Serialized Form (Gemma 1.31.10 API)

Package ubic.gemma.core.analysis.expression.coexpression
- Class ubic.gemma.core.analysis.expression.coexpression.CoexpressionMetaValueObject extends Object implements Serializable
  - Serialized Fields
    - errorState
      
      String errorState
      
      Error message for the client.
    - maxEdges
      
      int maxEdges
      
      Upper bound on how large we let the graph be from the server side. Can be overridden via the setter.
    - numDatasetsQueried
      
      int numDatasetsQueried
      
      How many data sets were actually used in the query; that is, which had coexpression analysis done.
    - queryGenes
      
      Collection<GeneValueObject> queryGenes
    - queryGenesOnly
      
      boolean queryGenesOnly
      
      if this was a "query genes only" search
    - queryStringency
      
      int queryStringency
      
      The stringency used in the initial query and after 'global' trimming.
    - results
      
      List<CoexpressionValueObjectExt> results
      
      Results for coexpression of the query gene with other 'found' genes (which could potentially include other query genes)
    - searchSettings
      
      CoexpressionSearchCommand searchSettings
      
      The original search settings.
    - summaries
      
      Map<Long,CoexpressionSummaryValueObject> summaries
      
      Summaries of results for each gene (map of gene ids to CoexpressionSummaryValueObject)
- Class ubic.gemma.core.analysis.expression.coexpression.CoexpressionSearchCommand extends Object implements Serializable
  - Serialized Fields
    - dirty
      
      boolean dirty
      
      Set to true to signal that the eeSet has been modified from its stored version.
    - eeIds
      
      Collection<Long> eeIds
    - eeQuery
      
      String eeQuery
      
      we're storing the actual ee ids in the command object; the query string is only here so we can use this object to store the state of the search form between visits...
    - eeSetId
      
      Long eeSetId
    - eeSetName
      
      String eeSetName
    - geneIds
      
      Collection<Long> geneIds
    - geneSetId
      
      Long geneSetId
    - queryGenesOnly
      
      boolean queryGenesOnly
    - quick
      
      boolean quick
      
      if set to true will do a quick coexpression search (without filling in various details)
    - stringency
      
      Integer stringency
    - taxonId
      
      Long taxonId
      
      as eeQuery above, the taxon is only here so we can use this object to store the entire state of the form...
    - useMyDatasets
      
      boolean useMyDatasets
- Class ubic.gemma.core.analysis.expression.coexpression.CoexpressionSummaryValueObject extends Object implements Serializable
  - Serialized Fields
    - coexpNodeDegree
      
      GeneCoexpressionNodeDegreeValueObject coexpNodeDegree
    - datasetsAvailable
      
      int datasetsAvailable
    - datasetsTested
      
      int datasetsTested
    - geneId
      
      long geneId
    - linksFound
      
      int linksFound
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
      
      what proportion of links to keep (possibly subject to FWE statistical significance threshold). 1.0 means keep everything. 0.01 means 1%.
    - checkCorrelationDistribution
      
      boolean checkCorrelationDistribution
    - checkForBatchEffect
      
      boolean checkForBatchEffect
    - checkForOutliers
      
      boolean checkForOutliers
    - correlationCacheThreshold
      
      double correlationCacheThreshold
      
      only used for internal cache during calculations.
    - fwe
      
      double fwe
      
      family-wise error rate threshold we use to select links
    - lowerCdfCutUsed
      
      boolean lowerCdfCutUsed
    - lowerTailCut
      
      double lowerTailCut
    - makeSampleCorrMatImages
      
      boolean makeSampleCorrMatImages
    - metric
      
      String metric
    - minNumPresent
      
      int minNumPresent
      
      How many samples must be present in a correlation pair to keep the data, taking into account missing values.
    - normalizationMethod
      
      LinkAnalysisConfig.NormalizationMethod normalizationMethod
    - omitNegLinks
      
      boolean omitNegLinks
      
      Remove negative correlated values at the end.
    - outputFile
      
      File outputFile
      
      Only used if textOut = true; if null, just write to stdout.
    - probeDegreeThreshold
      
      int probeDegreeThreshold
      
      Probes with more than this many links are removed. Zero means no action is taken.
    - 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
      
      If this is non-null, this was a subset analysis, for this factor value.
    - useWeights
      
      boolean useWeights
- Class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionMetaAnalysisValueObject extends Object implements Serializable
  - Serialized Fields
    - activeExperiments
      
      Collection<BioAssaySet> activeExperiments
    - fisherPValue
      
      Double fisherPValue
    - gene
      
      GeneValueObject gene
    - numExperimentsInScope
      
      int numExperimentsInScope
    - numMetThreshold
      
      int numMetThreshold
    - numSearchedExperiments
      
      int numSearchedExperiments
    - probeResults
      
      Collection<DifferentialExpressionValueObject> probeResults
    - sortKey
      
      String sortKey
- Class ubic.gemma.core.analysis.expression.diff.DiffExpressionSelectedFactorCommand extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - eeId
      
      Long eeId
    - efId
      
      Long efId
Package ubic.gemma.core.analysis.preprocess
- Class ubic.gemma.core.analysis.preprocess.FailedToComputeSingularValueDecomposition extends PreprocessingException implements Serializable
- Class ubic.gemma.core.analysis.preprocess.InsufficientProbesException extends InsufficientDataException implements Serializable
  
  serialVersionUID:
  
  1L
- Class ubic.gemma.core.analysis.preprocess.PreprocessingException extends RuntimeException implements Serializable
  
  serialVersionUID:
  
  -8463478950898408838L
- Class ubic.gemma.core.analysis.preprocess.QuantitationMismatchPreprocessingException extends PreprocessingException implements Serializable
- Class ubic.gemma.core.analysis.preprocess.SampleCoexpressionRelatedPreprocessingException extends PreprocessingException implements Serializable
- Class ubic.gemma.core.analysis.preprocess.SVDRelatedPreprocessingException extends PreprocessingException implements Serializable
  - Serialized Fields
    - cause
      
      SVDException cause
- Class ubic.gemma.core.analysis.preprocess.UnsupportedQuantitationScaleConversionException extends QuantitationTypeConversionException implements Serializable
Package ubic.gemma.core.analysis.preprocess.batcheffects
- Class ubic.gemma.core.analysis.preprocess.batcheffects.BatchConfound extends Object implements Serializable
  - Serialized Fields
    - chiSquare
      
      double chiSquare
    - df
      
      int df
    - ee
      
      BioAssaySet ee
    - ef
      
      ExperimentalFactor ef
    - numBatches
      
      int numBatches
    - p
      
      double p
- Class ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoMissingException extends BatchInfoPopulationException implements Serializable
- Class ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationException extends PreprocessingException implements Serializable
  
  serialVersionUID:
  
  -1770591991479420212L
- Class ubic.gemma.core.analysis.preprocess.batcheffects.FASTQHeadersPresentButNotUsableException extends BatchInfoPopulationException implements Serializable
  
  serialVersionUID:
  
  1917074433646650950L
- Class ubic.gemma.core.analysis.preprocess.batcheffects.SingletonBatchesException extends BatchInfoPopulationException implements Serializable
  
  serialVersionUID:
  
  9088141067684148902L
- Class ubic.gemma.core.analysis.preprocess.batcheffects.UnsupportedRawdataFileFormatException extends BatchInfoPopulationException implements Serializable
  
  serialVersionUID:
  
  1L
Package ubic.gemma.core.analysis.preprocess.filter
- Class ubic.gemma.core.analysis.preprocess.filter.FilterConfig extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - afterDistinctValueCut
      
      int afterDistinctValueCut
    - afterInitialFilter
      
      int afterInitialFilter
    - afterLowExpressionCut
      
      int afterLowExpressionCut
    - afterLowVarianceCut
      
      int afterLowVarianceCut
    - afterMinPresentFilter
      
      int afterMinPresentFilter
    - afterZeroVarianceCut
      
      int afterZeroVarianceCut
    - highExpressionCut
      
      double highExpressionCut
    - ignoreMinimumRowsThreshold
      
      boolean ignoreMinimumRowsThreshold
      
      If true, the MINIMUM_ROWS_TO_BOTHER is ignored.
    - ignoreMinimumSampleThreshold
      
      boolean ignoreMinimumSampleThreshold
      
      If true, MINIMUM_SAMPLE is ignored.
    - logTransform
      
      boolean logTransform
    - lowDistinctValueCut
      
      double lowDistinctValueCut
    - lowDistinctValueIsSet
      
      boolean lowDistinctValueIsSet
    - lowExpressionCut
      
      double lowExpressionCut
    - lowExpressionCutIsSet
      
      boolean lowExpressionCutIsSet
    - lowVarianceCut
      
      double lowVarianceCut
    - lowVarianceCutIsSet
      
      boolean lowVarianceCutIsSet
    - minPresentFraction
      
      double minPresentFraction
    - minPresentFractionIsSet
      
      boolean minPresentFractionIsSet
    - requireSequences
      
      boolean requireSequences
    - startingRows
      
      int startingRows
- Class ubic.gemma.core.analysis.preprocess.filter.FilteringException extends PreprocessingException implements Serializable
- Class ubic.gemma.core.analysis.preprocess.filter.InsufficientDataException extends FilteringException implements Serializable
  
  serialVersionUID:
  
  1L
- Class ubic.gemma.core.analysis.preprocess.filter.InsufficientSamplesException extends InsufficientDataException implements Serializable
  
  serialVersionUID:
  
  1L
- Class ubic.gemma.core.analysis.preprocess.filter.NoRowsLeftAfterFilteringException extends FilteringException implements Serializable
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
      
      In order like the rows of the v matrix.
    - 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
      
      Need to store the correlations of eigengenes with dates of assays, and also with factors. Statistics are rank-based correlations
    - factors
      
      Map<Long,List<Double>> factors
      
      Map of factors to the double-ized representations of them.
    - id
      
      Long id
      
      ID of the experiment this is for
    - variances
      
      double[] variances
      
      An array of values representing the fraction of the variance each component accounts for
    - 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.association.phenotype
- Class ubic.gemma.core.association.phenotype.EntityNotFoundException extends RuntimeException implements Serializable
  
  serialVersionUID:
  
  -4361183252269974829L
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.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.image
- Class ubic.gemma.core.image.ABALinkOutValueObject extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - abaGeneImageUrls
      
      Collection<String> abaGeneImageUrls
    - abaGeneUrl
      
      String abaGeneUrl
    - geneSymbol
      
      String geneSymbol
Package ubic.gemma.core.job
- Class ubic.gemma.core.job.TaskCommand extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - emailAlert
      
      boolean emailAlert
      
      Should an email be sent to the user when the job is done?
    - entityId
      
      Long entityId
      
      Convenience field to handle the common case where a primary key is all that is needed.
    - maxQueueMinutes
      
      Integer maxQueueMinutes
      
      How long we will allow this task to be queued before giving up.
    - maxRuntime
      
      int maxRuntime
    - persistJobDetails
      
      Boolean persistJobDetails
      
      If true, the jobDetails associated with this task will be persisted in the database. Consider setting to false for test jobs or other super-frequent maintenance tasks.
    - securityContext
      
      org.springframework.security.core.context.SecurityContext securityContext
      
      Used to propagate security to grid workers.
    - submitter
      
      String submitter
    - taskId
      
      String taskId
- Class ubic.gemma.core.job.TaskResult extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - answer
      
      Object answer
      
      The actual result object
    - exception
      
      Exception exception
      
      Set if failed.
    - taskID
      
      String taskID
      
      The task id
Package ubic.gemma.core.job.progress
- Class ubic.gemma.core.job.progress.ProgressData extends Object implements Serializable
  
  serialVersionUID:
  
  -4303625064082352461L
  - Serialized Fields
    - description
      
      String description
    - done
      
      boolean done
    - failed
      
      boolean failed
    - forwardingURL
      
      String forwardingURL
    - percent
      
      int percent
    - taskId
      
      String taskId
- Class ubic.gemma.core.job.progress.SubmittedTaskValueObject extends Object implements Serializable
  
  serialVersionUID:
  
  6757089319713433356L
  - Serialized Fields
    - done
      
      boolean done
    - emailAlert
      
      boolean emailAlert
    - finishTime
      
      Date finishTime
    - lastLogMessage
      
      String lastLogMessage
    - logMessages
      
      String logMessages
    - runningRemotely
      
      boolean runningRemotely
    - startTime
      
      Date startTime
    - submissionTime
      
      Date submissionTime
    - submitter
      
      String submitter
    - taskId
      
      String taskId
    - taskStatus
      
      String taskStatus
    - taskType
      
      String taskType
Package ubic.gemma.core.loader.entrez.pubmed
- Class ubic.gemma.core.loader.entrez.pubmed.ESearchException extends Exception implements Serializable
Package ubic.gemma.core.loader.expression.arrayDesign
- Class ubic.gemma.core.loader.expression.arrayDesign.Reporter extends AbstractDescribable implements Serializable
  
  serialVersionUID:
  
  3703827938981026012L
  - Serialized Fields
    - col
      
      Integer col
    - compositeSequence
      
      CompositeSequence compositeSequence
    - immobilizedCharacteristic
      
      BioSequence immobilizedCharacteristic
    - row
      
      Integer row
    - startInBioChar
      
      Long startInBioChar
    - strand
      
      String strand
Package ubic.gemma.core.loader.expression.geo
- Class ubic.gemma.core.loader.expression.geo.GeoSampleCorrespondence extends Object implements Serializable
  
  serialVersionUID:
  
  -5285504953530483114L
  - Serialized Fields
    - accToDataset
      
      Map<String,String> accToDataset
    - accToTitle
      
      Map<String,String> accToTitle
    - sets
      
      Collection<Set<String>> sets
Package ubic.gemma.core.loader.expression.geo.model
- Class ubic.gemma.core.loader.expression.geo.model.GeoContact extends Object implements Serializable
  
  serialVersionUID:
  
  -2042747972349661568L
  - Serialized Fields
    - address
      
      String address
    - city
      
      String city
    - country
      
      String country
    - department
      
      String department
    - email
      
      String email
    - fax
      
      String fax
    - institute
      
      String institute
    - laboratory
      
      String laboratory
    - name
      
      String name
    - phone
      
      String phone
    - postCode
      
      String postCode
    - state
      
      String state
    - webLink
      
      String webLink
- Class ubic.gemma.core.loader.expression.geo.model.GeoData extends Object implements Serializable
  
  serialVersionUID:
  
  -859220901359581113L
  - Serialized Fields
    - columnDescriptions
      
      List<String> columnDescriptions
    - columnNames
      
      List<String> columnNames
    - contact
      
      GeoContact contact
    - geoAccession
      
      String geoAccession
    - title
      
      String title
- Class ubic.gemma.core.loader.expression.geo.model.GeoDataset extends GeoData implements Serializable
  
  serialVersionUID:
  
  2659028881509672793L
  - Serialized Fields
    - completeness
      
      String completeness
    - datasetType
      
      String datasetType
    - description
      
      String description
    - experimentType
      
      GeoDataset.ExperimentType experimentType
    - featureCount
      
      String featureCount
    - numChannels
      
      int numChannels
    - numProbes
      
      int numProbes
    - numSamples
      
      int numSamples
    - order
      
      String order
    - organism
      
      String organism
    - platform
      
      GeoPlatform platform
    - platformType
      
      GeoDataset.PlatformType platformType
    - pubmedId
      
      String pubmedId
    - sampleType
      
      GeoDataset.SampleType sampleType
    - series
      
      Collection<GeoSeries> series
    - subsets
      
      Collection<GeoSubset> subsets
    - updateDate
      
      String updateDate
    - valueType
      
      GeoDataset.ValueType valueType
- Class ubic.gemma.core.loader.expression.geo.model.GeoPlatform extends GeoData implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - catalogNumbers
      
      Collection<String> catalogNumbers
    - coating
      
      String coating
    - contributer
      
      Collection<String> contributer
    - description
      
      String description
    - designElements
      
      Collection<String> designElements
    - distribution
      
      String distribution
    - id
      
      String id
    - lastUpdateDate
      
      String lastUpdateDate
    - manufactureProtocol
      
      String manufactureProtocol
    - manufacturer
      
      String manufacturer
    - organisms
      
      Collection<String> organisms
    - platformData
      
      List<List<String>> platformData
    - platformInformation
      
      Map<String,List<String>> platformInformation
      
      Store information on the platform here. Map of designElements to other information. This has to be lists so the values "line up".
    - probeNamesInGemma
      
      Map<String,String> probeNamesInGemma
      
      Map of original probe names provided by GEO to the names in Gemma (if this platform is already there). This is needed because probe names are sometimes changed after import. This map must be populated prior to import of the data.
    - pubMedIds
      
      Collection<Integer> pubMedIds
    - sample
      
      String sample
    - status
      
      String status
    - submissionDate
      
      String submissionDate
    - supplementaryFile
      
      String supplementaryFile
    - support
      
      String support
    - technology
      
      GeoDataset.PlatformType technology
    - useDataFromGEO
      
      boolean useDataFromGEO
      
      Will be set to false during parsing if data are missing.
    - webLink
      
      String webLink
    - webLinks
      
      Collection<String> webLinks
- Class ubic.gemma.core.loader.expression.geo.model.GeoRecord extends GeoData implements Serializable
  
  serialVersionUID:
  
  2060148205381855991L
  - Serialized Fields
    - contactName
      
      String contactName
    - correspondingExperiments
      
      Collection<Long> correspondingExperiments
    - libraryStrategy
      
      String libraryStrategy
    - meshHeadings
      
      String meshHeadings
    - numSamples
      
      int numSamples
    - organisms
      
      Collection<String> organisms
    - overallDesign
      
      String overallDesign
    - platform
      
      String platform
    - previousClicks
      
      int previousClicks
    - pubMedIds
      
      String pubMedIds
    - releaseDate
      
      Date releaseDate
    - sampleDetails
      
      String sampleDetails
    - sampleGEOAccessions
      
      Collection<String> sampleGEOAccessions
    - seriesType
      
      String seriesType
    - subSeries
      
      boolean subSeries
    - subSeriesOf
      
      String subSeriesOf
    - summary
      
      String summary
    - superSeries
      
      boolean superSeries
    - usable
      
      boolean usable
- Class ubic.gemma.core.loader.expression.geo.model.GeoSample extends GeoData implements Serializable
  
  serialVersionUID:
  
  -8820012224856178673L
  - Serialized Fields
    - anchor
      
      String anchor
    - channelCount
      
      int channelCount
    - channels
      
      List<GeoChannel> channels
    - dataProcessing
      
      String dataProcessing
    - description
      
      String description
    - hybProtocol
      
      String hybProtocol
    - id
      
      String id
    - isGenePix
      
      boolean isGenePix
    - lastUpdateDate
      
      String lastUpdateDate
    - libSource
      
      String libSource
    - libStrategy
      
      String libStrategy
    - mightNotHaveDataInFile
      
      boolean mightNotHaveDataInFile
    - platforms
      
      Collection<GeoPlatform> platforms
    - replicates
      
      Collection<GeoReplication> replicates
    - scanProtocol
      
      String scanProtocol
    - seriesAppearsIn
      
      Collection<String> seriesAppearsIn
    - status
      
      String status
    - submissionDate
      
      String submissionDate
    - supplementaryFile
      
      String supplementaryFile
    - tagCount
      
      int tagCount
    - tagLength
      
      int tagLength
    - titleInDataset
      
      String titleInDataset
      
      This is used to store the title for the sample as found in the GDS file, if it differs from the one in the GSE file
    - type
      
      String type
    - variables
      
      Collection<GeoVariable> variables
    - warnedAboutGenePix
      
      boolean warnedAboutGenePix
- Class ubic.gemma.core.loader.expression.geo.model.GeoSeries extends GeoData implements Serializable
  
  serialVersionUID:
  
  -1058350558444775537L
  - Serialized Fields
    - contributers
      
      Collection<GeoContact> contributers
    - dataSets
      
      Collection<GeoDataset> dataSets
    - isSubSeries
      
      boolean isSubSeries
    - isSuperSeries
      
      boolean isSuperSeries
    - keyWords
      
      Collection<String> keyWords
    - lastUpdateDate
      
      String lastUpdateDate
    - overallDesign
      
      String overallDesign
    - platformId
      
      String platformId
    - pubmedIds
      
      Collection<String> pubmedIds
    - replicates
      
      Map<Integer,GeoReplication> replicates
    - sampleCorrespondence
      
      GeoSampleCorrespondence sampleCorrespondence
    - samples
      
      Collection<GeoSample> samples
    - seriesId
      
      String seriesId
    - seriesTypes
      
      Collection<GeoSeries.SeriesType> seriesTypes
    - status
      
      String status
    - submissionDate
      
      String submissionDate
    - subSeries
      
      Collection<String> subSeries
    - summary
      
      String summary
    - supplementaryFile
      
      String supplementaryFile
    - values
      
      GeoValues values
    - variables
      
      Map<Integer,GeoVariable> variables
    - webLinks
      
      Collection<String> webLinks
- Class ubic.gemma.core.loader.expression.geo.model.GeoSubset extends GeoData implements Serializable
  
  serialVersionUID:
  
  2392295178038874633L
  - Serialized Fields
    - dataSet
      
      String dataSet
    - description
      
      String description
    - owningDataset
      
      GeoDataset owningDataset
    - samples
      
      Collection<GeoSample> samples
    - type
      
      GeoVariable.VariableType type
- Class ubic.gemma.core.loader.expression.geo.model.GeoValues extends Object implements Serializable
  
  serialVersionUID:
  
  3748363645735281578L
  - Serialized Fields
    - data
      
      Map<GeoPlatform,Map<Integer,Map<String,List<Object>>>> data
    - quantitationTypeIndexMap
      
      Map<GeoPlatform,Map<Integer,Collection<String>>> quantitationTypeIndexMap
    - quantitationTypeNameMap
      
      Map<GeoPlatform,Map<String,Integer>> quantitationTypeNameMap
    - sampleDimensions
      
      Map<GeoPlatform,Map<Integer,LinkedHashSet<GeoSample>>> sampleDimensions
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.expression.simple.model
- Class ubic.gemma.core.loader.expression.simple.model.SimpleExpressionExperimentMetaData extends TaskCommand implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - arrayDesignIds
      
      Collection<Long> arrayDesignIds
    - arrayDesigns
      
      Collection<ArrayDesign> arrayDesigns
    - description
      
      String description
    - experimentalDesignDescription
      
      String experimentalDesignDescription
    - experimentalDesignName
      
      String experimentalDesignName
    - externalReference
      
      DatabaseEntry externalReference
    - generalType
      
      GeneralType generalType
    - isBatchCorrected
      
      Boolean isBatchCorrected
    - isMaskedPreferred
      
      Boolean isMaskedPreferred
    - isRatio
      
      Boolean isRatio
    - name
      
      String name
    - probeIdsAreImageClones
      
      boolean probeIdsAreImageClones
    - pubMedId
      
      Integer pubMedId
      
      Publication reference.
    - quantitationTypeDescription
      
      String quantitationTypeDescription
    - quantitationTypeName
      
      String quantitationTypeName
    - scale
      
      ScaleType scale
    - shortName
      
      String shortName
    - sourceUrl
      
      String sourceUrl
    - taxon
      
      Taxon taxon
    - taxonId
      
      Long taxonId
    - technologyType
      
      TechnologyType technologyType
    - type
      
      StandardQuantitationType type
    - user
      
      Contact user
      
      The person who loaded this data.
Package ubic.gemma.core.loader.util
- Class ubic.gemma.core.loader.util.AlreadyExistsInSystemException extends RuntimeException implements Serializable
  
  serialVersionUID:
  
  5677999264920938691L
  - Serialized Fields
    - data
      
      Object data
Package ubic.gemma.core.loader.util.biomart
- Class ubic.gemma.core.loader.util.biomart.Ensembl2NcbiValueObject extends Object implements Serializable
  
  serialVersionUID:
  
  -859220901359582113L
  - Serialized Fields
    - enemblTranscriptId
      
      String enemblTranscriptId
    - ensembleGeneId
      
      String ensembleGeneId
    - ensemblPeptideId
      
      String ensemblPeptideId
    - hgcnId
      
      String hgcnId
    - ncbiGenes
      
      Collection<String> ncbiGenes
    - ncbiTaxonId
      
      Integer ncbiTaxonId
Package ubic.gemma.core.loader.util.parser
- Class ubic.gemma.core.loader.util.parser.FileFormatException extends RuntimeException implements Serializable
  
  serialVersionUID:
  
  -1984918923089214361L
Package ubic.gemma.core.ontology
- Class ubic.gemma.core.ontology.AbstractOntologyResourceSimple extends Object implements Serializable
  - Serialized Fields
    - label
      
      String label
    - uri
      
      String uri
- Class ubic.gemma.core.ontology.OntologyIndividualSimple extends AbstractOntologyResourceSimple implements Serializable
  - Serialized Fields
    - instanceOf
      
      OntologyTermSimple instanceOf
- Class ubic.gemma.core.ontology.OntologyPropertySimple extends AbstractOntologyResourceSimple implements Serializable
Package ubic.gemma.core.search
- Class ubic.gemma.core.search.BaseCodeOntologySearchException extends SearchException implements Serializable
  - Serialized Fields
    - cause
      
      OntologySearchException cause
- Class ubic.gemma.core.search.ParseSearchException extends SearchException implements Serializable
  - Serialized Fields
    - originalParseException
      
      ParseSearchException originalParseException
    - query
      
      String query
- Class ubic.gemma.core.search.SearchException extends Exception implements Serializable
- Class ubic.gemma.core.search.SearchTimeoutException extends SearchException implements Serializable
  - Serialized Fields
    - cause
      
      TimeoutException cause
Package ubic.gemma.core.search.lucene
- Class ubic.gemma.core.search.lucene.LuceneParseSearchException extends ParseSearchException implements Serializable
Package ubic.gemma.core.search.source
- Class ubic.gemma.core.search.source.HibernateSearchException extends SearchException implements Serializable
  - Serialized Fields
    - cause
      
      org.hibernate.search.SearchException cause
Package ubic.gemma.core.tasks.analysis.coexp
- Class ubic.gemma.core.tasks.analysis.coexp.LinkAnalysisTaskCommand extends TaskCommand implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - expressionExperiment
      
      ExpressionExperiment expressionExperiment
    - filterConfig
      
      FilterConfig filterConfig
    - linkAnalysisConfig
      
      LinkAnalysisConfig linkAnalysisConfig
Package ubic.gemma.core.tasks.analysis.diffex
- Class ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisRemoveTaskCommand extends DifferentialExpressionAnalysisTaskCommand implements Serializable
  
  serialVersionUID:
  
  -6881129987842634598L
  - Serialized Fields
    - toRemove
      
      DifferentialExpressionAnalysis toRemove
- Class ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisTaskCommand extends TaskCommand implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - analysisType
      
      DifferentialExpressionAnalyzerServiceImpl.AnalysisType analysisType
      
      Proposed analysis type. If null the system tries to figure it out.
    - expressionExperiment
      
      ExpressionExperiment expressionExperiment
    - factors
      
      Collection<ExperimentalFactor> factors
      
      The factors to actually use in the analysis. If null the system tries to figure it out.
    - forceAnalysis
      
      boolean forceAnalysis
    - includeInteractions
      
      boolean includeInteractions
      
      Whether interactions among the factors should be included. The implementation may limit this to two-way interactions for only up to two factors, so this may not have the effect desired.
    - moderateStatistics
      
      boolean moderateStatistics
      
      Whether to moderate test statistics via empirical Bayes
    - subsetFactor
      
      ExperimentalFactor subsetFactor
    - toRedo
      
      DifferentialExpressionAnalysis toRedo
    - useWeights
      
      boolean useWeights
      
      Whether to use weighted regression based on mean-variance relationships (voom)
- Class ubic.gemma.core.tasks.analysis.diffex.DiffExMetaAnalyzerTaskCommand extends TaskCommand implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - analysisResultSetIds
      
      Collection<Long> analysisResultSetIds
    - description
      
      String description
    - name
      
      String name
    - persist
      
      boolean persist
Package ubic.gemma.core.tasks.analysis.expression
- Class ubic.gemma.core.tasks.analysis.expression.BatchInfoFetchTaskCommand extends ExpressionExperimentReportTaskCommand implements Serializable
  
  serialVersionUID:
  
  -1901958943061377082L
- Class ubic.gemma.core.tasks.analysis.expression.BioAssayOutlierProcessingTaskCommand extends TaskCommand implements Serializable
  
  serialVersionUID:
  
  3083077516188614790L
  - Serialized Fields
    - bioAssayIds
      
      Collection<Long> bioAssayIds
    - revert
      
      boolean revert
- Class ubic.gemma.core.tasks.analysis.expression.ExpressionExperimentLoadTaskCommand extends TaskCommand implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - accession
      
      String accession
    - aggressiveQtRemoval
      
      boolean aggressiveQtRemoval
      
      Set to true to attempt to remove all unneeded quantitation types during parsing.
    - allowArrayExpressDesign
      
      boolean allowArrayExpressDesign
    - allowSubSeriesLoad
      
      boolean allowSubSeriesLoad
    - allowSuperSeriesLoad
      
      boolean allowSuperSeriesLoad
    - arrayDesignName
      
      String arrayDesignName
    - isArrayExpress
      
      boolean isArrayExpress
    - isSplitByPlatform
      
      boolean isSplitByPlatform
    - loadPlatformOnly
      
      boolean loadPlatformOnly
    - suppressMatching
      
      boolean suppressMatching
      
      Used to turn off 'bioassay to biomaterial' matching.
- Class ubic.gemma.core.tasks.analysis.expression.PreprocessTaskCommand extends TaskCommand implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - diagnosticsOnly
      
      boolean diagnosticsOnly
    - expressionExperiment
      
      ExpressionExperiment expressionExperiment
- Class ubic.gemma.core.tasks.analysis.expression.SvdTaskCommand extends TaskCommand implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - expressionExperiment
      
      ExpressionExperiment expressionExperiment
    - postProcessOnly
      
      boolean postProcessOnly
- Class ubic.gemma.core.tasks.analysis.expression.TwoChannelMissingValueTaskCommand extends TaskCommand implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - expressionExperiment
      
      ExpressionExperiment expressionExperiment
    - extraMissingValueIndicators
      
      Collection<Double> extraMissingValueIndicators
    - s2n
      
      double s2n
- Class ubic.gemma.core.tasks.analysis.expression.UpdateEEDetailsCommand extends TaskCommand implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - description
      
      String description
    - name
      
      String name
    - pubMedId
      
      String pubMedId
    - removePrimaryPublication
      
      boolean removePrimaryPublication
    - shortName
      
      String shortName
- Class ubic.gemma.core.tasks.analysis.expression.UpdatePubMedCommand extends TaskCommand implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - pubmedId
      
      String pubmedId
Package ubic.gemma.core.tasks.analysis.sequence
- Class ubic.gemma.core.tasks.analysis.sequence.ArrayDesignProbeMapTaskCommand extends TaskCommand implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - arrayDesign
      
      ArrayDesign arrayDesign
    - forceAnalysis
      
      boolean forceAnalysis
Package ubic.gemma.core.tasks.maintenance
- Class ubic.gemma.core.tasks.maintenance.CharacteristicUpdateCommand extends TaskCommand implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - annotationValueObjects
      
      Collection<AnnotationValueObject> annotationValueObjects
    - remove
      
      boolean remove
      
      If set to true, the annotations passed in will be deleted.
- Class ubic.gemma.core.tasks.maintenance.ExpressionExperimentReportTaskCommand extends TaskCommand implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - all
      
      boolean all
    - expressionExperiment
      
      ExpressionExperiment expressionExperiment
- Class ubic.gemma.core.tasks.maintenance.IndexerTaskCommand extends TaskCommand implements Serializable
  
  serialVersionUID:
  
  -8994831072852393919L
  - Serialized Fields
    - compassOn
      
      boolean compassOn
    - indexAD
      
      boolean indexAD
    - indexBibRef
      
      boolean indexBibRef
    - indexBioSequence
      
      boolean indexBioSequence
    - indexEE
      
      boolean indexEE
    - indexExperimentSet
      
      boolean indexExperimentSet
    - indexGene
      
      boolean indexGene
    - indexGeneSet
      
      boolean indexGeneSet
    - indexOntologies
      
      boolean indexOntologies
    - indexProbe
      
      boolean indexProbe
Package ubic.gemma.core.tasks.visualization
- Class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject extends Object implements Serializable
  - Serialized Fields
    - analysisId
      
      Long analysisId
    - analysisNotRun
      
      boolean analysisNotRun
    - baselineFactorValue
      
      String baselineFactorValue
    - baselineFactorValueId
      
      Long baselineFactorValueId
    - contrastsFactorValueIds
      
      List<Long> contrastsFactorValueIds
    - contrastsFactorValues
      
      Map<Long,String> contrastsFactorValues
    - datasetId
      
      Long datasetId
    - datasetLink
      
      String datasetLink
    - datasetName
      
      String datasetName
    - datasetShortName
      
      String datasetShortName
    - factorCategory
      
      String factorCategory
    - factorDescription
      
      String factorDescription
    - factorId
      
      Long factorId
    - factorName
      
      String factorName
    - numberOfProbes
      
      List<List<Integer>> numberOfProbes
    - numberOfProbesDiffExpressed
      
      int numberOfProbesDiffExpressed
    - numberOfProbesDownRegulated
      
      int numberOfProbesDownRegulated
    - numberOfProbesTotal
      
      int numberOfProbesTotal
    - numberOfProbesUpRegulated
      
      int numberOfProbesUpRegulated
    - qValues
      
      List<List<Double>> qValues
    - resultSetId
      
      Long resultSetId
    - visualizationValues
      
      List<List<Double>> visualizationValues
- Class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject extends Object implements Serializable
  - Serialized Fields
    - cellData
      
      Map<String,Map<Long,DifferentialExpressionGenesConditionsValueObject.Cell>> cellData
      
      Map of Condition IDs to map of Genes to the Cell holding the information for the results for that Gene x Condition combination.
    - conditions
      
      List<DifferentialExpressionGenesConditionsValueObject.Condition> conditions
    - genes
      
      List<DifferentialExpressionGenesConditionsValueObject.DiffExGene> genes
    - resultSetConditions
      
      Map<Long,Collection<DifferentialExpressionGenesConditionsValueObject.Condition>> resultSetConditions
- Class ubic.gemma.core.tasks.visualization.DifferentialExpressionSearchTaskCommand extends TaskCommand implements Serializable
  
  serialVersionUID:
  
  -8510536003059837349L
  - Serialized Fields
    - experimentGroup
      
      Collection<ExpressionExperimentDetailsValueObject> experimentGroup
    - experimentGroupName
      
      String experimentGroupName
    - geneGroup
      
      Collection<GeneValueObject> geneGroup
    - geneGroupName
      
      String geneGroupName
Package ubic.gemma.core.util
- Class ubic.gemma.core.util.GemmaRestApiClientException extends RuntimeException 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
- Class ubic.gemma.model.analysis.expression.ExpressionAnalysis extends Analysis implements Serializable
  
  serialVersionUID:
  
  7521985377825526643L
- Class ubic.gemma.model.analysis.expression.ExpressionExperimentSet extends AbstractAuditable implements Serializable
  
  serialVersionUID:
  
  -1034074709420077917L
  - Serialized Fields
    - experiments
      
      Set<BioAssaySet> experiments
    - taxon
      
      Taxon taxon
- Class ubic.gemma.model.analysis.expression.FactorAssociatedAnalysisResultSet extends AnalysisResultSet<R extends AnalysisResult> implements Serializable
  
  serialVersionUID:
  
  821072688513147160L
  - Serialized Fields
    - experimentalFactors
      
      Set<ExperimentalFactor> experimentalFactors
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
      
      At gene level.
- 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
      
      This serves as the primary key.
    - numDatasetsTestedIn
      
      int numDatasetsTestedIn
      
      we store this separately as a column in the DB, which is why it is a field. Otherwise we infer it from the data.
- 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.analysis.expression.diff
- Class ubic.gemma.model.analysis.expression.diff.ContrastResult extends Object implements Serializable
  
  serialVersionUID:
  
  -4310735803120153778L
  - Serialized Fields
    - coefficient
      
      Double coefficient
    - factorValue
      
      FactorValue factorValue
    - id
      
      Long id
    - logFoldChange
      
      Double logFoldChange
      
      TODO: rename this to log2FoldChange to avoid confusion with the logarithm base used.
    - pvalue
      
      Double pvalue
    - secondFactorValue
      
      FactorValue secondFactorValue
    - tStat
      
      Double tStat
- Class ubic.gemma.model.analysis.expression.diff.ContrastResultValueObject extends IdentifiableValueObject<ContrastResult> implements Serializable
  - Serialized Fields
    - coefficient
      
      Double coefficient
    - factorValue
      
      FactorValueBasicValueObject factorValue
    - factorValueId
      
      Long factorValueId
    - logFoldChange
      
      Double logFoldChange
    - pvalue
      
      Double pvalue
    - secondFactorValue
      
      FactorValueBasicValueObject secondFactorValue
    - secondFactorValueId
      
      Long secondFactorValueId
    - tStat
      
      Double tStat
- Class ubic.gemma.model.analysis.expression.diff.ContrastsValueObject extends Object implements Serializable
  - Serialized Fields
    - contrasts
      
      List<ContrastVO> contrasts
    - resultId
      
      Long resultId
- Class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysis extends SingleExperimentAnalysis implements Serializable
  
  serialVersionUID:
  
  -7855180617739271699L
  - Serialized Fields
    - resultSets
      
      Set<ExpressionAnalysisResultSet> resultSets
    - subsetFactorValue
      
      FactorValue subsetFactorValue
- Class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResult extends AnalysisResult implements Serializable
  
  serialVersionUID:
  
  8952834115689524169L
  - Serialized Fields
    - contrasts
      
      Set<ContrastResult> contrasts
    - correctedPvalue
      
      Double correctedPvalue
      
      Typically actually a qvalue.
    - correctedPValueBin
      
      Integer correctedPValueBin
    - id
      
      Long id
    - probe
      
      CompositeSequence probe
    - pvalue
      
      Double pvalue
    - rank
      
      Double rank
    - resultSet
      
      ExpressionAnalysisResultSet resultSet
- Class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResultSetValueObject extends AnalysisResultSetValueObject<DifferentialExpressionAnalysisResult,ExpressionAnalysisResultSet> implements Serializable
  - Serialized Fields
    - analysis
      
      DifferentialExpressionAnalysisValueObject analysis
    - baselineGroup
      
      FactorValueBasicValueObject baselineGroup
    - experimentalFactors
      
      Collection<ExperimentalFactorValueObject> experimentalFactors
    - results
      
      Collection<DifferentialExpressionAnalysisResultValueObject> results
      
      Related analysis results.
      Note that this field is excluded from the JSON serialization if left unset.
    - secondBaselineGroup
      
      FactorValueBasicValueObject secondBaselineGroup
    - taxa
      
      Set<TaxonValueObject> taxa
      
      When genes are included, this field is populated.
- Class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResultValueObject extends AnalysisResultValueObject<DifferentialExpressionAnalysisResult> implements Serializable
  - Serialized Fields
    - contrasts
      
      List<ContrastResultValueObject> contrasts
    - correctedPvalue
      
      Double correctedPvalue
    - genes
      
      List<GeneValueObject> genes
    - probeId
      
      Long probeId
    - probeName
      
      String probeName
    - pValue
      
      Double pValue
    - rank
      
      Double rank
- Class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisValueObject extends AnalysisValueObject<DifferentialExpressionAnalysis> implements Serializable
  
  serialVersionUID:
  
  622877438067070041L
  - Serialized Fields
    - arrayDesignsUsed
      
      Collection<Long> arrayDesignsUsed
    - experimentAnalyzedId
      
      Long experimentAnalyzedId
    - factorValuesUsed
      
      Map<Long,Collection<FactorValueValueObject>> factorValuesUsed
    - resultSets
      
      Collection<DiffExResultSetSummaryValueObject> resultSets
    - sourceExperimentId
      
      Long sourceExperimentId
    - subsetFactor
      
      ExperimentalFactorValueObject subsetFactor
    - subsetFactorId
      
      Long subsetFactorId
    - subsetFactorValue
      
      FactorValueValueObject subsetFactorValue
    - subsetFactorValueId
      
      Long subsetFactorValueId
- Class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionValueObject extends Object implements Serializable
  - Serialized Fields
    - contrasts
      
      ContrastsValueObject contrasts
    - corrP
      
      Double corrP
    - direction
      
      Direction direction
    - experimentalFactors
      
      Collection<ExperimentalFactorValueObject> experimentalFactors
    - expressionExperiment
      
      ExpressionExperimentValueObject expressionExperiment
    - fisherContribution
      
      Boolean fisherContribution
    - gene
      
      GeneValueObject gene
    - id
      
      Long id
    - metThreshold
      
      Boolean metThreshold
    - p
      
      Double p
    - probe
      
      String probe
    - probeId
      
      Long probeId
    - resultSetId
      
      Long resultSetId
    - sortKey
      
      String sortKey
- Class ubic.gemma.model.analysis.expression.diff.DiffExprGeneSearchResult extends Object implements Serializable
  
  serialVersionUID:
  
  -6199218806972657112L
  - Serialized Fields
    - analysisResultId
      
      Long analysisResultId
    - correctedPvalue
      
      Double correctedPvalue
    - geneId
      
      Long geneId
    - numberOfProbes
      
      int numberOfProbes
    - numberOfProbesDiffExpressed
      
      int numberOfProbesDiffExpressed
    - pvalue
      
      Double pvalue
    - resultSetId
      
      Long resultSetId
    - score
      
      Double score
- Class ubic.gemma.model.analysis.expression.diff.DiffExResultSetSummaryValueObject extends Object implements Serializable
  
  serialVersionUID:
  
  2063274043081170625L
  - Serialized Fields
    - analysisId
      
      Long analysisId
    - arrayDesignsUsed
      
      Collection<Long> arrayDesignsUsed
    - baselineGroup
      
      FactorValueValueObject baselineGroup
    - bioAssaySetAnalyzedId
      
      Long bioAssaySetAnalyzedId
      
      Analyzed BioAssaySet ID.
      This is redundant because of DifferentialExpressionAnalysisValueObject#getExperimentAnalyzedId(), and always displayed in that context in the RESTful API.
    - downregulatedCount
      
      Integer downregulatedCount
      
      Number of diffex probes in the Direction.DOWN hit list if available.
    - experimentalFactors
      
      Collection<ExperimentalFactorValueObject> experimentalFactors
    - factorIds
      
      Collection<Long> factorIds
    - id
      
      Long id
    - numberOfDiffExpressedProbes
      
      Integer numberOfDiffExpressedProbes
      
      Number of diffex probes in the Direction.EITHER hit list if available.
    - numberOfGenesAnalyzed
      
      Integer numberOfGenesAnalyzed
    - numberOfProbesAnalyzed
      
      Integer numberOfProbesAnalyzed
    - qValue
      
      Double qValue
      
      This is used once in the frontend, but never filled, so please ignore.
    - threshold
      
      Double threshold
      
      Threshold applied to the hitlist.
    - upregulatedCount
      
      Integer upregulatedCount
      
      Number of diffex probes in the Direction.UP hit list if available.
- Class ubic.gemma.model.analysis.expression.diff.ExpressionAnalysisResultSet extends FactorAssociatedAnalysisResultSet<DifferentialExpressionAnalysisResult> implements Serializable
  
  serialVersionUID:
  
  7226901182513177574L
  - Serialized Fields
    - analysis
      
      DifferentialExpressionAnalysis analysis
    - baselineGroup
      
      FactorValue baselineGroup
    - hitListSizes
      
      Set<HitListSize> hitListSizes
    - numberOfGenesTested
      
      Integer numberOfGenesTested
    - numberOfProbesTested
      
      Integer numberOfProbesTested
    - pvalueDistribution
      
      PvalueDistribution pvalueDistribution
    - results
      
      Set<DifferentialExpressionAnalysisResult> results
- Class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysis extends ExpressionAnalysis implements Serializable
  
  serialVersionUID:
  
  -2588180973962410595L
  - Serialized Fields
    - numGenesAnalyzed
      
      Integer numGenesAnalyzed
    - qvalueThresholdForStorage
      
      Double qvalueThresholdForStorage
    - results
      
      Set<GeneDifferentialExpressionMetaAnalysisResult> results
    - resultSetsIncluded
      
      Set<ExpressionAnalysisResultSet> resultSetsIncluded
- Class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisDetailValueObject extends Object implements Serializable
  
  serialVersionUID:
  
  3868004995989355452L
  - Serialized Fields
    - includedResultSetsInfo
      
      Collection<IncludedResultSetInfoValueObject> includedResultSetsInfo
    - numGenesAnalyzed
      
      Integer numGenesAnalyzed
    - results
      
      Collection<GeneDifferentialExpressionMetaAnalysisResultValueObject> results
- Class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisResult extends Object implements Serializable
  
  serialVersionUID:
  
  -6553250926957951550L
  - Serialized Fields
    - gene
      
      Gene gene
    - id
      
      Long id
    - meanLogFoldChange
      
      Double meanLogFoldChange
    - metaPvalue
      
      Double metaPvalue
    - metaPvalueRank
      
      Double metaPvalueRank
    - metaQvalue
      
      Double metaQvalue
    - resultsUsed
      
      Set<DifferentialExpressionAnalysisResult> resultsUsed
    - upperTail
      
      Boolean upperTail
- Class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisResultValueObject extends Object implements Serializable
  
  serialVersionUID:
  
  6099286095885830140L
  - Serialized Fields
    - geneName
      
      String geneName
    - geneSymbol
      
      String geneSymbol
    - metaPvalue
      
      Double metaPvalue
    - metaQvalue
      
      Double metaQvalue
    - upperTail
      
      Boolean upperTail
- Class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject extends Object implements Serializable
  
  serialVersionUID:
  
  -1856182824742323129L
  - Serialized Fields
    - description
      
      String description
    - diffExpressionEvidence
      
      DiffExpressionEvidenceValueObject diffExpressionEvidence
    - id
      
      Long id
    - isEditable
      
      boolean isEditable
    - isOwnedByCurrentUser
      
      boolean isOwnedByCurrentUser
    - isPublic
      
      boolean isPublic
    - isShared
      
      boolean isShared
    - name
      
      String name
    - numGenesAnalyzed
      
      Integer numGenesAnalyzed
    - numResults
      
      Integer numResults
    - numResultSetsIncluded
      
      Integer numResultSetsIncluded
- Class ubic.gemma.model.analysis.expression.diff.HitListSize extends Object implements Serializable
  
  serialVersionUID:
  
  -6398621486105806034L
  - Serialized Fields
    - direction
      
      Direction direction
    - id
      
      Long id
    - numberOfGenes
      
      Integer numberOfGenes
    - numberOfProbes
      
      Integer numberOfProbes
    - thresholdQvalue
      
      Double thresholdQvalue
- Class ubic.gemma.model.analysis.expression.diff.IncludedResultSetInfoValueObject extends Object implements Serializable
  
  serialVersionUID:
  
  -4660741839991839187L
  - Serialized Fields
    - analysisId
      
      Long analysisId
    - experimentId
      
      Long experimentId
    - resultSetId
      
      Long resultSetId
- Class ubic.gemma.model.analysis.expression.diff.PvalueDistribution extends Object implements Serializable
  
  serialVersionUID:
  
  -4783507721422402289L
  - Serialized Fields
    - binCounts
      
      byte[] binCounts
    - id
      
      Long id
    - numBins
      
      Integer numBins
Package ubic.gemma.model.analysis.expression.pca
- Class ubic.gemma.model.analysis.expression.pca.Eigenvalue extends Object implements Serializable
  
  serialVersionUID:
  
  -6675153115416719020L
  - Serialized Fields
    - componentNumber
      
      Integer componentNumber
    - id
      
      Long id
    - value
      
      Double value
    - varianceFraction
      
      Double varianceFraction
- Class ubic.gemma.model.analysis.expression.pca.Eigenvector extends Object implements Serializable
  
  serialVersionUID:
  
  5122763307995485698L
  - Serialized Fields
    - componentNumber
      
      Integer componentNumber
    - id
      
      Long id
    - vector
      
      byte[] vector
- Class ubic.gemma.model.analysis.expression.pca.PrincipalComponentAnalysis extends SingleExperimentAnalysis implements Serializable
  
  serialVersionUID:
  
  7046708934564931841L
  - Serialized Fields
    - bioAssayDimension
      
      BioAssayDimension bioAssayDimension
    - eigenValues
      
      Set<Eigenvalue> eigenValues
    - eigenVectors
      
      Set<Eigenvector> eigenVectors
    - maxNumProbesPerComponent
      
      Integer maxNumProbesPerComponent
    - numComponentsStored
      
      Integer numComponentsStored
    - probeLoadings
      
      Set<ProbeLoading> probeLoadings
- Class ubic.gemma.model.analysis.expression.pca.ProbeLoading extends Object implements Serializable
  
  serialVersionUID:
  
  -2328381846024383305L
  - Serialized Fields
    - componentNumber
      
      Integer componentNumber
    - id
      
      Long id
    - loading
      
      Double loading
    - loadingRank
      
      Integer loadingRank
    - probe
      
      CompositeSequence probe
Package ubic.gemma.model.association
- Class ubic.gemma.model.association.BioSequence2GeneProduct extends Object implements Serializable
  
  serialVersionUID:
  
  8361432485953690591L
  - Serialized Fields
    - bioSequence
      
      BioSequence bioSequence
    - geneProduct
      
      GeneProduct geneProduct
    - id
      
      Long id
    - overlap
      
      Integer overlap
    - score
      
      Double score
    - sourceAnalysis
      
      Analysis sourceAnalysis
    - specificity
      
      Double specificity
    - threePrimeDistance
      
      Long threePrimeDistance
    - threePrimeDistanceMeasurementMethod
      
      ThreePrimeDistanceMethod threePrimeDistanceMeasurementMethod
- Class ubic.gemma.model.association.Gene2GeneAssociation extends Object implements Serializable
  
  serialVersionUID:
  
  -322186137554528167L
  - Serialized Fields
    - firstGene
      
      Gene firstGene
    - id
      
      Long id
    - secondGene
      
      Gene secondGene
- Class ubic.gemma.model.association.Gene2GeneIdAssociation extends Object implements Serializable
  
  serialVersionUID:
  
  3735868529324395241L
  - Serialized Fields
    - firstGene
      
      Long firstGene
    - id
      
      Long id
    - secondGene
      
      Long secondGene
- Class ubic.gemma.model.association.Gene2GOAssociation extends Gene2OntologyEntryAssociationImpl implements Serializable
  
  serialVersionUID:
  
  -710930089869830248L
  - Serialized Fields
    - evidenceCode
      
      GOEvidenceCode evidenceCode
- Class ubic.gemma.model.association.Gene2OntologyEntryAssociation extends Object implements Serializable
  
  serialVersionUID:
  
  -6097916172357707966L
  - Serialized Fields
    - gene
      
      Gene gene
    - id
      
      Long id
    - ontologyEntry
      
      Characteristic ontologyEntry
- Class ubic.gemma.model.association.Gene2OntologyEntryAssociationImpl extends Gene2OntologyEntryAssociation implements Serializable
  
  serialVersionUID:
  
  -7343879715589606942L
- Class ubic.gemma.model.association.ReferenceAssociation extends BioSequence2GeneProduct implements Serializable
  
  serialVersionUID:
  
  -6338026603382275762L
  - Serialized Fields
    - referencedDatabaseEntry
      
      DatabaseEntry referencedDatabaseEntry
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
      
      we need to have the genes here as a denormalization. We store these links both ways for efficiency.
    - id
      
      Long id
    - linkId
      
      Long linkId
      
      Note that we do not make this a proper link to a Gene2GeneCoexpression entity, for simplicity, so we cant do some hql stuff.
    - secondGene
      
      Long secondGene
- Class ubic.gemma.model.association.coexpression.Gene2GeneCoexpression extends Gene2GeneIdAssociation implements Serializable
  
  serialVersionUID:
  
  6088623734153830393L
  - Serialized Fields
    - numDataSetsSupporting
      
      Integer numDataSetsSupporting
    - positiveCorrelation
      
      Boolean positiveCorrelation
      
      If true, this represents a positive correlation; false indicates it is negative (sorry, 0 doesn't exist, I guess we could use null).
    - supportDetails
      
      SupportDetails supportDetails
- Class ubic.gemma.model.association.coexpression.GeneCoexpressionNodeDegree extends Object implements Serializable
  
  serialVersionUID:
  
  -1456064687251594963L
  - Serialized Fields
    - geneId
      
      Long geneId
    - linkCountsNegative
      
      byte[] linkCountsNegative
      
      Byte format of a int array. the first value is 0; the other values is the number of links at support=index. Unlike the relativeLinkRanks these are not cumulative.
    - linkCountsPositive
      
      byte[] linkCountsPositive
      
      Byte format of a int array. the first value is 0; the other values is the number of links at support=index. Unlike the relativeLinkRanks these are not cumulative.
    - relativeLinkRanksNegative
      
      byte[] relativeLinkRanksNegative
      
      Normalized rank values for the node degree of this gene at each threshold of support; that is, "at or above" the threshold. The ranking is among all other genes for the taxon; the normalization factor is the node degree of the most hubby gene (computed separately for each support threshold).
    - relativeLinkRanksPositive
      
      byte[] relativeLinkRanksPositive
      
      Normalized rank values for the node degree of this gene at each threshold of support; that is, "at or above" the threshold. The ranking is among all other genes for the taxon; the normalization factor is the node degree of the most hubby gene (computed separately for each support threshold).
- 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.blacklist
- Class ubic.gemma.model.blacklist.BlacklistedEntity extends AbstractDescribable implements Serializable
  - Serialized Fields
    - externalAccession
      
      DatabaseEntry externalAccession
      
      The external accession
    - reason
      
      String reason
      
      The reason the entity was blacklisted.
    - shortName
      
      String shortName
- Class ubic.gemma.model.blacklist.BlacklistedExperiment extends BlacklistedEntity implements Serializable
- Class ubic.gemma.model.blacklist.BlacklistedPlatform extends BlacklistedEntity implements Serializable
- Class ubic.gemma.model.blacklist.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.common
- Class ubic.gemma.model.common.BaseValueObject extends Object implements Serializable
  
  serialVersionUID:
  
  -5290562301261202171L
  - Serialized Fields
    - accessDenied
      
      boolean accessDenied
    - errorFound
      
      boolean errorFound
    - objectAlreadyRemoved
      
      boolean objectAlreadyRemoved
    - userNotLoggedIn
      
      boolean userNotLoggedIn
    - valueObject
      
      Serializable valueObject
- Class ubic.gemma.model.common.IdentifiableValueObject extends Object implements Serializable
  - Serialized Fields
    - id
      
      Long id
Package ubic.gemma.model.common.auditAndSecurity
- Class ubic.gemma.model.common.auditAndSecurity.AbstractAuditable extends AbstractDescribable implements Serializable
  
  serialVersionUID:
  
  2797229483150957490L
  - Serialized Fields
    - auditTrail
      
      AuditTrail auditTrail
- 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.curation
- Class ubic.gemma.model.common.auditAndSecurity.curation.AbstractCuratableValueObject extends IdentifiableValueObject<C extends Curatable> implements Serializable
  - Serialized Fields
    - curationNote
      
      String curationNote
    - lastNeedsAttentionEvent
      
      AuditEventValueObject lastNeedsAttentionEvent
    - lastNoteUpdateEvent
      
      AuditEventValueObject lastNoteUpdateEvent
    - lastTroubledEvent
      
      AuditEventValueObject lastTroubledEvent
    - lastUpdated
      
      Date lastUpdated
    - needsAttention
      
      Boolean needsAttention
    - troubled
      
      Boolean troubled
- Class ubic.gemma.model.common.auditAndSecurity.curation.CurationDetails extends Object implements Serializable
  
  serialVersionUID:
  
  -3418540112052921387L
  - Serialized Fields
    - curationNote
      
      String curationNote
    - id
      
      Long id
    - lastNeedsAttentionEvent
      
      AuditEvent lastNeedsAttentionEvent
    - lastNoteUpdateEvent
      
      AuditEvent lastNoteUpdateEvent
    - lastTroubledEvent
      
      AuditEvent lastTroubledEvent
    - lastUpdated
      
      Date lastUpdated
    - needsAttention
      
      boolean needsAttention
    - troubled
      
      boolean troubled
Package ubic.gemma.model.common.auditAndSecurity.eventType
- Class ubic.gemma.model.common.auditAndSecurity.eventType.AlignmentBasedGeneMappingEvent extends ArrayDesignGeneMappingEvent implements Serializable
  
  serialVersionUID:
  
  7667960927701046528L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.AnalysisSuitabilityEvent extends AuditEventType implements Serializable
  
  serialVersionUID:
  
  7754007995197256846L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.AnnotationBasedGeneMappingEvent extends ArrayDesignGeneMappingEvent implements Serializable
  
  serialVersionUID:
  
  6216699496744292404L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.AnnotationEvent extends AuditEventType implements Serializable
  
  serialVersionUID:
  
  -7488448191665314917L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignAnalysisEvent extends AuditEventType implements Serializable
  
  serialVersionUID:
  
  -8391873112717801492L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignGeneMappingEvent extends ArrayDesignAnalysisEvent implements Serializable
  
  serialVersionUID:
  
  -7566135203525054499L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignMergeEvent extends ArrayDesignAnalysisEvent implements Serializable
  
  serialVersionUID:
  
  8243373027784116451L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignProbeRenamingEvent extends ArrayDesignAnalysisEvent implements Serializable
  
  serialVersionUID:
  
  -5458770150436736181L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignRepeatAnalysisEvent extends ArrayDesignAnalysisEvent implements Serializable
  
  serialVersionUID:
  
  -1315594279851821201L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignSequenceAnalysisEvent extends ArrayDesignAnalysisEvent implements Serializable
  
  serialVersionUID:
  
  8487897002282121437L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignSequenceRemoveEvent extends ArrayDesignAnalysisEvent implements Serializable
  
  serialVersionUID:
  
  -3044700012305059422L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignSequenceUpdateEvent extends ArrayDesignAnalysisEvent implements Serializable
  
  serialVersionUID:
  
  2502989996801972836L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignSubsumeCheckEvent extends ArrayDesignAnalysisEvent implements Serializable
  
  serialVersionUID:
  
  -6105886398033742202L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.AuditEventType extends Object implements Serializable
  
  serialVersionUID:
  
  -7397754091918396538L
  - Serialized Fields
    - id
      
      Long id
- Class ubic.gemma.model.common.auditAndSecurity.eventType.AutomatedAnnotationEvent extends AnnotationEvent implements Serializable
  
  serialVersionUID:
  
  8510568858539453569L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.BatchCorrectionEvent extends ExpressionExperimentAnalysisEvent implements Serializable
  
  serialVersionUID:
  
  -3061045506228031201L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.BatchInformationEvent extends ExpressionExperimentAnalysisEvent implements Serializable
- Class ubic.gemma.model.common.auditAndSecurity.eventType.BatchInformationFetchingEvent extends BatchInformationEvent implements Serializable
  
  serialVersionUID:
  
  4635587632131568136L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.BatchInformationMissingEvent extends BatchInformationEvent implements Serializable
- Class ubic.gemma.model.common.auditAndSecurity.eventType.BatchProblemsUpdateEvent extends ExpressionExperimentAnalysisEvent implements Serializable
  
  serialVersionUID:
  
  -3061045506228031201L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.BioMaterialMappingUpdate extends ExpressionExperimentAnalysisEvent implements Serializable
  
  serialVersionUID:
  
  -4390321148453980797L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.CommentedEvent extends AuditEventType implements Serializable
  
  serialVersionUID:
  
  -9053488530090657730L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.CurationDetailsEvent extends AuditEventType implements Serializable
  
  serialVersionUID:
  
  6621758826080039878L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.CurationNoteUpdateEvent extends CurationDetailsEvent implements Serializable
  
  serialVersionUID:
  
  -1180281595664872508L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.DataAddedEvent extends ExpressionExperimentAnalysisEvent implements Serializable
  
  serialVersionUID:
  
  -492849538043540166L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.DataRemovedEvent extends ExpressionExperimentAnalysisEvent implements Serializable
- Class ubic.gemma.model.common.auditAndSecurity.eventType.DataReplacedEvent extends ExpressionExperimentAnalysisEvent implements Serializable
  
  serialVersionUID:
  
  -3239733956797015820L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.DifferentialExpressionAnalysisEvent extends ExpressionExperimentAnalysisEvent implements Serializable
  
  serialVersionUID:
  
  -2254124666542924604L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.DifferentialExpressionSuitabilityEvent extends AnalysisSuitabilityEvent implements Serializable
  
  serialVersionUID:
  
  -3436468845066159993L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.DoesNotNeedAttentionEvent extends CurationDetailsEvent implements Serializable
  
  serialVersionUID:
  
  6425018808816856629L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.ExperimentalDesignUpdatedEvent extends AuditEventType implements Serializable
  
  serialVersionUID:
  
  6359338763821876809L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.ExpressionExperimentAnalysisEvent extends AuditEventType implements Serializable
  
  serialVersionUID:
  
  6359338763821876809L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.ExpressionExperimentPlatformSwitchEvent extends ExpressionExperimentAnalysisEvent implements Serializable
  
  serialVersionUID:
  
  2918272498309052073L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.ExpressionExperimentUpdateFromGEOEvent extends AuditEventType implements Serializable
  
  serialVersionUID:
  
  5823969791153895703L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.ExpressionExperimentVectorMergeEvent extends ExpressionExperimentAnalysisEvent implements Serializable
  
  serialVersionUID:
  
  3635469819668645913L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.FactorValueNeedsAttentionEvent extends NeedsAttentionEvent implements Serializable
- Class ubic.gemma.model.common.auditAndSecurity.eventType.FailedBatchInformationFetchingEvent extends BatchInformationFetchingEvent implements Serializable
- Class ubic.gemma.model.common.auditAndSecurity.eventType.FailedBatchInformationMissingEvent extends BatchInformationMissingEvent implements Serializable
  
  serialVersionUID:
  
  -3235885345623521195L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.FailedDataReplacedEvent extends DataReplacedEvent implements Serializable
  
  serialVersionUID:
  
  304758117763492676L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.FailedDifferentialExpressionAnalysisEvent extends NeedsAttentionEvent implements Serializable
  
  serialVersionUID:
  
  6904992064998125083L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.FailedLinkAnalysisEvent extends NeedsAttentionEvent implements Serializable
  
  serialVersionUID:
  
  1234186759038122633L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.FailedMeanVarianceUpdateEvent extends NeedsAttentionEvent implements Serializable
- Class ubic.gemma.model.common.auditAndSecurity.eventType.FailedMissingValueAnalysisEvent extends NeedsAttentionEvent implements Serializable
  
  serialVersionUID:
  
  -8827983770602337826L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.FailedPCAAnalysisEvent extends NeedsAttentionEvent implements Serializable
  
  serialVersionUID:
  
  -7055117029646665872L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.FailedProcessedVectorComputationEvent extends NeedsAttentionEvent implements Serializable
  
  serialVersionUID:
  
  -3296770035025801791L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.FailedSampleCorrelationAnalysisEvent extends NeedsAttentionEvent implements Serializable
- Class ubic.gemma.model.common.auditAndSecurity.eventType.GeeqEvent extends AuditEventType implements Serializable
  
  serialVersionUID:
  
  6621758826080039878L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.LinkAnalysisEvent extends ExpressionExperimentAnalysisEvent implements Serializable
  
  serialVersionUID:
  
  -9218026901325452759L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.MakePrivateEvent extends PermissionChangeEvent implements Serializable
  
  serialVersionUID:
  
  1858209889786173945L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.MakePublicEvent extends PermissionChangeEvent implements Serializable
  
  serialVersionUID:
  
  -2250506177437626685L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.ManualAnnotationEvent extends AnnotationEvent implements Serializable
  
  serialVersionUID:
  
  -4919680073334263746L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.MeanVarianceUpdateEvent extends ExpressionExperimentAnalysisEvent implements Serializable
- Class ubic.gemma.model.common.auditAndSecurity.eventType.MissingValueAnalysisEvent extends ExpressionExperimentAnalysisEvent implements Serializable
  
  serialVersionUID:
  
  -4000136638329943603L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.NeedsAttentionEvent extends CurationDetailsEvent implements Serializable
  
  serialVersionUID:
  
  -1180281595664872508L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.NotTroubledStatusFlagEvent extends CurationDetailsEvent implements Serializable
  
  serialVersionUID:
  
  -8586752080144045085L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.OutlierAnalysisEvent extends ExpressionExperimentAnalysisEvent implements Serializable
  
  serialVersionUID:
  
  681380361152118118L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.OutlierFoundAnalysisEvent extends OutlierAnalysisEvent implements Serializable
  
  serialVersionUID:
  
  -3797610069227351691L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.OutliersNotFoundAnalysisEvent extends OutlierAnalysisEvent implements Serializable
  
  serialVersionUID:
  
  -1857664606860041995L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.PCAAnalysisEvent extends ExpressionExperimentAnalysisEvent implements Serializable
  
  serialVersionUID:
  
  -7387174169412782003L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.PermissionChangeEvent extends AuditEventType implements Serializable
  
  serialVersionUID:
  
  -7205154783209555418L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.ProcessedVectorComputationEvent extends ExpressionExperimentAnalysisEvent implements Serializable
  
  serialVersionUID:
  
  3380481220417398475L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.RankComputationEvent extends ProcessedVectorComputationEvent implements Serializable
  
  serialVersionUID:
  
  7396366160834308993L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.ReleaseDetailsUpdateEvent extends VersionedEvent implements Serializable
- Class ubic.gemma.model.common.auditAndSecurity.eventType.ResetSuitabilityForDifferentialExpressionAnalysisEvent extends DifferentialExpressionSuitabilityEvent implements Serializable
  
  serialVersionUID:
  
  5909581992797452478L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.SampleCorrelationAnalysisEvent extends ExpressionExperimentAnalysisEvent implements Serializable
- Class ubic.gemma.model.common.auditAndSecurity.eventType.SampleRemovalEvent extends ExpressionExperimentAnalysisEvent implements Serializable
  
  serialVersionUID:
  
  6508357999103110838L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.SampleRemovalReversionEvent extends ExpressionExperimentAnalysisEvent implements Serializable
  
  serialVersionUID:
  
  -2893496636576496129L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.SingleBatchDeterminationEvent extends BatchInformationFetchingEvent implements Serializable
  
  serialVersionUID:
  
  -6544162258733474787L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.SingletonBatchInvalidEvent extends FailedBatchInformationFetchingEvent implements Serializable
  
  serialVersionUID:
  
  7917557159624872204L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.TooSmallDatasetLinkAnalysisEvent extends LinkAnalysisEvent implements Serializable
  
  serialVersionUID:
  
  3051344049635374788L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.TroubledStatusFlagEvent extends CurationDetailsEvent implements Serializable
  
  serialVersionUID:
  
  7335601529423635731L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.UninformativeFASTQHeadersForBatchingEvent extends FailedBatchInformationFetchingEvent implements Serializable
  
  serialVersionUID:
  
  8836148437542742955L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.UnsuitableForDifferentialExpressionAnalysisEvent extends DifferentialExpressionSuitabilityEvent implements Serializable
  
  serialVersionUID:
  
  4296161562091100967L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.VersionedEvent extends AuditEventType implements Serializable
Package ubic.gemma.model.common.description
- Class ubic.gemma.model.common.description.AnnotationValueObject extends IdentifiableValueObject<Characteristic> implements Serializable
  - Serialized Fields
    - className
      
      String className
    - classUri
      
      String classUri
    - description
      
      String description
    - evidenceCode
      
      String evidenceCode
    - objectClass
      
      String objectClass
    - parentDescription
      
      String parentDescription
    - parentLink
      
      String parentLink
    - parentName
      
      String parentName
    - parentOfParentDescription
      
      String parentOfParentDescription
    - parentOfParentLink
      
      String parentOfParentLink
    - parentOfParentName
      
      String parentOfParentName
    - termName
      
      String termName
    - termUri
      
      String termUri
- Class ubic.gemma.model.common.description.BibliographicReference extends AbstractDescribable implements Serializable
  
  serialVersionUID:
  
  5823969791153895703L
  - Serialized Fields
    - abstractText
      
      String abstractText
    - annotatedAbstract
      
      String annotatedAbstract
      
      Deprecated.
    - annotations
      
      Set<Characteristic> annotations
      
      Deprecated.
      never used
    - 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.
      do not rely on this field, it will be removed once the migration is completed.
      
      Indicate if this "old-style" characteristic has been migrated to a Statement. This is only meaningful for FactorValue characteristics.
    - originalValue
      
      String originalValue
      
      Stores the value this characteristic had before it was assigned a URI for the term.
    - 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
      
      child term from a root
    - numTimesUsed
      
      int numTimesUsed
    - ontologyUsed
      
      String ontologyUsed
      
      what Ontology uses this term
    - originalValue
      
      String originalValue
    - privateGeneCount
      
      long privateGeneCount
    - publicGeneCount
      
      long publicGeneCount
      
      number of occurrences in all genes
    - root
      
      boolean root
      
      root of a query
    - taxon
      
      String taxon
    - urlId
      
      String urlId
      
      id used by url on the client side
    - value
      
      String value
    - valueDefinition
      
      String valueDefinition
      
      The definition of the value, if it is an ontology term, as supplied by the ontology. If the value is free text, this will be empty
    - valueId
      
      String valueId
      
      A unique ontology identifier (i.e. IRI) for this characteristic.
    - valueUri
      
      String valueUri
- Class ubic.gemma.model.common.description.CitationValueObject extends Object implements Serializable
  - Serialized Fields
    - citation
      
      String citation
    - id
      
      Long id
      
      the DB id of the BibliographicReference being represented
    - 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
      
      Related external databases.
    - 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.measurement
- Class ubic.gemma.model.common.measurement.Measurement extends Object implements Serializable
  
  serialVersionUID:
  
  1833568047451431226L
  - Serialized Fields
    - id
      
      Long id
    - kindCV
      
      MeasurementKind kindCV
    - otherKind
      
      String otherKind
    - representation
      
      PrimitiveType representation
    - type
      
      MeasurementType type
    - unit
      
      Unit unit
    - value
      
      String value
- Class ubic.gemma.model.common.measurement.MeasurementValueObject extends IdentifiableValueObject<Measurement> implements Serializable
  - Serialized Fields
    - representation
      
      String representation
    - type
      
      String type
    - unit
      
      String unit
    - unitId
      
      Long unitId
    - value
      
      String value
- Class ubic.gemma.model.common.measurement.Unit extends Object implements Serializable
  
  serialVersionUID:
  
  6348133346610787608L
  - Serialized Fields
    - id
      
      Long id
    - unitNameCV
      
      String unitNameCV
Package ubic.gemma.model.common.protocol
- Class ubic.gemma.model.common.protocol.Protocol extends AbstractDescribable implements Serializable
  
  serialVersionUID:
  
  -1902891452989019766L
Package ubic.gemma.model.common.quantitationtype
- Class ubic.gemma.model.common.quantitationtype.QuantitationType extends AbstractDescribable implements Serializable
  
  serialVersionUID:
  
  -9139594736279728431L
  - Serialized Fields
    - generalType
      
      GeneralType generalType
    - isBackground
      
      boolean isBackground
      
      This will be false except for some Qts on two-colour platforms.
    - isBackgroundSubtracted
      
      boolean isBackgroundSubtracted
      
      True if this is explicitly background-subtracted by Gemma. This is not very important and would only apply to two-colour platforms since we don't background-subtract otherwise.
    - isBatchCorrected
      
      boolean isBatchCorrected
      
      Refers to batch correction by Gemma. This should only ever be true for the ProcessedData.
    - isMaskedPreferred
      
      boolean isMaskedPreferred
      
      Deprecated.
      this is useless as there can only be one QT for processed data per dataset.
      
      Indicate if this quantitation is the preferred for processed data.
    - isNormalized
      
      boolean isNormalized
      
      This is pretty confusing since we don't make clear what we mean by "normalized", so this isn't that useful. It might be wise to separate out "quantile normalized", but since we always quantile normalize ProcessedData, this isn't very useful.
    - isPreferred
      
      boolean isPreferred
      
      This is only useful for RawExpressionDataVectors; for the ProcessedData it is just confusing
    - isRatio
      
      boolean isRatio
    - isRecomputedFromRawData
      
      boolean isRecomputedFromRawData
      
      This is also confusing: it is an attempt to capture whether we just used the data from GEO (or whatever) or went back to raw CEL or fastq files.
    - representation
      
      PrimitiveType representation
    - scale
      
      ScaleType scale
    - type
      
      StandardQuantitationType type
- Class ubic.gemma.model.common.quantitationtype.QuantitationTypeValueObject extends IdentifiableValueObject<QuantitationType> implements Serializable
  
  serialVersionUID:
  
  7537853492100102404L
  - Serialized Fields
    - description
      
      String description
    - expressionExperimentId
      
      Long expressionExperimentId
      
      Associated expression experiment ID.
      This is unnecessary in the context of the RESTful API because vector types are always retrieved when the associated ExpressionExperiment is known.
    - generalType
      
      String generalType
    - isBackground
      
      Boolean isBackground
    - isBackgroundSubtracted
      
      Boolean isBackgroundSubtracted
    - isBatchCorrected
      
      Boolean isBatchCorrected
    - isMaskedPreferred
      
      Boolean isMaskedPreferred
    - isNormalized
      
      Boolean isNormalized
    - isPreferred
      
      Boolean isPreferred
    - isRatio
      
      Boolean isRatio
    - isRecomputedFromRawData
      
      Boolean isRecomputedFromRawData
    - name
      
      String name
    - representation
      
      String representation
    - scale
      
      String scale
    - type
      
      String type
    - vectorType
      
      String vectorType
      
      Vector type this QT is associated to.
      This only makes sense in the context of an associated EE.
Package ubic.gemma.model.common.search
- Class ubic.gemma.model.common.search.SearchSettings extends Object implements Serializable
  
  serialVersionUID:
  
  -982243911532743661L
  - Serialized Fields
    - fillResults
      
      boolean fillResults
      
      Indicate if results should be filled.
    - maxResults
      
      int maxResults
      
      Limit for the number of results per result type in SearchService.SearchResultMap.
      The default is relatively large and given by SearchSettings.DEFAULT_MAX_RESULTS_PER_RESULT_TYPE. Any value less than one indicate no limit.
    - mode
      
      SearchSettings.SearchMode mode
      
      Fast mode, return quickly.
    - platformConstraint
      
      ArrayDesign platformConstraint
    - query
      
      String query
      
      Processed query for performing a search.
    - resultTypes
      
      Set<Class<? extends Identifiable>> resultTypes
      
      Entities to retrieve.
    - 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.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
      
      Deprecated.
    - createDate
      
      Date createDate
    - dateCached
      
      String dateCached
    - description
      
      String description
    - designElementCount
      
      Integer designElementCount
    - expressionExperimentCount
      
      Long expressionExperimentCount
    - externalReferences
      
      Set<DatabaseEntryValueObject> externalReferences
      
      Main external reference.
    - hasBlatAssociations
      
      Boolean hasBlatAssociations
    - hasGeneAssociations
      
      Boolean hasGeneAssociations
    - hasSequenceAssociations
      
      Boolean hasSequenceAssociations
    - isAffymetrixAltCdf
      
      Boolean isAffymetrixAltCdf
    - isMerged
      
      Boolean isMerged
      
      Indicates this array design is the merger of other array designs.
    - isMergee
      
      Boolean isMergee
      
      Indicates that this array design has been merged into another.
    - isSubsumed
      
      Boolean isSubsumed
      
      Indicate if this array design is subsumed by some other array design.
    - isSubsumer
      
      Boolean isSubsumer
      
      Indicates if this array design subsumes some other array design(s)
    - lastGeneMapping
      
      Date lastGeneMapping
    - lastRepeatMask
      
      Date lastRepeatMask
    - lastSequenceAnalysis
      
      Date lastSequenceAnalysis
    - lastSequenceUpdate
      
      Date lastSequenceUpdate
    - name
      
      String name
    - numGenes
      
      String numGenes
      
      The number of unique genes that this array design maps to.
    - numProbeAlignments
      
      String numProbeAlignments
      
      The number of probes that have BLAT alignments.
    - numProbeSequences
      
      String numProbeSequences
      
      The number of probes that map to bioSequences.
    - numProbesToGenes
      
      String numProbesToGenes
      
      The number of probes that map to genes. This count includes probe-aligned regions, predicted genes, and known genes.
    - releaseUrl
      
      URL releaseUrl
    - releaseVersion
      
      String releaseVersion
    - shortName
      
      String shortName
    - switchedExpressionExperimentCount
      
      Long switchedExpressionExperimentCount
    - taxonObject
      
      TaxonValueObject taxonObject
    - technologyType
      
      String technologyType
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
      
      For RNA-seq representation of representative headers from the FASTQ file(s). If there is more than on FASTQ file, this string will contain multiple newline-delimited headers.
    - isOutlier
      
      Boolean isOutlier
    - metadata
      
      String metadata
    - originalPlatform
      
      ArrayDesign originalPlatform
      
      If the sample data was switched to another platform, this is what it was originally.
    - 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
      
      If this is a subset, or a padded, BioAssayDimensionValueObject, the sourceBioAssayDimension is the original.
- 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
    - expressionExperiment
      
      ExpressionExperiment expressionExperiment
    - 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
- 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
      
      Securable securityOwner
    - variances
      
      byte[] variances
- Class ubic.gemma.model.expression.bioAssayData.ProcessedExpressionDataVector extends DesignElementDataVector implements Serializable
  
  serialVersionUID:
  
  -3948846630785289034L
  - Serialized Fields
    - rankByMax
      
      Double rankByMax
    - rankByMean
      
      Double rankByMean
- Class ubic.gemma.model.expression.bioAssayData.RawExpressionDataVector extends DesignElementDataVector implements Serializable
  
  serialVersionUID:
  
  -7410374297463625206L
- Class ubic.gemma.model.expression.bioAssayData.SlicedDoubleVectorValueObject extends DoubleVectorValueObject implements Serializable
  - Serialized Fields
    - sourceVectorId
      
      Long sourceVectorId
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
      
      Indicate if this is using the BioMaterialValueObject.fVBasicVOs or BioMaterialValueObject.factorValueObjects for representing factor values.
    - bioAssayIds
      
      Collection<Long> bioAssayIds
      
      Related BioAssay IDs.
    - characteristicOriginalValues
      
      Map<String,String> characteristicOriginalValues
      
      Map of categories to original text values (for this biomaterial). This is only used for display and will only be populated if the original value is different from the value.
    - characteristics
      
      Collection<CharacteristicValueObject> characteristics
    - characteristicValues
      
      Map<String,String> characteristicValues
    - description
      
      String description
    - factorIdToFactorValueId
      
      Map<String,String> factorIdToFactorValueId
      
      Map of factor ids (factor232) to factor value (id or the actual value) for this biomaterial.
    - factors
      
      Map<String,String> factors
      
      Deprecated.
      
      Map of ids (factor232) to a representation of the factor (e.g., the name).
    - factorValueObjects
      
      Collection<FactorValueValueObject> factorValueObjects
    - factorValues
      
      Map<String,String> factorValues
      
      Map of ids (fv133) to a representation of the value (for this biomaterial.)
    - fastqHeaders
      
      String fastqHeaders
    - 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.designElement
- Class ubic.gemma.model.expression.designElement.CompositeSequence extends AbstractDescribable implements Serializable
  
  serialVersionUID:
  
  -3859507822452159349L
  - Serialized Fields
    - arrayDesign
      
      ArrayDesign arrayDesign
    - biologicalCharacteristic
      
      BioSequence biologicalCharacteristic
- Class ubic.gemma.model.expression.designElement.CompositeSequenceValueObject extends IdentifiableValueObject<CompositeSequence> implements Serializable
  
  serialVersionUID:
  
  4915680501039784666L
  - Serialized Fields
    - arrayDesign
      
      ArrayDesignValueObject arrayDesign
    - description
      
      String description
    - geneMappingSummaries
      
      Collection<GeneMappingSummary> geneMappingSummaries
    - name
      
      String name
Package ubic.gemma.model.expression.experiment
- Class ubic.gemma.model.expression.experiment.AbstractFactorValueValueObject extends IdentifiableValueObject<FactorValue> implements Serializable
  - Serialized Fields
    - characteristics
      
      List<CharacteristicValueObject> characteristics
      
      The characteristics associated with this factor value.
    - experimentalFactorCategory
      
      CharacteristicValueObject experimentalFactorCategory
      
      The experiment factor category.
    - experimentalFactorId
      
      Long experimentalFactorId
      
      The ID of the experimental factor this factor value belongs to.
    - measurement
      
      MeasurementValueObject measurement
      
      The measurement associated with this factor value.
    - ontologyId
      
      String ontologyId
      
      A unique ontology identifier (i.e. IRI) for this factor value.
    - statements
      
      List<StatementValueObject> statements
      
      The statements associated with this factor value.
    - summary
      
      String summary
      
      Human-readable summary of the factor value.
- Class ubic.gemma.model.expression.experiment.BioAssaySet extends Investigation implements Serializable
  
  serialVersionUID:
  
  2368063046639481521L
  - Serialized Fields
    - accession
      
      DatabaseEntry accession
    - bioAssays
      
      Set<BioAssay> bioAssays
- Class ubic.gemma.model.expression.experiment.ExperimentalDesign extends AbstractDescribable implements Serializable
  
  serialVersionUID:
  
  1734101852541885497L
  - Serialized Fields
    - experimentalFactors
      
      Set<ExperimentalFactor> experimentalFactors
    - normalizationDescription
      
      String normalizationDescription
    - qualityControlDescription
      
      String qualityControlDescription
    - replicateDescription
      
      String replicateDescription
    - types
      
      Set<Characteristic> types
- Class ubic.gemma.model.expression.experiment.ExperimentalFactor extends AbstractDescribable implements Serializable
  
  serialVersionUID:
  
  4615731059510436891L
  - Serialized Fields
    - annotations
      
      Set<Characteristic> annotations
      
      Deprecated.
    - category
      
      Characteristic category
    - experimentalDesign
      
      ExperimentalDesign experimentalDesign
    - factorValues
      
      Set<FactorValue> factorValues
    - securityOwner
      
      ExpressionExperiment securityOwner
    - type
      
      FactorType type
- Class ubic.gemma.model.expression.experiment.ExperimentalFactorValueObject extends IdentifiableValueObject<ExperimentalFactor> implements Serializable
  
  serialVersionUID:
  
  -2615804031123874251L
  - Serialized Fields
    - category
      
      String category
    - categoryUri
      
      String categoryUri
    - description
      
      String description
    - factorValues
      
      String factorValues
      
      Deprecated.
    - name
      
      String name
    - type
      
      String type
    - values
      
      Collection<FactorValueValueObject> values
- Class ubic.gemma.model.expression.experiment.ExpressionExperiment extends BioAssaySet implements Serializable
  
  serialVersionUID:
  
  -1342753625018841735L
  - Serialized Fields
    - allCharacteristics
      
      Set<Characteristic> allCharacteristics
    - batchConfound
      
      String batchConfound
      
      A string describing the batch confound if a batch effect is present and confounded with one of the experimental factor.
    - batchEffect
      
      BatchEffectType batchEffect
      
      Type of batch effect detected or corrected for. See BatchEffectType enum for possible values.
    - batchEffectStatistics
      
      String batchEffectStatistics
      
      Summary statistics of the batch effect, if present.
    - 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
      
      If this experiment was split off of a larger experiment, link to its relatives.
    - 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
      
      FIXME: rename this to hasUsableBatchInformation
    - 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
      
      If modifying the set is constrained by existing analyses.
    - name
      
      String name
    - numWithCoexpressionAnalysis
      
      Integer numWithCoexpressionAnalysis
    - numWithDifferentialExpressionAnalysis
      
      Integer numWithDifferentialExpressionAnalysis
    - shared
      
      boolean shared
    - size
      
      Integer size
    - taxonId
      
      Long taxonId
    - taxonName
      
      String taxonName
    - userCanWrite
      
      boolean userCanWrite
    - userOwned
      
      boolean userOwned
- Class ubic.gemma.model.expression.experiment.ExpressionExperimentSubSet extends BioAssaySet implements Serializable
  
  serialVersionUID:
  
  -1880425342951467283L
  - Serialized Fields
    - sourceExperiment
      
      ExpressionExperiment sourceExperiment
- Class ubic.gemma.model.expression.experiment.ExpressionExperimentSubsetValueObject extends ExpressionExperimentValueObject implements Serializable
  - Serialized Fields
    - sourceExperiment
      
      Long sourceExperiment
    - sourceExperimentShortName
      
      String sourceExperimentShortName
- Class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject extends AbstractCuratableValueObject<ExpressionExperiment> implements Serializable
  
  serialVersionUID:
  
  -6861385216096602508L
  - Serialized Fields
    - accession
      
      String accession
    - arrayDesignCount
      
      Long arrayDesignCount
    - batchConfound
      
      String batchConfound
    - batchEffect
      
      String batchEffect
      
      Batch effect type. See BatchEffectType enum for possible values.
    - batchEffectStatistics
      
      String batchEffectStatistics
      
      Summary statistics of a batch effect is present.
    - bioMaterialCount
      
      Integer bioMaterialCount
    - currentUserHasWritePermission
      
      Boolean currentUserHasWritePermission
    - currentUserIsOwner
      
      Boolean currentUserIsOwner
    - description
      
      String description
    - experimentalDesign
      
      Long experimentalDesign
    - externalDatabase
      
      String externalDatabase
    - externalDatabaseUri
      
      String externalDatabaseUri
    - externalUri
      
      String externalUri
    - geeq
      
      GeeqValueObject geeq
    - isPublic
      
      Boolean isPublic
    - isShared
      
      Boolean isShared
    - metadata
      
      String metadata
    - name
      
      String name
    - numberOfBioAssays
      
      Integer numberOfBioAssays
    - processedExpressionVectorCount
      
      Integer processedExpressionVectorCount
    - shortName
      
      String shortName
    - source
      
      String source
    - suitableForDEA
      
      Boolean suitableForDEA
    - taxonObject
      
      TaxonValueObject taxonObject
      
      FIXME: this should be named simply "taxon", but that field is already taken for Gemma Web, see ExpressionExperimentValueObject.getTaxon().
    - technologyType
      
      String technologyType
- Class ubic.gemma.model.expression.experiment.FactorValue extends Object implements Serializable
  
  serialVersionUID:
  
  -3783172994360698631L
  - Serialized Fields
    - characteristics
      
      Set<Statement> characteristics
    - experimentalFactor
      
      ExperimentalFactor experimentalFactor
    - id
      
      Long id
    - isBaseline
      
      Boolean isBaseline
    - measurement
      
      Measurement measurement
    - needsAttention
      
      boolean needsAttention
    - oldStyleCharacteristics
      
      Set<Characteristic> oldStyleCharacteristics
      
      Deprecated.
    - securityOwner
      
      ExpressionExperiment securityOwner
    - value
      
      String value
      
      Deprecated.
- Class ubic.gemma.model.expression.experiment.FactorValueBasicValueObject extends AbstractFactorValueValueObject implements Serializable
  
  serialVersionUID:
  
  3378801249808036785L
  - Serialized Fields
    - value
      
      String value
      
      Deprecated.
      use either #getCharacteristics() or #getMeasurement()
- Class ubic.gemma.model.expression.experiment.FactorValueValueObject extends AbstractFactorValueValueObject implements Serializable
  
  serialVersionUID:
  
  3378801249808036785L
  - Serialized Fields
    - category
      
      String category
      
      Deprecated.
    - categoryUri
      
      String categoryUri
      
      Deprecated.
    - charId
      
      Long charId
      
      Deprecated.
      
      It could be the id of the measurement if there is no characteristic.
    - factorId
      
      Long factorId
      
      Deprecated.
      
      ID of the experimental factor this FV belongs to.
    - needsAttention
      
      Boolean needsAttention
      
      Deprecated.
    - object
      
      String object
      
      Deprecated.
    - objectUri
      
      String objectUri
      
      Deprecated.
    - predicate
      
      String predicate
      
      Deprecated.
    - predicateUri
      
      String predicateUri
      
      Deprecated.
    - secondObject
      
      String secondObject
      
      Deprecated.
    - secondObjectUri
      
      String secondObjectUri
      
      Deprecated.
    - secondPredicate
      
      String secondPredicate
      
      Deprecated.
    - secondPredicateUri
      
      String secondPredicateUri
      
      Deprecated.
    - value
      
      String value
      
      Deprecated.
    - valueUri
      
      String valueUri
      
      Deprecated.
- Class ubic.gemma.model.expression.experiment.FreeTextExpressionExperimentResultsValueObject extends SessionBoundExpressionExperimentSetValueObject implements Serializable
  
  serialVersionUID:
  
  3557304710219740029L
  - Serialized Fields
    - queryString
      
      String queryString
- Class ubic.gemma.model.expression.experiment.Geeq extends Object implements Serializable
  
  serialVersionUID:
  
  4783171234360698630L
  - Serialized Fields
    - batchCorrected
      
      boolean batchCorrected
    - corrMatIssues
      
      byte corrMatIssues
    - detectedQualityScore
      
      double detectedQualityScore
    - detectedSuitabilityScore
      
      double detectedSuitabilityScore
    - id
      
      Long id
    - manualBatchConfoundActive
      
      boolean manualBatchConfoundActive
    - manualBatchEffectActive
      
      boolean manualBatchEffectActive
    - manualHasBatchConfound
      
      boolean manualHasBatchConfound
    - manualHasNoBatchEffect
      
      boolean manualHasNoBatchEffect
    - manualHasStrongBatchEffect
      
      boolean manualHasStrongBatchEffect
    - manualQualityOverride
      
      boolean manualQualityOverride
    - manualQualityScore
      
      double manualQualityScore
    - manualSuitabilityOverride
      
      boolean manualSuitabilityOverride
    - manualSuitabilityScore
      
      double manualSuitabilityScore
    - noVectors
      
      boolean noVectors
    - otherIssues
      
      String otherIssues
    - qScoreBatchConfound
      
      double qScoreBatchConfound
    - qScoreBatchEffect
      
      double qScoreBatchEffect
    - qScoreBatchInfo
      
      double qScoreBatchInfo
    - qScoreOutliers
      
      double qScoreOutliers
    - qScorePlatformsTech
      
      double qScorePlatformsTech
    - qScoreReplicates
      
      double qScoreReplicates
    - qScoreSampleCorrelationVariance
      
      double qScoreSampleCorrelationVariance
    - qScoreSampleMeanCorrelation
      
      double qScoreSampleMeanCorrelation
    - qScoreSampleMedianCorrelation
      
      double qScoreSampleMedianCorrelation
    - replicatesIssues
      
      byte replicatesIssues
    - sScoreAvgPlatformPopularity
      
      double sScoreAvgPlatformPopularity
    - sScoreAvgPlatformSize
      
      double sScoreAvgPlatformSize
    - sScoreMissingValues
      
      double sScoreMissingValues
    - sScorePlatformAmount
      
      double sScorePlatformAmount
    - sScorePlatformsTechMulti
      
      double sScorePlatformsTechMulti
    - sScorePublication
      
      double sScorePublication
    - sScoreRawData
      
      double sScoreRawData
    - sScoreSampleSize
      
      double sScoreSampleSize
- Class ubic.gemma.model.expression.experiment.GeeqAdminValueObject extends GeeqValueObject implements Serializable
  - Serialized Fields
    - detectedQualityScore
      
      double detectedQualityScore
    - detectedSuitabilityScore
      
      double detectedSuitabilityScore
    - manualBatchConfoundActive
      
      boolean manualBatchConfoundActive
    - manualBatchEffectActive
      
      boolean manualBatchEffectActive
    - manualHasBatchConfound
      
      boolean manualHasBatchConfound
    - manualHasNoBatchEffect
      
      boolean manualHasNoBatchEffect
    - manualHasStrongBatchEffect
      
      boolean manualHasStrongBatchEffect
    - manualQualityOverride
      
      boolean manualQualityOverride
    - manualQualityScore
      
      double manualQualityScore
    - manualSuitabilityOverride
      
      boolean manualSuitabilityOverride
    - manualSuitabilityScore
      
      double manualSuitabilityScore
    - otherIssues
      
      String otherIssues
    - qScoreBatchConfound
      
      double qScoreBatchConfound
    - qScoreBatchEffect
      
      double qScoreBatchEffect
- Class ubic.gemma.model.expression.experiment.GeeqValueObject extends IdentifiableValueObject<Geeq> implements Serializable
  - Serialized Fields
    - batchCorrected
      
      boolean batchCorrected
    - corrMatIssues
      
      byte corrMatIssues
    - noVectors
      
      boolean noVectors
    - publicQualityScore
      
      double publicQualityScore
    - publicSuitabilityScore
      
      double publicSuitabilityScore
    - qScoreBatchInfo
      
      double qScoreBatchInfo
    - qScoreOutliers
      
      double qScoreOutliers
    - qScorePlatformsTech
      
      double qScorePlatformsTech
    - qScorePublicBatchConfound
      
      double qScorePublicBatchConfound
    - qScorePublicBatchEffect
      
      double qScorePublicBatchEffect
    - qScoreReplicates
      
      double qScoreReplicates
    - qScoreSampleCorrelationVariance
      
      double qScoreSampleCorrelationVariance
    - qScoreSampleMeanCorrelation
      
      double qScoreSampleMeanCorrelation
    - qScoreSampleMedianCorrelation
      
      double qScoreSampleMedianCorrelation
    - replicatesIssues
      
      byte replicatesIssues
    - sScoreAvgPlatformPopularity
      
      double sScoreAvgPlatformPopularity
    - sScoreAvgPlatformSize
      
      double sScoreAvgPlatformSize
    - sScoreMissingValues
      
      double sScoreMissingValues
    - sScorePlatformAmount
      
      double sScorePlatformAmount
    - sScorePlatformsTechMulti
      
      double sScorePlatformsTechMulti
    - sScorePublication
      
      double sScorePublication
    - sScoreRawData
      
      double sScoreRawData
    - sScoreSampleSize
      
      double sScoreSampleSize
- Class ubic.gemma.model.expression.experiment.SessionBoundExpressionExperimentSetValueObject extends ExpressionExperimentSetValueObject implements Serializable
  
  serialVersionUID:
  
  2068650886972222818L
  - Serialized Fields
    - modified
      
      boolean modified
- Class ubic.gemma.model.expression.experiment.Statement extends Characteristic implements Serializable
  - Serialized Fields
    - object
      
      String object
      
      The object of the statement.
    - objectUri
      
      String objectUri
    - predicate
      
      String predicate
      
      The predicate of the statement.
    - predicateUri
      
      String predicateUri
      
      The predicate URI of the statement.
    - secondObject
      
      String secondObject
      
      The second object.
    - secondObjectUri
      
      String secondObjectUri
    - secondPredicate
      
      String secondPredicate
      
      The second predicate.
    - 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
      
      A unique ontology identifier (i.e. IRI) for this object.
    - 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
      
      A unique ontology identifier (i.e. IRI) for this subject.
    - 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.FreeTextGeneResultsValueObject extends SessionBoundGeneSetValueObject implements Serializable
  
  serialVersionUID:
  
  3557304710219740029L
  - Serialized Fields
    - queryString
      
      String queryString
- 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
      
      Indicate if this GeneProduct is dummy.
      Dummy GeneProduct are not listed in the Gene.getProducts() associations.
    - exons
      
      Set<PhysicalLocation> exons
      
      Only used in transient instances in sequence analysis. The entity relation in the database is never used and will be removed.
    - 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
      
      Gene IDs part of this gene set.
    - 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
      
      Gene aliases, sorted alphabetically.
    - associatedExperimentCount
      
      Integer associatedExperimentCount
      
      How many experiments "involve" (manipulate, etc.) this gene
    - compositeSequenceCount
      
      Integer compositeSequenceCount
    - description
      
      String description
    - ensemblId
      
      String ensemblId
    - geneSets
      
      Collection<GeneSetValueObject> geneSets
    - homologues
      
      Collection<GeneValueObject> homologues
    - includeTaxon
      
      boolean includeTaxon
    - isQuery
      
      Boolean isQuery
      
      Was this gene directly used in a query? Or is it inferred somehow. The default is true, use this when you need to differentiate
    - multifunctionalityRank
      
      Double multifunctionalityRank
    - name
      
      String name
    - ncbiId
      
      Integer ncbiId
    - nodeDegreeNegRanks
      
      double[] nodeDegreeNegRanks
    - nodeDegreePosRanks
      
      double[] nodeDegreePosRanks
    - nodeDegreesNeg
      
      int[] nodeDegreesNeg
      
      Array containing number of links supported by 0,1,2, .... data sets (value in first index is always 0) for negative correlation coexpression
    - nodeDegreesPos
      
      int[] nodeDegreesPos
      
      Array containing number of links supported by 0,1,2, .... data sets (value in first index is always 0) for positive coexpression
    - 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.GOGroupValueObject extends SessionBoundGeneSetValueObject implements Serializable
  
  serialVersionUID:
  
  -185326197992950287L
  - Serialized Fields
    - goId
      
      String goId
    - searchTerm
      
      String searchTerm
- 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
- Class ubic.gemma.model.genome.gene.PhenotypeGroupValueObject extends SessionBoundGeneSetValueObject implements Serializable
  
  serialVersionUID:
  
  -7264201170714207356L
  - Serialized Fields
    - phenotypeCategory
      
      String phenotypeCategory
    - phenotypeName
      
      String phenotypeName
    - searchTerm
      
      String searchTerm
- Class ubic.gemma.model.genome.gene.SessionBoundGeneSetValueObject extends GeneSetValueObject implements Serializable
  
  serialVersionUID:
  
  5073203626044664184L
  - Serialized Fields
    - modified
      
      boolean modified
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.
      
      Added field for the Candidate Gene Management System
    - 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
      
      phenotype present in the database
    - 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.hibernate
- Class ubic.gemma.persistence.hibernate.XSDEntityResolver extends DTDEntityResolver implements Serializable
Package ubic.gemma.persistence.service.analysis.expression.diff
- Class ubic.gemma.persistence.service.analysis.expression.diff.MissingResult extends DiffExprGeneSearchResult implements Serializable
  
  serialVersionUID:
  
  -2868418055346274525L
- Class ubic.gemma.persistence.service.analysis.expression.diff.NonRetainedResult extends DiffExprGeneSearchResult implements Serializable
  
  serialVersionUID:
  
  3501605965895623139L
Package ubic.gemma.persistence.service.association.coexpression
- Class ubic.gemma.persistence.service.association.coexpression.CoexpressionCacheValueObject extends Object implements Serializable
  
  serialVersionUID:
  
  184287422449009209L
  - Serialized Fields
    - coexGeneSymbol
      
      String coexGeneSymbol
    - coexpGene
      
      Long coexpGene
    - positiveCorrelation
      
      boolean positiveCorrelation
    - queryGene
      
      Long queryGene
    - queryGeneSymbol
      
      String queryGeneSymbol
    - support
      
      int support
    - supportDetailsId
      
      Long supportDetailsId
    - supportingDatasets
      
      Collection<Long> supportingDatasets
    - testedInDatasets
      
      ubic.gemma.persistence.service.association.coexpression.CompressedLongSet testedInDatasets
- Class ubic.gemma.persistence.service.association.coexpression.CoexpressionValueObject extends Object implements Serializable
  - Serialized Fields
    - coexGeneId
      
      Long coexGeneId
    - coexGeneSymbol
      
      String coexGeneSymbol
    - eeConstraint
      
      boolean eeConstraint
      
      If true, this means the results were trimmed to a subset.
    - fromCache
      
      boolean fromCache
      
      True if these data were pulled from the cache, or if they were put in the cache (so future queries will find them); false otherwise.
    - interQueryLink
      
      boolean interQueryLink
    - maxResults
      
      int maxResults
      
      the max results limit used in the query; 0 means no limit.
    - positiveCorrelation
      
      boolean positiveCorrelation
    - queryGeneId
      
      Long queryGeneId
    - queryGeneSymbol
      
      String queryGeneSymbol
    - queryStringency
      
      int queryStringency
      
      The stringency used in the query (will be 1 by default)
    - support
      
      Integer support
    - supportDetailsId
      
      Long supportDetailsId
    - supportingDatasets
      
      Set<Long> supportingDatasets
      
      The data sets which supported the link. If eeConstraint = true, this reflects only data sets which were in the query.
    - testedInDatasets
      
      Set<Long> testedInDatasets
      
      The data sets in which the link was tested. If eeConstraint = true, this reflects only data sets which were in the query.
Package ubic.gemma.persistence.service.common.quantitationtype
- Class ubic.gemma.persistence.service.common.quantitationtype.NonUniqueQuantitationTypeByNameException extends Exception implements Serializable
Package ubic.gemma.persistence.service.expression.experiment
- Class ubic.gemma.persistence.service.expression.experiment.FactorValueMigratorService.MigrationFailedException extends RuntimeException implements Serializable
  - Serialized Fields
    - migration
      
      FactorValueMigratorService.Migration migration
Package ubic.gemma.persistence.service.maintenance
- Class ubic.gemma.persistence.service.maintenance.Gene2CsStatus extends Object implements Serializable
  
  serialVersionUID:
  
  1956861185764899312L
  - Serialized Fields
    - annotation
      
      String annotation
    - error
      
      Exception error
    - lastUpdate
      
      Date lastUpdate
Package ubic.gemma.rest
- Class ubic.gemma.rest.DatasetsWebService.AnnotationWithUsageStatisticsValueObject extends AnnotationValueObject implements Serializable
  - Serialized Fields
    - numberOfExpressionExperiments
      
      Long numberOfExpressionExperiments
      
      Number of times the characteristic is mentioned among matching datasets.
    - parentTerms
      
      Set<DatasetsWebService.OntologyTermValueObject> parentTerms
      
      URIs of parent terms, or null if excluded.
- Class ubic.gemma.rest.DatasetsWebService.ArrayDesignWithUsageStatisticsValueObject extends ArrayDesignValueObject implements Serializable
  - Serialized Fields
    - numberOfExpressionExperimentsForTechnologyType
      
      Long numberOfExpressionExperimentsForTechnologyType
- Class ubic.gemma.rest.DatasetsWebService.DifferentialExpressionAnalysisResultByGeneValueObject extends DifferentialExpressionAnalysisResultValueObject implements Serializable
  - Serialized Fields
    - baseline
      
      FactorValueBasicValueObject baseline
    - experimentAnalyzedId
      
      Long experimentAnalyzedId
      
      The ID of the experiment analyzed which is either an ExpressionExperiment or an ExpressionExperimentSubSet.
    - resultSetId
      
      Long resultSetId
      
      The result set ID to which this result belong.
    - secondBaseline
      
      FactorValueBasicValueObject secondBaseline
    - sourceExperimentId
      
      Long sourceExperimentId
      
      The ID of the source experiment, which differs only if this result is from a subset. This is always referring to an ExpressionExperiment.
- Class ubic.gemma.rest.DatasetsWebService.ExpressionExperimentWithSearchResultValueObject extends ExpressionExperimentValueObject implements Serializable
  - Serialized Fields
    - searchResult
      
      SearchWebService.SearchResultValueObject<ExpressionExperimentValueObject> searchResult
- Class ubic.gemma.rest.DatasetsWebService.TaxonWithUsageStatisticsValueObject extends TaxonValueObject implements Serializable
  - Serialized Fields
    - numberOfExpressionExperiments
      
      Long numberOfExpressionExperiments
Package ubic.gemma.rest.serializers
- Class ubic.gemma.rest.serializers.AbstractFactorValueValueObjectSerializer extends com.fasterxml.jackson.databind.ser.std.StdSerializer<T extends AbstractFactorValueValueObject> implements Serializable
- Class ubic.gemma.rest.serializers.FactorValueBasicValueObjectSerializer extends AbstractFactorValueValueObjectSerializer<FactorValueBasicValueObject> implements Serializable
- Class ubic.gemma.rest.serializers.FactorValueValueObjectSerializer extends AbstractFactorValueValueObjectSerializer<FactorValueValueObject> implements Serializable
Package ubic.gemma.rest.util
- Class ubic.gemma.rest.util.EntityNotFoundException extends Exception implements Serializable
- Class ubic.gemma.rest.util.MalformedArgException extends javax.ws.rs.BadRequestException implements Serializable
Package ubic.gemma.web.controller.coexpressionSearch
- Class ubic.gemma.web.controller.coexpressionSearch.CoexSearchTaskCommand extends TaskCommand implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - searchOptions
      
      CoexpressionSearchCommand searchOptions
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.common.auditAndSecurity.recaptcha
- Class ubic.gemma.web.controller.common.auditAndSecurity.recaptcha.ReCaptchaException extends RuntimeException implements Serializable
Package ubic.gemma.web.controller.diff
- Class ubic.gemma.web.controller.diff.DiffExpressionSearchCommand extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - dirty
      
      boolean dirty
    - eeIds
      
      Collection<Long> eeIds
    - eeQuery
      
      String eeQuery
    - eeSetId
      
      Long eeSetId
    - eeSetName
      
      String eeSetName
    - geneIds
      
      Collection<Long> geneIds
    - selectedFactors
      
      Collection<DiffExpressionSelectedFactorCommand> selectedFactors
    - taxonId
      
      Long taxonId
    - threshold
      
      Double threshold
Package ubic.gemma.web.controller.expression.arrayDesign
- Class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignValueObjectExt extends ArrayDesignValueObject implements Serializable
  
  serialVersionUID:
  
  218696698777199533L
  - Serialized Fields
    - additionalTaxa
      
      Set<String> additionalTaxa
    - allParentsAnnotationLink
      
      String allParentsAnnotationLink
    - alternateNames
      
      Collection<String> alternateNames
    - alternative
      
      ArrayDesignValueObject alternative
    - bioProcessAnnotationLink
      
      String bioProcessAnnotationLink
    - colorString
      
      String colorString
    - mergees
      
      Collection<ArrayDesignValueObject> mergees
    - merger
      
      ArrayDesignValueObject merger
    - noParentsAnnotationLink
      
      String noParentsAnnotationLink
    - subsumees
      
      Collection<ArrayDesignValueObject> subsumees
    - subsumer
      
      ArrayDesignValueObject subsumer
Package ubic.gemma.web.controller.expression.experiment
- Class ubic.gemma.web.controller.expression.experiment.DesignMatrixRowValueObject extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - count
      
      int count
    - factors
      
      List<String> factors
    - factorTypes
      
      List<String> factorTypes
    - factorValueMap
      
      Map<String,String> factorValueMap
- Class ubic.gemma.web.controller.expression.experiment.ExperimentalFactorValueWebUIObject extends ExperimentalFactorValueObject implements Serializable
  - Serialized Fields
    - bioMaterialCharacteristicCategoryToUse
      
      String bioMaterialCharacteristicCategoryToUse
- Class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentDataFetchCommand extends TaskCommand implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - analysisId
      
      Long analysisId
    - experimentalDesignId
      
      Long experimentalDesignId
    - expressionExperimentId
      
      Long expressionExperimentId
    - filter
      
      boolean filter
    - forceRewrite
      
      boolean forceRewrite
    - format
      
      String format
    - quantitationTypeId
      
      Long quantitationTypeId
- Class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditValueObject extends ExpressionExperimentDetailsValueObject implements Serializable
  
  serialVersionUID:
  
  1630521876359566915L
  - Serialized Fields
    - bioAssays
      
      Collection<BioAssayValueObject> bioAssays
    - quantitationTypes
      
      Collection<QuantitationTypeValueObject> quantitationTypes
- Class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentLoadTaskCommand extends SimpleExpressionExperimentMetaData implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - arrayDesignName
      
      String arrayDesignName
    - originalFileName
      
      String originalFileName
    - serverFilePath
      
      String serverFilePath
    - taxonName
      
      String taxonName
    - validateOnly
      
      boolean validateOnly
Package ubic.gemma.web.controller.visualization
- Class ubic.gemma.web.controller.visualization.ExpressionExperimentVisualizationCommand extends Object implements Serializable
  
  serialVersionUID:
  
  2166768356457316142L
  - Serialized Fields
    - expressionExperimentId
      
      Long expressionExperimentId
    - maskMissing
      
      boolean maskMissing
    - name
      
      String name
    - quantitationType
      
      QuantitationType quantitationType
    - searchCriteria
      
      String searchCriteria
    - searchString
      
      String searchString
    - viewSampling
      
      boolean viewSampling
Package ubic.gemma.web.persistence
- Class ubic.gemma.web.persistence.AbstractSetListContainer extends Object implements Serializable
  
  serialVersionUID:
  
  -7207696842986893748L
  - Serialized Fields
    - allSessionBoundGroups
      
      List<GemmaSessionBackedValueObject> allSessionBoundGroups
    - largestSessionId
      
      Long largestSessionId
    - sessionBoundModifiedGroups
      
      List<GemmaSessionBackedValueObject> sessionBoundModifiedGroups
- Class ubic.gemma.web.persistence.ExperimentSetListContainer extends AbstractSetListContainer implements Serializable
  
  serialVersionUID:
  
  2031936160381488016L
- Class ubic.gemma.web.persistence.GeneSetListContainer extends AbstractSetListContainer implements Serializable
  
  serialVersionUID:
  
  2163440335723257830L
Package ubic.gemma.web.taglib
- Class ubic.gemma.web.taglib.ConstantsTag extends javax.servlet.jsp.tagext.TagSupport implements Serializable
  
  serialVersionUID:
  
  4937929483183805421L
  - Serialized Fields
    - clazz
      
      String clazz
      
      The class to expose the variables from.
    - scope
      
      String scope
      
      The scope to be put the variable in.
    - var
      
      String var
      
      The single variable to expose.
- Class ubic.gemma.web.taglib.DatabaseEntryTag extends javax.servlet.jsp.tagext.TagSupport implements Serializable
  
  serialVersionUID:
  
  -8225561718129593445L
  - Serialized Fields
    - databaseEntry
      
      DatabaseEntryValueObject databaseEntry
- Class ubic.gemma.web.taglib.ShortBibliographicReferenceTag extends javax.servlet.jsp.tagext.TagSupport implements Serializable
  
  serialVersionUID:
  
  -7325678534991860679L
  - Serialized Fields
    - citation
      
      BibliographicReference citation
Package ubic.gemma.web.taglib.arrayDesign
- Class ubic.gemma.web.taglib.arrayDesign.ArrayDesignGroupingTag extends javax.servlet.jsp.tagext.TagSupport implements Serializable
  
  serialVersionUID:
  
  -5646614364631502667L
  - Serialized Fields
    - subsumees
      
      Collection<ArrayDesign> subsumees
    - subsumer
      
      ArrayDesign subsumer
Package ubic.gemma.web.taglib.common.auditAndSecurity
- Class ubic.gemma.web.taglib.common.auditAndSecurity.ExceptionTag extends javax.servlet.jsp.tagext.TagSupport implements Serializable
  
  serialVersionUID:
  
  4323477499674966726L
  - Serialized Fields
    - exception
      
      Exception exception
    - showStackTrace
      
      Boolean showStackTrace
Package ubic.gemma.web.taglib.expression.experiment
- Class ubic.gemma.web.taglib.expression.experiment.AssayViewTag extends javax.servlet.jsp.tagext.TagSupport implements Serializable
  
  serialVersionUID:
  
  8754490187937841260L
  - Serialized Fields
    - bioAssays
      
      Collection<BioAssayValueObject> bioAssays
    - edit
      
      boolean edit
    - objectMapper
      
      com.fasterxml.jackson.databind.ObjectMapper objectMapper
      
      Jackson serializer to map objects to JSON.
- Class ubic.gemma.web.taglib.expression.experiment.ExperimentQCTag extends javax.servlet.jsp.tagext.TagSupport implements Serializable
  
  serialVersionUID:
  
  -466958848014180520L
  - Serialized Fields
    - eeid
      
      Long eeid
    - eeManagerId
      
      String eeManagerId
    - hasCorrDist
      
      boolean hasCorrDist
    - hasCorrMat
      
      boolean hasCorrMat
    - hasMeanVariance
      
      boolean hasMeanVariance
    - hasNodeDegreeDist
      
      boolean hasNodeDegreeDist
    - hasPCA
      
      boolean hasPCA
    - numFactors
      
      int numFactors
    - numOutliersRemoved
      
      int numOutliersRemoved
    - numPossibleOutliers
      
      int numPossibleOutliers
Package ubic.gemma.web.tasks.analysis.sequence
- Class ubic.gemma.web.tasks.analysis.sequence.ArrayDesignRepeatScanTaskCommand extends TaskCommand implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - arrayDesign
      
      ArrayDesign arrayDesign
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
      
      The property which supplies the option label visible to the end user.
    - value
      
      String value
      
      The property which supplies the value returned to the server.
- 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

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

Serialized Fields

errorState

maxEdges

numDatasetsQueried

queryGenes

queryGenesOnly

queryStringency

results

searchSettings

summaries

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

Serialized Fields

dirty

eeIds

eeQuery

eeSetId

eeSetName

geneIds

geneSetId

queryGenesOnly

quick

stringency

taxonId

useMyDatasets

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

Serialized Fields

coexpNodeDegree

datasetsAvailable

datasetsTested

geneId

linksFound

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