in class edu.jhu.tmaj.client.image.data.StaticFields

getTableForNode(DefaultMutableTreeNode) - Static method in class edu.jhu.tmaj.client.admin.data.DynamicTreeHelper

Returns the table the given node represents.

getTableModel() - Method in class edu.jhu.tmaj.client.image.DotTableFrame

getTableModel() - Method in class edu.jhu.tmaj.client.tables.data.TableData4

getTableName() - Method in enum edu.jhu.tmaj.beans.data.DatabaseTable

getTableName() - Method in enum edu.jhu.tmaj.beans.data.datatypes.DynamicEnumsTable

getTableName() - Method in enum edu.jhu.tmaj.beans.data.datatypes.FieldsTable

getTableName() - Method in enum edu.jhu.tmaj.beans.data.datatypes.LookupTable

getTableName() - Method in interface edu.jhu.tmaj.beans.data.datatypes.NameTable

Returns the name of the database table.

getTableName() - Method in enum edu.jhu.tmaj.beans.data.datatypes.TypesTable

getTableName() - Method in class edu.jhu.tmaj.beans.JBean

Returns the name of the database table to which this bean refers.

getTableName() - Method in enum edu.jhu.tmaj.client.image.data.MainTableSection

getTableName() - Method in class edu.jhu.tmaj.client.importer.specimens.data.TranslatedTable

getTableName() - Method in class edu.jhu.tmaj.client.tables.data.SearchTerm

getTableName(String) - Method in class edu.jhu.tmaj.database.sql.GeneralSQLMaker

Gets the sql-ready tablename given the table-name that tmaj uses.

getTableName() - Method in class edu.jhu.tmaj.database.sql.ModifySQL

Returns the tablename that is being updated.

getTableNumber(JBean) - Static method in class edu.jhu.tmaj.client.tables.logs.LogTableNumbers

getTableNumber(DatabaseTable) - Static method in class edu.jhu.tmaj.client.tables.logs.LogTableNumbers

getTabList() - Method in class edu.jhu.tmaj.client.tables.TabGroup

getTemporaryExcelFile(String) - Static method in class edu.jhu.tmaj.util.ExcelUtil

Returns the file path where a new Excel file can be placed.

getTestSQL() - Method in class edu.jhu.tmaj.database.conn.DatabaseParameters

getText(ArrayImageCell) - Static method in class edu.jhu.tmaj.client.image.data.ArrayImageRenderer

Returns "X" if the ArrayImage has been scored.

getTimeBetweenEvents(String, String) - Method in class edu.jhu.tmaj.util.StopWatch

getTissueBean() - Static method in class edu.jhu.tmaj.beans.cache.GenericBeans

getTissueDiagnosisBean(int) - Method in class edu.jhu.tmaj.beans.ArrayCoreReferenceBean

getTissueDiagnosisBean() - Static method in class edu.jhu.tmaj.beans.cache.GenericBeans

getTissueDiagnosisBean(int) - Method in class edu.jhu.tmaj.beans.CellLinesReferenceBean

getTissueDiagnosisID() - Method in class edu.jhu.tmaj.beans.misc.ArrayCoreRep

Gets the TissueDiagnosisID of the ArrayCore.

getTissueDiagnosisID() - Method in class edu.jhu.tmaj.client.arraybuilder.data.ArrayCoreCell

getTissueDiagnosisID() - Method in class edu.jhu.tmaj.client.arraybuilder.data.ArrayCoreData

getTissueDiagnosisID() - Method in class edu.jhu.tmaj.servlet.response.impl.ExpressEntryResponse

getTissueDiagnosisIDString(int) - Static method in class edu.jhu.tmaj.client.arraybuilder.TissueDiagnosisIDPanel

getTissueTypesList() - Method in class edu.jhu.tmaj.servlet.response.impl.UsedTissueTypesResponse

getTissueUsageBean() - Static method in class edu.jhu.tmaj.beans.cache.GenericBeans

getTitle() - Method in class edu.jhu.tmaj.beans.PaperBean

getTmajHomeDirectory() - Static method in class edu.jhu.tmaj.config.ClientConstants

getTopGrayPixels(JLabel, ImageIcon) - Static method in class edu.jhu.tmaj.client.image.GridLabel

getTotalChecked() - Method in class edu.jhu.tmaj.servlet.response.impl.GrossDescriptionWipeResponse

getTotalPixels() - Method in class edu.jhu.tmaj.beans.masks.results.FileStats

getTotalUpdated() - Method in class edu.jhu.tmaj.servlet.response.impl.GrossDescriptionWipeResponse

getTranslatedRecordsList(TableArray<String, String>, MetaDataConverter, int, SpecimenIdentifiersResponse) - Static method in class edu.jhu.tmaj.client.importer.specimens.data.DestinationUtils

Gets a List of Maps ready to be inserted into the database from a List of Maps that was read from a file.

getTreatment() - Method in class edu.jhu.tmaj.beans.CellLineExperimentBean

getTreeCellEditorComponent(JTree, Object, boolean, boolean, boolean, int) - Method in class edu.jhu.tmaj.client.image.MyTreeCellEditor

getTreeCellRendererComponent(JTree, Object, boolean, boolean, boolean, int, boolean) - Method in class edu.jhu.tmaj.client.admin.data.TreeRenderer

getTreeCellRendererComponent(JTree, Object, boolean, boolean, boolean, int, boolean) - Method in class edu.jhu.tmaj.client.image.MyTreeCellRenderer

getType() - Method in class edu.jhu.tmaj.beans.masks.AbstractMask

getType() - Method in interface edu.jhu.tmaj.beans.masks.Mask

getType() - Method in interface edu.jhu.tmaj.beans2.SwingColumn

getType() - Method in class edu.jhu.tmaj.client.frida.data.MaskChangeEvent

getType() - Method in enum edu.jhu.tmaj.config.ClientConstants.ClientConfigKey

getType() - Method in interface edu.jhu.tmaj.util.config.data.ConfigKey

Returns the type of the Config Key, such as a String or URL.

getTypeField() - Method in class edu.jhu.tmaj.beans.dynamic.DynamicJBean

Returns the TField column where the type of this DynamicBean is put.

getTypeField() - Method in class edu.jhu.tmaj.beans.dynamic.ScoredImageBean

getTypeField() - Method in class edu.jhu.tmaj.beans.dynamic.SpecimenBean

getTypeField() - Method in class edu.jhu.tmaj.beans.dynamic.TissueDiagnosisBean

getTypeID() - Method in class edu.jhu.tmaj.beans.dynamic.DynamicJBean

Returns the type of this DynamicBean, which determines which dynamic-fields will be displayed.

getTypeID() - Method in class edu.jhu.tmaj.servlet.response.impl.OriginalTypeResponse

getTypesTable() - Method in enum edu.jhu.tmaj.beans.data.datatypes.DynamicSection

Gets the Types table for this meta data section.

getUMeans() - Static method in class edu.jhu.tmaj.beans.masks.results.Analyzer2

Returns an array containing the first 20 uncalibrated means.

getUncompressedObjectSize(Object) - Static method in class edu.jhu.tmaj.util.ByteUtil

getUniqueList(List) - Static method in class edu.jhu.tmaj.client.image.data.RecentComboBox

Returns a List containing only unique elements from list

getUp(ArrayImageCell) - Method in class edu.jhu.tmaj.client.image.data.Navigator

Returns the ArrayImage that is directory above currentArrayImage in the ArraySlide.

getUpdatedColumnsForRow(int) - Method in class edu.jhu.tmaj.client.tables.data.ChangedCells

getUpdatedRows() - Method in class edu.jhu.tmaj.client.tables.data.ChangedCells

getUpdateSQL() - Method in class edu.jhu.tmaj.client.image.draw.AbstractDrawable

Returns a SQL statement to insert this shape into the database.

getUpdateSQL() - Method in interface edu.jhu.tmaj.client.image.draw.Drawable

Returns a SQL statement to update the shape in the database

getUpdateSQL() - Method in class edu.jhu.tmaj.client.image.draw.FreeHandDrawable

getUpdateSQL() - Method in class edu.jhu.tmaj.client.image.draw.LineDrawable

getUpdateSQL() - Method in class edu.jhu.tmaj.client.image.draw.PolygonDrawable

getUpdateSQL() - Method in class edu.jhu.tmaj.client.image.draw.RectangleDrawable

getUpdateSQL() - Method in class edu.jhu.tmaj.client.image.draw.TextDrawable

getUpdateSQL(UpdateSQL) - Method in class edu.jhu.tmaj.database.sql.GeneralSQLMaker

getUpdateSQL(UpdateSQL) - Method in interface edu.jhu.tmaj.database.sql.SQLMaker

Returns a UPDATE SQL string that is ready to be run on the database.

getUpdateStatements() - Method in class edu.jhu.tmaj.servlet.request.impl.GrossDescriptionWipeRequest

getUrineSampleBean() - Static method in class edu.jhu.tmaj.beans.cache.GenericBeans

getUrineUsageBean() - Static method in class edu.jhu.tmaj.beans.cache.GenericBeans

getURL() - Method in class edu.jhu.tmaj.client.image.data.PaperURL

getURL(ConfigKey) - Method in class edu.jhu.tmaj.util.config.data.ConstantsHolder

getUserBean() - Method in class edu.jhu.tmaj.beans.JBean

Returns the UserBean of the person reading and writing data to this bean.

getUserBean() - Static method in class edu.jhu.tmaj.client.shared.CurrentUser

Returns the UserBean of the person using this application.

getUserBean() - Method in class edu.jhu.tmaj.servlet.response.impl.LoginResponse

getUserID() - Method in class edu.jhu.tmaj.beans.IASessionBean

getUserID() - Method in class edu.jhu.tmaj.client.image.data.UserPermission

getUserID() - Method in class edu.jhu.tmaj.client.image.draw.AbstractDrawable

Returns the UserID of the person drawing this shape

getUserID() - Static method in class edu.jhu.tmaj.client.shared.CurrentUser

Gets the userID of the person currently logged on.

getUserID() - Method in class edu.jhu.tmaj.database.sql.InputLog

getUsername() - Method in class edu.jhu.tmaj.beans.UserBean

Returns the userName of the user.

getUsername() - Static method in class edu.jhu.tmaj.client.shared.CurrentUser

Returns the user name of the person using this application.

getUsername() - Method in class edu.jhu.tmaj.database.conn.DatabaseParameters

Gets the Username used to connect to the database, e.g.

getUsername() - Method in class edu.jhu.tmaj.servlet.request.BaseRequest

getUsername() - Method in interface edu.jhu.tmaj.servlet.request.CommandRequest

Gets the username of the user making this Request

getUsername() - Method in class edu.jhu.tmaj.servlet.request.impl.InitDatabaseRequest

This method should not be needed for this request.

getUsername() - Method in class edu.jhu.tmaj.util.data.UserCredentials

getUserPermissionsList(int) - Static method in class edu.jhu.tmaj.servlet.request.impl.UsersSessionsGetRequest

getUserPermissionsList() - Method in class edu.jhu.tmaj.servlet.response.impl.UsersSessionsGetResponse

getUsersArrayBlocksBean() - Static method in class edu.jhu.tmaj.beans.cache.CachedManyToManyBeans

getUsersForAdminUserID(int) - Method in class edu.jhu.tmaj.beans.manytomany.UsersUsersBean

getUsersProjectsBean() - Static method in class edu.jhu.tmaj.beans.cache.CachedManyToManyBeans

getUsersUsersBean() - Static method in class edu.jhu.tmaj.beans.cache.CachedManyToManyBeans

getUsersWithPublishedSessionsNode() - Static method in class edu.jhu.tmaj.client.image.data.PublishedSessionsNodes

Gets the 'Users who have published papers' Node with all proper sub nodes (users) attached.

getValue(double, Calibration) - Static method in class edu.jhu.tmaj.client.frida.data.CalibrationCalculator

getValue() - Method in class edu.jhu.tmaj.client.frida.gui.masks.color.FullSlider

Gets the current value of the Slider

getValue() - Method in class edu.jhu.tmaj.client.tables.data.Search

getValue(ClientConstants.ClientConfigKey) - Static method in class edu.jhu.tmaj.config.ClientConstants

getValue() - Method in class edu.jhu.tmaj.database.sql.LiteralValue

getValue() - Method in class edu.jhu.tmaj.servlet.response.impl.KeyValueGetResponse

getValue2() - Method in class edu.jhu.tmaj.client.tables.data.Search

getValueAt(int, int) - Method in class edu.jhu.tmaj.client.tables.data.GeneralTableModel

getValueFormat(String, String) - Static method in class edu.jhu.tmaj.beans.data.SqlFormatter

getValuesList() - Method in class edu.jhu.tmaj.database.sql.SQLValues

getVerifiedColumnIndex(C) - Method in interface edu.jhu.tmaj.util.file.TableArray

getVerifiedColumnIndex(C) - Method in class edu.jhu.tmaj.util.file.TableArrayImpl

getWantedColumnsString(Search) - Method in class edu.jhu.tmaj.beans.JBean

Returns a comma, delimited list of columnNames desired in a Search.

getWantedStaticColumnIdentifiers(Search) - Method in class edu.jhu.tmaj.beans.JBean

Returns a List of the ColumnIdentifiers that are desired by the end-user's search.

getWarnings() - Method in class edu.jhu.tmaj.servlet.request.impl.DetailsRequest

getWarnings() - Method in class edu.jhu.tmaj.servlet.response.impl.DetailsResponse

getWarnings() - Method in class edu.jhu.tmaj.servlet.response.impl.MachineScoresImportResponse

getWebSlideURL() - Method in class edu.jhu.tmaj.client.image.data.ArrayImageCell

getWhereClause(Search, JBean, String) - Static method in class edu.jhu.tmaj.beans.JBean

Returns the WHERE Clause of a SELECT statement given a Search.

getWhereSQLValues() - Method in class edu.jhu.tmaj.database.sql.DeleteSQL

getWhereSQLValues() - Method in class edu.jhu.tmaj.database.sql.UpdateSQL

getWidth() - Method in class edu.jhu.tmaj.beans.misc.ArrayImageCollectionBean

Returns the number of columns for this session's ArrayBlock.

getX() - Method in class edu.jhu.tmaj.beans.misc.ArrayCoreRep

Gets the X position of this ArrayCore in the ArrayBlock

getX() - Method in class edu.jhu.tmaj.util.data.Pair

getXPosition() - Method in class edu.jhu.tmaj.client.image.data.ArrayImageCell

Returns the X Position of this ArrayImage indicated in the ArrayCores table.

getY() - Method in class edu.jhu.tmaj.beans.misc.ArrayCoreRep

Gets the Y position of this ArrayCore in the ArrayBlock

getY() - Method in class edu.jhu.tmaj.util.data.Pair

getYPosition() - Method in class edu.jhu.tmaj.client.image.data.ArrayImageCell

Returns the Y Position of this ArrayImage indicated in the ArrayCores table.

getZ() - Method in class edu.jhu.tmaj.beans.ArraySlideBean

Returns the cut number of this array slide

GplPanel - Class in edu.jhu.tmaj.client.shared

GplPanel() - Constructor for class edu.jhu.tmaj.client.shared.GplPanel

GridBagPanelMaker - Class in edu.jhu.tmaj.client.tables

A Utility class for creating a component with a GridBagLayout.

GridBagPanelMaker() - Constructor for class edu.jhu.tmaj.client.tables.GridBagPanelMaker

GridLabel - Class in edu.jhu.tmaj.client.image

A JLabel that draws a Grid over itself when gridEnabled is true

GridLabel(String, int) - Constructor for class edu.jhu.tmaj.client.image.GridLabel

GrossDescriptionRequest - Class in edu.jhu.tmaj.servlet.request.impl

Obtains the GrossDescription and Diagnosis of a specimen in SingleInputPanel

GrossDescriptionRequest(int) - Constructor for class edu.jhu.tmaj.servlet.request.impl.GrossDescriptionRequest

GrossDescriptionResponse - Class in edu.jhu.tmaj.servlet.response.impl

Contains the GrossDescription and Diagnosis of a specimen.

GrossDescriptionResponse(String, String) - Constructor for class edu.jhu.tmaj.servlet.response.impl.GrossDescriptionResponse

GrossDescriptionWipeRequest - Class in edu.jhu.tmaj.servlet.request.impl

Removes the Patient Name from the GrossDescription.

GrossDescriptionWipeRequest() - Constructor for class edu.jhu.tmaj.servlet.request.impl.GrossDescriptionWipeRequest

GrossDescriptionWipeResponse - Class in edu.jhu.tmaj.servlet.response.impl

Contains the number of records checked and the number of records updated during a Gross Description Wipe.

GrossDescriptionWipeResponse(int, int) - Constructor for class edu.jhu.tmaj.servlet.response.impl.GrossDescriptionWipeResponse

GroupQueryFrame - Class in edu.jhu.tmaj.client.image.data

A GUI Frame for allowing the user to do GROUP-style queries on data.

GroupQueryFrame() - Constructor for class edu.jhu.tmaj.client.image.data.GroupQueryFrame

GROWTH_MEDIA_THIS_EXPERIMENT_FIELD - Static variable in class edu.jhu.tmaj.beans.CellLineExperimentBean

H

h - Variable in class edu.jhu.tmaj.beans.masks.data.HsbPixel

handleKeyPressed(KeyEvent) - Method in class edu.jhu.tmaj.client.image.draw.AbstractDrawable

Does nothing.

handleKeyPressed(KeyEvent) - Method in interface edu.jhu.tmaj.client.image.draw.Drawable

handleKeyPressed(KeyEvent) - Method in class edu.jhu.tmaj.client.image.draw.TextDrawable

handleMouseDragged(MouseEvent) - Method in class edu.jhu.tmaj.client.image.draw.AbstractDrawable

Moves the shape depending on difference between last point, if the user has finished drawing it.

handleMouseDragged(MouseEvent) - Method in interface edu.jhu.tmaj.client.image.draw.Drawable

handleMouseDragged(MouseEvent) - Method in class edu.jhu.tmaj.client.image.draw.FreeHandDrawable

handleMouseDragged(MouseEvent) - Method in class edu.jhu.tmaj.client.image.draw.LineDrawable

handleMouseDragged(MouseEvent) - Method in class edu.jhu.tmaj.client.image.draw.PolygonDrawable

handleMouseDragged(MouseEvent) - Method in class edu.jhu.tmaj.client.image.draw.RectangleDrawable

handleMouseDragged(MouseEvent) - Method in class edu.jhu.tmaj.client.image.draw.TextDrawable

handleMousePressed(MouseEvent) - Method in class edu.jhu.tmaj.client.image.draw.AbstractDrawable

Registers tempX and tempX if moving is allowed

handleMousePressed(MouseEvent) - Method in interface edu.jhu.tmaj.client.image.draw.Drawable

handleMousePressed(MouseEvent) - Method in class edu.jhu.tmaj.client.image.draw.FreeHandDrawable

handleMousePressed(MouseEvent) - Method in class edu.jhu.tmaj.client.image.draw.LineDrawable

handleMousePressed(MouseEvent) - Method in class edu.jhu.tmaj.client.image.draw.PolygonDrawable

handleMousePressed(MouseEvent) - Method in class edu.jhu.tmaj.client.image.draw.RectangleDrawable

handleMousePressed(MouseEvent) - Method in class edu.jhu.tmaj.client.image.draw.TextDrawable

handleMouseReleased(MouseEvent) - Method in class edu.jhu.tmaj.client.image.draw.AbstractDrawable

Indicate the user has finished drawing the shape

handleMouseReleased(MouseEvent) - Method in interface edu.jhu.tmaj.client.image.draw.Drawable

handleMouseReleased(MouseEvent) - Method in class edu.jhu.tmaj.client.image.draw.FreeHandDrawable

handleMouseReleased(MouseEvent) - Method in class edu.jhu.tmaj.client.image.draw.PolygonDrawable

Does nothing: unlike most shapes MouseReleased() does not mean the user is done drawing the shape

handleResponse(TranslatedRow, TranslatedRowResponse) - Method in class edu.jhu.tmaj.client.importer.specimens.UpdateTracker

handleResultSet(ResultSet) - Method in class edu.jhu.tmaj.database.DatabaseQuery

Called for every row the SELECT statement generates.

handleScoreData(ScoreData) - Method in class edu.jhu.tmaj.servlet.request.impl.ScoreDataHandler

handleWindowClosed() - Method in class edu.jhu.tmaj.client.image.data.IASessionWindowListener

handleWindowClosed() - Method in class edu.jhu.tmaj.client.image.data.SessionWindowListener

handleWindowClosed() - Method in class edu.jhu.tmaj.client.shared.ClosingWindowListener

Called when the window is closed for any reason.

HardConstants - Class in edu.jhu.tmaj.config

HAS_DRAWINGS_FIELD - Static variable in class edu.jhu.tmaj.servlet.request.impl.ScoredImageDetailsRequest

HAS_H_AND_E_FIELD - Static variable in class edu.jhu.tmaj.beans.BlockBean

hasAllAccess() - Method in enum edu.jhu.tmaj.beans.data.SpecimensAppPermission

Returns true if the user should see every record in the database, regardless of which specimens they have been assigned to.

hasArrayCoreID(Coordinate) - Method in class edu.jhu.tmaj.servlet.response.impl.ArrayImageCoresResponse

hasAtLeastOpenAccess() - Method in enum edu.jhu.tmaj.beans.data.SpecimensAppPermission

Returns true if a user will receive automatic access to 'requested' Specimens.

hasAtLeastReadAccess() - Method in enum edu.jhu.tmaj.beans.data.SpecimensAppPermission

hasColumn(String) - Method in class edu.jhu.tmaj.client.importer.specimens.data.TranslatedTable

hasForeignWritePermission() - Method in class edu.jhu.tmaj.beans.SessionBean

Returns true if another user other than the owner may write data to this session.

hasGroupAdminAccess() - Method in class edu.jhu.tmaj.beans.SessionBean

Returns true if the current user can access this session because it belongs to someone with their group.

hashCode() - Method in class edu.jhu.tmaj.beans.data.datatypes.LookupRecord

hashCode() - Method in class edu.jhu.tmaj.beans.data.StaticEnumeration

hashCode() - Method in class edu.jhu.tmaj.beans.dynamic.data.DynamicTField

hashCode() - Method in class edu.jhu.tmaj.beans.exfile.ExternalFile

hashCode() - Method in class edu.jhu.tmaj.beans.exfile.ExternalFolder

hashCode() - Method in class edu.jhu.tmaj.beans.JBean

Returns the ID of this bean.

hashCode() - Method in class edu.jhu.tmaj.beans.masks.color.SimpleRange

hashCode() - Method in class edu.jhu.tmaj.client.image.data.ArrayImageCell

hashCode() - Method in class edu.jhu.tmaj.client.image.data.SubTableSection

hashCode() - Method in class edu.jhu.tmaj.client.image.data.TableField

hashCode() - Method in class edu.jhu.tmaj.client.importer.specimens.data.RecordIdentifier

hashCode() - Method in class edu.jhu.tmaj.client.tables.data.SearchTerm

hashCode() - Method in class edu.jhu.tmaj.database.data.DatabaseField

hashCode() - Method in class edu.jhu.tmaj.util.data.Pair

hashCode() - Method in class edu.jhu.tmaj.util.data.Triplet

hashCode() - Method in interface edu.jhu.tmaj.util.file.TableArray

hashCode() - Method in class edu.jhu.tmaj.util.file.TableArrayImpl

hasUnsavedModifications() - Method in class edu.jhu.tmaj.client.arraybuilder.ArrayBuilderTable

hasWritePermission() - Method in enum edu.jhu.tmaj.beans.data.ArrayBuilderPermission

Returns true if a user can design an ArrayBlock, as oppose to just view them.

hasWritePermission() - Method in enum edu.jhu.tmaj.beans.data.SpecimensAppPermission

Returns false if the user may only view records, and not change them.

HeaderTableCellRenderer - Class in edu.jhu.tmaj.client.tables.data

A TableCellRenderer for TableHeaders that display required fields in Bold.

HeaderTableCellRenderer() - Constructor for class edu.jhu.tmaj.client.tables.data.HeaderTableCellRenderer

HeaderTableScrollPane - Class in edu.jhu.tmaj.client.image.data

A ScrollPane that displays row numbers for a JTable.

HeaderTableScrollPane(JTable, int, int) - Constructor for class edu.jhu.tmaj.client.image.data.HeaderTableScrollPane

Constructs this object

headWithTitle(String) - Static method in class edu.jhu.tmaj.servlet.ServletUtil

height - Variable in class edu.jhu.tmaj.client.image.data.Size

height - Variable in class edu.jhu.tmaj.client.image.draw.Dimension

height - Variable in class edu.jhu.tmaj.client.image.draw.RectangleDrawable

height - Variable in class edu.jhu.tmaj.client.image.draw.ShapeRecord

helpButtonPressed(Component) - Static method in class edu.jhu.tmaj.client.importer.AriolFileRenamerHelper

Display the help dialog.

HelpDialog - Class in edu.jhu.tmaj.client.shared

A dialog that contains a url where help information is available.

HelpDialog() - Constructor for class edu.jhu.tmaj.client.shared.HelpDialog

hideColumns(JTable, String[]) - Static method in class edu.jhu.tmaj.client.image.data.JTableUtil

Sets the width of all the columnames in columnNames[] to zero.

hideColumns() - Method in class edu.jhu.tmaj.client.tables.InputPanel4

Displays a HideColumnsFrame

HideColumnsDialog - Class in edu.jhu.tmaj.client.tables

A Frame that allows users to hide columns in a JTable by setting their width to zero.

HideColumnsTreeDialog - Class in edu.jhu.tmaj.client.image

HideColumnsTreeDialog() - Constructor for class edu.jhu.tmaj.client.image.HideColumnsTreeDialog

hideLegend() - Method in class edu.jhu.tmaj.client.arraybuilder.data.ColorLegend

HISTO_TECHNICIAN_FIELD - Static variable in class edu.jhu.tmaj.beans.SlideBean

HISTOLOGIC_TYPE_FIELD - Static variable in class edu.jhu.tmaj.servlet.request.impl.DiagnosisLookupRequest

HistoryDialog - Class in edu.jhu.tmaj.client.tables.logs

A Dialog that displays in table-format a history of the changes to a given record

HistoryRequest - Class in edu.jhu.tmaj.servlet.request.impl

A Request used to show the history of a specified record in TMAJ.

HistoryRequest(int, int) - Constructor for class edu.jhu.tmaj.servlet.request.impl.HistoryRequest

Constructs this request

HistoryResponse - Class in edu.jhu.tmaj.servlet.response.impl

A Response showing information about who modified a database record, and when they modified it.

HistoryResponse(List<String>, List<List>) - Constructor for class edu.jhu.tmaj.servlet.response.impl.HistoryResponse

Constructs this Response.

HoldPanel - Class in edu.jhu.tmaj.client.tables

A Panel where the supplied component may be hidden or shown by calling the setNormalComponentViewable method.

HoldPanel(Component) - Constructor for class edu.jhu.tmaj.client.tables.HoldPanel

HorizontalTable - Class in edu.jhu.tmaj.client.tables.data

A JTable that allows different ComboBoxes on different rows (normally it's columns)

HorizontalTable(TableModel) - Constructor for class edu.jhu.tmaj.client.tables.data.HorizontalTable

HOSPITAL_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.dynamic.SpecimenBean

HOSPITAL_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.PatientBean

HOST_ANIMAL_STRAIN_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.CellLineExperimentBean

HOST_ANIMAL_TYPE_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.CellLineExperimentBean

HsbPixel - Class in edu.jhu.tmaj.beans.masks.data

Represents a H, S, and B value ranging from 0 - 255.

HsbPixel(int, int, int) - Constructor for class edu.jhu.tmaj.beans.masks.data.HsbPixel

HsbRange - Class in edu.jhu.tmaj.beans.masks.color

Represents a mutable range of Hsb values that include all values that have been passed to the updateRange method.

HsbRangeComponent - Class in edu.jhu.tmaj.client.frida.gui.masks.color

A GUI component with 6 JSliders that represent a HSB range, from min to max.

HsbRangeComponent(HsbRange, ActionListener) - Constructor for class edu.jhu.tmaj.client.frida.gui.masks.color.HsbRangeComponent

Constructs this object.

hsbToColor(HsbPixel) - Static method in class edu.jhu.tmaj.beans.masks.data.PixelUtil

Converts an HsbPixel into a java.awt.Color

hsbToPixel(HsbPixel) - Static method in class edu.jhu.tmaj.beans.masks.data.PixelUtil

Converts an hsb pixel to a imagej-ready pixel.

I

IAQuery - Class in edu.jhu.tmaj.servlet.request.impl

IAQuery(ExpandingMap, String) - Constructor for class edu.jhu.tmaj.servlet.request.impl.IAQuery

IASessionBean - Class in edu.jhu.tmaj.beans

IASessionBean() - Constructor for class edu.jhu.tmaj.beans.IASessionBean

IASessionBean(int, int, String, int) - Constructor for class edu.jhu.tmaj.beans.IASessionBean

IASessionBeanHolder - Class in edu.jhu.tmaj.client.image.data

IASessionDialog - Class in edu.jhu.tmaj.client.image

IASessionGuis - Class in edu.jhu.tmaj.client.image.data

IASessionGuis() - Constructor for class edu.jhu.tmaj.client.image.data.IASessionGuis

IASessionWindowListener - Class in edu.jhu.tmaj.client.image.data

IconsHelper - Class in edu.jhu.tmaj.util.swing

This class became unused following the addition of icon images to the JAR file.

id - Variable in class edu.jhu.tmaj.beans.exfile.data.PartialFolder

ID_FIELD - Static variable in class edu.jhu.tmaj.beans.AnimalExperimentBean

ID_FIELD - Static variable in class edu.jhu.tmaj.beans.ArrayBlockBean

ID_FIELD - Static variable in class edu.jhu.tmaj.beans.ArrayCoreBean

ID_FIELD - Static variable in class edu.jhu.tmaj.beans.ArrayImageBean

ID_FIELD - Static variable in class edu.jhu.tmaj.beans.ArraySlideBean

ID_FIELD - Static variable in class edu.jhu.tmaj.beans.BlockBean

ID_FIELD - Static variable in class edu.jhu.tmaj.beans.BlockOrSlideExchangeBean

ID_FIELD - Static variable in class edu.jhu.tmaj.beans.BlockUsageAltBean

ID_FIELD - Static variable in class edu.jhu.tmaj.beans.BlockUsageBean

ID_FIELD - Static variable in class edu.jhu.tmaj.beans.BloodSampleBean

ID_FIELD - Static variable in class edu.jhu.tmaj.beans.BloodUsageBean

ID_FIELD - Static variable in class edu.jhu.tmaj.beans.CellLineBean

ID_FIELD - Static variable in class edu.jhu.tmaj.beans.CellLineExperimentBean

ID_FIELD - Static variable in class edu.jhu.tmaj.beans.dynamic.ScoredImageBean

ID_FIELD - Static variable in class edu.jhu.tmaj.beans.dynamic.SpecimenBean

ID_FIELD - Static variable in class edu.jhu.tmaj.beans.dynamic.TissueDiagnosisBean

ID_FIELD - Static variable in class edu.jhu.tmaj.beans.IASessionBean

ID_FIELD - Static variable in class edu.jhu.tmaj.beans.MachineSessionBean

ID_FIELD - Static variable in class edu.jhu.tmaj.beans.MolecularSampleBean

ID_FIELD - Static variable in class edu.jhu.tmaj.beans.MolecularUsageBean

ID_FIELD - Static variable in class edu.jhu.tmaj.beans.PaperBean

ID_FIELD - Static variable in class edu.jhu.tmaj.beans.PatientBean

ID_FIELD - Static variable in class edu.jhu.tmaj.beans.ProjectBean

ID_FIELD - Static variable in class edu.jhu.tmaj.beans.ProtocolBean

ID_FIELD - Static variable in class edu.jhu.tmaj.beans.ScanBean

ID_FIELD - Static variable in class edu.jhu.tmaj.beans.SessionBean

ID_FIELD - Static variable in class edu.jhu.tmaj.beans.SlideBean

ID_FIELD - Static variable in class edu.jhu.tmaj.beans.TissueSampleBean

ID_FIELD - Static variable in class edu.jhu.tmaj.beans.TissueUsageBean

ID_FIELD - Static variable in class edu.jhu.tmaj.beans.UrineUsageBean

ID_FIELD - Static variable in class edu.jhu.tmaj.beans.UserBean

IMAGE_ANALYSIS_SESSION_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.SessionBean

ImageAppGuis - Class in edu.jhu.tmaj.client.image.data

ImageAppGuis() - Constructor for class edu.jhu.tmaj.client.image.data.ImageAppGuis

imageClosed(ExternalFile, ImagePlus) - Method in class edu.jhu.tmaj.client.frida.gui.masks.color.ColorMaskGui

imageClosed(ExternalFile, ImagePlus) - Method in class edu.jhu.tmaj.client.frida.gui.masks.filter.FilterMaskGui

imageClosed(ExternalFile, ImagePlus) - Method in class edu.jhu.tmaj.client.frida.gui.masks.lasso.LassoMaskGui

imageClosed(ExternalFile, ImagePlus) - Method in interface edu.jhu.tmaj.client.frida.gui.shared.MaskPanelListener

ImageFilesUtil - Class in edu.jhu.tmaj.client.importer.images.data

ImageFilesUtil() - Constructor for class edu.jhu.tmaj.client.importer.images.data.ImageFilesUtil

ImageFrameKeyListener - Class in edu.jhu.tmaj.client.image

Contains KeyListener support for the ArrayImageFrame.

ImageFrameKeyListener(ArrayImageFrame) - Constructor for class edu.jhu.tmaj.client.image.ImageFrameKeyListener

ImageInfoRequest - Class in edu.jhu.tmaj.servlet.request.impl

Obtains information about an ArrayImageID, such as the original diagnosis.

ImageInfoRequest(int) - Constructor for class edu.jhu.tmaj.servlet.request.impl.ImageInfoRequest

ImageInfoResponse - Class in edu.jhu.tmaj.servlet.response.impl

Contains a string describing background information about an ArrayImage, including information from the specimen, donor-block, and tissue diagnosis.

ImageInfoResponse(String) - Constructor for class edu.jhu.tmaj.servlet.response.impl.ImageInfoResponse

imageLabel - Variable in class edu.jhu.tmaj.client.image.ArrayImagePanel

imageOpened(ExternalFile, ImagePlus) - Method in class edu.jhu.tmaj.client.frida.gui.masks.color.ColorMaskGui

imageOpened(ExternalFile, ImagePlus) - Method in class edu.jhu.tmaj.client.frida.gui.masks.filter.FilterMaskGui

imageOpened(ExternalFile, ImagePlus) - Method in class edu.jhu.tmaj.client.frida.gui.masks.lasso.LassoMaskGui

imageOpened(ExternalFile, ImagePlus) - Method in interface edu.jhu.tmaj.client.frida.gui.shared.MaskPanelListener

ImageOutputParser - Interface in edu.jhu.tmaj.client.importer.images.data

An ImageOutputParser parses images output from a system that scans TMA slides, such as Bacus or ChromaVision.

imagePlus - Variable in class edu.jhu.tmaj.client.frida.data.ImagePlusInfo

The ImagePlus the user will change around.

ImagePlusHolder - Class in edu.jhu.tmaj.client.frida.data

ImagePlusHolder() - Constructor for class edu.jhu.tmaj.client.frida.data.ImagePlusHolder

imagePlusHolder - Variable in class edu.jhu.tmaj.client.frida.gui.shared.GeneralMaskPanel

ImagePlusInfo - Class in edu.jhu.tmaj.client.frida.data

An ImagePlus and a copy of the ImagePlus with the original Pixels.

ImagePlusInfo(ImagePlus, ExternalFile) - Constructor for class edu.jhu.tmaj.client.frida.data.ImagePlusInfo

imageScrollPane - Variable in class edu.jhu.tmaj.client.image.ArrayImagePanel

ImagesDirectoryResponse - Class in edu.jhu.tmaj.servlet.response.impl

Contains a list of ArrayImageBeans that will go on to be put in the database; "NumberOfImagesAlreadyInserted", represents how many images have been inserted on this ArraySlide, and "NumberOfImagesWithNoArrayCore" represents how many of the files in the directory can not be inserted because an ArrayCore could not be located.

ImagesDirectoryResponse(List<ArrayImageU>, int, int, int, int) - Constructor for class edu.jhu.tmaj.servlet.response.impl.ImagesDirectoryResponse

ImageSize - Enum in edu.jhu.tmaj.client.image.data

The 4 sizes of ArrayImages in TMAJ.

ImagesScanLinkingHelper - Class in edu.jhu.tmaj.client.importer.images.data

ImagesScanLinkingHelper() - Constructor for class edu.jhu.tmaj.client.importer.images.data.ImagesScanLinkingHelper

ImagesUploadHelper - Class in edu.jhu.tmaj.client.importer.images.data

ImagesUploadHelper() - Constructor for class edu.jhu.tmaj.client.importer.images.data.ImagesUploadHelper

imp - Variable in class edu.jhu.tmaj.beans.masks.results.ParticleAnalyzer2

ImportAppGUI - Class in edu.jhu.tmaj.client.importer

The main gui class for the Import application.

ImportDBUtil - Class in edu.jhu.tmaj.client.importer.specimens.data

Database utility functions used in the import program.

IMPORTED_BY_USER_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.MachineSessionBean

ImportSpecimensPanel - Class in edu.jhu.tmaj.client.importer.specimens

A Panel used to import specimens and patients into the database from a tab-delimited file

ImportSpecimensPanel() - Constructor for class edu.jhu.tmaj.client.importer.specimens.ImportSpecimensPanel

INCLUDE_HOLES - Static variable in class edu.jhu.tmaj.beans.masks.results.ParticleAnalyzer2

Flood fill to ignore interior holes.

increment() - Method in class edu.jhu.tmaj.util.TextProgressMonitor

Increment the total number of parts completed.

incrementCounter() - Method in class edu.jhu.tmaj.beans.masks.results.Analyzer2

IndexablePanel - Interface in edu.jhu.tmaj.client.shared

Generally implemented by a JTabbedPane, these methods allow a foreign object to switch the panel to a different tab.

indexOf(String) - Method in class edu.jhu.tmaj.client.image.data.StringSet

infoButton - Variable in class edu.jhu.tmaj.client.image.ArrayImageFrame

InfoFrame - Class in edu.jhu.tmaj.client.image

A Frame containing background data for any ArrayImage, including the Specimen and donor-block information, as well as the original diagnosis.

InfoFrame() - Constructor for class edu.jhu.tmaj.client.image.InfoFrame

init() - Method in class edu.jhu.tmaj.client.samples.SamplesAppGUI

init() - Method in class edu.jhu.tmaj.client.specimens.SpecimensAppGUI

InitDatabaseRequest - Class in edu.jhu.tmaj.servlet.request.impl

This class allows the user to fill the database with sample data and a default user account when they are setting up the application for the first time, rather than having to run a platform-dependent database script separately.

InitDatabaseRequest() - Constructor for class edu.jhu.tmaj.servlet.request.impl.InitDatabaseRequest

InitDatabaseResponse - Class in edu.jhu.tmaj.servlet.response.impl

Contains a String identifying the changes made to initialize the database.

InitDatabaseResponse(String) - Constructor for class edu.jhu.tmaj.servlet.response.impl.InitDatabaseResponse

INITIAL_QUANTITY_FIELD - Static variable in class edu.jhu.tmaj.beans.BloodSampleBean

INITIAL_QUANTITY_FIELD - Static variable in class edu.jhu.tmaj.beans.TissueSampleBean

initialize(int) - Method in class edu.jhu.tmaj.beans.manytomany.ManyToManyBean

Initializes the bean for a particular user, which includes only some of the records in the ManyToMany table.

initialize() - Method in class edu.jhu.tmaj.beans.manytomany.ManyToManyBean

Initializes the bean with all the records found in the ManyToMany table

initialize(ArrayImageCollectionBean) - Method in class edu.jhu.tmaj.client.image.data.Navigator

Initializes the navigator by setting the the ArrayImageCollectionBean

initializeWithArrayBlock(int) - Method in class edu.jhu.tmaj.beans.ArrayCoreReferenceBean

Initializes the data in this class with an ArrayBlockID.

initializeWithArrayBlock(int) - Method in class edu.jhu.tmaj.beans.CellLinesReferenceBean

initializeWithTissueDiagnosisID(int) - Method in class edu.jhu.tmaj.beans.ArrayCoreReferenceBean

Initializes this bean with a TissueDiagnosisID.

initializeWithTissueDiagnosisID(int) - Method in class edu.jhu.tmaj.beans.CellLinesReferenceBean

initSliderSize(JSlider) - Static method in class edu.jhu.tmaj.client.frida.gui.masks.color.FullSlider

Initializes the Slider's ticks and size

INPUT_FIELD - Static variable in class edu.jhu.tmaj.beans.AnimalExperimentBean

INPUT_FIELD - Static variable in class edu.jhu.tmaj.beans.ArrayCoreBean

INPUT_FIELD - Static variable in class edu.jhu.tmaj.beans.BlockBean

INPUT_FIELD - Static variable in class edu.jhu.tmaj.beans.CellLineExperimentBean

INPUT_LOG_FIELD - Static variable in class edu.jhu.tmaj.beans.ArrayBlockBean

INPUT_LOG_FIELD - Static variable in class edu.jhu.tmaj.beans.ArraySlideBean

INPUT_LOG_FIELD - Static variable in class edu.jhu.tmaj.beans.BlockOrSlideExchangeBean

INPUT_LOG_FIELD - Static variable in class edu.jhu.tmaj.beans.BlockUsageBean

INPUT_LOG_FIELD - Static variable in class edu.jhu.tmaj.beans.dynamic.TissueDiagnosisBean

INPUT_LOG_FIELD - Static variable in class edu.jhu.tmaj.beans.PatientBean

INPUT_LOG_FIELD - Static variable in class edu.jhu.tmaj.beans.ProtocolBean

INPUT_LOG_FIELD - Static variable in class edu.jhu.tmaj.beans.ScanBean

INPUT_LOG_FIELD - Static variable in class edu.jhu.tmaj.beans.UrineUsageBean

INPUT_LOG_FIELD - Static variable in class edu.jhu.tmaj.beans.UserBean

InputAdapter - Class in edu.jhu.tmaj.client.image.draw

A convenience class that implements a MouseListener,MouseMotionListener, and KeyListener

InputAdapter() - Constructor for class edu.jhu.tmaj.client.image.draw.InputAdapter

InputLog - Class in edu.jhu.tmaj.database.sql

Represents the InputLog field in one record.

InputLog(int, String) - Constructor for class edu.jhu.tmaj.database.sql.InputLog

INPUTLOG_FIELD - Static variable in class edu.jhu.tmaj.beans.ArrayImageBean

INPUTLOG_FIELD - Static variable in class edu.jhu.tmaj.beans.BlockUsageAltBean

INPUTLOG_FIELD - Static variable in class edu.jhu.tmaj.beans.BloodSampleBean

INPUTLOG_FIELD - Static variable in class edu.jhu.tmaj.beans.BloodUsageBean

INPUTLOG_FIELD - Static variable in class edu.jhu.tmaj.beans.CellLineBean

INPUTLOG_FIELD - Static variable in class edu.jhu.tmaj.beans.dynamic.ScoredImageBean

INPUTLOG_FIELD - Static variable in class edu.jhu.tmaj.beans.dynamic.SpecimenBean

INPUTLOG_FIELD - Static variable in class edu.jhu.tmaj.beans.IASessionBean

INPUTLOG_FIELD - Static variable in class edu.jhu.tmaj.beans.MolecularSampleBean

INPUTLOG_FIELD - Static variable in class edu.jhu.tmaj.beans.MolecularUsageBean

INPUTLOG_FIELD - Static variable in class edu.jhu.tmaj.beans.PaperBean

INPUTLOG_FIELD - Static variable in class edu.jhu.tmaj.beans.ProjectBean

INPUTLOG_FIELD - Static variable in class edu.jhu.tmaj.beans.SlideBean

INPUTLOG_FIELD - Static variable in class edu.jhu.tmaj.beans.TissueSampleBean

INPUTLOG_FIELD - Static variable in class edu.jhu.tmaj.beans.TissueUsageBean

InputPanel4 - Class in edu.jhu.tmaj.client.tables

A Panel that turns a regular database table into a JTable with lots of functionality for adding, modifying, and deleting rows.

InputPanel4(TableData4) - Constructor for class edu.jhu.tmaj.client.tables.InputPanel4

InputPanelClipBoard - Class in edu.jhu.tmaj.client.tables.data

Allows users to cut and paste in the Tables.

inRange(HsbPixel) - Method in class edu.jhu.tmaj.beans.masks.color.HsbRange

Returns true if the pixel is in the range defined.

inRange(int) - Method in class edu.jhu.tmaj.beans.masks.color.SimpleRange

Returns true if the value is inside this range.

inRange(HsbPixel) - Method in class edu.jhu.tmaj.client.frida.gui.masks.color.HsbRangeComponent

insert() - Method in class edu.jhu.tmaj.beans.ArrayBlockBean

insert() - Method in class edu.jhu.tmaj.beans.dynamic.DynamicJBean

Performs an INSERT operation on the database with the data in this bean.

insert() - Method in class edu.jhu.tmaj.beans.dynamic.SpecimenBean

insert() - Method in class edu.jhu.tmaj.beans.JBean

Inserts the database row with the data in this Bean.

insert() - Method in class edu.jhu.tmaj.beans.ProjectBean

insert() - Method in class edu.jhu.tmaj.beans.SessionBean

insert() - Method in class edu.jhu.tmaj.beans.UserBean

Inserts this new user into the database, and assigns a random password.

insert() - Method in class edu.jhu.tmaj.client.importer.images.data.ArrayImage2

insertBeans(CacheableBean, String) - Method in class edu.jhu.tmaj.beans.data.StaticMetaData

insertColumn(int, C) - Method in interface edu.jhu.tmaj.util.file.TableArray

insertColumn(int, C) - Method in class edu.jhu.tmaj.util.file.TableArrayImpl

insertEnumerations(String[], String) - Method in class edu.jhu.tmaj.beans.data.StaticMetaData

insertEnumerations(List<StaticEnumeration>, String) - Method in class edu.jhu.tmaj.beans.data.StaticMetaData

insertHash(String, String, Map<String, String>, int) - Static method in class edu.jhu.tmaj.client.importer.specimens.data.ImportDBUtil

Inserts a record into a database tables based on values given in a Map.

insertIntoDatabase() - Method in interface edu.jhu.tmaj.client.tables.logs.ChangeLog

Inserts the ChangeLog into one of the Log-Recording tables in the Database.

insertIntoDatabase() - Method in class edu.jhu.tmaj.client.tables.logs.DeletionLog

insertIntoDatabase() - Method in class edu.jhu.tmaj.client.tables.logs.FieldUpdateLog

insertLookupTable(LookupTable, String) - Method in class edu.jhu.tmaj.beans.data.StaticMetaData

InsertSQL - Class in edu.jhu.tmaj.database.sql

Represents an Insert SQL statement.

insertSQL - Variable in class edu.jhu.tmaj.servlet.request.impl.ScoredImageInsert

insertUsersArrayBlocks(int, int) - Static method in class edu.jhu.tmaj.beans.manytomany.UsersArrayBlocksBean

insertUsersProjects(int, int) - Static method in class edu.jhu.tmaj.beans.manytomany.UsersProjectsBean

insertUsersSpecimens(int, int) - Static method in class edu.jhu.tmaj.beans.manytomany.UsersSpecimens

Inserts a record into the UsersSpecimens Table.

insertUsersUsers(int, int) - Static method in class edu.jhu.tmaj.beans.manytomany.UsersUsersBean

Inserts a record into the UsersUsers Table.

INSTITUTION_FIELD - Static variable in class edu.jhu.tmaj.beans.UserBean

intArrayToCommaParenthesisString(int[]) - Static method in class edu.jhu.tmaj.util.ListConvertUtil

Converts an array of ints to a comma-delimited String with parenthesis at the beginning and end.

IntegerCellRenderer - Class in edu.jhu.tmaj.client.tables.data

This cell renderer uses the same functionality as the default JTable renderer for integer cells, but enforces a consistent font across UI Look & Feel types.

IntegerCellRenderer() - Constructor for class edu.jhu.tmaj.client.tables.data.IntegerCellRenderer

InternalSecurityException - Exception in edu.jhu.tmaj.beans.data

Exception indicates the server is rejecting a client's request because of security.

InternalSecurityException(String) - Constructor for exception edu.jhu.tmaj.beans.data.InternalSecurityException

intersects(Set, Set) - Static method in class edu.jhu.tmaj.util.SetUtil

InvalidateMachineScoresRequest - Class in edu.jhu.tmaj.servlet.request.impl

A Request to set a MachineScore record as invalid (or valid).

InvalidateMachineScoresRequest(List<Integer>, boolean) - Constructor for class edu.jhu.tmaj.servlet.request.impl.InvalidateMachineScoresRequest

Constructs this object.

INVESTIGATOR_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.BlockOrSlideExchangeBean

IRB_CONTACT1_FIELD - Static variable in class edu.jhu.tmaj.beans.ProtocolBean

IRB_NUMBER_FIELD - Static variable in class edu.jhu.tmaj.beans.BlockUsageBean

IRB_NUMBER_FIELD - Static variable in class edu.jhu.tmaj.beans.BloodUsageBean

IRB_NUMBER_FIELD - Static variable in class edu.jhu.tmaj.beans.MolecularUsageBean

IRB_NUMBER_FIELD - Static variable in class edu.jhu.tmaj.beans.TissueUsageBean

IRB_NUMBER_FIELD - Static variable in class edu.jhu.tmaj.beans.UrineUsageBean

IRB_PROTOCOL_NUMBER_FIELD - Static variable in class edu.jhu.tmaj.beans.ProtocolBean

IS_BAD_FIELD - Static variable in class edu.jhu.tmaj.beans.ArrayImageBean

IS_CHECK_IN_FIELD - Static variable in class edu.jhu.tmaj.beans.BlockOrSlideExchangeBean

IS_DIVIDED_FIELD - Static variable in class edu.jhu.tmaj.beans.BlockBean

IS_FINAL_FIELD - Static variable in class edu.jhu.tmaj.beans.ArrayBlockBean

IS_FINAL_FIELD - Static variable in class edu.jhu.tmaj.beans.SessionBean

IS_LOOKUP_DISABLED_FIELD - Static variable in class edu.jhu.tmaj.beans.ProjectBean

IS_PUBLISHED_FIELD - Static variable in class edu.jhu.tmaj.beans.SessionBean

IS_XENOGRAFT_FIELD - Static variable in class edu.jhu.tmaj.beans.CellLineExperimentBean

isAdmin() - Method in class edu.jhu.tmaj.beans.UserBean

Returns true if the user is a group admin or full admin.

isAllIncludedInDefault() - Method in class edu.jhu.tmaj.beans.masks.lasso.LassoMask

isAnded - Variable in class edu.jhu.tmaj.beans.masks.meta.ActionMaskInfo

isArrayBlockBlank() - Method in class edu.jhu.tmaj.servlet.response.impl.IsArrayBlockBlankResponse

IsArrayBlockBlankRequest - Class in edu.jhu.tmaj.servlet.request.impl

A request that determines if an ArrayBlock has had a user put in information on it's cores.

IsArrayBlockBlankRequest(int) - Constructor for class edu.jhu.tmaj.servlet.request.impl.IsArrayBlockBlankRequest

IsArrayBlockBlankResponse - Class in edu.jhu.tmaj.servlet.response.impl

Contains a boolean on whether the ArrayBlock is blank, and if not, how many cores are designed.

IsArrayBlockBlankResponse(int) - Constructor for class edu.jhu.tmaj.servlet.response.impl.IsArrayBlockBlankResponse

isArrayImageIncluded(ArrayImageCell) - Static method in class edu.jhu.tmaj.client.image.data.Navigator

Returns true if the ArrayImage should be included in the navigator.

isArraySlideInAnyProject(int) - Method in class edu.jhu.tmaj.beans.manytomany.ProjectsArraySlidesBean

Returns true if the given ArraySlide has been assigned to one or more projects.

isAttached() - Method in class edu.jhu.tmaj.client.tables.Detacher

isBad() - Method in class edu.jhu.tmaj.client.image.data.ArrayImageCell

Returns true if there is an image present, but it is not worth viewing.

isCancelledGracefully() - Method in class edu.jhu.tmaj.util.swing.PublicSwingWorker

isCellEditable(int, int) - Method in class edu.jhu.tmaj.client.tables.data.BeanTableModel

Returns false if the row has been deleted or the column number is zero; otherwise, returns true.

isCellEditable(int, int) - Method in class edu.jhu.tmaj.client.tables.data.DynamicTableModel

isCellEditable(int, int) - Method in class edu.jhu.tmaj.client.tables.data.GeneralTableModel

Returns false.

isCellRelevant(JTable, int, int) - Static method in class edu.jhu.tmaj.client.tables.data.DynamicTableModel

isChecked - Variable in class edu.jhu.tmaj.client.image.CheckableObject

ISCHEMIC_ESTIMATED_TIME_FIELD - Static variable in class edu.jhu.tmaj.beans.TissueSampleBean

isClientViewable() - Method in enum edu.jhu.tmaj.servlet.request.impl.KeyValueGetRequest.KeyName

isColumnShown(JTable, int) - Static method in class edu.jhu.tmaj.client.image.data.JTableUtil

isCompatible(Object) - Method in class edu.jhu.tmaj.client.tables.data.ColumnSet

Returns true if the Data contain the same set of columns.

isCompleted - Variable in class edu.jhu.tmaj.client.image.draw.AbstractDrawable

isCompleted() - Method in class edu.jhu.tmaj.client.image.draw.AbstractDrawable

Returns true if the user is finished drawing the shape

isCompleted() - Method in interface edu.jhu.tmaj.client.image.draw.Drawable

Returns true if the user is finished drawing the shape.

isControl() - Method in class edu.jhu.tmaj.beans.misc.ArrayCoreRep

isControl() - Method in class edu.jhu.tmaj.client.arraybuilder.data.ArrayCoreCell

Returns true if the user has designated this ArrayCoreCell as a control.

isControl() - Method in class edu.jhu.tmaj.client.arraybuilder.data.ArrayCoreData

isDetached() - Method in class edu.jhu.tmaj.client.tables.Detacher

isDiagnosed() - Method in class edu.jhu.tmaj.client.image.data.ScoreData

Returns true if the user has assigned a Sub-Diagnosis (HistologicType)

isDisabled() - Method in class edu.jhu.tmaj.client.image.data.ArrayImageCell

Returns true if the ArrayImage actually has an image, and not just a place holder.

isDouble() - Method in enum edu.jhu.tmaj.beans.masks.results.MaskStats.StatName

isDrawingViewable() - Method in class edu.jhu.tmaj.client.image.TopMenu

Returns true if the user should be able to view drawing made on the image.

isEnumerated(String) - Method in class edu.jhu.tmaj.beans.data.StaticMetaData

Returns true if the column is enumerated, false if it is "type-in"

isEnumerated(int) - Method in class edu.jhu.tmaj.beans.dynamic.data.DynamicMetaData

Returns true if a DynamicField with primary key fieldID has any enumerations; Returns false if it is a field where the user types in the value.

isEnumerated() - Method in class edu.jhu.tmaj.beans.dynamic.data.DynamicValue

Returns true if the relevant data is in the EnumID column

isEnumerated(DatabaseField) - Method in class edu.jhu.tmaj.beans.dynamic.DynamicJBean

Returns true if the field is enumerated (has a drop down box.) This DynamicMetaData is checked if the TField is a DynamicField, whereas the staticMetaData is checked if the TField is not a DynamicTField.

isEnumerated(DatabaseField) - Method in class edu.jhu.tmaj.beans.JBean

Returns true if the column is enumerated (gives a comboBox of choices).

isError() - Method in class edu.jhu.tmaj.util.data.Status

isFilteredOut() - Method in class edu.jhu.tmaj.client.image.data.ArrayImageCell

Returns true if this image is not part of the images selected in a filter

isFilterOn() - Method in class edu.jhu.tmaj.client.image.data.ArrayImageCell

Returns true if a filter has been applied to this set of images

isFinal() - Method in class edu.jhu.tmaj.beans.ArrayBlockBean

Returns true if ArrayBlock has been set as final and can no longer be modified in ArrayBuilder.

isFinal() - Method in class edu.jhu.tmaj.beans.SessionBean

Returns true if this has been marked as a final session.

isFloat - Variable in enum edu.jhu.tmaj.client.importer.machscores.MachineScoreField

isFocusable() - Method in class edu.jhu.tmaj.client.image.draw.DrawableLabel

Returns true so the component can fire keyboard events

isFullAdmin() - Method in enum edu.jhu.tmaj.beans.data.AdminAppPermission

Returns true if the user is a full ("true") admin.

isFullAdmin() - Method in class edu.jhu.tmaj.beans.UserBean

isGenericShape() - Method in class edu.jhu.tmaj.beans.masks.lasso.Lasso

isGenericShape() - Method in class edu.jhu.tmaj.beans.masks.lasso.LassoedFile

isGridEnabled() - Method in class edu.jhu.tmaj.client.image.GridLabel

Returns true if this JLabel should draw the grid.

isGroupAdmin() - Method in class edu.jhu.tmaj.beans.UserBean

isGuest() - Method in class edu.jhu.tmaj.beans.UserBean

Returns true if the user's username is guest.

isHigherAccess(AdminAppPermission) - Method in enum edu.jhu.tmaj.beans.data.AdminAppPermission

isHigherAccess(ArrayBuilderPermission) - Method in enum edu.jhu.tmaj.beans.data.ArrayBuilderPermission

isHigherAccess(MetaDataAppPermission) - Method in enum edu.jhu.tmaj.beans.data.MetaDataAppPermission

isHigherAccess(PatientDataPermission) - Method in enum edu.jhu.tmaj.beans.data.PatientDataPermission

isHigherAccess(SpecimensAppPermission) - Method in enum edu.jhu.tmaj.beans.data.SpecimensAppPermission

isHighlighted() - Method in class edu.jhu.tmaj.client.image.draw.AbstractDrawable

Returns true if the drawable is selected

isHighlighted() - Method in interface edu.jhu.tmaj.client.image.draw.Drawable

Returns true if the shape is selected

isIASessionBeanInList(IASessionBean) - Method in class edu.jhu.tmaj.client.image.AbstractSessionsPanel

isIASessionOpen(IASessionBean) - Method in class edu.jhu.tmaj.client.image.OpenSessionsPanel

isImageAvailable() - Method in class edu.jhu.tmaj.client.image.ArrayImagePanel

isImageFile(File) - Static method in class edu.jhu.tmaj.client.importer.images.data.ImageFilesUtil

isImportedDataAssociatedWithScan(SelectedScan) - Static method in class edu.jhu.tmaj.servlet.request.impl.ScanDeleteRequest

isInverted - Variable in class edu.jhu.tmaj.beans.masks.meta.ActionMaskInfo

isIterationCountValid(int) - Static method in class edu.jhu.tmaj.beans.masks.filter.FilterMask

isLookupDisabled() - Method in class edu.jhu.tmaj.beans.ProjectBean

Returns true if the user should not be able to lookup the original diagnosis of the image in the Images application.

isLookupDisabledForProject(SessionBean) - Static method in class edu.jhu.tmaj.client.image.TopMenu

isLookupEnabled() - Method in class edu.jhu.tmaj.client.image.TopMenu

Returns true if diagnosis's (either general or specific) are being looked up for the user.

isMaximumParticleSizeFilterOn() - Method in class edu.jhu.tmaj.beans.masks.filter.FilterMask

isMinimumParticleSizeFilterOn() - Method in class edu.jhu.tmaj.beans.masks.filter.FilterMask

isModified() - Method in class edu.jhu.tmaj.beans.masks.lasso.LassoedFile

isNull() - Method in class edu.jhu.tmaj.beans.dynamic.data.DynamicValue

isNullOrEmpty(String) - Static method in class edu.jhu.tmaj.util.file.StringUtil

isOkay() - Method in class edu.jhu.tmaj.util.data.Status

isOnTheServer() - Static method in class edu.jhu.tmaj.config.ServerConstants

isOpen(ArrayBlockBean) - Method in class edu.jhu.tmaj.client.arraybuilder.OpenedArrayBlocksPanel

isOptionSet(ClientConstants.ClientConfigKey) - Static method in class edu.jhu.tmaj.config.ClientConstants

isOtherScored() - Method in class edu.jhu.tmaj.client.image.data.ScoreData

Returns true if the user has made a score to a field other than HistologicType, such as notes.

isParticleSizeValid(int) - Static method in class edu.jhu.tmaj.beans.masks.filter.FilterMask

isPatientInserted() - Method in class edu.jhu.tmaj.servlet.response.impl.TranslatedRowResponse

isPatientUpdated() - Method in class edu.jhu.tmaj.servlet.response.impl.TranslatedRowResponse

isPointNearLine(int, int, int, int, int, int) - Static method in class edu.jhu.tmaj.client.image.draw.LineDrawable

isPublished() - Method in class edu.jhu.tmaj.beans.SessionBean

Returns true if the session has been published, meaning its data can not be changed and all users may view the data.

isRandom() - Method in class edu.jhu.tmaj.client.image.TopMenu

Returns true if the ArrayImages should be viewed in a random order.

isRecordInUsersSpecimensTable(int, int) - Static method in class edu.jhu.tmaj.beans.manytomany.UsersSpecimens

Returns true if the UserID/SpecimenID pair is in the UsersSpecimens table.

isRedirectImage() - Static method in class edu.jhu.tmaj.beans.masks.results.Analyzer2

Returns true if an image is selected in the "Redirect To:" popup menu of the Analyze/Set Measurements dialog box.

isRequired() - Method in interface edu.jhu.tmaj.beans2.SwingColumn

isRequired - Variable in class edu.jhu.tmaj.client.tables.CheckBoxField

isRequired() - Method in enum edu.jhu.tmaj.config.ClientConstants.ClientConfigKey

isRequired() - Method in class edu.jhu.tmaj.database.data.DatabaseField

isRequired() - Method in interface edu.jhu.tmaj.util.config.data.ConfigKey

Returns true if the Config Key must be present and must have a value for TMAJ to work.

isReset() - Method in class edu.jhu.tmaj.beans.masks.color.CircleRange

isReset() - Method in class edu.jhu.tmaj.beans.masks.color.SimpleRange

isReversed - Variable in class edu.jhu.tmaj.client.admin.ManyDataPanel

isRowDeleted(TableModel, int) - Static method in class edu.jhu.tmaj.client.tables.data.BeanTableModel

isRowDeleted(int) - Method in class edu.jhu.tmaj.client.tables.data.ChangedCells

isRunningWindows() - Static method in class edu.jhu.tmaj.util.config.data.EnvironmentUtils

isSaveNecessary() - Method in class edu.jhu.tmaj.client.image.draw.ShapesFrame

isSaveNecessary(List) - Static method in class edu.jhu.tmaj.servlet.request.impl.ShapesSaveRequest

Returns true if the database must be written to reflect the changes the user made to the shapes.

isSelected() - Method in class edu.jhu.tmaj.client.arraybuilder.data.ArrayCoreCell

Returns true if the user has selected this cell.

isSelected() - Method in class edu.jhu.tmaj.client.image.data.ArrayImageCell

Returns true if the ArrayImage is currently selected by the user.

isSelected() - Method in class edu.jhu.tmaj.client.image.SelectableImage

isSessionBeanInList(SessionBean) - Method in class edu.jhu.tmaj.client.image.AbstractSessionsPanel

Returns true if the SessionBean is in the JList.

isSessionBlank(int) - Static method in class edu.jhu.tmaj.servlet.request.impl.CopySessionRequest

Returns true if there are no records for this session in the ArrayImageData and ArrayImageTypes table

isSessionIDinPaper(int, int) - Method in class edu.jhu.tmaj.beans.manytomany.PapersSessionsBean

isSessionOpen(SessionBean) - Method in class edu.jhu.tmaj.client.image.OpenSessionsPanel

isSharedOut() - Method in class edu.jhu.tmaj.beans.SessionBean

Returns true if this session has been shared to other users.

isShowing() - Method in class edu.jhu.tmaj.client.image.DotTableFrame

isSpecified() - Method in class edu.jhu.tmaj.client.tables.data.Search

isSpecimenInDatabase() - Method in class edu.jhu.tmaj.servlet.response.impl.CheckIfSpecimenExistsResponse

isSpecimenInserted() - Method in class edu.jhu.tmaj.servlet.response.impl.TranslatedRowResponse

isSpecimenUpdated() - Method in class edu.jhu.tmaj.servlet.response.impl.TranslatedRowResponse

isStringEmpty(String) - Static method in class edu.jhu.tmaj.util.StringFormatUtils

isSuccessful() - Method in interface edu.jhu.tmaj.servlet.response.CommandResponse

Returns true if the request completed successfully

isSuccessful() - Method in class edu.jhu.tmaj.servlet.response.ErrorResponse

Returns false

isSuccessful() - Method in class edu.jhu.tmaj.servlet.response.SuccessResponse

Returns true.

isTissueDiagnosisInDatabase() - Method in class edu.jhu.tmaj.servlet.response.impl.CheckIfSpecimenExistsResponse

isTissueDiagnosisLookedUp(int) - Method in class edu.jhu.tmaj.beans.ArrayCoreReferenceBean

Returns true if this bean has information about the specified TissueDiagnosisID

isTooLate(long) - Method in enum edu.jhu.tmaj.util.ObjectPool.WaitTime

isTopLevel() - Method in class edu.jhu.tmaj.beans.exfile.ExternalFolder

isTyped() - Method in class edu.jhu.tmaj.client.image.data.ScoreData

Returns true if the user has assigned a TissueType

isURLValid(String) - Static method in class edu.jhu.tmaj.util.URLUtil

isUseHardLinks() - Method in class edu.jhu.tmaj.client.image.data.ImageAppGuis

isValid() - Method in interface edu.jhu.tmaj.client.image.draw.Drawable

Returns true if the shape is "worth saving".

isValid() - Method in class edu.jhu.tmaj.client.image.draw.FreeHandDrawable

isValid() - Method in class edu.jhu.tmaj.client.image.draw.LineDrawable

isValid() - Method in class edu.jhu.tmaj.client.image.draw.PolygonDrawable

isValid() - Method in class edu.jhu.tmaj.client.image.draw.RectangleDrawable

isValid() - Method in class edu.jhu.tmaj.client.image.draw.TextDrawable

isViewPositionEnabled() - Method in class edu.jhu.tmaj.client.image.TopMenu

Returns true if the user can view the current x/y position of the ArrayImage in the corner.

isVisited() - Method in class edu.jhu.tmaj.client.image.data.ArrayImageCell

Returns true if the user has visited this ArrayImage since starting the application.

isWaitingAnOption() - Method in enum edu.jhu.tmaj.util.ObjectPool.WaitTime

isWrapping() - Method in class edu.jhu.tmaj.beans.masks.color.CircleRange

Returns true if the range "wraps" around 0.

isWritable(UserBean) - Method in class edu.jhu.tmaj.beans.SessionBean

isWritable() - Method in class edu.jhu.tmaj.client.arraybuilder.ArrayBlockFrame

Returns true if the user is allowed to make changes to the current ArrayBlock

isWritable() - Method in class edu.jhu.tmaj.client.image.ArrayImageFrame

ITALIC_FONT - Static variable in class edu.jhu.tmaj.client.tables.data.HeaderTableCellRenderer

ITERATION_COUNT_MAX_VALUE - Static variable in class edu.jhu.tmaj.beans.masks.filter.FilterMask

ITERATION_COUNT_MIN_VALUE - Static variable in class edu.jhu.tmaj.beans.masks.filter.FilterMask

IV_FILE_NAME - Static variable in class edu.jhu.tmaj.util.crypt.KeyManagementUtil

J

JBean - Class in edu.jhu.tmaj.beans

Represents a database table that can be converted into a Swing JTable and edited.

JBean(StaticMetaData) - Constructor for class edu.jhu.tmaj.beans.JBean

Constructs a JBean.

JNLP_LINK_FIELD - Static variable in class edu.jhu.tmaj.beans.PaperBean

jobIsDone() - Method in class edu.jhu.tmaj.client.shared.SimpleProgressDialog

join(MaskStats) - Method in class edu.jhu.tmaj.beans.masks.results.MaskStats

join(List, String) - Static method in class edu.jhu.tmaj.util.file.StringUtil

join(List, String, String) - Static method in class edu.jhu.tmaj.util.file.StringUtil

JOURNAL_REFERENCE_FIELD - Static variable in class edu.jhu.tmaj.beans.PaperBean

JpegCompressionUtil - Class in edu.jhu.tmaj.util

This plugin creates a 100 pixel wide 8-bit indexed color version of the active image.

JpegCompressionUtil() - Constructor for class edu.jhu.tmaj.util.JpegCompressionUtil

JTableUtil - Class in edu.jhu.tmaj.client.image.data

K

KeyListenerUtils - Class in edu.jhu.tmaj.util.swing

Utility methods for adding key listeners to components.

KeyManagementUtil - Class in edu.jhu.tmaj.util.crypt

A utility class for creating, storing, or getting a key or iv.

KeyManagementUtil() - Constructor for class edu.jhu.tmaj.util.crypt.KeyManagementUtil

keyPressed(KeyEvent) - Method in class edu.jhu.tmaj.client.image.draw.InputAdapter

keyPressed(KeyEvent) - Method in class edu.jhu.tmaj.client.image.draw.ShapeListener

keyPressed(KeyEvent) - Method in class edu.jhu.tmaj.client.image.ImageFrameKeyListener

keyReleased(KeyEvent) - Method in class edu.jhu.tmaj.client.image.draw.InputAdapter

keyTyped(KeyEvent) - Method in class edu.jhu.tmaj.client.image.draw.InputAdapter

KeyValueGetRequest - Class in edu.jhu.tmaj.servlet.request.impl

KeyValueGetRequest(KeyValueGetRequest.KeyName) - Constructor for class edu.jhu.tmaj.servlet.request.impl.KeyValueGetRequest

KeyValueGetRequest.KeyName - Enum in edu.jhu.tmaj.servlet.request.impl

KeyValueGetResponse - Class in edu.jhu.tmaj.servlet.response.impl

KeyValueGetResponse(String) - Constructor for class edu.jhu.tmaj.servlet.response.impl.KeyValueGetResponse

KeyValueSetRequest - Class in edu.jhu.tmaj.servlet.request.impl

L

LAB_OBTAINED_FIELD - Static variable in class edu.jhu.tmaj.beans.CellLineExperimentBean

LabelFocusMouseListener - Class in edu.jhu.tmaj.client.image.draw

A MouseListener that is attached to a JLabel, and when the mouse is pressed the JLabel gets the Focus.

LabelFocusMouseListener(JLabel) - Constructor for class edu.jhu.tmaj.client.image.draw.LabelFocusMouseListener

LARGE_SIZE_FILE_ID - Static variable in class edu.jhu.tmaj.beans.ArrayImageBean

Lasso - Class in edu.jhu.tmaj.beans.masks.lasso

A data class for storing free hand Lassos the user draws on an image.

LassoedFile - Class in edu.jhu.tmaj.beans.masks.lasso

LassoedFile(ExternalFile) - Constructor for class edu.jhu.tmaj.beans.masks.lasso.LassoedFile

LassoMask - Class in edu.jhu.tmaj.beans.masks.lasso

Represents a mask that the user draws with the free-hand (circle) tool on an image to select a region of interest.

LassoMask(String, boolean) - Constructor for class edu.jhu.tmaj.beans.masks.lasso.LassoMask

LassoMaskDatabaseUtil - Class in edu.jhu.tmaj.beans.masks.lasso

LassoMaskDatabaseUtil() - Constructor for class edu.jhu.tmaj.beans.masks.lasso.LassoMaskDatabaseUtil

LassoMaskDatabaseUtil.Reader - Class in edu.jhu.tmaj.beans.masks.lasso

LassoMaskDatabaseUtil.Reader() - Constructor for class edu.jhu.tmaj.beans.masks.lasso.LassoMaskDatabaseUtil.Reader

LassoMaskDatabaseUtil.Writer - Class in edu.jhu.tmaj.beans.masks.lasso

LassoMaskDatabaseUtil.Writer() - Constructor for class edu.jhu.tmaj.beans.masks.lasso.LassoMaskDatabaseUtil.Writer

LassoMaskGui - Class in edu.jhu.tmaj.client.frida.gui.masks.lasso

The GUI component for the Lasso Mask.

LassoMaskGui(LassoMask, List<ExternalFileCoordinate>, IASessionBean, ImageAppGuis) - Constructor for class edu.jhu.tmaj.client.frida.gui.masks.lasso.LassoMaskGui

lastParticle - Static variable in class edu.jhu.tmaj.beans.masks.results.Analyzer2

LESION_LETTER_FIELD - Static variable in class edu.jhu.tmaj.beans.dynamic.TissueDiagnosisBean

LevelMessages - Class in edu.jhu.tmaj.util.data

LevelMessages() - Constructor for class edu.jhu.tmaj.util.data.LevelMessages

LimitedToolBar - Class in edu.jhu.tmaj.client.frida.gui.shared

This class is used to show only part of the imageJ tool bar; Part of the tool-bar that is made available in this class in the zoom tool, the freehand-selection tool, and the hand tool.

LimitedToolBar(LimitedToolBar.ImageTool...) - Constructor for class edu.jhu.tmaj.client.frida.gui.shared.LimitedToolBar

LimitedToolBar.ImageTool - Enum in edu.jhu.tmaj.client.frida.gui.shared

Represents all the tools from ImageJ that this class will support.

LineDrawable - Class in edu.jhu.tmaj.client.image.draw

A line

LineDrawable(DrawableLabel) - Constructor for class edu.jhu.tmaj.client.image.draw.LineDrawable

LineupFrame - Class in edu.jhu.tmaj.client.image

A Frame that lines up mid-size ArrayImages side-to-side.

linkButton - Variable in class edu.jhu.tmaj.client.image.NavigationGUI

LinkGroup - Class in edu.jhu.tmaj.beans.manytomany

Links Integers to a Set.

LinkGroup() - Constructor for class edu.jhu.tmaj.beans.manytomany.LinkGroup

linkImagesToScanButton - Variable in class edu.jhu.tmaj.client.importer.images.ArrayImagesImportGui2

linkImagesToScanButtonPressed() - Method in class edu.jhu.tmaj.client.importer.images.ArrayImagesImportHelper

linkImagesWithScan(ExternalFolder, SelectedScan, Component) - Static method in class edu.jhu.tmaj.client.importer.images.data.ImagesScanLinkingHelper

LIST_VIEW_SIZE - Static variable in class edu.jhu.tmaj.client.image.ShareSessionDialog

ListConvertUtil - Class in edu.jhu.tmaj.util

Provides methods for converting and printing information about Collections and arrays.

listToCommaDelimitedString(List) - Static method in class edu.jhu.tmaj.util.ListConvertUtil

Converts a List to one big comma-delimited String.

listToDelimitedString(List, String) - Static method in class edu.jhu.tmaj.util.ListConvertUtil

Converts a list to a String where the elements of the list are delimited by the specified delimiter.

listToIntArray(List<Integer>) - Static method in class edu.jhu.tmaj.util.ListConvertUtil

Converts an int array to a List of Doubles.

listToString(List, String) - Static method in class edu.jhu.tmaj.util.ListConvertUtil

A useful join() function

listToTabDelimitedString(List) - Static method in class edu.jhu.tmaj.util.ListConvertUtil

Converts a list to a tab-delimited String

LiteralValue - Class in edu.jhu.tmaj.database.sql

Represents a value to be put in the database as-is.

LiteralValue(String) - Constructor for class edu.jhu.tmaj.database.sql.LiteralValue

loadShapesIntoDrawableLabel(int) - Method in class edu.jhu.tmaj.client.image.ArrayImagePanel

LOCATION_FIELD - Static variable in class edu.jhu.tmaj.beans.ArraySlideBean

LOCATION_FIELD - Static variable in class edu.jhu.tmaj.beans.MolecularSampleBean

LOCATION_FIELD - Static variable in class edu.jhu.tmaj.beans.SlideBean

LOCATION_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.BlockUsageAltBean

logDelete(JBean) - Static method in class edu.jhu.tmaj.client.tables.logs.BeanLogger

Logs the deletion of the JBean.

logger - Static variable in class edu.jhu.tmaj.servlet.request.impl.ScoredImageDetailsRequest

LoginDialog - Class in edu.jhu.tmaj.client.shared

A frame that displays a log-in prompt

LoginRequest - Class in edu.jhu.tmaj.servlet.request.impl

Returns a userbean containing all the permissions of the user given the user's username and password.

LoginRequest(String, String) - Constructor for class edu.jhu.tmaj.servlet.request.impl.LoginRequest

LoginResponse - Class in edu.jhu.tmaj.servlet.response.impl

The UserBean returned to the client when the client provides the UserBean's correct username and password.

LoginResponse(UserBean) - Constructor for class edu.jhu.tmaj.servlet.response.impl.LoginResponse

logIntoGUIAsGuest() - Static method in class edu.jhu.tmaj.client.shared.LoginDialog

LogoutRequest - Class in edu.jhu.tmaj.servlet.request.impl

Purely for logging purposes, this request ensures that a record will be appear in the log when a user logs out.

LogoutRequest() - Constructor for class edu.jhu.tmaj.servlet.request.impl.LogoutRequest

LogoutWindowListener - Class in edu.jhu.tmaj.client.shared

A WindowListener that informs the server the user has logged out when a specified window is closed

LogoutWindowListener() - Constructor for class edu.jhu.tmaj.client.shared.LogoutWindowListener

LogTableNumbers - Class in edu.jhu.tmaj.client.tables.logs

A utility class that gives each updatable table in TMAJ a unique table number.

logUpdate(JBean, GeneralTableModel, ChangedCells, int) - Static method in class edu.jhu.tmaj.client.tables.logs.BeanLogger

Logs changes to a JBean--All fields changed are recorded.

LookedUpDynamicEnumeration - Class in edu.jhu.tmaj.client.image.data

A DynamicEnumeration that has been automatically looked up by the software.

LookedUpDynamicEnumeration(DynamicEnumeration) - Constructor for class edu.jhu.tmaj.client.image.data.LookedUpDynamicEnumeration

LookedUpTableCellRenderer - Class in edu.jhu.tmaj.client.image.data

Highlights a TableCell yellow if it in an instance of LookedUpDynamicEnumeration.

LookedUpTableCellRenderer() - Constructor for class edu.jhu.tmaj.client.image.data.LookedUpTableCellRenderer

lookup(String, String) - Static method in class edu.jhu.tmaj.beans.UserBean

Returns a UserBean given a username and password.

lookup(int) - Method in class edu.jhu.tmaj.client.image.InfoFrame

Looks up the information for the specified ArrayImage and puts it into the TextField.

lookup(int) - Static method in class edu.jhu.tmaj.servlet.request.impl.ArrayCoresOpenRequest

Returns a List of ArrayCoreBeans from a specified ArrayBlockID

lookup(int, JTable, GeneralTableModel, JBean) - Static method in class edu.jhu.tmaj.servlet.request.impl.DiagnosisLookupRequest

Looks up the original Diagnosis and sets the appropriate ComboBox editor of the table

lookupExternalFileID(String, ExternalFolder) - Static method in class edu.jhu.tmaj.beans.exfile.data.FileGetUtil

lookupExternalFolder(String, ExternalFolder) - Static method in class edu.jhu.tmaj.beans.exfile.data.FolderGetUtil

LookupRecord - Class in edu.jhu.tmaj.beans.data.datatypes

A record from a lookup table.

LookupRecord(int, String) - Constructor for class edu.jhu.tmaj.beans.data.datatypes.LookupRecord

lookupStaticField(Map, Object, Map<Integer, LookupRecord>) - Static method in class edu.jhu.tmaj.servlet.request.impl.DetailsRequest

Given a Map and a key of that Map, changes the value of the key based on a Map lookup.

lookupStaticValuesInRecord(Map) - Method in class edu.jhu.tmaj.servlet.request.impl.ArrayCoreDetailsRequest

Looks up the TissueTypeID,SpecimenTypeID and Block Fixation fields

lookupStaticValuesInRecord(Map<TableField, Object>) - Method in class edu.jhu.tmaj.servlet.request.impl.DetailsRequest

lookupStaticValuesInRecord(Map) - Method in class edu.jhu.tmaj.servlet.request.impl.ScoredImageDetailsRequest

Lookups the TissueType,SpecimenType, and BlockFixationID from their respective tables

LookupTable - Enum in edu.jhu.tmaj.beans.data.datatypes

Represents tables in TMAJ that act as a lookup table, even though they may have many more records.

LookupTableRequest - Class in edu.jhu.tmaj.servlet.request.impl

Gets the data from a LookupTable.

LookupTableRequest(LookupTable) - Constructor for class edu.jhu.tmaj.servlet.request.impl.LookupTableRequest

LookupTableResponse - Class in edu.jhu.tmaj.servlet.response.impl

Contains a map with the primary key ids of the lookup table as its keys, and lookupRecords as it values.

LookupTableResponse(Map<Integer, LookupRecord>) - Constructor for class edu.jhu.tmaj.servlet.response.impl.LookupTableResponse

M

MachineScoreField - Enum in edu.jhu.tmaj.client.importer.machscores

Represents a field in the MachineScores table, (which is imported from a tab-delimited file).

MachineScoresImportPanel - Class in edu.jhu.tmaj.client.importer.machscores

MachineScoresImportPanel() - Constructor for class edu.jhu.tmaj.client.importer.machscores.MachineScoresImportPanel

MachineScoresImportRequest - Class in edu.jhu.tmaj.servlet.request.impl

Imports MachineScores, that is scores that are given automatically by an Imaging-Scanning machine, as opposed to by a human-being.

MachineScoresImportRequest(FilenameData, List<String>) - Constructor for class edu.jhu.tmaj.servlet.request.impl.MachineScoresImportRequest

Constructs this object

MachineScoresImportResponse - Class in edu.jhu.tmaj.servlet.response.impl

Contains a CompletionMessage, along with any warnings the Request generated while executing.

MachineScoresImportResponse() - Constructor for class edu.jhu.tmaj.servlet.response.impl.MachineScoresImportResponse

MachineScoresInfoRequest - Class in edu.jhu.tmaj.servlet.request.impl

Returns machine-scored data from the MachineScores table given an ArrayImageID.

MachineScoresInfoRequest(int) - Constructor for class edu.jhu.tmaj.servlet.request.impl.MachineScoresInfoRequest

MachineScoresInfoResponse - Class in edu.jhu.tmaj.servlet.response.impl

Contains a String with all the auto-scored data of a specified ArrayImage

MachineScoresInfoResponse(String) - Constructor for class edu.jhu.tmaj.servlet.response.impl.MachineScoresInfoResponse

MachineScoresInputDialog - Class in edu.jhu.tmaj.client.importer.machscores

MachineScoresInputDialog(Component) - Constructor for class edu.jhu.tmaj.client.importer.machscores.MachineScoresInputDialog

MachineScoresParser - Interface in edu.jhu.tmaj.servlet.request.impl

An interface that allows a tab-delimited file of MachineScores to be imported into TMAJ.

MachineScoresQuery - Class in edu.jhu.tmaj.servlet.request.impl

Add machine scores for every MachineScoresSession to the DotTableFrame.

MachineScoresQuery(ExpandingMap, String) - Constructor for class edu.jhu.tmaj.servlet.request.impl.MachineScoresQuery

MachineSessionBean - Class in edu.jhu.tmaj.beans

MachineSessionBean(StaticMetaData) - Constructor for class edu.jhu.tmaj.beans.MachineSessionBean

MachineSessionUtils - Class in edu.jhu.tmaj.client.importer.machscores

MachineSessionUtils() - Constructor for class edu.jhu.tmaj.client.importer.machscores.MachineSessionUtils

main(String[]) - Static method in class edu.jhu.tmaj.beans.masks.color.ActionList

Tests this class.

main(String[]) - Static method in class edu.jhu.tmaj.beans.masks.color.CircleRange

Performs a test of this class.

main(String[]) - Static method in class edu.jhu.tmaj.client.admin.MetaDataAdminPanel

main(String[]) - Static method in class edu.jhu.tmaj.client.image.PapersGUI

main(String[]) - Static method in class edu.jhu.tmaj.client.shared.MainApplicationGUI

main(String[]) - Static method in class edu.jhu.tmaj.database.test.Test

main(String[]) - Static method in class edu.jhu.tmaj.util.crypt.KeyManagementUtil

main(String[]) - Static method in class edu.jhu.tmaj.util.crypt.RandomString

main(String[]) - Static method in class edu.jhu.tmaj.util.crypt.StringDigest

main(String[]) - Static method in class edu.jhu.tmaj.util.swing.ColorContrastUtil

MainApplicationGUI - Class in edu.jhu.tmaj.client.shared

The first screen a user sees when they log into TMAJ.

mainPanel - Variable in class edu.jhu.tmaj.client.image.ShareSessionDialog

mainPanel - Variable in class edu.jhu.tmaj.client.importer.images.ArrayImagesImportGui2

MainTableSection - Enum in edu.jhu.tmaj.client.image.data

makeCompactGrid(Container, int, int) - Static method in class edu.jhu.tmaj.util.swing.SpringUtilities

makeCompactGrid(Container, int, int, int, int, int, int) - Static method in class edu.jhu.tmaj.util.swing.SpringUtilities

Aligns the first rows * cols components of parent in a grid.

makeCustomLut() - Method in class edu.jhu.tmaj.beans.masks.results.ParticleAnalyzer2

makeGrid(Container, int, int, int, int, int, int) - Static method in class edu.jhu.tmaj.util.swing.SpringUtilities

Aligns the first rows * cols components of parent in a grid.

ManyDataPanel - Class in edu.jhu.tmaj.client.admin

The GUI for the ManyToManyPanel, which the reverse direction is set and final.

ManyDataPanel(List<JBean>, List<JBean>, String, String, ManyToManyBean, boolean) - Constructor for class edu.jhu.tmaj.client.admin.ManyDataPanel

ManyToManyBean - Class in edu.jhu.tmaj.beans.manytomany

This Bean represents Many-To-Many tables.

ManyToManyBean(String, String, String) - Constructor for class edu.jhu.tmaj.beans.manytomany.ManyToManyBean

Constructs this object.

ManyToManyPanel - Class in edu.jhu.tmaj.client.admin

A Panel that displays two columns of keys that are linked with a ManyToManyTable, providing users with a graphical method of modifying a ManyToMany table.

ManyToManyPanel(JBean, JBean, String, String, ManyToManyBean) - Constructor for class edu.jhu.tmaj.client.admin.ManyToManyPanel

ManyToManyPanel(JBean, JBean, ManyToManyBean) - Constructor for class edu.jhu.tmaj.client.admin.ManyToManyPanel

A convenience constructor -- the headers are simply the bean titles.

ManyToManyResponse - Class in edu.jhu.tmaj.servlet.response.impl

Contains an initialized ManyToManyBean.

ManyToManyResponse(ManyToManyBean) - Constructor for class edu.jhu.tmaj.servlet.response.impl.ManyToManyResponse

ManyToManyTableRequest - Class in edu.jhu.tmaj.servlet.request.impl

This Request initializes a ManyToManyBean by calling its manyToManyBean.initialize() method.

ManyToManyTableRequest(ManyToManyBean, boolean) - Constructor for class edu.jhu.tmaj.servlet.request.impl.ManyToManyTableRequest

ManyToManyUpdateRequest - Class in edu.jhu.tmaj.servlet.request.impl

This Request is used to update a ManyToMany table.

ManyToManyUpdateRequest(ManyToManyBean, int, Set<Integer>, Set<Integer>, boolean) - Constructor for class edu.jhu.tmaj.servlet.request.impl.ManyToManyUpdateRequest

MARGIN - Static variable in class edu.jhu.tmaj.client.image.draw.AbstractDrawable

Specifies how close a mouse click must be to an shapes border for the program to select the shape

MARGINS_POSITIVE_FIELD - Static variable in class edu.jhu.tmaj.beans.dynamic.SpecimenBean

markBadImages() - Method in class edu.jhu.tmaj.client.image.MarkBadImagesFrame

Returns true if ArraySlideFrame is in markBadImages mode

MarkBadImagesFrame - Class in edu.jhu.tmaj.client.image

A Frame that allows the user to mark bad images on the ArraySlideFrame.

MarkBadImagesFrame(Navigator, ArrayImageCollectionBean) - Constructor for class edu.jhu.tmaj.client.image.MarkBadImagesFrame

markWidth - Static variable in class edu.jhu.tmaj.beans.masks.results.Analyzer2

Mask - Interface in edu.jhu.tmaj.beans.masks

Represents a Mask.

mask_maskStats - Variable in class edu.jhu.tmaj.beans.masks.results.FileStats

MaskChangeEvent - Class in edu.jhu.tmaj.client.frida.data

Represents an event where a mask is added or deleted or has its name changed.

MaskChangeEvent(MaskChangeEvent.MaskChangeEventType, Mask) - Constructor for class edu.jhu.tmaj.client.frida.data.MaskChangeEvent

MaskChangeEvent.MaskChangeEventType - Enum in edu.jhu.tmaj.client.frida.data

Represents several ways a user may change a mask.

maskChangeEventPerformed(MaskChangeEvent) - Method in interface edu.jhu.tmaj.client.frida.data.MaskChangeListener

MaskChangeListener - Interface in edu.jhu.tmaj.client.frida.data

A listener that listens for MaskChangeEvents.

MaskGui - Interface in edu.jhu.tmaj.client.frida.gui.masks

All Guis that return a Mask (Color, Lasso, and Meta) must implement this interface.

MaskIntensityStatUtil - Class in edu.jhu.tmaj.beans.masks.data

This class contains methods for getting a Stat object that contains statistics on the data analyzed.

maskName - Variable in class edu.jhu.tmaj.client.frida.gui.AddMaskDialog.BasicMaskInfo

maskNameAlreadyExists(String) - Method in class edu.jhu.tmaj.client.frida.gui.DefinedMasksGui

Returns true if there is already a defined mask with the supplied name.

MaskPanelListener - Interface in edu.jhu.tmaj.client.frida.gui.shared

MaskReadRequest - Class in edu.jhu.tmaj.servlet.request.impl

MaskReadRequest(int) - Constructor for class edu.jhu.tmaj.servlet.request.impl.MaskReadRequest

maskRepresentationPanel - Variable in class edu.jhu.tmaj.client.frida.gui.shared.GeneralMaskPanel

MaskRepresentationPanel - Class in edu.jhu.tmaj.client.frida.gui.shared

MaskRepresentationPanel(DefinedMasksGui, ImagePlusHolder) - Constructor for class edu.jhu.tmaj.client.frida.gui.shared.MaskRepresentationPanel

MASKS - Static variable in class edu.jhu.tmaj.beans.masks.results.ParticleAnalyzer2

MasksResponse - Class in edu.jhu.tmaj.servlet.response.impl

MasksResponse(List<Mask>) - Constructor for class edu.jhu.tmaj.servlet.response.impl.MasksResponse

MaskStats - Class in edu.jhu.tmaj.beans.masks.results

MaskStats() - Constructor for class edu.jhu.tmaj.beans.masks.results.MaskStats

MaskStats.StatName - Enum in edu.jhu.tmaj.beans.masks.results

MaskStatsWriteRequest - Class in edu.jhu.tmaj.servlet.request.impl

MaskStatsWriteRequest(AllFileStats) - Constructor for class edu.jhu.tmaj.servlet.request.impl.MaskStatsWriteRequest

MasksWriteRequest - Class in edu.jhu.tmaj.servlet.request.impl

MasksWriteRequest(List<Mask>, int) - Constructor for class edu.jhu.tmaj.servlet.request.impl.MasksWriteRequest

maskTableChanged() - Method in class edu.jhu.tmaj.client.frida.gui.shared.MaskRepresentationPanel

MaskType - Enum in edu.jhu.tmaj.beans.masks

Represents the 3 types of Masks currently in the program.

maskType - Variable in class edu.jhu.tmaj.client.frida.gui.AddMaskDialog.BasicMaskInfo

MaskUtil - Class in edu.jhu.tmaj.beans.masks.data

Contains utilties for handling mask arrays, which are representing as a boolean array where true values are said to be inside the mask, and false values are outside the mask.

MAX_SINGLE_VALUE - Static variable in class edu.jhu.tmaj.beans.data.SqlFormatter

The largest a value in a SQL String can be.

MAX_VALUE - Static variable in class edu.jhu.tmaj.beans.masks.data.HsbPixel

MAX_VALUES_IN_COMMA_LIST - Static variable in class edu.jhu.tmaj.beans.data.SqlFormatter

Oracle only allows 1000 values in a list that looks like SELECT * FROM Table WHERE ID IN ('n1','n2','n3'...'n1000') This resolves the error: java.sql.SQLException: ORA-01795: maximum number of expressions in a list is 1000

mayAccessAdminApp() - Method in enum edu.jhu.tmaj.beans.data.AdminAppPermission

Returns true if the user can get into the administrator application.

mayAccessApplication() - Method in enum edu.jhu.tmaj.beans.data.MetaDataAppPermission

mayAccessArrayBuilderApp() - Method in enum edu.jhu.tmaj.beans.data.ArrayBuilderPermission

Returns true if a user may get into the ArrayBuilder Application.

mayAccessSpecimensApplication() - Method in enum edu.jhu.tmaj.beans.data.SpecimensAppPermission

Returns true if a user may get into the Specimens App

mayChangeMetaData() - Method in enum edu.jhu.tmaj.beans.data.MetaDataAppPermission

measure() - Method in class edu.jhu.tmaj.beans.masks.results.Analyzer2

Measures the image or selection and adds the results to the default results table.

measureAngle(Roi) - Method in class edu.jhu.tmaj.beans.masks.results.Analyzer2

measureLength(Roi) - Method in class edu.jhu.tmaj.beans.masks.results.Analyzer2

measurePoint(Roi) - Method in class edu.jhu.tmaj.beans.masks.results.Analyzer2

MemoryUtil - Class in edu.jhu.tmaj.util

MemoryUtil() - Constructor for class edu.jhu.tmaj.util.MemoryUtil

MenuHelper - Class in edu.jhu.tmaj.client.shared

Holds the HELP and ABOUT MenuItems.

MenuHelper(String, Frame) - Constructor for class edu.jhu.tmaj.client.shared.MenuHelper

mergeCommonFieldNames(List, List<List>) - Static method in class edu.jhu.tmaj.client.tables.data.DynamicDataPrinter

MessageLabel - Class in edu.jhu.tmaj.client.frida.gui.shared

A JLabel for displaying either regular messages (in black) or error messages (in red).

MessageLabel() - Constructor for class edu.jhu.tmaj.client.frida.gui.shared.MessageLabel

Messages - Class in edu.jhu.tmaj.util.data

Represents a series of warning messages.

Messages() - Constructor for class edu.jhu.tmaj.util.data.Messages

MessagesResponse - Class in edu.jhu.tmaj.servlet.response.impl

MessagesResponse(Messages) - Constructor for class edu.jhu.tmaj.servlet.response.impl.MessagesResponse

META_DATA_APP_FIELD - Static variable in class edu.jhu.tmaj.beans.UserBean

MetaDataAddRequest - Class in edu.jhu.tmaj.servlet.request.impl

Used to add a record to one of the DynamicMeta Data sections.

MetaDataAddRequest(MetaDataAddRequest.AddOperation) - Constructor for class edu.jhu.tmaj.servlet.request.impl.MetaDataAddRequest

MetaDataAddRequest.AddOperation - Interface in edu.jhu.tmaj.servlet.request.impl

An operation that adds a new record to a MetaData table.

MetaDataAddRequest.EnumAdd - Class in edu.jhu.tmaj.servlet.request.impl

Add to a Enums table.

MetaDataAddRequest.EnumAdd(DynamicEnumsTable, int, String) - Constructor for class edu.jhu.tmaj.servlet.request.impl.MetaDataAddRequest.EnumAdd

MetaDataAddRequest.FieldAdd - Class in edu.jhu.tmaj.servlet.request.impl

Add to a Fields table.

MetaDataAddRequest.FieldAdd(FieldsTable, int, String) - Constructor for class edu.jhu.tmaj.servlet.request.impl.MetaDataAddRequest.FieldAdd

MetaDataAddRequest.TypeAdd - Class in edu.jhu.tmaj.servlet.request.impl

Adds to a Types table.

MetaDataAddRequest.TypeAdd(TypesTable, String) - Constructor for class edu.jhu.tmaj.servlet.request.impl.MetaDataAddRequest.TypeAdd

MetaDataAddResponse - Class in edu.jhu.tmaj.servlet.response.impl

Contains the primary key ID that the database assigned during the add.

MetaDataAddResponse(int) - Constructor for class edu.jhu.tmaj.servlet.response.impl.MetaDataAddResponse

MetaDataAdminPanel - Class in edu.jhu.tmaj.client.admin

A Panel that displays the design of the MetaData.

MetaDataAdminPanel() - Constructor for class edu.jhu.tmaj.client.admin.MetaDataAdminPanel

MetaDataAlterRequest - Class in edu.jhu.tmaj.servlet.request.impl

A Request to change the name of a MetaData record, or delete it.

MetaDataAlterRequest(MetaDataAlterRequest.AlterOperation) - Constructor for class edu.jhu.tmaj.servlet.request.impl.MetaDataAlterRequest

MetaDataAlterRequest.AlterOperation - Interface in edu.jhu.tmaj.servlet.request.impl

An operation that either changes the name of or deletes a Meta Data Record.

MetaDataAlterRequest.DeleteOperation - Class in edu.jhu.tmaj.servlet.request.impl

Delete a MetaData record.

MetaDataAlterRequest.DeleteOperation(NameTable, int) - Constructor for class edu.jhu.tmaj.servlet.request.impl.MetaDataAlterRequest.DeleteOperation

MetaDataAlterRequest.ModifyOperation - Class in edu.jhu.tmaj.servlet.request.impl

Change the name of a Meta Data record.

MetaDataAlterRequest.ModifyOperation(NameTable, int, String) - Constructor for class edu.jhu.tmaj.servlet.request.impl.MetaDataAlterRequest.ModifyOperation

MetaDataAppGUI - Class in edu.jhu.tmaj.client.admin

The gui for the meta data application.

MetaDataAppPermission - Enum in edu.jhu.tmaj.beans.data

Represents the user's permission to the Meta Data Application.

MetaDataConverter - Class in edu.jhu.tmaj.client.importer.specimens.data

A utility class used by the Specimen-Importer for importing dynamic-data.

MetaDataConverter(DynamicMetaData) - Constructor for class edu.jhu.tmaj.client.importer.specimens.data.MetaDataConverter

MetaMask - Class in edu.jhu.tmaj.beans.masks.meta

Represents a mask of masks.

MetaMask(String) - Constructor for class edu.jhu.tmaj.beans.masks.meta.MetaMask

MetaMask.ActionMaskInfoComparable - Class in edu.jhu.tmaj.beans.masks.meta

MetaMask.ActionMaskInfoComparable() - Constructor for class edu.jhu.tmaj.beans.masks.meta.MetaMask.ActionMaskInfoComparable

MetaMaskDatabaseUtil - Class in edu.jhu.tmaj.beans.masks.meta

MetaMaskDatabaseUtil() - Constructor for class edu.jhu.tmaj.beans.masks.meta.MetaMaskDatabaseUtil

MetaMaskDatabaseUtil.Reader - Class in edu.jhu.tmaj.beans.masks.meta

MetaMaskDatabaseUtil.Reader() - Constructor for class edu.jhu.tmaj.beans.masks.meta.MetaMaskDatabaseUtil.Reader

MetaMaskDatabaseUtil.Writer - Class in edu.jhu.tmaj.beans.masks.meta

MetaMaskDatabaseUtil.Writer() - Constructor for class edu.jhu.tmaj.beans.masks.meta.MetaMaskDatabaseUtil.Writer

MetaMaskGui - Class in edu.jhu.tmaj.client.frida.gui.masks.meta

The GUI component for the Meta Mask.

MetaMaskGui(MetaMask, IASessionBean, ImageAppGuis) - Constructor for class edu.jhu.tmaj.client.frida.gui.masks.meta.MetaMaskGui

MetaObject - Interface in edu.jhu.tmaj.beans.data

Either a Type, Field, or Enum record (for Meta Data).

MICROSCOPIST_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.dynamic.TissueDiagnosisBean

MID_SIZE_FILE_ID - Static variable in class edu.jhu.tmaj.beans.ArrayImageBean

midParameters - Variable in class edu.jhu.tmaj.client.importer.images.data.SizeParameters

MIN_NUMBER_OF_PASSWORD_CHARACTERS - Static variable in class edu.jhu.tmaj.client.shared.ChangePasswordDialog

MIN_VALUE - Static variable in class edu.jhu.tmaj.beans.masks.data.HsbPixel

ModifySQL - Class in edu.jhu.tmaj.database.sql

The superclass of BaseUpdateSQL and DeleteSQL.

ModifySQL(String) - Constructor for class edu.jhu.tmaj.database.sql.ModifySQL

Constructs this object.

MOLECULAR_PANEL_NAME - Static variable in class edu.jhu.tmaj.client.samples.SamplesAppGUI

MOLECULAR_SAMPLE_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.MolecularUsageBean

MOLECULAR_TYPE_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.MolecularSampleBean

MOLECULAR_USAGES_PANEL_NAME - Static variable in class edu.jhu.tmaj.client.samples.SamplesAppGUI

MolecularSampleBean - Class in edu.jhu.tmaj.beans

Represents a molecular sample obtained from either a blood, urine, block, or tissue sample.

MolecularSampleBean(StaticMetaData) - Constructor for class edu.jhu.tmaj.beans.MolecularSampleBean

MolecularUsageBean - Class in edu.jhu.tmaj.beans

Represents the MolecularUsages table.

MolecularUsageBean(StaticMetaData) - Constructor for class edu.jhu.tmaj.beans.MolecularUsageBean

MoreColors - Class in edu.jhu.tmaj.util.swing

A Utility class containing extra color constants.

mouseClicked(MouseEvent) - Method in class edu.jhu.tmaj.client.tables.data.ColumnExpanderMouseListener

mouseClicked(MouseEvent) - Method in class edu.jhu.tmaj.client.tables.data.ShowFrameMouseListener

mouseClicked(MouseEvent) - Method in class edu.jhu.tmaj.client.tables.data.SortFilterMouseListener

mouseClicked(MouseEvent) - Method in class edu.jhu.tmaj.client.tables.data.TableHeaderListener

mouseDragged(MouseEvent) - Method in class edu.jhu.tmaj.client.image.data.ScrollPaneMouseInputListener

Moves the scrollPane based on the difference between the new and old XY point

mouseDragged(MouseEvent) - Method in class edu.jhu.tmaj.client.image.draw.ShapeListener

Forward to currentDrawable

mousePressed(MouseEvent) - Method in class edu.jhu.tmaj.client.frida.gui.masks.color.FullSlider.HeldMouseListener

mousePressed(MouseEvent) - Method in class edu.jhu.tmaj.client.image.data.ScrollPaneMouseInputListener

Registers X and Y and changes the cursor to a hand.

mousePressed(MouseEvent) - Method in class edu.jhu.tmaj.client.image.draw.LabelFocusMouseListener

Gives focus to JLabel

mousePressed(MouseEvent) - Method in class edu.jhu.tmaj.client.image.draw.ShapeListener

mouseReleased(MouseEvent) - Method in class edu.jhu.tmaj.client.frida.gui.masks.color.FullSlider.HeldMouseListener

mouseReleased(MouseEvent) - Method in class edu.jhu.tmaj.client.image.data.ScrollPaneMouseInputListener

Changes the cursor back to normal

mouseReleased(MouseEvent) - Method in class edu.jhu.tmaj.client.image.draw.ShapeListener

Forward to currentDrawable

move(int, int) - Method in class edu.jhu.tmaj.client.image.draw.AbstractDrawable

Moves the shape by adding xDiff and YDiff to it's current x and y, respectively.

move(int, int) - Method in class edu.jhu.tmaj.client.image.draw.FreeHandDrawable

move(int, int) - Method in class edu.jhu.tmaj.client.image.draw.LineDrawable

move(int, int) - Method in class edu.jhu.tmaj.client.image.draw.PolygonDrawable

move(int, int) - Method in class edu.jhu.tmaj.client.image.draw.RectangleDrawable

move(int, int) - Method in class edu.jhu.tmaj.client.image.draw.TextDrawable

MySqlConnectionFactory - Class in edu.jhu.tmaj.database.conn

Generates database Connections to a MySQL database.

MySqlConnectionFactory(DatabaseParameters) - Constructor for class edu.jhu.tmaj.database.conn.MySqlConnectionFactory

MyTreeCellEditor - Class in edu.jhu.tmaj.client.image

MyTreeCellEditor(SpecialTree) - Constructor for class edu.jhu.tmaj.client.image.MyTreeCellEditor

MyTreeCellRenderer - Class in edu.jhu.tmaj.client.image

MyTreeCellRenderer() - Constructor for class edu.jhu.tmaj.client.image.MyTreeCellRenderer

N

n(double) - Method in class edu.jhu.tmaj.beans.masks.results.Analyzer2

Converts a number to a formatted string with a tab at the end.

n(double) - Method in class edu.jhu.tmaj.beans.masks.results.ParticleAnalyzer2

NAME_FIELD - Static variable in class edu.jhu.tmaj.beans.ArrayBlockBean

NAME_FIRST_FIELD - Static variable in class edu.jhu.tmaj.beans.PatientBean

NAME_FIRST_FIELD - Static variable in class edu.jhu.tmaj.beans.UserBean

NAME_LAST_FIELD - Static variable in class edu.jhu.tmaj.beans.PatientBean

NAME_LAST_FIELD - Static variable in class edu.jhu.tmaj.beans.UserBean

NameTable - Interface in edu.jhu.tmaj.beans.data.datatypes

A Database table that has a descriptive name field that represents the record.

navigationGUI - Variable in class edu.jhu.tmaj.client.image.ArrayImageFrame

NavigationGUI - Class in edu.jhu.tmaj.client.image

Allows users to go up and down, back and next on the ArrayImageFrame, or in another order they specify.

NavigationGUI(ArrayImageFrame, ImageAppGuis) - Constructor for class edu.jhu.tmaj.client.image.NavigationGUI

NavigationPanel - Class in edu.jhu.tmaj.client.frida.gui.shared

NavigationPanel(List<ExternalFileCoordinate>, ImagePlusHolder, IASessionBean, ImageAppGuis) - Constructor for class edu.jhu.tmaj.client.frida.gui.shared.NavigationPanel

Navigator - Class in edu.jhu.tmaj.client.image.data

A class that controls which ArrayImages are seen (as well as the order) when the user clicks the "Next" and "Back" buttons.

Navigator() - Constructor for class edu.jhu.tmaj.client.image.data.Navigator

NEW_LOCATION_FIELD - Static variable in class edu.jhu.tmaj.beans.BlockOrSlideExchangeBean

newTableData() - Method in class edu.jhu.tmaj.client.tables.data.TableData4

Performs the finally initialization of the table after the columns have been determined.

nextButton - Variable in class edu.jhu.tmaj.client.image.NavigationGUI

nextColumn() - Method in class edu.jhu.tmaj.client.tables.GridBagPanelMaker

nextRow() - Method in class edu.jhu.tmaj.client.tables.GridBagPanelMaker

NoArrayImageException - Exception in edu.jhu.tmaj.client.image.data

Thrown to indicate that an ArrayImage can not be located.

NoArrayImageException(String) - Constructor for exception edu.jhu.tmaj.client.image.data.NoArrayImageException

NodeMaker - Class in edu.jhu.tmaj.client.image.data

Contains helper methods for making the tree structure of Projects,ArraySlides,Scans,and Sessions in the ProjectFrame.

NodeMaker(boolean) - Constructor for class edu.jhu.tmaj.client.image.data.NodeMaker

Constructs this class, and initializes all nodes in JTree of the ProjectFrame.

NORMAL_FONT - Static variable in class edu.jhu.tmaj.client.tables.data.HeaderTableCellRenderer

NORMAL_SAMPLE_TEXT - Static variable in class edu.jhu.tmaj.client.arraybuilder.data.ArrayCoreCell

NOT_INFILE_LOCATION_FIELD - Static variable in class edu.jhu.tmaj.beans.BlockBean

notes - Variable in class edu.jhu.tmaj.servlet.request.impl.ArrayCoreC

NOTES_FIELD - Static variable in class edu.jhu.tmaj.beans.AnimalExperimentBean

NOTES_FIELD - Static variable in class edu.jhu.tmaj.beans.ArrayCoreBean

NOTES_FIELD - Static variable in class edu.jhu.tmaj.beans.ArraySlideBean

NOTES_FIELD - Static variable in class edu.jhu.tmaj.beans.BlockBean

NOTES_FIELD - Static variable in class edu.jhu.tmaj.beans.BlockOrSlideExchangeBean

NOTES_FIELD - Static variable in class edu.jhu.tmaj.beans.BlockUsageBean

NOTES_FIELD - Static variable in class edu.jhu.tmaj.beans.BloodSampleBean

NOTES_FIELD - Static variable in class edu.jhu.tmaj.beans.BloodUsageBean

NOTES_FIELD - Static variable in class edu.jhu.tmaj.beans.CellLineBean

NOTES_FIELD - Static variable in class edu.jhu.tmaj.beans.CellLineExperimentBean

NOTES_FIELD - Static variable in class edu.jhu.tmaj.beans.dynamic.ScoredImageBean

NOTES_FIELD - Static variable in class edu.jhu.tmaj.beans.dynamic.SpecimenBean

NOTES_FIELD - Static variable in class edu.jhu.tmaj.beans.dynamic.TissueDiagnosisBean

NOTES_FIELD - Static variable in class edu.jhu.tmaj.beans.IASessionBean

NOTES_FIELD - Static variable in class edu.jhu.tmaj.beans.MolecularSampleBean

NOTES_FIELD - Static variable in class edu.jhu.tmaj.beans.MolecularUsageBean

NOTES_FIELD - Static variable in class edu.jhu.tmaj.beans.PaperBean

NOTES_FIELD - Static variable in class edu.jhu.tmaj.beans.PatientBean

NOTES_FIELD - Static variable in class edu.jhu.tmaj.beans.ScanBean

NOTES_FIELD - Static variable in class edu.jhu.tmaj.beans.SessionBean

NOTES_FIELD - Static variable in class edu.jhu.tmaj.beans.SlideBean

NOTES_FIELD - Static variable in class edu.jhu.tmaj.beans.TissueSampleBean

NOTES_FIELD - Static variable in class edu.jhu.tmaj.beans.TissueUsageBean

NOTES_FIELD - Static variable in class edu.jhu.tmaj.beans.UrineUsageBean

NOTHING - Static variable in class edu.jhu.tmaj.beans.masks.results.ParticleAnalyzer2

NULL_STRING - Static variable in class edu.jhu.tmaj.database.sql.GeneralSQLMaker

NullBean - Class in edu.jhu.tmaj.beans

NullBean() - Constructor for class edu.jhu.tmaj.beans.NullBean

NUMBER_OF_ANIMALS_FIELD - Static variable in class edu.jhu.tmaj.beans.AnimalExperimentBean

NUMBER_OF_COLUMNS_FIELD - Static variable in class edu.jhu.tmaj.beans.ArrayBlockBean

NUMBER_OF_GROUPS_FIELD - Static variable in class edu.jhu.tmaj.beans.AnimalExperimentBean

NUMBER_OF_ROWS_FIELD - Static variable in class edu.jhu.tmaj.beans.ArrayBlockBean

NUMBER_OF_SPOTS_FIELD - Static variable in class edu.jhu.tmaj.beans.ArrayBlockBean

NumberedCheckBox - Class in edu.jhu.tmaj.client.tables

A JCheckBox with a position attached.

NumberedCheckBox(int, Object) - Constructor for class edu.jhu.tmaj.client.tables.NumberedCheckBox

numberOfColumns() - Method in interface edu.jhu.tmaj.util.file.TableArray

numberOfColumns() - Method in class edu.jhu.tmaj.util.file.TableArrayImpl

numberOfRows() - Method in interface edu.jhu.tmaj.util.file.TableArray

numberOfRows() - Method in class edu.jhu.tmaj.util.file.TableArrayImpl

O

object - Variable in class edu.jhu.tmaj.client.image.CheckableObject

OBJECT_TYPE_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.BlockOrSlideExchangeBean

objectClicked(CheckableObject) - Method in class edu.jhu.tmaj.client.image.SpecialTree

The user clicked a checkbox

ObjectPool - Class in edu.jhu.tmaj.util

A utility that manages a group of resources in a thread safe manner.

ObjectPool() - Constructor for class edu.jhu.tmaj.util.ObjectPool

Default constructor.

ObjectPool.WaitTime - Enum in edu.jhu.tmaj.util

OBJECTS_DESCRIPTIONS_FIELD - Static variable in class edu.jhu.tmaj.beans.BlockOrSlideExchangeBean

OpenedArrayBlocksPanel - Class in edu.jhu.tmaj.client.arraybuilder

A panel that shows all the ArrayBlocks the user has opened.

OpenedArrayBlocksPanel() - Constructor for class edu.jhu.tmaj.client.arraybuilder.OpenedArrayBlocksPanel

openFileUsingWindowsApp(File, Component) - Static method in class edu.jhu.tmaj.util.WindowsCommandUtil

Opens a file in windows

openIASession(IASessionBean) - Method in class edu.jhu.tmaj.client.image.ProjectsGUI

openLink(URL, Component) - Static method in class edu.jhu.tmaj.util.WindowsCommandUtil

openSession(SessionBean) - Method in class edu.jhu.tmaj.client.image.ProjectsGUI

OpenSessionsPanel - Class in edu.jhu.tmaj.client.image

The Panel on the ProjectFrame that lists all sessions the user currently has open.

OpenSessionsPanel(ImageAppGuis) - Constructor for class edu.jhu.tmaj.client.image.OpenSessionsPanel

OPTIONS - Static variable in class edu.jhu.tmaj.beans.masks.results.ParticleAnalyzer2

OptionsGUI - Class in edu.jhu.tmaj.client.shared

The GUI displayed when the options button is clicked.

OracleConnectionFactory - Class in edu.jhu.tmaj.database.conn

A ConnectionFactory that generates new connections to an Oracle database.

OracleConnectionFactory(DatabaseParameters) - Constructor for class edu.jhu.tmaj.database.conn.OracleConnectionFactory

OracleSQLMaker - Class in edu.jhu.tmaj.database.sql

A SQLMaker for an Oracle Database.

orderNumber - Variable in class edu.jhu.tmaj.beans.masks.meta.ActionMaskInfo

ORGAN_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.BlockUsageAltBean

ORGAN_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.CellLineBean

originalImagePlus - Variable in class edu.jhu.tmaj.client.frida.data.ImagePlusInfo

An ImagePlus that will not change, and that we can revert to if we ever need to.

OriginalTypeRequest - Class in edu.jhu.tmaj.servlet.request.impl

A Request that gets the original TissueType (assigned in TissueDiagnosis) of an ArrayImage.

OriginalTypeResponse - Class in edu.jhu.tmaj.servlet.response.impl

Contains an ArrayImageIDs original TissueTypeID in the TissueDiagnosis.

OriginalTypeResponse(int, boolean) - Constructor for class edu.jhu.tmaj.servlet.response.impl.OriginalTypeResponse

OUTLINES - Static variable in class edu.jhu.tmaj.beans.masks.results.ParticleAnalyzer2

OUTSIDE_ARRAY_CORE_NUMBER_FIELD - Static variable in class edu.jhu.tmaj.beans.ArrayCoreBean

OUTSIDE_BLOCK_NUMBER_FIELD - Static variable in class edu.jhu.tmaj.beans.BlockBean

OUTSIDE_RESEARCH_NUMBER_FIELD - Static variable in class edu.jhu.tmaj.beans.dynamic.SpecimenBean

OUTSIDE_SURG_PATH_NUMBER_FIELD - Static variable in class edu.jhu.tmaj.beans.dynamic.SpecimenBean

OUTSIDE_TD_NUMBER_FIELD - Static variable in class edu.jhu.tmaj.beans.dynamic.TissueDiagnosisBean

OvalDrawable - Class in edu.jhu.tmaj.client.image.draw

An oval

OvalDrawable(DrawableLabel) - Constructor for class edu.jhu.tmaj.client.image.draw.OvalDrawable

OvalDrawableHelper - Class in edu.jhu.tmaj.client.image.draw

A Helper class for Ovals that determines how close a mouse click needs to be to an oval for the oval to be considered selected.

OvalDrawableHelper() - Constructor for class edu.jhu.tmaj.client.image.draw.OvalDrawableHelper

override(File) - Method in class edu.jhu.tmaj.util.config.data.ConstantsHolder

Override the config file with another config file.

OWNER_USER_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.SessionBean

P

paint(Graphics) - Method in class edu.jhu.tmaj.client.image.GridLabel

paintComponent(Graphics) - Method in class edu.jhu.tmaj.client.image.draw.DrawableLabel

Overwritten to paint the Drawables if isActive is true

Pair - Class in edu.jhu.tmaj.util.data

Represents 2 integers.

Pair(int, int) - Constructor for class edu.jhu.tmaj.util.data.Pair

PanelForwarder - Class in edu.jhu.tmaj.client.shared

A Utility class that returns a 'forwarding' labeled '<<<' or '>>>'.

PaperBean - Class in edu.jhu.tmaj.beans

Represents a Published Paper.

PaperBean(StaticMetaData) - Constructor for class edu.jhu.tmaj.beans.PaperBean

PaperInputPanel - Class in edu.jhu.tmaj.client.image

An InputPanel for entering records into the Papers table.

PaperInputPanel(TableData4) - Constructor for class edu.jhu.tmaj.client.image.PaperInputPanel

PapersDialog - Class in edu.jhu.tmaj.client.image

An InputPanel listing all the Papers in TMAJ.

PapersGUI - Class in edu.jhu.tmaj.client.image

This application automatically logs into TMAJ as a guest, and starts the ProjectsFrame where only published papers can be viewed.

PapersSessionsBean - Class in edu.jhu.tmaj.beans.manytomany

Represents the ManyToMany table PapersSessions.

PapersSessionsBean() - Constructor for class edu.jhu.tmaj.beans.manytomany.PapersSessionsBean

PapersSessionsDialog - Class in edu.jhu.tmaj.client.image

A Dialog that displays a ManyToMany Panel for assigning sessions to papers.

PapersSessionsDialog(Frame) - Constructor for class edu.jhu.tmaj.client.image.PapersSessionsDialog

PaperURL - Class in edu.jhu.tmaj.client.image.data

The pdf URL of a paper.

PaperURL(URL) - Constructor for class edu.jhu.tmaj.client.image.data.PaperURL

parentComponent - Variable in class edu.jhu.tmaj.client.tables.data.TableData4

parentID - Variable in class edu.jhu.tmaj.beans.exfile.data.PartialFolder

PART_FIELD - Static variable in class edu.jhu.tmaj.beans.BlockBean

PART_NUMBER_FIELD - Static variable in class edu.jhu.tmaj.beans.BlockOrSlideExchangeBean

PartialFolder - Class in edu.jhu.tmaj.beans.exfile.data

PartialFolder(int, String, Integer) - Constructor for class edu.jhu.tmaj.beans.exfile.data.PartialFolder

PartialFolderCollection - Class in edu.jhu.tmaj.beans.exfile.data

PartialFolderCollection() - Constructor for class edu.jhu.tmaj.beans.exfile.data.PartialFolderCollection

PARTICLE_SIZE_MAX_VALUE - Static variable in class edu.jhu.tmaj.beans.masks.filter.FilterMask

PARTICLE_SIZE_MIN_VALUE - Static variable in class edu.jhu.tmaj.beans.masks.filter.FilterMask

ParticleAnalyzer2 - Class in edu.jhu.tmaj.beans.masks.results

Implements ImageJ's Analyze Particles command.

ParticleAnalyzer2(int, int, ResultsTable, double, double, double, double) - Constructor for class edu.jhu.tmaj.beans.masks.results.ParticleAnalyzer2

Constructs a ParticleAnalyzer.

ParticleAnalyzer2(int, int, ResultsTable, double, double) - Constructor for class edu.jhu.tmaj.beans.masks.results.ParticleAnalyzer2

Constructs a ParticleAnalyzer using the default min and max circularity values (0 and 1).

ParticleAnalyzer2() - Constructor for class edu.jhu.tmaj.beans.masks.results.ParticleAnalyzer2

Default constructor

ParticleStatsUtil - Class in edu.jhu.tmaj.beans.masks.results

ParticleStatsUtil() - Constructor for class edu.jhu.tmaj.beans.masks.results.ParticleStatsUtil

PASSAGE_NUMBER_FIELD - Static variable in class edu.jhu.tmaj.beans.CellLineExperimentBean

password - Variable in class edu.jhu.tmaj.servlet.request.BaseRequest

PASSWORD_REQUIREMENTS - Static variable in class edu.jhu.tmaj.client.shared.ChangePasswordDialog

PasswordDialog - Class in edu.jhu.tmaj.client.shared

A Dialog that prompts the user for a password.

passwordMeetsConditions(String) - Static method in class edu.jhu.tmaj.client.shared.ChangePasswordDialog

Returns true if the password is at least 6 characters, contains at least one number, and one letter

pasteInfo() - Method in class edu.jhu.tmaj.client.image.data.ArrayImagesClipBoard

Pastes the current information into the Table and ComboBox.

PATHOLOGISTS_FIELD - Static variable in class edu.jhu.tmaj.beans.dynamic.SpecimenBean

PATIENT_DATA_FIELD - Static variable in class edu.jhu.tmaj.beans.UserBean

PATIENT_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.dynamic.SpecimenBean

PATIENT_NUMBER_FIELD - Static variable in class edu.jhu.tmaj.beans.PatientBean

PATIENT_NUMBER_STRING - Static variable in class edu.jhu.tmaj.beans.PatientBean

PATIENT_PANEL_NAME - Static variable in class edu.jhu.tmaj.client.samples.SamplesAppGUI

PATIENT_PANEL_NAME - Static variable in class edu.jhu.tmaj.client.specimens.SpecimensAppGUI

PatientBean - Class in edu.jhu.tmaj.beans

Represents a record from the Patients Table.

PatientBean(StaticMetaData) - Constructor for class edu.jhu.tmaj.beans.PatientBean

PatientDataPermission - Enum in edu.jhu.tmaj.beans.data

PatientTranslatedTable - Class in edu.jhu.tmaj.client.importer.specimens.data

A Patient record that is ready to be written to the database.

PatientTranslatedTable() - Constructor for class edu.jhu.tmaj.client.importer.specimens.data.PatientTranslatedTable

patientTranslatedTable - Variable in class edu.jhu.tmaj.client.importer.specimens.data.TranslatedRow

PDF_LINK_FIELD - Static variable in class edu.jhu.tmaj.beans.PaperBean

PERCENT_TUMOR_FIELD - Static variable in class edu.jhu.tmaj.beans.BlockUsageAltBean

perform() - Method in class edu.jhu.tmaj.client.importer.images.data.RenameOp

Actually perform the renaming.

PERSON_OBTAINED_FROM_FIELD - Static variable in class edu.jhu.tmaj.beans.CellLineExperimentBean

PHONE_FIELD - Static variable in class edu.jhu.tmaj.beans.UserBean

PHYSICIANS_FIELD - Static variable in class edu.jhu.tmaj.beans.dynamic.SpecimenBean

PI_FIELD - Static variable in class edu.jhu.tmaj.beans.AnimalExperimentBean

PI_FIELD - Static variable in class edu.jhu.tmaj.beans.ProtocolBean

PI_USER_FIELD - Static variable in class edu.jhu.tmaj.beans.BlockUsageBean

PI_USER_FIELD - Static variable in class edu.jhu.tmaj.beans.BloodUsageBean

PI_USER_FIELD - Static variable in class edu.jhu.tmaj.beans.MolecularUsageBean

PI_USER_FIELD - Static variable in class edu.jhu.tmaj.beans.TissueUsageBean

PI_USER_FIELD - Static variable in class edu.jhu.tmaj.beans.UrineUsageBean

PickListEnumeration - Interface in edu.jhu.tmaj.beans.data

Either a StaticEnumeration or DynamicEnumeration.

pixelToColor(int) - Static method in class edu.jhu.tmaj.beans.masks.data.PixelUtil

Converts a int pixel into a java.awt.Color

pixelToHsb(int) - Static method in class edu.jhu.tmaj.beans.masks.data.PixelUtil

Converts an int pixel into an HsbPixel.

PixelUtil - Class in edu.jhu.tmaj.beans.masks.data

Contains utility methods for pixel conversion.

Point - Class in edu.jhu.tmaj.beans.masks.color

Represents a point on a graph.

Point(double, double) - Constructor for class edu.jhu.tmaj.beans.masks.color.Point

Point - Class in edu.jhu.tmaj.client.image.draw

A class that represents an x and y coordinate

Point(int, int) - Constructor for class edu.jhu.tmaj.client.image.draw.Point

pointsList - Variable in class edu.jhu.tmaj.client.image.draw.ShapeRecord

PolygonDrawable - Class in edu.jhu.tmaj.client.image.draw

A polygon

PolygonDrawable(DrawableLabel) - Constructor for class edu.jhu.tmaj.client.image.draw.PolygonDrawable

polygonToString(Polygon) - Static method in class edu.jhu.tmaj.beans.masks.lasso.Lasso

PooledConnectionManager - Class in edu.jhu.tmaj.database.conn

A connection factory that supports and reuses multiple connections to the database in a thread-safe manner.

PooledConnectionManager(ConnectionFactory, String) - Constructor for class edu.jhu.tmaj.database.conn.PooledConnectionManager

Constructs this object.

popupWidth - Variable in class edu.jhu.tmaj.client.image.data.SteppedComboBox

Position - Class in edu.jhu.tmaj.util.data

A pair where both x and y are greater than 0

Position(int, int) - Constructor for class edu.jhu.tmaj.util.data.Position

precision - Static variable in class edu.jhu.tmaj.beans.masks.results.Analyzer2

Preference - Enum in edu.jhu.tmaj.client.shared

PreferencesUtil - Class in edu.jhu.tmaj.util.config.data

Contains Utility methods for writing a preference file to a users hard-disk.

PreferencesUtil() - Constructor for class edu.jhu.tmaj.util.config.data.PreferencesUtil

PREFERRED_GROWTH_MEDIA_FIELD - Static variable in class edu.jhu.tmaj.beans.CellLineBean

prefixList(List, String) - Static method in class edu.jhu.tmaj.util.ListConvertUtil

PRIMARY_DIAGNOSIS_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.BlockUsageAltBean

PrimaryKeyComparator - Class in edu.jhu.tmaj.beans.data

A Comparator that sorts BasicTableBeans by their ID

PrimaryKeyComparator() - Constructor for class edu.jhu.tmaj.beans.data.PrimaryKeyComparator

primaryKeyID - Variable in class edu.jhu.tmaj.client.tables.logs.RecordModify

printManualUpdate(String) - Method in class edu.jhu.tmaj.util.TextProgressMonitor

printSizes(Component) - Static method in class edu.jhu.tmaj.util.swing.SpringUtilities

A debugging utility that prints to stdout the component's minimum, preferred, and maximum sizes.

PROCEDURE_TYPE_FIELD - Static variable in class edu.jhu.tmaj.beans.dynamic.SpecimenBean

PROCESSING_DATE_FIELD - Static variable in class edu.jhu.tmaj.beans.MolecularSampleBean

PROCESSING_FIELD - Static variable in class edu.jhu.tmaj.beans.dynamic.SpecimenBean

PROCESSING_TIME_FIELD - Static variable in class edu.jhu.tmaj.beans.BloodSampleBean

PROCESSING_TIME_FIELD - Static variable in class edu.jhu.tmaj.beans.TissueSampleBean

PROCESSOR_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.BloodSampleBean

PROCESSOR_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.TissueSampleBean

processRequest(UserBean) - Method in class edu.jhu.tmaj.servlet.request.BaseRequest

This request is executed on the server assuming the username and password returns a valid UserBean.

processRequest(UserBean) - Method in class edu.jhu.tmaj.servlet.request.impl.ArrayCoreReferenceRequest

Returns an Response that contains an ArrayCoreReferenceBean initialized with either an entire ArrayBlock of TissueDiagnosisIDs, or just one individual TissueDiagonsisID.

processRequest(UserBean) - Method in class edu.jhu.tmaj.servlet.request.impl.ArrayCoresOpenRequest

processRequest(UserBean) - Method in class edu.jhu.tmaj.servlet.request.impl.ArrayCoresSaveRequest

processRequest(UserBean) - Method in class edu.jhu.tmaj.servlet.request.impl.ArrayImageAddRequest

processRequest(UserBean) - Method in class edu.jhu.tmaj.servlet.request.impl.ArrayImageCollectionRequest

Initializes an ArrayImageCollectionBean with a sessionID, and puts it into a Response object.

processRequest(UserBean) - Method in class edu.jhu.tmaj.servlet.request.impl.ArrayImageCoresRequest

processRequest(UserBean) - Method in class edu.jhu.tmaj.servlet.request.impl.BadImagesUpdateRequest

processRequest(UserBean) - Method in class edu.jhu.tmaj.servlet.request.impl.CellLinesReferenceRequest

Returns an Response that contains an ArrayCoreReferenceBean initialized with either an entire ArrayBlock of TissueDiagnosisIDs, or just one individual TissueDiagonsisID.

processRequest(UserBean) - Method in class edu.jhu.tmaj.servlet.request.impl.ChangeLogsSaveRequest

processRequest(UserBean) - Method in class edu.jhu.tmaj.servlet.request.impl.ChangePasswordRequest

processRequest(UserBean) - Method in class edu.jhu.tmaj.servlet.request.impl.CheckIfSpecimenExistsRequest

processRequest(UserBean) - Method in class edu.jhu.tmaj.servlet.request.impl.CopyArrayBlockRequest

processRequest(UserBean) - Method in class edu.jhu.tmaj.servlet.request.impl.CopySessionRequest

processRequest(UserBean) - Method in class edu.jhu.tmaj.servlet.request.impl.DetailsRequest

processRequest(UserBean) - Method in class edu.jhu.tmaj.servlet.request.impl.DiagnosisLookupRequest

processRequest(UserBean) - Method in class edu.jhu.tmaj.servlet.request.impl.DynamicMetaDataRequest

processRequest(UserBean) - Method in class edu.jhu.tmaj.servlet.request.impl.EnumerationsRequest

processRequest(UserBean) - Method in class edu.jhu.tmaj.servlet.request.impl.ExpressEntryRequest

processRequest(UserBean) - Method in class edu.jhu.tmaj.servlet.request.impl.FileChecksumRequest

processRequest(UserBean) - Method in class edu.jhu.tmaj.servlet.request.impl.FileDeleteRequest

processRequest(UserBean) - Method in class edu.jhu.tmaj.servlet.request.impl.FileDownloadRequest

processRequest(UserBean) - Method in class edu.jhu.tmaj.servlet.request.impl.FilesGetRequest

processRequest(UserBean) - Method in class edu.jhu.tmaj.servlet.request.impl.FilesLargeGetRequest

processRequest(UserBean) - Method in class edu.jhu.tmaj.servlet.request.impl.FileUploadRequest

processRequest(UserBean) - Method in class edu.jhu.tmaj.servlet.request.impl.FolderCheckRequest

processRequest(UserBean) - Method in class edu.jhu.tmaj.servlet.request.impl.FolderCreateRequest

processRequest(UserBean) - Method in class edu.jhu.tmaj.servlet.request.impl.FolderDeleteRequest

processRequest(UserBean) - Method in class edu.jhu.tmaj.servlet.request.impl.FolderGetRequest

processRequest(UserBean) - Method in class edu.jhu.tmaj.servlet.request.impl.GrossDescriptionRequest

processRequest(UserBean) - Method in class edu.jhu.tmaj.servlet.request.impl.GrossDescriptionWipeRequest

processRequest(UserBean) - Method in class edu.jhu.tmaj.servlet.request.impl.HistoryRequest

processRequest(UserBean) - Method in class edu.jhu.tmaj.servlet.request.impl.ImageInfoRequest

processRequest(UserBean) - Method in class edu.jhu.tmaj.servlet.request.impl.InvalidateMachineScoresRequest

processRequest(UserBean) - Method in class edu.jhu.tmaj.servlet.request.impl.IsArrayBlockBlankRequest

processRequest(UserBean) - Method in class edu.jhu.tmaj.servlet.request.impl.KeyValueGetRequest

processRequest(UserBean) - Method in class edu.jhu.tmaj.servlet.request.impl.KeyValueSetRequest

processRequest(UserBean) - Method in class edu.jhu.tmaj.servlet.request.impl.LoginRequest

processRequest(UserBean) - Method in class edu.jhu.tmaj.servlet.request.impl.LogoutRequest

processRequest(UserBean) - Method in class edu.jhu.tmaj.servlet.request.impl.LookupTableRequest

processRequest(UserBean) - Method in class edu.jhu.tmaj.servlet.request.impl.MachineScoresImportRequest

processRequest(UserBean) - Method in class edu.jhu.tmaj.servlet.request.impl.MachineScoresInfoRequest

processRequest(UserBean) - Method in class edu.jhu.tmaj.servlet.request.impl.ManyToManyTableRequest

processRequest(UserBean) - Method in class edu.jhu.tmaj.servlet.request.impl.ManyToManyUpdateRequest

processRequest(UserBean) - Method in class edu.jhu.tmaj.servlet.request.impl.MaskReadRequest

processRequest(UserBean) - Method in class edu.jhu.tmaj.servlet.request.impl.MaskStatsWriteRequest

processRequest(UserBean) - Method in class edu.jhu.tmaj.servlet.request.impl.MasksWriteRequest

processRequest(UserBean) - Method in class edu.jhu.tmaj.servlet.request.impl.MetaDataAddRequest

processRequest(UserBean) - Method in class edu.jhu.tmaj.servlet.request.impl.MetaDataAlterRequest

processRequest(UserBean) - Method in class edu.jhu.tmaj.servlet.request.impl.OriginalTypeRequest

processRequest(UserBean) - Method in class edu.jhu.tmaj.servlet.request.impl.ProjectsArraySlidesAddRequest

processRequest(UserBean) - Method in class edu.jhu.tmaj.servlet.request.impl.QuantityLeftRequest

processRequest(UserBean) - Method in class edu.jhu.tmaj.servlet.request.impl.RecentSessionDeleteRequest

processRequest(UserBean) - Method in class edu.jhu.tmaj.servlet.request.impl.RecentSessionGetRequest

processRequest(UserBean) - Method in class edu.jhu.tmaj.servlet.request.impl.RecentSessionUpdateRequest

processRequest(UserBean) - Method in class edu.jhu.tmaj.servlet.request.impl.ScanCheckDataRequest

processRequest(UserBean) - Method in class edu.jhu.tmaj.servlet.request.impl.ScanDeleteRequest

processRequest(UserBean) - Method in class edu.jhu.tmaj.servlet.request.impl.SelectRequest

processRequest(UserBean) - Method in class edu.jhu.tmaj.servlet.request.impl.SessionDescriptionsRequest

processRequest(UserBean) - Method in class edu.jhu.tmaj.servlet.request.impl.ShapesLoadRequest

processRequest(UserBean) - Method in class edu.jhu.tmaj.servlet.request.impl.ShapesSaveRequest

processRequest(UserBean) - Method in class edu.jhu.tmaj.servlet.request.impl.SpecimenIdentifiersRequest

processRequest(UserBean) - Method in class edu.jhu.tmaj.servlet.request.impl.SpecimensAssignRequest

processRequest(UserBean) - Method in class edu.jhu.tmaj.servlet.request.impl.SurgPathNumberRequest

processRequest(UserBean) - Method in class edu.jhu.tmaj.servlet.request.impl.TranslatedRowRequest

processRequest(UserBean) - Method in class edu.jhu.tmaj.servlet.request.impl.UpdateRequest

Calls either the commit(), insert(), or delete() method on the Bean provided.

processRequest(UserBean) - Method in class edu.jhu.tmaj.servlet.request.impl.UsedTissueTypesRequest

processRequest(UserBean) - Method in class edu.jhu.tmaj.servlet.request.impl.UsersSessionsGetRequest

processRequest(UserBean) - Method in class edu.jhu.tmaj.servlet.request.impl.UsersSessionsSaveRequest

processStack - Variable in class edu.jhu.tmaj.beans.masks.results.ParticleAnalyzer2

progressBar - Variable in class edu.jhu.tmaj.client.importer.images.ArrayImagesImportGui2

ProgressLabel - Class in edu.jhu.tmaj.client.frida.gui.shared

A text label and a progress bar.

ProgressLabel() - Constructor for class edu.jhu.tmaj.client.frida.gui.shared.ProgressLabel

PROJECT_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.IASessionBean

PROJECT_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.SessionBean

PROJECT_NAME_FIELD - Static variable in class edu.jhu.tmaj.beans.ProjectBean

PROJECT_TITLE_FIELD - Static variable in class edu.jhu.tmaj.beans.BlockUsageBean

PROJECT_TITLE_FIELD - Static variable in class edu.jhu.tmaj.beans.BloodUsageBean

PROJECT_TITLE_FIELD - Static variable in class edu.jhu.tmaj.beans.MolecularUsageBean

PROJECT_TITLE_FIELD - Static variable in class edu.jhu.tmaj.beans.TissueUsageBean

PROJECT_TITLE_FIELD - Static variable in class edu.jhu.tmaj.beans.UrineUsageBean

ProjectBean - Class in edu.jhu.tmaj.beans

Represents the Projects Table.

ProjectBean() - Constructor for class edu.jhu.tmaj.beans.ProjectBean

ProjectsArraySlidesAddRequest - Class in edu.jhu.tmaj.servlet.request.impl

Adds a record to the ProjectsArraySlides table.

ProjectsArraySlidesAddRequest(int, int) - Constructor for class edu.jhu.tmaj.servlet.request.impl.ProjectsArraySlidesAddRequest

ProjectsArraySlidesBean - Class in edu.jhu.tmaj.beans.manytomany

Represents the ProjectsArraySlides table, a many-to-many table that links Projects to ArraySlides.

ProjectsArraySlidesBean() - Constructor for class edu.jhu.tmaj.beans.manytomany.ProjectsArraySlidesBean

ProjectSelectDialog - Class in edu.jhu.tmaj.client.importer.images

ProjectSelectDialog() - Constructor for class edu.jhu.tmaj.client.importer.images.ProjectSelectDialog

ProjectSessionType - Enum in edu.jhu.tmaj.beans.data

ProjectsGui - Class in edu.jhu.tmaj.client.frida.gui

ProjectsGui() - Constructor for class edu.jhu.tmaj.client.frida.gui.ProjectsGui

ProjectsGUI - Class in edu.jhu.tmaj.client.image

The initially displayed frame for the Image Analysis application that allows a user to pick a session to score.

ProjectsGUI(boolean) - Constructor for class edu.jhu.tmaj.client.image.ProjectsGUI

promptToOpenFile(JFileChooser, Component, Preference) - Static method in class edu.jhu.tmaj.util.FileManager

Open a file or directory

promptToOpenFiles(JFileChooser, Component, Preference) - Static method in class edu.jhu.tmaj.util.FileManager

promptToSaveFile(JFileChooser, Component, Preference, String) - Static method in class edu.jhu.tmaj.util.FileManager

Saves a file

PropertiesReaderUtil - Class in edu.jhu.tmaj.util.config.data

PropertiesReaderUtil() - Constructor for class edu.jhu.tmaj.util.config.data.PropertiesReaderUtil

PROTOCOL_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.BlockUsageAltBean

PROTOCOL_NAME_FIELD - Static variable in class edu.jhu.tmaj.beans.ProtocolBean

ProtocolBean - Class in edu.jhu.tmaj.beans

Represents the Protocols table.

ProtocolBean() - Constructor for class edu.jhu.tmaj.beans.ProtocolBean

PUB_MED_LINK_FIELD - Static variable in class edu.jhu.tmaj.beans.PaperBean

PublicSwingWorker<T,V> - Class in edu.jhu.tmaj.util.swing

PublicSwingWorker() - Constructor for class edu.jhu.tmaj.util.swing.PublicSwingWorker

PublishedSessionsNodes - Class in edu.jhu.tmaj.client.image.data

A Helper class for generating the Published Sessions Nodes in the JTree in the Projects Frame.

PublishedSessionsNodes() - Constructor for class edu.jhu.tmaj.client.image.data.PublishedSessionsNodes

purgeEmptyStrings(List<String>) - Static method in class edu.jhu.tmaj.util.ListConvertUtil

Returns a list where any strings that were empty have been removed.

PURPLE - Static variable in class edu.jhu.tmaj.util.swing.MoreColors

PURPOSE_FIELD - Static variable in class edu.jhu.tmaj.beans.ArrayBlockBean

Q

quality - Variable in class edu.jhu.tmaj.client.importer.images.data.SizeParameters.OneSizeParameters

QUANTITY_EXCHANGED_FIELD - Static variable in class edu.jhu.tmaj.beans.BlockOrSlideExchangeBean

QUANTITY_USED_FIELD - Static variable in class edu.jhu.tmaj.beans.BlockUsageBean

QUANTITY_USED_FIELD - Static variable in class edu.jhu.tmaj.beans.BloodUsageBean

QUANTITY_USED_FIELD - Static variable in class edu.jhu.tmaj.beans.MolecularUsageBean

QUANTITY_USED_FIELD - Static variable in class edu.jhu.tmaj.beans.TissueUsageBean

QUANTITY_USED_FIELD - Static variable in class edu.jhu.tmaj.beans.UrineUsageBean

QuantityLeftHelper - Class in edu.jhu.tmaj.client.samples

A class that determines how much of a samples quantity is left.

QuantityLeftRequest - Class in edu.jhu.tmaj.servlet.request.impl

An operation that determines how much is left of a particular sample.

QuantityLeftRequest(int, JBean, JBean) - Constructor for class edu.jhu.tmaj.servlet.request.impl.QuantityLeftRequest

QuantityLeftResponse - Class in edu.jhu.tmaj.servlet.response.impl

Contains the quantity left on a sample.

QuantityLeftResponse(int) - Constructor for class edu.jhu.tmaj.servlet.response.impl.QuantityLeftResponse

quote(String) - Static method in class edu.jhu.tmaj.util.StringQuoter

Returns a String that can be included in sybase SQL statement.

R

RACE_FIELD - Static variable in class edu.jhu.tmaj.beans.dynamic.SpecimenBean

RandomString - Class in edu.jhu.tmaj.util.crypt

Utility methods for generating random strings.

RandomString() - Constructor for class edu.jhu.tmaj.util.crypt.RandomString

readBinaryFile(File) - Method in interface edu.jhu.tmaj.util.file.FileUtil

readBinaryFile(File) - Method in class edu.jhu.tmaj.util.file.FileUtilImpl

readByteArrayFromFile(File) - Static method in class edu.jhu.tmaj.util.ByteUtil

readExternalPropertiesFile(File) - Static method in class edu.jhu.tmaj.util.config.data.PropertiesReaderUtil

Gets a properties file located outside the classes directory.

readFlatFile(File, String) - Method in interface edu.jhu.tmaj.util.file.FlatFileSyncer

Reads the supplied File and returns a TableArray based upon the file data.

readFlatFile(File, String) - Method in class edu.jhu.tmaj.util.file.FlatFileSyncerImpl

readInternalPropertiesFile(String) - Static method in class edu.jhu.tmaj.util.config.data.PropertiesReaderUtil

Get a properties values located in the directory where the class files are.

readTextFile(File) - Method in interface edu.jhu.tmaj.util.file.FileUtil

readTextFile(File) - Method in class edu.jhu.tmaj.util.file.FileUtilImpl

readXmlFromFile(File) - Static method in class edu.jhu.tmaj.util.XmlUtil

Gets the root element of an XML file.

readXmlFromInternalFile(String) - Static method in class edu.jhu.tmaj.util.XmlUtil

RECEIVER_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.CellLineBean

RecentComboBox - Class in edu.jhu.tmaj.client.image.data

A ComboBox that divides the elements into 2 sections: recently chosen elements and everything else.

RecentComboBox(List<Object>, List<Object>) - Constructor for class edu.jhu.tmaj.client.image.data.RecentComboBox

Initializes the ComboBox.

RecentSessionDeleteRequest - Class in edu.jhu.tmaj.servlet.request.impl

A Request that deletes all of a users records in the RecentSessions table.

RecentSessionDeleteRequest() - Constructor for class edu.jhu.tmaj.servlet.request.impl.RecentSessionDeleteRequest

RecentSessionGetRequest - Class in edu.jhu.tmaj.servlet.request.impl

A Request to get the most recently accessed sessions for a user.

RecentSessionGetRequest() - Constructor for class edu.jhu.tmaj.servlet.request.impl.RecentSessionGetRequest

RecentSessionGetResponse - Class in edu.jhu.tmaj.servlet.response.impl

RecentSessionGetResponse(List<DatedProjectSession>) - Constructor for class edu.jhu.tmaj.servlet.response.impl.RecentSessionGetResponse

RecentSessionsPanel - Class in edu.jhu.tmaj.client.image

A Panel showing a list of recent sessions the user has viewed.

RecentSessionsPanel(ProjectsGUI) - Constructor for class edu.jhu.tmaj.client.image.RecentSessionsPanel

RecentSessionUpdateRequest - Class in edu.jhu.tmaj.servlet.request.impl

Indicate a user has accessed a session, and to log it in the RecentSessions table.

RecentSessionUpdateRequest(int, ProjectSessionType) - Constructor for class edu.jhu.tmaj.servlet.request.impl.RecentSessionUpdateRequest

Constructs this request.

RECORD_STARTS - Static variable in class edu.jhu.tmaj.beans.masks.results.ParticleAnalyzer2

Record starting coordinates so outline can be recreated later using doWand(x,y).

recordAdd(DefaultMutableTreeNode, DefaultTreeModel) - Static method in class edu.jhu.tmaj.client.admin.data.TissueTypesSyncer

recordDelete(DefaultMutableTreeNode, DefaultTreeModel) - Static method in class edu.jhu.tmaj.client.admin.data.TissueTypesSyncer

recordEdit(DefaultMutableTreeNode, MetaObject, DefaultTreeModel) - Static method in class edu.jhu.tmaj.client.admin.data.TissueTypesSyncer

recordExists() - Method in class edu.jhu.tmaj.client.importer.specimens.data.TranslatedTable

RecordIdentifier - Class in edu.jhu.tmaj.client.importer.specimens.data

Represents the unique data portion of patient or a specimen.

RecordIdentifier(int, String) - Constructor for class edu.jhu.tmaj.client.importer.specimens.data.RecordIdentifier

RecordModify - Class in edu.jhu.tmaj.client.tables.logs

Represents a user modifying a unique record in a given TMAJ table.

RecordModify(int, int, int) - Constructor for class edu.jhu.tmaj.client.tables.logs.RecordModify

recordStarts - Variable in class edu.jhu.tmaj.beans.masks.results.ParticleAnalyzer2

RectangleDrawable - Class in edu.jhu.tmaj.client.image.draw

A rectangle

RectangleDrawable(DrawableLabel) - Constructor for class edu.jhu.tmaj.client.image.draw.RectangleDrawable

redo() - Method in class edu.jhu.tmaj.beans.masks.color.ActionList

Indicate a redo action; if undo() was previously called, this will put the action item that was undone back on the stack, so that when the user calls getActionList(), the item will be there.

referencedMask - Variable in class edu.jhu.tmaj.beans.masks.meta.ActionMaskInfo

refresh(List, List) - Method in class edu.jhu.tmaj.client.admin.ManyDataPanel

Refreshes data in both lists.

refresh() - Method in class edu.jhu.tmaj.client.admin.ManyToManyPanel

Refreshes data in both lists.

refresh(DefaultTreeModel) - Method in class edu.jhu.tmaj.client.image.data.NodeMaker

Refreses the SharedSessionsNode and PublishedSessions Node.

refreshCache(CacheableBean) - Static method in class edu.jhu.tmaj.beans.cache.CachedBeans

refreshFromDatabase() - Method in class edu.jhu.tmaj.client.image.RecentSessionsPanel

REGION_SIZE_FIELD - Static variable in class edu.jhu.tmaj.beans.dynamic.TissueDiagnosisBean

registerEvent(String) - Method in class edu.jhu.tmaj.util.StopWatch

releaseObject(Object) - Method in class edu.jhu.tmaj.util.ObjectPool

Returns the object to the pool.

reload() - Method in class edu.jhu.tmaj.client.image.ArrayImageFrame

removeAllObjects() - Method in class edu.jhu.tmaj.util.ObjectPool

Removes all elements from the pool.

removeColumn(int) - Method in interface edu.jhu.tmaj.util.file.TableArray

removeColumn(C) - Method in interface edu.jhu.tmaj.util.file.TableArray

removeColumn(int) - Method in class edu.jhu.tmaj.util.file.TableArrayImpl

removeColumn(C) - Method in class edu.jhu.tmaj.util.file.TableArrayImpl

removeCurrentSelection() - Method in class edu.jhu.tmaj.client.image.draw.ShapeListener

removeDeletedRow(int) - Method in class edu.jhu.tmaj.client.tables.data.ChangedCells

removeElementAt(int) - Method in class edu.jhu.tmaj.util.swing.GeneralListModel

removeExternalFolderButton - Variable in class edu.jhu.tmaj.client.importer.images.ArrayImagesImportGui2

removeExternalFolderButtonPressed() - Method in class edu.jhu.tmaj.client.importer.images.ArrayImagesImportHelper

removeFilterSort() - Method in class edu.jhu.tmaj.client.tables.SortFilterDialog

removeFromOpenedList(ArrayBlockFrame) - Method in class edu.jhu.tmaj.client.arraybuilder.OpenedArrayBlocksPanel

removeIASessionBean(IASessionBean) - Method in class edu.jhu.tmaj.client.image.AbstractSessionsPanel

removeKey(int, int) - Method in class edu.jhu.tmaj.beans.manytomany.LinkGroup

Removes a key mapping.

removeListDataListener(ListDataListener) - Method in class edu.jhu.tmaj.util.swing.GeneralListModel

removeObject(Object) - Method in class edu.jhu.tmaj.util.ObjectPool

Removes an element from the pool.

removePrimaryMask(Mask) - Method in class edu.jhu.tmaj.client.frida.gui.shared.MaskRepresentationPanel

removeRow(int) - Method in class edu.jhu.tmaj.client.tables.data.GeneralTableModel

removeRow(int) - Method in interface edu.jhu.tmaj.util.file.TableArray

removeRow(int) - Method in class edu.jhu.tmaj.util.file.TableArrayImpl

removeSessionBean(SessionBean) - Method in class edu.jhu.tmaj.client.image.AbstractSessionsPanel

removeUpdatedRow(int) - Method in class edu.jhu.tmaj.client.tables.data.ChangedCells

renameFields(List<TableField>) - Method in class edu.jhu.tmaj.servlet.request.impl.DetailsRequest

renameFields(List<TableField>) - Method in class edu.jhu.tmaj.servlet.request.impl.ScoredImageDetailsRequest

renameFile(File, String) - Method in interface edu.jhu.tmaj.util.file.FileUtil

renameFile(File, String) - Method in class edu.jhu.tmaj.util.file.FileUtilImpl

renameFilesInDirectory(File, Component, SimpleProgressDialog) - Static method in class edu.jhu.tmaj.client.importer.AriolFileRenamerHelper

Prepends the proper x and y coordinate information onto all the files in the directory.

RenameOp - Class in edu.jhu.tmaj.client.importer.images.data

Represents an operation where a file is renamed.

RenameOp(File, String) - Constructor for class edu.jhu.tmaj.client.importer.images.data.RenameOp

Constructs this object.

repaint(long, int, int, int, int) - Method in class edu.jhu.tmaj.util.swing.AbstractTableCellRenderer

Overridden for performance reasons

repaintDrawableLabel() - Method in class edu.jhu.tmaj.client.image.draw.AbstractDrawable

reset() - Method in class edu.jhu.tmaj.beans.masks.color.CircleRange

Resets this range so that no numbers are included.

reset() - Method in class edu.jhu.tmaj.beans.masks.color.HsbRange

Resets this range; this means nothing will be included.

reset() - Method in class edu.jhu.tmaj.beans.masks.color.SimpleRange

Resets this range; a reset range includes NO values.

reset() - Method in class edu.jhu.tmaj.beans.masks.results.Analyzer2

reset() - Method in class edu.jhu.tmaj.client.frida.gui.DefinedMasksGui

Clears all masks from the list, and disposes of all their guis.

reset() - Method in class edu.jhu.tmaj.client.frida.gui.masks.color.FullSlider

reset() - Method in class edu.jhu.tmaj.client.image.data.Navigator

Recalculates the ArrayImage sequence.

reset() - Static method in class edu.jhu.tmaj.client.shared.CurrentUser

Gets a fresh copy of the userBean data from the database.

RESET_MAX_VALUE - Static variable in class edu.jhu.tmaj.beans.masks.color.CircleRange

RESET_MIN_VALUE - Static variable in class edu.jhu.tmaj.beans.masks.color.CircleRange

resetCounter() - Static method in class edu.jhu.tmaj.beans.masks.results.Analyzer2

Sets the measurement counter to zero.

resetCounter - Variable in class edu.jhu.tmaj.beans.masks.results.ParticleAnalyzer2

resetRange() - Method in class edu.jhu.tmaj.client.frida.gui.masks.color.HsbRangeComponent

Resets the range and the JSliders that show that range.

ResizableTableComponentListener - Class in edu.jhu.tmaj.client.image.data

Added to a window with a JTable, this ComponentListener adjusts the row height of the JTable whenever the window is resized.

ResizableTableComponentListener(Component, JTable, HeaderTableScrollPane) - Constructor for class edu.jhu.tmaj.client.image.data.ResizableTableComponentListener

Initializes the ComponentListener.

retrieveImage(ArrayImageCell) - Static method in class edu.jhu.tmaj.client.image.data.ArrayImageRendererCache

retrieveIV() - Static method in class edu.jhu.tmaj.util.crypt.KeyManagementUtil

retrieveKey() - Static method in class edu.jhu.tmaj.util.crypt.KeyManagementUtil

returnConnection(Connection) - Method in interface edu.jhu.tmaj.database.conn.ConnectionManager

Gives a connection back to the ConnectionFactory telling indicating the connection can be re-issued.

returnConnection(Connection) - Method in class edu.jhu.tmaj.database.conn.PooledConnectionManager

returns the connection allowing other threads to use it.

revalidate() - Method in class edu.jhu.tmaj.util.swing.AbstractTableCellRenderer

Overridden for performance reasons

RGB - Static variable in class edu.jhu.tmaj.beans.masks.results.ParticleAnalyzer2

ROI_MASKS - Static variable in class edu.jhu.tmaj.beans.masks.results.ParticleAnalyzer2

RowHeaderList - Class in edu.jhu.tmaj.client.image.data

A row-header viewport for a JScrollPane.

RowHeaderList(JTable, int, int) - Constructor for class edu.jhu.tmaj.client.image.data.RowHeaderList

RowHeaderListRenderer - Class in edu.jhu.tmaj.client.image.data

A Renderer for the JList that serves the row-header viewpoint for the HeaderTableScrollPane.

RowHeaderListRenderer(int) - Constructor for class edu.jhu.tmaj.client.image.data.RowHeaderListRenderer

rt - Variable in class edu.jhu.tmaj.beans.masks.results.ParticleAnalyzer2

run(ImageProcessor) - Method in class edu.jhu.tmaj.beans.masks.results.Analyzer2

run(ImageProcessor) - Method in class edu.jhu.tmaj.beans.masks.results.ParticleAnalyzer2

runJob() - Method in class edu.jhu.tmaj.client.shared.SimpleProgressDialog

Overwrite this method with code that the task will run.

runQuery(String, ArrayImageCollectionBean) - Method in class edu.jhu.tmaj.servlet.request.impl.ScoreDataHandler

S

s - Variable in class edu.jhu.tmaj.beans.masks.data.HsbPixel

SamplesAppGUI - Class in edu.jhu.tmaj.client.samples

The main GUI class for the Samples Application for Cleveland Clinic.

save(int) - Method in class edu.jhu.tmaj.client.image.draw.ShapesFrame

Save shapes to the database

save() - Method in class edu.jhu.tmaj.client.tables.data.TableData4

Saves any changes the user has made to the table.

save() - Method in class edu.jhu.tmaj.client.tables.InputPanel4

Saves any changes the user has made to the table

saveColumnWidths(TableColumnModel) - Method in class edu.jhu.tmaj.client.tables.data.ColumnWidthData

Saves the widths of this TableColumnModel

SaveFrame - Class in edu.jhu.tmaj.client.image

A frame that pops up when a user right clicks an ArrayImage, it allows the user to save the image or see another version of the image.

SaveFrame(ArrayImageCell, ArrayImagePanel) - Constructor for class edu.jhu.tmaj.client.image.SaveFrame

saveImage(ExternalFile, ImagePlus) - Method in class edu.jhu.tmaj.client.frida.gui.shared.NavigationPanel

savePoints(Roi) - Method in class edu.jhu.tmaj.beans.masks.results.Analyzer2

savePreferences(Properties) - Static method in class edu.jhu.tmaj.beans.masks.results.Analyzer2

Called once when ImageJ quits.

savePreferences(Properties) - Static method in class edu.jhu.tmaj.beans.masks.results.ParticleAnalyzer2

Called once when ImageJ quits.

saveResults(ImageStatistics, Roi) - Method in class edu.jhu.tmaj.beans.masks.results.Analyzer2

Saves the measurements specified in the "Set Measurements" dialog, or by calling setMeasurements(), in the default results table.

saveResults(ImageStatistics, Roi) - Method in class edu.jhu.tmaj.beans.masks.results.ParticleAnalyzer2

Saves statistics for one particle in a results table.

saveToDatabaseMenuItemClicked() - Method in class edu.jhu.tmaj.client.arraybuilder.ArrayBlockFrame

Saves the ArrayBlock to the database

scale - Variable in class edu.jhu.tmaj.client.importer.images.data.SizeParameters.OneSizeParameters

SCAN_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.ArrayImageBean

SCAN_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.IASessionBean

SCAN_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.MachineSessionBean

SCAN_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.SessionBean

SCAN_NUMBER_FIELD - Static variable in class edu.jhu.tmaj.beans.ScanBean

SCAN_SCOPE_IMAGE_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.ScanBean

ScanBean - Class in edu.jhu.tmaj.beans

Represents a Scan of an ArraySlide.

ScanBean(StaticMetaData) - Constructor for class edu.jhu.tmaj.beans.ScanBean

scanBean - Variable in class edu.jhu.tmaj.client.importer.images.data.SelectedScan

ScanCheckDataRequest - Class in edu.jhu.tmaj.servlet.request.impl

ScanCheckDataRequest(SelectedScan) - Constructor for class edu.jhu.tmaj.servlet.request.impl.ScanCheckDataRequest

ScanDeleteRequest - Class in edu.jhu.tmaj.servlet.request.impl

ScanDeleteRequest(SelectedScan) - Constructor for class edu.jhu.tmaj.servlet.request.impl.ScanDeleteRequest

SCANNING_MACHINE_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.ScanBean

ScanningMachine - Enum in edu.jhu.tmaj.client.importer.data

The Machines that can scan an ArraySlide, namely the BLISS, ACIS, NIKON, and ARIOL.

scanningMachine - Variable in class edu.jhu.tmaj.client.importer.images.data.FilenameData

scanNumber - Variable in class edu.jhu.tmaj.client.importer.images.data.FilenameData

ScanScopeDialog - Class in edu.jhu.tmaj.client.shared

ScanScopeDialog() - Constructor for class edu.jhu.tmaj.client.shared.ScanScopeDialog

ScanScopeUtil - Class in edu.jhu.tmaj.client.arrays

ScanSelectDialog - Class in edu.jhu.tmaj.client.importer.images

ScanSelectDialog(Component) - Constructor for class edu.jhu.tmaj.client.importer.images.ScanSelectDialog

scanTextField - Variable in class edu.jhu.tmaj.client.importer.images.ArrayImagesImportGui2

SCORED_IMAGE_ID_FIELD - Static variable in class edu.jhu.tmaj.servlet.request.impl.ScoredImageDetailsRequest

ScoreData - Class in edu.jhu.tmaj.client.image.data

A Class that represents the what fields (not values) a user has assigned to a spot

ScoreData() - Constructor for class edu.jhu.tmaj.client.image.data.ScoreData

ScoreDataHandler - Class in edu.jhu.tmaj.servlet.request.impl

A class for running a SQL statement that will modify the ScoreData inside an ArrayImageCollectionBean.

ScoreDataHandler() - Constructor for class edu.jhu.tmaj.servlet.request.impl.ScoreDataHandler

ScoredImageBean - Class in edu.jhu.tmaj.beans.dynamic

A ScoredImage Bean represents an ArrayImage that has been scored by a user.

ScoredImageBean(StaticMetaData, DynamicMetaData, SessionBean) - Constructor for class edu.jhu.tmaj.beans.dynamic.ScoredImageBean

ScoredImageDetailsRequest - Class in edu.jhu.tmaj.servlet.request.impl

Retrieves information about every x and y position from a session (a scored array) and puts it into a table format (List of Lists).

ScoredImageDetailsRequest(int[], DynamicMetaData, DynamicMetaData, DynamicMetaData, Map<Integer, LookupRecord>, Map<Integer, LookupRecord>) - Constructor for class edu.jhu.tmaj.servlet.request.impl.ScoredImageDetailsRequest

Since this is executed on the server side, the request must pass in the cached MetaData from MyBeans

ScoredImageInsert - Class in edu.jhu.tmaj.servlet.request.impl

ScoredImageInsert(InsertSQL, int) - Constructor for class edu.jhu.tmaj.servlet.request.impl.ScoredImageInsert

ScoredImageQuery - Class in edu.jhu.tmaj.servlet.request.impl

Adds data from the ScoredImages table to the field_value maps in mapList.

ScoredImageQuery(List<Map>, String) - Constructor for class edu.jhu.tmaj.servlet.request.impl.ScoredImageQuery

SCOREDIMAGES_INPUT_LOG_FIELD - Static variable in class edu.jhu.tmaj.servlet.request.impl.ScoredImageDetailsRequest

SCOREDIMAGES_NOTES_FIELD - Static variable in class edu.jhu.tmaj.servlet.request.impl.ScoredImageDetailsRequest

SCOREDIMAGES_TISSUETYPEID_FIELD - Static variable in class edu.jhu.tmaj.servlet.request.impl.ScoredImageDetailsRequest

SCORING_STRATEGY_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.SessionBean

SCORING_STRATEGY_TISSUE_TYPE_ID - Static variable in class edu.jhu.tmaj.beans.dynamic.data.ArrayImageDynamicField

The DynamicTypeID assigned to DynamicFields who are a ScoringStrategy field, not a regular Dynamic Field

scoringStrategyID_dynamicFields - Variable in class edu.jhu.tmaj.beans.dynamic.data.ArrayImageDynamicMetaData

scrollPane - Variable in class edu.jhu.tmaj.client.tables.data.TableData4

ScrollPaneMouseInputListener - Class in edu.jhu.tmaj.client.image.data

A MouseListener and MouseMotionListener that scrolls a JScrollPane.

ScrollPaneMouseInputListener(JScrollPane) - Constructor for class edu.jhu.tmaj.client.image.data.ScrollPaneMouseInputListener

Search - Class in edu.jhu.tmaj.client.tables.data

Represents a Search done from an InputPanel Gui.

search() - Method in class edu.jhu.tmaj.client.tables.data.TableData4

Performs a search on the database and fills the table with the found rows

search() - Method in class edu.jhu.tmaj.client.tables.InputPanel4

Searches the database for any records that match the search-fields and puts the records in the table

SearchDialog - Class in edu.jhu.tmaj.client.tables

The dialog displayed when the user presses the search button on an InputPanel.

SearchTerm - Class in edu.jhu.tmaj.client.tables.data

A tablename and a fieldname

SearchTerm(String, DatabaseField) - Constructor for class edu.jhu.tmaj.client.tables.data.SearchTerm

SECONDARY_DIAGNOSIS_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.BlockUsageAltBean

SECONDARY_HISTOLOGIC_TYPE_FIELD - Static variable in class edu.jhu.tmaj.servlet.request.impl.DiagnosisLookupRequest

SECONDARY_USER_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.PaperBean

SECRET_KEY_FILE_NAME - Static variable in class edu.jhu.tmaj.util.crypt.KeyManagementUtil

seek(JScrollPane, JTable, int) - Static method in class edu.jhu.tmaj.client.tables.FindFrame

Scrolls the scrollPane to a specified row number in the JTable

select() - Method in class edu.jhu.tmaj.client.image.data.ArrayImageCell

Indicate user has selected this image to be viewed.

SelectableImage - Class in edu.jhu.tmaj.client.image

An ArrayImage that the user can select or unselect.

SelectableImage(ArrayImageCell) - Constructor for class edu.jhu.tmaj.client.image.SelectableImage

SelectedScan - Class in edu.jhu.tmaj.client.importer.images.data

SelectedScan(ArrayBlockBean, ArraySlideBean, ScanBean) - Constructor for class edu.jhu.tmaj.client.importer.images.data.SelectedScan

selectedScanMatchesFolderName(SelectedScan, String) - Static method in class edu.jhu.tmaj.client.importer.images.data.FolderNameUtil

SelectRequest - Class in edu.jhu.tmaj.servlet.request.impl

Gets a SelectResponse from a JBean.

SelectRequest(JBean, Search) - Constructor for class edu.jhu.tmaj.servlet.request.impl.SelectRequest

SelectResponse - Class in edu.jhu.tmaj.servlet.response.impl

Contains a List of BasicTableBeans and columnIdentifiers.

SelectResponse(List<JBean>, List) - Constructor for class edu.jhu.tmaj.servlet.response.impl.SelectResponse

selectScanButton - Variable in class edu.jhu.tmaj.client.importer.images.ArrayImagesImportGui2

selectScanButtonPressed() - Method in class edu.jhu.tmaj.client.importer.images.ArrayImagesImportHelper

SelectSQL - Class in edu.jhu.tmaj.database.sql

Represents a SELECT SQL statement.

sendRequest(CommandRequest) - Method in class edu.jhu.tmaj.servlet.CommandServletClient

Sends the ServerRequest object to the server to be executed.

sendRequest(KeyValueGetRequest.KeyName, String) - Static method in class edu.jhu.tmaj.servlet.request.impl.KeyValueSetRequest

SeparatedComboBoxRenderer - Class in edu.jhu.tmaj.client.image.data

A ComboBox that allows its items to be separated with a JSeparator.

SeparatedComboBoxRenderer() - Constructor for class edu.jhu.tmaj.client.image.data.SeparatedComboBoxRenderer

SEPARATOR - Static variable in class edu.jhu.tmaj.client.image.data.DividedComboBox

ServerConstants - Class in edu.jhu.tmaj.config

ServletUtil - Class in edu.jhu.tmaj.servlet

A class used to generate the header for an HTML document.

ServletUtil() - Constructor for class edu.jhu.tmaj.servlet.ServletUtil

SESSION_DESCRIPTION_FIELD - Static variable in class edu.jhu.tmaj.beans.IASessionBean

SESSION_DESCRIPTION_FIELD - Static variable in class edu.jhu.tmaj.beans.SessionBean

SESSION_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.dynamic.ScoredImageBean

SESSION_ID_POSITION - Static variable in class edu.jhu.tmaj.beans.dynamic.ScoredImageBean

SessionBean - Class in edu.jhu.tmaj.beans

Represents the Sessions Table.

SessionBean() - Constructor for class edu.jhu.tmaj.beans.SessionBean

SessionBean(int, int, String, int) - Constructor for class edu.jhu.tmaj.beans.SessionBean

sessionBean - Variable in class edu.jhu.tmaj.client.image.ArrayImageFrame

SessionBeansHolder - Class in edu.jhu.tmaj.client.image.data

Contains initialized Beans used in the Images application.

SessionCreateDialog - Class in edu.jhu.tmaj.client.image

SessionDescriptionsRequest - Class in edu.jhu.tmaj.servlet.request.impl

This request is used by AnalysisFrame to return a description of the users sessions.

SessionDescriptionsRequest() - Constructor for class edu.jhu.tmaj.servlet.request.impl.SessionDescriptionsRequest

SessionDescriptionsRequest.Column - Enum in edu.jhu.tmaj.servlet.request.impl

SessionDescriptionsResponse - Class in edu.jhu.tmaj.servlet.response.impl

SessionDescriptionsResponse(List<Map<SessionDescriptionsRequest.Column, String>>) - Constructor for class edu.jhu.tmaj.servlet.response.impl.SessionDescriptionsResponse

SessionDialog - Class in edu.jhu.tmaj.client.image

A frame that allows users to modify session information, including the ability to publish sessions

SessionGuis - Class in edu.jhu.tmaj.client.image.data

SessionGuis() - Constructor for class edu.jhu.tmaj.client.image.data.SessionGuis

SESSIONID_FIELD - Static variable in class edu.jhu.tmaj.servlet.request.impl.ScoredImageDetailsRequest

SessionWindowListener - Class in edu.jhu.tmaj.client.image.data

A WindowListener attached to the ArraySlideFrame so that when it is closed, the session is removed from the active sessions list.

setActive(boolean) - Method in class edu.jhu.tmaj.client.image.draw.DrawableLabel

Sets whether the label will paint the Drawables

setAllComboBoxes() - Method in class edu.jhu.tmaj.client.tables.data.TableData4

Sets enumerated columns to JComboBoxes containing the proper choices.

setArrayCoreData(ArrayCoreData) - Method in class edu.jhu.tmaj.client.arraybuilder.CoreDataPanel

Sets up all TextFields in this GUI to point to the correct TissueDiagnosis,Block, Specimen, and Patient.

setArrayCoreData(ArrayCoreData) - Method in class edu.jhu.tmaj.client.arraybuilder.TissueDiagnosisIDPanel

Sets the values in this panel to that of ArrayCoreData.

setArrayImage(ArrayImageCell) - Method in class edu.jhu.tmaj.client.image.ArrayImageFrame

setArrayImage(ArrayImageCell) - Method in class edu.jhu.tmaj.client.image.ArraySlideFrame

setArrayImage(ArrayImageCell) - Method in interface edu.jhu.tmaj.client.image.data.ArrayImageSettable

setArrayImage(ArrayImageCell) - Method in class edu.jhu.tmaj.client.image.DotTableFrame

Highlight the row that is represents the supplied ArrayImage.

setArrayImageEnumID(int) - Method in class edu.jhu.tmaj.servlet.response.impl.DiagnosisLookupResponse

setArrayImageFieldID(int) - Method in class edu.jhu.tmaj.servlet.response.impl.DiagnosisLookupResponse

setArrayImageFrame(ArrayImageFrame) - Method in class edu.jhu.tmaj.client.image.data.SessionGuis

setArraySlideFrame(ArraySlideFrame) - Method in class edu.jhu.tmaj.client.image.data.SessionGuis

setBooleanField(DatabaseField, Boolean) - Method in class edu.jhu.tmaj.beans.JBean

Sets a field of type TFieldType.BOOLEAN

setCalibrationCoefficient1(Double) - Method in class edu.jhu.tmaj.beans.IASessionBean

setCalibrationCoefficient2(Double) - Method in class edu.jhu.tmaj.beans.IASessionBean

setCalibrationCoefficient3(Double) - Method in class edu.jhu.tmaj.beans.IASessionBean

setCalibrationCoefficient4(Double) - Method in class edu.jhu.tmaj.beans.IASessionBean

setCalibrationCoefficient5(Double) - Method in class edu.jhu.tmaj.beans.IASessionBean

setCalibrationFunction(String) - Method in class edu.jhu.tmaj.beans.IASessionBean

setCalibrationFunction(CalibrationFunction) - Method in class edu.jhu.tmaj.client.frida.data.Calibration

setCell(int, int) - Method in class edu.jhu.tmaj.client.tables.SortFilterDialog

setCell(int, int, T) - Method in interface edu.jhu.tmaj.util.file.TableArray

setCell(int, C, T) - Method in interface edu.jhu.tmaj.util.file.TableArray

setCell(int, int, T) - Method in class edu.jhu.tmaj.util.file.TableArrayImpl

setCell(int, C, T) - Method in class edu.jhu.tmaj.util.file.TableArrayImpl

setCellSize(HeaderTableScrollPane, JTable, int, int) - Static method in class edu.jhu.tmaj.client.image.ThumbnailsMenuHelper

setCellValue(int, DatabaseField, Object) - Method in class edu.jhu.tmaj.client.tables.data.TableData4

setCellView(CellView) - Method in class edu.jhu.tmaj.client.arraybuilder.data.ArrayCoreRenderer

setChangedCells(ChangedCells) - Method in class edu.jhu.tmaj.client.tables.data.BeanTableModel

setCoefficient1(Double) - Method in class edu.jhu.tmaj.client.frida.data.Calibration

setCoefficient2(Double) - Method in class edu.jhu.tmaj.client.frida.data.Calibration

setCoefficient3(Double) - Method in class edu.jhu.tmaj.client.frida.data.Calibration

setCoefficient4(Double) - Method in class edu.jhu.tmaj.client.frida.data.Calibration

setCoefficient5(Double) - Method in class edu.jhu.tmaj.client.frida.data.Calibration

setColorLegendDisplayed(boolean) - Method in class edu.jhu.tmaj.client.arraybuilder.ArrayBuilderTable

Display a legend showing which colors are mapped to which TissueTypes.

setColorMaskID(Integer) - Method in class edu.jhu.tmaj.beans.masks.color.ColorMask

setColorsUse(boolean) - Method in class edu.jhu.tmaj.client.arraybuilder.ArrayBuilderTable

Turns the color-scheme on or off.

setColumn(int, C) - Method in interface edu.jhu.tmaj.util.file.TableArray

setColumn(int, C) - Method in class edu.jhu.tmaj.util.file.TableArrayImpl

setColumnIdentifiers(List) - Method in class edu.jhu.tmaj.client.tables.data.GeneralTableModel

setColumns(List<C>) - Method in interface edu.jhu.tmaj.util.file.TableArray

setColumns(List<C>) - Method in class edu.jhu.tmaj.util.file.TableArrayImpl

setColumnViewable(JTable, int, boolean) - Static method in class edu.jhu.tmaj.client.image.data.JTableUtil

Hides or unhides a column in the JTable.

setColumnViewable(JTable, GeneralTableModel, Object, boolean) - Static method in class edu.jhu.tmaj.client.image.data.JTableUtil

setColumnWidths(JTable, int) - Static method in class edu.jhu.tmaj.client.image.data.JTableUtil

Used for setting the column-width-minimum to zero for all the columns in a jtable, allowing the user to "hide" columns

setColumnWidthsToMinimum(JTable, TableModel) - Static method in class edu.jhu.tmaj.client.image.data.JTableUtil

Set the column-width-minimum to zero for all the columns in a jtable, allowing the user to "hide" columns

setComboBox(SelectedScan) - Method in class edu.jhu.tmaj.client.importer.images.ArrayImagesImportHelper

setComboBox(JTable, int, List) - Static method in class edu.jhu.tmaj.client.tables.data.TableData4

Sets the cell editor of the specified column to a ComboBox containing all the choices in enumerationList.

setCompletionMessage(String) - Method in class edu.jhu.tmaj.servlet.response.impl.MachineScoresImportResponse

setControlName(String) - Method in class edu.jhu.tmaj.beans.misc.ArrayCoreRep

setCoordinate(Coordinate) - Method in class edu.jhu.tmaj.client.frida.gui.DefinedMasksGui

setCoordinate(Coordinate) - Method in class edu.jhu.tmaj.client.frida.gui.FridaGui

setCoordinate(Coordinate) - Method in class edu.jhu.tmaj.client.frida.gui.masks.color.ColorMaskGui

setCoordinate(Coordinate) - Method in class edu.jhu.tmaj.client.frida.gui.masks.filter.FilterMaskGui

setCoordinate(Coordinate) - Method in class edu.jhu.tmaj.client.frida.gui.masks.lasso.LassoMaskGui

setCoordinate(Coordinate) - Method in interface edu.jhu.tmaj.client.frida.gui.masks.MaskGui

setCoordinate(Coordinate) - Method in class edu.jhu.tmaj.client.frida.gui.masks.meta.MetaMaskGui

setCoordinate(Coordinate) - Method in class edu.jhu.tmaj.client.frida.gui.shared.GeneralMaskPanel

setCoordinate(Coordinate) - Method in class edu.jhu.tmaj.client.frida.gui.shared.NavigationPanel

setCoordinate(int, int) - Method in class edu.jhu.tmaj.client.image.data.IASessionGuis

setCoordinate(int, int, SessionBean) - Method in class edu.jhu.tmaj.client.image.data.ImageAppGuis

Sets the X,Y coordinate for All SessionGuis and IASessionGuis

setCoordinate(int, int, IASessionBean) - Method in class edu.jhu.tmaj.client.image.data.ImageAppGuis

setCoordinate(int, int) - Method in class edu.jhu.tmaj.client.image.data.SessionGuis

setCreationDate(Date) - Method in class edu.jhu.tmaj.beans.IASessionBean

setCreationDate(Date) - Method in class edu.jhu.tmaj.beans.SessionBean

setData() - Method in class edu.jhu.tmaj.client.image.ArrayImageFrameTable

setData(List<List>, List) - Method in class edu.jhu.tmaj.client.tables.data.GeneralTableModel

setData(List, List) - Method in class edu.jhu.tmaj.client.tables.data.TableData4

setDataList(List) - Method in class edu.jhu.tmaj.client.tables.data.GeneralTableModel

setDataList(List) - Method in class edu.jhu.tmaj.util.swing.GeneralListModel

setDateField(DatabaseField, Date) - Method in class edu.jhu.tmaj.beans.JBean

setDefaultHeadings() - Static method in class edu.jhu.tmaj.beans.masks.results.Analyzer2

Sets the default headings ("Area", "Mean", etc.).

setDiagnosed(boolean) - Method in class edu.jhu.tmaj.client.image.data.ScoreData

setDisplayedIndex(String) - Method in class edu.jhu.tmaj.client.tables.TabGroup

setDotTableFrame(DotTableFrame) - Method in class edu.jhu.tmaj.client.image.data.SessionGuis

setDoubleField(DatabaseField, Double) - Method in class edu.jhu.tmaj.beans.JBean

Sets a field of type TFieldType.DOUBLE

setDoubleStat(MaskStats.StatName, Double) - Method in class edu.jhu.tmaj.beans.masks.results.MaskStats

setDrawableLabel(DrawableLabel) - Method in class edu.jhu.tmaj.client.image.draw.AbstractDrawable

Sets the DrawableLabel on which this shape is being drawn

setDrawableLabel(DrawableLabel) - Method in class edu.jhu.tmaj.servlet.response.impl.ShapesSaveResponse

setDrawableToDelete(Drawable) - Static method in class edu.jhu.tmaj.client.image.draw.ShapeListener

setDrawButtonEnabled(boolean) - Method in class edu.jhu.tmaj.client.image.ArrayImageFrame

setEditable(boolean) - Method in class edu.jhu.tmaj.client.frida.gui.masks.color.FullSlider

setEditingDisabled(boolean) - Method in class edu.jhu.tmaj.client.tables.data.BeanTableModel

setEnabled(boolean) - Method in class edu.jhu.tmaj.client.frida.gui.DefinedMasksGui

setEnabled(boolean) - Method in class edu.jhu.tmaj.client.frida.gui.shared.LimitedToolBar

Sets buttons as enabled or disabled

setEnabled(boolean) - Method in class edu.jhu.tmaj.client.importer.images.ArrayImagesImportGui2

setErrorMessage(String) - Method in class edu.jhu.tmaj.client.frida.gui.shared.MessageLabel

setErrorMessage(String) - Method in class edu.jhu.tmaj.client.frida.gui.shared.ProgressLabel

setExistingFields(List<TranslatedRow>, int, SpecimenIdentifiersResponse) - Static method in class edu.jhu.tmaj.servlet.request.impl.SpecimenIdentifiersRequest

Sets the recordExists and primaryKeyID fields in the Translated table.

setExtras(ArraySlideBean, ScanBean, UserBean) - Method in class edu.jhu.tmaj.beans.SessionBean

setFailureMessage(String) - Method in class edu.jhu.tmaj.servlet.response.impl.DiagnosisLookupResponse

setFilteredOut(boolean) - Method in class edu.jhu.tmaj.client.image.data.ArrayImageCell

setFilterMaskID(Integer) - Method in class edu.jhu.tmaj.beans.masks.filter.FilterMask

setFilterMaskType(FilterMaskType) - Method in class edu.jhu.tmaj.beans.masks.filter.FilterMask

setFilterOn(boolean) - Method in class edu.jhu.tmaj.client.image.data.ArrayImageCell

setFridaGui(FridaGui) - Method in class edu.jhu.tmaj.client.image.data.IASessionGuis

setGridEnabled(boolean) - Method in class edu.jhu.tmaj.client.image.GridLabel

setGridSpacing(int) - Method in class edu.jhu.tmaj.client.image.GridLabel

setHideOutputImage(boolean) - Method in class edu.jhu.tmaj.beans.masks.results.ParticleAnalyzer2

Set 'hideOutputImage' true to not display the "Show:" image.

setIASessionID(Integer) - Method in class edu.jhu.tmaj.beans.SessionBean

setID(int) - Method in class edu.jhu.tmaj.beans.JBean

Sets the id of this bean.

setID(Integer) - Method in class edu.jhu.tmaj.beans.masks.AbstractMask

setID(Integer) - Method in class edu.jhu.tmaj.beans.masks.lasso.LassoedFile

setID(Integer) - Method in interface edu.jhu.tmaj.beans.masks.Mask

setID(Integer) - Method in class edu.jhu.tmaj.beans.masks.meta.ActionMaskInfo

setImage(ExternalFile, ImagePlus) - Method in class edu.jhu.tmaj.client.frida.gui.shared.NavigationPanel

setImagePathNames(ArrayImageCell) - Method in class edu.jhu.tmaj.client.image.ArrayImagePanel

Sets a new path for the image, and then reloads the image

setIndex(int) - Method in class edu.jhu.tmaj.client.specimens.SpecimenSingleInputPanel

setIndex(String) - Method in class edu.jhu.tmaj.client.tables.DoubleTabbedPane

Sets the selected pane for this DoubleTabbedPane.

setIndex(int) - Method in class edu.jhu.tmaj.client.tables.SingleInputPanel

setInputMask(Mask) - Method in class edu.jhu.tmaj.beans.masks.filter.FilterMask

setIntegerField(DatabaseField, Integer) - Method in class edu.jhu.tmaj.beans.JBean

Sets a field of type TFieldType.INTEGER

setIntegerStat(MaskStats.StatName, Integer) - Method in class edu.jhu.tmaj.beans.masks.results.MaskStats

setIsAllIncludedInDefault(boolean) - Method in class edu.jhu.tmaj.beans.masks.lasso.LassoMask

setIsBad(boolean) - Method in class edu.jhu.tmaj.client.image.data.ArrayImageCell

Sets whether this ArrayImage has an image worth viewing.

setIsCompleted(boolean) - Method in class edu.jhu.tmaj.client.image.draw.AbstractDrawable

Sets whether the user has finished drawing the shape

setIsCompleted(boolean) - Method in interface edu.jhu.tmaj.client.image.draw.Drawable

setIsFinal(boolean) - Method in class edu.jhu.tmaj.beans.SessionBean

setIsGenericShape(boolean) - Method in class edu.jhu.tmaj.beans.masks.lasso.LassoedFile

setIsHighlighted(boolean) - Method in class edu.jhu.tmaj.client.image.draw.AbstractDrawable

setIsHighlighted(boolean) - Method in interface edu.jhu.tmaj.client.image.draw.Drawable

setIsOn(boolean) - Method in class edu.jhu.tmaj.client.image.data.ResizableTableComponentListener

Sets whether this listener will take action when the window is resized.

setIsPublished(boolean) - Method in class edu.jhu.tmaj.beans.SessionBean

setIterationCount(int) - Method in class edu.jhu.tmaj.beans.masks.filter.FilterMask

setKey(Preference, String) - Static method in class edu.jhu.tmaj.util.config.data.PreferencesUtil

setKeySet(int, Set<Integer>, boolean) - Method in class edu.jhu.tmaj.beans.manytomany.ManyToManyBean

setLabelMessage(String, boolean) - Method in class edu.jhu.tmaj.client.importer.images.ArrayImagesImportGui2

setLasso(Lasso) - Method in class edu.jhu.tmaj.beans.masks.lasso.LassoedFile

setLassoMaskID(Integer) - Method in class edu.jhu.tmaj.beans.masks.lasso.LassoMask

setLookAndFeel() - Static method in class edu.jhu.tmaj.client.shared.MainApplicationGUI

setMaximumParticleSize(int) - Method in class edu.jhu.tmaj.beans.masks.filter.FilterMask

setMaximumParticleSizeFilterOn(boolean) - Method in class edu.jhu.tmaj.beans.masks.filter.FilterMask

setMeasurement(int, boolean) - Static method in class edu.jhu.tmaj.beans.masks.results.Analyzer2

Sets the specified system-wide measurement option.

setMeasurements(int) - Static method in class edu.jhu.tmaj.beans.masks.results.Analyzer2

Sets the system-wide measurement options.

setMessage(String) - Method in class edu.jhu.tmaj.client.frida.gui.shared.MessageLabel

setMessage(String) - Method in class edu.jhu.tmaj.client.frida.gui.shared.ProgressLabel

setMinimumParticleSize(int) - Method in class edu.jhu.tmaj.beans.masks.filter.FilterMask

setMinimumParticleSizeFilterOn(boolean) - Method in class edu.jhu.tmaj.beans.masks.filter.FilterMask

setName(String) - Method in class edu.jhu.tmaj.beans.exfile.ExternalFolder

setName(String) - Method in class edu.jhu.tmaj.beans.masks.AbstractMask

setName(String) - Method in interface edu.jhu.tmaj.beans.masks.Mask

setNavigator(Navigator) - Method in class edu.jhu.tmaj.client.image.data.SessionGuis

setNormalComponentViewable(boolean) - Method in class edu.jhu.tmaj.client.tables.HoldPanel

setNotes(String) - Method in class edu.jhu.tmaj.beans.IASessionBean

setNotes(String) - Method in class edu.jhu.tmaj.beans.SessionBean

setObjectSelected(Object, boolean) - Method in class edu.jhu.tmaj.client.image.SpecialTree

setOption(String, boolean) - Static method in class edu.jhu.tmaj.beans.masks.results.Analyzer2

setOptions(GenericDialog) - Method in class edu.jhu.tmaj.beans.masks.results.Analyzer2

setOriginalDataList(List) - Method in class edu.jhu.tmaj.client.tables.SortFilterDialog

Sets the data list that contains all rows, which is displayed initially and when the user removes the filter and sort.

setOtherScored(boolean) - Method in class edu.jhu.tmaj.client.image.data.ScoreData

setPanelToIndex(int) - Method in interface edu.jhu.tmaj.client.shared.IndexablePanel

setPassword(String) - Method in class edu.jhu.tmaj.beans.UserBean

Sets the digested password of this UserBean.

setPopupWidth(int) - Method in class edu.jhu.tmaj.client.image.data.SteppedComboBox

Sets the width of the popup frame that is displayed when the user clicks on the ComboBox.

setPrecision(int) - Static method in class edu.jhu.tmaj.beans.masks.results.Analyzer2

Sets the number of digits displayed to the right of decimal point.

setPrimaryMaskAsFirstRow(Mask) - Method in class edu.jhu.tmaj.client.frida.gui.shared.MaskRepresentationPanel

setProgressValue(int) - Method in class edu.jhu.tmaj.util.swing.PublicSwingWorker

setProjectID(Integer) - Method in class edu.jhu.tmaj.beans.IASessionBean

setRange(int, int) - Method in class edu.jhu.tmaj.beans.masks.color.CircleRange

setRange(CircleRange) - Method in class edu.jhu.tmaj.beans.masks.color.CircleRange

setRange(CircleRange, SimpleRange, SimpleRange) - Method in class edu.jhu.tmaj.beans.masks.color.HsbRange

Sets this range to an absolute value.

setRange(HsbRange) - Method in class edu.jhu.tmaj.beans.masks.color.HsbRange

setRange(SimpleRange) - Method in class edu.jhu.tmaj.beans.masks.color.SimpleRange

setRange(HsbRange) - Method in class edu.jhu.tmaj.client.frida.gui.masks.color.HsbRangeComponent

setRecordDoesExist(int) - Method in class edu.jhu.tmaj.client.importer.specimens.data.TranslatedTable

setRecordDoesNotExist() - Method in class edu.jhu.tmaj.client.importer.specimens.data.TranslatedTable

setRedirectImage(ImagePlus) - Static method in class edu.jhu.tmaj.beans.masks.results.Analyzer2

setReducedFont(Component) - Static method in class edu.jhu.tmaj.client.tables.InputPanel4

setResultsTable(ResultsTable) - Static method in class edu.jhu.tmaj.beans.masks.results.Analyzer2

setReverseEnabled(boolean) - Method in class edu.jhu.tmaj.client.admin.ManyToManyPanel

setRow(int, List<T>) - Method in interface edu.jhu.tmaj.util.file.TableArray

setRow(int, List<T>) - Method in class edu.jhu.tmaj.util.file.TableArrayImpl

setRowHeight(int) - Method in class edu.jhu.tmaj.client.image.data.HeaderTableScrollPane

setRowHeight(int) - Method in class edu.jhu.tmaj.client.image.data.RowHeaderList

setRows(List<List<T>>) - Method in interface edu.jhu.tmaj.util.file.TableArray

setRows(List<List<T>>) - Method in class edu.jhu.tmaj.util.file.TableArrayImpl

setScanID(Integer) - Method in class edu.jhu.tmaj.beans.IASessionBean

setScoreData(ScoreData) - Method in class edu.jhu.tmaj.client.image.data.ArrayImageCell

setScoringStrategyID(Integer) - Method in class edu.jhu.tmaj.beans.SessionBean

setSelected(boolean) - Method in class edu.jhu.tmaj.client.arraybuilder.data.ArrayCoreCell

setSession(SessionBean) - Method in class edu.jhu.tmaj.client.image.DotTableFrame

setSessionDescription(String) - Method in class edu.jhu.tmaj.beans.IASessionBean

setSessionDescription(String) - Method in class edu.jhu.tmaj.beans.SessionBean

setShapeID(int) - Method in class edu.jhu.tmaj.client.image.draw.AbstractDrawable

Sets the unique ShapeID of this shape in the database table Shapes

setShapeID(int) - Method in interface edu.jhu.tmaj.client.image.draw.Drawable

setSharedOut(boolean) - Method in class edu.jhu.tmaj.beans.SessionBean

setShowDetails(CellView) - Method in class edu.jhu.tmaj.client.arraybuilder.ArrayBuilderTable

setSize(ImageSize) - Method in class edu.jhu.tmaj.client.image.ArrayImagePanel

Sets a new size, and then reloads the image

setSpecifiedArrayImagesList(List<ArrayImageCell>) - Method in class edu.jhu.tmaj.client.image.data.Navigator

setStatus(DrawableStatus) - Method in class edu.jhu.tmaj.client.image.draw.AbstractDrawable

setStatus(DrawableStatus) - Method in interface edu.jhu.tmaj.client.image.draw.Drawable

setStringField(DatabaseField, String) - Method in class edu.jhu.tmaj.beans.JBean

Sets a field of type TFieldType.STRING

setTableModelFromData(GeneralTableModel) - Method in class edu.jhu.tmaj.servlet.response.impl.SessionDescriptionsResponse

setThresholdLevels(ImagePlus, ImageProcessor) - Method in class edu.jhu.tmaj.beans.masks.results.ParticleAnalyzer2

setTissueDiagnosisID(int) - Method in class edu.jhu.tmaj.beans.misc.ArrayCoreRep

Changes the TissueDiagnosisID where this ArrayCore came from.

setTitle(String) - Method in class edu.jhu.tmaj.client.image.DotTableFrame

setToCommaDelimitedString(Set) - Static method in class edu.jhu.tmaj.util.ListConvertUtil

setTool(LimitedToolBar.ImageTool) - Method in class edu.jhu.tmaj.client.frida.gui.shared.LimitedToolBar

setTyped(boolean) - Method in class edu.jhu.tmaj.client.image.data.ScoreData

setTypeID(int) - Method in class edu.jhu.tmaj.beans.dynamic.DynamicJBean

Sets the Type of this DynamicBean.

setUnsavedMeasurements(boolean) - Static method in class edu.jhu.tmaj.beans.masks.results.Analyzer2

setup(String, ImagePlus) - Method in class edu.jhu.tmaj.beans.masks.results.Analyzer2

setup(String, ImagePlus) - Method in class edu.jhu.tmaj.beans.masks.results.ParticleAnalyzer2

setupTableModel(GeneralTableModel, int[], Component) - Static method in class edu.jhu.tmaj.client.image.DotTableFrame

Sets the data in a tableModel to include detailed information about the specified sessions.

setUseColors(boolean) - Method in class edu.jhu.tmaj.client.arraybuilder.data.ArrayCoreRenderer

setUseHardLinks(boolean) - Method in class edu.jhu.tmaj.client.image.data.ImageAppGuis

setUserBean(UserBean) - Method in class edu.jhu.tmaj.beans.JBean

Sets the User who is reading and writing information to this bean.

setUserBean(UserBean) - Static method in class edu.jhu.tmaj.client.shared.CurrentUser

setUserID(Integer) - Method in class edu.jhu.tmaj.beans.IASessionBean

setUserID(int) - Method in class edu.jhu.tmaj.client.image.draw.AbstractDrawable

setUserID(int) - Method in interface edu.jhu.tmaj.client.image.draw.Drawable

Used only for setting the InputLog in the shapes table

setUsername(String) - Method in class edu.jhu.tmaj.beans.UserBean

setUseThumbnails(boolean) - Method in class edu.jhu.tmaj.client.image.data.ArrayImageRenderer

SetUtil - Class in edu.jhu.tmaj.util

SetUtil() - Constructor for class edu.jhu.tmaj.util.SetUtil

setValue(int) - Method in class edu.jhu.tmaj.client.frida.gui.masks.color.FullSlider

Sets the current value of the Slider

setValue(int) - Method in class edu.jhu.tmaj.client.frida.gui.shared.ProgressLabel

setValueAt(Object, int, int) - Method in class edu.jhu.tmaj.client.tables.data.GeneralTableModel

setVisible(boolean) - Method in class edu.jhu.tmaj.client.image.DotTableFrame

setVisible(boolean) - Method in class edu.jhu.tmaj.client.importer.machscores.MachineScoresInputDialog

setXYPanelEnabled(boolean) - Method in class edu.jhu.tmaj.client.image.ArrayImageFrame

shapeID - Variable in class edu.jhu.tmaj.client.image.draw.ShapeRecord

ShapeListener - Class in edu.jhu.tmaj.client.image.draw

Added to a DrawableLabel, this listener class processes mouseEvents and keyEvents and uses them to either create new shapes, select selects, or forward the mouseEvent or keyEvent to the currently selected shape.

ShapeListener(DrawableLabel, List, ShapesFrame) - Constructor for class edu.jhu.tmaj.client.image.draw.ShapeListener

ShapeRecord - Class in edu.jhu.tmaj.client.image.draw

Represents a record in the Shapes database table.

ShapeRecord() - Constructor for class edu.jhu.tmaj.client.image.draw.ShapeRecord

shapesFrame - Variable in class edu.jhu.tmaj.client.image.ArrayImageFrame

ShapesFrame - Class in edu.jhu.tmaj.client.image.draw

A window that allows the user to select a shape(arrows,rectangles,etc) for drawing, as well as a default option for selecting existing shapes.

ShapesFrame(DrawableLabel) - Constructor for class edu.jhu.tmaj.client.image.draw.ShapesFrame

ShapesLoadRequest - Class in edu.jhu.tmaj.servlet.request.impl

Returns Shapes associated with a specified arrayImageID and SessionID

ShapesLoadRequest(int) - Constructor for class edu.jhu.tmaj.servlet.request.impl.ShapesLoadRequest

ShapesLoadResponse - Class in edu.jhu.tmaj.servlet.response.impl

Contains a List of ShapeRecords that will be displayed on an ArrayImage for the user.

ShapesLoadResponse(List<ShapeRecord>) - Constructor for class edu.jhu.tmaj.servlet.response.impl.ShapesLoadResponse

ShapesQuery - Class in edu.jhu.tmaj.servlet.request.impl

Add data from the shapes table to the supplied expandingMap.

ShapesQuery(ExpandingMap, String) - Constructor for class edu.jhu.tmaj.servlet.request.impl.ShapesQuery

ShapesSaveRequest - Class in edu.jhu.tmaj.servlet.request.impl

Saves shapes to a specified scoredImageID.

ShapesSaveRequest(List, int) - Constructor for class edu.jhu.tmaj.servlet.request.impl.ShapesSaveRequest

ShapesSaveResponse - Class in edu.jhu.tmaj.servlet.response.impl

Contains a List of Drawables

ShapesSaveResponse(List<Drawable>) - Constructor for class edu.jhu.tmaj.servlet.response.impl.ShapesSaveResponse

SharedNodes - Class in edu.jhu.tmaj.client.image.data

Contains helper methods for generating the Shared Sessions Tree Structure in the Project Frame.

SharedNodes() - Constructor for class edu.jhu.tmaj.client.image.data.SharedNodes

ShareSessionDialog - Class in edu.jhu.tmaj.client.image

A GUI that allows users to share their sessions with other users.

SHORT - Static variable in class edu.jhu.tmaj.beans.masks.results.ParticleAnalyzer2

SHORT_DESCRIPTION_FIELD - Static variable in class edu.jhu.tmaj.beans.MachineSessionBean

SHORT_DESCRIPTION_FIELD - Static variable in class edu.jhu.tmaj.beans.ScanBean

SHORT_TITLE_FIELD - Static variable in class edu.jhu.tmaj.beans.PaperBean

ShortenedFile - Class in edu.jhu.tmaj.client.importer.data

A File whose toString() method only returned the file name and not the entire path.

ShortenedFile(File) - Constructor for class edu.jhu.tmaj.client.importer.data.ShortenedFile

SHOULD_DISPLAY_PATIENTS_TAB - Static variable in class edu.jhu.tmaj.client.specimens.SpecimensAppGUI

shouldDisplayInputLogColumn() - Method in class edu.jhu.tmaj.client.image.TopMenu

shouldPointActivate(int, int) - Method in interface edu.jhu.tmaj.client.image.draw.Drawable

Returns true if the x and y are close enough to the border of the shape to "Select" the shape

shouldPointActivate(int, int) - Method in class edu.jhu.tmaj.client.image.draw.FreeHandDrawable

shouldPointActivate(int, int) - Method in class edu.jhu.tmaj.client.image.draw.LineDrawable

shouldPointActivate(int, int) - Method in class edu.jhu.tmaj.client.image.draw.OvalDrawable

shouldPointActivate(int, int, Rectangle) - Static method in class edu.jhu.tmaj.client.image.draw.OvalDrawableHelper

shouldPointActivate(int, int) - Method in class edu.jhu.tmaj.client.image.draw.PolygonDrawable

shouldPointActivate(int, int) - Method in class edu.jhu.tmaj.client.image.draw.RectangleDrawable

shouldPointActivate(int, int) - Method in class edu.jhu.tmaj.client.image.draw.TextDrawable

show(JTable, GeneralTableModel, Component) - Static method in class edu.jhu.tmaj.client.tables.HideColumnsDialog

SHOW_MASKS - Static variable in class edu.jhu.tmaj.beans.masks.results.ParticleAnalyzer2

Display image containing binary masks of measured particles.

SHOW_NONE - Static variable in class edu.jhu.tmaj.beans.masks.results.ParticleAnalyzer2

Do not display particle outline image.

SHOW_OUTLINES - Static variable in class edu.jhu.tmaj.beans.masks.results.ParticleAnalyzer2

Display image containing outlines of measured particles.

SHOW_PROGRESS - Static variable in class edu.jhu.tmaj.beans.masks.results.ParticleAnalyzer2

Display a progress bar.

SHOW_RESULTS - Static variable in class edu.jhu.tmaj.beans.masks.results.ParticleAnalyzer2

Display results in the ImageJ console.

SHOW_ROI_MASKS - Static variable in class edu.jhu.tmaj.beans.masks.results.ParticleAnalyzer2

Display image containing grayscales masks that identify measured particles.

SHOW_SUMMARY - Static variable in class edu.jhu.tmaj.beans.masks.results.ParticleAnalyzer2

Obsolete

showAddDialog(Component, DefinedMasksGui) - Static method in class edu.jhu.tmaj.client.frida.gui.AddMaskDialog

Displays a dialog that lets users add a NEW mask.

showChoice - Static variable in class edu.jhu.tmaj.beans.masks.results.ParticleAnalyzer2

showDebugParticleStats(ImagePlus, boolean[], double, double) - Static method in class edu.jhu.tmaj.beans.masks.results.ParticleStatsUtil

showDialog() - Method in class edu.jhu.tmaj.beans.masks.results.ParticleAnalyzer2

Displays a modal options dialog.

showDialog() - Method in class edu.jhu.tmaj.client.image.AddUserDialog

showDialog(SessionBean, Component) - Static method in class edu.jhu.tmaj.client.image.CopySessionDialog

showDialog(Frame) - Static method in class edu.jhu.tmaj.client.image.PapersDialog

showDialog(Frame) - Static method in class edu.jhu.tmaj.client.shared.AboutDialog

showDialog(int[], Frame) - Static method in class edu.jhu.tmaj.client.specimens.AssignSpecimensDialog

showDialog() - Method in class edu.jhu.tmaj.client.tables.DetachableIndicesDialog

showEditDialog(Component, DefinedMasksGui, Mask) - Static method in class edu.jhu.tmaj.client.frida.gui.AddMaskDialog

Displays a dialog that lets the user change only the mask-name (not the mask-type) of an EXISTING mask.

showError(String, Component) - Static method in class edu.jhu.tmaj.util.swing.DialogUtil

Displays an error message

showErrorDialog(String) - Method in class edu.jhu.tmaj.client.importer.images.ArrayImagesImportGui2

showErrorDialog(String, String) - Method in class edu.jhu.tmaj.client.importer.images.ArrayImagesImportGui2

showException(Throwable, String, Component) - Static method in class edu.jhu.tmaj.util.swing.DialogUtil

showFrame() - Static method in class edu.jhu.tmaj.client.admin.AdminGUI

showFrame() - Static method in class edu.jhu.tmaj.client.admin.MetaDataAppGUI

showFrame() - Static method in class edu.jhu.tmaj.client.arraybuilder.ArrayBuilderGUI

Display the ArrayBuilder Application.

showFrame() - Static method in class edu.jhu.tmaj.client.arrays.ArrayManagerAppGUI

Show the ArrayManager application.

showFrame() - Static method in class edu.jhu.tmaj.client.image.ProjectsGUI

showFrame() - Static method in class edu.jhu.tmaj.client.importer.ImportAppGUI

Create and show the import Application.

showFrame() - Static method in class edu.jhu.tmaj.client.samples.SamplesAppGUI

showFrame() - Static method in class edu.jhu.tmaj.client.specimens.AnimalExperimentsFrame

showFrame() - Static method in class edu.jhu.tmaj.client.specimens.BlockOrSlideExchangesFrame

showFrame() - Static method in class edu.jhu.tmaj.client.specimens.CellLinesFrame

showFrame() - Static method in class edu.jhu.tmaj.client.specimens.SpecimensAppGUI

ShowFrameMouseListener - Class in edu.jhu.tmaj.client.tables.data

Added to a component, this class will display a frame when the user right clicks on the component.

ShowFrameMouseListener(JFrame) - Constructor for class edu.jhu.tmaj.client.tables.data.ShowFrameMouseListener

showHelpDialog(String, Frame) - Static method in class edu.jhu.tmaj.client.shared.HelpDialog

showInformation(String, Component) - Static method in class edu.jhu.tmaj.util.swing.DialogUtil

Displays an information message

showLookupDialog(Frame) - Static method in class edu.jhu.tmaj.client.arraybuilder.ExpressEntryDialog

Displays this dialog and returns a TissueDiagnosisID.

showMessage(String) - Method in class edu.jhu.tmaj.client.image.DownloadImagesPanel

showMessage(String) - Method in class edu.jhu.tmaj.client.importer.images.ArrayImagesImportGui2

showMessageDialog(String) - Method in class edu.jhu.tmaj.client.importer.images.ArrayImagesImportGui2

showMessageDialog(String, String) - Method in class edu.jhu.tmaj.client.importer.images.ArrayImagesImportGui2

showProgress - Variable in class edu.jhu.tmaj.beans.masks.results.ParticleAnalyzer2

showResults - Variable in class edu.jhu.tmaj.beans.masks.results.ParticleAnalyzer2

showResults() - Method in class edu.jhu.tmaj.beans.masks.results.ParticleAnalyzer2

showSizeDistribution - Variable in class edu.jhu.tmaj.beans.masks.results.ParticleAnalyzer2

showURLDialog(URL, String, String, Frame) - Static method in class edu.jhu.tmaj.client.shared.UrlDialog

showWarning(String, Component) - Static method in class edu.jhu.tmaj.util.swing.DialogUtil

Displays a warning message

showWarningDialog(String, String) - Method in class edu.jhu.tmaj.client.importer.images.ArrayImagesImportGui2

shrinkButton(JComponent) - Static method in class edu.jhu.tmaj.client.tables.InputPanel4

Shrinks a JButton by lessening its font and margin in the interests of saving space.

shrinkFont(JComponent) - Static method in class edu.jhu.tmaj.client.tables.SortFilterDialog

SimpleProgressDialog - Class in edu.jhu.tmaj.client.shared

This class is used to display a dialog containing an indeterminate ProgressBar.

SimpleProgressDialog(String, Component) - Constructor for class edu.jhu.tmaj.client.shared.SimpleProgressDialog

SimpleRange - Class in edu.jhu.tmaj.beans.masks.color

Represents a range of values no smaller than MIN, and no larger than MAX.

singleCheckBox - Variable in class edu.jhu.tmaj.client.tables.InputPanel4

SingleInputPanel - Class in edu.jhu.tmaj.client.tables

Similar to a normal InputPanel except that the data for one row is displayed on the entire screen.

SingleInputPanel(JTable, GeneralTableModel, JScrollPane) - Constructor for class edu.jhu.tmaj.client.tables.SingleInputPanel

singleTableModel - Variable in class edu.jhu.tmaj.client.tables.SingleInputPanel

size() - Method in class edu.jhu.tmaj.client.image.data.FastCollection

Size - Class in edu.jhu.tmaj.client.image.data

Represents height and width

Size(int, int) - Constructor for class edu.jhu.tmaj.client.image.data.Size

SIZE_OF_POINTS_LIST_FIELD - Static variable in class edu.jhu.tmaj.client.image.draw.PolygonDrawable

sizeButton - Variable in class edu.jhu.tmaj.client.image.ArrayImageFrame

SizeParameters - Class in edu.jhu.tmaj.client.importer.images.data

SizeParameters(SizeParameters.OneSizeParameters, SizeParameters.OneSizeParameters, SizeParameters.OneSizeParameters) - Constructor for class edu.jhu.tmaj.client.importer.images.data.SizeParameters

SizeParameters.OneSizeParameters - Class in edu.jhu.tmaj.client.importer.images.data

SizeParameters.OneSizeParameters(double, int) - Constructor for class edu.jhu.tmaj.client.importer.images.data.SizeParameters.OneSizeParameters

SizeParametersGui - Class in edu.jhu.tmaj.client.importer.images

SizeParametersGui(Component) - Constructor for class edu.jhu.tmaj.client.importer.images.SizeParametersGui

slice - Variable in class edu.jhu.tmaj.beans.masks.results.ParticleAnalyzer2

SLIDE_FIXATION_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.BlockUsageAltBean

SLIDE_TYPE_FIELD - Static variable in class edu.jhu.tmaj.beans.SlideBean

SlideBean - Class in edu.jhu.tmaj.beans

Represents the Slides table.

SlideBean(StaticMetaData) - Constructor for class edu.jhu.tmaj.beans.SlideBean

SLIDES_PANEL_NAME - Static variable in class edu.jhu.tmaj.client.specimens.SpecimensAppGUI

SMALL_SIZE_FILE_ID - Static variable in class edu.jhu.tmaj.beans.ArrayImageBean

smallParameters - Variable in class edu.jhu.tmaj.client.importer.images.data.SizeParameters

SortFilterDialog - Class in edu.jhu.tmaj.client.tables

A Frame that allows the sorting rows in a JTable (based upon TableComparitor) and the filtering of rows based upon user input.

SortFilterDialog(JTable, GeneralTableModel, JScrollPane, TableData4) - Constructor for class edu.jhu.tmaj.client.tables.SortFilterDialog

SortFilterMouseListener - Class in edu.jhu.tmaj.client.tables.data

Added to a JTable, this MouseListener listens for a right mouse click and then displays a SortFilter Frame.

SortFilterMouseListener(SortFilterDialog, JTable, Component) - Constructor for class edu.jhu.tmaj.client.tables.data.SortFilterMouseListener

sortListOfMaps(List<Map>) - Method in class edu.jhu.tmaj.servlet.request.impl.ArrayCoreDetailsRequest

Sorts the List by Y then by X

sortListOfMaps(List<Map>) - Method in class edu.jhu.tmaj.servlet.request.impl.DetailsRequest

Sorts the final List, usually by rowIdentifiers.

sortListOfMaps(List<Map>) - Method in class edu.jhu.tmaj.servlet.request.impl.ScoredImageDetailsRequest

Sorts a List of Maps by the sessionid,y,x fields found in each of the Maps

source - Variable in enum edu.jhu.tmaj.client.importer.machscores.MachineScoreField

SOURCE_FIELD - Static variable in class edu.jhu.tmaj.beans.ArrayBlockBean

SOURCE_FIELD - Static variable in class edu.jhu.tmaj.beans.ProjectBean

sourceScoredImageID - Variable in class edu.jhu.tmaj.servlet.request.impl.ScoredImageInsert

SpecialTree - Class in edu.jhu.tmaj.client.image

SpecialTree(Object) - Constructor for class edu.jhu.tmaj.client.image.SpecialTree

SPECIES_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.CellLineBean

SPECIMEN_APP_FIELD - Static variable in class edu.jhu.tmaj.beans.UserBean

SPECIMEN_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.BlockBean

SPECIMEN_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.BloodSampleBean

SPECIMEN_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.CellLineExperimentBean

SPECIMEN_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.TissueSampleBean

SPECIMEN_LIST_FIELD - Static variable in class edu.jhu.tmaj.beans.dynamic.SpecimenBean

SPECIMEN_PANEL_NAME - Static variable in class edu.jhu.tmaj.client.samples.SamplesAppGUI

SPECIMEN_PANEL_NAME - Static variable in class edu.jhu.tmaj.client.specimens.SpecimensAppGUI

SPECIMEN_TYPE_FIELD - Static variable in class edu.jhu.tmaj.servlet.request.impl.ScoredImageDetailsRequest

SPECIMEN_TYPE_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.dynamic.SpecimenBean

SpecimenBean - Class in edu.jhu.tmaj.beans.dynamic

Represents the Specimens table, with the accompaning dynamic table, SpecimenData.

SpecimenBean(StaticMetaData, DynamicMetaData) - Constructor for class edu.jhu.tmaj.beans.dynamic.SpecimenBean

SPECIMENID_FIELD - Static variable in class edu.jhu.tmaj.beans.CellLineBean

SPECIMENID_FIELD - Static variable in class edu.jhu.tmaj.servlet.request.impl.ScoredImageDetailsRequest

SpecimenIdentifiersRequest - Class in edu.jhu.tmaj.servlet.request.impl

Gets information that can be used to uniquely identify a specimen or patient record, for example the Hospital and the SurgPathNumber.

SpecimenIdentifiersRequest() - Constructor for class edu.jhu.tmaj.servlet.request.impl.SpecimenIdentifiersRequest

SpecimenIdentifiersResponse - Class in edu.jhu.tmaj.servlet.response.impl

Contain two Maps that help identify if a specimen or patient is in the database.

SpecimenIdentifiersResponse(Map<RecordIdentifier, Integer>, Map<RecordIdentifier, Integer>) - Constructor for class edu.jhu.tmaj.servlet.response.impl.SpecimenIdentifiersResponse

SpecimenInfoDisplay - Class in edu.jhu.tmaj.client.specimens

SpecimenInfoDisplay(SurgPathNumberRequest.TableType, JTable) - Constructor for class edu.jhu.tmaj.client.specimens.SpecimenInfoDisplay

SpecimenInputPanel - Class in edu.jhu.tmaj.client.specimens

An InputPanel for entering detailed specimen information

SpecimenInputPanel(TableData4) - Constructor for class edu.jhu.tmaj.client.specimens.SpecimenInputPanel

specimenInputPanel - Variable in class edu.jhu.tmaj.client.specimens.SpecimensAppGUI

SpecimensAppGUI - Class in edu.jhu.tmaj.client.specimens

Main class for the Specimens application.

SpecimensAppPermission - Enum in edu.jhu.tmaj.beans.data

The permission level a user has for the Specimens Application.

SpecimensAssignRequest - Class in edu.jhu.tmaj.servlet.request.impl

A Request that assigns specimens to a user so that the user may access them.

SpecimensAssignRequest(int, int[]) - Constructor for class edu.jhu.tmaj.servlet.request.impl.SpecimensAssignRequest

SpecimenSingleInputPanel - Class in edu.jhu.tmaj.client.specimens

A SingleInputPanel for the Specimens table that displays only one specimen at a time, and includes JTextAreas for the lengthy GrossDescription and Diagnosis fields.

SpecimenSingleInputPanel(JTable, GeneralTableModel, JScrollPane) - Constructor for class edu.jhu.tmaj.client.specimens.SpecimenSingleInputPanel

SpecimenTranslatedTable - Class in edu.jhu.tmaj.client.importer.specimens.data

A Specimens record from a tab-delimited file that is ready to be written to the database.

SpecimenTranslatedTable(MetaDataConverter) - Constructor for class edu.jhu.tmaj.client.importer.specimens.data.SpecimenTranslatedTable

specimenTranslatedTable - Variable in class edu.jhu.tmaj.client.importer.specimens.data.TranslatedRow

split(String, String) - Static method in class edu.jhu.tmaj.util.file.StringUtil

SpringUtilities - Class in edu.jhu.tmaj.util.swing

A 1.4 file that provides utility methods for creating form- or grid-style layouts with SpringLayout.

SpringUtilities() - Constructor for class edu.jhu.tmaj.util.swing.SpringUtilities

SQL - Interface in edu.jhu.tmaj.database.sql

Represents a INSERT,UPDATE, or SELECT SQL statement.

SqlFormatter - Class in edu.jhu.tmaj.beans.data

SQLMaker - Interface in edu.jhu.tmaj.database.sql

Turns SQL objects into database-ready sql.

SQLMakerGetter - Class in edu.jhu.tmaj.database.sql

A utility class that returns a SQLMaker given a proper database type (such as Oracle).

SQLServerConnectionFactory - Class in edu.jhu.tmaj.database.conn

A ConnectionFactory to a Microsoft SQLServer database.

SQLServerConnectionFactory(DatabaseParameters) - Constructor for class edu.jhu.tmaj.database.conn.SQLServerConnectionFactory

SQLValues - Class in edu.jhu.tmaj.database.sql

The fields and the values in an INSERT or UPDATE SQL statement.

SQLValues() - Constructor for class edu.jhu.tmaj.database.sql.SQLValues

stain - Variable in class edu.jhu.tmaj.client.importer.images.data.FilenameData

STAIN_FIELD - Static variable in class edu.jhu.tmaj.beans.ArraySlideBean

STAIN_FIELD - Static variable in class edu.jhu.tmaj.beans.SlideBean

STAINING_USER_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.ArraySlideBean

StandardImageOutputParser - Class in edu.jhu.tmaj.client.importer.data

The standard ImageOutputParser; ideally all image scanning systems would give us their image filenames in this format.

StandardImageOutputParser() - Constructor for class edu.jhu.tmaj.client.importer.data.StandardImageOutputParser

StandardizedCellEditor - Class in edu.jhu.tmaj.client.tables.data

This cell editor has the same functionality as the Sun JTable default editors, but enforces a standard font and size across Look & Feel UI types.

StandardizedCellEditor(int) - Constructor for class edu.jhu.tmaj.client.tables.data.StandardizedCellEditor

Constructs a standardized cell editor with an alignment key from JTextField, such as: JTextField.LEFT JTextField.RIGHT JTextField.CENTER JTextField.LEADING JTextField.TRAILING

start() - Method in class edu.jhu.tmaj.util.TextProgressMonitor

Indicate to user task has begun.

START_DATE_FIELD - Static variable in class edu.jhu.tmaj.beans.AnimalExperimentBean

STARTING_NUMBER_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.BlockUsageAltBean

startTaskAndShowDialog() - Method in class edu.jhu.tmaj.client.shared.SimpleProgressDialog

stateChanged(ChangeEvent) - Method in class edu.jhu.tmaj.client.tables.TabChangeListener

Called when one of the user click one of the tabs of the sub-tabbedPanes, this will change the title of the main-tabbedPane.

StaticDestination - Class in edu.jhu.tmaj.client.importer.specimens.data

A table and a fieldname for the import.

StaticDestination(StaticDestination.DestinationTable, String) - Constructor for class edu.jhu.tmaj.client.importer.specimens.data.StaticDestination

StaticDestination.DestinationTable - Enum in edu.jhu.tmaj.client.importer.specimens.data

Either Patients or Specimens.

StaticEnumeration - Class in edu.jhu.tmaj.beans.data

Represent a record in a static Lookup table.

StaticEnumeration(int, String) - Constructor for class edu.jhu.tmaj.beans.data.StaticEnumeration

Initializes this class.

StaticFields - Class in edu.jhu.tmaj.client.image.data

StaticFields() - Constructor for class edu.jhu.tmaj.client.image.data.StaticFields

StaticMetaData - Class in edu.jhu.tmaj.beans.data

Contains information about standard (non-dynamic) "Lookup" tables for an InputPanel.

StaticMetaData() - Constructor for class edu.jhu.tmaj.beans.data.StaticMetaData

staticMetaData - Variable in class edu.jhu.tmaj.beans.JBean

Status - Class in edu.jhu.tmaj.util.data

Represents the status of a process, indicating where an error has occured, and if so, what is the error.

Status(boolean, String) - Constructor for class edu.jhu.tmaj.util.data.Status

STATUS_FIELD - Static variable in class edu.jhu.tmaj.beans.ArrayBlockBean

statusLabel - Variable in class edu.jhu.tmaj.client.importer.images.ArrayImagesImportGui2

SteppedComboBox - Class in edu.jhu.tmaj.client.image.data

A ComboBox that allows the popup dialog to be wider than the actual ComboBox.

SteppedComboBox(List) - Constructor for class edu.jhu.tmaj.client.image.data.SteppedComboBox

SteppedComboBoxUI - Class in edu.jhu.tmaj.client.image.data

The UI for a SteppedComboBox.

SteppedComboBoxUI() - Constructor for class edu.jhu.tmaj.client.image.data.SteppedComboBoxUI

stopCellEditing() - Method in class edu.jhu.tmaj.client.tables.data.StandardizedCellEditor

stopCellEditting(JTable) - Static method in class edu.jhu.tmaj.client.tables.data.TableData4

Stop Table editting, such that if a user is editting a cell, the value typed-in in stored in the TableModel.

StopWatch - Class in edu.jhu.tmaj.util

Class provides methods that allow tasks to be timed.

StopWatch() - Constructor for class edu.jhu.tmaj.util.StopWatch

STORAGE_CONDITION_FIELD - Static variable in class edu.jhu.tmaj.beans.BloodSampleBean

STORAGE_CONDITION_FIELD - Static variable in class edu.jhu.tmaj.beans.TissueSampleBean

STORAGE_LOCATION_FIELD - Static variable in class edu.jhu.tmaj.beans.BloodSampleBean

STORAGE_LOCATION_FIELD - Static variable in class edu.jhu.tmaj.beans.TissueSampleBean

STORAGE_TEMPERATURE_FIELD - Static variable in class edu.jhu.tmaj.beans.SlideBean

STORAGE_TYPE_FIELD - Static variable in class edu.jhu.tmaj.beans.SlideBean

STORAGE_TYPE_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.BlockUsageAltBean

STRAIN_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.CellLineBean

string1 - Variable in class edu.jhu.tmaj.client.tables.data.TwoStrings

string2 - Variable in class edu.jhu.tmaj.client.tables.data.TwoStrings

stringArrayToString(String[], String) - Static method in class edu.jhu.tmaj.util.ListConvertUtil

Converts an array of Strings one big comma-delimited String.

StringDigest - Class in edu.jhu.tmaj.util.crypt

Utility for digesting strings using a one way hash algorithm

StringDigest() - Constructor for class edu.jhu.tmaj.util.crypt.StringDigest

StringFormatUtils - Class in edu.jhu.tmaj.util

Contains utility methods for formatting Strings.

StringQuoter - Class in edu.jhu.tmaj.util

A Utility class for preparing strings that are put in SQL statements.

StringSet - Class in edu.jhu.tmaj.client.image.data

A Set of case-insensitive Strings.

StringSet(String[]) - Constructor for class edu.jhu.tmaj.client.image.data.StringSet

stringToFloatArray(String) - Static method in class edu.jhu.tmaj.beans.masks.lasso.Lasso

stringToPolygon(String) - Static method in class edu.jhu.tmaj.beans.masks.lasso.Lasso

stringToURL(String) - Static method in class edu.jhu.tmaj.util.URLUtil

Convert a String to a URL without requiring the user to catch the MalformedURL Exception.

StringUtil - Class in edu.jhu.tmaj.util.file

STUDY_NAME_FIELD - Static variable in class edu.jhu.tmaj.beans.BlockOrSlideExchangeBean

SubMap - Class in edu.jhu.tmaj.beans.data

A Map that links a primary key to a map of values for that primary key.

SubMap(Object) - Constructor for class edu.jhu.tmaj.beans.data.SubMap

SubTableSection - Class in edu.jhu.tmaj.client.image.data

SubTableSection(MainTableSection, String) - Constructor for class edu.jhu.tmaj.client.image.data.SubTableSection

SuccessResponse - Class in edu.jhu.tmaj.servlet.response

Every ServerResponse except the ErrorResponse extend this class.

SuccessResponse() - Constructor for class edu.jhu.tmaj.servlet.response.SuccessResponse

summarize() - Method in class edu.jhu.tmaj.beans.masks.results.Analyzer2

summarizeAreas() - Method in class edu.jhu.tmaj.beans.masks.results.Analyzer2

SUPPLIER_FIELD - Static variable in class edu.jhu.tmaj.beans.CellLineBean

SURG_PATH_NUMBER_FIELD - Static variable in class edu.jhu.tmaj.beans.BlockOrSlideExchangeBean

SURG_PATH_NUMBER_FIELD - Static variable in class edu.jhu.tmaj.beans.dynamic.SpecimenBean

SURG_PATH_NUMBER_STRING - Static variable in class edu.jhu.tmaj.beans.dynamic.SpecimenBean

SurgPathNumberRequest - Class in edu.jhu.tmaj.servlet.request.impl

SurgPathNumberRequest(SurgPathNumberRequest.TableType, int) - Constructor for class edu.jhu.tmaj.servlet.request.impl.SurgPathNumberRequest

SurgPathNumberRequest.TableType - Enum in edu.jhu.tmaj.servlet.request.impl

SurgPathNumberResponse - Class in edu.jhu.tmaj.servlet.response.impl

SurgPathNumberResponse(String) - Constructor for class edu.jhu.tmaj.servlet.response.impl.SurgPathNumberResponse

SwingBean - Class in edu.jhu.tmaj.beans2

SwingBean() - Constructor for class edu.jhu.tmaj.beans2.SwingBean

SwingCell - Interface in edu.jhu.tmaj.beans2

The value in a swing cell

SwingColumn - Interface in edu.jhu.tmaj.beans2

SwingColumnType - Enum in edu.jhu.tmaj.beans2

Date, Enumerated, etc

SwingMap - Interface in edu.jhu.tmaj.beans2

This class maps SwingColumns to SwingCells representing one row.

SwingRowConvertable - Interface in edu.jhu.tmaj.beans2

Beans that can be converted into a Swing Table row will implement this class.

SybaseConnectionFactory - Class in edu.jhu.tmaj.database.conn

Generates new connections to a Sybase database.

SybaseConnectionFactory(DatabaseParameters) - Constructor for class edu.jhu.tmaj.database.conn.SybaseConnectionFactory

syncColorMask(ColorMask) - Static method in class edu.jhu.tmaj.beans.masks.color.ColorMaskDatabaseUtil.Writer

syncDatabase(int, Set<Integer>, Set<Integer>, boolean) - Method in class edu.jhu.tmaj.beans.manytomany.ManyToManyBean

Writes the database for the new keys assigned to the individual key.

syncDynamicData() - Method in class edu.jhu.tmaj.beans.dynamic.DynamicJBean

Writes the dynamic data in this bean to the database.

syncFilterMask(FilterMask) - Static method in class edu.jhu.tmaj.beans.masks.filter.FilterMaskDatabaseUtil.Writer

syncLassoMask(LassoMask) - Static method in class edu.jhu.tmaj.beans.masks.lasso.LassoMaskDatabaseUtil.Writer

syncMetaMask(MetaMask) - Static method in class edu.jhu.tmaj.beans.masks.meta.MetaMaskDatabaseUtil.Writer

T

Tab - Class in edu.jhu.tmaj.client.tables

Represents a sub-tab in a DoubleTabbedPane.

Tab(String, Component) - Constructor for class edu.jhu.tmaj.client.tables.Tab

TAB - Static variable in interface edu.jhu.tmaj.util.file.FlatFileSyncer

TabChangeListener - Class in edu.jhu.tmaj.client.tables

Added to a Sub-TabbedPane, this change listener changes the main-TabbedPane's title as indexes on the sub-tabbedPane are selected.

TabChangeListener(JTabbedPane, JTabbedPane, int) - Constructor for class edu.jhu.tmaj.client.tables.TabChangeListener

Constructs this object.

TabGroup - Class in edu.jhu.tmaj.client.tables

Represents a main-tab on a DoubleTabbedPane.

TabGroup(String, List<Tab>) - Constructor for class edu.jhu.tmaj.client.tables.TabGroup

Constructs a TabGroup that has one or more components.

TabGroup(String, Component) - Constructor for class edu.jhu.tmaj.client.tables.TabGroup

Constructs a TabGroup that only has one component

table - Variable in class edu.jhu.tmaj.client.importer.specimens.data.StaticDestination

table - Variable in class edu.jhu.tmaj.client.tables.data.TableData4

table - Variable in class edu.jhu.tmaj.client.tables.InputPanel4

TableArray<C,T> - Interface in edu.jhu.tmaj.util.file

TableArrayImpl<C,T> - Class in edu.jhu.tmaj.util.file

TableArrayImpl() - Constructor for class edu.jhu.tmaj.util.file.TableArrayImpl

TableColumnModelAdapter - Class in edu.jhu.tmaj.client.tables.data

A convenience class that implements a TableColumnModelListener with empty methods

TableColumnModelAdapter() - Constructor for class edu.jhu.tmaj.client.tables.data.TableColumnModelAdapter

TableComparator - Class in edu.jhu.tmaj.client.tables.data

A Comparator that is used to sort rows in a JTable.

TableComparator(int) - Constructor for class edu.jhu.tmaj.client.tables.data.TableComparator

Constructs this object.

tableData - Variable in class edu.jhu.tmaj.client.tables.InputPanel4

TableData4 - Class in edu.jhu.tmaj.client.tables.data

The helper class for the InputPanel.

TableData4(JBean, boolean) - Constructor for class edu.jhu.tmaj.client.tables.data.TableData4

TableData4(JBean, boolean, BeanTableModel) - Constructor for class edu.jhu.tmaj.client.tables.data.TableData4

Constructs this object.

TableData4(JBean) - Constructor for class edu.jhu.tmaj.client.tables.data.TableData4

TableField - Class in edu.jhu.tmaj.client.image.data

A FieldName and a TableName.

TableField(DatabaseField, TableSection) - Constructor for class edu.jhu.tmaj.client.image.data.TableField

TableField(String, TableSection) - Constructor for class edu.jhu.tmaj.client.image.data.TableField

TableFieldComparator - Class in edu.jhu.tmaj.client.image.data

A Compartor used to compare TableFields used in DetailsRequest.

TableFieldRenderer - Class in edu.jhu.tmaj.client.image.data

A Renderer for TableFields, which are the objects found in the columns of the DotTableFrame.

TableFieldRenderer() - Constructor for class edu.jhu.tmaj.client.image.data.TableFieldRenderer

TableHeaderListener - Class in edu.jhu.tmaj.client.tables.data

Added to a JTableHeader, this listener selects or de-selects columns where appropriate.

TableHeaderListener(JTable, JPanel) - Constructor for class edu.jhu.tmaj.client.tables.data.TableHeaderListener

tableModel - Variable in class edu.jhu.tmaj.client.tables.data.TableData4

tableModel - Variable in class edu.jhu.tmaj.client.tables.InputPanel4

tableNumber - Variable in class edu.jhu.tmaj.client.tables.logs.RecordModify

tableScrollPane - Variable in class edu.jhu.tmaj.client.tables.InputPanel4

tableSection - Variable in class edu.jhu.tmaj.client.image.data.TableField

TableSection - Interface in edu.jhu.tmaj.client.image.data

TableSectionComparator - Class in edu.jhu.tmaj.client.image.data

TD_PANEL_NAME - Static variable in class edu.jhu.tmaj.client.specimens.SpecimensAppGUI

TD_TYPE_FIELD - Static variable in class edu.jhu.tmaj.servlet.request.impl.ScoredImageDetailsRequest

TECH_USER_FIELD - Static variable in class edu.jhu.tmaj.beans.BlockUsageBean

TECH_USER_FIELD - Static variable in class edu.jhu.tmaj.beans.BloodUsageBean

TECH_USER_FIELD - Static variable in class edu.jhu.tmaj.beans.MolecularUsageBean

TECH_USER_FIELD - Static variable in class edu.jhu.tmaj.beans.TissueUsageBean

TECH_USER_FIELD - Static variable in class edu.jhu.tmaj.beans.UrineUsageBean

TECHNICIAN_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.BlockUsageAltBean

TERTIARY_DIAGNOSIS_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.BlockUsageAltBean

Test - Class in edu.jhu.tmaj.database.test

Test() - Constructor for class edu.jhu.tmaj.database.test.Test

testExtra() - Method in enum edu.jhu.tmaj.beans.data.datatypes.DynamicSection

testExtra2() - Method in enum edu.jhu.tmaj.beans.data.datatypes.DynamicSection

TEXT_FILE_FILTER - Static variable in class edu.jhu.tmaj.util.swing.DefaultFileFilter

textDisplay - Variable in class edu.jhu.tmaj.client.image.draw.ShapeRecord

TextDrawable - Class in edu.jhu.tmaj.client.image.draw

Text drawn onto an image

TextDrawable(DrawableLabel) - Constructor for class edu.jhu.tmaj.client.image.draw.TextDrawable

TextProgressMonitor - Class in edu.jhu.tmaj.util

A Class used to monitor the progress of a long text-based task.

TextProgressMonitor(long, String) - Constructor for class edu.jhu.tmaj.util.TextProgressMonitor

TextProgressMonitor(long, String, boolean) - Constructor for class edu.jhu.tmaj.util.TextProgressMonitor

Construct this object.

throwCatchedException(String, Exception) - Static method in class edu.jhu.tmaj.util.ErrorUtil

throwCatchedSQLException(String, Exception) - Static method in class edu.jhu.tmaj.util.ErrorUtil

throwFatalCatchedException(String, Exception) - Static method in class edu.jhu.tmaj.util.ErrorUtil

throwNewException(String) - Static method in class edu.jhu.tmaj.util.ErrorUtil

throwNewFatalException(String) - Static method in class edu.jhu.tmaj.util.ErrorUtil

THUMB_SIZE_FILE_ID - Static variable in class edu.jhu.tmaj.beans.ArrayImageBean

ThumbnailsMenuHelper - Class in edu.jhu.tmaj.client.image

A class that controls how thumbnails are displayed on the ArraySlideFrame, as well as allowing the user to download thumbs to their local disk.

ThumbnailsMenuHelper(ResizableTableComponentListener, ArrayImageRenderer, JTable, ArrayImageCollectionBean, HeaderTableScrollPane) - Constructor for class edu.jhu.tmaj.client.image.ThumbnailsMenuHelper

thumbParameters - Variable in class edu.jhu.tmaj.client.importer.images.data.SizeParameters

TISSUE_BANK_NUMBER_FIELD - Static variable in class edu.jhu.tmaj.beans.BloodSampleBean

TISSUE_BANK_NUMBER_FIELD - Static variable in class edu.jhu.tmaj.beans.TissueSampleBean

TISSUE_DIAGNOSIS_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.ArrayCoreBean

TISSUE_DIAGNOSIS_PANEL_NAME - Static variable in class edu.jhu.tmaj.client.samples.SamplesAppGUI

TISSUE_PANEL_NAME - Static variable in class edu.jhu.tmaj.client.samples.SamplesAppGUI

TISSUE_SAMPLE_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.MolecularSampleBean

TISSUE_SAMPLE_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.TissueUsageBean

TISSUE_TYPE_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.dynamic.ScoredImageBean

TISSUE_TYPE_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.dynamic.TissueDiagnosisBean

TISSUE_TYPE_ID_POSITION - Static variable in class edu.jhu.tmaj.beans.dynamic.ScoredImageBean

TISSUE_USAGES_PANEL_NAME - Static variable in class edu.jhu.tmaj.client.samples.SamplesAppGUI

TissueDiagnosisBean - Class in edu.jhu.tmaj.beans.dynamic

Represents the table TissueDiagnosis and accompaining Dynamic table, TissueDiagnosisData.

TissueDiagnosisBean(StaticMetaData, DynamicMetaData) - Constructor for class edu.jhu.tmaj.beans.dynamic.TissueDiagnosisBean

tissueDiagnosisID - Variable in class edu.jhu.tmaj.servlet.request.impl.ArrayCoreC

TISSUEDIAGNOSISID_FIELD - Static variable in class edu.jhu.tmaj.servlet.request.impl.ScoredImageDetailsRequest

tissueDiagnosisIDPanel - Variable in class edu.jhu.tmaj.client.arraybuilder.ArrayBuilderTable

TissueDiagnosisIDPanel - Class in edu.jhu.tmaj.client.arraybuilder

Represents a panel located at the top of the ArrayBuilder application.

TissueDiagnosisIDPanel() - Constructor for class edu.jhu.tmaj.client.arraybuilder.TissueDiagnosisIDPanel

tissueDiagnosisInputPanel - Variable in class edu.jhu.tmaj.client.specimens.SpecimensAppGUI

TissueSampleBean - Class in edu.jhu.tmaj.beans

Represents a Tissue Sample used in Cleveland Clinic's Samples Application.

TissueSampleBean(StaticMetaData) - Constructor for class edu.jhu.tmaj.beans.TissueSampleBean

tissueTypeComboBox - Variable in class edu.jhu.tmaj.client.image.ArrayImageFrameTable

TissueTypesSyncer - Class in edu.jhu.tmaj.client.admin.data

Since the TissueTypes table is shared in the TissueDiagnosis AND ScoredImages section, something must be done to keep the two in sync in the tree.

TissueTypesSyncer() - Constructor for class edu.jhu.tmaj.client.admin.data.TissueTypesSyncer

tissueTypeTextField - Variable in class edu.jhu.tmaj.client.image.ArrayImageFrameTable

TissueUsageBean - Class in edu.jhu.tmaj.beans

Represents a usage of a Tissue Sample.

TissueUsageBean(StaticMetaData) - Constructor for class edu.jhu.tmaj.beans.TissueUsageBean

TITLE_FIELD - Static variable in class edu.jhu.tmaj.beans.AnimalExperimentBean

TITLE_FIELD - Static variable in class edu.jhu.tmaj.beans.PaperBean

toggleSelect() - Method in class edu.jhu.tmaj.client.image.SelectableImage

toolBar - Variable in class edu.jhu.tmaj.client.frida.gui.shared.GeneralMaskPanel

topMenu - Variable in class edu.jhu.tmaj.client.image.ArrayImageFrame

TopMenu - Class in edu.jhu.tmaj.client.image

The options menu for the ArrayImageFrame

TopMenu(ArrayImageFrame) - Constructor for class edu.jhu.tmaj.client.image.TopMenu

toString() - Method in class edu.jhu.tmaj.beans.AnimalExperimentBean

toString() - Method in class edu.jhu.tmaj.beans.ArrayBlockBean

toString() - Method in class edu.jhu.tmaj.beans.ArraySlideBean

toString() - Method in class edu.jhu.tmaj.beans.BlockOrSlideExchangeBean

toString() - Method in class edu.jhu.tmaj.beans.data.datatypes.LookupRecord

toString() - Method in class edu.jhu.tmaj.beans.data.DatedProjectSession

toString() - Method in class edu.jhu.tmaj.beans.data.PrimaryKeyComparator

toString() - Method in class edu.jhu.tmaj.beans.data.StaticEnumeration

Returns the name of the enumeration

toString() - Method in class edu.jhu.tmaj.beans.dynamic.data.DynamicEnumeration

toString() - Method in class edu.jhu.tmaj.beans.dynamic.data.DynamicValue

toString() - Method in class edu.jhu.tmaj.beans.exfile.data.ExternalFileCoordinate

toString() - Method in class edu.jhu.tmaj.beans.exfile.ExternalFile

toString() - Method in class edu.jhu.tmaj.beans.exfile.ExternalFolder

toString() - Method in class edu.jhu.tmaj.beans.IASessionBean

toString() - Method in class edu.jhu.tmaj.beans.JBean

Returns the primary key name of the bean's table, along with the bean's ID.

toString() - Method in class edu.jhu.tmaj.beans.masks.AbstractMask

toString() - Method in class edu.jhu.tmaj.beans.masks.color.ActionList

toString() - Method in class edu.jhu.tmaj.beans.masks.color.CircleRange

toString() - Method in class edu.jhu.tmaj.beans.masks.color.HsbRange

toString() - Method in class edu.jhu.tmaj.beans.masks.color.SimpleRange

toString() - Method in class edu.jhu.tmaj.beans.masks.data.HsbPixel

toString() - Method in class edu.jhu.tmaj.beans.masks.results.MaskStats

toString() - Method in class edu.jhu.tmaj.beans.misc.ArrayCoreRep

toString() - Method in class edu.jhu.tmaj.beans.misc.ArrayImageCollectionBean

toString() - Method in class edu.jhu.tmaj.beans.NullBean

toString() - Method in class edu.jhu.tmaj.beans.PaperBean

toString() - Method in class edu.jhu.tmaj.beans.ProjectBean

toString() - Method in class edu.jhu.tmaj.beans.ProtocolBean

toString() - Method in class edu.jhu.tmaj.beans.ScanBean

toString() - Method in class edu.jhu.tmaj.beans.SessionBean

toString() - Method in class edu.jhu.tmaj.beans.SlideBean

toString() - Method in class edu.jhu.tmaj.beans.UserBean

toString() - Method in class edu.jhu.tmaj.client.arraybuilder.ArrayBlockFrame

toString() - Method in class edu.jhu.tmaj.client.arraybuilder.data.ArrayCoreCell

toString() - Method in class edu.jhu.tmaj.client.image.CheckableObject

toString() - Method in class edu.jhu.tmaj.client.image.data.ArrayImageCell

toString() - Method in class edu.jhu.tmaj.client.image.data.FastCollection

toString() - Method in class edu.jhu.tmaj.client.image.data.PaperURL

toString() - Method in class edu.jhu.tmaj.client.image.data.Size

toString() - Method in class edu.jhu.tmaj.client.image.data.SubTableSection

toString() - Method in class edu.jhu.tmaj.client.image.data.TableField

toString() - Method in class edu.jhu.tmaj.client.image.data.UserPermission

toString() - Method in class edu.jhu.tmaj.client.image.draw.LineDrawable

toString() - Method in class edu.jhu.tmaj.client.image.draw.OvalDrawable

toString() - Method in class edu.jhu.tmaj.client.image.draw.RectangleDrawable

toString() - Method in class edu.jhu.tmaj.client.image.draw.TextDrawable

toString() - Method in class edu.jhu.tmaj.client.importer.data.ShortenedFile

toString() - Method in class edu.jhu.tmaj.client.importer.images.data.ArrayImage2

toString() - Method in class edu.jhu.tmaj.client.importer.images.data.ArrayImageU

toString() - Method in class edu.jhu.tmaj.client.importer.images.data.FilenameData

toString() - Method in class edu.jhu.tmaj.client.importer.images.data.SelectedScan

toString() - Method in class edu.jhu.tmaj.client.importer.specimens.data.DynamicDestination

toString() - Method in class edu.jhu.tmaj.client.importer.specimens.data.StaticDestination

toString() - Method in class edu.jhu.tmaj.client.importer.specimens.data.TranslatedRow

toString() - Method in class edu.jhu.tmaj.client.importer.specimens.data.TranslatedTable

toString() - Method in class edu.jhu.tmaj.client.tables.data.Search

toString() - Method in class edu.jhu.tmaj.client.tables.data.SearchTerm

toString() - Method in class edu.jhu.tmaj.client.tables.InputPanel4

toString() - Method in class edu.jhu.tmaj.client.tables.TabGroup

toString() - Method in class edu.jhu.tmaj.database.conn.DatabaseParameters

toString() - Method in class edu.jhu.tmaj.database.data.DatabaseField

toString() - Method in class edu.jhu.tmaj.database.sql.DeleteSQL

toString() - Method in class edu.jhu.tmaj.database.sql.InsertSQL

toString() - Method in class edu.jhu.tmaj.database.sql.SQLValues

toString() - Method in class edu.jhu.tmaj.database.sql.UpdateSQL

toString() - Method in class edu.jhu.tmaj.servlet.request.impl.ArrayCoreDetailsRequest

toString() - Method in class edu.jhu.tmaj.servlet.request.impl.ArrayCoreReferenceRequest

toString() - Method in class edu.jhu.tmaj.servlet.request.impl.ArrayCoresOpenRequest

toString() - Method in class edu.jhu.tmaj.servlet.request.impl.ArrayCoresSaveRequest

toString() - Method in class edu.jhu.tmaj.servlet.request.impl.ArrayImageAddRequest

toString() - Method in class edu.jhu.tmaj.servlet.request.impl.ArrayImageCollectionRequest

toString() - Method in class edu.jhu.tmaj.servlet.request.impl.CellLinesReferenceRequest

toString() - Method in class edu.jhu.tmaj.servlet.request.impl.ChangePasswordRequest

toString() - Method in class edu.jhu.tmaj.servlet.request.impl.CopyArrayBlockRequest

toString() - Method in class edu.jhu.tmaj.servlet.request.impl.CopySessionRequest

toString() - Method in class edu.jhu.tmaj.servlet.request.impl.DiagnosisLookupRequest

toString() - Method in class edu.jhu.tmaj.servlet.request.impl.DynamicMetaDataRequest

toString() - Method in class edu.jhu.tmaj.servlet.request.impl.EnumerationsRequest

toString() - Method in class edu.jhu.tmaj.servlet.request.impl.ExpressEntryRequest

toString() - Method in class edu.jhu.tmaj.servlet.request.impl.FileDownloadRequest

toString() - Method in class edu.jhu.tmaj.servlet.request.impl.FileUploadRequest

toString() - Method in class edu.jhu.tmaj.servlet.request.impl.GrossDescriptionRequest

toString() - Method in class edu.jhu.tmaj.servlet.request.impl.HistoryRequest

toString() - Method in class edu.jhu.tmaj.servlet.request.impl.ImageInfoRequest

toString() - Method in class edu.jhu.tmaj.servlet.request.impl.KeyValueGetRequest

toString() - Method in class edu.jhu.tmaj.servlet.request.impl.LoginRequest

toString() - Method in class edu.jhu.tmaj.servlet.request.impl.LogoutRequest

toString() - Method in class edu.jhu.tmaj.servlet.request.impl.LookupTableRequest

toString() - Method in class edu.jhu.tmaj.servlet.request.impl.ManyToManyTableRequest

toString() - Method in class edu.jhu.tmaj.servlet.request.impl.ManyToManyUpdateRequest

toString() - Method in class edu.jhu.tmaj.servlet.request.impl.ProjectsArraySlidesAddRequest

toString() - Method in class edu.jhu.tmaj.servlet.request.impl.ScoredImageDetailsRequest

toString() - Method in class edu.jhu.tmaj.servlet.request.impl.SelectRequest

toString() - Method in class edu.jhu.tmaj.servlet.request.impl.ShapesLoadRequest

toString() - Method in class edu.jhu.tmaj.servlet.request.impl.ShapesSaveRequest

toString() - Method in class edu.jhu.tmaj.servlet.request.impl.TranslatedRowRequest

toString() - Method in class edu.jhu.tmaj.servlet.request.impl.UpdateRequest

toString() - Method in class edu.jhu.tmaj.servlet.request.impl.UsersSessionsSaveRequest

toString() - Method in class edu.jhu.tmaj.servlet.response.ErrorResponse

toString() - Method in class edu.jhu.tmaj.servlet.response.impl.DiagnosisLookupResponse

toString() - Method in class edu.jhu.tmaj.servlet.response.impl.FileDownloadResponse

toString() - Method in class edu.jhu.tmaj.servlet.response.SuccessResponse

toString() - Method in class edu.jhu.tmaj.util.data.Messages

toString() - Method in class edu.jhu.tmaj.util.data.Pair

toString() - Method in class edu.jhu.tmaj.util.data.Triplet

toString() - Method in class edu.jhu.tmaj.util.file.TableArrayImpl

toStringAlt() - Method in class edu.jhu.tmaj.beans.exfile.ExternalFile

toStringAlt() - Method in class edu.jhu.tmaj.beans.exfile.ExternalFolder

toSwingMap() - Method in interface edu.jhu.tmaj.beans2.SwingRowConvertable

TOTAL_VALUES - Static variable in class edu.jhu.tmaj.beans.masks.data.HsbPixel

totalPixels - Variable in class edu.jhu.tmaj.beans.masks.results.FileStats

translateBeanListToTableList(List<JBean>, List<DatabaseField>) - Static method in class edu.jhu.tmaj.client.tables.data.TableData4

Converts a List of Beans to a List of Lists, making it ready to be inserted into a JTable

TranslatedRow - Class in edu.jhu.tmaj.client.importer.specimens.data

A TranslatedRow is data parsed from one row in the tab-delimited file that has been translated into a format that can be directly written to the database.

TranslatedRow(MetaDataConverter) - Constructor for class edu.jhu.tmaj.client.importer.specimens.data.TranslatedRow

TranslatedRowRequest - Class in edu.jhu.tmaj.servlet.request.impl

Writes a TranslatedRow to the database.

TranslatedRowRequest(TranslatedRow) - Constructor for class edu.jhu.tmaj.servlet.request.impl.TranslatedRowRequest

TranslatedRowResponse - Class in edu.jhu.tmaj.servlet.response.impl

Contains information on how many specimens/patients were inserted or updated.

TranslatedRowResponse(WriteType, WriteType) - Constructor for class edu.jhu.tmaj.servlet.response.impl.TranslatedRowResponse

TranslatedTable - Class in edu.jhu.tmaj.client.importer.specimens.data

A Table that is ready to be written to the database, as all the column-names match those in the database.

TranslatedTable(String, String) - Constructor for class edu.jhu.tmaj.client.importer.specimens.data.TranslatedTable

TREATMENT_FIELD - Static variable in class edu.jhu.tmaj.beans.CellLineExperimentBean

TreeDataPrinter - Class in edu.jhu.tmaj.client.admin.data

Used to print out a description of our meta data to a text file.

TreeDataPrinter() - Constructor for class edu.jhu.tmaj.client.admin.data.TreeDataPrinter

TreeRenderer - Class in edu.jhu.tmaj.client.admin.data

A TreeCellRenderer that uses a different color for the node depending on the node's user object.

TreeRenderer() - Constructor for class edu.jhu.tmaj.client.admin.data.TreeRenderer

TreeUtils - Class in edu.jhu.tmaj.client.admin.data

Utilities for the JTree in the MetaData application.

TreeUtils() - Constructor for class edu.jhu.tmaj.client.admin.data.TreeUtils

Triplet - Class in edu.jhu.tmaj.util.data

Represents 3 points, an X, Y, and Z.

Triplet(int, int, int) - Constructor for class edu.jhu.tmaj.util.data.Triplet

truncateString(String, int) - Static method in class edu.jhu.tmaj.util.StringFormatUtils

Returns a string no longer than maxLength; if s exceeds maxLength, ".." is appended after the string is truncated.

TUMOR_BANK_NUMBER_FIELD - Static variable in class edu.jhu.tmaj.beans.dynamic.SpecimenBean

TUMORIGENIC_FIELD - Static variable in class edu.jhu.tmaj.beans.CellLineBean

TwoSQLStatements - Class in edu.jhu.tmaj.database.sql

An INSERT statement in which a value is automatically assigned, and a SELECT statement that gets that value.

TwoSQLStatements(String, String) - Constructor for class edu.jhu.tmaj.database.sql.TwoSQLStatements

TwoStrings - Class in edu.jhu.tmaj.client.tables.data

Represents the cell-value for one column in 2 different rows.

TwoStrings(String, String) - Constructor for class edu.jhu.tmaj.client.tables.data.TwoStrings

type - Variable in class edu.jhu.tmaj.client.image.draw.ShapeRecord

TYPE_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.BlockUsageAltBean

TYPE_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.MolecularSampleBean

TypesTable - Enum in edu.jhu.tmaj.beans.data.datatypes

The 3 dynamic sections for the 2 types tables in TMAJ: SpecimenTypes and TissueTypes.

U

undo() - Method in class edu.jhu.tmaj.beans.masks.color.ActionList

Indicate an undo action, so that the next time the user calls getActionList(), the last action will be left off.

undoRenaming(File, Component, SimpleProgressDialog) - Static method in class edu.jhu.tmaj.client.importer.AriolFileRenamerHelper

Undoes the renaming this class performed.

unsignedIntToByte(int) - Static method in class edu.jhu.tmaj.beans.masks.data.PixelUtil

Converts an unsigned int from 0 - 255 into a byte (-128 to 127).

upButton - Variable in class edu.jhu.tmaj.client.image.NavigationGUI

update(ArrayCoreReferenceBean) - Method in class edu.jhu.tmaj.beans.ArrayCoreReferenceBean

Adds the information in this ArrayCoreReferenceBean with that of the specified ArrayCoreReferenceBean.

update(CellLinesReferenceBean) - Method in class edu.jhu.tmaj.beans.CellLinesReferenceBean

update() - Method in class edu.jhu.tmaj.beans.dynamic.DynamicJBean

Performs an UPDATE operation on the database with the data in this bean.

update() - Method in class edu.jhu.tmaj.beans.JBean

Updates the database row with the data in this Bean.

update() - Method in class edu.jhu.tmaj.beans.SessionBean

update(SwingMap) - Method in interface edu.jhu.tmaj.beans2.SwingRowConvertable

UPDATE_TIME - Static variable in class edu.jhu.tmaj.util.TextProgressMonitor

updateArrayCoreReferenceBean(ArrayCoreReferenceBean, int, ArrayCoreReferenceRequest.ReferenceRequestType) - Static method in class edu.jhu.tmaj.client.arraybuilder.ArrayBuilderGUI

Updates the ArrayCoreReferenceBean with new information, such as data from a new ArrayBlock, or new tissueDiagosis's entered in to the current ArrayBlock.

updateCache(CacheableBean, JBean) - Static method in class edu.jhu.tmaj.beans.cache.CachedBeans

updateCacheForBean(JBean) - Static method in class edu.jhu.tmaj.beans.cache.CachedBeans

updateCellLinesReferenceBean(CellLinesReferenceBean, int, CellLinesReferenceRequest.ReferenceRequestType) - Static method in class edu.jhu.tmaj.client.arraybuilder.ArrayBuilderGUI

updateDirtyRows() - Method in class edu.jhu.tmaj.client.tables.data.TableData4

Inserts or Updates any rows that have had their data changed (by the user typing in data on one of the row's cells).

updateHash(String, Map<String, String>, String, int, int) - Static method in class edu.jhu.tmaj.client.importer.specimens.data.ImportDBUtil

Updates a record in a table based on values from a Map.

updateHeadings() - Method in class edu.jhu.tmaj.beans.masks.results.Analyzer2

Redisplays the results table.

updateMacroOptions() - Method in class edu.jhu.tmaj.beans.masks.results.ParticleAnalyzer2

updateMask(Mask) - Method in class edu.jhu.tmaj.beans.masks.AbstractMask

updateMask(Mask) - Method in interface edu.jhu.tmaj.beans.masks.Mask

updateMaskSpecifics(Mask) - Method in class edu.jhu.tmaj.beans.masks.AbstractMask

updateMaskSpecifics(Mask) - Method in class edu.jhu.tmaj.beans.masks.color.ColorMask

updateMaskSpecifics(Mask) - Method in class edu.jhu.tmaj.beans.masks.filter.FilterMask

updateMaskSpecifics(Mask) - Method in class edu.jhu.tmaj.beans.masks.lasso.LassoMask

updateMaskSpecifics(Mask) - Method in class edu.jhu.tmaj.beans.masks.meta.MetaMask

updateRecentIASession(IASessionBean) - Method in class edu.jhu.tmaj.client.image.RecentSessionsPanel

updateRecentSession(SessionBean) - Method in class edu.jhu.tmaj.client.image.RecentSessionsPanel

UpdateRequest - Class in edu.jhu.tmaj.servlet.request.impl

Modifies the specified bean in the database with either an update, insert, or delete.

UpdateRequest(JBean, UpdateRequestType) - Constructor for class edu.jhu.tmaj.servlet.request.impl.UpdateRequest

UpdateRequestType - Enum in edu.jhu.tmaj.beans.data

The different types of an UpdateRequest

UpdateResponse - Class in edu.jhu.tmaj.servlet.response.impl

Contains a JBean, possibly with an updated PrimaryKey ID if an INSERT was performed.

UpdateResponse(JBean) - Constructor for class edu.jhu.tmaj.servlet.response.impl.UpdateResponse

updateSingleRecord(UpdateSQL) - Method in class edu.jhu.tmaj.database.DatabaseUtil

updateSliceSummary() - Method in class edu.jhu.tmaj.beans.masks.results.ParticleAnalyzer2

UpdateSQL - Class in edu.jhu.tmaj.database.sql

Represents an UPDATE SQL statement.

UpdateTracker - Class in edu.jhu.tmaj.client.importer.specimens

A class that keeps track of how many patients and specimens have been updated, as well as how many were inserted since they did not already exist in the database.

UpdateTracker() - Constructor for class edu.jhu.tmaj.client.importer.specimens.UpdateTracker

updateY(int, int) - Static method in class edu.jhu.tmaj.beans.masks.results.Analyzer2

Returns an updated Y coordinate based on the current "Invert Y Coordinates" flag.

updateY(double, int) - Static method in class edu.jhu.tmaj.beans.masks.results.Analyzer2

Returns an updated Y coordinate based on the current "Invert Y Coordinates" flag.

uploadButtonPressed() - Method in class edu.jhu.tmaj.client.importer.images.ArrayImagesImportHelper

uploadFile(ExternalFolder, File) - Method in class edu.jhu.tmaj.beans.exfile.data.ExternalFileClient

uploadImagesButton - Variable in class edu.jhu.tmaj.client.importer.images.ArrayImagesImportGui2

uploadImagesInBackground(SelectedScan, File, JProgressBar, PublicSwingWorker, Component, SizeParameters) - Static method in class edu.jhu.tmaj.client.importer.images.data.ImagesUploadHelper

URINE_PANEL_NAME - Static variable in class edu.jhu.tmaj.client.samples.SamplesAppGUI

URINE_SAMPLE_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.MolecularSampleBean

URINE_SAMPLE_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.UrineUsageBean

URINE_USAGES_PANEL_NAME - Static variable in class edu.jhu.tmaj.client.samples.SamplesAppGUI

UrineSampleBean - Class in edu.jhu.tmaj.beans

Represents Urine Samples.

UrineSampleBean(StaticMetaData) - Constructor for class edu.jhu.tmaj.beans.UrineSampleBean

UrineUsageBean - Class in edu.jhu.tmaj.beans

A table that represents usages of Urine Samples.

UrineUsageBean(StaticMetaData) - Constructor for class edu.jhu.tmaj.beans.UrineUsageBean

UrlDialog - Class in edu.jhu.tmaj.client.shared

URLUtil - Class in edu.jhu.tmaj.util

USAGE_DATE_FIELD - Static variable in class edu.jhu.tmaj.beans.BlockUsageBean

USAGE_DATE_FIELD - Static variable in class edu.jhu.tmaj.beans.BloodUsageBean

USAGE_DATE_FIELD - Static variable in class edu.jhu.tmaj.beans.MolecularUsageBean

USAGE_DATE_FIELD - Static variable in class edu.jhu.tmaj.beans.TissueUsageBean

USAGE_DATE_FIELD - Static variable in class edu.jhu.tmaj.beans.UrineUsageBean

UsedTissueTypesRequest - Class in edu.jhu.tmaj.servlet.request.impl

Retrieves all TissueTypes relevant for a session.

UsedTissueTypesRequest(int) - Constructor for class edu.jhu.tmaj.servlet.request.impl.UsedTissueTypesRequest

UsedTissueTypesResponse - Class in edu.jhu.tmaj.servlet.response.impl

Contains a list of integers where the integers are tissueTypeIDs that have been used in the original arrayBlock.

UsedTissueTypesResponse(List<Integer>) - Constructor for class edu.jhu.tmaj.servlet.response.impl.UsedTissueTypesResponse

USER_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.IASessionBean

USER_ID_FIELD - Static variable in class edu.jhu.tmaj.beans.PaperBean

UserBean - Class in edu.jhu.tmaj.beans

Represents the User table, which contains information such as username,password, and permissions of any person using TMAJ.

UserBean() - Constructor for class edu.jhu.tmaj.beans.UserBean

userBean - Variable in class edu.jhu.tmaj.servlet.request.impl.DetailsRequest

UserBeanLimited - Class in edu.jhu.tmaj.beans

A subclass of the UserBean that only returns a subset of all the userBeans.

UserBeanLimited() - Constructor for class edu.jhu.tmaj.beans.UserBeanLimited

UserCredentials - Class in edu.jhu.tmaj.util.data

Represents a username and a password.

UserCredentials(String, String) - Constructor for class edu.jhu.tmaj.util.data.UserCredentials

userID - Variable in class edu.jhu.tmaj.client.image.draw.AbstractDrawable

userID - Variable in class edu.jhu.tmaj.client.tables.logs.RecordModify

UserInputPanel - Class in edu.jhu.tmaj.client.admin

A InputPanel that provides for adding, modifying, and deleting users

UserInputPanel(TableData4) - Constructor for class edu.jhu.tmaj.client.admin.UserInputPanel

userMayAccessSpecimen(UserBean, int) - Static method in class edu.jhu.tmaj.servlet.request.impl.Verifier

Returns true if the user is an admin, has open access, or an entry exists in UsersSpecimens.

username - Variable in class edu.jhu.tmaj.servlet.request.BaseRequest

USERNAME_FIELD - Static variable in class edu.jhu.tmaj.beans.UserBean

UserPermission - Class in edu.jhu.tmaj.client.image.data

A UserID and a PermissionType (READ OR WRITE).

UserPermission(int, char) - Constructor for class edu.jhu.tmaj.client.image.data.UserPermission

UserPermission.PermissionType - Enum in edu.jhu.tmaj.client.image.data

Either READ or WRITE.

UsersArrayBlocksBean - Class in edu.jhu.tmaj.beans.manytomany

Represents the UsersArrayBlocks table, a many-to-many table that links users to ArrayBlocks.

UsersArrayBlocksBean() - Constructor for class edu.jhu.tmaj.beans.manytomany.UsersArrayBlocksBean

UsersProjectsBean - Class in edu.jhu.tmaj.beans.manytomany

This class represents the many-to-many table UsersProjects, linking users to projects.

UsersProjectsBean() - Constructor for class edu.jhu.tmaj.beans.manytomany.UsersProjectsBean

UsersSessionsGetRequest - Class in edu.jhu.tmaj.servlet.request.impl

Gets the users who have permission to a sessionID, other than the session's owner.

UsersSessionsGetRequest(int) - Constructor for class edu.jhu.tmaj.servlet.request.impl.UsersSessionsGetRequest

UsersSessionsGetResponse - Class in edu.jhu.tmaj.servlet.response.impl

Contains a List of UserPermissions for a particular Session.

UsersSessionsGetResponse(List) - Constructor for class edu.jhu.tmaj.servlet.response.impl.UsersSessionsGetResponse

UsersSessionsSaveRequest - Class in edu.jhu.tmaj.servlet.request.impl

Sends a request that alters the user permissions for a Session.

UsersSessionsSaveRequest(int, List) - Constructor for class edu.jhu.tmaj.servlet.request.impl.UsersSessionsSaveRequest

UsersSpecimens - Class in edu.jhu.tmaj.beans.manytomany

Represents the table UsersSpecimens, where users are assigned to specimens.

UsersSpecimens() - Constructor for class edu.jhu.tmaj.beans.manytomany.UsersSpecimens

UsersUsersBean - Class in edu.jhu.tmaj.beans.manytomany

A ManyToMany Beans that links group admins to people (users) in their group.

UsersUsersBean() - Constructor for class edu.jhu.tmaj.beans.manytomany.UsersUsersBean

usesGrid() - Method in class edu.jhu.tmaj.client.image.TopMenu

Returns true if a grid should be displayed over the image.

V

validate() - Method in class edu.jhu.tmaj.util.swing.AbstractTableCellRenderer

Overridden for performance reasons

validateFileName(String) - Static method in class edu.jhu.tmaj.beans.exfile.ExternalFile

value - Variable in class edu.jhu.tmaj.client.tables.data.StandardizedCellEditor

valueChanged(ListSelectionEvent) - Method in class edu.jhu.tmaj.client.image.ClearingListSelectionListener

valueOf(String) - Static method in enum edu.jhu.tmaj.beans.cache.CacheableBean

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum edu.jhu.tmaj.beans.cache.CacheableDynamicMetaData

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum edu.jhu.tmaj.beans.cache.CacheableStaticMetaData

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum edu.jhu.tmaj.beans.ColorCodedObject

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum edu.jhu.tmaj.beans.data.AdminAppPermission

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum edu.jhu.tmaj.beans.data.ArrayBuilderPermission

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum edu.jhu.tmaj.beans.data.DatabaseTable

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum edu.jhu.tmaj.beans.data.datatypes.DynamicEnumsTable

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum edu.jhu.tmaj.beans.data.datatypes.DynamicSection

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum edu.jhu.tmaj.beans.data.datatypes.EnumerationGroup

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum edu.jhu.tmaj.beans.data.datatypes.FieldsTable

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum edu.jhu.tmaj.beans.data.datatypes.LookupTable

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum edu.jhu.tmaj.beans.data.datatypes.TypesTable

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum edu.jhu.tmaj.beans.data.MetaDataAppPermission

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum edu.jhu.tmaj.beans.data.PatientDataPermission

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum edu.jhu.tmaj.beans.data.ProjectSessionType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum edu.jhu.tmaj.beans.data.SpecimensAppPermission

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum edu.jhu.tmaj.beans.data.UpdateRequestType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum edu.jhu.tmaj.beans.dynamic.data.ArrayImageDynamicField.AIDynamicFieldType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum edu.jhu.tmaj.beans.masks.filter.FilterMaskType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum edu.jhu.tmaj.beans.masks.MaskType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum edu.jhu.tmaj.beans.masks.results.MaskStats.StatName

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum edu.jhu.tmaj.beans2.SwingColumnType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum edu.jhu.tmaj.client.arraybuilder.data.ArrayBlockExporter.ArrayExportFormat

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum edu.jhu.tmaj.client.arraybuilder.data.CellView

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum edu.jhu.tmaj.client.frida.data.CalibrationFunction

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum edu.jhu.tmaj.client.frida.data.MaskChangeEvent.MaskChangeEventType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum edu.jhu.tmaj.client.frida.gui.shared.LimitedToolBar.ImageTool

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum edu.jhu.tmaj.client.image.data.ImageSize

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum edu.jhu.tmaj.client.image.data.MainTableSection

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum edu.jhu.tmaj.client.image.data.UserPermission.PermissionType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum edu.jhu.tmaj.client.image.draw.DrawableStatus

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum edu.jhu.tmaj.client.importer.data.ScanningMachine

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum edu.jhu.tmaj.client.importer.machscores.MachineScoreField

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum edu.jhu.tmaj.client.importer.specimens.data.StaticDestination.DestinationTable

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum edu.jhu.tmaj.client.importer.specimens.data.WriteType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum edu.jhu.tmaj.client.shared.Preference

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum edu.jhu.tmaj.config.ClientConstants.ClientConfigKey

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum edu.jhu.tmaj.database.data.DatabaseFieldType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum edu.jhu.tmaj.database.data.DatabaseType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum edu.jhu.tmaj.servlet.request.impl.ArrayCoreReferenceRequest.ReferenceRequestType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum edu.jhu.tmaj.servlet.request.impl.CellLinesReferenceRequest.ReferenceRequestType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum edu.jhu.tmaj.servlet.request.impl.KeyValueGetRequest.KeyName

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum edu.jhu.tmaj.servlet.request.impl.SessionDescriptionsRequest.Column

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum edu.jhu.tmaj.servlet.request.impl.SurgPathNumberRequest.TableType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum edu.jhu.tmaj.util.config.data.ConfigKeyType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum edu.jhu.tmaj.util.ObjectPool.WaitTime

Returns the enum constant of this type with the specified name.

values() - Static method in enum edu.jhu.tmaj.beans.cache.CacheableBean

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum edu.jhu.tmaj.beans.cache.CacheableDynamicMetaData

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum edu.jhu.tmaj.beans.cache.CacheableStaticMetaData

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum edu.jhu.tmaj.beans.ColorCodedObject

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum edu.jhu.tmaj.beans.data.AdminAppPermission

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum edu.jhu.tmaj.beans.data.ArrayBuilderPermission

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum edu.jhu.tmaj.beans.data.DatabaseTable

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum edu.jhu.tmaj.beans.data.datatypes.DynamicEnumsTable

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum edu.jhu.tmaj.beans.data.datatypes.DynamicSection

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum edu.jhu.tmaj.beans.data.datatypes.EnumerationGroup

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum edu.jhu.tmaj.beans.data.datatypes.FieldsTable

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum edu.jhu.tmaj.beans.data.datatypes.LookupTable

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum edu.jhu.tmaj.beans.data.datatypes.TypesTable

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum edu.jhu.tmaj.beans.data.MetaDataAppPermission

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum edu.jhu.tmaj.beans.data.PatientDataPermission

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum edu.jhu.tmaj.beans.data.ProjectSessionType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum edu.jhu.tmaj.beans.data.SpecimensAppPermission

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum edu.jhu.tmaj.beans.data.UpdateRequestType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum edu.jhu.tmaj.beans.dynamic.data.ArrayImageDynamicField.AIDynamicFieldType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum edu.jhu.tmaj.beans.masks.filter.FilterMaskType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum edu.jhu.tmaj.beans.masks.MaskType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum edu.jhu.tmaj.beans.masks.results.MaskStats.StatName

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum edu.jhu.tmaj.beans2.SwingColumnType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum edu.jhu.tmaj.client.arraybuilder.data.ArrayBlockExporter.ArrayExportFormat

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum edu.jhu.tmaj.client.arraybuilder.data.CellView

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum edu.jhu.tmaj.client.frida.data.CalibrationFunction

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum edu.jhu.tmaj.client.frida.data.MaskChangeEvent.MaskChangeEventType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum edu.jhu.tmaj.client.frida.gui.shared.LimitedToolBar.ImageTool

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum edu.jhu.tmaj.client.image.data.ImageSize

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum edu.jhu.tmaj.client.image.data.MainTableSection

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum edu.jhu.tmaj.client.image.data.UserPermission.PermissionType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum edu.jhu.tmaj.client.image.draw.DrawableStatus

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum edu.jhu.tmaj.client.importer.data.ScanningMachine

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum edu.jhu.tmaj.client.importer.machscores.MachineScoreField

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum edu.jhu.tmaj.client.importer.specimens.data.StaticDestination.DestinationTable

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum edu.jhu.tmaj.client.importer.specimens.data.WriteType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum edu.jhu.tmaj.client.shared.Preference

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum edu.jhu.tmaj.config.ClientConstants.ClientConfigKey

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum edu.jhu.tmaj.database.data.DatabaseFieldType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum edu.jhu.tmaj.database.data.DatabaseType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum edu.jhu.tmaj.servlet.request.impl.ArrayCoreReferenceRequest.ReferenceRequestType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum edu.jhu.tmaj.servlet.request.impl.CellLinesReferenceRequest.ReferenceRequestType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum edu.jhu.tmaj.servlet.request.impl.KeyValueGetRequest.KeyName

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum edu.jhu.tmaj.servlet.request.impl.SessionDescriptionsRequest.Column

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum edu.jhu.tmaj.servlet.request.impl.SurgPathNumberRequest.TableType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum edu.jhu.tmaj.util.config.data.ConfigKeyType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum edu.jhu.tmaj.util.ObjectPool.WaitTime

Returns an array containing the constants of this enum type, in the order they are declared.

VariedSizeFolders - Class in edu.jhu.tmaj.client.importer.images.data

VariedSizeFolders(ExternalFolder, ExternalFolder, ExternalFolder) - Constructor for class edu.jhu.tmaj.client.importer.images.data.VariedSizeFolders

VariedSizeFolders() - Constructor for class edu.jhu.tmaj.client.importer.images.data.VariedSizeFolders

VariedSizeImages - Class in edu.jhu.tmaj.client.image.data

VariedSizeImages(ExternalFile, ExternalFile, ExternalFile, ExternalFile) - Constructor for class edu.jhu.tmaj.client.image.data.VariedSizeImages

Verifier - Class in edu.jhu.tmaj.servlet.request.impl

Utility class that verifies server Requests based on the UserBean obtained from the username/password submitted.

Verifier() - Constructor for class edu.jhu.tmaj.servlet.request.impl.Verifier

verify() - Method in class edu.jhu.tmaj.beans.ArrayBlockBean

verify() - Method in class edu.jhu.tmaj.beans.JBean

Overwritten by subclasses, this method may throw an exception before an insert() or update() is done if there is something wrong with the JBean.

verify() - Method in class edu.jhu.tmaj.beans.UserBean

verifyChecksum(ExternalFile) - Static method in class edu.jhu.tmaj.servlet.request.impl.FileDeleteRequest

verifyChildrenNames(Element, String...) - Static method in class edu.jhu.tmaj.util.XmlUtil

Throws an exception if the element's children don't have the supplied names.

verifyElementName(Element, String) - Static method in class edu.jhu.tmaj.util.XmlUtil

Throws an exception if the element doesn't have the supplied name.

verifyFileInRoot(File, File) - Static method in class edu.jhu.tmaj.util.FilePathUtils

verifyFileIsAbsolute(File) - Static method in class edu.jhu.tmaj.util.FilePathUtils

verifyFileName(String) - Static method in class edu.jhu.tmaj.util.FilePathUtils

verifyFirstChildrenNames(Element, String...) - Static method in class edu.jhu.tmaj.util.XmlUtil

verifyRootDirectory(File) - Static method in class edu.jhu.tmaj.util.FilePathUtils

verifyUser(UserBean) - Method in class edu.jhu.tmaj.servlet.request.impl.ArrayCoreDetailsRequest

Returns true if the user can access the requested ArrayBlockID and the ArrayBuilder application.

verifyUser(UserBean) - Method in class edu.jhu.tmaj.servlet.request.impl.DetailsRequest

Throws an exception if the user is not allowed to make this Request

verifyUser(UserBean) - Method in class edu.jhu.tmaj.servlet.request.impl.ScoredImageDetailsRequest

verifyUserIsAdmin(UserBean) - Static method in class edu.jhu.tmaj.servlet.request.impl.Verifier

verifyUserMayAccessArrayBuilder(UserBean) - Static method in class edu.jhu.tmaj.servlet.request.impl.Verifier

verifyUserMayAccessArrayImage(int, int) - Static method in class edu.jhu.tmaj.servlet.request.impl.Verifier

verifyUserMayAccessImagesApp(UserBean) - Static method in class edu.jhu.tmaj.servlet.request.impl.Verifier

verifyUserMayAccessImportApp(UserBean) - Static method in class edu.jhu.tmaj.servlet.request.impl.Verifier

verifyUserMayAccessInputApp(UserBean) - Static method in class edu.jhu.tmaj.servlet.request.impl.Verifier

verifyUserMayAccessMetaDataApp(UserBean) - Static method in class edu.jhu.tmaj.servlet.request.impl.Verifier

verifyUserMayAccessSession(UserBean, int) - Static method in class edu.jhu.tmaj.servlet.request.impl.Verifier

verifyUserMayAccessSessions(UserBean, int[]) - Static method in class edu.jhu.tmaj.servlet.request.impl.Verifier

verifyUserMayAccessSpecimen(UserBean, int) - Static method in class edu.jhu.tmaj.servlet.request.impl.Verifier

verifyUserOwnsSession(int, int) - Static method in class edu.jhu.tmaj.servlet.request.impl.Verifier

verifyUsersArrayBlocks(UserBean, int) - Static method in class edu.jhu.tmaj.servlet.request.impl.Verifier

VERSION_NUMBER - Static variable in class edu.jhu.tmaj.config.HardConstants

viewScanDataButton - Variable in class edu.jhu.tmaj.client.importer.images.ArrayImagesImportGui2

viewScanDataButtonPressed() - Method in class edu.jhu.tmaj.client.importer.images.ArrayImagesImportHelper

viewServerImagesDirectoryButton - Variable in class edu.jhu.tmaj.client.importer.images.ArrayImagesImportGui2

viewServerImagesDirectoryButtonPressed() - Method in class edu.jhu.tmaj.client.importer.images.ArrayImagesImportHelper

viewSourceDirectoryButton - Variable in class edu.jhu.tmaj.client.importer.images.ArrayImagesImportGui2

viewSourceDirectoryButtonPressed() - Method in class edu.jhu.tmaj.client.importer.images.ArrayImagesImportHelper

VOLUME_FIELD - Static variable in class edu.jhu.tmaj.beans.MolecularSampleBean

W

warningsWereGenerated() - Method in class edu.jhu.tmaj.servlet.response.impl.DetailsResponse

wasTypeLookedUp() - Method in class edu.jhu.tmaj.servlet.response.impl.OriginalTypeResponse

WHITE_VALUE - Static variable in class edu.jhu.tmaj.client.frida.data.CalibrationCalculator

width - Variable in class edu.jhu.tmaj.client.image.data.Size

width - Variable in class edu.jhu.tmaj.client.image.draw.Dimension

width - Variable in class edu.jhu.tmaj.client.image.draw.RectangleDrawable

width - Variable in class edu.jhu.tmaj.client.image.draw.ShapeRecord

willLookupDiagnosis() - Method in class edu.jhu.tmaj.client.image.TopMenu

Returns true if both the general type and specific diagnosis should be looked up in TissueDiagnosis.

windowClosed(WindowEvent) - Method in class edu.jhu.tmaj.client.image.data.DisposeRelatedWindowsListener

windowClosed(WindowEvent) - Method in class edu.jhu.tmaj.client.shared.ClosingWindowListener

Called when a window is closed programatically, e.g.

windowClosed(WindowEvent) - Method in class edu.jhu.tmaj.client.shared.LogoutWindowListener

windowClosing(WindowEvent) - Method in class edu.jhu.tmaj.client.image.data.DisposeRelatedWindowsListener

windowClosing(WindowEvent) - Method in class edu.jhu.tmaj.client.shared.ClosingWindowListener

Called when the user closes the window.

windowClosing(WindowEvent) - Method in class edu.jhu.tmaj.client.shared.LogoutWindowListener

WindowsCommandUtil - Class in edu.jhu.tmaj.util

WindowsCommandUtil() - Constructor for class edu.jhu.tmaj.util.WindowsCommandUtil

write(List<ArrayCoreRep>, int, int) - Static method in class edu.jhu.tmaj.servlet.request.impl.ArrayCoresSaveRequest

Writes a List of ArrayCoreBeans to the database.

writeBinaryFile(File, byte[]) - Method in interface edu.jhu.tmaj.util.file.FileUtil

writeBinaryFile(File, byte[]) - Method in class edu.jhu.tmaj.util.file.FileUtilImpl

writeByteArrayToFile(File, byte[]) - Static method in class edu.jhu.tmaj.util.ByteUtil

writeFlatFile(TableArray, File, String) - Method in interface edu.jhu.tmaj.util.file.FlatFileSyncer

Writes the supplied tableArray to the supplied file using the supplied delimiter to separate columns.

writeFlatFile(TableArray, File, String) - Method in class edu.jhu.tmaj.util.file.FlatFileSyncerImpl

writeTextFile(File, List<String>) - Method in interface edu.jhu.tmaj.util.file.FileUtil

writeTextFile(File, List<String>) - Method in class edu.jhu.tmaj.util.file.FileUtilImpl

writeToDatabase() - Method in class edu.jhu.tmaj.client.arraybuilder.ArrayBuilderTable

Sends a Request to write the ArrayCores to the database for the specified ArrayBlockID.

writeToDatabase(int) - Method in class edu.jhu.tmaj.client.importer.specimens.data.PatientTranslatedTable

writeToDatabase(int) - Method in class edu.jhu.tmaj.client.importer.specimens.data.SpecimenTranslatedTable

writeToDatabase(int) - Method in class edu.jhu.tmaj.client.importer.specimens.data.TranslatedTable

writeToDatabase(AllFileStats) - Static method in class edu.jhu.tmaj.servlet.request.impl.MaskStatsWriteRequest

writeToDatabase(List<Mask>, int) - Static method in class edu.jhu.tmaj.servlet.request.impl.MasksWriteRequest

writeToDatabase() - Method in interface edu.jhu.tmaj.servlet.request.impl.MetaDataAddRequest.AddOperation

Commit the operation to the database by executing a SQL statement.

writeToDatabase() - Method in class edu.jhu.tmaj.servlet.request.impl.MetaDataAddRequest.EnumAdd

writeToDatabase() - Method in class edu.jhu.tmaj.servlet.request.impl.MetaDataAddRequest.FieldAdd

writeToDatabase() - Method in class edu.jhu.tmaj.servlet.request.impl.MetaDataAddRequest.TypeAdd

writeToDatabase() - Method in interface edu.jhu.tmaj.servlet.request.impl.MetaDataAlterRequest.AlterOperation

writeToDatabase() - Method in class edu.jhu.tmaj.servlet.request.impl.MetaDataAlterRequest.DeleteOperation

writeToDatabase() - Method in class edu.jhu.tmaj.servlet.request.impl.MetaDataAlterRequest.ModifyOperation

WriteType - Enum in edu.jhu.tmaj.client.importer.specimens.data

Either INSERT or UPDATE, the action to be done on the database.

X

x - Variable in class edu.jhu.tmaj.beans.masks.color.Point

x - Variable in class edu.jhu.tmaj.client.image.draw.Point

x - Variable in class edu.jhu.tmaj.client.image.draw.RectangleDrawable

x - Variable in class edu.jhu.tmaj.client.image.draw.ShapeRecord

x - Variable in class edu.jhu.tmaj.servlet.request.impl.ArrayCoreC

x - Variable in class edu.jhu.tmaj.util.data.Pair

x1 - Variable in class edu.jhu.tmaj.client.image.draw.LineDrawable

x2 - Variable in class edu.jhu.tmaj.client.image.draw.LineDrawable

x2 - Variable in class edu.jhu.tmaj.client.image.draw.ShapeRecord

X_FIELD - Static variable in class edu.jhu.tmaj.beans.ArrayCoreBean

X_FIELD - Static variable in class edu.jhu.tmaj.servlet.request.impl.ScoredImageDetailsRequest

XENOGRAFT_TIME_IN_HOST_FIELD - Static variable in class edu.jhu.tmaj.beans.CellLineExperimentBean

XmlUtil - Class in edu.jhu.tmaj.util

Y

y - Variable in class edu.jhu.tmaj.beans.masks.color.Point

y - Variable in class edu.jhu.tmaj.client.image.draw.Point

y - Variable in class edu.jhu.tmaj.client.image.draw.RectangleDrawable

y - Variable in class edu.jhu.tmaj.client.image.draw.ShapeRecord

y - Variable in class edu.jhu.tmaj.servlet.request.impl.ArrayCoreC

y - Variable in class edu.jhu.tmaj.util.data.Pair

y1 - Variable in class edu.jhu.tmaj.client.image.draw.LineDrawable

y2 - Variable in class edu.jhu.tmaj.client.image.draw.LineDrawable

y2 - Variable in class edu.jhu.tmaj.client.image.draw.ShapeRecord

Y_FIELD - Static variable in class edu.jhu.tmaj.beans.ArrayCoreBean

Y_FIELD - Static variable in class edu.jhu.tmaj.servlet.request.impl.ScoredImageDetailsRequest

Z

Z_FIELD - Static variable in class edu.jhu.tmaj.beans.ArraySlideBean

zeroPad(int, int) - Static method in class edu.jhu.tmaj.util.StringFormatUtils

Puts zeros at the beginning of a string if string length is less than min length.

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z