Class DatasetsWebService.SampleCorrelationMatrixValueObject

java.lang.Object

ubic.gemma.rest.DatasetsWebService.SampleCorrelationMatrixValueObject

Enclosing class:

DatasetsWebService

public static final class DatasetsWebService.SampleCorrelationMatrixValueObject
extends Object

Wire shape for DatasetsWebService.getDatasetSampleCorrelation(DatasetArg, DatasetsWebService.CorrelationMatrixChoice): a symmetric N×N Pearson correlation matrix with bioAssay ids + short names parallel to the rows/columns.

Author:

tesarst

Constructor Summary

Constructors

Constructor	Description
SampleCorrelationMatrixValueObject(DoubleMatrix<BioAssay,BioAssay> matrix, String matrixKind, Set<Long> actualOutlierIds, Set<Long> predictedOutlierIds)

Method Summary

Modifier and Type	Method	Description
boolean	equals(Object o)
Long[]	getActualOutlierBioAssayIds()	BioAssay ids the curator has explicitly flagged as outliers (BioAssay.getIsOutlier()).
Long[]	getBioAssayIds()	BioAssay ids in the order the rows / columns of values appear.
String[]	getBioAssayShortNames()	BioAssay short names parallel to bioAssayIds, for axis labels.
String	getFilterDescription()	Currently always null; placeholder for a probe-filter caption once SampleCoexpressionAnalysisService surfaces it.
String	getMatrix()	Which stored matrix this is: "regressed" (major factors regressed out) or "full" (none regressed).
String	getMethod()	Currently always "pearson" — Gemma's only supported correlation method here.
Long[]	getPredictedOutlierBioAssayIds()	BioAssay ids the median-correlation algorithm flags as outliers (OutlierDetectionService.getOutlierDetails(ExpressionExperiment)).
double[][]	getValues()	Symmetric, row-major, N×N Pearson correlation matrix.
int	hashCode()
String	toString()

Methods inherited from class Object

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

Constructor Details

SampleCorrelationMatrixValueObject

public SampleCorrelationMatrixValueObject(DoubleMatrix<BioAssay,BioAssay> matrix,
 String matrixKind,
 Set<Long> actualOutlierIds,
 Set<Long> predictedOutlierIds)

Method Details

getBioAssayIds

public Long[] getBioAssayIds()

BioAssay ids in the order the rows / columns of values appear.

getBioAssayShortNames

public String[] getBioAssayShortNames()

BioAssay short names parallel to bioAssayIds, for axis labels. Entries may be null for assays whose name has not been set.

getValues

public double[][] getValues()

Symmetric, row-major, N×N Pearson correlation matrix. values[i][j] is the correlation in [-1, 1] between the i'th and j'th bioAssay. Always sent UNMASKED — the UI applies any outlier-driven masking interactively.

getActualOutlierBioAssayIds

public Long[] getActualOutlierBioAssayIds()

BioAssay ids the curator has explicitly flagged as outliers (BioAssay.getIsOutlier()).

getPredictedOutlierBioAssayIds

public Long[] getPredictedOutlierBioAssayIds()

BioAssay ids the median-correlation algorithm flags as outliers (OutlierDetectionService.getOutlierDetails(ExpressionExperiment)). May overlap with actualOutlierBioAssayIds or stand alone.

getMatrix

public String getMatrix()

Which stored matrix this is: "regressed" (major factors regressed out) or "full" (none regressed). A caller asking for best gets one or the other and this is how it tells.

getFilterDescription

@Nullable
public String getFilterDescription()

Currently always null; placeholder for a probe-filter caption once SampleCoexpressionAnalysisService surfaces it.

getMethod

@Nullable
public String getMethod()

Currently always "pearson" — Gemma's only supported correlation method here.

equals

public boolean equals(Object o)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object

toString

public String toString()

Overrides:

toString in class Object