Serialized Form

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

Serialized Fields

result

DifferentialExpressionAnalysisFilterResult result

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

class InvalidQuantitationTypeConversionException extends AnalysisException implements Serializable

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

class MeanVarianceFailureException extends AnalysisException implements Serializable

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

class MultipleBaselinesRequireSubsetException 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.ExpressionExperimentFilterConfig

class ExpressionExperimentFilterConfig extends Object implements Serializable

Serialized Fields

highExpressionCut

double highExpressionCut

ignoreMinimumDesignElementsThreshold

boolean ignoreMinimumDesignElementsThreshold

ignoreMinimumSamplesThreshold

boolean ignoreMinimumSamplesThreshold

lowDistinctValueCut

double lowDistinctValueCut

lowExpressionCut

double lowExpressionCut

lowVarianceCut

double lowVarianceCut

maskOutliers

boolean maskOutliers

minPresentCount

int minPresentCount

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

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

class NoSamplesException extends InsufficientSamplesException implements Serializable

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

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

class SVDException extends Exception implements Serializable

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

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.expression.singleCell

Exception Class ubic.gemma.core.loader.expression.singleCell.NonUniqueCellLevelCharacteristicsByNameException

class NonUniqueCellLevelCharacteristicsByNameException extends NonUniqueDescribableByNameException implements Serializable

Exception Class ubic.gemma.core.loader.expression.singleCell.NonUniqueCellTypeAssignmentByNameException

class NonUniqueCellTypeAssignmentByNameException extends NonUniqueDescribableByNameException 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.ontology

Class ubic.gemma.core.ontology.ObsoleteTermCorrectionResult

class ObsoleteTermCorrectionResult extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

characteristicsRewritten

int characteristicsRewritten

dryRun

boolean dryRun

experimentsAffected

int experimentsAffected

resync

ObsoleteTermCorrectionResult.Resync resync

skippedDeferred

List<String> skippedDeferred

skippedNotCorrectable

List<String> skippedNotCorrectable

terms

List<ObsoleteTermCorrectionResult.TermCorrection> terms

Class ubic.gemma.core.ontology.ObsoleteTermCorrectionResult.Resync

class Resync extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

annotationRelationRowsWritten

int annotationRelationRowsWritten

ee2cRowsWritten

int ee2cRowsWritten

experimentsResynced

int experimentsResynced

resyncFailures

List<String> resyncFailures

Class ubic.gemma.core.ontology.ObsoleteTermCorrectionResult.TermCorrection

class TermCorrection extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

characteristicsRewritten

int characteristicsRewritten

experimentsAffected

int experimentsAffected

fromLabel

String fromLabel

fromUri

String fromUri

inCategory

int inCategory

inObject

int inObject

inPredicate

int inPredicate

inValue

int inValue

resolvedVia

String resolvedVia

toLabel

String toLabel

toUri

String toUri

Class ubic.gemma.core.ontology.ObsoleteTermUsage

class ObsoleteTermUsage extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

autoCorrectable

boolean autoCorrectable

blockedReason

String blockedReason

considerUris

List<String> considerUris

experimentCount

long experimentCount

label

String label

replacedByLabel

String replacedByLabel

replacedByUri

String replacedByUri

replacementHops

int replacementHops

resolvedVia

String resolvedVia

storedValue

String storedValue

uri

String uri

usedAsCategory

boolean usedAsCategory

usedAsTerm

boolean usedAsTerm

Package ubic.gemma.core.ontology.ols

Class ubic.gemma.core.ontology.ols.OlsTerm

class OlsTerm extends Object implements Serializable

Serialized Fields

found

boolean found

iri

String iri

label

String label

Exception Class ubic.gemma.core.ontology.ols.OlsUnavailableException

class OlsUnavailableException extends Exception 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.source

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

class HibernateSearchException extends SearchException implements Serializable

Serialized Fields

cause

org.hibernate.search.util.common.SearchException cause

Package ubic.gemma.core.security.acl.domain

Class ubic.gemma.core.security.acl.domain.AclEntry

class AclEntry extends Object implements Serializable

serialVersionUID:

-4697361841061166973L

Serialized Fields

aceOrder

int aceOrder

acl

org.springframework.security.acls.model.Acl acl

granting

boolean granting

id

Long id

mask

int mask

sid

AclSid sid

Class ubic.gemma.core.security.acl.domain.AclGrantedAuthoritySid

class AclGrantedAuthoritySid extends AclSid implements Serializable

serialVersionUID:

7755206462003052441L

Serialized Fields

grantedAuthority

String grantedAuthority

Class ubic.gemma.core.security.acl.domain.AclImpl

class AclImpl extends Object implements Serializable

serialVersionUID:

-953242274878593548L

Serialized Fields

entries

List<AclEntry> entries

objectIdentity

AclObjectIdentity objectIdentity

parentAcl

org.springframework.security.acls.model.Acl parentAcl

Class ubic.gemma.core.security.acl.domain.AclObjectIdentity

class AclObjectIdentity extends Object implements Serializable

serialVersionUID:

-6715898560226971244L

Serialized Fields

entries

Set<AclEntry> entries

entriesInheriting

boolean entriesInheriting

id

Long id

identifier

Long identifier

objectIdClass

Long objectIdClass

ownerSid

AclSid ownerSid

parentObject

AclObjectIdentity parentObject

type

String type

Class ubic.gemma.core.security.acl.domain.AclPrincipalSid

class AclPrincipalSid extends AclSid implements Serializable

serialVersionUID:

-4679911678447417301L

Serialized Fields

principal

String principal

Class ubic.gemma.core.security.acl.domain.AclSid

class AclSid extends Object implements Serializable

serialVersionUID:

-3256613712125656321L

Serialized Fields

id

Long id

Package ubic.gemma.core.security.audit

Class ubic.gemma.core.security.audit.AuditedEvent

class AuditedEvent extends org.springframework.context.ApplicationEvent implements Serializable

Serialized Fields

auditEvent

AuditEvent auditEvent

eventType

AuditEventType eventType

payload

AuditEventPayload payload

target

Auditable target

Package ubic.gemma.core.security.authentication

Class ubic.gemma.core.security.authentication.UserDetailsImpl

class UserDetailsImpl extends Object implements Serializable

serialVersionUID:

1650537135541038216L

Serialized Fields

email

String email

enabled

boolean enabled

grantedAuthorities

Collection<org.springframework.security.core.GrantedAuthority> grantedAuthorities

password

String password

signupToken

String signupToken

signupTokenDatestamp

Date signupTokenDatestamp

userName

String userName

Exception Class ubic.gemma.core.security.authentication.UserExistsException

class UserExistsException extends Exception implements Serializable

serialVersionUID:

-6191531408977402526L

Package ubic.gemma.core.tasks.analysis.diffex

Class ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisRemoveTaskCommand

class DifferentialExpressionAnalysisRemoveTaskCommand extends DifferentialExpressionAnalysisTaskCommand implements Serializable

serialVersionUID:

-6881129987842634598L

Serialized Fields

toRemove

DifferentialExpressionAnalysis toRemove

Class ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisTaskCommand

class DifferentialExpressionAnalysisTaskCommand extends TaskCommand implements Serializable

serialVersionUID:

1L

Serialized Fields

analysisType

AnalysisType analysisType

expressionExperiment

ExpressionExperiment expressionExperiment

factors

Collection<ExperimentalFactor> factors

forceAnalysis

boolean forceAnalysis

includeInteractions

boolean includeInteractions

moderateStatistics

boolean moderateStatistics

subsetFactor

ExperimentalFactor subsetFactor

toRedo

DifferentialExpressionAnalysis toRedo

useWeights

boolean useWeights

Class ubic.gemma.core.tasks.analysis.diffex.DiffExMetaAnalyzerTaskCommand

class DiffExMetaAnalyzerTaskCommand extends TaskCommand implements Serializable

serialVersionUID:

1L

Serialized Fields

analysisResultSetIds

Collection<Long> analysisResultSetIds

description

String description

name

String name

persist

boolean persist

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.util.math.linearmodels

Class ubic.gemma.core.util.math.linearmodels.AnovaEffect

class AnovaEffect extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

dof

double dof

effectName

String effectName

fStat

double fStat

isInteraction

boolean isInteraction

isResiduals

boolean isResiduals

meanSq

double meanSq

pValue

double pValue

ssQ

double ssQ

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

Class ubic.gemma.model.analysis.AnalysisResultSetValueObject

class AnalysisResultSetValueObject extends IdentifiableValueObject<R extends AnalysisResultSet<K>> implements Serializable

Class ubic.gemma.model.analysis.AnalysisResultValueObject

class AnalysisResultValueObject extends IdentifiableValueObject<A extends AnalysisResult> implements Serializable

Class ubic.gemma.model.analysis.AnalysisValueObject

class AnalysisValueObject extends IdentifiableValueObject<T extends Analysis> implements Serializable

Serialized Fields

name

String name

protocol

ProtocolValueObject protocol

Class ubic.gemma.model.analysis.CellTypeAssignmentValueObject

class CellTypeAssignmentValueObject extends AnalysisValueObject<CellTypeAssignment> implements Serializable

Serialized Fields

cellTypeIds

List<Long> cellTypeIds

cellTypes

Set<CharacteristicValueObject> cellTypes

isPreferred

boolean isPreferred

numberOfAssignedCells

Integer numberOfAssignedCells

numberOfAssignedCellsByCellType

Map<Long,Integer> numberOfAssignedCellsByCellType

Class ubic.gemma.model.analysis.ProtocolValueObject

class ProtocolValueObject extends IdentifiableValueObject<Protocol> implements Serializable

Serialized Fields

description

String description

name

String name

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

resultSetId

Long resultSetId

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

class DifferentialExpressionAnalysisValueObject extends AnalysisValueObject<DifferentialExpressionAnalysis> implements Serializable

serialVersionUID:

622877438067070041L

Serialized Fields

arrayDesignsUsed

Collection<Long> arrayDesignsUsed

bioAssaysAnalyzed

Collection<BioAssayValueObject> bioAssaysAnalyzed

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

bioAssaysAnalyzed

Collection<BioAssayValueObject> bioAssaysAnalyzed

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

threshold

Double threshold

upregulatedCount

Integer upregulatedCount

Class ubic.gemma.model.analysis.expression.diff.DiffExResultSetSummaryValueObject.Prefetch

class Prefetch extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

baselineGroup

FactorValue baselineGroup

experimentalFactors

Set<ExperimentalFactor> experimentalFactors

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

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

class ResultSetCountsValueObject extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

downregulatedCount

Integer downregulatedCount

numberOfDiffExpressedProbes

Integer numberOfDiffExpressedProbes

numberOfGenesAnalyzed

Integer numberOfGenesAnalyzed

numberOfProbesAnalyzed

Integer numberOfProbesAnalyzed

threshold

Double threshold

upregulatedCount

Integer upregulatedCount

Package ubic.gemma.model.common

Class ubic.gemma.model.common.BaseValueObject

class BaseValueObject extends Object implements Serializable

serialVersionUID:

-5290562301261202171L

Serialized Fields

accessDenied

boolean accessDenied

errorFound

boolean errorFound

objectAlreadyRemoved

boolean objectAlreadyRemoved

userNotLoggedIn

boolean userNotLoggedIn

valueObject

Serializable valueObject

Class ubic.gemma.model.common.IdentifiableValueObject

class IdentifiableValueObject extends Object implements Serializable

Serialized Fields

id

Long id

Exception Class ubic.gemma.model.common.NonUniqueDescribableByNameException

class NonUniqueDescribableByNameException extends IllegalArgumentException implements Serializable

Package ubic.gemma.model.common.auditAndSecurity.curation

Class ubic.gemma.model.common.auditAndSecurity.curation.AbstractCuratableValueObject

class AbstractCuratableValueObject extends IdentifiableValueObject<C extends Curatable> implements Serializable

Serialized Fields

curationNote

String curationNote

lastNeedsAttentionEvent

AuditEventValueObject lastNeedsAttentionEvent

lastNoteUpdateEvent

AuditEventValueObject lastNoteUpdateEvent

lastTroubledEvent

AuditEventValueObject lastTroubledEvent

lastUpdated

Date lastUpdated

needsAttention

boolean needsAttention

troubled

boolean troubled

Class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetSummaryValueObject

class AnnotationSetSummaryValueObject extends IdentifiableValueObject<AnnotationSet> implements Serializable

serialVersionUID:

1L

Serialized Fields

agentName

String agentName

agentVersion

String agentVersion

createdAt

Date createdAt

createdBy

String createdBy

datasetShortName

String datasetShortName

factorCount

Integer factorCount

finalizedAt

Date finalizedAt

finalizedBy

String finalizedBy

investigationId

Long investigationId

kind

AgentCurationKind kind

model

String model

parentId

Long parentId

payloadSize

Long payloadSize

ranAt

Date ranAt

role

AnnotationSetRole role

runId

String runId

runSha

String runSha

source

AnnotationSetSource source

status

String status

tagCount

Integer tagCount

updatedAt

Date updatedAt

Class ubic.gemma.model.common.auditAndSecurity.curation.CurationDetailsValueObject

class CurationDetailsValueObject extends IdentifiableValueObject<CurationDetails> implements Serializable

Serialized Fields

curationNote

String curationNote

curationPending

Boolean curationPending

lastNeedsAttentionEvent

AuditEventValueObject lastNeedsAttentionEvent

lastNoteUpdateEvent

AuditEventValueObject lastNoteUpdateEvent

lastTroubledEvent

AuditEventValueObject lastTroubledEvent

lastUpdated

Date lastUpdated

needsAttention

boolean needsAttention

troubled

boolean troubled

Class ubic.gemma.model.common.auditAndSecurity.curation.CurationLock

class CurationLock extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

agentName

String agentName

expiresAt

Date expiresAt

investigation

Investigation investigation

investigationId

Long investigationId

lockedAt

Date lockedAt

lockedBy

String lockedBy

runId

String runId

stolenAt

Date stolenAt

stolenFrom

String stolenFrom

Class ubic.gemma.model.common.auditAndSecurity.curation.TicketEventValueObject

class TicketEventValueObject extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

actorId

Long actorId

actorName

String actorName

id

Long id

occurredAt

Date occurredAt

payload

String payload

type

TicketEventType type

Class ubic.gemma.model.common.auditAndSecurity.curation.TicketSearchHitValueObject

class TicketSearchHitValueObject extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

id

Long id

priority

TicketPriority priority

state

TicketState state

targetCount

long targetCount

title

String title

type

TicketType type

updatedAt

Date updatedAt

Class ubic.gemma.model.common.auditAndSecurity.curation.TicketSummaryForTargetValueObject

class TicketSummaryForTargetValueObject extends TicketSearchHitValueObject implements Serializable

serialVersionUID:

1L

Serialized Fields

targetStatus

TicketTargetStatus targetStatus

Class ubic.gemma.model.common.auditAndSecurity.curation.TicketTargetValueObject

class TicketTargetValueObject extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

displayLabel

String displayLabel

displayName

String displayName

id

Long id

screeningResult

ScreeningResult screeningResult

screeningResultReason

String screeningResultReason

status

TicketTargetStatus status

targetId

Long targetId

targetType

TicketTargetType targetType

Class ubic.gemma.model.common.auditAndSecurity.curation.TicketValueObject

class TicketValueObject extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

acceptsTargets

boolean acceptsTargets

assigneeId

Long assigneeId

assigneeName

String assigneeName

body

String body

createdAt

Date createdAt

dueDate

Date dueDate

events

List<TicketEventValueObject> events

externalIssueSyncState

ExternalIssueSyncState externalIssueSyncState

externalIssueUrl

String externalIssueUrl

id

Long id

mode

TicketMode mode

payload

String payload

payloadSchemaVersion

Integer payloadSchemaVersion

priority

TicketPriority priority

reporterId

Long reporterId

reporterName

String reporterName

state

TicketState state

targets

List<TicketTargetValueObject> targets

title

String title

type

TicketType type

updatedAt

Date updatedAt

Package ubic.gemma.model.common.description

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

class AnnotationValueObject extends IdentifiableValueObject<Characteristic> implements Serializable

Serialized Fields

category

String category

categoryUri

String categoryUri

description

String description

evidenceCode

String evidenceCode

object

String object

objectClass

String objectClass

objectUri

String objectUri

parentDescription

String parentDescription

parentLink

String parentLink

parentName

String parentName

parentOfParentDescription

String parentOfParentDescription

parentOfParentLink

String parentOfParentLink

parentOfParentName

String parentOfParentName

predicate

String predicate

predicateUri

String predicateUri

secondObject

String secondObject

secondObjectUri

String secondObjectUri

secondPredicate

String secondPredicate

secondPredicateUri

String secondPredicateUri

supportingEvidence

com.fasterxml.jackson.databind.JsonNode supportingEvidence

value

String value

valueUri

String valueUri

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

supplementary

boolean supplementary

supportingEvidence

com.fasterxml.jackson.databind.JsonNode supportingEvidence

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

label

String label

uri

String uri

Class ubic.gemma.model.common.description.DatasetPublicationValueObject

class DatasetPublicationValueObject extends BibliographicReferenceValueObject implements Serializable

Serialized Fields

association

PublicationAssociationValueObject association

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

isSingleCellPreferred

boolean isSingleCellPreferred

name

String name

representation

String representation

scale

String scale

type

String type

vectorType

String vectorType

Package ubic.gemma.model.expression.bioAssay

Class ubic.gemma.model.expression.bioAssay.BioAssayValueObject

class BioAssayValueObject extends IdentifiableValueObject<BioAssay> implements Serializable

serialVersionUID:

9164284536309673585L

Serialized Fields

accession

DatabaseEntryValueObject accession

arrayDesign

ArrayDesignValueObject arrayDesign

description

String description

extractedMolecule

ExtractedMolecule extractedMolecule

librarySelection

String librarySelection

libraryStrategy

String libraryStrategy

metadata

String metadata

name

String name

numberOfCells

Integer numberOfCells

numberOfCellsByDesignElements

Integer numberOfCellsByDesignElements

numberOfDesignElements

Integer numberOfDesignElements

originalPlatform

ArrayDesignValueObject originalPlatform

outlier

boolean outlier

predictedOutlier

Boolean predictedOutlier

processingDate

Date processingDate

sample

BioMaterialValueObject sample

sequencePairedReads

Boolean sequencePairedReads

sequenceReadCount

Long sequenceReadCount

sequenceReadLength

Integer sequenceReadLength

shortName

String shortName

sourceBioAssayId

Long sourceBioAssayId

userFlaggedOutlier

boolean userFlaggedOutlier

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

numberOfCells

int[] numberOfCells

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

correctedPvalue

Double correctedPvalue

elements

List<ExperimentExpressionLevelsValueObject.VectorElementValueObject> elements

geneEnsemblId

String geneEnsemblId

geneNcbiId

Integer geneNcbiId

geneOfficialName

String geneOfficialName

geneOfficialSymbol

String geneOfficialSymbol

log2FoldChange

Double log2FoldChange

pvalue

Double pvalue

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.biomaterial

Class ubic.gemma.model.expression.biomaterial.BioMaterialValueObject

class BioMaterialValueObject extends IdentifiableValueObject<BioMaterial> implements Serializable

serialVersionUID:

-145137827948521045L

Serialized Fields

assayDescription

String assayDescription

assayName

String assayName

assayProcessingDate

Date assayProcessingDate

basicFVs

boolean basicFVs

bioAssayIds

Collection<Long> bioAssayIds

characteristicOriginalValues

Map<String,String> characteristicOriginalValues

characteristics

Collection<CharacteristicValueObject> characteristics

characteristicValues

Map<String,String> characteristicValues

description

String description

factorIdToFactorValueId

Map<String,String> factorIdToFactorValueId

factorValueObjects

Collection<FactorValueValueObject> factorValueObjects

factorValues

Map<String,String> factorValues

fastqHeaders

String fastqHeaders

fVBasicVOs

Collection<FactorValueBasicValueObject> fVBasicVOs

name

String name

sourceBioMaterialId

Long sourceBioMaterialId

statements

Collection<StatementValueObject> statements

Package ubic.gemma.model.expression.experiment

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

class AbstractFactorValueValueObject extends IdentifiableValueObject<FactorValue> implements Serializable

Serialized Fields

baseline

Boolean baseline

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

supportingEvidence

com.fasterxml.jackson.databind.JsonNode supportingEvidence

Class ubic.gemma.model.expression.experiment.DesignApplyOutcome

class DesignApplyOutcome extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

applied

boolean applied

design

ExperimentalDesignValueObject design

preflightAtApply

DesignPreflightReport preflightAtApply

Class ubic.gemma.model.expression.experiment.DesignPreflightReport

class DesignPreflightReport extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

blockers

List<DesignPreflightReport.Blocker> blockers

differentialExpressionAnalysesToDelete

List<DesignPreflightReport.AnalysisRef> differentialExpressionAnalysesToDelete

factorsToDelete

List<DesignPreflightReport.EntityRef> factorsToDelete

factorsToUpdate

List<DesignPreflightReport.EntityRef> factorsToUpdate

factorValuesToDelete

List<DesignPreflightReport.EntityRef> factorValuesToDelete

factorValuesToUpdate

List<DesignPreflightReport.EntityRef> factorValuesToUpdate

subsetsWithStaleAnchor

List<DesignPreflightReport.SubsetRef> subsetsWithStaleAnchor

summary

DesignPreflightReport.Summary summary

Class ubic.gemma.model.expression.experiment.DesignPreflightReport.AnalysisRef

class AnalysisRef extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

id

Long id

name

String name

subsetFactorValueId

Long subsetFactorValueId

Class ubic.gemma.model.expression.experiment.DesignPreflightReport.Blocker

class Blocker extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

bioMaterialId

Long bioMaterialId

factorId

Long factorId

factorValueId

Long factorValueId

message

String message

statementId

Long statementId

type

String type

Class ubic.gemma.model.expression.experiment.DesignPreflightReport.EntityRef

class EntityRef extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

id

Long id

name

String name

Class ubic.gemma.model.expression.experiment.DesignPreflightReport.SubsetRef

class SubsetRef extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

id

Long id

lostFactorValueIds

List<Long> lostFactorValueIds

name

String name

Class ubic.gemma.model.expression.experiment.DesignPreflightReport.Summary

class Summary extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

biomaterialsWithChangedAssignments

int biomaterialsWithChangedAssignments

differentialExpressionAnalysesToDelete

int differentialExpressionAnalysesToDelete

factorsToCreate

int factorsToCreate

factorsToDelete

int factorsToDelete

factorsToUpdate

int factorsToUpdate

factorValuesToCreate

int factorValuesToCreate

factorValuesToDelete

int factorValuesToDelete

factorValuesToUpdate

int factorValuesToUpdate

subsetsWithStaleAnchor

int subsetsWithStaleAnchor

Class ubic.gemma.model.expression.experiment.ExperimentalDesignValueObject

class ExperimentalDesignValueObject extends IdentifiableValueObject<ExperimentalDesign> implements Serializable

serialVersionUID:

1L

Serialized Fields

bioMaterialAssignments

List<ExperimentalDesignValueObject.BioMaterialFactorValueAssignment> bioMaterialAssignments

description

String description

experimentalFactors

List<ExperimentalDesignValueObject.ExperimentalFactorEntry> experimentalFactors

name

String name

normalizationDescription

String normalizationDescription

qualityControlDescription

String qualityControlDescription

replicateDescription

String replicateDescription

Class ubic.gemma.model.expression.experiment.ExperimentalFactorValueObject

class ExperimentalFactorValueObject extends IdentifiableValueObject<ExperimentalFactor> implements Serializable

serialVersionUID:

-2615804031123874251L

Serialized Fields

baselineRelevance

String baselineRelevance

baselineRelevanceReason

String baselineRelevanceReason

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

differentialAnalysisEventType

String differentialAnalysisEventType

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

lastArrayDesignUpdateDate

String lastArrayDesignUpdateDate

linkAnalysisEventType

String linkAnalysisEventType

missingValueAnalysisEventType

String missingValueAnalysisEventType

numAnnotations

Long numAnnotations

numPopulatedFactors

Long numPopulatedFactors

pcaAnalysisEventType

String pcaAnalysisEventType

primaryCitation

CitationValueObject primaryCitation

processedDataVectorComputationEventType

String processedDataVectorComputationEventType

QChtml

String QChtml

sampleRemovedFlags

Collection<AuditEventValueObject> sampleRemovedFlags

secondaryAccession

String secondaryAccession

secondaryExternalDatabase

String secondaryExternalDatabase

secondaryExternalUri

String secondaryExternalUri

Class ubic.gemma.model.expression.experiment.ExpressionExperimentReferenceValueObject

class ExpressionExperimentReferenceValueObject extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

id

Long id

name

String name

shortName

String shortName

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

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

dateCreated

Date dateCreated

description

String description

doi

String doi

experimentalDesign

Long experimentalDesign

externalDatabase

String externalDatabase

externalDatabaseUri

String externalDatabaseUri

externalLabel

String externalLabel

externalUri

String externalUri

geeq

GeeqValueObject geeq

isPublic

boolean isPublic

isShared

boolean isShared

isSingleCell

boolean isSingleCell

metadata

String metadata

minPvalue

Double minPvalue

name

String name

numberOfBioAssays

Integer numberOfBioAssays

numberOfCellIds

Integer numberOfCellIds

numberOfCells

Integer numberOfCells

originalPlatforms

List<ArrayDesignReferenceValueObject> originalPlatforms

otherParts

List<ExpressionExperimentReferenceValueObject> otherParts

platforms

List<ArrayDesignReferenceValueObject> platforms

processedExpressionVectorCount

Integer processedExpressionVectorCount

pubmedId

String pubmedId

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

manualBatchConfoundActive

boolean manualBatchConfoundActive

manualBatchEffectActive

boolean manualBatchEffectActive

manualHasBatchConfound

boolean manualHasBatchConfound

manualHasNoBatchEffect

boolean manualHasNoBatchEffect

manualHasStrongBatchEffect

boolean manualHasStrongBatchEffect

manualQualityOverride

boolean manualQualityOverride

manualQualityScore

double manualQualityScore

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

lastComputed

Date lastComputed

noVectors

boolean noVectors

publicQualityScore

double publicQualityScore

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

Class ubic.gemma.model.expression.experiment.GeoScrapeWatermark

class GeoScrapeWatermark extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

criteriaApplied

String criteriaApplied

errorMessage

String errorMessage

id

Long id

recordsMatched

int recordsMatched

recordsScanned

int recordsScanned

scanFrom

Date scanFrom

scannedAt

Date scannedAt

scanTo

Date scanTo

status

GeoScrapeWatermark.Status status

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

evidenceCode

String evidenceCode

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

supportingEvidence

com.fasterxml.jackson.databind.JsonNode supportingEvidence

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.model.util

Exception Class ubic.gemma.model.util.UninitializedCollectionException

class UninitializedCollectionException extends RuntimeException implements Serializable

Package ubic.gemma.persistence.hibernate

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.common.auditAndSecurity.curation

Exception Class ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationLockService.CurationLockedException

class CurationLockedException extends RuntimeException implements Serializable

serialVersionUID:

1L

Serialized Fields

heldBy

String heldBy

Package ubic.gemma.persistence.service.common.description

Exception Class ubic.gemma.persistence.service.common.description.PublicationAssociationConflictException

class PublicationAssociationConflictException extends IllegalArgumentException implements Serializable

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.DisallowedWorkflowTransitionException

class DisallowedWorkflowTransitionException extends RuntimeException implements Serializable

Serialized Fields

allowedNextStates

Set<WorkflowState> allowedNextStates

currentState

WorkflowState currentState

targetState

WorkflowState targetState

Exception Class ubic.gemma.persistence.service.expression.experiment.PreboardedExperimentService.AccessionAlreadyExistsException

class AccessionAlreadyExistsException extends Exception implements Serializable

Serialized Fields

existingId

Long existingId

existingType

String existingType

Exception Class ubic.gemma.persistence.service.expression.experiment.PreboardedExperimentService.PreboardedAlreadyPromotedException

class PreboardedAlreadyPromotedException extends Exception implements Serializable

Serialized Fields

preboardedId

Long preboardedId

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.persistence.util

Exception Class ubic.gemma.persistence.util.UnsupportedEntityUrlException

class UnsupportedEntityUrlException extends RuntimeException implements Serializable

Serialized Fields

entityType

Class<? extends Identifiable> entityType

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

Class ubic.gemma.rest.GeneWebService.CompositeSequenceSummaryValueObject

class CompositeSequenceSummaryValueObject extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

genes

List<GeneValueObject> genes

numBlatHits

Integer numBlatHits

numGenes

int numGenes

probe

CompositeSequenceValueObject probe

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.CurationCommitConflictException

class CurationCommitConflictException extends jakarta.ws.rs.ClientErrorException implements Serializable

Serialized Fields

reason

CurationCommitConflictException.Reason reason

Exception Class ubic.gemma.rest.util.EntityNotFoundException

class EntityNotFoundException extends Exception implements Serializable

Exception Class ubic.gemma.rest.util.MalformedArgException

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

Exception Class ubic.gemma.rest.util.OntologyTermValidationException

class OntologyTermValidationException extends RuntimeException implements Serializable

Serialized Fields

violations

List<OntologyTermValidationException.Located> violations

Exception Class ubic.gemma.rest.util.UnknownQueryParameterException

class UnknownQueryParameterException extends MalformedArgException implements Serializable

Serialized Fields

acceptedParameters

Set<String> acceptedParameters

unknownParameters

List<String> unknownParameters