Serialized Form (Gemma 1.31.0-SNAPSHOT Test API)

Package ubic.gemma.core.analysis.expression.coexpression.links
- Class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - absoluteValue
      
      boolean absoluteValue
    - arrayName
      
      String arrayName
    - cdfCut
      
      double cdfCut
    - checkCorrelationDistribution
      
      boolean checkCorrelationDistribution
    - checkForBatchEffect
      
      boolean checkForBatchEffect
    - checkForOutliers
      
      boolean checkForOutliers
    - correlationCacheThreshold
      
      double correlationCacheThreshold
    - fwe
      
      double fwe
    - lowerCdfCutUsed
      
      boolean lowerCdfCutUsed
    - lowerTailCut
      
      double lowerTailCut
    - makeSampleCorrMatImages
      
      boolean makeSampleCorrMatImages
    - metric
      
      String metric
    - minNumPresent
      
      int minNumPresent
    - normalizationMethod
      
      LinkAnalysisConfig.NormalizationMethod normalizationMethod
    - omitNegLinks
      
      boolean omitNegLinks
    - outputFile
      
      File outputFile
    - probeDegreeThreshold
      
      int probeDegreeThreshold
    - singularThreshold
      
      LinkAnalysisConfig.SingularThreshold singularThreshold
    - subset
      
      boolean subset
    - subsetSize
      
      double subsetSize
    - subsetUsed
      
      boolean subsetUsed
    - textOut
      
      boolean textOut
    - upperCdfCutUsed
      
      boolean upperCdfCutUsed
    - upperTailCut
      
      double upperTailCut
    - useDb
      
      boolean useDb
- Class ubic.gemma.core.analysis.expression.coexpression.links.UnsuitableForAnalysisException extends RuntimeException implements Serializable
  
  serialVersionUID:
  
  -4436136164850796179L
Package ubic.gemma.core.analysis.expression.diff
- Class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig extends Object implements Serializable
  
  serialVersionUID:
  
  622877438067070041L
  - Serialized Fields
    - analysisType
      
      DifferentialExpressionAnalyzerServiceImpl.AnalysisType analysisType
    - baseLineFactorValues
      
      Map<ExperimentalFactor,FactorValue> baseLineFactorValues
    - ebayes
      
      boolean ebayes
    - factorsToInclude
      
      List<ExperimentalFactor> factorsToInclude
    - interactionsToInclude
      
      Collection<Collection<ExperimentalFactor>> interactionsToInclude
    - makeArchiveFile
      
      boolean makeArchiveFile
    - persist
      
      boolean persist
    - subsetFactor
      
      ExperimentalFactor subsetFactor
    - subsetFactorValue
      
      FactorValue subsetFactorValue
    - useWeights
      
      boolean useWeights
- Class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionMetaAnalysisValueObject extends Object implements Serializable
  - Serialized Fields
    - activeExperiments
      
      Collection<BioAssaySet> activeExperiments
    - fisherPValue
      
      Double fisherPValue
    - gene
      
      GeneValueObject gene
    - numExperimentsInScope
      
      int numExperimentsInScope
    - numMetThreshold
      
      int numMetThreshold
    - numSearchedExperiments
      
      int numSearchedExperiments
    - probeResults
      
      Collection<DifferentialExpressionValueObject> probeResults
    - sortKey
      
      String sortKey
- Class ubic.gemma.core.analysis.expression.diff.DiffExpressionSelectedFactorCommand extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - eeId
      
      Long eeId
    - efId
      
      Long efId
Package ubic.gemma.core.analysis.preprocess
- Class ubic.gemma.core.analysis.preprocess.FailedToComputeSingularValueDecomposition extends PreprocessingException implements Serializable
- Class ubic.gemma.core.analysis.preprocess.InsufficientProbesException extends InsufficientDataException implements Serializable
  
  serialVersionUID:
  
  1L
- Class ubic.gemma.core.analysis.preprocess.PreprocessingException extends RuntimeException implements Serializable
  
  serialVersionUID:
  
  -8463478950898408838L
- Class ubic.gemma.core.analysis.preprocess.QuantitationMismatchPreprocessingException extends PreprocessingException implements Serializable
- Class ubic.gemma.core.analysis.preprocess.SampleCoexpressionRelatedPreprocessingException extends PreprocessingException implements Serializable
- Class ubic.gemma.core.analysis.preprocess.SVDRelatedPreprocessingException extends PreprocessingException implements Serializable
  - Serialized Fields
    - cause
      
      SVDException cause
- Class ubic.gemma.core.analysis.preprocess.UnsupportedQuantitationScaleConversionException extends QuantitationTypeConversionException implements Serializable
Package ubic.gemma.core.analysis.preprocess.batcheffects
- Class ubic.gemma.core.analysis.preprocess.batcheffects.BatchConfound extends Object implements Serializable
  - Serialized Fields
    - chiSquare
      
      double chiSquare
    - df
      
      int df
    - ee
      
      BioAssaySet ee
    - ef
      
      ExperimentalFactor ef
    - numBatches
      
      int numBatches
    - p
      
      double p
- Class ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationException extends PreprocessingException implements Serializable
  
  serialVersionUID:
  
  -1770591991479420212L
- Class ubic.gemma.core.analysis.preprocess.batcheffects.FASTQHeadersPresentButNotUsableException extends BatchInfoPopulationException implements Serializable
  
  serialVersionUID:
  
  1917074433646650950L
- Class ubic.gemma.core.analysis.preprocess.batcheffects.SingletonBatchesException extends BatchInfoPopulationException implements Serializable
  
  serialVersionUID:
  
  9088141067684148902L
- Class ubic.gemma.core.analysis.preprocess.batcheffects.UnsupportedRawdataFileFormatException extends BatchInfoPopulationException implements Serializable
  
  serialVersionUID:
  
  1L
Package ubic.gemma.core.analysis.preprocess.svd
- Class ubic.gemma.core.analysis.preprocess.svd.SVDException extends Exception implements Serializable
- Class ubic.gemma.core.analysis.preprocess.svd.SVDValueObject extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - bioMaterialIds
      
      Long[] bioMaterialIds
    - dateCorrelations
      
      Map<Integer,Double> dateCorrelations
    - datePVals
      
      Map<Integer,Double> datePVals
    - dates
      
      List<Date> dates
    - factorCorrelations
      
      Map<Integer,Map<Long,Double>> factorCorrelations
    - factorPvals
      
      Map<Integer,Map<Long,Double>> factorPvals
    - factors
      
      Map<Long,List<Double>> factors
    - id
      
      Long id
    - variances
      
      double[] variances
    - vMatrix
      
      DoubleMatrix<Long,Integer> vMatrix
Package ubic.gemma.core.analysis.report
- Class ubic.gemma.core.analysis.report.AuditableObject extends Object implements Serializable
  
  serialVersionUID:
  
  -7862129089784691035L
  - Serialized Fields
    - date
      
      Date date
    - id
      
      Long id
    - type
      
      String type

Package ubic.gemma.core.analysis.sequence

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

Serialized Fields

arrayDesignId
```
Long arrayDesignId
```
arrayDesignName
```
String arrayDesignName
```
arrayDesignShortName
```
String arrayDesignShortName
```
bioSequenceId
```
String bioSequenceId
```
bioSequenceName
```
String bioSequenceName
```
bioSequenceNcbiId
```
String bioSequenceNcbiId
```
compositeSequenceDescription
```
String compositeSequenceDescription
```
compositeSequenceId
```
String compositeSequenceId
```
compositeSequenceName
```
String compositeSequenceName
```

geneProducts

Map<Long,GeneProductValueObject> geneProducts

genes
```
Map<Long,GeneValueObject> genes
```
numBlatHits
```
Integer numBlatHits
```

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

serialVersionUID:: 8899320580201273360L

Serialized Fields

blatResult
```
BlatResultValueObject blatResult
```
blatResultId
```
String blatResultId
```

compositeSequence

CompositeSequenceValueObject compositeSequence

geneProductIdGeneMap

Map<String,GeneValueObject> geneProductIdGeneMap

geneProductIdMap

Map<String,GeneProductValueObject> geneProductIdMap

geneProductMap

Map<GeneProductValueObject,GeneValueObject> geneProductMap

identity
```
double identity
```
score
```
double score
```

Package ubic.gemma.core.datastructure.matrix
- Class ubic.gemma.core.datastructure.matrix.BaseExpressionDataMatrix extends Object implements Serializable
  - Serialized Fields
    - bioAssayDimensions
      
      Map<CompositeSequence,BioAssayDimension> bioAssayDimensions
    - columnAssayMap
      
      Map<BioAssay,Integer> columnAssayMap
    - columnBioAssayMapByInteger
      
      Map<Integer,Collection<BioAssay>> columnBioAssayMapByInteger
    - columnBioMaterialMap
      
      Map<BioMaterial,Integer> columnBioMaterialMap
    - columnBioMaterialMapByInteger
      
      Map<Integer,BioMaterial> columnBioMaterialMapByInteger
    - expressionExperiment
      
      ExpressionExperiment expressionExperiment
    - quantitationTypes
      
      Collection<QuantitationType> quantitationTypes
    - rowDesignElementMapByInteger
      
      Map<Integer,CompositeSequence> rowDesignElementMapByInteger
    - rowElementMap
      
      Map<CompositeSequence,Integer> rowElementMap
    - rowElements
      
      List<ExpressionDataMatrixRowElement> rowElements
- Class ubic.gemma.core.datastructure.matrix.EmptyExpressionMatrix extends BaseExpressionDataMatrix<Object> implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - numCols
      
      int numCols
- Class ubic.gemma.core.datastructure.matrix.ExpressionDataBooleanMatrix extends BaseExpressionDataMatrix<Boolean> implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - matrix
      
      ObjectMatrixImpl<CompositeSequence,Integer,Boolean> matrix
- Class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix extends BaseExpressionDataMatrix<Double> implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - matrix
      
      DoubleMatrix<CompositeSequence,BioMaterial> matrix
    - ranks
      
      Map<CompositeSequence,Double> ranks
- Class ubic.gemma.core.datastructure.matrix.ExpressionDataIntegerMatrix extends BaseExpressionDataMatrix<Integer> implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - matrix
      
      IntegerMatrix<CompositeSequence,Integer> matrix
- Class ubic.gemma.core.datastructure.matrix.ExpressionDataStringMatrix extends BaseExpressionDataMatrix<String> implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - matrix
      
      StringMatrix<Integer,Integer> matrix
- Class ubic.gemma.core.datastructure.matrix.ExpressionDataTestMatrix extends ExpressionDataDoubleMatrix implements Serializable
  
  serialVersionUID:
  
  1L
- Class ubic.gemma.core.datastructure.matrix.InferredQuantitationMismatchException extends QuantitationMismatchException implements Serializable
  - Serialized Fields
    - inferredQuantitationType
      
      QuantitationType inferredQuantitationType
- Class ubic.gemma.core.datastructure.matrix.QuantitationMismatchException extends Exception implements Serializable
  - Serialized Fields
    - quantitationType
      
      QuantitationType quantitationType
- Class ubic.gemma.core.datastructure.matrix.QuantitationTypeConversionException extends RuntimeException implements Serializable
- Class ubic.gemma.core.datastructure.matrix.SuspiciousValuesForQuantitationException extends QuantitationMismatchException implements Serializable
  - Serialized Fields
    - suspiciousValues
      
      List<SuspiciousValuesForQuantitationException.SuspiciousValueResult> suspiciousValues
Package ubic.gemma.core.job
- Class ubic.gemma.core.job.TaskCommand extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - emailAlert
      
      boolean emailAlert
    - entityId
      
      Long entityId
    - maxQueueMinutes
      
      Integer maxQueueMinutes
    - maxRuntime
      
      int maxRuntime
    - persistJobDetails
      
      Boolean persistJobDetails
    - securityContext
      
      org.springframework.security.core.context.SecurityContext securityContext
    - submitter
      
      String submitter
    - taskId
      
      String taskId
- Class ubic.gemma.core.job.TaskResult extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - answer
      
      Object answer
    - exception
      
      Exception exception
    - taskID
      
      String taskID
Package ubic.gemma.core.loader.entrez.pubmed
- Class ubic.gemma.core.loader.entrez.pubmed.ESearchException extends Exception implements Serializable
Package ubic.gemma.core.loader.expression.arrayDesign
- Class ubic.gemma.core.loader.expression.arrayDesign.Reporter extends AbstractDescribable implements Serializable
  
  serialVersionUID:
  
  3703827938981026012L
  - Serialized Fields
    - col
      
      Integer col
    - compositeSequence
      
      CompositeSequence compositeSequence
    - immobilizedCharacteristic
      
      BioSequence immobilizedCharacteristic
    - row
      
      Integer row
    - startInBioChar
      
      Long startInBioChar
    - strand
      
      String strand
Package ubic.gemma.core.loader.expression.geo
- Class ubic.gemma.core.loader.expression.geo.GeoSampleCorrespondence extends Object implements Serializable
  
  serialVersionUID:
  
  -5285504953530483114L
  - Serialized Fields
    - accToDataset
      
      Map<String,String> accToDataset
    - accToTitle
      
      Map<String,String> accToTitle
    - sets
      
      Collection<Set<String>> sets
Package ubic.gemma.core.loader.expression.geo.service
- Class ubic.gemma.core.loader.expression.geo.service.IOExceptionWithRetry extends IOException implements Serializable
  - Serialized Fields
    - errorFromPreviousAttempt
      
      IOExceptionWithRetry errorFromPreviousAttempt
Package ubic.gemma.core.loader.util
- Class ubic.gemma.core.loader.util.AlreadyExistsInSystemException extends RuntimeException implements Serializable
  
  serialVersionUID:
  
  5677999264920938691L
  - Serialized Fields
    - data
      
      Object data
Package ubic.gemma.core.ontology
- Class ubic.gemma.core.ontology.AbstractOntologyResourceSimple extends Object implements Serializable
  - Serialized Fields
    - label
      
      String label
    - uri
      
      String uri
- Class ubic.gemma.core.ontology.OntologyIndividualSimple extends AbstractOntologyResourceSimple implements Serializable
  - Serialized Fields
    - instanceOf
      
      OntologyTermSimple instanceOf
- Class ubic.gemma.core.ontology.OntologyPropertySimple extends AbstractOntologyResourceSimple implements Serializable
Package ubic.gemma.core.search
- Class ubic.gemma.core.search.BaseCodeOntologySearchException extends SearchException implements Serializable
  - Serialized Fields
    - cause
      
      OntologySearchException cause
- Class ubic.gemma.core.search.SearchException extends Exception implements Serializable
Package ubic.gemma.core.search.source
- Class ubic.gemma.core.search.source.HibernateSearchException extends SearchException implements Serializable
  - Serialized Fields
    - cause
      
      org.hibernate.search.SearchException cause
Package ubic.gemma.core.util
- Class ubic.gemma.core.util.StrictBeanDefinitionValidatorTest.TestAnnotatedVo extends Object implements Serializable
- Class ubic.gemma.core.util.StrictBeanDefinitionValidatorTest.TestImplicitValueObject extends Object implements Serializable
Package ubic.gemma.model.analysis
- Class ubic.gemma.model.analysis.Analysis extends AbstractDescribable implements Serializable
  
  serialVersionUID:
  
  -7666181528240555473L
  - Serialized Fields
    - protocol
      
      Protocol protocol
- Class ubic.gemma.model.analysis.AnalysisResultSet extends Object implements Serializable
  
  serialVersionUID:
  
  -6749501453616281312L
  - Serialized Fields
    - id
      
      Long id
- Class ubic.gemma.model.analysis.AnalysisResultSetValueObject extends IdentifiableValueObject<R extends AnalysisResultSet<K>> implements Serializable
- Class ubic.gemma.model.analysis.AnalysisResultValueObject extends IdentifiableValueObject<A extends AnalysisResult> implements Serializable
- Class ubic.gemma.model.analysis.AnalysisValueObject extends IdentifiableValueObject<T extends Analysis> implements Serializable
- Class ubic.gemma.model.analysis.Investigation extends AbstractAuditable implements Serializable
  
  serialVersionUID:
  
  -5191564466698945873L
  - Serialized Fields
    - characteristics
      
      Set<Characteristic> characteristics
    - otherRelevantPublications
      
      Set<BibliographicReference> otherRelevantPublications
    - owner
      
      Contact owner
    - primaryPublication
      
      BibliographicReference primaryPublication
- Class ubic.gemma.model.analysis.SingleExperimentAnalysis extends ExpressionAnalysis implements Serializable
  
  serialVersionUID:
  
  -6301345978501023402L
  - Serialized Fields
    - experimentAnalyzed
      
      BioAssaySet experimentAnalyzed
    - numberOfElementsAnalyzed
      
      Integer numberOfElementsAnalyzed
Package ubic.gemma.model.analysis.expression.coexpression
- Class ubic.gemma.model.analysis.expression.coexpression.CoexpressionAnalysis extends SingleExperimentAnalysis implements Serializable
  
  serialVersionUID:
  
  -2036918876881877628L
  - Serialized Fields
    - coexpCorrelationDistribution
      
      CoexpCorrelationDistribution coexpCorrelationDistribution
    - numberOfLinks
      
      Integer numberOfLinks
- Class ubic.gemma.model.analysis.expression.coexpression.GeneCoexpressedGenes extends IdArray implements Serializable
  
  serialVersionUID:
  
  6715464097628664297L
  - Serialized Fields
    - geneId
      
      Long geneId
- Class ubic.gemma.model.analysis.expression.coexpression.GeneCoexpressionTestedIn extends IdArray implements Serializable
  
  serialVersionUID:
  
  3122664964809277501L
  - Serialized Fields
    - geneId
      
      Long geneId
    - numDatasetsTestedIn
      
      int numDatasetsTestedIn
- Class ubic.gemma.model.analysis.expression.coexpression.HumanCoexpressionSupportDetailsImpl extends SupportDetails implements Serializable
  
  serialVersionUID:
  
  -5002268300977281525L
- Class ubic.gemma.model.analysis.expression.coexpression.IdArray extends Object implements Serializable
  
  serialVersionUID:
  
  -7563304392793946778L
  - Serialized Fields
    - data
      
      com.googlecode.javaewah.EWAHCompressedBitmap data
- Class ubic.gemma.model.analysis.expression.coexpression.IdArrayValueObject extends IdArray implements Serializable
  
  serialVersionUID:
  
  3449107398932831708L
- Class ubic.gemma.model.analysis.expression.coexpression.MouseCoexpressionSupportDetailsImpl extends SupportDetails implements Serializable
  
  serialVersionUID:
  
  3935257719971070260L
- Class ubic.gemma.model.analysis.expression.coexpression.OtherCoexpressionSupportDetailsImpl extends SupportDetails implements Serializable
  
  serialVersionUID:
  
  1730038206222335399L
- Class ubic.gemma.model.analysis.expression.coexpression.RatCoexpressionSupportDetailsImpl extends SupportDetails implements Serializable
  
  serialVersionUID:
  
  3067914341922800267L
- Class ubic.gemma.model.analysis.expression.coexpression.SampleCoexpressionAnalysis extends SingleExperimentAnalysis implements Serializable
  
  serialVersionUID:
  
  5006465967597402551L
  - Serialized Fields
    - fullCoexpressionMatrix
      
      SampleCoexpressionMatrix fullCoexpressionMatrix
    - regressedCoexpressionMatrix
      
      SampleCoexpressionMatrix regressedCoexpressionMatrix
- Class ubic.gemma.model.analysis.expression.coexpression.SampleCoexpressionMatrix extends Object implements Serializable
  
  serialVersionUID:
  
  8168483585163161355L
  - Serialized Fields
    - bioAssayDimension
      
      BioAssayDimension bioAssayDimension
    - coexpressionMatrix
      
      byte[] coexpressionMatrix
    - id
      
      Long id
- Class ubic.gemma.model.analysis.expression.coexpression.SupportDetails extends IdArray implements Serializable
  
  serialVersionUID:
  
  -8148641748805015611L
  - Serialized Fields
    - firstGeneId
      
      Long firstGeneId
    - id
      
      Long id
    - isPositive
      
      Boolean isPositive
    - secondGeneId
      
      Long secondGeneId
Package ubic.gemma.model.association.coexpression
- Class ubic.gemma.model.association.coexpression.ExperimentCoexpressionLink extends Object implements Serializable
  
  serialVersionUID:
  
  -3850440587168527052L
  - Serialized Fields
    - experiment
      
      BioAssaySet experiment
    - firstGene
      
      Long firstGene
    - id
      
      Long id
    - linkId
      
      Long linkId
    - secondGene
      
      Long secondGene
- Class ubic.gemma.model.association.coexpression.Gene2GeneCoexpression extends Gene2GeneIdAssociation implements Serializable
  
  serialVersionUID:
  
  6088623734153830393L
  - Serialized Fields
    - numDataSetsSupporting
      
      Integer numDataSetsSupporting
    - positiveCorrelation
      
      Boolean positiveCorrelation
    - supportDetails
      
      SupportDetails supportDetails
- Class ubic.gemma.model.association.coexpression.GeneCoexpressionNodeDegree extends Object implements Serializable
  
  serialVersionUID:
  
  -1456064687251594963L
  - Serialized Fields
    - geneId
      
      Long geneId
    - linkCountsNegative
      
      byte[] linkCountsNegative
    - linkCountsPositive
      
      byte[] linkCountsPositive
    - relativeLinkRanksNegative
      
      byte[] relativeLinkRanksNegative
    - relativeLinkRanksPositive
      
      byte[] relativeLinkRanksPositive
- Class ubic.gemma.model.association.coexpression.GeneCoexpressionNodeDegreeValueObject extends Object implements Serializable
  - Serialized Fields
    - geneId
      
      Long geneId
    - nodeDegreesNeg
      
      TreeMap<Integer,Integer> nodeDegreesNeg
    - nodeDegreesPos
      
      TreeMap<Integer,Integer> nodeDegreesPos
    - relDegreesNeg
      
      TreeMap<Integer,Double> relDegreesNeg
    - relDegreesPos
      
      TreeMap<Integer,Double> relDegreesPos
- Class ubic.gemma.model.association.coexpression.HumanExperimentCoexpressionLinkImpl extends ExperimentCoexpressionLink implements Serializable
  
  serialVersionUID:
  
  8753430934473629791L
- Class ubic.gemma.model.association.coexpression.HumanGeneCoExpression extends Gene2GeneCoexpression implements Serializable
  
  serialVersionUID:
  
  -908571853818330702L
- Class ubic.gemma.model.association.coexpression.HumanGeneCoExpressionImpl extends HumanGeneCoExpression implements Serializable
  
  serialVersionUID:
  
  -1143581426457333084L
- Class ubic.gemma.model.association.coexpression.MouseExperimentCoexpressionLinkImpl extends ExperimentCoexpressionLink implements Serializable
  
  serialVersionUID:
  
  498137981864642L
- Class ubic.gemma.model.association.coexpression.MouseGeneCoExpression extends Gene2GeneCoexpression implements Serializable
  
  serialVersionUID:
  
  6475614056538630827L
- Class ubic.gemma.model.association.coexpression.MouseGeneCoExpressionImpl extends MouseGeneCoExpression implements Serializable
  
  serialVersionUID:
  
  9197559725933952760L
- Class ubic.gemma.model.association.coexpression.OtherExperimentCoexpressionLinkImpl extends ExperimentCoexpressionLink implements Serializable
  
  serialVersionUID:
  
  -1684811922186491341L
- Class ubic.gemma.model.association.coexpression.OtherGeneCoExpression extends Gene2GeneCoexpression implements Serializable
  
  serialVersionUID:
  
  7730779544234187004L
- Class ubic.gemma.model.association.coexpression.OtherGeneCoExpressionImpl extends OtherGeneCoExpression implements Serializable
  
  serialVersionUID:
  
  -2419886942835022490L
- Class ubic.gemma.model.association.coexpression.RatExperimentCoexpressionLinkImpl extends ExperimentCoexpressionLink implements Serializable
  
  serialVersionUID:
  
  -3635504802405373650L
- Class ubic.gemma.model.association.coexpression.RatGeneCoExpression extends Gene2GeneCoexpression implements Serializable
  
  serialVersionUID:
  
  -151363121627382446L
- Class ubic.gemma.model.association.coexpression.RatGeneCoExpressionImpl extends RatGeneCoExpression implements Serializable
  
  serialVersionUID:
  
  5889802151081696108L
Package ubic.gemma.model.association.phenotype
- Class ubic.gemma.model.association.phenotype.DataAnalysisEvidence extends PhenotypeAssociation implements Serializable
  
  serialVersionUID:
  
  -1823081475754671450L
- Class ubic.gemma.model.association.phenotype.DifferentialExpressionEvidence extends DataAnalysisEvidence implements Serializable
  
  serialVersionUID:
  
  1056186800210320618L
  - Serialized Fields
    - geneDifferentialExpressionMetaAnalysisResult
      
      GeneDifferentialExpressionMetaAnalysisResult geneDifferentialExpressionMetaAnalysisResult
      
      Deprecated.
    - selectionThreshold
      
      Double selectionThreshold
      
      Deprecated.
- Class ubic.gemma.model.association.phenotype.ExperimentalEvidence extends PhenotypeAssociation implements Serializable
  
  serialVersionUID:
  
  -1310307976449116756L
  - Serialized Fields
    - experiment
      
      Investigation experiment
      
      Deprecated.
- Class ubic.gemma.model.association.phenotype.GenericEvidence extends PhenotypeAssociation implements Serializable
  
  serialVersionUID:
  
  9049824856704318367L
- Class ubic.gemma.model.association.phenotype.GenericExperiment extends Investigation implements Serializable
  
  serialVersionUID:
  
  -1322252603261082189L
- Class ubic.gemma.model.association.phenotype.LiteratureEvidence extends PhenotypeAssociation implements Serializable
  
  serialVersionUID:
  
  -4106020347488355001L
- Class ubic.gemma.model.association.phenotype.PhenotypeAssociation extends AbstractAuditable implements Serializable
  
  serialVersionUID:
  
  -1734685902449428500L
  - Serialized Fields
    - associationType
      
      Characteristic associationType
      
      Deprecated.
    - evidenceCode
      
      GOEvidenceCode evidenceCode
      
      Deprecated.
    - evidenceSource
      
      DatabaseEntry evidenceSource
      
      Deprecated.
    - gene
      
      Gene gene
      
      Deprecated.
    - isNegativeEvidence
      
      Boolean isNegativeEvidence
      
      Deprecated.
    - lastUpdated
      
      Date lastUpdated
      
      Deprecated.
    - mappingType
      
      PhenotypeMappingType mappingType
      
      Deprecated.
    - originalPhenotype
      
      String originalPhenotype
      
      Deprecated.
    - phenotypeAssociationPublications
      
      Set<PhenotypeAssociationPublication> phenotypeAssociationPublications
      
      Deprecated.
    - phenotypes
      
      Set<Characteristic> phenotypes
      
      Deprecated.
    - relationship
      
      String relationship
      
      Deprecated.
    - score
      
      String score
      
      Deprecated.
    - scoreType
      
      QuantitationType scoreType
      
      Deprecated.
    - strength
      
      Double strength
      
      Deprecated.
- Class ubic.gemma.model.association.phenotype.PhenotypeAssociationPublication extends Object implements Serializable
  
  serialVersionUID:
  
  -4156623260205197700L
  - Serialized Fields
    - citation
      
      BibliographicReference citation
      
      Deprecated.
    - id
      
      Long id
      
      Deprecated.
    - type
      
      String type
      
      Deprecated.
- Class ubic.gemma.model.association.phenotype.PhenotypeMappingType extends Object implements Serializable
  
  serialVersionUID:
  
  -3336933794060950406L
  - Serialized Fields
    - value
      
      String value
      
      Deprecated.
Package ubic.gemma.model.common.auditAndSecurity
- Class ubic.gemma.model.common.auditAndSecurity.AuditEvent extends Object implements Serializable
  
  serialVersionUID:
  
  -1212093157703833905L
  - Serialized Fields
    - action
      
      AuditAction action
    - date
      
      Date date
    - detail
      
      String detail
    - eventType
      
      AuditEventType eventType
    - id
      
      Long id
    - note
      
      String note
    - performer
      
      User performer
- Class ubic.gemma.model.common.auditAndSecurity.AuditEventValueObject extends IdentifiableValueObject<AuditEvent> implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - action
      
      String action
    - date
      
      Date date
    - detail
      
      String detail
    - eventType
      
      AuditEventType eventType
    - note
      
      String note
    - performer
      
      String performer
- Class ubic.gemma.model.common.auditAndSecurity.AuditTrail extends Object implements Serializable
  
  serialVersionUID:
  
  -7450755789163303140L
  - Serialized Fields
    - events
      
      List<AuditEvent> events
    - id
      
      Long id
- Class ubic.gemma.model.common.auditAndSecurity.Contact extends AbstractDescribable implements Serializable
  
  serialVersionUID:
  
  2410750024818017046L
  - Serialized Fields
    - email
      
      String email
- Class ubic.gemma.model.common.auditAndSecurity.GroupAuthority extends Object implements Serializable
  
  serialVersionUID:
  
  6376142653264312139L
  - Serialized Fields
    - authority
      
      String authority
    - id
      
      Long id
- Class ubic.gemma.model.common.auditAndSecurity.GroupAuthorityImpl extends GroupAuthority implements Serializable
  
  serialVersionUID:
  
  6376142653264312139L
- Class ubic.gemma.model.common.auditAndSecurity.JobInfo extends Object implements Serializable
  
  serialVersionUID:
  
  -4998165708433543706L
  - Serialized Fields
    - description
      
      String description
    - endTime
      
      Date endTime
    - failedMessage
      
      String failedMessage
    - id
      
      Long id
    - messages
      
      String messages
    - phases
      
      Integer phases
    - runningStatus
      
      Boolean runningStatus
    - startTime
      
      Date startTime
    - taskId
      
      String taskId
    - user
      
      User user
- Class ubic.gemma.model.common.auditAndSecurity.Person extends Contact implements Serializable
  
  serialVersionUID:
  
  -7873047856249494633L
  - Serialized Fields
    - lastName
      
      String lastName
      
      Deprecated.
- Class ubic.gemma.model.common.auditAndSecurity.User extends Person implements Serializable
  
  serialVersionUID:
  
  5910497757956461559L
  - Serialized Fields
    - enabled
      
      Boolean enabled
    - groups
      
      Set<UserGroup> groups
    - jobs
      
      Set<JobInfo> jobs
    - password
      
      String password
    - passwordHint
      
      String passwordHint
    - signupToken
      
      String signupToken
    - signupTokenDatestamp
      
      Date signupTokenDatestamp
    - userName
      
      String userName
- Class ubic.gemma.model.common.auditAndSecurity.UserGroup extends AbstractAuditable implements Serializable
  
  serialVersionUID:
  
  5795744069086222179L
  - Serialized Fields
    - authorities
      
      Set<gemma.gsec.model.GroupAuthority> authorities
    - groupMembers
      
      Set<gemma.gsec.model.User> groupMembers
- Class ubic.gemma.model.common.auditAndSecurity.UserQuery extends Object implements Serializable
  
  serialVersionUID:
  
  -2790140985613402440L
  - Serialized Fields
    - autoRunFrequencyHours
      
      Integer autoRunFrequencyHours
    - id
      
      Long id
    - lastUsed
      
      Date lastUsed
    - name
      
      String name
    - searchSettings
      
      SearchSettings searchSettings
    - url
      
      String url
Package ubic.gemma.model.common.auditAndSecurity.eventType
- Class ubic.gemma.model.common.auditAndSecurity.eventType.AlignmentBasedGeneMappingEvent extends ArrayDesignGeneMappingEvent implements Serializable
  
  serialVersionUID:
  
  7667960927701046528L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.AnalysisSuitabilityEvent extends AuditEventType implements Serializable
  
  serialVersionUID:
  
  7754007995197256846L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.AnnotationBasedGeneMappingEvent extends ArrayDesignGeneMappingEvent implements Serializable
  
  serialVersionUID:
  
  6216699496744292404L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.AnnotationEvent extends AuditEventType implements Serializable
  
  serialVersionUID:
  
  -7488448191665314917L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignAnalysisEvent extends AuditEventType implements Serializable
  
  serialVersionUID:
  
  -8391873112717801492L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignGeneMappingEvent extends ArrayDesignAnalysisEvent implements Serializable
  
  serialVersionUID:
  
  -7566135203525054499L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignMergeEvent extends ArrayDesignAnalysisEvent implements Serializable
  
  serialVersionUID:
  
  8243373027784116451L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignProbeRenamingEvent extends ArrayDesignAnalysisEvent implements Serializable
  
  serialVersionUID:
  
  -5458770150436736181L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignRepeatAnalysisEvent extends ArrayDesignAnalysisEvent implements Serializable
  
  serialVersionUID:
  
  -1315594279851821201L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignSequenceAnalysisEvent extends ArrayDesignAnalysisEvent implements Serializable
  
  serialVersionUID:
  
  8487897002282121437L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignSequenceRemoveEvent extends ArrayDesignAnalysisEvent implements Serializable
  
  serialVersionUID:
  
  -3044700012305059422L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignSequenceUpdateEvent extends ArrayDesignAnalysisEvent implements Serializable
  
  serialVersionUID:
  
  2502989996801972836L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignSubsumeCheckEvent extends ArrayDesignAnalysisEvent implements Serializable
  
  serialVersionUID:
  
  -6105886398033742202L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.AuditEventType extends Object implements Serializable
  
  serialVersionUID:
  
  -7397754091918396538L
  - Serialized Fields
    - id
      
      Long id
- Class ubic.gemma.model.common.auditAndSecurity.eventType.AutomatedAnnotationEvent extends AnnotationEvent implements Serializable
  
  serialVersionUID:
  
  8510568858539453569L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.BatchCorrectionEvent extends ExpressionExperimentAnalysisEvent implements Serializable
  
  serialVersionUID:
  
  -3061045506228031201L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.BatchInformationEvent extends ExpressionExperimentAnalysisEvent implements Serializable
- Class ubic.gemma.model.common.auditAndSecurity.eventType.BatchInformationFetchingEvent extends BatchInformationEvent implements Serializable
  
  serialVersionUID:
  
  4635587632131568136L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.BatchInformationMissingEvent extends BatchInformationEvent implements Serializable
- Class ubic.gemma.model.common.auditAndSecurity.eventType.BatchProblemsUpdateEvent extends ExpressionExperimentAnalysisEvent implements Serializable
  
  serialVersionUID:
  
  -3061045506228031201L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.BioMaterialMappingUpdate extends ExpressionExperimentAnalysisEvent implements Serializable
  
  serialVersionUID:
  
  -4390321148453980797L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.CommentedEvent extends AuditEventType implements Serializable
  
  serialVersionUID:
  
  -9053488530090657730L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.CurationDetailsEvent extends AuditEventType implements Serializable
  
  serialVersionUID:
  
  6621758826080039878L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.CurationNoteUpdateEvent extends CurationDetailsEvent implements Serializable
  
  serialVersionUID:
  
  -1180281595664872508L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.DataAddedEvent extends ExpressionExperimentAnalysisEvent implements Serializable
  
  serialVersionUID:
  
  -492849538043540166L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.DataReplacedEvent extends ExpressionExperimentAnalysisEvent implements Serializable
  
  serialVersionUID:
  
  -3239733956797015820L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.DifferentialExpressionAnalysisEvent extends ExpressionExperimentAnalysisEvent implements Serializable
  
  serialVersionUID:
  
  -2254124666542924604L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.DifferentialExpressionSuitabilityEvent extends AnalysisSuitabilityEvent implements Serializable
  
  serialVersionUID:
  
  -3436468845066159993L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.DoesNotNeedAttentionEvent extends CurationDetailsEvent implements Serializable
  
  serialVersionUID:
  
  6425018808816856629L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.ExperimentalDesignUpdatedEvent extends AuditEventType implements Serializable
  
  serialVersionUID:
  
  6359338763821876809L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.ExpressionExperimentAnalysisEvent extends AuditEventType implements Serializable
  
  serialVersionUID:
  
  6359338763821876809L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.ExpressionExperimentPlatformSwitchEvent extends ExpressionExperimentAnalysisEvent implements Serializable
  
  serialVersionUID:
  
  2918272498309052073L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.ExpressionExperimentUpdateFromGEOEvent extends AuditEventType implements Serializable
  
  serialVersionUID:
  
  5823969791153895703L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.ExpressionExperimentVectorMergeEvent extends ExpressionExperimentAnalysisEvent implements Serializable
  
  serialVersionUID:
  
  3635469819668645913L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.FactorValueNeedsAttentionEvent extends NeedsAttentionEvent implements Serializable
- Class ubic.gemma.model.common.auditAndSecurity.eventType.FailedBatchInformationFetchingEvent extends BatchInformationFetchingEvent implements Serializable
- Class ubic.gemma.model.common.auditAndSecurity.eventType.FailedBatchInformationMissingEvent extends BatchInformationMissingEvent implements Serializable
  
  serialVersionUID:
  
  -3235885345623521195L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.FailedDataReplacedEvent extends DataReplacedEvent implements Serializable
  
  serialVersionUID:
  
  304758117763492676L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.FailedDifferentialExpressionAnalysisEvent extends NeedsAttentionEvent implements Serializable
  
  serialVersionUID:
  
  6904992064998125083L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.FailedLinkAnalysisEvent extends NeedsAttentionEvent implements Serializable
  
  serialVersionUID:
  
  1234186759038122633L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.FailedMeanVarianceUpdateEvent extends NeedsAttentionEvent implements Serializable
- Class ubic.gemma.model.common.auditAndSecurity.eventType.FailedMissingValueAnalysisEvent extends NeedsAttentionEvent implements Serializable
  
  serialVersionUID:
  
  -8827983770602337826L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.FailedPCAAnalysisEvent extends NeedsAttentionEvent implements Serializable
  
  serialVersionUID:
  
  -7055117029646665872L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.FailedProcessedVectorComputationEvent extends NeedsAttentionEvent implements Serializable
  
  serialVersionUID:
  
  -3296770035025801791L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.FailedSampleCorrelationAnalysisEvent extends NeedsAttentionEvent implements Serializable
- Class ubic.gemma.model.common.auditAndSecurity.eventType.GeeqEvent extends AuditEventType implements Serializable
  
  serialVersionUID:
  
  6621758826080039878L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.LinkAnalysisEvent extends ExpressionExperimentAnalysisEvent implements Serializable
  
  serialVersionUID:
  
  -9218026901325452759L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.MakePrivateEvent extends PermissionChangeEvent implements Serializable
  
  serialVersionUID:
  
  1858209889786173945L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.MakePublicEvent extends PermissionChangeEvent implements Serializable
  
  serialVersionUID:
  
  -2250506177437626685L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.ManualAnnotationEvent extends AnnotationEvent implements Serializable
  
  serialVersionUID:
  
  -4919680073334263746L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.MeanVarianceUpdateEvent extends ExpressionExperimentAnalysisEvent implements Serializable
- Class ubic.gemma.model.common.auditAndSecurity.eventType.MissingValueAnalysisEvent extends ExpressionExperimentAnalysisEvent implements Serializable
  
  serialVersionUID:
  
  -4000136638329943603L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.NeedsAttentionEvent extends CurationDetailsEvent implements Serializable
  
  serialVersionUID:
  
  -1180281595664872508L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.NotTroubledStatusFlagEvent extends CurationDetailsEvent implements Serializable
  
  serialVersionUID:
  
  -8586752080144045085L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.OutlierAnalysisEvent extends ExpressionExperimentAnalysisEvent implements Serializable
  
  serialVersionUID:
  
  681380361152118118L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.OutlierFoundAnalysisEvent extends OutlierAnalysisEvent implements Serializable
  
  serialVersionUID:
  
  -3797610069227351691L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.OutliersNotFoundAnalysisEvent extends OutlierAnalysisEvent implements Serializable
  
  serialVersionUID:
  
  -1857664606860041995L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.PCAAnalysisEvent extends ExpressionExperimentAnalysisEvent implements Serializable
  
  serialVersionUID:
  
  -7387174169412782003L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.PermissionChangeEvent extends AuditEventType implements Serializable
  
  serialVersionUID:
  
  -7205154783209555418L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.ProcessedVectorComputationEvent extends ExpressionExperimentAnalysisEvent implements Serializable
  
  serialVersionUID:
  
  3380481220417398475L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.RankComputationEvent extends ProcessedVectorComputationEvent implements Serializable
  
  serialVersionUID:
  
  7396366160834308993L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.ReleaseDetailsUpdateEvent extends VersionedEvent implements Serializable
- Class ubic.gemma.model.common.auditAndSecurity.eventType.ResetSuitabilityForDifferentialExpressionAnalysisEvent extends DifferentialExpressionSuitabilityEvent implements Serializable
  
  serialVersionUID:
  
  5909581992797452478L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.SampleCorrelationAnalysisEvent extends ExpressionExperimentAnalysisEvent implements Serializable
- Class ubic.gemma.model.common.auditAndSecurity.eventType.SampleRemovalEvent extends ExpressionExperimentAnalysisEvent implements Serializable
  
  serialVersionUID:
  
  6508357999103110838L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.SampleRemovalReversionEvent extends ExpressionExperimentAnalysisEvent implements Serializable
  
  serialVersionUID:
  
  -2893496636576496129L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.SingleBatchDeterminationEvent extends BatchInformationFetchingEvent implements Serializable
  
  serialVersionUID:
  
  -6544162258733474787L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.SingletonBatchInvalidEvent extends FailedBatchInformationFetchingEvent implements Serializable
  
  serialVersionUID:
  
  7917557159624872204L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.TooSmallDatasetLinkAnalysisEvent extends LinkAnalysisEvent implements Serializable
  
  serialVersionUID:
  
  3051344049635374788L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.TroubledStatusFlagEvent extends CurationDetailsEvent implements Serializable
  
  serialVersionUID:
  
  7335601529423635731L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.UninformativeFASTQHeadersForBatchingEvent extends FailedBatchInformationFetchingEvent implements Serializable
  
  serialVersionUID:
  
  8836148437542742955L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.UnsuitableForDifferentialExpressionAnalysisEvent extends DifferentialExpressionSuitabilityEvent implements Serializable
  
  serialVersionUID:
  
  4296161562091100967L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.VersionedEvent extends AuditEventType implements Serializable
Package ubic.gemma.model.common.description
- Class ubic.gemma.model.common.description.AnnotationValueObject extends IdentifiableValueObject<Characteristic> implements Serializable
  - Serialized Fields
    - className
      
      String className
    - classUri
      
      String classUri
    - description
      
      String description
    - evidenceCode
      
      String evidenceCode
    - objectClass
      
      String objectClass
    - parentDescription
      
      String parentDescription
    - parentLink
      
      String parentLink
    - parentName
      
      String parentName
    - parentOfParentDescription
      
      String parentOfParentDescription
    - parentOfParentLink
      
      String parentOfParentLink
    - parentOfParentName
      
      String parentOfParentName
    - termName
      
      String termName
    - termUri
      
      String termUri
- Class ubic.gemma.model.common.description.BibliographicReference extends AbstractDescribable implements Serializable
  
  serialVersionUID:
  
  5823969791153895703L
  - Serialized Fields
    - abstractText
      
      String abstractText
    - annotatedAbstract
      
      String annotatedAbstract
      
      Deprecated.
    - annotations
      
      Set<Characteristic> annotations
      
      Deprecated.
    - authorList
      
      String authorList
    - chemicals
      
      Set<Compound> chemicals
    - citation
      
      String citation
    - editor
      
      String editor
    - fullTextUri
      
      String fullTextUri
    - issue
      
      String issue
    - keywords
      
      Set<Keyword> keywords
    - meshTerms
      
      Set<MedicalSubjectHeading> meshTerms
    - pages
      
      String pages
    - pubAccession
      
      DatabaseEntry pubAccession
    - publication
      
      String publication
    - publicationDate
      
      Date publicationDate
    - publisher
      
      String publisher
    - retracted
      
      Boolean retracted
    - title
      
      String title
    - volume
      
      String volume
- Class ubic.gemma.model.common.description.BibliographicReferenceValueObject extends IdentifiableValueObject<BibliographicReference> implements Serializable
  - Serialized Fields
    - abstractText
      
      String abstractText
    - authorList
      
      String authorList
    - bibliographicPhenotypes
      
      Collection<BibliographicPhenotypesValueObject> bibliographicPhenotypes
    - chemicalsTerms
      
      Collection<String> chemicalsTerms
    - citation
      
      CitationValueObject citation
    - experiments
      
      Collection<ExpressionExperimentValueObject> experiments
    - issue
      
      String issue
    - meshTerms
      
      Collection<String> meshTerms
    - pages
      
      String pages
    - pubAccession
      
      String pubAccession
    - publication
      
      String publication
    - publicationDate
      
      Date publicationDate
    - publisher
      
      String publisher
    - retracted
      
      boolean retracted
    - title
      
      String title
    - volume
      
      String volume
- Class ubic.gemma.model.common.description.BibRefAnnotation extends Object implements Serializable
  
  serialVersionUID:
  
  -2925637697790915030L
  - Serialized Fields
    - id
      
      Long id
    - isMajorTopic
      
      Boolean isMajorTopic
    - term
      
      String term
- Class ubic.gemma.model.common.description.Characteristic extends AbstractDescribable implements Serializable
  
  serialVersionUID:
  
  -7242166109264718620L
  - Serialized Fields
    - category
      
      String category
    - categoryUri
      
      String categoryUri
    - evidenceCode
      
      GOEvidenceCode evidenceCode
    - migratedToStatement
      
      boolean migratedToStatement
      
      Deprecated.
    - originalValue
      
      String originalValue
    - value
      
      String value
    - valueUri
      
      String valueUri
- Class ubic.gemma.model.common.description.CharacteristicValueObject extends IdentifiableValueObject<Characteristic> implements Serializable
  - Serialized Fields
    - alreadyPresentInDatabase
      
      boolean alreadyPresentInDatabase
    - alreadyPresentOnGene
      
      boolean alreadyPresentOnGene
    - category
      
      String category
    - categoryUri
      
      String categoryUri
    - child
      
      boolean child
    - numTimesUsed
      
      int numTimesUsed
    - ontologyUsed
      
      String ontologyUsed
    - privateGeneCount
      
      long privateGeneCount
    - publicGeneCount
      
      long publicGeneCount
    - root
      
      boolean root
    - taxon
      
      String taxon
    - urlId
      
      String urlId
    - value
      
      String value
    - valueDefinition
      
      String valueDefinition
    - valueId
      
      String valueId
    - valueUri
      
      String valueUri
- Class ubic.gemma.model.common.description.CitationValueObject extends Object implements Serializable
  - Serialized Fields
    - citation
      
      String citation
    - id
      
      Long id
    - pubmedAccession
      
      String pubmedAccession
    - pubmedURL
      
      String pubmedURL
    - retracted
      
      boolean retracted
- Class ubic.gemma.model.common.description.DatabaseEntry extends Object implements Serializable
  
  serialVersionUID:
  
  5418961655066735636L
  - Serialized Fields
    - accession
      
      String accession
    - accessionVersion
      
      String accessionVersion
    - externalDatabase
      
      ExternalDatabase externalDatabase
    - id
      
      Long id
    - Uri
      
      String Uri
      
      Deprecated.
- Class ubic.gemma.model.common.description.DatabaseEntryValueObject extends IdentifiableValueObject<DatabaseEntry> implements Serializable
  
  serialVersionUID:
  
  -527323410580090L
  - Serialized Fields
    - accession
      
      String accession
    - externalDatabase
      
      ExternalDatabaseValueObject externalDatabase
- Class ubic.gemma.model.common.description.ExternalDatabase extends AbstractDescribable implements Serializable
  
  serialVersionUID:
  
  6807023718405086508L
  - Serialized Fields
    - auditTrail
      
      AuditTrail auditTrail
    - databaseSupplier
      
      Contact databaseSupplier
    - externalDatabases
      
      Set<ExternalDatabase> externalDatabases
    - ftpUri
      
      String ftpUri
    - lastUpdated
      
      Date lastUpdated
    - localInstallDbName
      
      String localInstallDbName
    - releaseUrl
      
      URL releaseUrl
    - releaseVersion
      
      String releaseVersion
    - type
      
      DatabaseType type
    - webUri
      
      String webUri
- Class ubic.gemma.model.common.description.ExternalDatabaseValueObject extends IdentifiableValueObject<ExternalDatabase> implements Serializable
  
  serialVersionUID:
  
  -1714429166594162374L
  - Serialized Fields
    - checked
      
      boolean checked
    - description
      
      String description
    - externalDatabases
      
      Set<ExternalDatabaseValueObject> externalDatabases
    - lastUpdated
      
      Date lastUpdated
    - name
      
      String name
    - releaseUrl
      
      URL releaseUrl
    - releaseVersion
      
      String releaseVersion
    - uri
      
      String uri
- Class ubic.gemma.model.common.description.Keyword extends BibRefAnnotation implements Serializable
  
  serialVersionUID:
  
  2663428244994277220L
- Class ubic.gemma.model.common.description.LocalFile extends Object implements Serializable
  
  serialVersionUID:
  
  5057142607188347151L
  - Serialized Fields
    - id
      
      Long id
    - localURL
      
      URI localURL
    - remoteURL
      
      URI remoteURL
    - size
      
      Long size
    - version
      
      String version
- Class ubic.gemma.model.common.description.MedicalSubjectHeading extends BibRefAnnotation implements Serializable
  
  serialVersionUID:
  
  7820807342851172028L
  - Serialized Fields
    - qualifiers
      
      Set<MedicalSubjectHeading> qualifiers
Package ubic.gemma.model.common.search
- Class ubic.gemma.model.common.search.SearchSettings extends Object implements Serializable
  
  serialVersionUID:
  
  -982243911532743661L
  - Serialized Fields
    - fillResults
      
      boolean fillResults
    - maxResults
      
      int maxResults
    - mode
      
      SearchSettings.SearchMode mode
    - platformConstraint
      
      ArrayDesign platformConstraint
    - query
      
      String query
    - resultTypes
      
      Set<Class<? extends Identifiable>> resultTypes
    - taxon
      
      Taxon taxon
    - useCharacteristics
      
      boolean useCharacteristics
    - useDatabase
      
      boolean useDatabase
    - useGo
      
      boolean useGo
    - useIndices
      
      boolean useIndices
- Class ubic.gemma.model.common.search.SearchSettingsValueObject extends Object implements Serializable
  
  serialVersionUID:
  
  -934534534L
  - Serialized Fields
    - maxResults
      
      Integer maxResults
    - platformConstraint
      
      ArrayDesign platformConstraint
    - query
      
      String query
    - searchBibrefs
      
      Boolean searchBibrefs
    - searchBioSequences
      
      Boolean searchBioSequences
    - searchExperiments
      
      Boolean searchExperiments
    - searchExperimentSets
      
      Boolean searchExperimentSets
    - searchGenes
      
      Boolean searchGenes
    - searchGeneSets
      
      Boolean searchGeneSets
    - searchPhenotypes
      
      Boolean searchPhenotypes
    - searchPlatforms
      
      Boolean searchPlatforms
    - searchProbes
      
      Boolean searchProbes
    - taxon
      
      Taxon taxon
    - termUri
      
      String termUri
    - useCharacteristics
      
      Boolean useCharacteristics
    - useDatabase
      
      Boolean useDatabase
    - useGo
      
      Boolean useGo
    - useIndices
      
      Boolean useIndices
Package ubic.gemma.model.expression
- Class ubic.gemma.model.expression.BlacklistedEntity extends AbstractDescribable implements Serializable
  - Serialized Fields
    - externalAccession
      
      DatabaseEntry externalAccession
    - reason
      
      String reason
    - shortName
      
      String shortName
- Class ubic.gemma.model.expression.BlacklistedValueObject extends IdentifiableValueObject<BlacklistedEntity> implements Serializable
  
  serialVersionUID:
  
  -4817418347388923905L
  - Serialized Fields
    - accession
      
      String accession
    - externalDatabase
      
      ExternalDatabaseValueObject externalDatabase
    - name
      
      String name
    - reason
      
      String reason
    - shortName
      
      String shortName
    - type
      
      String type
Package ubic.gemma.model.expression.arrayDesign
- Class ubic.gemma.model.expression.arrayDesign.AlternateName extends Object implements Serializable
  
  serialVersionUID:
  
  -1208836332065611893L
  - Serialized Fields
    - id
      
      Long id
    - name
      
      String name
- Class ubic.gemma.model.expression.arrayDesign.ArrayDesign extends AbstractAuditable implements Serializable
  
  serialVersionUID:
  
  -7566439134502613470L
  - Serialized Fields
    - advertisedNumberOfDesignElements
      
      Integer advertisedNumberOfDesignElements
    - alternateNames
      
      Set<AlternateName> alternateNames
    - alternativeTo
      
      ArrayDesign alternativeTo
    - compositeSequences
      
      Set<CompositeSequence> compositeSequences
    - curationDetails
      
      CurationDetails curationDetails
    - designProvider
      
      Contact designProvider
    - externalReferences
      
      Set<DatabaseEntry> externalReferences
    - mergedInto
      
      ArrayDesign mergedInto
    - mergees
      
      Set<ArrayDesign> mergees
    - primaryTaxon
      
      Taxon primaryTaxon
    - shortName
      
      String shortName
    - subsumedArrayDesigns
      
      Set<ArrayDesign> subsumedArrayDesigns
    - subsumingArrayDesign
      
      ArrayDesign subsumingArrayDesign
    - technologyType
      
      TechnologyType technologyType
- Class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject extends AbstractCuratableValueObject<ArrayDesign> implements Serializable
  
  serialVersionUID:
  
  -8259245319391937522L
  - Serialized Fields
    - blackListed
      
      Boolean blackListed
    - color
      
      String color
    - dateCached
      
      String dateCached
    - description
      
      String description
    - designElementCount
      
      Integer designElementCount
    - expressionExperimentCount
      
      Long expressionExperimentCount
    - externalReferences
      
      Set<DatabaseEntryValueObject> externalReferences
    - hasBlatAssociations
      
      Boolean hasBlatAssociations
    - hasGeneAssociations
      
      Boolean hasGeneAssociations
    - hasSequenceAssociations
      
      Boolean hasSequenceAssociations
    - isAffymetrixAltCdf
      
      Boolean isAffymetrixAltCdf
    - isMerged
      
      Boolean isMerged
    - isMergee
      
      Boolean isMergee
    - isSubsumed
      
      Boolean isSubsumed
    - isSubsumer
      
      Boolean isSubsumer
    - lastGeneMapping
      
      Date lastGeneMapping
    - lastRepeatMask
      
      Date lastRepeatMask
    - lastSequenceAnalysis
      
      Date lastSequenceAnalysis
    - lastSequenceUpdate
      
      Date lastSequenceUpdate
    - name
      
      String name
    - numGenes
      
      String numGenes
    - numProbeAlignments
      
      String numProbeAlignments
    - numProbeSequences
      
      String numProbeSequences
    - numProbesToGenes
      
      String numProbesToGenes
    - releaseUrl
      
      URL releaseUrl
    - releaseVersion
      
      String releaseVersion
    - shortName
      
      String shortName
    - switchedExpressionExperimentCount
      
      Long switchedExpressionExperimentCount
    - taxonObject
      
      TaxonValueObject taxonObject
    - technologyType
      
      String technologyType
- Class ubic.gemma.model.expression.arrayDesign.BlacklistedPlatform extends BlacklistedEntity implements Serializable
Package ubic.gemma.model.expression.bioAssay
- Class ubic.gemma.model.expression.bioAssay.BioAssay extends AbstractDescribable implements Serializable
  
  serialVersionUID:
  
  -7868768731812964045L
  - Serialized Fields
    - accession
      
      DatabaseEntry accession
    - arrayDesignUsed
      
      ArrayDesign arrayDesignUsed
    - fastqHeaders
      
      String fastqHeaders
    - isOutlier
      
      Boolean isOutlier
    - metadata
      
      String metadata
    - originalPlatform
      
      ArrayDesign originalPlatform
    - processingDate
      
      Date processingDate
    - sampleUsed
      
      BioMaterial sampleUsed
    - sequencePairedReads
      
      Boolean sequencePairedReads
    - sequenceReadCount
      
      Long sequenceReadCount
    - sequenceReadLength
      
      Integer sequenceReadLength
- Class ubic.gemma.model.expression.bioAssay.BioAssayValueObject extends IdentifiableValueObject<BioAssay> implements Serializable
  
  serialVersionUID:
  
  9164284536309673585L
  - Serialized Fields
    - accession
      
      DatabaseEntryValueObject accession
    - arrayDesign
      
      ArrayDesignValueObject arrayDesign
    - description
      
      String description
    - metadata
      
      String metadata
    - name
      
      String name
    - originalPlatform
      
      ArrayDesignValueObject originalPlatform
    - outlier
      
      Boolean outlier
    - predictedOutlier
      
      Boolean predictedOutlier
    - processingDate
      
      Date processingDate
    - sample
      
      BioMaterialValueObject sample
    - sequencePairedReads
      
      Boolean sequencePairedReads
    - sequenceReadCount
      
      Long sequenceReadCount
    - sequenceReadLength
      
      Integer sequenceReadLength
    - userFlaggedOutlier
      
      Boolean userFlaggedOutlier
Package ubic.gemma.model.expression.bioAssayData
- Class ubic.gemma.model.expression.bioAssayData.BioAssayDimension extends AbstractDescribable implements Serializable
  
  serialVersionUID:
  
  -3786404705366085672L
  - Serialized Fields
    - bioAssays
      
      List<BioAssay> bioAssays
- Class ubic.gemma.model.expression.bioAssayData.BioAssayDimensionValueObject extends IdentifiableValueObject<BioAssayDimension> implements Serializable
  
  serialVersionUID:
  
  -8686807689616396835L
  - Serialized Fields
    - bioAssays
      
      List<BioAssayValueObject> bioAssays
    - description
      
      String description
    - isReordered
      
      boolean isReordered
    - isSubset
      
      boolean isSubset
    - name
      
      String name
    - sourceBioAssayDimension
      
      BioAssayDimensionValueObject sourceBioAssayDimension
- Class ubic.gemma.model.expression.bioAssayData.BooleanVectorValueObject extends DataVectorValueObject implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - data
      
      boolean[] data
- Class ubic.gemma.model.expression.bioAssayData.DataVector extends Object implements Serializable
  
  serialVersionUID:
  
  -5823802521832643417L
  - Serialized Fields
    - data
      
      byte[] data
    - id
      
      Long id
    - quantitationType
      
      QuantitationType quantitationType
- Class ubic.gemma.model.expression.bioAssayData.DataVectorValueObject extends IdentifiableValueObject<DataVector> implements Serializable
  
  serialVersionUID:
  
  4291090102921066018L
  - Serialized Fields
    - bioAssayDimension
      
      BioAssayDimensionValueObject bioAssayDimension
    - designElement
      
      CompositeSequenceValueObject designElement
    - expressionExperiment
      
      ExpressionExperimentValueObject expressionExperiment
    - genes
      
      Collection<Long> genes
    - quantitationType
      
      QuantitationTypeValueObject quantitationType
- Class ubic.gemma.model.expression.bioAssayData.DesignElementDataVector extends DataVector implements Serializable
  
  serialVersionUID:
  
  -4185333066166517308L
  - Serialized Fields
    - bioAssayDimension
      
      BioAssayDimension bioAssayDimension
    - designElement
      
      CompositeSequence designElement
- Class ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject extends DataVectorValueObject implements Serializable
  
  serialVersionUID:
  
  -5116242513725297615L
  - Serialized Fields
    - data
      
      double[] data
    - masked
      
      boolean masked
    - pvalue
      
      Double pvalue
    - rank
      
      Double rank
    - rankByMax
      
      Double rankByMax
    - rankByMean
      
      Double rankByMean
    - reorganized
      
      boolean reorganized
    - sliced
      
      boolean sliced
    - sourceVectorId
      
      Long sourceVectorId
- Class ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject extends Object implements Serializable
  - Serialized Fields
    - datasetId
      
      long datasetId
    - geneExpressionLevels
      
      LinkedList<ExperimentExpressionLevelsValueObject.GeneElementExpressionsValueObject> geneExpressionLevels
- Class ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject.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 extends Object implements Serializable
  - Serialized Fields
    - bioAssayExpressionLevels
      
      Map<String,Double> bioAssayExpressionLevels
    - designElementName
      
      String designElementName
- Class ubic.gemma.model.expression.bioAssayData.MeanVarianceRelation extends Object implements Serializable
  
  serialVersionUID:
  
  -1442923993171126882L
  - Serialized Fields
    - id
      
      Long id
    - means
      
      byte[] means
    - securityOwner
      
      gemma.gsec.model.Securable securityOwner
    - variances
      
      byte[] variances
- Class ubic.gemma.model.expression.bioAssayData.ProcessedExpressionDataVector extends DesignElementDataVector implements Serializable
  
  serialVersionUID:
  
  -3948846630785289034L
  - Serialized Fields
    - expressionExperiment
      
      ExpressionExperiment expressionExperiment
    - rankByMax
      
      Double rankByMax
    - rankByMean
      
      Double rankByMean
- Class ubic.gemma.model.expression.bioAssayData.RawExpressionDataVector extends DesignElementDataVector implements Serializable
  
  serialVersionUID:
  
  -7410374297463625206L
  - Serialized Fields
    - expressionExperiment
      
      ExpressionExperiment expressionExperiment
Package ubic.gemma.model.expression.biomaterial
- Class ubic.gemma.model.expression.biomaterial.BioMaterial extends AbstractDescribable implements Serializable
  
  serialVersionUID:
  
  4374359557498220256L
  - Serialized Fields
    - bioAssaysUsedIn
      
      Set<BioAssay> bioAssaysUsedIn
    - characteristics
      
      Set<Characteristic> characteristics
    - externalAccession
      
      DatabaseEntry externalAccession
    - factorValues
      
      Set<FactorValue> factorValues
    - sourceTaxon
      
      Taxon sourceTaxon
    - treatments
      
      Set<Treatment> treatments
- Class ubic.gemma.model.expression.biomaterial.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
    - characteristics
      
      Collection<CharacteristicValueObject> characteristics
    - characteristicValues
      
      Map<String,String> characteristicValues
    - description
      
      String description
    - factorIdToFactorValueId
      
      Map<String,String> factorIdToFactorValueId
    - factors
      
      Map<String,String> factors
      
      Deprecated.
    - factorValueObjects
      
      Collection<FactorValueValueObject> factorValueObjects
    - factorValues
      
      Map<String,String> factorValues
    - fVBasicVOs
      
      Collection<FactorValueBasicValueObject> fVBasicVOs
    - name
      
      String name
- Class ubic.gemma.model.expression.biomaterial.Compound extends AbstractDescribable implements Serializable
  
  serialVersionUID:
  
  -6782144197298874202L
  - Serialized Fields
    - registryNumber
      
      String registryNumber
- Class ubic.gemma.model.expression.biomaterial.Treatment extends AbstractDescribable implements Serializable
  
  serialVersionUID:
  
  265514192370169605L
  - Serialized Fields
    - orderApplied
      
      Integer orderApplied
Package ubic.gemma.model.expression.experiment
- Class ubic.gemma.model.expression.experiment.BioAssaySet extends Investigation implements Serializable
  
  serialVersionUID:
  
  2368063046639481521L
  - Serialized Fields
    - accession
      
      DatabaseEntry accession
    - bioAssays
      
      Set<BioAssay> bioAssays
- Class ubic.gemma.model.expression.experiment.BlacklistedExperiment extends BlacklistedEntity implements Serializable
- Class ubic.gemma.model.expression.experiment.ExperimentalDesign extends AbstractDescribable implements Serializable
  
  serialVersionUID:
  
  1734101852541885497L
  - Serialized Fields
    - experimentalFactors
      
      Set<ExperimentalFactor> experimentalFactors
    - normalizationDescription
      
      String normalizationDescription
    - qualityControlDescription
      
      String qualityControlDescription
    - replicateDescription
      
      String replicateDescription
    - types
      
      Set<Characteristic> types
- Class ubic.gemma.model.expression.experiment.ExperimentalFactor extends AbstractDescribable implements Serializable
  
  serialVersionUID:
  
  4615731059510436891L
  - Serialized Fields
    - annotations
      
      Set<Characteristic> annotations
      
      Deprecated.
    - category
      
      Characteristic category
    - experimentalDesign
      
      ExperimentalDesign experimentalDesign
    - factorValues
      
      Set<FactorValue> factorValues
    - securityOwner
      
      ExpressionExperiment securityOwner
    - type
      
      FactorType type
- Class ubic.gemma.model.expression.experiment.ExperimentalFactorValueObject extends IdentifiableValueObject<ExperimentalFactor> implements Serializable
  
  serialVersionUID:
  
  -2615804031123874251L
  - Serialized Fields
    - category
      
      String category
    - categoryUri
      
      String categoryUri
    - description
      
      String description
    - factorValues
      
      String factorValues
      
      Deprecated.
    - name
      
      String name
    - type
      
      String type
    - values
      
      Collection<FactorValueValueObject> values
- Class ubic.gemma.model.expression.experiment.ExpressionExperiment extends BioAssaySet implements Serializable
  
  serialVersionUID:
  
  -1342753625018841735L
  - Serialized Fields
    - allCharacteristics
      
      Set<Characteristic> allCharacteristics
    - batchConfound
      
      String batchConfound
    - batchEffect
      
      BatchEffectType batchEffect
    - batchEffectStatistics
      
      String batchEffectStatistics
    - curationDetails
      
      CurationDetails curationDetails
    - experimentalDesign
      
      ExperimentalDesign experimentalDesign
    - geeq
      
      Geeq geeq
    - meanVarianceRelation
      
      MeanVarianceRelation meanVarianceRelation
    - metadata
      
      String metadata
    - numberOfDataVectors
      
      Integer numberOfDataVectors
    - numberOfSamples
      
      Integer numberOfSamples
    - otherParts
      
      Set<ExpressionExperiment> otherParts
    - processedExpressionDataVectors
      
      Set<ProcessedExpressionDataVector> processedExpressionDataVectors
    - quantitationTypes
      
      Set<QuantitationType> quantitationTypes
    - rawExpressionDataVectors
      
      Set<RawExpressionDataVector> rawExpressionDataVectors
    - shortName
      
      String shortName
    - source
      
      String source
    - taxon
      
      Taxon taxon
- Class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject extends ExpressionExperimentValueObject implements Serializable
  
  serialVersionUID:
  
  -1219449523930648392L
  - Serialized Fields
    - arrayDesigns
      
      Collection<ArrayDesignValueObject> arrayDesigns
    - batchFetchEventType
      
      String batchFetchEventType
    - dateArrayDesignLastUpdated
      
      Date dateArrayDesignLastUpdated
    - dateBatchFetch
      
      Date dateBatchFetch
    - dateCached
      
      Date dateCached
    - dateDifferentialAnalysis
      
      Date dateDifferentialAnalysis
    - dateLinkAnalysis
      
      Date dateLinkAnalysis
    - dateMissingValueAnalysis
      
      Date dateMissingValueAnalysis
    - datePcaAnalysis
      
      Date datePcaAnalysis
    - dateProcessedDataVectorComputation
      
      Date dateProcessedDataVectorComputation
    - differentialExpressionAnalyses
      
      Collection<DifferentialExpressionAnalysisValueObject> differentialExpressionAnalyses
    - expressionExperimentSets
      
      Collection<ExpressionExperimentSetValueObject> expressionExperimentSets
    - hasBatchInformation
      
      boolean hasBatchInformation
    - hasBothIntensities
      
      Boolean hasBothIntensities
    - hasCoexpressionAnalysis
      
      Boolean hasCoexpressionAnalysis
    - hasDifferentialExpressionAnalysis
      
      Boolean hasDifferentialExpressionAnalysis
    - hasEitherIntensity
      
      Boolean hasEitherIntensity
    - hasMultiplePreferredQuantitationTypes
      
      Boolean hasMultiplePreferredQuantitationTypes
    - hasMultipleTechnologyTypes
      
      Boolean hasMultipleTechnologyTypes
    - isRNASeq
      
      Boolean isRNASeq
    - lastArrayDesignUpdateDate
      
      String lastArrayDesignUpdateDate
    - linkAnalysisEventType
      
      String linkAnalysisEventType
    - minPvalue
      
      Double minPvalue
    - missingValueAnalysisEventType
      
      String missingValueAnalysisEventType
    - numAnnotations
      
      Long numAnnotations
    - numPopulatedFactors
      
      Long numPopulatedFactors
    - originalPlatforms
      
      Collection<ArrayDesignValueObject> originalPlatforms
    - otherParts
      
      Collection<ExpressionExperimentValueObject> otherParts
    - pcaAnalysisEventType
      
      String pcaAnalysisEventType
    - primaryCitation
      
      CitationValueObject primaryCitation
    - processedDataVectorComputationEventType
      
      String processedDataVectorComputationEventType
    - pubmedId
      
      Integer pubmedId
    - QChtml
      
      String QChtml
    - reprocessedFromRawData
      
      boolean reprocessedFromRawData
    - sampleRemovedFlags
      
      Collection<AuditEventValueObject> sampleRemovedFlags
    - secondaryAccession
      
      String secondaryAccession
    - secondaryExternalDatabase
      
      String secondaryExternalDatabase
    - secondaryExternalUri
      
      String secondaryExternalUri
- Class ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject extends IdentifiableValueObject<ExpressionExperimentSet> implements Serializable
  
  serialVersionUID:
  
  -6852364688337216390L
  - Serialized Fields
    - description
      
      String description
    - expressionExperimentIds
      
      Collection<Long> expressionExperimentIds
    - isPublic
      
      boolean isPublic
    - modifiable
      
      boolean modifiable
    - name
      
      String name
    - numWithCoexpressionAnalysis
      
      Integer numWithCoexpressionAnalysis
    - numWithDifferentialExpressionAnalysis
      
      Integer numWithDifferentialExpressionAnalysis
    - shared
      
      boolean shared
    - size
      
      Integer size
    - taxonId
      
      Long taxonId
    - taxonName
      
      String taxonName
    - userCanWrite
      
      boolean userCanWrite
    - userOwned
      
      boolean userOwned
- Class ubic.gemma.model.expression.experiment.ExpressionExperimentSubSet extends BioAssaySet implements Serializable
  
  serialVersionUID:
  
  -1880425342951467283L
  - Serialized Fields
    - sourceExperiment
      
      ExpressionExperiment sourceExperiment
- Class ubic.gemma.model.expression.experiment.ExpressionExperimentSubsetValueObject extends ExpressionExperimentValueObject implements Serializable
  - Serialized Fields
    - sourceExperiment
      
      Long sourceExperiment
- Class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject extends AbstractCuratableValueObject<ExpressionExperiment> implements Serializable
  
  serialVersionUID:
  
  -6861385216096602508L
  - Serialized Fields
    - accession
      
      String accession
    - arrayDesignCount
      
      Long arrayDesignCount
    - batchConfound
      
      String batchConfound
    - batchEffect
      
      String batchEffect
    - batchEffectStatistics
      
      String batchEffectStatistics
    - bioMaterialCount
      
      Integer bioMaterialCount
    - currentUserHasWritePermission
      
      Boolean currentUserHasWritePermission
    - currentUserIsOwner
      
      Boolean currentUserIsOwner
    - description
      
      String description
    - experimentalDesign
      
      Long experimentalDesign
    - externalDatabase
      
      String externalDatabase
    - externalUri
      
      String externalUri
    - geeq
      
      GeeqValueObject geeq
    - isPublic
      
      Boolean isPublic
    - isShared
      
      Boolean isShared
    - metadata
      
      String metadata
    - name
      
      String name
    - numberOfBioAssays
      
      Integer numberOfBioAssays
    - processedExpressionVectorCount
      
      Integer processedExpressionVectorCount
    - shortName
      
      String shortName
    - source
      
      String source
    - suitableForDEA
      
      Boolean suitableForDEA
    - taxonObject
      
      TaxonValueObject taxonObject
    - technologyType
      
      String technologyType
- Class ubic.gemma.model.expression.experiment.FactorValue extends Object implements Serializable
  
  serialVersionUID:
  
  -3783172994360698631L
  - Serialized Fields
    - characteristics
      
      Set<Statement> characteristics
    - experimentalFactor
      
      ExperimentalFactor experimentalFactor
    - id
      
      Long id
    - isBaseline
      
      Boolean isBaseline
    - measurement
      
      Measurement measurement
    - needsAttention
      
      boolean needsAttention
    - oldStyleCharacteristics
      
      Set<Characteristic> oldStyleCharacteristics
      
      Deprecated.
    - securityOwner
      
      ExpressionExperiment securityOwner
    - value
      
      String value
      
      Deprecated.
- Class ubic.gemma.model.expression.experiment.FactorValueBasicValueObject extends IdentifiableValueObject<FactorValue> implements Serializable
  
  serialVersionUID:
  
  3378801249808036785L
  - Serialized Fields
    - characteristics
      
      List<CharacteristicValueObject> characteristics
    - experimentalFactorCategory
      
      CharacteristicValueObject experimentalFactorCategory
    - experimentalFactorId
      
      Long experimentalFactorId
    - measurement
      
      MeasurementValueObject measurement
    - ontologyId
      
      String ontologyId
    - statements
      
      List<StatementValueObject> statements
    - summary
      
      String summary
    - value
      
      String value
      
      Deprecated.
- Class ubic.gemma.model.expression.experiment.FactorValueValueObject extends IdentifiableValueObject<FactorValue> implements Serializable
  
  serialVersionUID:
  
  3378801249808036785L
  - Serialized Fields
    - category
      
      String category
      
      Deprecated.
    - categoryUri
      
      String categoryUri
      
      Deprecated.
    - characteristics
      
      List<CharacteristicValueObject> characteristics
      
      Deprecated.
    - charId
      
      Long charId
      
      Deprecated.
    - description
      
      String description
      
      Deprecated.
    - experimentalFactorCategory
      
      CharacteristicValueObject experimentalFactorCategory
      
      Deprecated.
    - experimentalFactorId
      
      Long experimentalFactorId
      
      Deprecated.
    - factorId
      
      Long factorId
      
      Deprecated.
    - factorValue
      
      String factorValue
      
      Deprecated.
    - measurementObject
      
      MeasurementValueObject measurementObject
      
      Deprecated.
    - needsAttention
      
      Boolean needsAttention
      
      Deprecated.
    - object
      
      String object
      
      Deprecated.
    - objectUri
      
      String objectUri
      
      Deprecated.
    - ontologyId
      
      String ontologyId
      
      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.
    - statements
      
      List<StatementValueObject> statements
      
      Deprecated.
    - summary
      
      String summary
      
      Deprecated.
    - value
      
      String value
      
      Deprecated.
    - valueUri
      
      String valueUri
      
      Deprecated.
- Class ubic.gemma.model.expression.experiment.FreeTextExpressionExperimentResultsValueObject extends SessionBoundExpressionExperimentSetValueObject implements Serializable
  
  serialVersionUID:
  
  3557304710219740029L
  - Serialized Fields
    - queryString
      
      String queryString
- Class ubic.gemma.model.expression.experiment.Geeq extends Object implements Serializable
  
  serialVersionUID:
  
  4783171234360698630L
  - Serialized Fields
    - batchCorrected
      
      boolean batchCorrected
    - corrMatIssues
      
      byte corrMatIssues
    - detectedQualityScore
      
      double detectedQualityScore
    - detectedSuitabilityScore
      
      double detectedSuitabilityScore
    - id
      
      Long id
    - manualBatchConfoundActive
      
      boolean manualBatchConfoundActive
    - manualBatchEffectActive
      
      boolean manualBatchEffectActive
    - manualHasBatchConfound
      
      boolean manualHasBatchConfound
    - manualHasNoBatchEffect
      
      boolean manualHasNoBatchEffect
    - manualHasStrongBatchEffect
      
      boolean manualHasStrongBatchEffect
    - manualQualityOverride
      
      boolean manualQualityOverride
    - manualQualityScore
      
      double manualQualityScore
    - manualSuitabilityOverride
      
      boolean manualSuitabilityOverride
    - manualSuitabilityScore
      
      double manualSuitabilityScore
    - noVectors
      
      boolean noVectors
    - otherIssues
      
      String otherIssues
    - qScoreBatchConfound
      
      double qScoreBatchConfound
    - qScoreBatchEffect
      
      double qScoreBatchEffect
    - qScoreBatchInfo
      
      double qScoreBatchInfo
    - qScoreOutliers
      
      double qScoreOutliers
    - qScorePlatformsTech
      
      double qScorePlatformsTech
    - qScoreReplicates
      
      double qScoreReplicates
    - qScoreSampleCorrelationVariance
      
      double qScoreSampleCorrelationVariance
    - qScoreSampleMeanCorrelation
      
      double qScoreSampleMeanCorrelation
    - qScoreSampleMedianCorrelation
      
      double qScoreSampleMedianCorrelation
    - replicatesIssues
      
      byte replicatesIssues
    - sScoreAvgPlatformPopularity
      
      double sScoreAvgPlatformPopularity
    - sScoreAvgPlatformSize
      
      double sScoreAvgPlatformSize
    - sScoreMissingValues
      
      double sScoreMissingValues
    - sScorePlatformAmount
      
      double sScorePlatformAmount
    - sScorePlatformsTechMulti
      
      double sScorePlatformsTechMulti
    - sScorePublication
      
      double sScorePublication
    - sScoreRawData
      
      double sScoreRawData
    - sScoreSampleSize
      
      double sScoreSampleSize
- Class ubic.gemma.model.expression.experiment.GeeqAdminValueObject extends GeeqValueObject implements Serializable
  - Serialized Fields
    - detectedQualityScore
      
      double detectedQualityScore
    - detectedSuitabilityScore
      
      double detectedSuitabilityScore
    - manualBatchConfoundActive
      
      boolean manualBatchConfoundActive
    - manualBatchEffectActive
      
      boolean manualBatchEffectActive
    - manualHasBatchConfound
      
      boolean manualHasBatchConfound
    - manualHasNoBatchEffect
      
      boolean manualHasNoBatchEffect
    - manualHasStrongBatchEffect
      
      boolean manualHasStrongBatchEffect
    - manualQualityOverride
      
      boolean manualQualityOverride
    - manualQualityScore
      
      double manualQualityScore
    - manualSuitabilityOverride
      
      boolean manualSuitabilityOverride
    - manualSuitabilityScore
      
      double manualSuitabilityScore
    - otherIssues
      
      String otherIssues
    - qScoreBatchConfound
      
      double qScoreBatchConfound
    - qScoreBatchEffect
      
      double qScoreBatchEffect
- Class ubic.gemma.model.expression.experiment.GeeqValueObject extends IdentifiableValueObject<Geeq> implements Serializable
  - Serialized Fields
    - batchCorrected
      
      boolean batchCorrected
    - corrMatIssues
      
      byte corrMatIssues
    - noVectors
      
      boolean noVectors
    - publicQualityScore
      
      double publicQualityScore
    - publicSuitabilityScore
      
      double publicSuitabilityScore
    - qScoreBatchInfo
      
      double qScoreBatchInfo
    - qScoreOutliers
      
      double qScoreOutliers
    - qScorePlatformsTech
      
      double qScorePlatformsTech
    - qScorePublicBatchConfound
      
      double qScorePublicBatchConfound
    - qScorePublicBatchEffect
      
      double qScorePublicBatchEffect
    - qScoreReplicates
      
      double qScoreReplicates
    - qScoreSampleCorrelationVariance
      
      double qScoreSampleCorrelationVariance
    - qScoreSampleMeanCorrelation
      
      double qScoreSampleMeanCorrelation
    - qScoreSampleMedianCorrelation
      
      double qScoreSampleMedianCorrelation
    - replicatesIssues
      
      byte replicatesIssues
    - sScoreAvgPlatformPopularity
      
      double sScoreAvgPlatformPopularity
    - sScoreAvgPlatformSize
      
      double sScoreAvgPlatformSize
    - sScoreMissingValues
      
      double sScoreMissingValues
    - sScorePlatformAmount
      
      double sScorePlatformAmount
    - sScorePlatformsTechMulti
      
      double sScorePlatformsTechMulti
    - sScorePublication
      
      double sScorePublication
    - sScoreRawData
      
      double sScoreRawData
    - sScoreSampleSize
      
      double sScoreSampleSize
- Class ubic.gemma.model.expression.experiment.SessionBoundExpressionExperimentSetValueObject extends ExpressionExperimentSetValueObject implements Serializable
  
  serialVersionUID:
  
  2068650886972222818L
  - Serialized Fields
    - modified
      
      boolean modified
- Class ubic.gemma.model.expression.experiment.Statement extends Characteristic implements Serializable
  - Serialized Fields
    - object
      
      String object
    - objectUri
      
      String objectUri
    - predicate
      
      String predicate
    - predicateUri
      
      String predicateUri
    - secondObject
      
      String secondObject
    - secondObjectUri
      
      String secondObjectUri
    - secondPredicate
      
      String secondPredicate
    - secondPredicateUri
      
      String secondPredicateUri
- Class ubic.gemma.model.expression.experiment.StatementValueObject extends IdentifiableValueObject<Statement> implements Serializable
  - Serialized Fields
    - category
      
      String category
    - categoryUri
      
      String categoryUri
    - object
      
      String object
    - objectId
      
      String objectId
    - objectUri
      
      String objectUri
    - predicate
      
      String predicate
    - predicateUri
      
      String predicateUri
    - secondObject
      
      String secondObject
    - secondObjectUri
      
      String secondObjectUri
    - secondPredicate
      
      String secondPredicate
    - secondPredicateUri
      
      String secondPredicateUri
    - subject
      
      String subject
    - subjectId
      
      String subjectId
    - subjectUri
      
      String subjectUri
Package ubic.gemma.model.genome
- Class ubic.gemma.model.genome.Chromosome extends Object implements Serializable
  
  serialVersionUID:
  
  7394734846565885136L
  - Serialized Fields
    - assemblyDatabase
      
      ExternalDatabase assemblyDatabase
    - id
      
      Long id
    - name
      
      String name
    - sequence
      
      BioSequence sequence
    - taxon
      
      Taxon taxon
- Class ubic.gemma.model.genome.ChromosomeFeature extends AbstractDescribable implements Serializable
  
  serialVersionUID:
  
  -8627296370886752496L
  - Serialized Fields
    - physicalLocation
      
      PhysicalLocation physicalLocation
    - previousNcbiId
      
      String previousNcbiId
- Class ubic.gemma.model.genome.ChromosomeLocation extends Object implements Serializable
  
  serialVersionUID:
  
  -4932607147290671454L
  - Serialized Fields
    - chromosome
      
      Chromosome chromosome
    - id
      
      Long id
- Class ubic.gemma.model.genome.Gene extends ChromosomeFeature implements Serializable
  
  serialVersionUID:
  
  -5693198926006383546L
  - Serialized Fields
    - accessions
      
      Set<DatabaseEntry> accessions
    - aliases
      
      Set<GeneAlias> aliases
    - ensemblId
      
      String ensemblId
    - multifunctionality
      
      Multifunctionality multifunctionality
    - ncbiGeneId
      
      Integer ncbiGeneId
    - officialName
      
      String officialName
    - officialSymbol
      
      String officialSymbol
    - phenotypeAssociations
      
      Set<PhenotypeAssociation> phenotypeAssociations
      
      Deprecated.
    - products
      
      Set<GeneProduct> products
    - taxon
      
      Taxon taxon
- Class ubic.gemma.model.genome.GeneOntologyTermValueObject extends Object implements Serializable
  - Serialized Fields
    - comment
      
      String comment
    - goId
      
      String goId
    - isObsolete
      
      boolean isObsolete
    - label
      
      String label
    - localName
      
      String localName
    - term
      
      String term
    - uri
      
      String uri
- Class ubic.gemma.model.genome.PhysicalLocation extends ChromosomeLocation implements Serializable
  
  serialVersionUID:
  
  -6580769809003779541L
  - Serialized Fields
    - bin
      
      Integer bin
    - nucleotide
      
      Long nucleotide
    - nucleotideLength
      
      Integer nucleotideLength
    - strand
      
      String strand
- Class ubic.gemma.model.genome.PhysicalLocationValueObject extends IdentifiableValueObject<PhysicalLocation> implements Serializable
  - Serialized Fields
    - bin
      
      Integer bin
    - chromosome
      
      String chromosome
    - nucleotide
      
      Long nucleotide
    - nucleotideLength
      
      Integer nucleotideLength
    - strand
      
      String strand
    - taxon
      
      TaxonValueObject taxon
- Class ubic.gemma.model.genome.Taxon extends Object implements Serializable
  
  serialVersionUID:
  
  9219471082900615778L
  - Serialized Fields
    - commonName
      
      String commonName
    - externalDatabase
      
      ExternalDatabase externalDatabase
    - id
      
      Long id
    - isGenesUsable
      
      boolean isGenesUsable
    - ncbiId
      
      Integer ncbiId
    - scientificName
      
      String scientificName
    - secondaryNcbiId
      
      Integer secondaryNcbiId
- Class ubic.gemma.model.genome.TaxonValueObject extends IdentifiableValueObject<Taxon> implements Serializable
  - Serialized Fields
    - commonName
      
      String commonName
    - externalDatabase
      
      ExternalDatabaseValueObject externalDatabase
    - isGenesUsable
      
      Boolean isGenesUsable
    - isSpecies
      
      Boolean isSpecies
    - ncbiId
      
      Integer ncbiId
    - scientificName
      
      String scientificName
Package ubic.gemma.model.genome.biosequence
- Class ubic.gemma.model.genome.biosequence.BioSequence extends AbstractDescribable implements Serializable
  
  serialVersionUID:
  
  -6620431603579954167L
  - Serialized Fields
    - bioSequence2GeneProduct
      
      Set<BioSequence2GeneProduct> bioSequence2GeneProduct
    - fractionRepeats
      
      Double fractionRepeats
    - isApproximateLength
      
      Boolean isApproximateLength
    - isCircular
      
      Boolean isCircular
    - length
      
      Long length
    - polymerType
      
      PolymerType polymerType
    - sequence
      
      String sequence
    - sequenceDatabaseEntry
      
      DatabaseEntry sequenceDatabaseEntry
    - taxon
      
      Taxon taxon
    - type
      
      SequenceType type
Package ubic.gemma.model.genome.gene
- Class ubic.gemma.model.genome.gene.DatabaseBackedGeneSetValueObject extends GeneSetValueObject implements Serializable
  
  serialVersionUID:
  
  -1360523793656012770L
- Class ubic.gemma.model.genome.gene.GeneAlias extends Object implements Serializable
  
  serialVersionUID:
  
  -4156628260205167700L
  - Serialized Fields
    - alias
      
      String alias
    - id
      
      Long id
- Class ubic.gemma.model.genome.gene.GeneProduct extends ChromosomeFeature implements Serializable
  
  serialVersionUID:
  
  8414732389521430535L
  - Serialized Fields
    - accessions
      
      Set<DatabaseEntry> accessions
    - dummy
      
      boolean dummy
    - exons
      
      Set<PhysicalLocation> exons
    - gene
      
      Gene gene
    - ncbiGi
      
      String ncbiGi
- Class ubic.gemma.model.genome.gene.GeneProductValueObject extends IdentifiableValueObject<GeneProduct> implements Serializable
  
  serialVersionUID:
  
  1156628868995566223L
  - Serialized Fields
    - chromosome
      
      String chromosome
    - geneId
      
      Long geneId
    - name
      
      String name
    - ncbiId
      
      String ncbiId
    - nucleotideEnd
      
      Long nucleotideEnd
      
      Deprecated.
    - nucleotideStart
      
      Long nucleotideStart
    - strand
      
      String strand
- Class ubic.gemma.model.genome.gene.GeneSet extends AbstractAuditable implements Serializable
  
  serialVersionUID:
  
  4357218100681569138L
  - Serialized Fields
    - characteristics
      
      Set<Characteristic> characteristics
    - literatureSources
      
      Set<BibliographicReference> literatureSources
    - members
      
      Set<GeneSetMember> members
    - sourceAccession
      
      DatabaseEntry sourceAccession
- Class ubic.gemma.model.genome.gene.GeneSetMember extends Object implements Serializable
  
  serialVersionUID:
  
  -926690781193097196L
  - Serialized Fields
    - gene
      
      Gene gene
    - id
      
      Long id
    - score
      
      Double score
- Class ubic.gemma.model.genome.gene.GeneSetValueObject extends IdentifiableValueObject<GeneSet> implements Serializable
  
  serialVersionUID:
  
  6212231006289412683L
  - Serialized Fields
    - description
      
      String description
    - geneIds
      
      Collection<Long> geneIds
    - isPublic
      
      boolean isPublic
    - isShared
      
      boolean isShared
    - name
      
      String name
    - size
      
      Long size
    - taxon
      
      TaxonValueObject taxon
    - userOwned
      
      boolean userOwned
- Class ubic.gemma.model.genome.gene.GeneValueObject extends IdentifiableValueObject<Gene> implements Serializable
  
  serialVersionUID:
  
  -7098036090107647318L
  - Serialized Fields
    - accessions
      
      Set<DatabaseEntryValueObject> accessions
    - aliases
      
      SortedSet<String> aliases
    - associatedExperimentCount
      
      Integer associatedExperimentCount
    - compositeSequenceCount
      
      Integer compositeSequenceCount
    - description
      
      String description
    - ensemblId
      
      String ensemblId
    - geneSets
      
      Collection<GeneSetValueObject> geneSets
    - homologues
      
      Collection<GeneValueObject> homologues
    - isQuery
      
      Boolean isQuery
    - multifunctionalityRank
      
      Double multifunctionalityRank
    - name
      
      String name
    - ncbiId
      
      Integer ncbiId
    - nodeDegreeNegRanks
      
      double[] nodeDegreeNegRanks
    - nodeDegreePosRanks
      
      double[] nodeDegreePosRanks
    - nodeDegreesNeg
      
      int[] nodeDegreesNeg
    - nodeDegreesPos
      
      int[] nodeDegreesPos
    - numGoTerms
      
      Integer numGoTerms
    - officialName
      
      String officialName
    - officialSymbol
      
      String officialSymbol
    - phenotypes
      
      Collection<CharacteristicValueObject> phenotypes
    - platformCount
      
      Integer platformCount
    - score
      
      Double score
    - taxon
      
      TaxonValueObject taxon
- Class ubic.gemma.model.genome.gene.Multifunctionality extends Object implements Serializable
  
  serialVersionUID:
  
  1842256912459855071L
  - Serialized Fields
    - id
      
      Long id
    - numGoTerms
      
      Integer numGoTerms
    - rank
      
      Double rank
    - score
      
      Double score
Package ubic.gemma.model.genome.gene.phenotype.valueObject
- Class ubic.gemma.model.genome.gene.phenotype.valueObject.BibliographicPhenotypesValueObject extends Object implements Serializable
  - Serialized Fields
    - evidenceId
      
      Long evidenceId
    - geneName
      
      String geneName
    - geneNCBI
      
      Integer geneNCBI
    - phenotypesValues
      
      Set<CharacteristicValueObject> phenotypesValues
- Class ubic.gemma.model.genome.gene.phenotype.valueObject.DiffExpressionEvidenceValueObject extends EvidenceValueObject<DifferentialExpressionEvidence> implements Serializable
  
  serialVersionUID:
  
  7262262666070114995L
  - Serialized Fields
    - geneDifferentialExpressionMetaAnalysisId
      
      Long geneDifferentialExpressionMetaAnalysisId
    - geneDifferentialExpressionMetaAnalysisResultId
      
      Long geneDifferentialExpressionMetaAnalysisResultId
    - geneDifferentialExpressionMetaAnalysisSummaryValueObject
      
      GeneDifferentialExpressionMetaAnalysisSummaryValueObject geneDifferentialExpressionMetaAnalysisSummaryValueObject
    - meanLogFoldChange
      
      Double meanLogFoldChange
    - metaPvalue
      
      Double metaPvalue
    - metaPvalueRank
      
      Double metaPvalueRank
    - metaQvalue
      
      Double metaQvalue
    - numEvidenceFromSameMetaAnalysis
      
      Long numEvidenceFromSameMetaAnalysis
    - selectionThreshold
      
      Double selectionThreshold
    - upperTail
      
      Boolean upperTail
- Class ubic.gemma.model.genome.gene.phenotype.valueObject.DumpsValueObject extends Object implements Serializable
  - Serialized Fields
    - lastModified
      
      String lastModified
    - name
      
      String name
    - url
      
      String url
- Class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceSecurityValueObject extends Object implements Serializable
  - Serialized Fields
    - currentUserHasWritePermission
      
      boolean currentUserHasWritePermission
    - currentUserIsOwner
      
      boolean currentUserIsOwner
    - isPublik
      
      boolean isPublik
    - isShared
      
      boolean isShared
    - owner
      
      String owner
- Class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceSourceValueObject extends DatabaseEntryValueObject implements Serializable
  
  serialVersionUID:
  
  4085159943613845499L
  - Serialized Fields
    - externalUrl
      
      String externalUrl
- Class ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceValueObject extends IdentifiableValueObject<E extends PhenotypeAssociation> implements Serializable
  
  serialVersionUID:
  
  -2483508971580975L
  - Serialized Fields
    - className
      
      String className
    - containQueryPhenotype
      
      boolean containQueryPhenotype
    - description
      
      String description
    - evidenceCode
      
      String evidenceCode
    - evidenceSecurityValueObject
      
      EvidenceSecurityValueObject evidenceSecurityValueObject
    - evidenceSource
      
      EvidenceSourceValueObject evidenceSource
    - externalUrl
      
      String externalUrl
    - geneId
      
      Long geneId
    - geneNCBI
      
      Integer geneNCBI
    - geneOfficialName
      
      String geneOfficialName
    - geneOfficialSymbol
      
      String geneOfficialSymbol
    - isHomologueEvidence
      
      boolean isHomologueEvidence
    - isNegativeEvidence
      
      boolean isNegativeEvidence
    - lastUpdated
      
      Long lastUpdated
    - originalPhenotype
      
      String originalPhenotype
    - phenotypeAssPubVO
      
      Set<PhenotypeAssPubValueObject> phenotypeAssPubVO
    - phenotypeMapping
      
      String phenotypeMapping
    - phenotypes
      
      Set<CharacteristicValueObject> phenotypes
    - relationship
      
      String relationship
    - scoreValueObject
      
      ScoreValueObject scoreValueObject
    - taxonCommonName
      
      String taxonCommonName
- Class ubic.gemma.model.genome.gene.phenotype.valueObject.ExperimentalEvidenceValueObject extends EvidenceValueObject<ExperimentalEvidence> implements Serializable
  
  serialVersionUID:
  
  4243531745086284715L
  - Serialized Fields
    - experimentCharacteristics
      
      Collection<CharacteristicValueObject> experimentCharacteristics
      
      Deprecated.
- Class ubic.gemma.model.genome.gene.phenotype.valueObject.ExternalDatabaseStatisticsValueObject extends Object implements Serializable
  - Serialized Fields
    - description
      
      String description
    - lastUpdateDate
      
      Date lastUpdateDate
    - name
      
      String name
    - numEvidence
      
      Long numEvidence
    - numGenes
      
      Long numGenes
    - numPhenotypes
      
      Long numPhenotypes
    - numPublications
      
      Long numPublications
    - pathToDownloadFile
      
      String pathToDownloadFile
    - webUri
      
      String webUri
- Class ubic.gemma.model.genome.gene.phenotype.valueObject.GeneEvidenceValueObject extends GeneValueObject implements Serializable
  
  serialVersionUID:
  
  -3484291071757959936L
  - Serialized Fields
    - evidence
      
      Collection<EvidenceValueObject<? extends PhenotypeAssociation>> evidence
      
      Deprecated.
    - phenotypesValueUri
      
      Set<String> phenotypesValueUri
      
      Deprecated.
- Class ubic.gemma.model.genome.gene.phenotype.valueObject.GenericEvidenceValueObject extends EvidenceValueObject<GenericEvidence> implements Serializable
  
  serialVersionUID:
  
  754768748091915831L
- Class ubic.gemma.model.genome.gene.phenotype.valueObject.LiteratureEvidenceValueObject extends EvidenceValueObject<LiteratureEvidence> implements Serializable
  
  serialVersionUID:
  
  -4401437961722829548L
- Class ubic.gemma.model.genome.gene.phenotype.valueObject.PhenotypeAssPubValueObject extends Object implements Serializable
  - Serialized Fields
    - citationValueObject
      
      CitationValueObject citationValueObject
    - type
      
      String type
- Class ubic.gemma.model.genome.gene.phenotype.valueObject.PhenotypeValueObject extends Object implements Serializable
  - Serialized Fields
    - value
      
      String value
    - valueUri
      
      String valueUri
- Class ubic.gemma.model.genome.gene.phenotype.valueObject.ScoreValueObject extends Object implements Serializable
  - Serialized Fields
    - scoreName
      
      String scoreName
    - scoreValue
      
      String scoreValue
    - strength
      
      Double strength
- Class ubic.gemma.model.genome.gene.phenotype.valueObject.SimpleTreeValueObject extends Object implements Serializable
  - Serialized Fields
    - _is_leaf
      
      boolean _is_leaf
    - _parent
      
      String _parent
    - children
      
      List<String> children
    - dbPhenotype
      
      boolean dbPhenotype
    - privateGeneCount
      
      long privateGeneCount
    - publicGeneCount
      
      long publicGeneCount
    - urlId
      
      String urlId
    - value
      
      String value
    - valueUri
      
      String valueUri
- Class ubic.gemma.model.genome.gene.phenotype.valueObject.TreeCharacteristicValueObject extends CharacteristicValueObject implements Serializable
  - Serialized Fields
    - _id
      
      String _id
    - children
      
      TreeSet<TreeCharacteristicValueObject> children
    - dbPhenotype
      
      boolean dbPhenotype
    - publicGenesNBCI
      
      HashSet<Integer> publicGenesNBCI
    - rootOfTree
      
      String rootOfTree
- Class ubic.gemma.model.genome.gene.phenotype.valueObject.ValidateEvidenceValueObject extends Object implements Serializable
  - Serialized Fields
    - accessDenied
      
      boolean accessDenied
    - descriptionInvalidSymbol
      
      boolean descriptionInvalidSymbol
    - evidenceNotFound
      
      boolean evidenceNotFound
    - lastUpdateDifferent
      
      boolean lastUpdateDifferent
    - problematicEvidenceIds
      
      Set<Long> problematicEvidenceIds
    - pubmedIdInvalid
      
      boolean pubmedIdInvalid
    - sameEvidenceFound
      
      boolean sameEvidenceFound
    - sameGeneAndOnePhenotypeAnnotated
      
      boolean sameGeneAndOnePhenotypeAnnotated
    - sameGeneAndPhenotypeChildOrParentAnnotated
      
      boolean sameGeneAndPhenotypeChildOrParentAnnotated
    - sameGeneAndPhenotypesAnnotated
      
      boolean sameGeneAndPhenotypesAnnotated
    - sameGeneAnnotated
      
      boolean sameGeneAnnotated
    - userNotLoggedIn
      
      boolean userNotLoggedIn
Package ubic.gemma.model.genome.sequenceAnalysis
- Class ubic.gemma.model.genome.sequenceAnalysis.AnnotationAssociation extends BioSequence2GeneProduct implements Serializable
  
  serialVersionUID:
  
  8648644792470060326L
  - Serialized Fields
    - source
      
      ExternalDatabase source
- Class ubic.gemma.model.genome.sequenceAnalysis.BioSequenceValueObject extends IdentifiableValueObject<BioSequence> implements Serializable
  - Serialized Fields
    - description
      
      String description
    - fractionRepeats
      
      Double fractionRepeats
    - length
      
      Long length
    - name
      
      String name
    - sequence
      
      String sequence
    - sequenceDatabaseEntry
      
      DatabaseEntryValueObject sequenceDatabaseEntry
    - taxon
      
      TaxonValueObject taxon
    - type
      
      SequenceTypeValueObject type
- Class ubic.gemma.model.genome.sequenceAnalysis.BlatAssociation extends BioSequence2GeneProduct implements Serializable
  
  serialVersionUID:
  
  -4620329339018727407L
  - Serialized Fields
    - blatResult
      
      BlatResult blatResult
- Class ubic.gemma.model.genome.sequenceAnalysis.BlatResult extends SequenceSimilaritySearchResult implements Serializable
  
  serialVersionUID:
  
  5703130745858235525L
  - Serialized Fields
    - blockCount
      
      Integer blockCount
    - blockSizes
      
      String blockSizes
    - matches
      
      Integer matches
    - mismatches
      
      Integer mismatches
    - ns
      
      Integer ns
    - queryEnd
      
      Integer queryEnd
    - queryGapBases
      
      Integer queryGapBases
    - queryGapCount
      
      Integer queryGapCount
    - queryStart
      
      Integer queryStart
    - queryStarts
      
      String queryStarts
    - repMatches
      
      Integer repMatches
    - strand
      
      String strand
    - targetEnd
      
      Long targetEnd
    - targetGapBases
      
      Integer targetGapBases
    - targetGapCount
      
      Integer targetGapCount
    - targetStart
      
      Long targetStart
    - targetStarts
      
      String targetStarts
- Class ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject extends IdentifiableValueObject<BlatResult> implements Serializable
  - Serialized Fields
    - blockCount
      
      Integer blockCount
    - blockSizes
      
      String blockSizes
    - identity
      
      Double identity
    - matches
      
      Integer matches
    - mismatches
      
      Integer mismatches
    - ns
      
      Integer ns
    - queryEnd
      
      Integer queryEnd
    - queryGapBases
      
      Integer queryGapBases
    - queryGapCount
      
      Integer queryGapCount
    - querySequence
      
      BioSequenceValueObject querySequence
    - queryStart
      
      Integer queryStart
    - queryStarts
      
      String queryStarts
    - repMatches
      
      Integer repMatches
    - score
      
      Double score
    - strand
      
      String strand
    - targetChromosomeName
      
      String targetChromosomeName
    - targetDatabase
      
      String targetDatabase
    - targetEnd
      
      Long targetEnd
    - targetGapBases
      
      Integer targetGapBases
    - targetGapCount
      
      Integer targetGapCount
    - targetStart
      
      Long targetStart
    - targetStarts
      
      String targetStarts
    - taxon
      
      TaxonValueObject taxon
- Class ubic.gemma.model.genome.sequenceAnalysis.SequenceSimilaritySearchResult extends Object implements Serializable
  
  serialVersionUID:
  
  -7196820023599562042L
  - Serialized Fields
    - id
      
      Long id
    - querySequence
      
      BioSequence querySequence
    - searchedDatabase
      
      ExternalDatabase searchedDatabase
    - targetAlignedRegion
      
      PhysicalLocation targetAlignedRegion
    - targetChromosome
      
      Chromosome targetChromosome
    - targetSequence
      
      BioSequence targetSequence
- Class ubic.gemma.model.genome.sequenceAnalysis.SequenceTypeValueObject extends Object implements Serializable
  - Serialized Fields
    - value
      
      String value
Package ubic.gemma.persistence.service
- Class ubic.gemma.persistence.service.AbstractServiceTest.ExceptionWithMessage extends Exception implements Serializable
- Class ubic.gemma.persistence.service.AbstractServiceTest.ExceptionWithoutMessage extends Exception implements Serializable
Package ubic.gemma.persistence.service.analysis.expression.diff
- Class ubic.gemma.persistence.service.analysis.expression.diff.MissingResult extends DiffExprGeneSearchResult implements Serializable
  
  serialVersionUID:
  
  -2868418055346274525L
- Class ubic.gemma.persistence.service.analysis.expression.diff.NonRetainedResult extends DiffExprGeneSearchResult implements Serializable
  
  serialVersionUID:
  
  3501605965895623139L
Package ubic.gemma.persistence.service.expression.experiment
- Class ubic.gemma.persistence.service.expression.experiment.FactorValueMigratorService.MigrationFailedException extends RuntimeException implements Serializable
  - Serialized Fields
    - migration
      
      FactorValueMigratorService.Migration migration
Package ubic.gemma.persistence.util
- Class ubic.gemma.persistence.util.TaskCancelledException extends RuntimeException implements Serializable
  
  serialVersionUID:
  
  7343146551545342910L
Package ubic.gemma.rest
- Class ubic.gemma.rest.DatasetsWebService.AnnotationWithUsageStatisticsValueObject extends AnnotationValueObject implements Serializable
  - Serialized Fields
    - numberOfExpressionExperiments
      
      Long numberOfExpressionExperiments
    - parentTerms
      
      Set<DatasetsWebService.OntologyTermValueObject> parentTerms
- Class ubic.gemma.rest.DatasetsWebService.ArrayDesignWithUsageStatisticsValueObject extends ArrayDesignValueObject implements Serializable
  - Serialized Fields
    - numberOfExpressionExperimentsForTechnologyType
      
      Long numberOfExpressionExperimentsForTechnologyType
- Class ubic.gemma.rest.DatasetsWebService.ExpressionExperimentWithSearchResultValueObject extends ExpressionExperimentValueObject implements Serializable
  - Serialized Fields
    - searchResult
      
      SearchWebService.SearchResultValueObject<ExpressionExperimentValueObject> searchResult
- Class ubic.gemma.rest.DatasetsWebService.TaxonWithUsageStatisticsValueObject extends TaxonValueObject implements Serializable
  - Serialized Fields
    - numberOfExpressionExperiments
      
      Long numberOfExpressionExperiments
Package ubic.gemma.rest.serializers
- Class ubic.gemma.rest.serializers.AbstractFactorValueValueObjectSerializer extends com.fasterxml.jackson.databind.ser.std.StdSerializer<T extends Object> implements Serializable
- Class ubic.gemma.rest.serializers.FactorValueBasicValueObjectSerializer extends AbstractFactorValueValueObjectSerializer<FactorValueBasicValueObject> implements Serializable
- Class ubic.gemma.rest.serializers.FactorValueValueObjectSerializer extends AbstractFactorValueValueObjectSerializer<FactorValueValueObject> implements Serializable
Package ubic.gemma.rest.util
- Class ubic.gemma.rest.util.EntityNotFoundException extends Exception implements Serializable
- Class ubic.gemma.rest.util.MalformedArgException extends javax.ws.rs.BadRequestException implements Serializable
Package ubic.gemma.web.controller.common.auditAndSecurity
- Class ubic.gemma.web.controller.common.auditAndSecurity.FileUpload extends Object implements Serializable
  
  serialVersionUID:
  
  537156568346654834L
  - Serialized Fields
    - file
      
      byte[] file
    - localPath
      
      String localPath
- Class ubic.gemma.web.controller.common.auditAndSecurity.SidValueObject extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - authority
      
      String authority
    - principal
      
      boolean principal
Package ubic.gemma.web.controller.expression.arrayDesign
- Class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignValueObjectExt extends ArrayDesignValueObject implements Serializable
  
  serialVersionUID:
  
  218696698777199533L
  - Serialized Fields
    - additionalTaxa
      
      Set<String> additionalTaxa
    - allParentsAnnotationLink
      
      String allParentsAnnotationLink
    - alternateNames
      
      Collection<String> alternateNames
    - alternative
      
      ArrayDesignValueObject alternative
    - bioProcessAnnotationLink
      
      String bioProcessAnnotationLink
    - colorString
      
      String colorString
    - mergees
      
      Collection<ArrayDesignValueObject> mergees
    - merger
      
      ArrayDesignValueObject merger
    - noParentsAnnotationLink
      
      String noParentsAnnotationLink
    - subsumees
      
      Collection<ArrayDesignValueObject> subsumees
    - subsumer
      
      ArrayDesignValueObject subsumer
Package ubic.gemma.web.controller.expression.experiment
- Class ubic.gemma.web.controller.expression.experiment.DesignMatrixRowValueObject extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - count
      
      int count
    - factors
      
      List<String> factors
    - factorTypes
      
      List<String> factorTypes
    - factorValueMap
      
      Map<String,String> factorValueMap
- Class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentDataFetchCommand extends TaskCommand implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - analysisId
      
      Long analysisId
    - experimentalDesignId
      
      Long experimentalDesignId
    - expressionExperimentId
      
      Long expressionExperimentId
    - filter
      
      boolean filter
    - forceRewrite
      
      boolean forceRewrite
    - format
      
      String format
    - quantitationTypeId
      
      Long quantitationTypeId
- Class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditValueObject extends ExpressionExperimentDetailsValueObject implements Serializable
  
  serialVersionUID:
  
  1630521876359566915L
  - Serialized Fields
    - bioAssays
      
      Collection<BioAssayValueObject> bioAssays
    - quantitationTypes
      
      Collection<QuantitationTypeValueObject> quantitationTypes
- Class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentLoadTaskCommand extends SimpleExpressionExperimentMetaData implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - arrayDesignName
      
      String arrayDesignName
    - originalFileName
      
      String originalFileName
    - serverFilePath
      
      String serverFilePath
    - taxonName
      
      String taxonName
    - validateOnly
      
      boolean validateOnly
Package ubic.gemma.web.util
- Class ubic.gemma.web.util.ConfigurationCookie extends javax.servlet.http.Cookie implements Serializable
  - Serialized Fields
    - configuration
      
      org.apache.commons.configuration2.PropertiesConfiguration configuration
- Class ubic.gemma.web.util.EntityNotFoundException extends RuntimeException implements Serializable
  
  serialVersionUID:
  
  -4361183252269974819L
- Class ubic.gemma.web.util.LabelValue extends Object implements Serializable
  
  serialVersionUID:
  
  3485837885293359602L
  - Serialized Fields
    - label
      
      String label
    - value
      
      String value
- Class ubic.gemma.web.util.ServiceUnavailableException extends RuntimeException implements Serializable
Package ubic.gemma.web.util.upload
- Class ubic.gemma.web.util.upload.CommonsMultipartFile extends Object implements Serializable
  
  serialVersionUID:
  
  6483196912349343465L
  - Serialized Fields
    - fileItem
      
      org.apache.commons.fileupload.FileItem fileItem
      
      Deprecated.
    - size
      
      long size
      
      Deprecated.
- Class ubic.gemma.web.util.upload.UploadInfo extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - bytesRead
      
      long bytesRead
    - fileIndex
      
      int fileIndex
    - status
      
      String status
    - totalSize
      
      long totalSize

Serialized Form

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

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

Serialized Fields

absoluteValue

arrayName

cdfCut

checkCorrelationDistribution

checkForBatchEffect

checkForOutliers

correlationCacheThreshold

fwe

lowerCdfCutUsed

lowerTailCut

makeSampleCorrMatImages

metric

minNumPresent

normalizationMethod

omitNegLinks

outputFile

probeDegreeThreshold

singularThreshold

subset

subsetSize

subsetUsed

textOut

upperCdfCutUsed

upperTailCut

useDb

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

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

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

Serialized Fields

analysisType

baseLineFactorValues

ebayes

factorsToInclude

interactionsToInclude

makeArchiveFile

persist

subsetFactor

subsetFactorValue

useWeights

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

Serialized Fields

activeExperiments

fisherPValue

gene

numExperimentsInScope

numMetThreshold

numSearchedExperiments

probeResults

sortKey

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

Serialized Fields

eeId

efId

Package ubic.gemma.core.analysis.preprocess

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

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

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

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

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

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

Serialized Fields

cause

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

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

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

Serialized Fields

chiSquare

df

ee

ef

numBatches

p

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

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

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

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