Class ExperimentExpressionLevelsValueObject

java.lang.Object

ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject

All Implemented Interfaces:

Serializable

public class ExperimentExpressionLevelsValueObject
extends Object
implements Serializable

See Also:

• Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	ExperimentExpressionLevelsValueObject.GeneDiffExStats	Per-gene differential-expression statistics carried alongside expression levels for the /datasets/{dataset}/expressions/differential endpoint.
static class	ExperimentExpressionLevelsValueObject.GeneElementExpressionsValueObject
static class	ExperimentExpressionLevelsValueObject.VectorElementValueObject

Field Summary

Fields

Modifier and Type	Field	Description
static final String	OPT_AVG
static final String	OPT_PICK_MAX
static final String	OPT_PICK_VAR

Constructor Summary

Constructors

Constructor	Description
ExperimentExpressionLevelsValueObject()
ExperimentExpressionLevelsValueObject(long datasetId, Map<Gene, List<DoubleVectorValueObject>> vectorsPerGene, boolean keepGeneNonSpecific, String conslidationMode)
ExperimentExpressionLevelsValueObject(long datasetId, Map<Gene, List<DoubleVectorValueObject>> vectorsPerGene, boolean keepGeneNonSpecific, String conslidationMode, Map<Gene, ExperimentExpressionLevelsValueObject.GeneDiffExStats> diffExStatsPerGene)	Variant that carries per-gene differential-expression statistics for the contrast represented by the result-set used to build the response.

Method Summary

Modifier and Type	Method	Description
long	getDatasetId()
LinkedList<ExperimentExpressionLevelsValueObject.GeneElementExpressionsValueObject>	getGeneExpressionLevels()
void	roundValuesForJson()	Round every expression value and per-gene statistic in this response to RoundingUtils.JSON_SIGNIFICANT_DIGITS significant digits.

Methods inherited from class Object

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

Field Details

OPT_PICK_MAX

public static final String OPT_PICK_MAX

See Also:

• Constant Field Values

OPT_PICK_VAR

public static final String OPT_PICK_VAR

See Also:

• Constant Field Values

OPT_AVG

public static final String OPT_AVG

See Also:

• Constant Field Values

Constructor Details

ExperimentExpressionLevelsValueObject

public ExperimentExpressionLevelsValueObject()

ExperimentExpressionLevelsValueObject

public ExperimentExpressionLevelsValueObject(long datasetId,
 Map<Gene, List<DoubleVectorValueObject>> vectorsPerGene,
 boolean keepGeneNonSpecific,
 @Nullable
 String conslidationMode)

ExperimentExpressionLevelsValueObject

public ExperimentExpressionLevelsValueObject(long datasetId,
 Map<Gene, List<DoubleVectorValueObject>> vectorsPerGene,
 boolean keepGeneNonSpecific,
 @Nullable
 String conslidationMode,
 Map<Gene, ExperimentExpressionLevelsValueObject.GeneDiffExStats> diffExStatsPerGene)

Variant that carries per-gene differential-expression statistics for the contrast represented by the result-set used to build the response. See geneOfficialName accessors on ExperimentExpressionLevelsValueObject.GeneElementExpressionsValueObject for the exposed fields.

Method Details

roundValuesForJson

public void roundValuesForJson()

Round every expression value and per-gene statistic in this response to RoundingUtils.JSON_SIGNIFICANT_DIGITS significant digits.

Gemma's expression data descends from 16-bit measurements and these values are plotted rather than recomputed from; the digits this drops are also incompressible, so they cost the most on the largest responses. The REST layer applies this unless the caller asks for precise=true.

Mutates in place. That is safe here and only here: the producer builds a fresh value object per request, and VectorElementValueObject copies each vector's values into its own map, so the cached DoubleVectorValueObject arrays are never reached.

getDatasetId

public long getDatasetId()

getGeneExpressionLevels

public LinkedList<ExperimentExpressionLevelsValueObject.GeneElementExpressionsValueObject> getGeneExpressionLevels()