Uses of Class
MaHybridSample

Packages that use MaHybridSample

Uses of MaHybridSample in

Fields in declared as MaHybridSample

(package private) MaHybridSample	ArrayScroller.msR link to global MaHybridSample instance
(package private) MaHybridSample[]	ClusterGenes.msEPlist list of expression profile samples [1:nEPmsList] where genes are to be checked normally this is mae.msListE[1:mae.nHP_E].
(package private) MaHybridSample[]	ClusterSamples.msList list of samples H.P.s to cluster
(package private) MaHybridSample[]	Condition.msCond [0:nMScond-1] elements of the list
(package private) MaHybridSample	Draw2Dplot.ms link to global MaHybridSample instance
private MaHybridSample	DrawHistogram.ms link to global MaHybridSample instance
private MaHybridSample	DrawScatterPlot.ms link to global instance
private static MaHybridSample	EventMenu.oldMS save old value of MaHybridSample mae.ms
(package private) static MaHybridSample	MAExplorer.ms Current hybridized sample
(package private) static MaHybridSample	MAExplorer.msPrev Previous (last current) hybridized sample for garbage collection
(package private) static MaHybridSample	MAExplorer.msX Current HP-X hybridized sample
(package private) static MaHybridSample	MAExplorer.msY Current HP-Y hybridized sample
private MaHybridSample	MJAgene.msW
private MaHybridSample	MaHPquantTable.ms HP sample that owns this table instance
private MaHybridSample[]	PopupHPChooser.msListXo initial HP-X sample list on starting chooser
private MaHybridSample[]	PopupHPChooser.msListYo initial HP-Y sample list on starting chooser
private MaHybridSample[]	PopupHPChooser.msListEo initial HP-E sample list on starting chooser
private MaHybridSample[]	PopupHPChooser.msList List of ALL initial samples in DB
private MaHybridSample[]	PopupHPChooser.msListrXY rem(X+Y) = mxListo - msListXo - msListYo
private MaHybridSample[]	PopupHPChooser.msListrE rem(E) = mxListo - msListEo
(package private) static MaHybridSample[]	SampleSets.msListX X-axis [1:nHP_X]
(package private) static MaHybridSample[]	SampleSets.msListY Y-axis [1:nHP_Y]
(package private) static MaHybridSample[]	SampleSets.msListE Expression Profile [1:nHP_E]
(package private) static MaHybridSample[]	SampleSets.msList total HP list [1:nHP] for all active samples
(package private) MaHybridSample	ScrollableImageCanvas.msR link to current sample
(package private) static MaHybridSample	SpotData.ms HP where this data came from

Methods in that return MaHybridSample

(package private) MaHybridSample[]	Condition.getHPlist() getHPlist() - get sample list for condition [1:nMScond]
(package private) MaHybridSample	MAExplorer.createSample(int hpNbr, java.lang.String hpName, java.lang.String sampleID, java.lang.String databaseFileID, java.lang.String oImageName, java.lang.String oMenuName, java.lang.String fullStageText, java.lang.String projectName, boolean needLoginFlag, boolean swapCy5Cy3DataFlag) createSample() - create and return a MaHybridSample hybridized sample object.
(package private) static MaHybridSample	MJAbase.chkGetHP(int sampleNbr) chkGetHP() - check HP sample # to make sure it is legal and within the legal range and get MaHybidSample ms.

Methods in with parameters of type MaHybridSample

(package private) boolean	ClusterGenes.createClusterMethod(GeneList complexClusterCL, int nbrOfClusters, MaHybridSample[] msEPlist, int nEPmsList, int method, boolean resetFlag) createClusterMethod() - create instance of new cluster method
(package private) boolean	CompositeDatabase.calcHistOfF1F2Ratios(GeneList ml, MaHybridSample ms) calcHistOfF1F2Ratios() - compute histogram of F1/F2 ratios for spots which are selected in the GeneList ml.
(package private) boolean	CompositeDatabase.setIntensHistCLfromIntenRange(GeneList resultCL, MaHybridSample ms, float intensLB, float intensUB, boolean outsideRangeFlag) setIntensHistCLfromIntensRange() - set GeneList of (F1+F2)/2 in intensity range
(package private) boolean	CompositeDatabase.setRatioHistCLfromF1F2Ratios(GeneList resultCL, MaHybridSample ms, float ratioLB, float ratioUB, boolean outsideRangeFlag) setRatioHistCLfromF1F2Ratios() - set GeneList of F1/F2 ratios in ratio range
(package private) boolean	CompositeDatabase.setRatioHistCLfromHP_XYratios(GeneList resultCL, MaHybridSample msX, MaHybridSample msY, float ratioLB, float ratioUB, boolean outsideRangeFlag) setRatioHistCLfromHP_XYRatios() - set GeneList of X/Y ratios in ratio range
(package private) java.lang.String	CompositeDatabase.lookupHPcoords(int x, int y, int distThreshold, boolean useFieldNameFlag, MaHybridSample ms) lookupHPcoords() - lookup closest gene name by (x,y) in sample pseudoarray and set current gene if < distThreshold away, else return "".
(package private) void	CompositeDatabase.setOBJtoGID(int gid, MaHybridSample ms) setOBJtoGID() - set the current gene xxxOBJ values to the specified GID.
(package private) int	CompositeDatabase.getNormHP_XandYdata(float[] xList, float[] yList, int[] propList, GeneList ml, MaHybridSample msX, MaHybridSample msY, boolean setPropsFlag, boolean filterByMLflag) getNormHP_XandYdata() - get normalized list spot (HP-X,HP-Y) data passing data filter ml or mae.fc.workingCL.
(package private) int	CompositeDatabase.getRawHP_XandYdata(float[] xData, float[] yData, float[] xBkgd, float[] yBkgd, int[] propList, GeneList ml, MaHybridSample msX, MaHybridSample msY, boolean setPropsFlag, boolean filterByMLflag) getRawHP_XandYdata() - get list raw spot (HP-X,HP-Y) data passing data filter ml or mae.fc.workingCL.
(package private) int	Condition.addCondList(java.lang.String conditionName, MaHybridSample[] msList, int msListLength, int offset) addCondList() - add conditionName Condition list with msList[] data
(package private) boolean	Condition.addHPtoCondList(MaHybridSample ms) addHPtoCondList() - add Sample to condition list.
(package private) boolean	Condition.rmvHPfromCondList(MaHybridSample ms) rmvHPfromCondList() - remove Sample from condition list
(package private) boolean	Condition.isHPinCondList(MaHybridSample ms) isHPinCondList() - is Sample in condition list
private void	DrawPseudoImage.drawGridLabelsInImage(MaHybridSample ms, java.awt.Graphics g, boolean isRatioPlot, boolean isDualPseudoImageFlag) drawGridLabelsInImage() - draw ms.textQ[] in the image at (x,y)[] locations.
(package private) void	DrawPseudoImage.drawPseudoImage(java.awt.Graphics gi, int piWidth, int piHeight, int plotMode, MaHybridSample ms) drawPseudoImage() - draw pseudoarray image of filled grayscale circles using the totC[] density values.
(package private) boolean	Filter.setHP_XY_t_TestCL(GeneList t_TestResultCL, GeneList genesToTestCL, MaHybridSample msX, MaHybridSample msY, float pValueThr) setHP_XY_t_TestCL() - set GeneList of genes passing HP-X,HP-Y t-Test with a pValue better than pValueThr. Compute the means and std deviations using the f1,f2 values for each sample.
(package private) boolean	Filter.setThresholdsCL(GeneList genesToTestCL, GeneList passedCL, MaHybridSample msX, MaHybridSample msY, boolean testGrayFlag) setThresholdsCL() - set GeneList of thresholded F1,F2 or HP_X,HP_Y intensity or ratio range where the threshold for rangeType [T1:T2] or [R1:R2] and rangeMode is RANGE_INSIDE, RANGE_OUTSIDE.
(package private) boolean	Filter.setCy3Cy5RatiosCL(GeneList genesToTestCL, GeneList passedCL, MaHybridSample msX, boolean useCy5Cy3flag) setCy3Cy5RatiosCL() - Set GeneList of thresholded genes for Cy3/Cy5 ratio range where the threshold for rangeType [CR1:CR2] and rangeMode RANGE_INSIDE, RANGE_OUTSIDE.
(package private) static int	MJAbase.lookupHPsampleNbr(MaHybridSample ms) lookupHPsampleNbr() - lookup MaHybidSample's sampleNbr.
(package private) static int	SampleSets.lookupHPsampleNbr(MaHybridSample ms) lookupHPsampleNbr() - lookup MaHybidSample's sampleNbr.
(package private) boolean	SampleSets.addHPtoDB(MaHybridSample ms, int i) addHPtoDB() - set HP sample to active database entry i
(package private) boolean	SampleSets.addNewHPtoDB(MaHybridSample ms) addNewHPtoDB() - add new HP sample to end of active database list
(package private) boolean	SampleSets.addHPtoXset(MaHybridSample ms) addHPtoXset() - add HP sample to HP-X set
(package private) boolean	SampleSets.addHPtoYset(MaHybridSample ms) addHPtoYset() - add HP sample to HP-Y set
(package private) boolean	SampleSets.addHPtoElist(MaHybridSample ms) addHPtoElist() - add HP sample to end of HP-E list
(package private) boolean	SampleSets.rmvHPfromXset(MaHybridSample ms) rmvHPfromXset() - remove HP sample from HP-X set
(package private) boolean	SampleSets.rmvHPfromYset(MaHybridSample ms) rmvHPfromYset() - remove HP sample from HP-Y set
(package private) boolean	SampleSets.rmvHPfromElist(MaHybridSample ms) rmvHPfromElist() - remove HP sample from HP-E list
private void	SampleSets.assignHPtoAxis(int n, int axis, MaHybridSample ms) assignHPtoAxis() - assign sample to current HP-X or HP-Y sample This is the default.
(package private) void	ScrollableImageCanvas.setObjState(MaHybridSample ms, int xObj, int yObj) setObjState() - change the object position
(package private) void	ScrollableImageCanvas.setImgPos(MaHybridSample ms, int xImg, int yImg) setImgPos() - set the Image position.
(package private) static void	SpotData.setSpotData(MaHybridSample msS, int x, int y, int gid, float tot) setSpotData() - set the default STATIC spot data by (x,y).
(package private) static void	SpotData.setSpotData(MaHybridSample msS, java.awt.Point xy, int gid, float tot) setSpotData() - set the default STATIC spot data by Point xy.
(package private) static void	SpotData.setSpotData1(MaHybridSample msS, java.awt.Point xy, int gid, float tot) setSpotData1() - set the default STATIC spot data by Point xy.
(package private) static void	SpotData.setSpotData2(MaHybridSample msS, java.awt.Point xy, int gid, float tot) setSpotData2() - set the default STATIC spot data by Point xy.
(package private) java.lang.String	SpotFeatures.getSpotMeasurementStr(int gid, MaHybridSample ms) getSpotMeasurementStr() - return pretty-print spot measurement string.
(package private) java.lang.String	SpotFeatures.getXYG(java.awt.Point xy, MaHybridSample ms) getXYG() - return pretty-print string for status of x,y,grayvalue string.
(package private) java.lang.String	SpotFeatures.getSpotFeatures(java.awt.Point xy, MaHybridSample ms) getSpotFeatures() - get spot coords and features associated with spot at (x,y)
(package private) java.lang.String	SpotFeatures.getSpotGenomicData(java.awt.Point xy, MaHybridSample ms) getSpotGenomicData() - get additional genomic name features by (x,y) coordindate of current spot for sample if the features exist.
(package private) void	SpotFeatures.showValidSpotInfo(java.awt.Point xyObj, MaHybridSample ms) showValidSpotInfo() - show spot gene info if valid obj else no-op
(package private) boolean	Util.popupImageOfHPsample(MaHybridSample ms) popupImageOfHPsample() - popup image of current gene in Web browser.

Constructors in with parameters of type MaHybridSample

ClusterGenes(GeneList complexClusterCL, MaHybridSample[] msEPlist, int nEPmsList)
ClusterGenes() - constructor to create instance of new cluster method

ClusterSamples(MAExplorer mae, GeneList mList, MaHybridSample[] msList, int nMSlist)
ClusterSamples() - constructor

Condition(java.lang.String condName, MaHybridSample[] msList, int msListLength, int offset)
Condition() - constructor to create a new condition with list of samples.

MaHPquantTable(MAExplorer mae, MaHybridSample ms, java.lang.String fileName, java.lang.String hpName, boolean swapCy5Cy3DataFlag)
MaHPquantTable() - constructor to read the .quant file table and setup MaHybridSample

ScrollableImageCanvas(MaHybridSample ms, int preferredWidth, int preferredHeight, ArrayScroller is)
ScrollableImageCanvas() - constructor for scrollable pseudoarray image canvas.