Serialized Form

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

Class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig

class 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

logTransform

boolean logTransform

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

Exception Class ubic.gemma.core.analysis.expression.coexpression.links.UnsuitableForAnalysisException

class UnsuitableForAnalysisException extends RuntimeException implements Serializable

serialVersionUID:

-4436136164850796179L

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

Exception Class ubic.gemma.core.analysis.expression.diff.AllAnalysesFailedException

class AllAnalysesFailedException extends AnalysisException implements Serializable

Exception Class ubic.gemma.core.analysis.expression.diff.AllSubSetAnalysesFailedException

class AllSubSetAnalysesFailedException extends AllAnalysesFailedException implements Serializable

Exception Class ubic.gemma.core.analysis.expression.diff.AnalysisException

class AnalysisException extends RuntimeException implements Serializable

Serialized Fields

config

DifferentialExpressionAnalysisConfig config

Class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionMetaAnalysisValueObject

class 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

class DiffExpressionSelectedFactorCommand extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

eeId

Long eeId

efId

Long efId

Exception Class ubic.gemma.core.analysis.expression.diff.EbayesFailureException

class EbayesFailureException extends AnalysisException implements Serializable

Exception Class ubic.gemma.core.analysis.expression.diff.FilteringRelatedAnalysisException

class FilteringRelatedAnalysisException extends AnalysisException implements Serializable

Exception Class ubic.gemma.core.analysis.expression.diff.InvalidQuantitationTypeConversionException

class InvalidQuantitationTypeConversionException extends AnalysisException implements Serializable

Exception Class ubic.gemma.core.analysis.expression.diff.NoFactorLeftForAnalysisException

class NoFactorLeftForAnalysisException extends AnalysisException implements Serializable

Package ubic.gemma.core.analysis.preprocess

Exception Class ubic.gemma.core.analysis.preprocess.FilteringRelatedPreprocessingException

class FilteringRelatedPreprocessingException extends PreprocessingException implements Serializable

Serialized Fields

cause

FilteringException cause

Class ubic.gemma.core.analysis.preprocess.OutlierDetails

class OutlierDetails extends Object implements Serializable

Serialized Fields

bioAssayId

Long bioAssayId

firstQuartile

double firstQuartile

medianCorrelation

double medianCorrelation

thirdQuartile

double thirdQuartile

Exception Class ubic.gemma.core.analysis.preprocess.PreprocessingException

class PreprocessingException extends RuntimeException implements Serializable

serialVersionUID:

-8463478950898408838L

Exception Class ubic.gemma.core.analysis.preprocess.QuantitationTypeConversionRelatedPreprocessingException

class QuantitationTypeConversionRelatedPreprocessingException extends PreprocessingException implements Serializable

Serialized Fields

cause

QuantitationTypeConversionException cause

Exception Class ubic.gemma.core.analysis.preprocess.QuantitationTypeDetectionRelatedPreprocessingException

class QuantitationTypeDetectionRelatedPreprocessingException extends PreprocessingException implements Serializable

Serialized Fields

cause

QuantitationTypeDetectionException cause

Exception Class ubic.gemma.core.analysis.preprocess.SampleCoexpressionRelatedPreprocessingException

class SampleCoexpressionRelatedPreprocessingException extends PreprocessingException implements Serializable

Exception Class ubic.gemma.core.analysis.preprocess.SVDRelatedPreprocessingException

class SVDRelatedPreprocessingException extends PreprocessingException implements Serializable

Serialized Fields

cause

SVDException cause

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

Exception Class ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoMissingException

class BatchInfoMissingException extends BatchInfoPopulationException implements Serializable

Exception Class ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationException

class BatchInfoPopulationException extends PreprocessingException implements Serializable

serialVersionUID:

-1770591991479420212L

Exception Class ubic.gemma.core.analysis.preprocess.batcheffects.FASTQHeadersPresentButNotUsableException

class FASTQHeadersPresentButNotUsableException extends BatchInfoPopulationException implements Serializable

serialVersionUID:

1917074433646650950L

Exception Class ubic.gemma.core.analysis.preprocess.batcheffects.SingletonBatchesException

class SingletonBatchesException extends BatchInfoPopulationException implements Serializable

serialVersionUID:

9088141067684148902L

Exception Class ubic.gemma.core.analysis.preprocess.batcheffects.UnsupportedRawdataFileFormatException

class UnsupportedRawdataFileFormatException extends BatchInfoPopulationException implements Serializable

serialVersionUID:

1L

Package ubic.gemma.core.analysis.preprocess.convert

Exception Class ubic.gemma.core.analysis.preprocess.convert.QuantitationTypeConversionException

class QuantitationTypeConversionException extends Exception implements Serializable

Exception Class ubic.gemma.core.analysis.preprocess.convert.UnsupportedQuantitationRepresentationConversionException

class UnsupportedQuantitationRepresentationConversionException extends UnsupportedQuantitationTypeConversionException implements Serializable

Exception Class ubic.gemma.core.analysis.preprocess.convert.UnsupportedQuantitationScaleConversionException

class UnsupportedQuantitationScaleConversionException extends UnsupportedQuantitationTypeConversionException implements Serializable

Exception Class ubic.gemma.core.analysis.preprocess.convert.UnsupportedQuantitationTypeConversionException

class UnsupportedQuantitationTypeConversionException extends QuantitationTypeConversionException implements Serializable

Package ubic.gemma.core.analysis.preprocess.detect

Exception Class ubic.gemma.core.analysis.preprocess.detect.InferredQuantitationMismatchException

class InferredQuantitationMismatchException extends QuantitationMismatchException implements Serializable

Serialized Fields

inferredQuantitationType

QuantitationType inferredQuantitationType

Exception Class ubic.gemma.core.analysis.preprocess.detect.QuantitationMismatchException

class QuantitationMismatchException extends QuantitationTypeDetectionException implements Serializable

Serialized Fields

quantitationType

QuantitationType quantitationType

Exception Class ubic.gemma.core.analysis.preprocess.detect.QuantitationTypeDetectionException

class QuantitationTypeDetectionException extends Exception implements Serializable

Exception Class ubic.gemma.core.analysis.preprocess.detect.SuspiciousValuesForQuantitationException

class SuspiciousValuesForQuantitationException extends QuantitationMismatchException implements Serializable

Serialized Fields

suspiciousValues

List<SuspiciousValuesForQuantitationException.SuspiciousValueResult> suspiciousValues

Package ubic.gemma.core.analysis.preprocess.filter

Class ubic.gemma.core.analysis.preprocess.filter.FilterConfig

class FilterConfig extends Object implements Serializable

Serialized Fields

highExpressionCut

double highExpressionCut

ignoreMinimumRowsThreshold

boolean ignoreMinimumRowsThreshold

ignoreMinimumSampleThreshold

boolean ignoreMinimumSampleThreshold

lowDistinctValueCut

double lowDistinctValueCut

lowDistinctValueIsSet

boolean lowDistinctValueIsSet

lowExpressionCut

double lowExpressionCut

lowVarianceCut

double lowVarianceCut

minPresentFraction

double minPresentFraction

requireSequences

boolean requireSequences

Exception Class ubic.gemma.core.analysis.preprocess.filter.FilteringException

class FilteringException extends Exception implements Serializable

Exception Class ubic.gemma.core.analysis.preprocess.filter.InsufficientDataException

class InsufficientDataException extends FilteringException implements Serializable

Exception Class ubic.gemma.core.analysis.preprocess.filter.InsufficientDesignElementsException

class InsufficientDesignElementsException extends InsufficientDataException implements Serializable

Exception Class ubic.gemma.core.analysis.preprocess.filter.InsufficientSamplesException

class InsufficientSamplesException extends InsufficientDataException implements Serializable

serialVersionUID:

1L

Exception Class ubic.gemma.core.analysis.preprocess.filter.NoDesignElementsException

class NoDesignElementsException extends InsufficientDesignElementsException implements Serializable

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

Exception Class ubic.gemma.core.analysis.preprocess.svd.SVDException

class SVDException extends Exception implements Serializable

Class ubic.gemma.core.analysis.preprocess.svd.SVDResult

class SVDResult extends Object implements Serializable

Serialized Fields

bioAssays

List<BioAssay> bioAssays

bioMaterials

List<BioMaterial> bioMaterials

dateCorrelations

Map<Integer,Double> dateCorrelations

datePVals

Map<Integer,Double> datePVals

dates

List<Date> dates

experimentAnalyzed

ExpressionExperiment experimentAnalyzed

factorCorrelations

Map<Integer,Map<ExperimentalFactor,Double>> factorCorrelations

factorPVals

Map<Integer,Map<ExperimentalFactor,Double>> factorPVals

factors

Map<ExperimentalFactor,List<Number>> factors

variances

double[] variances

vMatrix

DoubleMatrix<BioMaterial,Integer> vMatrix

Package ubic.gemma.core.analysis.report

Class ubic.gemma.core.analysis.report.AuditableObject

class 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

class 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

Package ubic.gemma.core.analysis.singleCell.aggregate

Exception Class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellAggregationException

class SingleCellAggregationException extends RuntimeException implements Serializable

Exception Class ubic.gemma.core.analysis.singleCell.aggregate.UnsupportedScaleTypeForSingleCellAggregationException

class UnsupportedScaleTypeForSingleCellAggregationException extends SingleCellAggregationException implements Serializable

Package ubic.gemma.core.job

Class ubic.gemma.core.job.TaskCommand

class TaskCommand extends Object implements Serializable

Serialized Fields

emailAlert

boolean emailAlert

maxQueueMillis

long maxQueueMillis

maxRuntimeMillis

long maxRuntimeMillis

persistJobDetails

Boolean persistJobDetails

securityContext

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

submitter

String submitter

Class ubic.gemma.core.job.TaskResult

class TaskResult extends Object implements Serializable

Serialized Fields

answer

Serializable answer

Package ubic.gemma.core.job.progress

Class ubic.gemma.core.job.progress.ProgressData

class 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

Package ubic.gemma.core.loader.entrez

Exception Class ubic.gemma.core.loader.entrez.EntrezException

class EntrezException extends RuntimeException implements Serializable

Serialized Fields

errors

List<String> errors

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

Class ubic.gemma.core.loader.expression.arrayDesign.Reporter

class 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

class 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.singleCell

Exception Class ubic.gemma.core.loader.expression.geo.singleCell.NoSingleCellDataFoundException

class NoSingleCellDataFoundException extends Exception implements Serializable

Package ubic.gemma.core.loader.util

Exception Class ubic.gemma.core.loader.util.AlreadyExistsInSystemException

class AlreadyExistsInSystemException extends RuntimeException implements Serializable

serialVersionUID:

5677999264920938691L

Serialized Fields

data

Object data

Package ubic.gemma.core.loader.util.anndata

Exception Class ubic.gemma.core.loader.util.anndata.AnnDataException

class AnnDataException extends RuntimeException implements Serializable

Exception Class ubic.gemma.core.loader.util.anndata.InvalidEncodingAttributeException

class InvalidEncodingAttributeException extends AnnDataException implements Serializable

Exception Class ubic.gemma.core.loader.util.anndata.MissingEncodingAttributeException

class MissingEncodingAttributeException extends AnnDataException implements Serializable

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

Class ubic.gemma.core.loader.util.biomart.Ensembl2NcbiValueObject

class 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.loader.util.hdf5

Exception Class ubic.gemma.core.loader.util.hdf5.H5Exception

class H5Exception extends RuntimeException implements Serializable

Serialized Fields

cause

hdf.hdf5lib.exceptions.HDF5Exception cause

Exception Class ubic.gemma.core.loader.util.hdf5.TruncatedH5FileException

class TruncatedH5FileException extends IOException implements Serializable

Package ubic.gemma.core.search

Exception Class ubic.gemma.core.search.BaseCodeOntologySearchException

class BaseCodeOntologySearchException extends SearchException implements Serializable

Serialized Fields

cause

OntologySearchException cause

Exception Class ubic.gemma.core.search.ParseSearchException

class ParseSearchException extends SearchException implements Serializable

Serialized Fields

originalParseException

ParseSearchException originalParseException

query

String query

Exception Class ubic.gemma.core.search.SearchException

class SearchException extends Exception implements Serializable

Exception Class ubic.gemma.core.search.SearchTimeoutException

class SearchTimeoutException extends SearchException implements Serializable

Serialized Fields

cause

TimeoutException cause

Package ubic.gemma.core.search.lucene

Exception Class ubic.gemma.core.search.lucene.LuceneParseSearchException

class LuceneParseSearchException extends ParseSearchException implements Serializable

Package ubic.gemma.core.search.source

Exception Class ubic.gemma.core.search.source.HibernateSearchException

class HibernateSearchException extends SearchException implements Serializable

Serialized Fields

cause

org.hibernate.search.SearchException cause

Package ubic.gemma.core.util

Exception Class ubic.gemma.core.util.GemmaRestApiClientException

class GemmaRestApiClientException extends RuntimeException implements Serializable

Class ubic.gemma.core.util.StrictBeanDefinitionValidatorTest.TestAnnotatedVo

class TestAnnotatedVo extends Object implements Serializable

Class ubic.gemma.core.util.StrictBeanDefinitionValidatorTest.TestImplicitValueObject

class TestImplicitValueObject extends Object implements Serializable

Package ubic.gemma.core.visualization

Class ubic.gemma.core.visualization.ExpressionDataHeatmap

class ExpressionDataHeatmap extends Object implements Serializable

Serialized Fields

assayIndex

int[] assayIndex

assays

List<BioAssay> assays

bioAssaySet

BioAssaySet bioAssaySet

cellLevelCharacteristics

CellLevelCharacteristics cellLevelCharacteristics

cellSize

int cellSize

designElements

Slice<CompositeSequence> designElements

dimension

BioAssayDimension dimension

focusedCellLevelCharacteristic

Characteristic focusedCellLevelCharacteristic

genes

List<Gene> genes

singleCellQuantitationType

QuantitationType singleCellQuantitationType

transpose

boolean transpose

vectors

Slice<? extends BulkExpressionDataVector> vectors

Class ubic.gemma.core.visualization.SingleCellSparsityHeatmap

class SingleCellSparsityHeatmap extends Object implements Serializable

Serialized Fields

cellSize

int cellSize

designElementsPerSample

Map<BioAssay,Long> designElementsPerSample

dimension

BioAssayDimension dimension

expressionExperiment

ExpressionExperiment expressionExperiment

samples

List<BioAssay> samples

singleCellDimension

SingleCellDimension singleCellDimension

subSets

List<ExpressionExperimentSubSet> subSets

transpose

boolean transpose

type

SingleCellSparsityHeatmap.SingleCellHeatmapType type

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

Class ubic.gemma.model.analysis.expression.diff.ContrastResultValueObject

class 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

class ContrastsValueObject extends Object implements Serializable

Serialized Fields

contrasts

List<ContrastVO> contrasts

resultId

Long resultId

Class ubic.gemma.model.analysis.expression.diff.ContrastVO

class ContrastVO extends Object implements Serializable

Serialized Fields

factorValueId

Long factorValueId

id

Long id

logFoldChange

Double logFoldChange

pvalue

Double pvalue

secondFactorValueId

Long secondFactorValueId

Class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResultSetValueObject

class 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

class 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

class 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

class DifferentialExpressionValueObject extends Object implements Serializable

Serialized Fields

contrasts

ContrastsValueObject contrasts

corrP

Double corrP

direction

Direction direction

experimentalFactors

Collection<ExperimentalFactorValueObject> experimentalFactors

expressionExperiment

BioAssaySetValueObject 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

class 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

class 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.GeneDifferentialExpressionMetaAnalysisDetailValueObject

class 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.GeneDifferentialExpressionMetaAnalysisResultValueObject

class 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.IncludedResultSetInfoValueObject

class IncludedResultSetInfoValueObject extends Object implements Serializable

serialVersionUID:

-4660741839991839187L

Serialized Fields

analysisId

Long analysisId

experimentId

Long experimentId

resultSetId

Long resultSetId

Package ubic.gemma.model.association.coexpression

Class ubic.gemma.model.association.coexpression.GeneCoexpressionNodeDegreeValueObject

class 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

Package ubic.gemma.model.common.description

Class ubic.gemma.model.common.description.AnnotationValueObject

class 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.BibliographicReferenceValueObject

class BibliographicReferenceValueObject extends IdentifiableValueObject<BibliographicReference> implements Serializable

Serialized Fields

abstractText

String abstractText

authorList

String authorList

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.CharacteristicValueObject

class 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

class 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.DatabaseEntryValueObject

class DatabaseEntryValueObject extends IdentifiableValueObject<DatabaseEntry> implements Serializable

serialVersionUID:

-527323410580090L

Serialized Fields

accession

String accession

externalDatabase

ExternalDatabaseValueObject externalDatabase

Class ubic.gemma.model.common.description.ExternalDatabaseValueObject

class 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

Package ubic.gemma.model.common.quantitationtype

Class ubic.gemma.model.common.quantitationtype.QuantitationTypeValueObject

class QuantitationTypeValueObject extends IdentifiableValueObject<QuantitationType> implements Serializable

serialVersionUID:

7537853492100102404L

Serialized Fields

description

String description

expressionExperimentId

Long expressionExperimentId

generalType

String generalType

isBackground

boolean isBackground

isBackgroundSubtracted

boolean isBackgroundSubtracted

isBatchCorrected

boolean isBatchCorrected

isMaskedPreferred

boolean isMaskedPreferred

Deprecated.

isNormalized

boolean isNormalized

isPreferred

boolean isPreferred

isRatio

boolean isRatio

isRecomputedFromRawData

boolean isRecomputedFromRawData

name

String name

representation

String representation

scale

String scale

type

String type

vectorType

String vectorType

Package ubic.gemma.model.common.search

Class ubic.gemma.model.common.search.SearchSettingsValueObject

class 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

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.bioAssayData

Class ubic.gemma.model.expression.bioAssayData.BioAssayDimensionValueObject

class BioAssayDimensionValueObject extends IdentifiableValueObject<BioAssayDimension> implements Serializable

serialVersionUID:

-8686807689616396835L

Serialized Fields

bioAssays

List<BioAssayValueObject> bioAssays

description

String description

Deprecated.

isReordered

boolean isReordered

isSubset

boolean isSubset

name

String name

Deprecated.

sourceBioAssayDimension

BioAssayDimensionValueObject sourceBioAssayDimension

Class ubic.gemma.model.expression.bioAssayData.BooleanVectorValueObject

class BooleanVectorValueObject extends DataVectorValueObject implements Serializable

Serialized Fields

data

boolean[] data

Class ubic.gemma.model.expression.bioAssayData.CellLevelCharacteristicsValueObject

class CellLevelCharacteristicsValueObject extends IdentifiableValueObject<CellLevelCharacteristics> implements Serializable

Serialized Fields

characteristicIds

List<Long> characteristicIds

characteristics

Set<CharacteristicValueObject> characteristics

numberOfAssignedCells

Integer numberOfAssignedCells

Class ubic.gemma.model.expression.bioAssayData.DataVectorValueObject

class DataVectorValueObject extends IdentifiableValueObject<DataVector> implements Serializable

Serialized Fields

bioAssayDimension

BioAssayDimensionValueObject bioAssayDimension

designElement

CompositeSequenceValueObject designElement

expressionExperiment

BioAssaySetValueObject expressionExperiment

genes

Collection<Long> genes

quantitationType

QuantitationTypeValueObject quantitationType

Class ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject

class DoubleVectorValueObject extends DataVectorValueObject implements Serializable

Serialized Fields

data

double[] data

masked

boolean masked

pvalue

Double pvalue

rank

Double rank

rankByMax

Double rankByMax

rankByMean

Double rankByMean

reorganized

boolean reorganized

Class ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject

class ExperimentExpressionLevelsValueObject extends Object implements Serializable

Serialized Fields

datasetId

long datasetId

geneExpressionLevels

LinkedList<ExperimentExpressionLevelsValueObject.GeneElementExpressionsValueObject> geneExpressionLevels

Class ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject.GeneElementExpressionsValueObject

class GeneElementExpressionsValueObject extends Object implements Serializable

Serialized Fields

elements

List<ExperimentExpressionLevelsValueObject.VectorElementValueObject> elements

geneNcbiId

Integer geneNcbiId

geneOfficialSymbol

String geneOfficialSymbol

Class ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject.VectorElementValueObject

class VectorElementValueObject extends Object implements Serializable

Serialized Fields

bioAssayExpressionLevels

Map<String,Double> bioAssayExpressionLevels

designElementName

String designElementName

Class ubic.gemma.model.expression.bioAssayData.SingleCellDimensionValueObject

class SingleCellDimensionValueObject extends IdentifiableValueObject<SingleCellDimension> implements Serializable

Serialized Fields

bioAssayIds

List<Long> bioAssayIds

cellIds

List<String> cellIds

cellLevelCharacteristics

Set<CellLevelCharacteristicsValueObject> cellLevelCharacteristics

cellTypeAssignments

Set<CellTypeAssignmentValueObject> cellTypeAssignments

numberOfCellIds

int numberOfCellIds

Class ubic.gemma.model.expression.bioAssayData.SlicedDoubleVectorValueObject

class SlicedDoubleVectorValueObject extends DoubleVectorValueObject implements Serializable

Serialized Fields

sourceVectorId

Long sourceVectorId

Package ubic.gemma.model.expression.experiment

Class ubic.gemma.model.expression.experiment.AbstractFactorValueValueObject

class 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.ExperimentalFactorValueObject

class 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.ExpressionExperimentDetailsValueObject

class ExpressionExperimentDetailsValueObject extends ExpressionExperimentValueObject implements Serializable

serialVersionUID:

-1219449523930648392L

Serialized Fields

arrayDesigns

Collection<ArrayDesignValueObject> arrayDesigns

batchFetchEventType

String batchFetchEventType

cellBrowserDatasetName

String cellBrowserDatasetName

cellBrowserUrl

String cellBrowserUrl

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

font

String font

hasBatchInformation

boolean hasBatchInformation

hasBothIntensities

boolean hasBothIntensities

hasCellBrowser

boolean hasCellBrowser

hasCoexpressionAnalysis

boolean hasCoexpressionAnalysis

hasDifferentialExpressionAnalysis

boolean hasDifferentialExpressionAnalysis

hasEitherIntensity

boolean hasEitherIntensity

hasMultiplePreferredQuantitationTypes

boolean hasMultiplePreferredQuantitationTypes

hasMultipleTechnologyTypes

boolean hasMultipleTechnologyTypes

isReprocessedFromRawData

boolean isReprocessedFromRawData

isRNASeq

boolean isRNASeq

isSingleCell

boolean isSingleCell

lastArrayDesignUpdateDate

String lastArrayDesignUpdateDate

linkAnalysisEventType

String linkAnalysisEventType

missingValueAnalysisEventType

String missingValueAnalysisEventType

numAnnotations

Long numAnnotations

numberOfCellIds

Integer numberOfCellIds

numberOfCells

Integer numberOfCells

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

sampleRemovedFlags

Collection<AuditEventValueObject> sampleRemovedFlags

secondaryAccession

String secondaryAccession

secondaryExternalDatabase

String secondaryExternalDatabase

secondaryExternalUri

String secondaryExternalUri

Class ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject

class 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.ExpressionExperimentSubsetValueObject

class ExpressionExperimentSubsetValueObject extends IdentifiableValueObject<ExpressionExperimentSubSet> implements Serializable

Serialized Fields

accession

String accession

Deprecated.

bioAssays

Collection<BioAssayValueObject> bioAssays

characteristics

Collection<CharacteristicValueObject> characteristics

description

String description

isPublic

boolean isPublic

isShared

boolean isShared

minPvalue

Double minPvalue

name

String name

numberOfBioAssays

Integer numberOfBioAssays

sourceExperimentId

Long sourceExperimentId

sourceExperimentShortName

String sourceExperimentShortName

userCanWrite

boolean userCanWrite

userOwned

boolean userOwned

Class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject

class 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

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

minPvalue

Double minPvalue

name

String name

numberOfBioAssays

Integer numberOfBioAssays

processedExpressionVectorCount

Integer processedExpressionVectorCount

shortName

String shortName

source

String source

suitableForDEA

Boolean suitableForDEA

taxonObject

TaxonValueObject taxonObject

technologyType

String technologyType

userCanWrite

boolean userCanWrite

userOwned

boolean userOwned

Class ubic.gemma.model.expression.experiment.FactorValueBasicValueObject

class FactorValueBasicValueObject extends AbstractFactorValueValueObject implements Serializable

serialVersionUID:

3378801249808036785L

Serialized Fields

value

String value

Deprecated.

Class ubic.gemma.model.expression.experiment.FactorValueValueObject

class 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

class FreeTextExpressionExperimentResultsValueObject extends SessionBoundExpressionExperimentSetValueObject implements Serializable

serialVersionUID:

3557304710219740029L

Serialized Fields

queryString

String queryString

Class ubic.gemma.model.expression.experiment.GeeqAdminValueObject

class 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

class 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

class SessionBoundExpressionExperimentSetValueObject extends ExpressionExperimentSetValueObject implements Serializable

serialVersionUID:

2068650886972222818L

Serialized Fields

modified

boolean modified

Class ubic.gemma.model.expression.experiment.StatementValueObject

class 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.GeneOntologyTermValueObject

class 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.PhysicalLocationValueObject

class 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.TaxonValueObject

class 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.persistence.hibernate

Class ubic.gemma.persistence.hibernate.HibernateTransactionManager

class HibernateTransactionManager extends org.springframework.orm.hibernate4.HibernateTransactionManager implements Serializable

Class ubic.gemma.persistence.hibernate.LocalSessionFactoryBuilder

class LocalSessionFactoryBuilder extends org.springframework.orm.hibernate4.LocalSessionFactoryBuilder implements Serializable

Class ubic.gemma.persistence.hibernate.XSDEntityResolver

class XSDEntityResolver extends DTDEntityResolver implements Serializable

Package ubic.gemma.persistence.service

Exception Class ubic.gemma.persistence.service.AbstractServiceTest.ExceptionWithMessage

class ExceptionWithMessage extends Exception implements Serializable

Exception Class ubic.gemma.persistence.service.AbstractServiceTest.ExceptionWithoutMessage

class ExceptionWithoutMessage extends Exception implements Serializable

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

Class ubic.gemma.persistence.service.analysis.expression.diff.MissingResult

class MissingResult extends DiffExprGeneSearchResult implements Serializable

serialVersionUID:

-2868418055346274525L

Class ubic.gemma.persistence.service.analysis.expression.diff.NonRetainedResult

class NonRetainedResult extends DiffExprGeneSearchResult implements Serializable

serialVersionUID:

3501605965895623139L

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

Class ubic.gemma.persistence.service.association.coexpression.CoexpressionCacheValueObject

class 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

class 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

Exception Class ubic.gemma.persistence.service.common.quantitationtype.NonUniqueQuantitationTypeByNameException

class NonUniqueQuantitationTypeByNameException extends Exception implements Serializable

Package ubic.gemma.persistence.service.expression.bioAssayData

Class ubic.gemma.persistence.service.expression.bioAssayData.NegativeBinomialDistribution

class NegativeBinomialDistribution extends org.apache.commons.math3.distribution.AbstractIntegerDistribution implements Serializable

Serialized Fields

distribution

NegativeBinomial distribution

i

int i

v

double v

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

Exception Class ubic.gemma.persistence.service.expression.experiment.FactorValueMigratorService.MigrationFailedException

class MigrationFailedException extends RuntimeException implements Serializable

Serialized Fields

migration

FactorValueMigratorService.Migration migration

Package ubic.gemma.persistence.service.maintenance

Class ubic.gemma.persistence.service.maintenance.Gene2CsStatus

class 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

class AnnotationWithUsageStatisticsValueObject extends AnnotationValueObject implements Serializable

Serialized Fields

numberOfExpressionExperiments

Long numberOfExpressionExperiments

parentTerms

Set<DatasetsWebService.OntologyTermValueObject> parentTerms

Class ubic.gemma.rest.DatasetsWebService.ArrayDesignWithUsageStatisticsValueObject

class ArrayDesignWithUsageStatisticsValueObject extends ArrayDesignValueObject implements Serializable

Serialized Fields

numberOfExpressionExperimentsForTechnologyType

Long numberOfExpressionExperimentsForTechnologyType

Class ubic.gemma.rest.DatasetsWebService.DifferentialExpressionAnalysisResultByGeneValueObject

class 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.ExpressionExperimentSubsetWithFactorValuesObject

class ExpressionExperimentSubsetWithFactorValuesObject extends ExpressionExperimentSubsetValueObject implements Serializable

Serialized Fields

factorValues

List<FactorValueBasicValueObject> factorValues

Class ubic.gemma.rest.DatasetsWebService.ExpressionExperimentSubSetWithGroupsValueObject

class ExpressionExperimentSubSetWithGroupsValueObject extends ExpressionExperimentSubsetValueObject implements Serializable

Serialized Fields

subSetGroupIds

List<Long> subSetGroupIds

Class ubic.gemma.rest.DatasetsWebService.ExpressionExperimentWithSearchResultValueObject

class ExpressionExperimentWithSearchResultValueObject extends ExpressionExperimentValueObject implements Serializable

Serialized Fields

searchResult

SearchWebService.SearchResultValueObject<ExpressionExperimentValueObject> searchResult

Class ubic.gemma.rest.DatasetsWebService.TaxonWithUsageStatisticsValueObject

class TaxonWithUsageStatisticsValueObject extends TaxonValueObject implements Serializable

Serialized Fields

numberOfExpressionExperiments

Long numberOfExpressionExperiments

Package ubic.gemma.rest.serializers

Class ubic.gemma.rest.serializers.AbstractFactorValueValueObjectSerializer

class AbstractFactorValueValueObjectSerializer extends com.fasterxml.jackson.databind.ser.std.StdSerializer<T extends AbstractFactorValueValueObject> implements Serializable

Class ubic.gemma.rest.serializers.FactorValueBasicValueObjectSerializer

class FactorValueBasicValueObjectSerializer extends AbstractFactorValueValueObjectSerializer<FactorValueBasicValueObject> implements Serializable

Class ubic.gemma.rest.serializers.FactorValueValueObjectSerializer

class FactorValueValueObjectSerializer extends AbstractFactorValueValueObjectSerializer<FactorValueValueObject> implements Serializable

Package ubic.gemma.rest.util

Exception Class ubic.gemma.rest.util.EntityNotFoundException

class EntityNotFoundException extends Exception implements Serializable

Exception Class ubic.gemma.rest.util.MalformedArgException

class MalformedArgException extends javax.ws.rs.BadRequestException implements Serializable

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

Class ubic.gemma.web.controller.common.auditAndSecurity.FileUpload

class FileUpload extends Object implements Serializable

serialVersionUID:

537156568346654834L

Serialized Fields

file

byte[] file

localPath

String localPath

Class ubic.gemma.web.controller.common.auditAndSecurity.SidValueObject

class SidValueObject extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

authority

String authority

principal

boolean principal

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

Exception Class ubic.gemma.web.controller.common.auditAndSecurity.recaptcha.ReCaptchaException

class ReCaptchaException extends RuntimeException implements Serializable

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

Class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignValueObjectExt

class 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

class 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

class ExperimentalFactorValueWebUIObject extends ExperimentalFactorValueObject implements Serializable

Serialized Fields

bioMaterialCharacteristicCategoryToUse

String bioMaterialCharacteristicCategoryToUse

Class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentDataFetchCommand

class 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

class ExpressionExperimentEditValueObject extends ExpressionExperimentDetailsValueObject implements Serializable

serialVersionUID:

1630521876359566915L

Serialized Fields

bioAssays

Collection<BioAssayValueObject> bioAssays

quantitationTypes

Collection<QuantitationTypeValueObject> quantitationTypes

Class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentUploadResponse

class ExpressionExperimentUploadResponse extends Object implements Serializable

Serialized Fields

error

boolean error

errorMessage

String errorMessage

taskId

Long taskId

Class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentCommandValidation

class SimpleExpressionExperimentCommandValidation extends Object implements Serializable

Serialized Fields

arrayDesignMatchesDataFile

boolean arrayDesignMatchesDataFile

arrayDesignMismatchProblemMessage

String arrayDesignMismatchProblemMessage

dataFileFormatProblemMessage

String dataFileFormatProblemMessage

dataFileIsValidFormat

boolean dataFileIsValidFormat

isValid

boolean isValid

nonMatchingProbeNameExamples

Collection<String> nonMatchingProbeNameExamples

numberMatchingProbes

int numberMatchingProbes

numberOfNonMatchingProbes

int numberOfNonMatchingProbes

numColumns

int numColumns

numRows

int numRows

otherProblemsMessage

String otherProblemsMessage

quantitationTypeIsValid

boolean quantitationTypeIsValid

quantitationTypeProblemMessage

String quantitationTypeProblemMessage

shortNameIsUnique

boolean shortNameIsUnique

Class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentLoadTaskCommand

class SimpleExpressionExperimentLoadTaskCommand extends TaskCommand implements Serializable

serialVersionUID:

1L

Serialized Fields

arrayDesignIds

Collection<Long> arrayDesignIds

description

String description

isRatio

Boolean isRatio

name

String name

originalFileName

String originalFileName

pubMedId

Integer pubMedId

quantitationTypeDescription

String quantitationTypeDescription

quantitationTypeName

String quantitationTypeName

scale

ScaleType scale

serverFilePath

String serverFilePath

shortName

String shortName

taxonId

Long taxonId

validateOnly

boolean validateOnly

Package ubic.gemma.web.controller.job

Class ubic.gemma.web.controller.job.SubmittedTaskValueObject

class 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