Package ubic.gemma.model.expression.bioAssayData

Class SingleCellExpressionDataVectorUtils

java.lang.Object

ubic.gemma.model.expression.bioAssayData.SingleCellExpressionDataVectorUtils

public class SingleCellExpressionDataVectorUtils
extends Object

Utilities for working with SingleCellExpressionDataVector.

Author:

poirigui

Constructor Summary

Constructors

Constructor	Description
SingleCellExpressionDataVectorUtils()

Method Summary

Modifier and Type	Method	Description
static Consumer<SingleCellExpressionDataVector>	createStreamMonitor(ExpressionExperiment ee, QuantitationType qt, String logCategory, int reportFrequency, long numVecs)	Create a consumer for a Stream that will report progress of retrieving single-cell vectors.
static double[]	getSampleDataAsDoubles(SingleCellExpressionDataVector vector, int sampleIndex)	Obtain the data of a sample.
static double[]	getSampleDataAsDoubles(SingleCellExpressionDataVector vector, int sampleIndex, CellLevelCharacteristics cellLevelCharacteristics, int row)
static double[]	getSampleDataAsDoubles(SingleCellExpressionDataVector vector, DoubleBuffer buffer, int sampleIndex)
static double[]	getSampleDataAsDoubles(SingleCellExpressionDataVector vector, DoubleBuffer data, int sampleIndex, CellLevelCharacteristics cellLevelCharacteristics, int row)	Obtain the data of a sample.
static double[]	getSampleDataAsDoubles(SingleCellExpressionDataVector vector, BioAssay sample)
static float[]	getSampleDataAsFloats(SingleCellExpressionDataVector vector, int sampleIndex)	Obtain the data of a sample.
static float[]	getSampleDataAsFloats(SingleCellExpressionDataVector vector, int sampleIndex, CellLevelCharacteristics cellLevelCharacteristics, int row)
static float[]	getSampleDataAsFloats(SingleCellExpressionDataVector vector, FloatBuffer buffer, int sampleIndex)
static float[]	getSampleDataAsFloats(SingleCellExpressionDataVector vector, FloatBuffer data, int sampleIndex, CellLevelCharacteristics cellLevelCharacteristics, int row)	Obtain the data of a sample.
static int[]	getSampleDataAsInts(SingleCellExpressionDataVector vector, int sampleIndex)
static int[]	getSampleDataAsInts(SingleCellExpressionDataVector vector, int sampleIndex, CellLevelCharacteristics cellLevelCharacteristics, int row)
static int[]	getSampleDataAsInts(SingleCellExpressionDataVector vector, IntBuffer buffer, int sampleIndex)
static int[]	getSampleDataAsInts(SingleCellExpressionDataVector vector, IntBuffer data, int sampleIndex, CellLevelCharacteristics cellLevelCharacteristics, int row)
static long[]	getSampleDataAsLongs(SingleCellExpressionDataVector vector, int sampleIndex)
static long[]	getSampleDataAsLongs(SingleCellExpressionDataVector vector, int sampleIndex, CellLevelCharacteristics cellLevelCharacteristics, int row)
static long[]	getSampleDataAsLongs(SingleCellExpressionDataVector vector, LongBuffer buffer, int sampleIndex)
static long[]	getSampleDataAsLongs(SingleCellExpressionDataVector vector, LongBuffer data, int sampleIndex, CellLevelCharacteristics cellLevelCharacteristics, int row)
static int	getSampleEnd(SingleCellDimension dimension, int[] dataIndices, int sampleIndex, int after)	Only exposed for internal use, prefer getSampleEnd(SingleCellExpressionDataVector, int, int).
static int	getSampleEnd(SingleCellExpressionDataVector vector, int sampleIndex, int after)	Get the *exclusive* index of the last cell for a given sample.
static int	getSampleEnd(SingleCellExpressionDataVector vector, BioAssay sample)
static int	getSampleEnd(SingleCellExpressionDataVector vector, BioAssay sample, int after)
static int	getSampleStart(SingleCellExpressionDataVector vector, int sampleIndex, int after)	Get the index of the first cell for a given sample.
static int	getSampleStart(SingleCellExpressionDataVector vector, BioAssay sample)
static int	getSampleStart(SingleCellExpressionDataVector vector, BioAssay sample, int after)

Methods inherited from class java.lang.Object

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

Constructor Details

SingleCellExpressionDataVectorUtils

public SingleCellExpressionDataVectorUtils()

Method Details

getSampleStart

public static int getSampleStart(SingleCellExpressionDataVector vector,
 BioAssay sample)

See Also:

• getSampleStart(SingleCellExpressionDataVector, int, int)

getSampleStart

public static int getSampleStart(SingleCellExpressionDataVector vector,
 BioAssay sample,
 int after)

See Also:

• getSampleStart(SingleCellExpressionDataVector, int, int)

getSampleStart

public static int getSampleStart(SingleCellExpressionDataVector vector,
 int sampleIndex,
 int after)

Get the index of the first cell for a given sample.

Parameters:

vector - vector

sampleIndex - index of the sample in the single-cell dimension, see

invalid reference

SingleCellDimension#getBioAssays()

after - starting position for the search

getSampleEnd

public static int getSampleEnd(SingleCellExpressionDataVector vector,
 BioAssay sample)

getSampleEnd

public static int getSampleEnd(SingleCellExpressionDataVector vector,
 BioAssay sample,
 int after)

getSampleEnd

public static int getSampleEnd(SingleCellExpressionDataVector vector,
 int sampleIndex,
 int after)

Get the *exclusive* index of the last cell for a given sample.

Parameters:

vector - vector

sampleIndex - index of the sample in the single-cell dimension, see

invalid reference

SingleCellDimension#getBioAssays()

after - starting position for the search, if you previously called getSampleStart(SingleCellExpressionDataVector, int, int), you should use this value here to save some time

getSampleEnd

public static int getSampleEnd(SingleCellDimension dimension,
 int[] dataIndices,
 int sampleIndex,
 int after)

Only exposed for internal use, prefer getSampleEnd(SingleCellExpressionDataVector, int, int).

getSampleDataAsDoubles

public static double[] getSampleDataAsDoubles(SingleCellExpressionDataVector vector,
 BioAssay sample)

getSampleDataAsFloats

public static float[] getSampleDataAsFloats(SingleCellExpressionDataVector vector,
 int sampleIndex)

Obtain the data of a sample.

getSampleDataAsFloats

public static float[] getSampleDataAsFloats(SingleCellExpressionDataVector vector,
 FloatBuffer buffer,
 int sampleIndex)

getSampleDataAsDoubles

public static double[] getSampleDataAsDoubles(SingleCellExpressionDataVector vector,
 int sampleIndex)

Obtain the data of a sample.

getSampleDataAsDoubles

public static double[] getSampleDataAsDoubles(SingleCellExpressionDataVector vector,
 DoubleBuffer buffer,
 int sampleIndex)

getSampleDataAsInts

public static int[] getSampleDataAsInts(SingleCellExpressionDataVector vector,
 int sampleIndex)

getSampleDataAsInts

public static int[] getSampleDataAsInts(SingleCellExpressionDataVector vector,
 IntBuffer buffer,
 int sampleIndex)

getSampleDataAsLongs

public static long[] getSampleDataAsLongs(SingleCellExpressionDataVector vector,
 int sampleIndex)

getSampleDataAsLongs

public static long[] getSampleDataAsLongs(SingleCellExpressionDataVector vector,
 LongBuffer buffer,
 int sampleIndex)

getSampleDataAsFloats

public static float[] getSampleDataAsFloats(SingleCellExpressionDataVector vector,
 int sampleIndex,
 CellLevelCharacteristics cellLevelCharacteristics,
 int row)

getSampleDataAsFloats

public static float[] getSampleDataAsFloats(SingleCellExpressionDataVector vector,
 FloatBuffer data,
 int sampleIndex,
 CellLevelCharacteristics cellLevelCharacteristics,
 int row)

Obtain the data of a sample.

getSampleDataAsDoubles

public static double[] getSampleDataAsDoubles(SingleCellExpressionDataVector vector,
 int sampleIndex,
 CellLevelCharacteristics cellLevelCharacteristics,
 int row)

getSampleDataAsDoubles

public static double[] getSampleDataAsDoubles(SingleCellExpressionDataVector vector,
 DoubleBuffer data,
 int sampleIndex,
 CellLevelCharacteristics cellLevelCharacteristics,
 int row)

Obtain the data of a sample.

getSampleDataAsInts

public static int[] getSampleDataAsInts(SingleCellExpressionDataVector vector,
 int sampleIndex,
 CellLevelCharacteristics cellLevelCharacteristics,
 int row)

getSampleDataAsInts

public static int[] getSampleDataAsInts(SingleCellExpressionDataVector vector,
 IntBuffer data,
 int sampleIndex,
 CellLevelCharacteristics cellLevelCharacteristics,
 int row)

getSampleDataAsLongs

public static long[] getSampleDataAsLongs(SingleCellExpressionDataVector vector,
 int sampleIndex,
 CellLevelCharacteristics cellLevelCharacteristics,
 int row)

getSampleDataAsLongs

public static long[] getSampleDataAsLongs(SingleCellExpressionDataVector vector,
 LongBuffer data,
 int sampleIndex,
 CellLevelCharacteristics cellLevelCharacteristics,
 int row)

createStreamMonitor

public static Consumer<SingleCellExpressionDataVector> createStreamMonitor(ExpressionExperiment ee,
 QuantitationType qt,
 String logCategory,
 int reportFrequency,
 long numVecs)

Create a consumer for a Stream that will report progress of retrieving single-cell vectors.

The logging is similar to that of ProgressReporter.