edu.jhu.tmaj.beans.dynamic
Class TissueDiagnosisBean

java.lang.Object
  edu.jhu.tmaj.beans.JBean
      edu.jhu.tmaj.beans.dynamic.DynamicJBean
          edu.jhu.tmaj.beans.dynamic.TissueDiagnosisBean

All Implemented Interfaces:

java.io.Serializable, java.lang.Comparable

public final class TissueDiagnosisBean
extends DynamicJBean
implements java.io.Serializable

Represents the table TissueDiagnosis and accompaining Dynamic table, TissueDiagnosisData. A TissueDiagnosis (sometimes called sub-block) is a region on a donor-block that has been circled and given a diagnosis. For example, a block may have 3 circles on it. The first circle might represent an area of normal tissue, the second circle an area of cancer tissue, and third circle another area of cancer tissue. Each circle represents one TissueDiagnosis or sub-block. Physically a TissueDiagonsis is 3-dimensional, since a block is also 3-dimensional. Each of the TissueDiagnosis's on a block is given a lesion letter, and physically written on the block. Generally the first lesion letter is A, second is B, and so on. Thus, if you know the block and a lesion letter, you can uniquely identify a TissueDiagnosis. The TissueDiagonisBean is a dynamicBean, thus based on different types (it's tissuetype) the user will pick from different fields. For example, if a circled-area is diagnosised as "Prostate Cancer", different fields will appear that if it type is called "Normal Bladder Tissue". Notes: In practice, the very top of a block is cut off to make an h&e-stained slide. The circled-areas are actually drawn onto this slide and labeled, not the block itself. But the slide (which is 2-dimensional) will represent the block (which is 3-dimensional). Note: The diagnosis may change and you go deeper into the block. Remember the slide used to make the diagnosis was cut from the very top of the block. So the top of the block may be cancer, but as you go lower it may turn to normal again. This is one reason why all tissue is "re-diagnonsed" in the images application. How ArrayBlocks are created from TissueDiagnosis's:
A hollow cylinder is inserted into the circled area and tissue is obtained from the donor-block. The tissue is then placed in a specified coordinate (e.g. x=1,y=4) of the array-block (or receipient-block).

See Also:

Serialized Form

Field Summary

static DatabaseField	AREA_FIELD
static DatabaseField	BLOCK_ID_FIELD
static DatabaseField	CELL_LINE_EXPERIMENT_ID_FIELD
static DatabaseField	ID_FIELD
static DatabaseField	INPUT_LOG_FIELD
static DatabaseField	LESION_LETTER_FIELD
static DatabaseField	MICROSCOPIST_ID_FIELD
static DatabaseField	NOTES_FIELD
static DatabaseField	OUTSIDE_TD_NUMBER_FIELD
static DatabaseField	REGION_SIZE_FIELD
static DatabaseField	TISSUE_TYPE_ID_FIELD

Fields inherited from class edu.jhu.tmaj.beans.dynamic.DynamicJBean

dynamicMetaData

Fields inherited from class edu.jhu.tmaj.beans.JBean

staticMetaData

Constructor Summary

TissueDiagnosisBean(StaticMetaData staticMetaData, DynamicMetaData dynamicMetaData)

Method Summary

int	getBlockID() Returns the BlockID on which this TissueDiagnosis has been circled.
java.lang.Integer	getCellLineExperimentID()
(package private) java.lang.String	getDynamicSQL(Search search) Returns a SQL statement that will pull records from the DynamicData table (e.g.
java.lang.String	getDynamicTableName() Returns the name of the Table that contains the DynamicData for this Bean, for example, SpecimenData.
DatabaseField[]	getFieldsArray() Returns an Array of TFields representing the columnnames of this bean.
java.lang.String	getLesionLetter() Returns the letter assigned to the circle.
JBean	getNewInstance() Returns a new instance of this bean.
java.lang.String	getOutsideTDNumber()
java.lang.String	getSQL(Search search) Returns a SELECT SQL statement given a Search.
DatabaseTable	getTable()
DatabaseField	getTypeField() Returns the TField column where the type of this DynamicBean is put.

Methods inherited from class edu.jhu.tmaj.beans.dynamic.DynamicJBean

addDynamicValue, createFromSwingMap, getBeanList, getColumnIdentifiers, getDynamicBaseSQL, getDynamicColumnIdentifiers, getDynamicMetaData, getEnumerations, getSwingHash, getSwingToBeanObject, getTypeID, insert, isEnumerated, setTypeID, syncDynamicData, update

Methods inherited from class edu.jhu.tmaj.beans.JBean

compareTo, createFromResultSet, delete, equals, getAllStaticColumnIdentifiers, getBaseSQL, getBeanInDatabase, getBeanList, getClassForType, getDateField, getDefaultBeanObjectForType, getDefaultSwingObjectForType, getDoubleField, getFieldValue, getID_Bean_Map, getID, getIntegerField, getNonNullString, getPrimaryKeyField, getPrimaryKeyName, getSelectResponse, getStaticMetaData, getStringField, getTableName, getUserBean, getWhereClause, hashCode, setDoubleField, setID, setIntegerField, setUserBean, toString, verify

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Field Detail

ID_FIELD

public static final DatabaseField ID_FIELD

TISSUE_TYPE_ID_FIELD

public static final DatabaseField TISSUE_TYPE_ID_FIELD

BLOCK_ID_FIELD

public static final DatabaseField BLOCK_ID_FIELD

LESION_LETTER_FIELD

public static final DatabaseField LESION_LETTER_FIELD

OUTSIDE_TD_NUMBER_FIELD

public static final DatabaseField OUTSIDE_TD_NUMBER_FIELD

MICROSCOPIST_ID_FIELD

public static final DatabaseField MICROSCOPIST_ID_FIELD

CELL_LINE_EXPERIMENT_ID_FIELD

public static final DatabaseField CELL_LINE_EXPERIMENT_ID_FIELD

AREA_FIELD

public static final DatabaseField AREA_FIELD

REGION_SIZE_FIELD

public static final DatabaseField REGION_SIZE_FIELD

NOTES_FIELD

public static final DatabaseField NOTES_FIELD

INPUT_LOG_FIELD

public static final DatabaseField INPUT_LOG_FIELD

Constructor Detail

TissueDiagnosisBean

public TissueDiagnosisBean(StaticMetaData staticMetaData,
                           DynamicMetaData dynamicMetaData)

Method Detail

getBlockID

public int getBlockID()

Returns the BlockID on which this TissueDiagnosis has been circled.

getLesionLetter

public java.lang.String getLesionLetter()

Returns the letter assigned to the circle.

getOutsideTDNumber

public java.lang.String getOutsideTDNumber()

getCellLineExperimentID

public java.lang.Integer getCellLineExperimentID()

getNewInstance

public JBean getNewInstance()

Description copied from class: JBean

Returns a new instance of this bean.

Specified by:

getNewInstance in class JBean

getTypeField

public DatabaseField getTypeField()

Description copied from class: DynamicJBean

Returns the TField column where the type of this DynamicBean is put.

Specified by:

getTypeField in class DynamicJBean

getDynamicTableName

public java.lang.String getDynamicTableName()

Description copied from class: DynamicJBean

Returns the name of the Table that contains the DynamicData for this Bean, for example, SpecimenData.

Specified by:

getDynamicTableName in class DynamicJBean

getTable

public DatabaseTable getTable()

Specified by:

getTable in class JBean

getFieldsArray

public DatabaseField[] getFieldsArray()

Description copied from class: JBean

Returns an Array of TFields representing the columnnames of this bean.

Specified by:

getFieldsArray in class JBean

getDynamicSQL

java.lang.String getDynamicSQL(Search search)

Description copied from class: DynamicJBean

Returns a SQL statement that will pull records from the DynamicData table (e.g. SpecimenData)

Overrides:

getDynamicSQL in class DynamicJBean

getSQL

public java.lang.String getSQL(Search search)

Description copied from class: JBean

Returns a SELECT SQL statement given a Search.

Overrides:

getSQL in class JBean