edu.jhu.tmaj.beans.misc
Class ArrayCoreRep

java.lang.Object
  edu.jhu.tmaj.beans.misc.ArrayCoreRep

All Implemented Interfaces:

java.io.Serializable

public final class ArrayCoreRep
extends java.lang.Object
implements java.io.Serializable

Represents the table ArrayCores. An ArrayCore is a "cylinder" that is put into an ArrayBlock. These cylinders are made by poking the TissueDiagnosis sub-section of a donor-block with a hollow cylinder tube. The TissueDiagnosis (Sub-Block) area can be poked multiple times, thus a single TissueDiagnosis can be used for multiple ArrayCores. An ArrayCore can be uniquely identified by knowing the ArrayBlock, and the X and Y coordinate.

Using Controls in ArrayBlocks

Why Controls Are Used

Controls are used for quality-control. An ArrayBlock made to study prostate cancer will obviously have most of the ArrayCores come from Prostate Donor Blocks. However when designing the ArrayBlock, the technician puts tissue from the Brain in columns 5,10 and 15, and 20. All the other columns have prostate tissue. The brain tissue is used as a control here. A pathologist can easily tell if an image is brain tissue. So when they look at the images from this ArrayBlock, they will expect to see brain tissue in these preset columns. If they do not, they know something went wrong in the creation of the ArrayBlock.

How to represent a control in the Database

The database does not keep track of the exact block from where control tissue is obtained. Rather all control tissue uses a hard-coded TissueDiagnosisID of CoreTableData.CONTROL_TISSUE_DIAGNOSIS_ID. This class has a String value named control which stores the organ-type of the control tissue, if control tissue is used. So in our example, control would have value "Brain". e

See Also:

Serialized Form

Field Summary

static int	CONTROL_TISSUE_DIAGNOSIS_ID The TissueDiagnosisID for Controls.
static int	DUMMY_TISSUE_DIAGNOSIS_ID The tissueDiagnosisID assigned to ArrayCores that are null.

Constructor Summary

ArrayCoreRep(int arrayBlockID, Coordinate c, int tissueDiagnosisID, java.lang.String control)

Method Summary

int	getArrayBlockID() Returns the ArrayBlock of which this ArrayCore is part.
java.lang.String	getControlName() Returns the Control name of the ArrayCoreBean.
Coordinate	getCoordinate() Returns the position of this ArrayCore in the ArrayBlock, for example, x=5,y=10.
int	getTissueDiagnosisID() Gets the TissueDiagnosisID of the ArrayCore.
int	getX() Gets the X position of this ArrayCore in the ArrayBlock
int	getY() Gets the Y position of this ArrayCore in the ArrayBlock
boolean	isControl()
void	setControlName(java.lang.String control)
void	setTissueDiagnosisID(int tissueDiagnosisID) Changes the TissueDiagnosisID where this ArrayCore came from.
java.lang.String	toString()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

DUMMY_TISSUE_DIAGNOSIS_ID

public static final int DUMMY_TISSUE_DIAGNOSIS_ID

The tissueDiagnosisID assigned to ArrayCores that are null. All ArrayCores must have a TissueDiagnosisID. (The database is set up to demand this, since TissueDiagnosisID is a required field in the ArrayCores table.) If the programs wants to assign a blank or null to a coordinate, they use this value.

See Also:

Constant Field Values

CONTROL_TISSUE_DIAGNOSIS_ID

public static final int CONTROL_TISSUE_DIAGNOSIS_ID

The TissueDiagnosisID for Controls. The database does not track which specimen and block a control comes from, so we use this default TissueDiagnosisID.

See Also:

Constant Field Values

Constructor Detail

ArrayCoreRep

public ArrayCoreRep(int arrayBlockID,
                    Coordinate c,
                    int tissueDiagnosisID,
                    java.lang.String control)

Method Detail

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

isControl

public boolean isControl()

getControlName

public java.lang.String getControlName()

Returns the Control name of the ArrayCoreBean. If the ArrayCore is a control, a default TissueDiagnosisID is assigned (CoreTableData.CONTROL_TISSUE_DIAGNOSIS_ID) and a control name is given (for example, "Kidney"). Most ArrayCores are not controls and this field simply returns an empty string.

getTissueDiagnosisID

public int getTissueDiagnosisID()

Gets the TissueDiagnosisID of the ArrayCore. The TissueDiagnosisID is the original circled area on the donor-block that is poked with a hollow cylinder.

getX

public int getX()

Gets the X position of this ArrayCore in the ArrayBlock

getY

public int getY()

Gets the Y position of this ArrayCore in the ArrayBlock

getArrayBlockID

public int getArrayBlockID()

Returns the ArrayBlock of which this ArrayCore is part.

getCoordinate

public Coordinate getCoordinate()

Returns the position of this ArrayCore in the ArrayBlock, for example, x=5,y=10.

setTissueDiagnosisID

public void setTissueDiagnosisID(int tissueDiagnosisID)

Changes the TissueDiagnosisID where this ArrayCore came from.

setControlName

public void setControlName(java.lang.String control)