Serialized Form

Package ubic.gemma.core.analysis.expression.coexpression.links

Class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

absoluteValue

boolean absoluteValue

arrayName

String arrayName

cdfCut

double cdfCut

checkCorrelationDistribution

boolean checkCorrelationDistribution

checkForBatchEffect

boolean checkForBatchEffect

checkForOutliers

boolean checkForOutliers

correlationCacheThreshold

double correlationCacheThreshold

fwe

double fwe

lowerCdfCutUsed

boolean lowerCdfCutUsed

lowerTailCut

double lowerTailCut

makeSampleCorrMatImages

boolean makeSampleCorrMatImages

metric

String metric

minNumPresent

int minNumPresent

normalizationMethod

LinkAnalysisConfig.NormalizationMethod normalizationMethod

omitNegLinks

boolean omitNegLinks

outputFile

File outputFile

probeDegreeThreshold

int probeDegreeThreshold

singularThreshold

LinkAnalysisConfig.SingularThreshold singularThreshold

subset

boolean subset

subsetSize

double subsetSize

subsetUsed

boolean subsetUsed

textOut

boolean textOut

upperCdfCutUsed

boolean upperCdfCutUsed

upperTailCut

double upperTailCut

useDb

boolean useDb

Class ubic.gemma.core.analysis.expression.coexpression.links.UnsuitableForAnalysisException extends RuntimeException implements Serializable

serialVersionUID:

-4436136164850796179L

Package ubic.gemma.core.analysis.expression.diff

Class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig extends Object implements Serializable

serialVersionUID:

622877438067070041L

Serialized Fields

analysisType

DifferentialExpressionAnalyzerServiceImpl.AnalysisType analysisType

baseLineFactorValues

Map<ExperimentalFactor,FactorValue> baseLineFactorValues

ebayes

boolean ebayes

factorsToInclude

List<ExperimentalFactor> factorsToInclude

interactionsToInclude

Collection<Collection<ExperimentalFactor>> interactionsToInclude

makeArchiveFile

boolean makeArchiveFile

persist

boolean persist

subsetFactor

ExperimentalFactor subsetFactor

subsetFactorValue

FactorValue subsetFactorValue

useWeights

boolean useWeights

Class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionMetaAnalysisValueObject extends Object implements Serializable

Serialized Fields

activeExperiments

Collection<BioAssaySet> activeExperiments

fisherPValue

Double fisherPValue

gene

GeneValueObject gene

numExperimentsInScope

int numExperimentsInScope

numMetThreshold

int numMetThreshold

numSearchedExperiments

int numSearchedExperiments

probeResults

Collection<DifferentialExpressionValueObject> probeResults

sortKey

String sortKey

Class ubic.gemma.core.analysis.expression.diff.DiffExpressionSelectedFactorCommand extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

eeId

Long eeId

efId

Long efId

Package ubic.gemma.core.analysis.preprocess

Class ubic.gemma.core.analysis.preprocess.FailedToComputeSingularValueDecomposition extends PreprocessingException implements Serializable

Class ubic.gemma.core.analysis.preprocess.InsufficientProbesException extends InsufficientDataException implements Serializable

serialVersionUID:

1L

Class ubic.gemma.core.analysis.preprocess.PreprocessingException extends RuntimeException implements Serializable

serialVersionUID:

-8463478950898408838L

Class ubic.gemma.core.analysis.preprocess.QuantitationMismatchPreprocessingException extends PreprocessingException implements Serializable

Class ubic.gemma.core.analysis.preprocess.SampleCoexpressionRelatedPreprocessingException extends PreprocessingException implements Serializable

Class ubic.gemma.core.analysis.preprocess.SVDRelatedPreprocessingException extends PreprocessingException implements Serializable

Serialized Fields

cause

SVDException cause

Class ubic.gemma.core.analysis.preprocess.UnsupportedQuantitationScaleConversionException extends QuantitationTypeConversionException implements Serializable

Package ubic.gemma.core.analysis.preprocess.batcheffects

Class ubic.gemma.core.analysis.preprocess.batcheffects.BatchConfound extends Object implements Serializable

Serialized Fields

chiSquare

double chiSquare

df

int df

ee

BioAssaySet ee

ef

ExperimentalFactor ef

numBatches

int numBatches

p

double p

Class ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoMissingException extends BatchInfoPopulationException implements Serializable

Class ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationException extends PreprocessingException implements Serializable

serialVersionUID:

-1770591991479420212L

Class ubic.gemma.core.analysis.preprocess.batcheffects.FASTQHeadersPresentButNotUsableException extends BatchInfoPopulationException implements Serializable

serialVersionUID:

1917074433646650950L

Class ubic.gemma.core.analysis.preprocess.batcheffects.SingletonBatchesException extends BatchInfoPopulationException implements Serializable

serialVersionUID:

9088141067684148902L

Class ubic.gemma.core.analysis.preprocess.batcheffects.UnsupportedRawdataFileFormatException extends BatchInfoPopulationException implements Serializable

serialVersionUID:

1L

Package ubic.gemma.core.analysis.preprocess.svd

Class ubic.gemma.core.analysis.preprocess.svd.SVDException extends Exception implements Serializable

Class ubic.gemma.core.analysis.preprocess.svd.SVDValueObject extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

bioMaterialIds

Long[] bioMaterialIds

dateCorrelations

Map<Integer,Double> dateCorrelations

datePVals

Map<Integer,Double> datePVals

dates

List<Date> dates

factorCorrelations

Map<Integer,Map<Long,Double>> factorCorrelations

factorPvals

Map<Integer,Map<Long,Double>> factorPvals

factors

Map<Long,List<Double>> factors

id

Long id

variances

double[] variances

vMatrix

DoubleMatrix<Long,Integer> vMatrix

Package ubic.gemma.core.analysis.report

Class ubic.gemma.core.analysis.report.AuditableObject extends Object implements Serializable

serialVersionUID:

-7862129089784691035L

Serialized Fields

date

Date date

id

Long id

type

String type

Package ubic.gemma.core.analysis.sequence

Class ubic.gemma.core.analysis.sequence.CompositeSequenceMapValueObject extends Object implements Serializable

Serialized Fields

arrayDesignId

Long arrayDesignId

arrayDesignName

String arrayDesignName

arrayDesignShortName

String arrayDesignShortName

bioSequenceId

String bioSequenceId

bioSequenceName

String bioSequenceName

bioSequenceNcbiId

String bioSequenceNcbiId

compositeSequenceDescription

String compositeSequenceDescription

compositeSequenceId

String compositeSequenceId

compositeSequenceName

String compositeSequenceName

geneProducts

Map<Long,GeneProductValueObject> geneProducts

genes

Map<Long,GeneValueObject> genes

numBlatHits

Integer numBlatHits

Class ubic.gemma.core.analysis.sequence.GeneMappingSummary extends Object implements Serializable

serialVersionUID:

8899320580201273360L

Serialized Fields

blatResult

BlatResultValueObject blatResult

blatResultId

String blatResultId

compositeSequence

CompositeSequenceValueObject compositeSequence

geneProductIdGeneMap

Map<String,GeneValueObject> geneProductIdGeneMap

geneProductIdMap

Map<String,GeneProductValueObject> geneProductIdMap

geneProductMap

Map<GeneProductValueObject,GeneValueObject> geneProductMap

identity

double identity

score

double score

Package ubic.gemma.core.datastructure.matrix

Class ubic.gemma.core.datastructure.matrix.BaseExpressionDataMatrix extends Object implements Serializable

Serialized Fields

bioAssayDimensions

Map<CompositeSequence,BioAssayDimension> bioAssayDimensions

columnAssayMap

Map<BioAssay,Integer> columnAssayMap

columnBioAssayMapByInteger

Map<Integer,Collection<BioAssay>> columnBioAssayMapByInteger

columnBioMaterialMap

Map<BioMaterial,Integer> columnBioMaterialMap

columnBioMaterialMapByInteger

Map<Integer,BioMaterial> columnBioMaterialMapByInteger

expressionExperiment

ExpressionExperiment expressionExperiment

quantitationTypes

Collection<QuantitationType> quantitationTypes

rowDesignElementMapByInteger

Map<Integer,CompositeSequence> rowDesignElementMapByInteger

rowElementMap

Map<CompositeSequence,Integer> rowElementMap

rowElements

List<ExpressionDataMatrixRowElement> rowElements

Class ubic.gemma.core.datastructure.matrix.EmptyExpressionMatrix extends BaseExpressionDataMatrix<Object> implements Serializable

serialVersionUID:

1L

Serialized Fields

numCols

int numCols

Class ubic.gemma.core.datastructure.matrix.ExpressionDataBooleanMatrix extends BaseExpressionDataMatrix<Boolean> implements Serializable

serialVersionUID:

1L

Serialized Fields

matrix

ObjectMatrixImpl<CompositeSequence,Integer,Boolean> matrix

Class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix extends BaseExpressionDataMatrix<Double> implements Serializable

serialVersionUID:

1L

Serialized Fields

matrix

DoubleMatrix<CompositeSequence,BioMaterial> matrix

ranks

Map<CompositeSequence,Double> ranks

Class ubic.gemma.core.datastructure.matrix.ExpressionDataIntegerMatrix extends BaseExpressionDataMatrix<Integer> implements Serializable

serialVersionUID:

1L

Serialized Fields

matrix

IntegerMatrix<CompositeSequence,Integer> matrix

Class ubic.gemma.core.datastructure.matrix.ExpressionDataStringMatrix extends BaseExpressionDataMatrix<String> implements Serializable

serialVersionUID:

1L

Serialized Fields

matrix

StringMatrix<Integer,Integer> matrix

Class ubic.gemma.core.datastructure.matrix.ExpressionDataTestMatrix extends ExpressionDataDoubleMatrix implements Serializable

serialVersionUID:

1L

Class ubic.gemma.core.datastructure.matrix.InferredQuantitationMismatchException extends QuantitationMismatchException implements Serializable

Serialized Fields

inferredQuantitationType

QuantitationType inferredQuantitationType

Class ubic.gemma.core.datastructure.matrix.QuantitationMismatchException extends Exception implements Serializable

Serialized Fields

quantitationType

QuantitationType quantitationType

Class ubic.gemma.core.datastructure.matrix.QuantitationTypeConversionException extends RuntimeException implements Serializable

Class ubic.gemma.core.datastructure.matrix.SuspiciousValuesForQuantitationException extends QuantitationMismatchException implements Serializable

Serialized Fields

suspiciousValues

List<SuspiciousValuesForQuantitationException.SuspiciousValueResult> suspiciousValues

Package ubic.gemma.core.job

Class ubic.gemma.core.job.TaskCommand extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

emailAlert

boolean emailAlert

entityId

Long entityId

maxQueueMinutes

Integer maxQueueMinutes

maxRuntime

int maxRuntime

persistJobDetails

Boolean persistJobDetails

securityContext

org.springframework.security.core.context.SecurityContext securityContext

submitter

String submitter

taskId

String taskId

Class ubic.gemma.core.job.TaskResult extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

answer

Object answer

exception

Exception exception

taskID

String taskID

Package ubic.gemma.core.job.progress

Class ubic.gemma.core.job.progress.ProgressData extends Object implements Serializable

serialVersionUID:

-4303625064082352461L

Serialized Fields

description

String description

done

boolean done

failed

boolean failed

forwardingURL

String forwardingURL

percent

int percent

taskId

String taskId

Class ubic.gemma.core.job.progress.SubmittedTaskValueObject extends Object implements Serializable

serialVersionUID:

6757089319713433356L

Serialized Fields

done

boolean done

emailAlert

boolean emailAlert

finishTime

Date finishTime

lastLogMessage

String lastLogMessage

logMessages

String logMessages

runningRemotely

boolean runningRemotely

startTime

Date startTime

submissionTime

Date submissionTime

submitter

String submitter

taskId

String taskId

taskStatus

String taskStatus

taskType

String taskType

Package ubic.gemma.core.loader.entrez.pubmed

Class ubic.gemma.core.loader.entrez.pubmed.ESearchException extends Exception implements Serializable

Package ubic.gemma.core.loader.expression.arrayDesign

Class ubic.gemma.core.loader.expression.arrayDesign.Reporter extends AbstractDescribable implements Serializable

serialVersionUID:

3703827938981026012L

Serialized Fields

col

Integer col

compositeSequence

CompositeSequence compositeSequence

immobilizedCharacteristic

BioSequence immobilizedCharacteristic

row

Integer row

startInBioChar

Long startInBioChar

strand

String strand

Package ubic.gemma.core.loader.expression.geo

Class ubic.gemma.core.loader.expression.geo.GeoSampleCorrespondence extends Object implements Serializable

serialVersionUID:

-5285504953530483114L

Serialized Fields

accToDataset

Map<String,String> accToDataset

accToTitle

Map<String,String> accToTitle

sets

Collection<Set<String>> sets

Package ubic.gemma.core.loader.expression.geo.service

Class ubic.gemma.core.loader.expression.geo.service.IOExceptionWithRetry extends IOException implements Serializable

Serialized Fields

errorFromPreviousAttempt

IOExceptionWithRetry errorFromPreviousAttempt

Package ubic.gemma.core.loader.util

Class ubic.gemma.core.loader.util.AlreadyExistsInSystemException extends RuntimeException implements Serializable

serialVersionUID:

5677999264920938691L

Serialized Fields

data

Object data

Package ubic.gemma.core.loader.util.biomart

Class ubic.gemma.core.loader.util.biomart.Ensembl2NcbiValueObject extends Object implements Serializable

serialVersionUID:

-859220901359582113L

Serialized Fields

enemblTranscriptId

String enemblTranscriptId

ensembleGeneId

String ensembleGeneId

ensemblPeptideId

String ensemblPeptideId

hgcnId

String hgcnId

ncbiGenes

Collection<String> ncbiGenes

ncbiTaxonId

Integer ncbiTaxonId

Package ubic.gemma.core.ontology

Class ubic.gemma.core.ontology.AbstractOntologyResourceSimple extends Object implements Serializable

Serialized Fields

label

String label

uri

String uri

Class ubic.gemma.core.ontology.OntologyIndividualSimple extends AbstractOntologyResourceSimple implements Serializable

Serialized Fields

instanceOf

OntologyTermSimple instanceOf

Class ubic.gemma.core.ontology.OntologyPropertySimple extends AbstractOntologyResourceSimple implements Serializable

Package ubic.gemma.core.search

Class ubic.gemma.core.search.BaseCodeOntologySearchException extends SearchException implements Serializable

Serialized Fields

cause

OntologySearchException cause

Class ubic.gemma.core.search.ParseSearchException extends SearchException implements Serializable

Serialized Fields

originalParseException

ParseSearchException originalParseException

query

String query

Class ubic.gemma.core.search.SearchException extends Exception implements Serializable

Class ubic.gemma.core.search.SearchTimeoutException extends SearchException implements Serializable

Serialized Fields

cause

TimeoutException cause

Package ubic.gemma.core.search.lucene

Class ubic.gemma.core.search.lucene.LuceneParseSearchException extends ParseSearchException implements Serializable

Package ubic.gemma.core.search.source

Class ubic.gemma.core.search.source.HibernateSearchException extends SearchException implements Serializable

Serialized Fields

cause

org.hibernate.search.SearchException cause

Package ubic.gemma.core.util

Class ubic.gemma.core.util.GemmaRestApiClientException extends RuntimeException implements Serializable

Class ubic.gemma.core.util.StrictBeanDefinitionValidatorTest.TestAnnotatedVo extends Object implements Serializable

Class ubic.gemma.core.util.StrictBeanDefinitionValidatorTest.TestImplicitValueObject extends Object implements Serializable

Package ubic.gemma.model.analysis.expression.diff

Class ubic.gemma.model.analysis.expression.diff.ContrastResult extends Object implements Serializable

serialVersionUID:

-4310735803120153778L

Serialized Fields

coefficient

Double coefficient

factorValue

FactorValue factorValue

id

Long id

logFoldChange

Double logFoldChange

pvalue

Double pvalue

secondFactorValue

FactorValue secondFactorValue

tStat

Double tStat

Class ubic.gemma.model.analysis.expression.diff.ContrastResultValueObject extends IdentifiableValueObject<ContrastResult> implements Serializable

Serialized Fields

coefficient

Double coefficient

factorValue

FactorValueBasicValueObject factorValue

factorValueId

Long factorValueId

logFoldChange

Double logFoldChange

pvalue

Double pvalue

secondFactorValue

FactorValueBasicValueObject secondFactorValue

secondFactorValueId

Long secondFactorValueId

tStat

Double tStat

Class ubic.gemma.model.analysis.expression.diff.ContrastsValueObject extends Object implements Serializable

Serialized Fields

contrasts

List<ContrastVO> contrasts

resultId

Long resultId

Class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysis extends SingleExperimentAnalysis implements Serializable

serialVersionUID:

-7855180617739271699L

Serialized Fields

resultSets

Set<ExpressionAnalysisResultSet> resultSets

subsetFactorValue

FactorValue subsetFactorValue

Class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResult extends AnalysisResult implements Serializable

serialVersionUID:

8952834115689524169L

Serialized Fields

contrasts

Set<ContrastResult> contrasts

correctedPvalue

Double correctedPvalue

correctedPValueBin

Integer correctedPValueBin

id

Long id

probe

CompositeSequence probe

pvalue

Double pvalue

rank

Double rank

resultSet

ExpressionAnalysisResultSet resultSet

Class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResultSetValueObject extends AnalysisResultSetValueObject<DifferentialExpressionAnalysisResult,ExpressionAnalysisResultSet> implements Serializable

Serialized Fields

analysis

DifferentialExpressionAnalysisValueObject analysis

baselineGroup

FactorValueBasicValueObject baselineGroup

experimentalFactors

Collection<ExperimentalFactorValueObject> experimentalFactors

results

Collection<DifferentialExpressionAnalysisResultValueObject> results

secondBaselineGroup

FactorValueBasicValueObject secondBaselineGroup

taxa

Set<TaxonValueObject> taxa

Class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResultValueObject extends AnalysisResultValueObject<DifferentialExpressionAnalysisResult> implements Serializable

Serialized Fields

contrasts

List<ContrastResultValueObject> contrasts

correctedPvalue

Double correctedPvalue

genes

List<GeneValueObject> genes

probeId

Long probeId

probeName

String probeName

pValue

Double pValue

rank

Double rank

Class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisValueObject extends AnalysisValueObject<DifferentialExpressionAnalysis> implements Serializable

serialVersionUID:

622877438067070041L

Serialized Fields

arrayDesignsUsed

Collection<Long> arrayDesignsUsed

experimentAnalyzedId

Long experimentAnalyzedId

factorValuesUsed

Map<Long,Collection<FactorValueValueObject>> factorValuesUsed

resultSets

Collection<DiffExResultSetSummaryValueObject> resultSets

sourceExperimentId

Long sourceExperimentId

subsetFactor

ExperimentalFactorValueObject subsetFactor

subsetFactorId

Long subsetFactorId

subsetFactorValue

FactorValueValueObject subsetFactorValue

subsetFactorValueId

Long subsetFactorValueId

Class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionValueObject extends Object implements Serializable

Serialized Fields

contrasts

ContrastsValueObject contrasts

corrP

Double corrP

direction

Direction direction

experimentalFactors

Collection<ExperimentalFactorValueObject> experimentalFactors

expressionExperiment

ExpressionExperimentValueObject expressionExperiment

fisherContribution

Boolean fisherContribution

gene

GeneValueObject gene

id

Long id

metThreshold

Boolean metThreshold

p

Double p

probe

String probe

probeId

Long probeId

resultSetId

Long resultSetId

sortKey

String sortKey

Class ubic.gemma.model.analysis.expression.diff.DiffExprGeneSearchResult extends Object implements Serializable

serialVersionUID:

-6199218806972657112L

Serialized Fields

analysisResultId

Long analysisResultId

correctedPvalue

Double correctedPvalue

geneId

Long geneId

numberOfProbes

int numberOfProbes

numberOfProbesDiffExpressed

int numberOfProbesDiffExpressed

pvalue

Double pvalue

resultSetId

Long resultSetId

score

Double score

Class ubic.gemma.model.analysis.expression.diff.DiffExResultSetSummaryValueObject extends Object implements Serializable

serialVersionUID:

2063274043081170625L

Serialized Fields

analysisId

Long analysisId

arrayDesignsUsed

Collection<Long> arrayDesignsUsed

baselineGroup

FactorValueValueObject baselineGroup

bioAssaySetAnalyzedId

Long bioAssaySetAnalyzedId

downregulatedCount

Integer downregulatedCount

experimentalFactors

Collection<ExperimentalFactorValueObject> experimentalFactors

factorIds

Collection<Long> factorIds

id

Long id

numberOfDiffExpressedProbes

Integer numberOfDiffExpressedProbes

numberOfGenesAnalyzed

Integer numberOfGenesAnalyzed

numberOfProbesAnalyzed

Integer numberOfProbesAnalyzed

qValue

Double qValue

threshold

Double threshold

upregulatedCount

Integer upregulatedCount

Class ubic.gemma.model.analysis.expression.diff.ExpressionAnalysisResultSet extends FactorAssociatedAnalysisResultSet<DifferentialExpressionAnalysisResult> implements Serializable

serialVersionUID:

7226901182513177574L

Serialized Fields

analysis

DifferentialExpressionAnalysis analysis

baselineGroup

FactorValue baselineGroup

hitListSizes

Set<HitListSize> hitListSizes

numberOfGenesTested

Integer numberOfGenesTested

numberOfProbesTested

Integer numberOfProbesTested

pvalueDistribution

PvalueDistribution pvalueDistribution

results

Set<DifferentialExpressionAnalysisResult> results

Class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysis extends ExpressionAnalysis implements Serializable

serialVersionUID:

-2588180973962410595L

Serialized Fields

numGenesAnalyzed

Integer numGenesAnalyzed

qvalueThresholdForStorage

Double qvalueThresholdForStorage

results

Set<GeneDifferentialExpressionMetaAnalysisResult> results

resultSetsIncluded

Set<ExpressionAnalysisResultSet> resultSetsIncluded

Class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisDetailValueObject extends Object implements Serializable

serialVersionUID:

3868004995989355452L

Serialized Fields

includedResultSetsInfo

Collection<IncludedResultSetInfoValueObject> includedResultSetsInfo

numGenesAnalyzed

Integer numGenesAnalyzed

results

Collection<GeneDifferentialExpressionMetaAnalysisResultValueObject> results

Class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisResult extends Object implements Serializable

serialVersionUID:

-6553250926957951550L

Serialized Fields

gene

Gene gene

id

Long id

meanLogFoldChange

Double meanLogFoldChange

metaPvalue

Double metaPvalue

metaPvalueRank

Double metaPvalueRank

metaQvalue

Double metaQvalue

resultsUsed

Set<DifferentialExpressionAnalysisResult> resultsUsed

upperTail

Boolean upperTail

Class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisResultValueObject extends Object implements Serializable

serialVersionUID:

6099286095885830140L

Serialized Fields

geneName

String geneName

geneSymbol

String geneSymbol

metaPvalue

Double metaPvalue

metaQvalue

Double metaQvalue

upperTail

Boolean upperTail

Class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject extends Object implements Serializable

serialVersionUID:

-1856182824742323129L

Serialized Fields

description

String description

diffExpressionEvidence

DiffExpressionEvidenceValueObject diffExpressionEvidence

id

Long id

isEditable

boolean isEditable

isOwnedByCurrentUser

boolean isOwnedByCurrentUser

isPublic

boolean isPublic

isShared

boolean isShared

name

String name

numGenesAnalyzed

Integer numGenesAnalyzed

numResults

Integer numResults

numResultSetsIncluded

Integer numResultSetsIncluded

Class ubic.gemma.model.analysis.expression.diff.HitListSize extends Object implements Serializable

serialVersionUID:

-6398621486105806034L

Serialized Fields

direction

Direction direction

id

Long id

numberOfGenes

Integer numberOfGenes

numberOfProbes

Integer numberOfProbes

thresholdQvalue

Double thresholdQvalue

Class ubic.gemma.model.analysis.expression.diff.IncludedResultSetInfoValueObject extends Object implements Serializable

serialVersionUID:

-4660741839991839187L

Serialized Fields

analysisId

Long analysisId

experimentId

Long experimentId

resultSetId

Long resultSetId

Class ubic.gemma.model.analysis.expression.diff.PvalueDistribution extends Object implements Serializable

serialVersionUID:

-4783507721422402289L

Serialized Fields

binCounts

byte[] binCounts

id

Long id

numBins

Integer numBins

Package ubic.gemma.model.association.coexpression

Class ubic.gemma.model.association.coexpression.ExperimentCoexpressionLink extends Object implements Serializable

serialVersionUID:

-3850440587168527052L

Serialized Fields

experiment

BioAssaySet experiment

firstGene

Long firstGene

id

Long id

linkId

Long linkId

secondGene

Long secondGene

Class ubic.gemma.model.association.coexpression.Gene2GeneCoexpression extends Gene2GeneIdAssociation implements Serializable

serialVersionUID:

6088623734153830393L

Serialized Fields

numDataSetsSupporting

Integer numDataSetsSupporting

positiveCorrelation

Boolean positiveCorrelation

supportDetails

SupportDetails supportDetails

Class ubic.gemma.model.association.coexpression.GeneCoexpressionNodeDegree extends Object implements Serializable

serialVersionUID:

-1456064687251594963L

Serialized Fields

geneId

Long geneId

linkCountsNegative

byte[] linkCountsNegative

linkCountsPositive

byte[] linkCountsPositive

relativeLinkRanksNegative

byte[] relativeLinkRanksNegative

relativeLinkRanksPositive

byte[] relativeLinkRanksPositive

Class ubic.gemma.model.association.coexpression.GeneCoexpressionNodeDegreeValueObject extends Object implements Serializable

Serialized Fields

geneId

Long geneId

nodeDegreesNeg

TreeMap<Integer,Integer> nodeDegreesNeg

nodeDegreesPos

TreeMap<Integer,Integer> nodeDegreesPos

relDegreesNeg

TreeMap<Integer,Double> relDegreesNeg

relDegreesPos

TreeMap<Integer,Double> relDegreesPos

Class ubic.gemma.model.association.coexpression.HumanExperimentCoexpressionLinkImpl extends ExperimentCoexpressionLink implements Serializable

serialVersionUID:

8753430934473629791L

Class ubic.gemma.model.association.coexpression.HumanGeneCoExpression extends Gene2GeneCoexpression implements Serializable

serialVersionUID:

-908571853818330702L

Class ubic.gemma.model.association.coexpression.HumanGeneCoExpressionImpl extends HumanGeneCoExpression implements Serializable

serialVersionUID:

-1143581426457333084L

Class ubic.gemma.model.association.coexpression.MouseExperimentCoexpressionLinkImpl extends ExperimentCoexpressionLink implements Serializable

serialVersionUID:

498137981864642L

Class ubic.gemma.model.association.coexpression.MouseGeneCoExpression extends Gene2GeneCoexpression implements Serializable

serialVersionUID:

6475614056538630827L

Class ubic.gemma.model.association.coexpression.MouseGeneCoExpressionImpl extends MouseGeneCoExpression implements Serializable

serialVersionUID:

9197559725933952760L

Class ubic.gemma.model.association.coexpression.OtherExperimentCoexpressionLinkImpl extends ExperimentCoexpressionLink implements Serializable

serialVersionUID:

-1684811922186491341L

Class ubic.gemma.model.association.coexpression.OtherGeneCoExpression extends Gene2GeneCoexpression implements Serializable

serialVersionUID:

7730779544234187004L

Class ubic.gemma.model.association.coexpression.OtherGeneCoExpressionImpl extends OtherGeneCoExpression implements Serializable

serialVersionUID:

-2419886942835022490L

Class ubic.gemma.model.association.coexpression.RatExperimentCoexpressionLinkImpl extends ExperimentCoexpressionLink implements Serializable

serialVersionUID:

-3635504802405373650L

Class ubic.gemma.model.association.coexpression.RatGeneCoExpression extends Gene2GeneCoexpression implements Serializable

serialVersionUID:

-151363121627382446L

Class ubic.gemma.model.association.coexpression.RatGeneCoExpressionImpl extends RatGeneCoExpression implements Serializable

serialVersionUID:

5889802151081696108L

Package ubic.gemma.model.common.auditAndSecurity.eventType

Class ubic.gemma.model.common.auditAndSecurity.eventType.AlignmentBasedGeneMappingEvent extends ArrayDesignGeneMappingEvent implements Serializable

serialVersionUID:

7667960927701046528L

Class ubic.gemma.model.common.auditAndSecurity.eventType.AnalysisSuitabilityEvent extends AuditEventType implements Serializable

serialVersionUID:

7754007995197256846L

Class ubic.gemma.model.common.auditAndSecurity.eventType.AnnotationBasedGeneMappingEvent extends ArrayDesignGeneMappingEvent implements Serializable

serialVersionUID:

6216699496744292404L

Class ubic.gemma.model.common.auditAndSecurity.eventType.AnnotationEvent extends AuditEventType implements Serializable

serialVersionUID:

-7488448191665314917L

Class ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignAnalysisEvent extends AuditEventType implements Serializable

serialVersionUID:

-8391873112717801492L

Class ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignGeneMappingEvent extends ArrayDesignAnalysisEvent implements Serializable

serialVersionUID:

-7566135203525054499L

Class ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignMergeEvent extends ArrayDesignAnalysisEvent implements Serializable

serialVersionUID:

8243373027784116451L

Class ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignProbeRenamingEvent extends ArrayDesignAnalysisEvent implements Serializable

serialVersionUID:

-5458770150436736181L

Class ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignRepeatAnalysisEvent extends ArrayDesignAnalysisEvent implements Serializable

serialVersionUID:

-1315594279851821201L

Class ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignSequenceAnalysisEvent extends ArrayDesignAnalysisEvent implements Serializable

serialVersionUID:

8487897002282121437L

Class ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignSequenceRemoveEvent extends ArrayDesignAnalysisEvent implements Serializable

serialVersionUID:

-3044700012305059422L

Class ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignSequenceUpdateEvent extends ArrayDesignAnalysisEvent implements Serializable

serialVersionUID:

2502989996801972836L

Class ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignSubsumeCheckEvent extends ArrayDesignAnalysisEvent implements Serializable

serialVersionUID:

-6105886398033742202L

Class ubic.gemma.model.common.auditAndSecurity.eventType.AuditEventType extends Object implements Serializable

serialVersionUID:

-7397754091918396538L

Serialized Fields

id

Long id

Class ubic.gemma.model.common.auditAndSecurity.eventType.AutomatedAnnotationEvent extends AnnotationEvent implements Serializable

serialVersionUID:

8510568858539453569L

Class ubic.gemma.model.common.auditAndSecurity.eventType.BatchCorrectionEvent extends ExpressionExperimentAnalysisEvent implements Serializable

serialVersionUID:

-3061045506228031201L

Class ubic.gemma.model.common.auditAndSecurity.eventType.BatchInformationEvent extends ExpressionExperimentAnalysisEvent implements Serializable

Class ubic.gemma.model.common.auditAndSecurity.eventType.BatchInformationFetchingEvent extends BatchInformationEvent implements Serializable

serialVersionUID:

4635587632131568136L

Class ubic.gemma.model.common.auditAndSecurity.eventType.BatchInformationMissingEvent extends BatchInformationEvent implements Serializable

Class ubic.gemma.model.common.auditAndSecurity.eventType.BatchProblemsUpdateEvent extends ExpressionExperimentAnalysisEvent implements Serializable

serialVersionUID:

-3061045506228031201L

Class ubic.gemma.model.common.auditAndSecurity.eventType.BioMaterialMappingUpdate extends ExpressionExperimentAnalysisEvent implements Serializable

serialVersionUID:

-4390321148453980797L

Class ubic.gemma.model.common.auditAndSecurity.eventType.CommentedEvent extends AuditEventType implements Serializable

serialVersionUID:

-9053488530090657730L

Class ubic.gemma.model.common.auditAndSecurity.eventType.CurationDetailsEvent extends AuditEventType implements Serializable

serialVersionUID:

6621758826080039878L

Class ubic.gemma.model.common.auditAndSecurity.eventType.CurationNoteUpdateEvent extends CurationDetailsEvent implements Serializable

serialVersionUID:

-1180281595664872508L

Class ubic.gemma.model.common.auditAndSecurity.eventType.DataAddedEvent extends ExpressionExperimentAnalysisEvent implements Serializable

serialVersionUID:

-492849538043540166L

Class ubic.gemma.model.common.auditAndSecurity.eventType.DataRemovedEvent extends ExpressionExperimentAnalysisEvent implements Serializable

Class ubic.gemma.model.common.auditAndSecurity.eventType.DataReplacedEvent extends ExpressionExperimentAnalysisEvent implements Serializable

serialVersionUID:

-3239733956797015820L

Class ubic.gemma.model.common.auditAndSecurity.eventType.DifferentialExpressionAnalysisEvent extends ExpressionExperimentAnalysisEvent implements Serializable

serialVersionUID:

-2254124666542924604L

Class ubic.gemma.model.common.auditAndSecurity.eventType.DifferentialExpressionSuitabilityEvent extends AnalysisSuitabilityEvent implements Serializable

serialVersionUID:

-3436468845066159993L

Class ubic.gemma.model.common.auditAndSecurity.eventType.DoesNotNeedAttentionEvent extends CurationDetailsEvent implements Serializable

serialVersionUID:

6425018808816856629L

Class ubic.gemma.model.common.auditAndSecurity.eventType.ExperimentalDesignUpdatedEvent extends AuditEventType implements Serializable

serialVersionUID:

6359338763821876809L

Class ubic.gemma.model.common.auditAndSecurity.eventType.ExpressionExperimentAnalysisEvent extends AuditEventType implements Serializable

serialVersionUID:

6359338763821876809L

Class ubic.gemma.model.common.auditAndSecurity.eventType.ExpressionExperimentPlatformSwitchEvent extends ExpressionExperimentAnalysisEvent implements Serializable

serialVersionUID:

2918272498309052073L

Class ubic.gemma.model.common.auditAndSecurity.eventType.ExpressionExperimentUpdateFromGEOEvent extends AuditEventType implements Serializable

serialVersionUID:

5823969791153895703L

Class ubic.gemma.model.common.auditAndSecurity.eventType.ExpressionExperimentVectorMergeEvent extends ExpressionExperimentAnalysisEvent implements Serializable

serialVersionUID:

3635469819668645913L

Class ubic.gemma.model.common.auditAndSecurity.eventType.FactorValueNeedsAttentionEvent extends NeedsAttentionEvent implements Serializable

Class ubic.gemma.model.common.auditAndSecurity.eventType.FailedBatchInformationFetchingEvent extends BatchInformationFetchingEvent implements Serializable

Class ubic.gemma.model.common.auditAndSecurity.eventType.FailedBatchInformationMissingEvent extends BatchInformationMissingEvent implements Serializable

serialVersionUID:

-3235885345623521195L

Class ubic.gemma.model.common.auditAndSecurity.eventType.FailedDataReplacedEvent extends DataReplacedEvent implements Serializable

serialVersionUID:

304758117763492676L

Class ubic.gemma.model.common.auditAndSecurity.eventType.FailedDifferentialExpressionAnalysisEvent extends NeedsAttentionEvent implements Serializable

serialVersionUID:

6904992064998125083L

Class ubic.gemma.model.common.auditAndSecurity.eventType.FailedLinkAnalysisEvent extends NeedsAttentionEvent implements Serializable

serialVersionUID:

1234186759038122633L

Class ubic.gemma.model.common.auditAndSecurity.eventType.FailedMeanVarianceUpdateEvent extends NeedsAttentionEvent implements Serializable

Class ubic.gemma.model.common.auditAndSecurity.eventType.FailedMissingValueAnalysisEvent extends NeedsAttentionEvent implements Serializable

serialVersionUID:

-8827983770602337826L

Class ubic.gemma.model.common.auditAndSecurity.eventType.FailedPCAAnalysisEvent extends NeedsAttentionEvent implements Serializable

serialVersionUID:

-7055117029646665872L

Class ubic.gemma.model.common.auditAndSecurity.eventType.FailedProcessedVectorComputationEvent extends NeedsAttentionEvent implements Serializable

serialVersionUID:

-3296770035025801791L

Class ubic.gemma.model.common.auditAndSecurity.eventType.FailedSampleCorrelationAnalysisEvent extends NeedsAttentionEvent implements Serializable

Class ubic.gemma.model.common.auditAndSecurity.eventType.GeeqEvent extends AuditEventType implements Serializable

serialVersionUID:

6621758826080039878L

Class ubic.gemma.model.common.auditAndSecurity.eventType.LinkAnalysisEvent extends ExpressionExperimentAnalysisEvent implements Serializable

serialVersionUID:

-9218026901325452759L

Class ubic.gemma.model.common.auditAndSecurity.eventType.MakePrivateEvent extends PermissionChangeEvent implements Serializable

serialVersionUID:

1858209889786173945L

Class ubic.gemma.model.common.auditAndSecurity.eventType.MakePublicEvent extends PermissionChangeEvent implements Serializable

serialVersionUID:

-2250506177437626685L

Class ubic.gemma.model.common.auditAndSecurity.eventType.ManualAnnotationEvent extends AnnotationEvent implements Serializable

serialVersionUID:

-4919680073334263746L

Class ubic.gemma.model.common.auditAndSecurity.eventType.MeanVarianceUpdateEvent extends ExpressionExperimentAnalysisEvent implements Serializable

Class ubic.gemma.model.common.auditAndSecurity.eventType.MissingValueAnalysisEvent extends ExpressionExperimentAnalysisEvent implements Serializable

serialVersionUID:

-4000136638329943603L

Class ubic.gemma.model.common.auditAndSecurity.eventType.NeedsAttentionEvent extends CurationDetailsEvent implements Serializable

serialVersionUID:

-1180281595664872508L

Class ubic.gemma.model.common.auditAndSecurity.eventType.NotTroubledStatusFlagEvent extends CurationDetailsEvent implements Serializable

serialVersionUID:

-8586752080144045085L

Class ubic.gemma.model.common.auditAndSecurity.eventType.OutlierAnalysisEvent extends ExpressionExperimentAnalysisEvent implements Serializable

serialVersionUID:

681380361152118118L

Class ubic.gemma.model.common.auditAndSecurity.eventType.OutlierFoundAnalysisEvent extends OutlierAnalysisEvent implements Serializable

serialVersionUID:

-3797610069227351691L

Class ubic.gemma.model.common.auditAndSecurity.eventType.OutliersNotFoundAnalysisEvent extends OutlierAnalysisEvent implements Serializable

serialVersionUID:

-1857664606860041995L

Class ubic.gemma.model.common.auditAndSecurity.eventType.PCAAnalysisEvent extends ExpressionExperimentAnalysisEvent implements Serializable

serialVersionUID:

-7387174169412782003L

Class ubic.gemma.model.common.auditAndSecurity.eventType.PermissionChangeEvent extends AuditEventType implements Serializable

serialVersionUID:

-7205154783209555418L

Class ubic.gemma.model.common.auditAndSecurity.eventType.ProcessedVectorComputationEvent extends ExpressionExperimentAnalysisEvent implements Serializable

serialVersionUID:

3380481220417398475L

Class ubic.gemma.model.common.auditAndSecurity.eventType.RankComputationEvent extends ProcessedVectorComputationEvent implements Serializable

serialVersionUID:

7396366160834308993L

Class ubic.gemma.model.common.auditAndSecurity.eventType.ReleaseDetailsUpdateEvent extends VersionedEvent implements Serializable

Class ubic.gemma.model.common.auditAndSecurity.eventType.ResetSuitabilityForDifferentialExpressionAnalysisEvent extends DifferentialExpressionSuitabilityEvent implements Serializable

serialVersionUID:

5909581992797452478L

Class ubic.gemma.model.common.auditAndSecurity.eventType.SampleCorrelationAnalysisEvent extends ExpressionExperimentAnalysisEvent implements Serializable

Class ubic.gemma.model.common.auditAndSecurity.eventType.SampleRemovalEvent extends ExpressionExperimentAnalysisEvent implements Serializable

serialVersionUID:

6508357999103110838L

Class ubic.gemma.model.common.auditAndSecurity.eventType.SampleRemovalReversionEvent extends ExpressionExperimentAnalysisEvent implements Serializable

serialVersionUID:

-2893496636576496129L

Class ubic.gemma.model.common.auditAndSecurity.eventType.SingleBatchDeterminationEvent extends BatchInformationFetchingEvent implements Serializable

serialVersionUID:

-6544162258733474787L

Class ubic.gemma.model.common.auditAndSecurity.eventType.SingletonBatchInvalidEvent extends FailedBatchInformationFetchingEvent implements Serializable

serialVersionUID:

7917557159624872204L

Class ubic.gemma.model.common.auditAndSecurity.eventType.TooSmallDatasetLinkAnalysisEvent extends LinkAnalysisEvent implements Serializable

serialVersionUID:

3051344049635374788L

Class ubic.gemma.model.common.auditAndSecurity.eventType.TroubledStatusFlagEvent extends CurationDetailsEvent implements Serializable

serialVersionUID:

7335601529423635731L

Class ubic.gemma.model.common.auditAndSecurity.eventType.UninformativeFASTQHeadersForBatchingEvent extends FailedBatchInformationFetchingEvent implements Serializable

serialVersionUID:

8836148437542742955L

Class ubic.gemma.model.common.auditAndSecurity.eventType.UnsuitableForDifferentialExpressionAnalysisEvent extends DifferentialExpressionSuitabilityEvent implements Serializable

serialVersionUID:

4296161562091100967L

Class ubic.gemma.model.common.auditAndSecurity.eventType.VersionedEvent extends AuditEventType implements Serializable

Package ubic.gemma.model.common.description

Class ubic.gemma.model.common.description.AnnotationValueObject extends IdentifiableValueObject<Characteristic> implements Serializable

Serialized Fields

className

String className

classUri

String classUri

description

String description

evidenceCode

String evidenceCode

objectClass

String objectClass

parentDescription

String parentDescription

parentLink

String parentLink

parentName

String parentName

parentOfParentDescription

String parentOfParentDescription

parentOfParentLink

String parentOfParentLink

parentOfParentName

String parentOfParentName

termName

String termName

termUri

String termUri

Class ubic.gemma.model.common.description.BibliographicReference extends AbstractDescribable implements Serializable

serialVersionUID:

5823969791153895703L

Serialized Fields

abstractText

String abstractText

annotatedAbstract

String annotatedAbstract

Deprecated.

annotations

Set<Characteristic> annotations

Deprecated.

authorList

String authorList

chemicals

Set<Compound> chemicals

citation

String citation

editor

String editor

fullTextUri

String fullTextUri

issue

String issue

keywords

Set<Keyword> keywords

meshTerms

Set<MedicalSubjectHeading> meshTerms

pages

String pages

pubAccession

DatabaseEntry pubAccession

publication

String publication

publicationDate

Date publicationDate

publisher

String publisher

retracted

Boolean retracted

title

String title

volume

String volume

Class ubic.gemma.model.common.description.BibliographicReferenceValueObject extends IdentifiableValueObject<BibliographicReference> implements Serializable

Serialized Fields

abstractText

String abstractText

authorList

String authorList

bibliographicPhenotypes

Collection<BibliographicPhenotypesValueObject> bibliographicPhenotypes

chemicalsTerms

Collection<String> chemicalsTerms

citation

CitationValueObject citation

experiments

Collection<ExpressionExperimentValueObject> experiments

issue

String issue

meshTerms

Collection<String> meshTerms

pages

String pages

pubAccession

String pubAccession

publication

String publication

publicationDate

Date publicationDate

publisher

String publisher

retracted

boolean retracted

title

String title

volume

String volume

Class ubic.gemma.model.common.description.BibRefAnnotation extends Object implements Serializable

serialVersionUID:

-2925637697790915030L

Serialized Fields

id

Long id

isMajorTopic

Boolean isMajorTopic

term

String term

Class ubic.gemma.model.common.description.Characteristic extends AbstractDescribable implements Serializable

serialVersionUID:

-7242166109264718620L

Serialized Fields

category

String category

categoryUri

String categoryUri

evidenceCode

GOEvidenceCode evidenceCode

migratedToStatement

boolean migratedToStatement

Deprecated.

originalValue

String originalValue

value

String value

valueUri

String valueUri

Class ubic.gemma.model.common.description.CharacteristicValueObject extends IdentifiableValueObject<Characteristic> implements Serializable

Serialized Fields

alreadyPresentInDatabase

boolean alreadyPresentInDatabase

alreadyPresentOnGene

boolean alreadyPresentOnGene

category

String category

categoryUri

String categoryUri

child

boolean child

numTimesUsed

int numTimesUsed

ontologyUsed

String ontologyUsed

originalValue

String originalValue

privateGeneCount

long privateGeneCount

publicGeneCount

long publicGeneCount

root

boolean root

taxon

String taxon

urlId

String urlId

value

String value

valueDefinition

String valueDefinition

valueId

String valueId

valueUri

String valueUri

Class ubic.gemma.model.common.description.CitationValueObject extends Object implements Serializable

Serialized Fields

citation

String citation

id

Long id

pubmedAccession

String pubmedAccession

pubmedURL

String pubmedURL

retracted

boolean retracted

Class ubic.gemma.model.common.description.DatabaseEntry extends Object implements Serializable

serialVersionUID:

5418961655066735636L

Serialized Fields

accession

String accession

accessionVersion

String accessionVersion

externalDatabase

ExternalDatabase externalDatabase

id

Long id

Uri

String Uri

Deprecated.

Class ubic.gemma.model.common.description.DatabaseEntryValueObject extends IdentifiableValueObject<DatabaseEntry> implements Serializable

serialVersionUID:

-527323410580090L

Serialized Fields

accession

String accession

externalDatabase

ExternalDatabaseValueObject externalDatabase

Class ubic.gemma.model.common.description.ExternalDatabase extends AbstractDescribable implements Serializable

serialVersionUID:

6807023718405086508L

Serialized Fields

auditTrail

AuditTrail auditTrail

databaseSupplier

Contact databaseSupplier

externalDatabases

Set<ExternalDatabase> externalDatabases

ftpUri

String ftpUri

lastUpdated

Date lastUpdated

localInstallDbName

String localInstallDbName

releaseUrl

URL releaseUrl

releaseVersion

String releaseVersion

type

DatabaseType type

webUri

String webUri

Class ubic.gemma.model.common.description.ExternalDatabaseValueObject extends IdentifiableValueObject<ExternalDatabase> implements Serializable

serialVersionUID:

-1714429166594162374L

Serialized Fields

checked

boolean checked

description

String description

externalDatabases

Set<ExternalDatabaseValueObject> externalDatabases

lastUpdated

Date lastUpdated

name

String name

releaseUrl

URL releaseUrl

releaseVersion

String releaseVersion

uri

String uri

Class ubic.gemma.model.common.description.Keyword extends BibRefAnnotation implements Serializable

serialVersionUID:

2663428244994277220L

Class ubic.gemma.model.common.description.LocalFile extends Object implements Serializable

serialVersionUID:

5057142607188347151L

Serialized Fields

id

Long id

localURL

URI localURL

remoteURL

URI remoteURL

size

Long size

version

String version

Class ubic.gemma.model.common.description.MedicalSubjectHeading extends BibRefAnnotation implements Serializable

serialVersionUID:

7820807342851172028L

Serialized Fields

qualifiers

Set<MedicalSubjectHeading> qualifiers

Package ubic.gemma.model.common.search

Class ubic.gemma.model.common.search.SearchSettings extends Object implements Serializable

serialVersionUID:

-982243911532743661L

Serialized Fields

experimentConstraint

ExpressionExperiment experimentConstraint

fillResults

boolean fillResults

maxResults

int maxResults

mode

SearchSettings.SearchMode mode

platformConstraint

ArrayDesign platformConstraint

query

String query

resultTypes

Set<Class<? extends Identifiable>> resultTypes

taxonConstraint

Taxon taxonConstraint

useCharacteristics

boolean useCharacteristics

useDatabase

boolean useDatabase

useGo

boolean useGo

useIndices

boolean useIndices

Class ubic.gemma.model.common.search.SearchSettingsValueObject extends Object implements Serializable

serialVersionUID:

-934534534L

Serialized Fields

maxResults

Integer maxResults

platformConstraint

ArrayDesign platformConstraint

query

String query

searchBibrefs

Boolean searchBibrefs

searchBioSequences

Boolean searchBioSequences

searchExperiments

Boolean searchExperiments

searchExperimentSets

Boolean searchExperimentSets

searchGenes

Boolean searchGenes

searchGeneSets

Boolean searchGeneSets

searchPhenotypes

Boolean searchPhenotypes

searchPlatforms

Boolean searchPlatforms

searchProbes

Boolean searchProbes

taxon

Taxon taxon

termUri

String termUri

useCharacteristics

Boolean useCharacteristics

useDatabase

Boolean useDatabase

useGo

Boolean useGo

useIndices

Boolean useIndices

Package ubic.gemma.model.expression.experiment

Class ubic.gemma.model.expression.experiment.AbstractFactorValueValueObject extends IdentifiableValueObject<FactorValue> implements Serializable

Serialized Fields

characteristics

List<CharacteristicValueObject> characteristics

experimentalFactorCategory

CharacteristicValueObject experimentalFactorCategory

experimentalFactorId

Long experimentalFactorId

experimentalFactorType

String experimentalFactorType

measurementObject

MeasurementValueObject measurementObject

ontologyId

String ontologyId

statements

List<StatementValueObject> statements

summary

String summary

Class ubic.gemma.model.expression.experiment.BioAssaySet extends Investigation implements Serializable

serialVersionUID:

2368063046639481521L

Serialized Fields

accession

DatabaseEntry accession

bioAssays

Set<BioAssay> bioAssays

Class ubic.gemma.model.expression.experiment.ExperimentalDesign extends AbstractDescribable implements Serializable

serialVersionUID:

1734101852541885497L

Serialized Fields

experimentalFactors

Set<ExperimentalFactor> experimentalFactors

normalizationDescription

String normalizationDescription

qualityControlDescription

String qualityControlDescription

replicateDescription

String replicateDescription

types

Set<Characteristic> types

Class ubic.gemma.model.expression.experiment.ExperimentalFactor extends AbstractDescribable implements Serializable

serialVersionUID:

4615731059510436891L

Serialized Fields

annotations

Set<Characteristic> annotations

Deprecated.

category

Characteristic category

experimentalDesign

ExperimentalDesign experimentalDesign

factorValues

Set<FactorValue> factorValues

securityOwner

ExpressionExperiment securityOwner

type

FactorType type

Class ubic.gemma.model.expression.experiment.ExperimentalFactorValueObject extends IdentifiableValueObject<ExperimentalFactor> implements Serializable

serialVersionUID:

-2615804031123874251L

Serialized Fields

category

String category

categoryUri

String categoryUri

description

String description

factorValues

String factorValues

Deprecated.

name

String name

type

String type

values

Collection<FactorValueValueObject> values

Class ubic.gemma.model.expression.experiment.ExpressionExperiment extends BioAssaySet implements Serializable

serialVersionUID:

-1342753625018841735L

Serialized Fields

allCharacteristics

Set<Characteristic> allCharacteristics

batchConfound

String batchConfound

batchEffect

BatchEffectType batchEffect

batchEffectStatistics

String batchEffectStatistics

curationDetails

CurationDetails curationDetails

experimentalDesign

ExperimentalDesign experimentalDesign

geeq

Geeq geeq

meanVarianceRelation

MeanVarianceRelation meanVarianceRelation

metadata

String metadata

numberOfDataVectors

Integer numberOfDataVectors

numberOfSamples

Integer numberOfSamples

otherParts

Set<ExpressionExperiment> otherParts

processedExpressionDataVectors

Set<ProcessedExpressionDataVector> processedExpressionDataVectors

quantitationTypes

Set<QuantitationType> quantitationTypes

rawExpressionDataVectors

Set<RawExpressionDataVector> rawExpressionDataVectors

shortName

String shortName

source

String source

taxon

Taxon taxon

Class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject extends ExpressionExperimentValueObject implements Serializable

serialVersionUID:

-1219449523930648392L

Serialized Fields

arrayDesigns

Collection<ArrayDesignValueObject> arrayDesigns

batchFetchEventType

String batchFetchEventType

dateArrayDesignLastUpdated

Date dateArrayDesignLastUpdated

dateBatchFetch

Date dateBatchFetch

dateCached

Date dateCached

dateDifferentialAnalysis

Date dateDifferentialAnalysis

dateLinkAnalysis

Date dateLinkAnalysis

dateMissingValueAnalysis

Date dateMissingValueAnalysis

datePcaAnalysis

Date datePcaAnalysis

dateProcessedDataVectorComputation

Date dateProcessedDataVectorComputation

differentialExpressionAnalyses

Collection<DifferentialExpressionAnalysisValueObject> differentialExpressionAnalyses

expressionExperimentSets

Collection<ExpressionExperimentSetValueObject> expressionExperimentSets

hasBatchInformation

boolean hasBatchInformation

hasBothIntensities

Boolean hasBothIntensities

hasCoexpressionAnalysis

Boolean hasCoexpressionAnalysis

hasDifferentialExpressionAnalysis

Boolean hasDifferentialExpressionAnalysis

hasEitherIntensity

Boolean hasEitherIntensity

hasMultiplePreferredQuantitationTypes

Boolean hasMultiplePreferredQuantitationTypes

hasMultipleTechnologyTypes

Boolean hasMultipleTechnologyTypes

isRNASeq

Boolean isRNASeq

lastArrayDesignUpdateDate

String lastArrayDesignUpdateDate

linkAnalysisEventType

String linkAnalysisEventType

minPvalue

Double minPvalue

missingValueAnalysisEventType

String missingValueAnalysisEventType

numAnnotations

Long numAnnotations

numPopulatedFactors

Long numPopulatedFactors

originalPlatforms

Collection<ArrayDesignValueObject> originalPlatforms

otherParts

Collection<ExpressionExperimentValueObject> otherParts

pcaAnalysisEventType

String pcaAnalysisEventType

primaryCitation

CitationValueObject primaryCitation

processedDataVectorComputationEventType

String processedDataVectorComputationEventType

pubmedId

Integer pubmedId

QChtml

String QChtml

reprocessedFromRawData

boolean reprocessedFromRawData

sampleRemovedFlags

Collection<AuditEventValueObject> sampleRemovedFlags

secondaryAccession

String secondaryAccession

secondaryExternalDatabase

String secondaryExternalDatabase

secondaryExternalUri

String secondaryExternalUri

Class ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject extends IdentifiableValueObject<ExpressionExperimentSet> implements Serializable

serialVersionUID:

-6852364688337216390L

Serialized Fields

description

String description

expressionExperimentIds

Collection<Long> expressionExperimentIds

isPublic

boolean isPublic

modifiable

boolean modifiable

name

String name

numWithCoexpressionAnalysis

Integer numWithCoexpressionAnalysis

numWithDifferentialExpressionAnalysis

Integer numWithDifferentialExpressionAnalysis

shared

boolean shared

size

Integer size

taxonId

Long taxonId

taxonName

String taxonName

userCanWrite

boolean userCanWrite

userOwned

boolean userOwned

Class ubic.gemma.model.expression.experiment.ExpressionExperimentSubSet extends BioAssaySet implements Serializable

serialVersionUID:

-1880425342951467283L

Serialized Fields

sourceExperiment

ExpressionExperiment sourceExperiment

Class ubic.gemma.model.expression.experiment.ExpressionExperimentSubsetValueObject extends ExpressionExperimentValueObject implements Serializable

Serialized Fields

sourceExperiment

Long sourceExperiment

sourceExperimentShortName

String sourceExperimentShortName

Class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject extends AbstractCuratableValueObject<ExpressionExperiment> implements Serializable

serialVersionUID:

-6861385216096602508L

Serialized Fields

accession

String accession

arrayDesignCount

Long arrayDesignCount

batchConfound

String batchConfound

batchEffect

String batchEffect

batchEffectStatistics

String batchEffectStatistics

bioMaterialCount

Integer bioMaterialCount

characteristics

Set<CharacteristicValueObject> characteristics

currentUserHasWritePermission

Boolean currentUserHasWritePermission

currentUserIsOwner

Boolean currentUserIsOwner

description

String description

experimentalDesign

Long experimentalDesign

externalDatabase

String externalDatabase

externalDatabaseUri

String externalDatabaseUri

externalUri

String externalUri

geeq

GeeqValueObject geeq

isPublic

Boolean isPublic

isShared

Boolean isShared

metadata

String metadata

name

String name

numberOfBioAssays

Integer numberOfBioAssays

processedExpressionVectorCount

Integer processedExpressionVectorCount

shortName

String shortName

source

String source

suitableForDEA

Boolean suitableForDEA

taxonObject

TaxonValueObject taxonObject

technologyType

String technologyType

Class ubic.gemma.model.expression.experiment.FactorValue extends Object implements Serializable

serialVersionUID:

-3783172994360698631L

Serialized Fields

characteristics

Set<Statement> characteristics

experimentalFactor

ExperimentalFactor experimentalFactor

id

Long id

isBaseline

Boolean isBaseline

measurement

Measurement measurement

needsAttention

boolean needsAttention

oldStyleCharacteristics

Set<Characteristic> oldStyleCharacteristics

Deprecated.

securityOwner

ExpressionExperiment securityOwner

value

String value

Deprecated.

Class ubic.gemma.model.expression.experiment.FactorValueBasicValueObject extends AbstractFactorValueValueObject implements Serializable

serialVersionUID:

3378801249808036785L

Serialized Fields

value

String value

Deprecated.

Class ubic.gemma.model.expression.experiment.FactorValueValueObject extends AbstractFactorValueValueObject implements Serializable

serialVersionUID:

3378801249808036785L

Serialized Fields

category

String category

Deprecated.

categoryUri

String categoryUri

Deprecated.

charId

Long charId

Deprecated.

factorId

Long factorId

Deprecated.

needsAttention

Boolean needsAttention

Deprecated.

object

String object

Deprecated.

objectUri

String objectUri

Deprecated.

predicate

String predicate

Deprecated.

predicateUri

String predicateUri

Deprecated.

secondObject

String secondObject

Deprecated.

secondObjectUri

String secondObjectUri

Deprecated.

secondPredicate

String secondPredicate

Deprecated.

secondPredicateUri

String secondPredicateUri

Deprecated.

value

String value

Deprecated.

valueUri

String valueUri

Deprecated.

Class ubic.gemma.model.expression.experiment.FreeTextExpressionExperimentResultsValueObject extends SessionBoundExpressionExperimentSetValueObject implements Serializable

serialVersionUID:

3557304710219740029L

Serialized Fields

queryString

String queryString

Class ubic.gemma.model.expression.experiment.Geeq extends Object implements Serializable

serialVersionUID:

4783171234360698630L

Serialized Fields

batchCorrected

boolean batchCorrected

corrMatIssues

byte corrMatIssues

detectedQualityScore

double detectedQualityScore

detectedSuitabilityScore

double detectedSuitabilityScore

id

Long id

manualBatchConfoundActive

boolean manualBatchConfoundActive

manualBatchEffectActive

boolean manualBatchEffectActive

manualHasBatchConfound

boolean manualHasBatchConfound

manualHasNoBatchEffect

boolean manualHasNoBatchEffect

manualHasStrongBatchEffect

boolean manualHasStrongBatchEffect

manualQualityOverride

boolean manualQualityOverride

manualQualityScore

double manualQualityScore

manualSuitabilityOverride

boolean manualSuitabilityOverride

manualSuitabilityScore

double manualSuitabilityScore

noVectors

boolean noVectors

otherIssues

String otherIssues

qScoreBatchConfound

double qScoreBatchConfound

qScoreBatchEffect

double qScoreBatchEffect

qScoreBatchInfo

double qScoreBatchInfo

qScoreOutliers

double qScoreOutliers

qScorePlatformsTech

double qScorePlatformsTech

qScoreReplicates

double qScoreReplicates

qScoreSampleCorrelationVariance

double qScoreSampleCorrelationVariance

qScoreSampleMeanCorrelation

double qScoreSampleMeanCorrelation

qScoreSampleMedianCorrelation

double qScoreSampleMedianCorrelation

replicatesIssues

byte replicatesIssues

sScoreAvgPlatformPopularity

double sScoreAvgPlatformPopularity

sScoreAvgPlatformSize

double sScoreAvgPlatformSize

sScoreMissingValues

double sScoreMissingValues

sScorePlatformAmount

double sScorePlatformAmount

sScorePlatformsTechMulti

double sScorePlatformsTechMulti

sScorePublication

double sScorePublication

sScoreRawData

double sScoreRawData

sScoreSampleSize

double sScoreSampleSize

Class ubic.gemma.model.expression.experiment.GeeqAdminValueObject extends GeeqValueObject implements Serializable

Serialized Fields

detectedQualityScore

double detectedQualityScore

detectedSuitabilityScore

double detectedSuitabilityScore

manualBatchConfoundActive

boolean manualBatchConfoundActive

manualBatchEffectActive

boolean manualBatchEffectActive

manualHasBatchConfound

boolean manualHasBatchConfound

manualHasNoBatchEffect

boolean manualHasNoBatchEffect

manualHasStrongBatchEffect

boolean manualHasStrongBatchEffect

manualQualityOverride

boolean manualQualityOverride

manualQualityScore

double manualQualityScore

manualSuitabilityOverride

boolean manualSuitabilityOverride

manualSuitabilityScore

double manualSuitabilityScore

otherIssues

String otherIssues

qScoreBatchConfound

double qScoreBatchConfound

qScoreBatchEffect

double qScoreBatchEffect

Class ubic.gemma.model.expression.experiment.GeeqValueObject extends IdentifiableValueObject<Geeq> implements Serializable

Serialized Fields

batchCorrected

boolean batchCorrected

corrMatIssues

byte corrMatIssues

noVectors

boolean noVectors

publicQualityScore

double publicQualityScore

publicSuitabilityScore

double publicSuitabilityScore

qScoreBatchInfo

double qScoreBatchInfo

qScoreOutliers

double qScoreOutliers

qScorePlatformsTech

double qScorePlatformsTech

qScorePublicBatchConfound

double qScorePublicBatchConfound

qScorePublicBatchEffect

double qScorePublicBatchEffect

qScoreReplicates

double qScoreReplicates

qScoreSampleCorrelationVariance

double qScoreSampleCorrelationVariance

qScoreSampleMeanCorrelation

double qScoreSampleMeanCorrelation

qScoreSampleMedianCorrelation

double qScoreSampleMedianCorrelation

replicatesIssues

byte replicatesIssues

sScoreAvgPlatformPopularity

double sScoreAvgPlatformPopularity

sScoreAvgPlatformSize

double sScoreAvgPlatformSize

sScoreMissingValues

double sScoreMissingValues

sScorePlatformAmount

double sScorePlatformAmount

sScorePlatformsTechMulti

double sScorePlatformsTechMulti

sScorePublication

double sScorePublication

sScoreRawData

double sScoreRawData

sScoreSampleSize

double sScoreSampleSize

Class ubic.gemma.model.expression.experiment.SessionBoundExpressionExperimentSetValueObject extends ExpressionExperimentSetValueObject implements Serializable

serialVersionUID:

2068650886972222818L

Serialized Fields

modified

boolean modified

Class ubic.gemma.model.expression.experiment.Statement extends Characteristic implements Serializable

Serialized Fields

object

String object

objectUri

String objectUri

predicate

String predicate

predicateUri

String predicateUri

secondObject

String secondObject

secondObjectUri

String secondObjectUri

secondPredicate

String secondPredicate

secondPredicateUri

String secondPredicateUri

Class ubic.gemma.model.expression.experiment.StatementValueObject extends IdentifiableValueObject<Statement> implements Serializable

Serialized Fields

category

String category

categoryUri

String categoryUri

object

String object

objectId

String objectId

objectUri

String objectUri

predicate

String predicate

predicateUri

String predicateUri

secondObject

String secondObject

secondObjectUri

String secondObjectUri

secondPredicate

String secondPredicate

secondPredicateUri

String secondPredicateUri

subject

String subject

subjectId

String subjectId

subjectUri

String subjectUri

Package ubic.gemma.model.genome

Class ubic.gemma.model.genome.Chromosome extends Object implements Serializable

serialVersionUID:

7394734846565885136L

Serialized Fields

assemblyDatabase

ExternalDatabase assemblyDatabase

id

Long id

name

String name

sequence

BioSequence sequence

taxon

Taxon taxon

Class ubic.gemma.model.genome.ChromosomeFeature extends AbstractDescribable implements Serializable

serialVersionUID:

-8627296370886752496L

Serialized Fields

physicalLocation

PhysicalLocation physicalLocation

previousNcbiId

String previousNcbiId

Class ubic.gemma.model.genome.ChromosomeLocation extends Object implements Serializable

serialVersionUID:

-4932607147290671454L

Serialized Fields

chromosome

Chromosome chromosome

id

Long id

Class ubic.gemma.model.genome.Gene extends ChromosomeFeature implements Serializable

serialVersionUID:

-5693198926006383546L

Serialized Fields

accessions

Set<DatabaseEntry> accessions

aliases

Set<GeneAlias> aliases

ensemblId

String ensemblId

multifunctionality

Multifunctionality multifunctionality

ncbiGeneId

Integer ncbiGeneId

officialName

String officialName

officialSymbol

String officialSymbol

phenotypeAssociations

Set<PhenotypeAssociation> phenotypeAssociations

Deprecated.

products

Set<GeneProduct> products

taxon

Taxon taxon

Class ubic.gemma.model.genome.GeneOntologyTermValueObject extends Object implements Serializable

Serialized Fields

comment

String comment

goId

String goId

isObsolete

boolean isObsolete

label

String label

localName

String localName

term

String term

uri

String uri

Class ubic.gemma.model.genome.PhysicalLocation extends ChromosomeLocation implements Serializable

serialVersionUID:

-6580769809003779541L

Serialized Fields

bin

Integer bin

nucleotide

Long nucleotide

nucleotideLength

Integer nucleotideLength

strand

String strand

Class ubic.gemma.model.genome.PhysicalLocationValueObject extends IdentifiableValueObject<PhysicalLocation> implements Serializable

Serialized Fields

bin

Integer bin

chromosome

String chromosome

nucleotide

Long nucleotide

nucleotideLength

Integer nucleotideLength

strand

String strand

taxon

TaxonValueObject taxon

Class ubic.gemma.model.genome.Taxon extends Object implements Serializable

serialVersionUID:

9219471082900615778L

Serialized Fields

commonName

String commonName

externalDatabase

ExternalDatabase externalDatabase

id

Long id

isGenesUsable

boolean isGenesUsable

ncbiId

Integer ncbiId

scientificName

String scientificName

secondaryNcbiId

Integer secondaryNcbiId

Class ubic.gemma.model.genome.TaxonValueObject extends IdentifiableValueObject<Taxon> implements Serializable

Serialized Fields

commonName

String commonName

externalDatabase

ExternalDatabaseValueObject externalDatabase

isGenesUsable

Boolean isGenesUsable

isSpecies

Boolean isSpecies

ncbiId

Integer ncbiId

scientificName

String scientificName

Package ubic.gemma.model.genome.biosequence

Class ubic.gemma.model.genome.biosequence.BioSequence extends AbstractDescribable implements Serializable

serialVersionUID:

-6620431603579954167L

Serialized Fields

bioSequence2GeneProduct

Set<BioSequence2GeneProduct> bioSequence2GeneProduct

fractionRepeats

Double fractionRepeats

isApproximateLength

Boolean isApproximateLength

isCircular

Boolean isCircular

length

Long length

polymerType

PolymerType polymerType

sequence

String sequence

sequenceDatabaseEntry

DatabaseEntry sequenceDatabaseEntry

taxon

Taxon taxon

type

SequenceType type

Package ubic.gemma.persistence.hibernate

Class ubic.gemma.persistence.hibernate.XSDEntityResolver extends DTDEntityResolver implements Serializable

Package ubic.gemma.persistence.service

Class ubic.gemma.persistence.service.AbstractServiceTest.ExceptionWithMessage extends Exception implements Serializable

Class ubic.gemma.persistence.service.AbstractServiceTest.ExceptionWithoutMessage extends Exception implements Serializable

Package ubic.gemma.persistence.service.analysis.expression.diff

Class ubic.gemma.persistence.service.analysis.expression.diff.MissingResult extends DiffExprGeneSearchResult implements Serializable

serialVersionUID:

-2868418055346274525L

Class ubic.gemma.persistence.service.analysis.expression.diff.NonRetainedResult extends DiffExprGeneSearchResult implements Serializable

serialVersionUID:

3501605965895623139L

Package ubic.gemma.persistence.service.association.coexpression

Class ubic.gemma.persistence.service.association.coexpression.CoexpressionCacheValueObject extends Object implements Serializable

serialVersionUID:

184287422449009209L

Serialized Fields

coexGeneSymbol

String coexGeneSymbol

coexpGene

Long coexpGene

positiveCorrelation

boolean positiveCorrelation

queryGene

Long queryGene

queryGeneSymbol

String queryGeneSymbol

support

int support

supportDetailsId

Long supportDetailsId

supportingDatasets

Collection<Long> supportingDatasets

testedInDatasets

ubic.gemma.persistence.service.association.coexpression.CompressedLongSet testedInDatasets

Class ubic.gemma.persistence.service.association.coexpression.CoexpressionValueObject extends Object implements Serializable

Serialized Fields

coexGeneId

Long coexGeneId

coexGeneSymbol

String coexGeneSymbol

eeConstraint

boolean eeConstraint

fromCache

boolean fromCache

interQueryLink

boolean interQueryLink

maxResults

int maxResults

positiveCorrelation

boolean positiveCorrelation

queryGeneId

Long queryGeneId

queryGeneSymbol

String queryGeneSymbol

queryStringency

int queryStringency

support

Integer support

supportDetailsId

Long supportDetailsId

supportingDatasets

Set<Long> supportingDatasets

testedInDatasets

Set<Long> testedInDatasets

Package ubic.gemma.persistence.service.common.quantitationtype

Class ubic.gemma.persistence.service.common.quantitationtype.NonUniqueQuantitationTypeByNameException extends Exception implements Serializable

Package ubic.gemma.persistence.service.expression.experiment

Class ubic.gemma.persistence.service.expression.experiment.FactorValueMigratorService.MigrationFailedException extends RuntimeException implements Serializable

Serialized Fields

migration

FactorValueMigratorService.Migration migration

Package ubic.gemma.persistence.service.maintenance

Class ubic.gemma.persistence.service.maintenance.Gene2CsStatus extends Object implements Serializable

serialVersionUID:

1956861185764899312L

Serialized Fields

annotation

String annotation

error

Exception error

lastUpdate

Date lastUpdate

Package ubic.gemma.rest

Class ubic.gemma.rest.DatasetsWebService.AnnotationWithUsageStatisticsValueObject extends AnnotationValueObject implements Serializable

Serialized Fields

numberOfExpressionExperiments

Long numberOfExpressionExperiments

parentTerms

Set<DatasetsWebService.OntologyTermValueObject> parentTerms

Class ubic.gemma.rest.DatasetsWebService.ArrayDesignWithUsageStatisticsValueObject extends ArrayDesignValueObject implements Serializable

Serialized Fields

numberOfExpressionExperimentsForTechnologyType

Long numberOfExpressionExperimentsForTechnologyType

Class ubic.gemma.rest.DatasetsWebService.DifferentialExpressionAnalysisResultByGeneValueObject extends DifferentialExpressionAnalysisResultValueObject implements Serializable

Serialized Fields

baseline

FactorValueBasicValueObject baseline

experimentAnalyzedId

Long experimentAnalyzedId

resultSetId

Long resultSetId

secondBaseline

FactorValueBasicValueObject secondBaseline

sourceExperimentId

Long sourceExperimentId

Class ubic.gemma.rest.DatasetsWebService.ExpressionExperimentWithSearchResultValueObject extends ExpressionExperimentValueObject implements Serializable

Serialized Fields

searchResult

SearchWebService.SearchResultValueObject<ExpressionExperimentValueObject> searchResult

Class ubic.gemma.rest.DatasetsWebService.TaxonWithUsageStatisticsValueObject extends TaxonValueObject implements Serializable

Serialized Fields

numberOfExpressionExperiments

Long numberOfExpressionExperiments

Package ubic.gemma.rest.serializers

Class ubic.gemma.rest.serializers.AbstractFactorValueValueObjectSerializer extends com.fasterxml.jackson.databind.ser.std.StdSerializer<T extends AbstractFactorValueValueObject> implements Serializable

Class ubic.gemma.rest.serializers.FactorValueBasicValueObjectSerializer extends AbstractFactorValueValueObjectSerializer<FactorValueBasicValueObject> implements Serializable

Class ubic.gemma.rest.serializers.FactorValueValueObjectSerializer extends AbstractFactorValueValueObjectSerializer<FactorValueValueObject> implements Serializable

Package ubic.gemma.rest.util

Class ubic.gemma.rest.util.EntityNotFoundException extends Exception implements Serializable

Class ubic.gemma.rest.util.MalformedArgException extends javax.ws.rs.BadRequestException implements Serializable

Package ubic.gemma.web.controller.common.auditAndSecurity

Class ubic.gemma.web.controller.common.auditAndSecurity.FileUpload extends Object implements Serializable

serialVersionUID:

537156568346654834L

Serialized Fields

file

byte[] file

localPath

String localPath

Class ubic.gemma.web.controller.common.auditAndSecurity.SidValueObject extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

authority

String authority

principal

boolean principal

Package ubic.gemma.web.controller.diff

Class ubic.gemma.web.controller.diff.DiffExpressionSearchCommand extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

dirty

boolean dirty

eeIds

Collection<Long> eeIds

eeQuery

String eeQuery

eeSetId

Long eeSetId

eeSetName

String eeSetName

geneIds

Collection<Long> geneIds

selectedFactors

Collection<DiffExpressionSelectedFactorCommand> selectedFactors

taxonId

Long taxonId

threshold

Double threshold

Package ubic.gemma.web.controller.expression.arrayDesign

Class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignValueObjectExt extends ArrayDesignValueObject implements Serializable

serialVersionUID:

218696698777199533L

Serialized Fields

additionalTaxa

Set<String> additionalTaxa

allParentsAnnotationLink

String allParentsAnnotationLink

alternateNames

Collection<String> alternateNames

alternative

ArrayDesignValueObject alternative

bioProcessAnnotationLink

String bioProcessAnnotationLink

colorString

String colorString

mergees

Collection<ArrayDesignValueObject> mergees

merger

ArrayDesignValueObject merger

noParentsAnnotationLink

String noParentsAnnotationLink

subsumees

Collection<ArrayDesignValueObject> subsumees

subsumer

ArrayDesignValueObject subsumer

Package ubic.gemma.web.controller.expression.experiment

Class ubic.gemma.web.controller.expression.experiment.DesignMatrixRowValueObject extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

count

int count

factors

List<String> factors

factorTypes

List<String> factorTypes

factorValueMap

Map<String,String> factorValueMap

Class ubic.gemma.web.controller.expression.experiment.ExperimentalFactorValueWebUIObject extends ExperimentalFactorValueObject implements Serializable

Serialized Fields

bioMaterialCharacteristicCategoryToUse

String bioMaterialCharacteristicCategoryToUse

Class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentDataFetchCommand extends TaskCommand implements Serializable

serialVersionUID:

1L

Serialized Fields

analysisId

Long analysisId

experimentalDesignId

Long experimentalDesignId

expressionExperimentId

Long expressionExperimentId

filter

boolean filter

forceRewrite

boolean forceRewrite

format

String format

quantitationTypeId

Long quantitationTypeId

Class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditValueObject extends ExpressionExperimentDetailsValueObject implements Serializable

serialVersionUID:

1630521876359566915L

Serialized Fields

bioAssays

Collection<BioAssayValueObject> bioAssays

quantitationTypes

Collection<QuantitationTypeValueObject> quantitationTypes

Class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentLoadTaskCommand extends SimpleExpressionExperimentMetaData implements Serializable

serialVersionUID:

1L

Serialized Fields

arrayDesignName

String arrayDesignName

originalFileName

String originalFileName

serverFilePath

String serverFilePath

taxonName

String taxonName

validateOnly

boolean validateOnly

Package ubic.gemma.web.util

Class ubic.gemma.web.util.ConfigurationCookie extends javax.servlet.http.Cookie implements Serializable

Serialized Fields

configuration

org.apache.commons.configuration2.PropertiesConfiguration configuration

Class ubic.gemma.web.util.EntityNotFoundException extends RuntimeException implements Serializable

serialVersionUID:

-4361183252269974819L

Class ubic.gemma.web.util.LabelValue extends Object implements Serializable

serialVersionUID:

3485837885293359602L

Serialized Fields

label

String label

value

String value

Class ubic.gemma.web.util.ServiceUnavailableException extends RuntimeException implements Serializable

Package ubic.gemma.web.util.upload

Class ubic.gemma.web.util.upload.CommonsMultipartFile extends Object implements Serializable

serialVersionUID:

6483196912349343465L

Serialized Fields

fileItem

org.apache.commons.fileupload.FileItem fileItem

Deprecated.

size

long size

Deprecated.

Class ubic.gemma.web.util.upload.UploadInfo extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

bytesRead

long bytesRead

fileIndex

int fileIndex

status

String status

totalSize

long totalSize