Serialized Form (Gemma 1.29.12 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<E> 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<E> 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<K,V> 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.
    - quick
```
boolean quick
```
      if set to true will do a quick coexpression search (without filling in various details)
    - eeIds
```
Collection<E> 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
```
    - geneSetId
```
Long geneSetId
```
    - geneIds
```
Collection<E> geneIds
```
    - queryGenesOnly
```
boolean queryGenesOnly
```
    - stringency
```
Integer stringency
```
    - useMyDatasets
```
boolean useMyDatasets
```
    - 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...
- Class ubic.gemma.core.analysis.expression.coexpression.CoexpressionSummaryValueObject extends Object implements Serializable
  - Serialized Fields
    - geneId
```
long geneId
```
    - coexpNodeDegree
```
GeneCoexpressionNodeDegreeValueObject coexpNodeDegree
```
    - datasetsAvailable
```
int datasetsAvailable
```
    - datasetsTested
```
int datasetsTested
```
    - 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
```
    - correlationCacheThreshold
```
double correlationCacheThreshold
```
      only used for internal cache during calculations.
    - checkForBatchEffect
```
boolean checkForBatchEffect
```
    - checkForOutliers
```
boolean checkForOutliers
```
    - 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<K,V> baseLineFactorValues
```
    - ebayes
```
boolean ebayes
```
    - factorsToInclude
```
List<E> factorsToInclude
```
    - interactionsToInclude
```
Collection<E> interactionsToInclude
```
    - 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
```
    - makeArchiveFile
```
boolean makeArchiveFile
```
- Class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionMetaAnalysisValueObject extends Object implements Serializable
  - Serialized Fields
    - gene
```
GeneValueObject gene
```
    - sortKey
```
String sortKey
```
    - fisherPValue
```
Double fisherPValue
```
    - numSearchedExperiments
```
int numSearchedExperiments
```
    - numExperimentsInScope
```
int numExperimentsInScope
```
    - numMetThreshold
```
int numMetThreshold
```
    - activeExperiments
```
Collection<E> activeExperiments
```
    - probeResults
```
Collection<E> probeResults
```
- 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.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
```
    - p
```
double p
```
    - numBatches
```
int numBatches
```
- 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
```
    - lowExpressionCut
```
double lowExpressionCut
```
    - lowExpressionCutIsSet
```
boolean lowExpressionCutIsSet
```
    - lowVarianceCut
```
double lowVarianceCut
```
    - lowVarianceCutIsSet
```
boolean lowVarianceCutIsSet
```
    - minPresentFraction
```
double minPresentFraction
```
    - minPresentFractionIsSet
```
boolean minPresentFractionIsSet
```
    - requireSequences
```
boolean requireSequences
```
    - startingRows
```
int startingRows
```
    - lowDistinctValueIsSet
```
boolean lowDistinctValueIsSet
```
- 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<K,V> dateCorrelations
```
    - datePVals
```
Map<K,V> datePVals
```
    - dates
```
List<E> dates
```
    - factorCorrelations
```
Map<K,V> factorCorrelations
```
    - factorPvals
```
Map<K,V> factorPvals
```
      Need to store the correlations of eigengenes with dates of assays, and also with factors. Statistics are rank-based correlations
    - factors
```
Map<K,V> 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
```
ubic.basecode.dataStructure.matrix.DoubleMatrix<R,C> vMatrix
```
Package ubic.gemma.core.analysis.report
- Class ubic.gemma.core.analysis.report.AuditableObject extends Object implements Serializable
  
  serialVersionUID:
  
  -7862129089784691035L
  - Serialized Fields
    - type
```
String type
```
    - id
```
Long id
```
    - date
```
Date date
```
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<K,V> geneProducts
```
    - genes
```
Map<K,V> genes
```
    - numBlatHits
```
Integer numBlatHits
```
- Class ubic.gemma.core.analysis.sequence.GeneMappingSummary extends Object implements Serializable
  
  serialVersionUID:
  
  8899320580201273360L
  - Serialized Fields
    - geneProductIdMap
```
Map<K,V> geneProductIdMap
```
    - geneProductIdGeneMap
```
Map<K,V> geneProductIdGeneMap
```
    - blatResult
```
BlatResultValueObject blatResult
```
    - geneProductMap
```
Map<K,V> geneProductMap
```
    - compositeSequence
```
CompositeSequenceValueObject compositeSequence
```
    - identity
```
double identity
```
    - score
```
double score
```
    - blatResultId
```
String blatResultId
```
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
    - expressionExperiment
```
ExpressionExperiment expressionExperiment
```
    - quantitationTypes
```
Collection<E> quantitationTypes
```
    - bioAssayDimensions
```
Map<K,V> bioAssayDimensions
```
    - columnAssayMap
```
Map<K,V> columnAssayMap
```
    - columnBioMaterialMap
```
Map<K,V> columnBioMaterialMap
```
    - columnBioAssayMapByInteger
```
Map<K,V> columnBioAssayMapByInteger
```
    - columnBioMaterialMapByInteger
```
Map<K,V> columnBioMaterialMapByInteger
```
    - rowElementMap
```
Map<K,V> rowElementMap
```
    - rowDesignElementMapByInteger
```
Map<K,V> rowDesignElementMapByInteger
```
    - rowElements
```
List<E> 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
```
ubic.basecode.dataStructure.matrix.ObjectMatrixImpl<R,C,V> matrix
```
- Class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix extends BaseExpressionDataMatrix<Double> implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - matrix
```
ubic.basecode.dataStructure.matrix.DoubleMatrix<R,C> matrix
```
    - ranks
```
Map<K,V> ranks
```
- Class ubic.gemma.core.datastructure.matrix.ExpressionDataIntegerMatrix extends BaseExpressionDataMatrix<Integer> implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - matrix
```
ubic.basecode.dataStructure.matrix.IntegerMatrix<R,C> matrix
```
- Class ubic.gemma.core.datastructure.matrix.ExpressionDataStringMatrix extends BaseExpressionDataMatrix<String> implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - matrix
```
ubic.basecode.dataStructure.matrix.StringMatrix<R,C> 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<E> suspiciousValues
```
Package ubic.gemma.core.genome.gene
- Class ubic.gemma.core.genome.gene.FreeTextGeneResultsValueObject extends SessionBoundGeneSetValueObject implements Serializable
  
  serialVersionUID:
  
  3557304710219740029L
  - Serialized Fields
    - queryString
```
String queryString
```
- Class ubic.gemma.core.genome.gene.GOGroupValueObject extends SessionBoundGeneSetValueObject implements Serializable
  
  serialVersionUID:
  
  -185326197992950287L
  - Serialized Fields
    - goId
```
String goId
```
    - searchTerm
```
String searchTerm
```
- Class ubic.gemma.core.genome.gene.PhenotypeGroupValueObject extends SessionBoundGeneSetValueObject implements Serializable
  
  serialVersionUID:
  
  -7264201170714207356L
  - Serialized Fields
    - phenotypeCategory
```
String phenotypeCategory
```
    - phenotypeName
```
String phenotypeName
```
    - searchTerm
```
String searchTerm
```
- Class ubic.gemma.core.genome.gene.SessionBoundGeneSetValueObject extends GeneSetValueObject implements Serializable
  
  serialVersionUID:
  
  5073203626044664184L
  - Serialized Fields
    - modified
```
boolean modified
```
Package ubic.gemma.core.image
- Class ubic.gemma.core.image.ABALinkOutValueObject extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - abaGeneImageUrls
```
Collection<E> 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.
    - 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
```
    - maxQueueMinutes
```
Integer maxQueueMinutes
```
      How long we will allow this task to be queued before giving up.
    - maxRuntime
```
int maxRuntime
```
- 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
    - percent
```
int percent
```
    - description
```
String description
```
    - done
```
boolean done
```
    - forwardingURL
```
String forwardingURL
```
    - taskId
```
String taskId
```
    - failed
```
boolean failed
```
- Class ubic.gemma.core.job.progress.SubmittedTaskValueObject extends Object implements Serializable
  
  serialVersionUID:
  
  6757089319713433356L
  - Serialized Fields
    - taskId
```
String taskId
```
    - submissionTime
```
Date submissionTime
```
    - startTime
```
Date startTime
```
    - finishTime
```
Date finishTime
```
    - submitter
```
String submitter
```
    - taskType
```
String taskType
```
    - logMessages
```
String logMessages
```
    - runningRemotely
```
boolean runningRemotely
```
    - done
```
boolean done
```
    - emailAlert
```
boolean emailAlert
```
    - taskStatus
```
String taskStatus
```
    - lastLogMessage
```
String lastLogMessage
```
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
    - row
```
Integer row
```
    - col
```
Integer col
```
    - startInBioChar
```
Long startInBioChar
```
    - strand
```
String strand
```
    - compositeSequence
```
CompositeSequence compositeSequence
```
    - immobilizedCharacteristic
```
BioSequence immobilizedCharacteristic
```
Package ubic.gemma.core.loader.expression.geo
- Class ubic.gemma.core.loader.expression.geo.GeoSampleCorrespondence extends Object implements Serializable
  
  serialVersionUID:
  
  -5285504953530483114L
  - Serialized Fields
    - sets
```
Collection<E> sets
```
    - accToTitle
```
Map<K,V> accToTitle
```
    - accToDataset
```
Map<K,V> accToDataset
```
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
    - city
```
String city
```
    - department
```
String department
```
    - email
```
String email
```
    - fax
```
String fax
```
    - institute
```
String institute
```
    - name
```
String name
```
    - phone
```
String phone
```
    - postCode
```
String postCode
```
    - state
```
String state
```
    - webLink
```
String webLink
```
    - country
```
String country
```
- Class ubic.gemma.core.loader.expression.geo.model.GeoData extends Object implements Serializable
  
  serialVersionUID:
  
  -859220901359581113L
  - Serialized Fields
    - columnNames
```
List<E> columnNames
```
    - columnDescriptions
```
List<E> columnDescriptions
```
    - 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
    - experimentType
```
GeoDataset.ExperimentType experimentType
```
    - completeness
```
String completeness
```
    - datasetType
```
String datasetType
```
    - description
```
String description
```
    - featureCount
```
String featureCount
```
    - numChannels
```
int numChannels
```
    - 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<E> series
```
    - subsets
```
Collection<E> 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<E> catalogNumbers
```
    - coating
```
String coating
```
    - contributer
```
Collection<E> contributer
```
    - description
```
String description
```
    - designElements
```
Collection<E> designElements
```
    - distribution
```
String distribution
```
    - lastUpdateDate
```
String lastUpdateDate
```
    - manufactureProtocol
```
String manufactureProtocol
```
    - manufacturer
```
String manufacturer
```
    - organisms
```
Collection<E> organisms
```
    - platformData
```
List<E> platformData
```
    - platformInformation
```
Map<K,V> 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<K,V> 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<E> pubMedIds
```
    - sample
```
String sample
```
    - supplementaryFile
```
String supplementaryFile
```
    - support
```
String support
```
    - technology
```
GeoDataset.PlatformType technology
```
    - useDataFromGEO
```
boolean useDataFromGEO
```
      Will be set to false during parsing if data are missing.
    - webLinks
```
Collection<E> webLinks
```
- Class ubic.gemma.core.loader.expression.geo.model.GeoRecord extends GeoData implements Serializable
  
  serialVersionUID:
  
  2060148205381855991L
  - Serialized Fields
    - contactName
```
String contactName
```
    - correspondingExperiments
```
Collection<E> correspondingExperiments
```
    - meshHeadings
```
String meshHeadings
```
    - numSamples
```
int numSamples
```
    - organisms
```
Collection<E> organisms
```
    - platform
```
String platform
```
    - libraryStrategy
```
String libraryStrategy
```
    - previousClicks
```
int previousClicks
```
    - pubMedIds
```
String pubMedIds
```
    - releaseDate
```
Date releaseDate
```
    - sampleDetails
```
String sampleDetails
```
    - sampleGEOAccessions
```
Collection<E> sampleGEOAccessions
```
    - seriesType
```
String seriesType
```
    - subSeries
```
boolean subSeries
```
    - subSeriesOf
```
String subSeriesOf
```
    - summary
```
String summary
```
    - overallDesign
```
String overallDesign
```
    - 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
```
    - channels
```
List<E> channels
```
    - dataProcessing
```
String dataProcessing
```
    - description
```
String description
```
    - hybProtocol
```
String hybProtocol
```
    - isGenePix
```
boolean isGenePix
```
    - lastUpdateDate
```
String lastUpdateDate
```
    - libSource
```
String libSource
```
    - libStrategy
```
String libStrategy
```
    - mightNotHaveDataInFile
```
boolean mightNotHaveDataInFile
```
    - platforms
```
Collection<E> platforms
```
    - replicates
```
Collection<E> replicates
```
    - scanProtocol
```
String scanProtocol
```
    - seriesAppearsIn
```
Collection<E> seriesAppearsIn
```
    - 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<E> variables
```
    - warnedAboutGenePix
```
boolean warnedAboutGenePix
```
- Class ubic.gemma.core.loader.expression.geo.model.GeoSeries extends GeoData implements Serializable
  
  serialVersionUID:
  
  -1058350558444775537L
  - Serialized Fields
    - samples
```
Collection<E> samples
```
    - seriesTypes
```
Collection<E> seriesTypes
```
    - subSeries
```
Collection<E> subSeries
```
    - variables
```
Map<K,V> variables
```
    - contributers
```
Collection<E> contributers
```
    - dataSets
```
Collection<E> dataSets
```
    - isSubSeries
```
boolean isSubSeries
```
    - isSuperSeries
```
boolean isSuperSeries
```
    - keyWords
```
Collection<E> keyWords
```
    - lastUpdateDate
```
String lastUpdateDate
```
    - overallDesign
```
String overallDesign
```
    - pubmedIds
```
Collection<E> pubmedIds
```
    - replicates
```
Map<K,V> replicates
```
    - sampleCorrespondence
```
GeoSampleCorrespondence sampleCorrespondence
```
    - summary
```
String summary
```
    - supplementaryFile
```
String supplementaryFile
```
    - values
```
GeoValues values
```
    - webLinks
```
Collection<E> webLinks
```
- Class ubic.gemma.core.loader.expression.geo.model.GeoSubset extends GeoData implements Serializable
  
  serialVersionUID:
  
  2392295178038874633L
  - Serialized Fields
    - owningDataset
```
GeoDataset owningDataset
```
    - description
```
String description
```
    - samples
```
Collection<E> samples
```
    - type
```
GeoVariable.VariableType type
```
- Class ubic.gemma.core.loader.expression.geo.model.GeoValues extends Object implements Serializable
  
  serialVersionUID:
  
  3748363645735281578L
  - Serialized Fields
    - data
```
Map<K,V> data
```
    - quantitationTypeIndexMap
```
Map<K,V> quantitationTypeIndexMap
```
    - quantitationTypeNameMap
```
Map<K,V> quantitationTypeNameMap
```
    - sampleDimensions
```
Map<K,V> sampleDimensions
```
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<E> arrayDesignIds
```
    - arrayDesigns
```
Collection<E> arrayDesigns
```
    - taxon
```
Taxon taxon
```
    - taxonId
```
Long taxonId
```
    - 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
```
    - 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
    - ncbiGenes
```
Collection<E> ncbiGenes
```
    - enemblTranscriptId
```
String enemblTranscriptId
```
    - ensembleGeneId
```
String ensembleGeneId
```
    - ensemblPeptideId
```
String ensemblPeptideId
```
    - hgcnId
```
String hgcnId
```
    - 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.search
- Class ubic.gemma.core.search.BaseCodeOntologySearchException extends SearchException implements Serializable
  - Serialized Fields
    - cause
```
ubic.basecode.ontology.search.OntologySearchException cause
```
- Class ubic.gemma.core.search.CompassSearchException extends SearchException implements Serializable
  - Serialized Fields
    - cause
```
org.compass.core.CompassException cause
```
- Class ubic.gemma.core.search.SearchException extends Exception implements Serializable
Package ubic.gemma.core.tasks.analysis.coexp
- Class ubic.gemma.core.tasks.analysis.coexp.LinkAnalysisTaskCommand extends TaskCommand implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - filterConfig
```
FilterConfig filterConfig
```
    - linkAnalysisConfig
```
LinkAnalysisConfig linkAnalysisConfig
```
    - expressionExperiment
```
ExpressionExperiment expressionExperiment
```
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<E> 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<E> analysisResultSetIds
```
    - name
```
String name
```
    - description
```
String description
```
    - 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
    - revert
```
boolean revert
```
    - bioAssayIds
```
Collection<E> bioAssayIds
```
- 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
```
    - allowSuperSeriesLoad
```
boolean allowSuperSeriesLoad
```
    - allowSubSeriesLoad
```
boolean allowSubSeriesLoad
```
    - 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
    - postProcessOnly
```
boolean postProcessOnly
```
    - expressionExperiment
```
ExpressionExperiment expressionExperiment
```
- Class ubic.gemma.core.tasks.analysis.expression.TwoChannelMissingValueTaskCommand extends TaskCommand implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - expressionExperiment
```
ExpressionExperiment expressionExperiment
```
    - s2n
```
double s2n
```
    - extraMissingValueIndicators
```
Collection<E> extraMissingValueIndicators
```
- Class ubic.gemma.core.tasks.analysis.expression.UpdateEEDetailsCommand extends TaskCommand implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - shortName
```
String shortName
```
    - name
```
String name
```
    - description
```
String description
```
    - pubMedId
```
String pubMedId
```
    - removePrimaryPublication
```
boolean removePrimaryPublication
```
- 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
    - forceAnalysis
```
boolean forceAnalysis
```
    - arrayDesign
```
ArrayDesign arrayDesign
```
Package ubic.gemma.core.tasks.maintenance
- Class ubic.gemma.core.tasks.maintenance.CharacteristicUpdateCommand extends TaskCommand implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - annotationValueObjects
```
Collection<E> 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
    - expressionExperiment
```
ExpressionExperiment expressionExperiment
```
    - all
```
boolean all
```
- Class ubic.gemma.core.tasks.maintenance.IndexerResult extends TaskResult implements Serializable
  
  serialVersionUID:
  
  -150285942553712429L
  - Serialized Fields
    - pathToArrayIndex
```
String pathToArrayIndex
```
    - pathToBibliographicIndex
```
String pathToBibliographicIndex
```
    - pathToBiosequenceIndex
```
String pathToBiosequenceIndex
```
    - pathToExperimentSetIndex
```
String pathToExperimentSetIndex
```
    - pathToExpressionIndex
```
String pathToExpressionIndex
```
    - pathToGeneIndex
```
String pathToGeneIndex
```
    - pathToGeneSetIndex
```
String pathToGeneSetIndex
```
    - pathToProbeIndex
```
String pathToProbeIndex
```
- 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
    - datasetName
```
String datasetName
```
    - datasetShortName
```
String datasetShortName
```
    - datasetLink
```
String datasetLink
```
    - datasetId
```
Long datasetId
```
    - analysisId
```
Long analysisId
```
    - analysisNotRun
```
boolean analysisNotRun
```
    - resultSetId
```
Long resultSetId
```
    - factorId
```
Long factorId
```
    - factorName
```
String factorName
```
    - factorCategory
```
String factorCategory
```
    - factorDescription
```
String factorDescription
```
    - numberOfProbesTotal
```
int numberOfProbesTotal
```
    - numberOfProbesDiffExpressed
```
int numberOfProbesDiffExpressed
```
    - numberOfProbesUpRegulated
```
int numberOfProbesUpRegulated
```
    - numberOfProbesDownRegulated
```
int numberOfProbesDownRegulated
```
    - visualizationValues
```
List<E> visualizationValues
```
    - qValues
```
List<E> qValues
```
    - numberOfProbes
```
List<E> numberOfProbes
```
    - contrastsFactorValues
```
Map<K,V> contrastsFactorValues
```
    - contrastsFactorValueIds
```
List<E> contrastsFactorValueIds
```
    - baselineFactorValue
```
String baselineFactorValue
```
    - baselineFactorValueId
```
Long baselineFactorValueId
```
- Class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject extends Object implements Serializable
  - Serialized Fields
    - cellData
```
Map<K,V> cellData
```
      Map of Condition IDs to map of Genes to the Cell holding the information for the results for that Gene x Condition combination.
    - resultSetConditions
```
Map<K,V> resultSetConditions
```
    - conditions
```
List<E> conditions
```
    - genes
```
List<E> genes
```
- Class ubic.gemma.core.tasks.visualization.DifferentialExpressionSearchTaskCommand extends TaskCommand implements Serializable
  
  serialVersionUID:
  
  -8510536003059837349L
  - Serialized Fields
    - geneGroup
```
Collection<E> geneGroup
```
    - experimentGroup
```
Collection<E> experimentGroup
```
    - geneGroupName
```
String geneGroupName
```
    - experimentGroupName
```
String experimentGroupName
```
Package ubic.gemma.model
- Class ubic.gemma.model.BaseValueObject extends Object implements Serializable
  
  serialVersionUID:
  
  -5290562301261202171L
  - Serialized Fields
    - valueObject
```
Serializable valueObject
```
    - errorFound
```
boolean errorFound
```
    - accessDenied
```
boolean accessDenied
```
    - userNotLoggedIn
```
boolean userNotLoggedIn
```
    - objectAlreadyRemoved
```
boolean objectAlreadyRemoved
```
- Class ubic.gemma.model.IdentifiableValueObject extends Object implements Serializable
  - Serialized Fields
    - id
```
Long id
```
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<E> characteristics
```
    - otherRelevantPublications
```
Set<E> 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
    - taxon
```
Taxon taxon
```
    - experiments
```
Set<E> experiments
```
- Class ubic.gemma.model.analysis.expression.FactorAssociatedAnalysisResultSet extends AnalysisResultSet<R extends AnalysisResult> implements Serializable
  
  serialVersionUID:
  
  821072688513147160L
  - Serialized Fields
    - experimentalFactors
```
Set<E> 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
    - id
```
Long id
```
    - firstGeneId
```
Long firstGeneId
```
    - secondGeneId
```
Long secondGeneId
```
    - isPositive
```
Boolean isPositive
```
Package ubic.gemma.model.analysis.expression.diff
- Class ubic.gemma.model.analysis.expression.diff.ContrastResult extends Object implements Serializable
  
  serialVersionUID:
  
  -4310735803120153778L
  - Serialized Fields
    - pvalue
```
Double pvalue
```
    - tStat
```
Double tStat
```
    - coefficient
```
Double coefficient
```
    - logFoldChange
```
Double logFoldChange
```
      TODO: rename this to log2FoldChange to avoid confusion with the logarithm base used.
    - id
```
Long id
```
    - factorValue
```
FactorValue factorValue
```
    - secondFactorValue
```
FactorValue secondFactorValue
```
- Class ubic.gemma.model.analysis.expression.diff.ContrastResultValueObject extends IdentifiableValueObject<ContrastResult> implements Serializable
  - Serialized Fields
    - pvalue
```
Double pvalue
```
    - tStat
```
Double tStat
```
    - coefficient
```
Double coefficient
```
    - logFoldChange
```
Double logFoldChange
```
    - factorValue
```
FactorValueBasicValueObject factorValue
```
    - secondFactorValue
```
FactorValueBasicValueObject secondFactorValue
```
- Class ubic.gemma.model.analysis.expression.diff.ContrastsValueObject extends Object implements Serializable
  - Serialized Fields
    - contrasts
```
List<E> contrasts
```
    - resultId
```
Long resultId
```
- Class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysis extends SingleExperimentAnalysis implements Serializable
  
  serialVersionUID:
  
  -7855180617739271699L
  - Serialized Fields
    - subsetFactorValue
```
FactorValue subsetFactorValue
```
    - resultSets
```
Set<E> resultSets
```
- Class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResult extends AnalysisResult implements Serializable
  
  serialVersionUID:
  
  8952834115689524169L
  - Serialized Fields
    - pvalue
```
Double pvalue
```
    - correctedPvalue
```
Double correctedPvalue
```
      Typically actually a qvalue.
    - rank
```
Double rank
```
    - correctedPValueBin
```
Integer correctedPValueBin
```
    - id
```
Long id
```
    - contrasts
```
Set<E> contrasts
```
    - resultSet
```
ExpressionAnalysisResultSet resultSet
```
    - probe
```
CompositeSequence probe
```
- Class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResultSetValueObject extends AnalysisResultSetValueObject<DifferentialExpressionAnalysisResult,ExpressionAnalysisResultSet> implements Serializable
  - Serialized Fields
    - analysis
```
DifferentialExpressionAnalysisValueObject analysis
```
    - experimentalFactors
```
Collection<E> experimentalFactors
```
    - results
```
Collection<E> results
```
      Related analysis results. Note that this field is excluded from the JSON serialization if left unset.
- Class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResultValueObject extends AnalysisResultValueObject<DifferentialExpressionAnalysisResult> implements Serializable
  - Serialized Fields
    - probeId
```
Long probeId
```
    - probeName
```
String probeName
```
    - genes
```
List<E> genes
```
    - pValue
```
Double pValue
```
    - correctedPvalue
```
Double correctedPvalue
```
    - rank
```
Double rank
```
    - contrasts
```
List<E> contrasts
```
- Class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisValueObject extends AnalysisValueObject<DifferentialExpressionAnalysis> implements Serializable
  
  serialVersionUID:
  
  622877438067070041L
  - Serialized Fields
    - factorValuesUsed
```
Map<K,V> factorValuesUsed
```
    - resultSets
```
Collection<E> resultSets
```
    - arrayDesignsUsed
```
Collection<E> arrayDesignsUsed
```
    - bioAssaySetId
```
Long bioAssaySetId
```
    - sourceExperiment
```
Long sourceExperiment
```
    - subsetFactor
```
ExperimentalFactorValueObject subsetFactor
```
    - subsetFactorValue
```
FactorValueValueObject subsetFactorValue
```
- 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<E> 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
```
    - resultSetId
```
Long resultSetId
```
    - geneId
```
Long geneId
```
    - numberOfProbes
```
int numberOfProbes
```
    - numberOfProbesDiffExpressed
```
int numberOfProbesDiffExpressed
```
    - score
```
Double score
```
    - pvalue
```
Double pvalue
```
    - correctedPvalue
```
Double correctedPvalue
```
- Class ubic.gemma.model.analysis.expression.diff.DiffExResultSetSummaryValueObject extends Object implements Serializable
  
  serialVersionUID:
  
  2063274043081170625L
  - Serialized Fields
    - id
```
Long id
```
    - analysisId
```
Long analysisId
```
    - arrayDesignsUsed
```
Collection<E> arrayDesignsUsed
```
    - baselineGroup
```
FactorValueValueObject baselineGroup
```
    - experimentalFactors
```
Collection<E> experimentalFactors
```
    - factorIds
```
Collection<E> factorIds
```
    - bioAssaySetAnalyzedId
```
Long bioAssaySetAnalyzedId
```
      Analyzed BioAssaySet ID.
      This is redundant because of DifferentialExpressionAnalysisValueObject#getBioAssaySetId(), and always displayed in that context in the RESTful API.
    - 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.
    - numberOfDiffExpressedProbes
```
Integer numberOfDiffExpressedProbes
```
      Number of diffex probes in the Direction.EITHER hit list if available.
    - upregulatedCount
```
Integer upregulatedCount
```
      Number of diffex probes in the Direction.UP hit list if available.
    - downregulatedCount
```
Integer downregulatedCount
```
      Number of diffex probes in the Direction.DOWN hit list if available.
- Class ubic.gemma.model.analysis.expression.diff.ExpressionAnalysisResultSet extends FactorAssociatedAnalysisResultSet<DifferentialExpressionAnalysisResult> implements Serializable
  
  serialVersionUID:
  
  7226901182513177574L
  - Serialized Fields
    - numberOfProbesTested
```
Integer numberOfProbesTested
```
    - numberOfGenesTested
```
Integer numberOfGenesTested
```
    - baselineGroup
```
FactorValue baselineGroup
```
    - results
```
Set<E> results
```
    - analysis
```
DifferentialExpressionAnalysis analysis
```
    - pvalueDistribution
```
PvalueDistribution pvalueDistribution
```
    - hitListSizes
```
Set<E> hitListSizes
```
- Class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysis extends ExpressionAnalysis implements Serializable
  
  serialVersionUID:
  
  -2588180973962410595L
  - Serialized Fields
    - numGenesAnalyzed
```
Integer numGenesAnalyzed
```
    - qvalueThresholdForStorage
```
Double qvalueThresholdForStorage
```
    - resultSetsIncluded
```
Set<E> resultSetsIncluded
```
    - results
```
Set<E> results
```
- Class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisDetailValueObject extends Object implements Serializable
  
  serialVersionUID:
  
  3868004995989355452L
  - Serialized Fields
    - numGenesAnalyzed
```
Integer numGenesAnalyzed
```
    - includedResultSetsInfo
```
Collection<E> includedResultSetsInfo
```
    - results
```
Collection<E> results
```
- Class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisResult extends Object implements Serializable
  
  serialVersionUID:
  
  -6553250926957951550L
  - Serialized Fields
    - metaPvalue
```
Double metaPvalue
```
    - metaQvalue
```
Double metaQvalue
```
    - meanLogFoldChange
```
Double meanLogFoldChange
```
    - metaPvalueRank
```
Double metaPvalueRank
```
    - upperTail
```
Boolean upperTail
```
    - id
```
Long id
```
    - gene
```
Gene gene
```
    - resultsUsed
```
Set<E> resultsUsed
```
- Class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisResultValueObject extends Object implements Serializable
  
  serialVersionUID:
  
  6099286095885830140L
  - Serialized Fields
    - geneSymbol
```
String geneSymbol
```
    - geneName
```
String geneName
```
    - 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
    - thresholdQvalue
```
Double thresholdQvalue
```
    - numberOfProbes
```
Integer numberOfProbes
```
    - direction
```
Direction direction
```
    - numberOfGenes
```
Integer numberOfGenes
```
    - id
```
Long id
```
- Class ubic.gemma.model.analysis.expression.diff.HitListSizeImpl extends HitListSize implements Serializable
  
  serialVersionUID:
  
  -6398621486105806034L
- Class ubic.gemma.model.analysis.expression.diff.IncludedResultSetInfoValueObject extends Object implements Serializable
  
  serialVersionUID:
  
  -4660741839991839187L
  - Serialized Fields
    - experimentId
```
Long experimentId
```
    - analysisId
```
Long analysisId
```
    - resultSetId
```
Long resultSetId
```
- Class ubic.gemma.model.analysis.expression.diff.PvalueDistribution extends Object implements Serializable
  
  serialVersionUID:
  
  -4783507721422402289L
  - Serialized Fields
    - numBins
```
Integer numBins
```
    - binCounts
```
byte[] binCounts
```
    - id
```
Long id
```
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
```
    - value
```
Double value
```
    - varianceFraction
```
Double varianceFraction
```
    - id
```
Long id
```
- Class ubic.gemma.model.analysis.expression.pca.Eigenvector extends Object implements Serializable
  
  serialVersionUID:
  
  5122763307995485698L
  - Serialized Fields
    - componentNumber
```
Integer componentNumber
```
    - vector
```
byte[] vector
```
    - id
```
Long id
```
- Class ubic.gemma.model.analysis.expression.pca.PrincipalComponentAnalysis extends SingleExperimentAnalysis implements Serializable
  
  serialVersionUID:
  
  7046708934564931841L
  - Serialized Fields
    - numComponentsStored
```
Integer numComponentsStored
```
    - maxNumProbesPerComponent
```
Integer maxNumProbesPerComponent
```
    - bioAssayDimension
```
BioAssayDimension bioAssayDimension
```
    - probeLoadings
```
Set<E> probeLoadings
```
    - eigenValues
```
Set<E> eigenValues
```
    - eigenVectors
```
Set<E> eigenVectors
```
- Class ubic.gemma.model.analysis.expression.pca.ProbeLoading extends Object implements Serializable
  
  serialVersionUID:
  
  -2328381846024383305L
  - Serialized Fields
    - componentNumber
```
Integer componentNumber
```
    - loading
```
Double loading
```
    - loadingRank
```
Integer loadingRank
```
    - id
```
Long id
```
    - probe
```
CompositeSequence probe
```
Package ubic.gemma.model.association
- Class ubic.gemma.model.association.BioSequence2GeneProduct extends Object implements Serializable
  
  serialVersionUID:
  
  8361432485953690591L
  - Serialized Fields
    - id
```
Long id
```
    - sourceAnalysis
```
Analysis sourceAnalysis
```
    - overlap
```
Integer overlap
```
    - score
```
Double score
```
    - threePrimeDistance
```
Long threePrimeDistance
```
    - threePrimeDistanceMeasurementMethod
```
ThreePrimeDistanceMethod threePrimeDistanceMeasurementMethod
```
    - specificity
```
Double specificity
```
    - bioSequence
```
BioSequence bioSequence
```
    - geneProduct
```
GeneProduct geneProduct
```
- Class ubic.gemma.model.association.Gene2GeneAssociation extends Object implements Serializable
  
  serialVersionUID:
  
  -322186137554528167L
  - Serialized Fields
    - id
```
Long id
```
    - firstGene
```
Gene firstGene
```
    - secondGene
```
Gene secondGene
```
- Class ubic.gemma.model.association.Gene2GeneIdAssociation extends Object implements Serializable
  
  serialVersionUID:
  
  3735868529324395241L
  - Serialized Fields
    - id
```
Long id
```
    - firstGene
```
Long firstGene
```
    - 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
    - id
```
Long id
```
    - gene
```
Gene gene
```
    - 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
```
- Class ubic.gemma.model.association.ReferenceAssociationImpl extends ReferenceAssociation implements Serializable
  
  serialVersionUID:
  
  -1476215275010160696L
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
    - 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
```
    - numDataSetsSupporting
```
Integer numDataSetsSupporting
```
- 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<K,V> nodeDegreesNeg
```
    - nodeDegreesPos
```
TreeMap<K,V> nodeDegreesPos
```
    - relDegreesNeg
```
TreeMap<K,V> relDegreesNeg
```
    - relDegreesPos
```
TreeMap<K,V> 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
    - selectionThreshold
```
Double selectionThreshold
```
      Deprecated.
    - geneDifferentialExpressionMetaAnalysisResult
```
GeneDifferentialExpressionMetaAnalysisResult geneDifferentialExpressionMetaAnalysisResult
```
      Deprecated.
- Class ubic.gemma.model.association.phenotype.DifferentialExpressionEvidenceImpl extends DifferentialExpressionEvidence implements Serializable
  
  serialVersionUID:
  
  -8941882468429643554L
- 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
    - evidenceCode
```
GOEvidenceCode evidenceCode
```
      Deprecated.
    - isNegativeEvidence
```
Boolean isNegativeEvidence
```
      Deprecated.
    - score
```
String score
```
      Deprecated.
    - strength
```
Double strength
```
      Deprecated.
    - gene
```
Gene gene
```
      Deprecated.
    - phenotypes
```
Set<E> phenotypes
```
      Deprecated.
    - associationType
```
Characteristic associationType
```
      Deprecated.
    - evidenceSource
```
DatabaseEntry evidenceSource
```
      Deprecated.
    - scoreType
```
QuantitationType scoreType
```
      Deprecated.
    - phenotypeAssociationPublications
```
Set<E> phenotypeAssociationPublications
```
      Deprecated.
    - mappingType
```
PhenotypeMappingType mappingType
```
      Deprecated.
    - originalPhenotype
```
String originalPhenotype
```
      Deprecated.
    - relationship
```
String relationship
```
      Deprecated.
    - lastUpdated
```
Date lastUpdated
```
      Deprecated.
- Class ubic.gemma.model.association.phenotype.PhenotypeAssociationPublication extends Object implements Serializable
  
  serialVersionUID:
  
  -4156623260205197700L
  - Serialized Fields
    - id
```
Long id
```
      Deprecated.
    - type
```
String type
```
      Deprecated.
    - citation
```
BibliographicReference citation
```
      Deprecated.
- Class ubic.gemma.model.association.phenotype.PhenotypeAssociationPublicationImpl extends PhenotypeAssociationPublication implements Serializable
  
  serialVersionUID:
  
  -4156623110205197711L
- Class ubic.gemma.model.association.phenotype.PhenotypeMappingType extends Object implements Serializable
  
  serialVersionUID:
  
  -3336933794060950406L
  - Serialized Fields
    - value
```
String value
```
      Deprecated.
Package ubic.gemma.model.common
- Class ubic.gemma.model.common.AbstractAuditable extends AbstractDescribable implements Serializable
  
  serialVersionUID:
  
  2797229483150957490L
  - Serialized Fields
    - auditTrail
```
AuditTrail auditTrail
```
Package ubic.gemma.model.common.auditAndSecurity
- Class ubic.gemma.model.common.auditAndSecurity.AuditEvent extends Object implements Serializable
  
  serialVersionUID:
  
  -1212093157703833905L
  - Serialized Fields
    - action
```
AuditAction action
```
    - date
```
Date date
```
    - detail
```
String detail
```
    - eventType
```
AuditEventType eventType
```
    - id
```
Long id
```
    - note
```
String note
```
    - performer
```
User performer
```
- Class ubic.gemma.model.common.auditAndSecurity.AuditEventValueObject extends IdentifiableValueObject<AuditEvent> implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - performer
```
String performer
```
    - date
```
Date date
```
    - action
```
String action
```
    - note
```
String note
```
    - detail
```
String detail
```
    - eventType
```
AuditEventType eventType
```
- Class ubic.gemma.model.common.auditAndSecurity.AuditTrail extends Object implements Serializable
  
  serialVersionUID:
  
  -7450755789163303140L
  - Serialized Fields
    - id
```
Long id
```
    - events
```
List<E> events
```
- 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
    - runningStatus
```
Boolean runningStatus
```
    - failedMessage
```
String failedMessage
```
    - startTime
```
Date startTime
```
    - endTime
```
Date endTime
```
    - phases
```
Integer phases
```
    - description
```
String description
```
    - messages
```
String messages
```
    - taskId
```
String taskId
```
    - id
```
Long id
```
    - 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
    - userName
```
String userName
```
    - password
```
String password
```
    - passwordHint
```
String passwordHint
```
    - enabled
```
Boolean enabled
```
    - signupToken
```
String signupToken
```
    - signupTokenDatestamp
```
Date signupTokenDatestamp
```
    - jobs
```
Set<E> jobs
```
    - groups
```
Set<E> groups
```
- Class ubic.gemma.model.common.auditAndSecurity.UserGroup extends AbstractAuditable implements Serializable
  
  serialVersionUID:
  
  5795744069086222179L
  - Serialized Fields
    - groupMembers
```
Set<E> groupMembers
```
    - authorities
```
Set<E> authorities
```
- Class ubic.gemma.model.common.auditAndSecurity.UserQuery extends Object implements Serializable
  
  serialVersionUID:
  
  -2790140985613402440L
  - Serialized Fields
    - url
```
String url
```
    - name
```
String name
```
    - lastUsed
```
Date lastUsed
```
    - autoRunFrequencyHours
```
Integer autoRunFrequencyHours
```
    - id
```
Long id
```
    - searchSettings
```
SearchSettings searchSettings
```
Package ubic.gemma.model.common.auditAndSecurity.curation
- Class ubic.gemma.model.common.auditAndSecurity.curation.AbstractCuratableValueObject extends IdentifiableValueObject<C extends Curatable> implements Serializable
  - Serialized Fields
    - lastUpdated
```
Date lastUpdated
```
    - troubled
```
Boolean troubled
```
    - lastTroubledEvent
```
AuditEventValueObject lastTroubledEvent
```
    - needsAttention
```
Boolean needsAttention
```
    - lastNeedsAttentionEvent
```
AuditEventValueObject lastNeedsAttentionEvent
```
    - curationNote
```
String curationNote
```
    - lastNoteUpdateEvent
```
AuditEventValueObject lastNoteUpdateEvent
```
- Class ubic.gemma.model.common.auditAndSecurity.curation.CurationDetails extends Object implements Serializable
  
  serialVersionUID:
  
  -3418540112052921387L
  - Serialized Fields
    - id
```
Long id
```
    - lastUpdated
```
Date lastUpdated
```
    - lastNeedsAttentionEvent
```
AuditEvent lastNeedsAttentionEvent
```
    - needsAttention
```
Boolean needsAttention
```
    - lastTroubledEvent
```
AuditEvent lastTroubledEvent
```
    - troubled
```
Boolean troubled
```
    - lastNoteUpdateEvent
```
AuditEvent lastNoteUpdateEvent
```
    - curationNote
```
String curationNote
```
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.BatchInformationFetchingEvent extends ExpressionExperimentAnalysisEvent implements Serializable
  
  serialVersionUID:
  
  4635587632131568136L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.BatchProblemsUpdateEvent extends ExpressionExperimentAnalysisEvent implements Serializable
  
  serialVersionUID:
  
  -3061045506228031201L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.BioMaterialMappingUpdate extends ExpressionExperimentAnalysisEvent implements Serializable
  
  serialVersionUID:
  
  -4390321148453980797L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.CommentedEvent extends AuditEventType implements Serializable
  
  serialVersionUID:
  
  -9053488530090657730L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.CurationDetailsEvent extends AuditEventType implements Serializable
  
  serialVersionUID:
  
  6621758826080039878L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.CurationNoteUpdateEvent extends CurationDetailsEvent implements Serializable
  
  serialVersionUID:
  
  -1180281595664872508L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.DataAddedEvent extends ExpressionExperimentAnalysisEvent implements Serializable
  
  serialVersionUID:
  
  -492849538043540166L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.DataReplacedEvent extends ExpressionExperimentAnalysisEvent implements Serializable
  
  serialVersionUID:
  
  -3239733956797015820L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.DifferentialExpressionAnalysisEvent extends ExpressionExperimentAnalysisEvent implements Serializable
  
  serialVersionUID:
  
  -2254124666542924604L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.DifferentialExpressionSuitabilityEvent extends AnalysisSuitabilityEvent implements Serializable
  
  serialVersionUID:
  
  -3436468845066159993L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.DoesNotNeedAttentionEvent extends CurationDetailsEvent implements Serializable
  
  serialVersionUID:
  
  6425018808816856629L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.ExperimentalDesignUpdatedEvent extends AuditEventType implements Serializable
  
  serialVersionUID:
  
  6359338763821876809L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.ExpressionExperimentAnalysisEvent extends AuditEventType implements Serializable
  
  serialVersionUID:
  
  6359338763821876809L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.ExpressionExperimentPlatformSwitchEvent extends ExpressionExperimentAnalysisEvent implements Serializable
  
  serialVersionUID:
  
  2918272498309052073L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.ExpressionExperimentVectorMergeEvent extends ExpressionExperimentAnalysisEvent implements Serializable
  
  serialVersionUID:
  
  3635469819668645913L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.FailedBatchInformationFetchingEvent extends BatchInformationFetchingEvent implements Serializable
  
  serialVersionUID:
  
  -3776787605548724345L
- Class ubic.gemma.model.common.auditAndSecurity.eventType.FailedBatchInformationMissingEvent extends FailedBatchInformationFetchingEvent 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.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.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.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.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
    - classUri
```
String classUri
```
    - className
```
String className
```
    - termUri
```
String termUri
```
    - termName
```
String termName
```
    - description
```
String description
```
    - evidenceCode
```
String evidenceCode
```
    - objectClass
```
String objectClass
```
    - parentName
```
String parentName
```
    - parentDescription
```
String parentDescription
```
    - parentLink
```
String parentLink
```
    - parentOfParentName
```
String parentOfParentName
```
    - parentOfParentDescription
```
String parentOfParentDescription
```
    - parentOfParentLink
```
String parentOfParentLink
```
- Class ubic.gemma.model.common.description.BibliographicReference extends AbstractDescribable implements Serializable
  
  serialVersionUID:
  
  5823969791153895703L
  - Serialized Fields
    - authorList
```
String authorList
```
    - title
```
String title
```
    - publisher
```
String publisher
```
    - editor
```
String editor
```
    - volume
```
String volume
```
    - issue
```
String issue
```
    - pages
```
String pages
```
    - publication
```
String publication
```
    - fullTextUri
```
String fullTextUri
```
    - abstractText
```
String abstractText
```
    - citation
```
String citation
```
    - publicationDate
```
Date publicationDate
```
    - annotatedAbstract
```
String annotatedAbstract
```
    - pubAccession
```
DatabaseEntry pubAccession
```
    - retracted
```
Boolean retracted
```
    - annotations
```
Set<E> annotations
```
      Deprecated. never used
    - meshTerms
```
Set<E> meshTerms
```
    - keywords
```
Set<E> keywords
```
    - chemicals
```
Set<E> chemicals
```
- Class ubic.gemma.model.common.description.BibliographicReferenceValueObject extends IdentifiableValueObject<BibliographicReference> implements Serializable
  - Serialized Fields
    - abstractText
```
String abstractText
```
    - authorList
```
String authorList
```
    - citation
```
CitationValueObject citation
```
    - experiments
```
Collection<E> experiments
```
    - issue
```
String issue
```
    - pages
```
String pages
```
    - pubAccession
```
String pubAccession
```
    - publication
```
String publication
```
    - publicationDate
```
Date publicationDate
```
    - publisher
```
String publisher
```
    - title
```
String title
```
    - volume
```
String volume
```
    - meshTerms
```
Collection<E> meshTerms
```
    - chemicalsTerms
```
Collection<E> chemicalsTerms
```
    - bibliographicPhenotypes
```
Collection<E> bibliographicPhenotypes
```
    - retracted
```
boolean retracted
```
- 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.BibRefAnnotationImpl extends BibRefAnnotation implements Serializable
  
  serialVersionUID:
  
  -6053053643577550669L
- Class ubic.gemma.model.common.description.Characteristic extends AbstractDescribable implements Serializable
  
  serialVersionUID:
  
  -7242166109264718620L
  - Serialized Fields
    - category
```
String category
```
    - categoryUri
```
String categoryUri
```
    - evidenceCode
```
GOEvidenceCode evidenceCode
```
    - 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.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
```
    - Uri
```
String Uri
```
    - id
```
Long id
```
    - externalDatabase
```
ExternalDatabase externalDatabase
```
- 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
    - localInstallDbName
```
String localInstallDbName
```
    - webUri
```
String webUri
```
    - ftpUri
```
String ftpUri
```
    - type
```
DatabaseType type
```
    - databaseSupplier
```
Contact databaseSupplier
```
    - externalDatabases
```
Set<E> externalDatabases
```
      Related external databases.
    - auditTrail
```
AuditTrail auditTrail
```
    - releaseVersion
```
String releaseVersion
```
    - releaseUrl
```
URL releaseUrl
```
    - lastUpdated
```
Date lastUpdated
```
- Class ubic.gemma.model.common.description.ExternalDatabaseValueObject extends IdentifiableValueObject<ExternalDatabase> implements Serializable
  
  serialVersionUID:
  
  -1714429166594162374L
  - Serialized Fields
    - name
```
String name
```
    - description
```
String description
```
    - uri
```
String uri
```
    - releaseVersion
```
String releaseVersion
```
    - releaseUrl
```
URL releaseUrl
```
    - lastUpdated
```
Date lastUpdated
```
    - externalDatabases
```
Set<E> externalDatabases
```
    - checked
```
boolean checked
```
- Class ubic.gemma.model.common.description.Keyword extends BibRefAnnotationImpl implements Serializable
  
  serialVersionUID:
  
  2663428244994277220L
- Class ubic.gemma.model.common.description.LocalFile extends Object implements Serializable
  
  serialVersionUID:
  
  5057142607188347151L
  - Serialized Fields
    - localURL
```
URI localURL
```
    - remoteURL
```
URI remoteURL
```
    - version
```
String version
```
    - size
```
Long size
```
    - id
```
Long id
```
- Class ubic.gemma.model.common.description.MedicalSubjectHeading extends BibRefAnnotationImpl implements Serializable
  
  serialVersionUID:
  
  7820807342851172028L
  - Serialized Fields
    - qualifiers
```
Set<E> qualifiers
```
Package ubic.gemma.model.common.measurement
- Class ubic.gemma.model.common.measurement.Measurement extends Object implements Serializable
  
  serialVersionUID:
  
  1833568047451431226L
  - Serialized Fields
    - type
```
MeasurementType type
```
    - value
```
String value
```
    - kindCV
```
MeasurementKind kindCV
```
    - otherKind
```
String otherKind
```
    - representation
```
PrimitiveType representation
```
    - id
```
Long id
```
    - unit
```
Unit unit
```
- Class ubic.gemma.model.common.measurement.MeasurementImpl extends Measurement implements Serializable
  
  serialVersionUID:
  
  -5572865478492871637L
- Class ubic.gemma.model.common.measurement.MeasurementValueObject extends IdentifiableValueObject implements Serializable
  - Serialized Fields
    - value
```
String value
```
    - unit
```
String unit
```
    - unitId
```
Long unitId
```
    - type
```
String type
```
    - representation
```
String representation
```
- Class ubic.gemma.model.common.measurement.Unit extends Object implements Serializable
  
  serialVersionUID:
  
  6348133346610787608L
  - Serialized Fields
    - unitNameCV
```
String unitNameCV
```
    - id
```
Long id
```
- Class ubic.gemma.model.common.measurement.UnitImpl extends Unit implements Serializable
  
  serialVersionUID:
  
  -6113027641969468902L
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
    - 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
    - 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.
    - isRatio
```
boolean isRatio
```
    - generalType
```
GeneralType generalType
```
    - representation
```
PrimitiveType representation
```
    - scale
```
ScaleType scale
```
    - type
```
StandardQuantitationType type
```
- Class ubic.gemma.model.common.quantitationtype.QuantitationTypeImpl extends QuantitationType implements Serializable
  
  serialVersionUID:
  
  -352202738189491165L
- Class ubic.gemma.model.common.quantitationtype.QuantitationTypeValueObject extends IdentifiableValueObject<QuantitationType> implements Serializable
  
  serialVersionUID:
  
  7537853492100102404L
  - Serialized Fields
    - description
```
String description
```
    - 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
```
    - 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.
    - 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
    - query
```
String query
```
      Processed query for performing a search.
    - resultTypes
```
Set<E> resultTypes
```
      Entities to retrieve.
    - platformConstraint
```
ArrayDesign platformConstraint
```
    - taxon
```
Taxon taxon
```
    - useCharacteristics
```
Boolean useCharacteristics
```
    - useDatabase
```
Boolean useDatabase
```
    - useGo
```
Boolean useGo
```
    - useIndices
```
Boolean useIndices
```
    - doHighlighting
```
boolean doHighlighting
```
      Highlight part of the search result as per SearchResult#getHighlightedText(). Overhead can be reduced by disabling highlighting if not needed.
    - 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.
- Class ubic.gemma.model.common.search.SearchSettingsValueObject extends Object implements Serializable
  
  serialVersionUID:
  
  -934534534L
  - Serialized Fields
    - maxResults
```
Integer maxResults
```
    - platformConstraint
```
ArrayDesign platformConstraint
```
    - query
```
String query
```
    - searchBibrefs
```
Boolean searchBibrefs
```
    - searchBioSequences
```
Boolean searchBioSequences
```
    - searchExperiments
```
Boolean searchExperiments
```
    - searchExperimentSets
```
Boolean searchExperimentSets
```
    - searchGenes
```
Boolean searchGenes
```
    - searchGeneSets
```
Boolean searchGeneSets
```
    - searchPhenotypes
```
Boolean searchPhenotypes
```
    - searchPlatforms
```
Boolean searchPlatforms
```
    - searchProbes
```
Boolean searchProbes
```
    - taxon
```
Taxon taxon
```
    - termUri
```
String termUri
```
    - useCharacteristics
```
Boolean useCharacteristics
```
    - useDatabase
```
Boolean useDatabase
```
    - useGo
```
Boolean useGo
```
    - useIndices
```
Boolean useIndices
```
Package ubic.gemma.model.expression
- Class ubic.gemma.model.expression.BlacklistedEntity extends AbstractDescribable implements Serializable
  - Serialized Fields
    - externalAccession
```
DatabaseEntry externalAccession
```
      The external accession
    - reason
```
String reason
```
      The reason the entity was blacklisted.
    - shortName
```
String shortName
```
- Class ubic.gemma.model.expression.BlacklistedValueObject extends IdentifiableValueObject<BlacklistedEntity> implements Serializable
  
  serialVersionUID:
  
  -4817418347388923905L
  - Serialized Fields
    - accession
```
String accession
```
    - externalDatabase
```
ExternalDatabaseValueObject externalDatabase
```
    - name
```
String name
```
    - reason
```
String reason
```
    - shortName
```
String shortName
```
    - type
```
String type
```
Package ubic.gemma.model.expression.arrayDesign
- Class ubic.gemma.model.expression.arrayDesign.AlternateName extends Object implements Serializable
  
  serialVersionUID:
  
  -1208836332065611893L
  - Serialized Fields
    - name
```
String name
```
    - id
```
Long id
```
- Class ubic.gemma.model.expression.arrayDesign.AlternateNameImpl extends AlternateName implements Serializable
  
  serialVersionUID:
  
  -1208836332065611893L
- Class ubic.gemma.model.expression.arrayDesign.ArrayDesign extends AbstractAuditable implements Serializable
  
  serialVersionUID:
  
  -7566439134502613470L
  - Serialized Fields
    - advertisedNumberOfDesignElements
```
Integer advertisedNumberOfDesignElements
```
    - alternateNames
```
Set<E> alternateNames
```
    - alternativeTo
```
ArrayDesign alternativeTo
```
    - compositeSequences
```
Set<E> compositeSequences
```
    - curationDetails
```
CurationDetails curationDetails
```
    - designProvider
```
Contact designProvider
```
    - externalReferences
```
Set<E> externalReferences
```
    - mergedInto
```
ArrayDesign mergedInto
```
    - mergees
```
Set<E> mergees
```
    - primaryTaxon
```
Taxon primaryTaxon
```
    - shortName
```
String shortName
```
    - subsumedArrayDesigns
```
Set<E> subsumedArrayDesigns
```
    - subsumingArrayDesign
```
ArrayDesign subsumingArrayDesign
```
    - technologyType
```
TechnologyType technologyType
```
- Class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject extends AbstractCuratableValueObject<ArrayDesign> implements Serializable
  
  serialVersionUID:
  
  -8259245319391937522L
  - Serialized Fields
    - blackListed
```
Boolean blackListed
```
    - color
```
String color
```
    - dateCached
```
String dateCached
```
    - description
```
String description
```
    - designElementCount
```
Integer designElementCount
```
    - expressionExperimentCount
```
Long expressionExperimentCount
```
    - 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.
    - shortName
```
String shortName
```
    - switchedExpressionExperimentCount
```
Long switchedExpressionExperimentCount
```
    - taxonObject
```
TaxonValueObject taxonObject
```
    - technologyType
```
String technologyType
```
    - releaseVersion
```
String releaseVersion
```
    - releaseUrl
```
URL releaseUrl
```
    - externalReferences
```
Set<E> externalReferences
```
      Main external reference.
- Class ubic.gemma.model.expression.arrayDesign.BlacklistedPlatform extends BlacklistedEntity implements Serializable
Package ubic.gemma.model.expression.bioAssay
- Class ubic.gemma.model.expression.bioAssay.BioAssay extends AbstractDescribable implements Serializable
  
  serialVersionUID:
  
  -7868768731812964045L
  - Serialized Fields
    - sequencePairedReads
```
Boolean sequencePairedReads
```
    - isOutlier
```
Boolean isOutlier
```
    - processingDate
```
Date processingDate
```
    - sequenceReadCount
```
Integer sequenceReadCount
```
    - sequenceReadLength
```
Integer sequenceReadLength
```
    - arrayDesignUsed
```
ArrayDesign arrayDesignUsed
```
    - originalPlatform
```
ArrayDesign originalPlatform
```
      If the sample data was switched to another platform, this is what it was originally.
    - sampleUsed
```
BioMaterial sampleUsed
```
    - accession
```
DatabaseEntry accession
```
    - metadata
```
String metadata
```
    - 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.
- 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
```
Integer 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<E> bioAssays
```
- Class ubic.gemma.model.expression.bioAssayData.BioAssayDimensionValueObject extends IdentifiableValueObject<BioAssayDimension> implements Serializable
  
  serialVersionUID:
  
  -8686807689616396835L
  - Serialized Fields
    - bioAssays
```
List<E> bioAssays
```
    - description
```
String description
```
    - name
```
String name
```
    - isReordered
```
boolean isReordered
```
    - isSubset
```
boolean isSubset
```
    - 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
```
    - id
```
Long id
```
    - quantitationType
```
QuantitationType quantitationType
```
- Class ubic.gemma.model.expression.bioAssayData.DataVectorValueObject extends IdentifiableValueObject<DataVector> implements Serializable
  
  serialVersionUID:
  
  4291090102921066018L
  - Serialized Fields
    - expressionExperiment
```
ExpressionExperimentValueObject expressionExperiment
```
    - designElement
```
CompositeSequenceValueObject designElement
```
    - quantitationType
```
QuantitationTypeValueObject quantitationType
```
    - genes
```
Collection<E> genes
```
    - bioAssayDimension
```
BioAssayDimensionValueObject bioAssayDimension
```
- 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
```
    - reorganized
```
boolean reorganized
```
    - sliced
```
boolean sliced
```
    - pvalue
```
Double pvalue
```
    - rank
```
Double rank
```
    - rankByMax
```
Double rankByMax
```
    - rankByMean
```
Double rankByMean
```
    - sourceVectorId
```
Long sourceVectorId
```
      Will only be non-null if the id is null, when we have a 'slice' of the data
- Class ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject extends Object implements Serializable
  - Serialized Fields
    - datasetId
```
long datasetId
```
    - geneExpressionLevels
```
LinkedList<E> geneExpressionLevels
```
- Class ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject.GeneElementExpressionsValueObject extends Object implements Serializable
  - Serialized Fields
    - geneOfficialSymbol
```
String geneOfficialSymbol
```
    - geneNcbiId
```
Integer geneNcbiId
```
    - elements
```
List<E> elements
```
- Class ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject.VectorElementValueObject extends Object implements Serializable
  - Serialized Fields
    - designElementName
```
String designElementName
```
    - bioAssayExpressionLevels
```
Map<K,V> bioAssayExpressionLevels
```
- Class ubic.gemma.model.expression.bioAssayData.MeanVarianceRelation extends Object implements Serializable
  
  serialVersionUID:
  
  -1442923993171126882L
  - Serialized Fields
    - securityOwner
```
gemma.gsec.model.Securable securityOwner
```
    - means
```
byte[] means
```
    - variances
```
byte[] variances
```
    - id
```
Long id
```
- Class ubic.gemma.model.expression.bioAssayData.ProcessedExpressionDataVector extends DesignElementDataVector implements Serializable
  
  serialVersionUID:
  
  -3948846630785289034L
  - Serialized Fields
    - rankByMean
```
Double rankByMean
```
    - rankByMax
```
Double rankByMax
```
    - expressionExperiment
```
ExpressionExperiment expressionExperiment
```
- Class ubic.gemma.model.expression.bioAssayData.RawExpressionDataVector extends DesignElementDataVector implements Serializable
  
  serialVersionUID:
  
  -7410374297463625206L
  - Serialized Fields
    - expressionExperiment
```
ExpressionExperiment expressionExperiment
```
Package ubic.gemma.model.expression.biomaterial
- Class ubic.gemma.model.expression.biomaterial.BioMaterial extends AbstractDescribable implements Serializable
  
  serialVersionUID:
  
  4374359557498220256L
  - Serialized Fields
    - sourceTaxon
```
Taxon sourceTaxon
```
    - factorValues
```
Set<E> factorValues
```
    - bioAssaysUsedIn
```
Set<E> bioAssaysUsedIn
```
    - treatments
```
Set<E> treatments
```
    - characteristics
```
Set<E> characteristics
```
    - externalAccession
```
DatabaseEntry externalAccession
```
- Class ubic.gemma.model.expression.biomaterial.BioMaterialValueObject extends IdentifiableValueObject<BioMaterial> implements Serializable
  
  serialVersionUID:
  
  -145137827948521045L
  - Serialized Fields
    - name
```
String name
```
    - description
```
String description
```
    - assayName
```
String assayName
```
    - assayDescription
```
String assayDescription
```
    - bioAssayIds
```
Collection<E> bioAssayIds
```
      Related BioAssay IDs.
    - characteristics
```
Collection<E> characteristics
```
    - characteristicValues
```
Map<K,V> characteristicValues
```
    - basicFVs
```
boolean basicFVs
```
      Indicate if this is using the BioMaterialValueObject.fVBasicVOs or BioMaterialValueObject.factorValueObjects for representing factor values.
    - fVBasicVOs
```
Collection<E> fVBasicVOs
```
    - factorValueObjects
```
Collection<E> factorValueObjects
```
    - factorValues
```
Map<K,V> factorValues
```
      Map of ids (fv133) to a representation of the value (for this biomaterial.)
    - factorIdToFactorValueId
```
Map<K,V> factorIdToFactorValueId
```
      Map of factor ids (factor232) to factor value (id or the actual value) for this biomaterial.
    - factors
```
Map<K,V> factors
```
      Map of ids (factor232) to a representation of the factor (e.g., the name).
    - assayProcessingDate
```
Date assayProcessingDate
```
- 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
    - biologicalCharacteristic
```
BioSequence biologicalCharacteristic
```
    - arrayDesign
```
ArrayDesign arrayDesign
```
- Class ubic.gemma.model.expression.designElement.CompositeSequenceValueObject extends IdentifiableValueObject<CompositeSequence> implements Serializable
  
  serialVersionUID:
  
  4915680501039784666L
  - Serialized Fields
    - name
```
String name
```
    - description
```
String description
```
    - arrayDesign
```
ArrayDesignValueObject arrayDesign
```
    - geneMappingSummaries
```
Collection<E> geneMappingSummaries
```
Package ubic.gemma.model.expression.experiment
- Class ubic.gemma.model.expression.experiment.BioAssaySet extends Investigation implements Serializable
  
  serialVersionUID:
  
  2368063046639481521L
  - Serialized Fields
    - accession
```
DatabaseEntry accession
```
    - bioAssays
```
Set<E> bioAssays
```
- Class ubic.gemma.model.expression.experiment.BlacklistedExperiment extends BlacklistedEntity implements Serializable
- Class ubic.gemma.model.expression.experiment.ExperimentalDesign extends AbstractDescribable implements Serializable
  
  serialVersionUID:
  
  1734101852541885497L
  - Serialized Fields
    - replicateDescription
```
String replicateDescription
```
    - qualityControlDescription
```
String qualityControlDescription
```
    - normalizationDescription
```
String normalizationDescription
```
    - experimentalFactors
```
Set<E> experimentalFactors
```
    - types
```
Set<E> types
```
- Class ubic.gemma.model.expression.experiment.ExperimentalFactor extends AbstractDescribable implements Serializable
  
  serialVersionUID:
  
  4615731059510436891L
  - Serialized Fields
    - annotations
```
Set<E> annotations
```
    - category
```
Characteristic category
```
    - experimentalDesign
```
ExperimentalDesign experimentalDesign
```
    - factorValues
```
Set<E> 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
```
    - name
```
String name
```
    - type
```
String type
```
    - values
```
Collection<E> values
```
- Class ubic.gemma.model.expression.experiment.ExpressionExperiment extends BioAssaySet implements Serializable
  
  serialVersionUID:
  
  -1342753625018841735L
  - Serialized Fields
    - batchConfound
```
String batchConfound
```
    - batchEffect
```
String batchEffect
```
    - curationDetails
```
CurationDetails curationDetails
```
    - experimentalDesign
```
ExperimentalDesign experimentalDesign
```
    - geeq
```
Geeq geeq
```
    - meanVarianceRelation
```
MeanVarianceRelation meanVarianceRelation
```
    - metadata
```
String metadata
```
    - numberOfDataVectors
```
Integer numberOfDataVectors
```
    - numberOfSamples
```
Integer numberOfSamples
```
    - taxon
```
Taxon taxon
```
    - otherParts
```
Set<E> otherParts
```
      If this experiment was split off of a larger experiment, link to its relatives.
    - processedExpressionDataVectors
```
Set<E> processedExpressionDataVectors
```
    - quantitationTypes
```
Set<E> quantitationTypes
```
    - rawExpressionDataVectors
```
Set<E> rawExpressionDataVectors
```
    - shortName
```
String shortName
```
    - source
```
String source
```
- Class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject extends ExpressionExperimentValueObject implements Serializable
  
  serialVersionUID:
  
  -1219449523930648392L
  - Serialized Fields
    - arrayDesigns
```
Collection<E> 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<E> differentialExpressionAnalyses
```
    - expressionExperimentSets
```
Collection<E> expressionExperimentSets
```
    - hasBatchInformation
```
boolean hasBatchInformation
```
    - hasBothIntensities
```
Boolean hasBothIntensities
```
    - hasCoexpressionAnalysis
```
Boolean hasCoexpressionAnalysis
```
    - hasDifferentialExpressionAnalysis
```
Boolean hasDifferentialExpressionAnalysis
```
    - hasEitherIntensity
```
Boolean hasEitherIntensity
```
    - hasMultiplePreferredQuantitationTypes
```
Boolean hasMultiplePreferredQuantitationTypes
```
    - hasMultipleTechnologyTypes
```
Boolean hasMultipleTechnologyTypes
```
    - isRNASeq
```
Boolean isRNASeq
```
    - lastArrayDesignUpdateDate
```
String lastArrayDesignUpdateDate
```
    - linkAnalysisEventType
```
String linkAnalysisEventType
```
    - minPvalue
```
Double minPvalue
```
    - missingValueAnalysisEventType
```
String missingValueAnalysisEventType
```
    - numAnnotations
```
Long numAnnotations
```
    - numPopulatedFactors
```
Long numPopulatedFactors
```
    - originalPlatforms
```
Collection<E> originalPlatforms
```
    - otherParts
```
Collection<E> otherParts
```
    - pcaAnalysisEventType
```
String pcaAnalysisEventType
```
    - primaryCitation
```
CitationValueObject primaryCitation
```
    - processedDataVectorComputationEventType
```
String processedDataVectorComputationEventType
```
    - pubmedId
```
Integer pubmedId
```
    - QChtml
```
String QChtml
```
    - reprocessedFromRawData
```
boolean reprocessedFromRawData
```
    - sampleRemovedFlags
```
Collection<E> 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<E> expressionExperimentIds
```
    - isPublic
```
boolean isPublic
```
    - modifiable
```
boolean modifiable
```
      If modifying the set is constrained by existing analyses.
    - name
```
String name
```
    - size
```
Integer size
```
    - numWithCoexpressionAnalysis
```
Integer numWithCoexpressionAnalysis
```
    - numWithDifferentialExpressionAnalysis
```
Integer numWithDifferentialExpressionAnalysis
```
    - shared
```
boolean shared
```
    - taxonId
```
Long taxonId
```
    - taxonName
```
String taxonName
```
    - userCanWrite
```
boolean userCanWrite
```
    - userOwned
```
boolean userOwned
```
- Class ubic.gemma.model.expression.experiment.ExpressionExperimentSubSet extends BioAssaySet implements Serializable
  
  serialVersionUID:
  
  -1880425342951467283L
  - Serialized Fields
    - sourceExperiment
```
ExpressionExperiment sourceExperiment
```
- Class ubic.gemma.model.expression.experiment.ExpressionExperimentSubsetValueObject extends ExpressionExperimentValueObject implements Serializable
  - Serialized Fields
    - sourceExperiment
```
Long sourceExperiment
```
- Class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject extends AbstractCuratableValueObject<ExpressionExperiment> implements Serializable
  
  serialVersionUID:
  
  -6861385216096602508L
  - Serialized Fields
    - numberOfBioAssays
```
Integer numberOfBioAssays
```
    - description
```
String description
```
    - name
```
String name
```
    - accession
```
String accession
```
    - arrayDesignCount
```
Long arrayDesignCount
```
    - batchConfound
```
String batchConfound
```
    - batchEffect
```
String batchEffect
```
    - bioMaterialCount
```
Integer bioMaterialCount
```
    - currentUserHasWritePermission
```
Boolean currentUserHasWritePermission
```
    - currentUserIsOwner
```
Boolean currentUserIsOwner
```
    - experimentalDesign
```
Long experimentalDesign
```
    - externalDatabase
```
String externalDatabase
```
    - externalUri
```
String externalUri
```
    - geeq
```
GeeqValueObject geeq
```
    - isPublic
```
Boolean isPublic
```
    - isShared
```
Boolean isShared
```
    - metadata
```
String metadata
```
    - 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
    - securityOwner
```
ExpressionExperiment securityOwner
```
    - value
```
String value
```
      Deprecated.
      
      Use FactorValue.characteristics instead.
    - isBaseline
```
Boolean isBaseline
```
    - id
```
Long id
```
    - experimentalFactor
```
ExperimentalFactor experimentalFactor
```
    - measurement
```
Measurement measurement
```
    - characteristics
```
Set<E> characteristics
```
- Class ubic.gemma.model.expression.experiment.FactorValueBasicValueObject extends IdentifiableValueObject<FactorValue> implements Serializable
  
  serialVersionUID:
  
  3378801249808036785L
  - Serialized Fields
    - isBaseline
```
boolean isBaseline
```
    - characteristics
```
Collection<E> characteristics
```
    - experimentalFactorCategory
```
CharacteristicBasicValueObject experimentalFactorCategory
```
    - measurement
```
MeasurementValueObject measurement
```
    - value
```
String value
```
    - summary
```
String summary
```
    - experimentalFactorId
```
Long experimentalFactorId
```
- Class ubic.gemma.model.expression.experiment.FactorValueValueObject extends IdentifiableValueObject<FactorValue> implements Serializable
  
  serialVersionUID:
  
  3378801249808036785L
  - Serialized Fields
    - category
```
String category
```
      Deprecated.
    - categoryUri
```
String categoryUri
```
      Deprecated.
    - description
```
String description
```
      Deprecated.
    - factor
```
String factor
```
      Deprecated.
    - value
```
String value
```
      Deprecated.
    - valueUri
```
String valueUri
```
      Deprecated.
    - charId
```
Long charId
```
      Deprecated.
      
      It could be the id of the measurement if there is no characteristic.
    - factorId
```
Long factorId
```
      Deprecated.
    - isBaseline
```
boolean isBaseline
```
      Deprecated.
    - measurement
```
boolean measurement
```
      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
    - id
```
Long id
```
    - detectedQualityScore
```
double detectedQualityScore
```
    - manualQualityScore
```
double manualQualityScore
```
    - manualQualityOverride
```
boolean manualQualityOverride
```
    - detectedSuitabilityScore
```
double detectedSuitabilityScore
```
    - manualSuitabilityScore
```
double manualSuitabilityScore
```
    - manualSuitabilityOverride
```
boolean manualSuitabilityOverride
```
    - sScorePublication
```
double sScorePublication
```
    - sScorePlatformAmount
```
double sScorePlatformAmount
```
    - sScorePlatformsTechMulti
```
double sScorePlatformsTechMulti
```
    - sScoreAvgPlatformPopularity
```
double sScoreAvgPlatformPopularity
```
    - sScoreAvgPlatformSize
```
double sScoreAvgPlatformSize
```
    - sScoreSampleSize
```
double sScoreSampleSize
```
    - sScoreRawData
```
double sScoreRawData
```
    - sScoreMissingValues
```
double sScoreMissingValues
```
    - noVectors
```
boolean noVectors
```
    - qScoreOutliers
```
double qScoreOutliers
```
    - corrMatIssues
```
byte corrMatIssues
```
    - qScoreSampleMeanCorrelation
```
double qScoreSampleMeanCorrelation
```
    - qScoreSampleMedianCorrelation
```
double qScoreSampleMedianCorrelation
```
    - qScoreSampleCorrelationVariance
```
double qScoreSampleCorrelationVariance
```
    - qScorePlatformsTech
```
double qScorePlatformsTech
```
    - qScoreReplicates
```
double qScoreReplicates
```
    - replicatesIssues
```
byte replicatesIssues
```
    - qScoreBatchInfo
```
double qScoreBatchInfo
```
    - batchCorrected
```
boolean batchCorrected
```
    - qScoreBatchEffect
```
double qScoreBatchEffect
```
    - manualHasStrongBatchEffect
```
boolean manualHasStrongBatchEffect
```
    - manualHasNoBatchEffect
```
boolean manualHasNoBatchEffect
```
    - manualBatchEffectActive
```
boolean manualBatchEffectActive
```
    - qScoreBatchConfound
```
double qScoreBatchConfound
```
    - manualHasBatchConfound
```
boolean manualHasBatchConfound
```
    - manualBatchConfoundActive
```
boolean manualBatchConfoundActive
```
    - otherIssues
```
String otherIssues
```
- Class ubic.gemma.model.expression.experiment.GeeqAdminValueObject extends GeeqValueObject implements Serializable
  - Serialized Fields
    - detectedQualityScore
```
double detectedQualityScore
```
    - manualQualityScore
```
double manualQualityScore
```
    - manualQualityOverride
```
boolean manualQualityOverride
```
    - detectedSuitabilityScore
```
double detectedSuitabilityScore
```
    - manualSuitabilityScore
```
double manualSuitabilityScore
```
    - manualSuitabilityOverride
```
boolean manualSuitabilityOverride
```
    - qScoreBatchEffect
```
double qScoreBatchEffect
```
    - manualHasStrongBatchEffect
```
boolean manualHasStrongBatchEffect
```
    - manualHasNoBatchEffect
```
boolean manualHasNoBatchEffect
```
    - manualBatchEffectActive
```
boolean manualBatchEffectActive
```
    - qScoreBatchConfound
```
double qScoreBatchConfound
```
    - manualHasBatchConfound
```
boolean manualHasBatchConfound
```
    - manualBatchConfoundActive
```
boolean manualBatchConfoundActive
```
    - otherIssues
```
String otherIssues
```
- Class ubic.gemma.model.expression.experiment.GeeqValueObject extends IdentifiableValueObject<Geeq> implements Serializable
  - Serialized Fields
    - publicQualityScore
```
double publicQualityScore
```
    - publicSuitabilityScore
```
double publicSuitabilityScore
```
    - sScorePublication
```
double sScorePublication
```
    - sScorePlatformAmount
```
double sScorePlatformAmount
```
    - sScorePlatformsTechMulti
```
double sScorePlatformsTechMulti
```
    - sScoreAvgPlatformPopularity
```
double sScoreAvgPlatformPopularity
```
    - sScoreAvgPlatformSize
```
double sScoreAvgPlatformSize
```
    - sScoreSampleSize
```
double sScoreSampleSize
```
    - sScoreRawData
```
double sScoreRawData
```
    - sScoreMissingValues
```
double sScoreMissingValues
```
    - qScoreOutliers
```
double qScoreOutliers
```
    - qScoreSampleMeanCorrelation
```
double qScoreSampleMeanCorrelation
```
    - qScoreSampleMedianCorrelation
```
double qScoreSampleMedianCorrelation
```
    - qScoreSampleCorrelationVariance
```
double qScoreSampleCorrelationVariance
```
    - qScorePlatformsTech
```
double qScorePlatformsTech
```
    - qScoreReplicates
```
double qScoreReplicates
```
    - qScoreBatchInfo
```
double qScoreBatchInfo
```
    - qScorePublicBatchEffect
```
double qScorePublicBatchEffect
```
    - qScorePublicBatchConfound
```
double qScorePublicBatchConfound
```
    - noVectors
```
boolean noVectors
```
    - corrMatIssues
```
byte corrMatIssues
```
    - replicatesIssues
```
byte replicatesIssues
```
    - batchCorrected
```
boolean batchCorrected
```
- Class ubic.gemma.model.expression.experiment.SessionBoundExpressionExperimentSetValueObject extends ExpressionExperimentSetValueObject implements Serializable
  
  serialVersionUID:
  
  2068650886972222818L
  - Serialized Fields
    - modified
```
boolean modified
```
Package ubic.gemma.model.genome
- Class ubic.gemma.model.genome.Chromosome extends Object implements Serializable
  
  serialVersionUID:
  
  7394734846565885136L
  - Serialized Fields
    - name
```
String name
```
    - assemblyDatabase
```
ExternalDatabase assemblyDatabase
```
    - sequence
```
BioSequence sequence
```
    - taxon
```
Taxon taxon
```
    - id
```
Long id
```
- Class ubic.gemma.model.genome.ChromosomeFeature extends AbstractDescribable implements Serializable
  
  serialVersionUID:
  
  -8627296370886752496L
  - Serialized Fields
    - previousNcbiId
```
String previousNcbiId
```
    - physicalLocation
```
PhysicalLocation physicalLocation
```
- Class ubic.gemma.model.genome.ChromosomeLocation extends Object implements Serializable
  
  serialVersionUID:
  
  -4932607147290671454L
  - Serialized Fields
    - id
```
Long id
```
    - chromosome
```
Chromosome chromosome
```
- Class ubic.gemma.model.genome.Gene extends ChromosomeFeature implements Serializable
  
  serialVersionUID:
  
  -5693198926006383546L
  - Serialized Fields
    - officialSymbol
```
String officialSymbol
```
    - officialName
```
String officialName
```
    - ncbiGeneId
```
Integer ncbiGeneId
```
    - ensemblId
```
String ensemblId
```
    - products
```
Set<E> products
```
    - aliases
```
Set<E> aliases
```
    - taxon
```
Taxon taxon
```
    - accessions
```
Set<E> accessions
```
    - multifunctionality
```
Multifunctionality multifunctionality
```
    - phenotypeAssociations
```
Set<E> phenotypeAssociations
```
- Class ubic.gemma.model.genome.GeneOntologyTermValueObject extends Object implements Serializable
  - Serialized Fields
    - goId
```
String goId
```
    - label
```
String label
```
    - uri
```
String uri
```
    - comment
```
String comment
```
    - localName
```
String localName
```
    - term
```
String term
```
    - isObsolete
```
boolean isObsolete
```
- Class ubic.gemma.model.genome.PhysicalLocation extends ChromosomeLocation implements Serializable
  
  serialVersionUID:
  
  -6580769809003779541L
  - Serialized Fields
    - nucleotide
```
Long nucleotide
```
    - nucleotideLength
```
Integer nucleotideLength
```
    - strand
```
String strand
```
    - bin
```
Integer bin
```
- Class ubic.gemma.model.genome.PhysicalLocationValueObject extends IdentifiableValueObject<PhysicalLocation> implements Serializable
  - Serialized Fields
    - nucleotide
```
Long nucleotide
```
    - nucleotideLength
```
Integer nucleotideLength
```
    - strand
```
String strand
```
    - bin
```
Integer bin
```
    - chromosome
```
String chromosome
```
    - taxon
```
TaxonValueObject taxon
```
- Class ubic.gemma.model.genome.Taxon extends Object implements Serializable
  
  serialVersionUID:
  
  9219471082900615778L
  - Serialized Fields
    - scientificName
```
String scientificName
```
    - commonName
```
String commonName
```
    - ncbiId
```
Integer ncbiId
```
    - isGenesUsable
```
boolean isGenesUsable
```
    - secondaryNcbiId
```
Integer secondaryNcbiId
```
    - id
```
Long id
```
    - externalDatabase
```
ExternalDatabase externalDatabase
```
- Class ubic.gemma.model.genome.TaxonValueObject extends IdentifiableValueObject<Taxon> implements Serializable
  - Serialized Fields
    - scientificName
```
String scientificName
```
    - commonName
```
String commonName
```
    - ncbiId
```
Integer ncbiId
```
    - isSpecies
```
Boolean isSpecies
```
    - isGenesUsable
```
Boolean isGenesUsable
```
    - externalDatabase
```
ExternalDatabaseValueObject externalDatabase
```
Package ubic.gemma.model.genome.biosequence
- Class ubic.gemma.model.genome.biosequence.BioSequence extends AbstractDescribable implements Serializable
  
  serialVersionUID:
  
  -6620431603579954167L
  - Serialized Fields
    - length
```
Long length
```
    - sequence
```
String sequence
```
    - isApproximateLength
```
Boolean isApproximateLength
```
    - isCircular
```
Boolean isCircular
```
    - polymerType
```
PolymerType polymerType
```
    - type
```
SequenceType type
```
    - fractionRepeats
```
Double fractionRepeats
```
    - sequenceDatabaseEntry
```
DatabaseEntry sequenceDatabaseEntry
```
    - taxon
```
Taxon taxon
```
    - bioSequence2GeneProduct
```
Set<E> bioSequence2GeneProduct
```
Package ubic.gemma.model.genome.gene
- Class ubic.gemma.model.genome.gene.DatabaseBackedGeneSetValueObject extends GeneSetValueObject implements Serializable
  
  serialVersionUID:
  
  -1360523793656012770L
- Class ubic.gemma.model.genome.gene.GeneAlias extends Object implements Serializable
  
  serialVersionUID:
  
  -4156628260205167700L
  - Serialized Fields
    - alias
```
String alias
```
    - id
```
Long id
```
- Class ubic.gemma.model.genome.gene.GeneProduct extends ChromosomeFeature implements Serializable
  
  serialVersionUID:
  
  8414732389521430535L
  - Serialized Fields
    - ncbiGi
```
String ncbiGi
```
    - accessions
```
Set<E> accessions
```
    - exons
```
Set<E> 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
```
- Class ubic.gemma.model.genome.gene.GeneProductValueObject extends IdentifiableValueObject<GeneProduct> implements Serializable
  
  serialVersionUID:
  
  1156628868995566223L
  - Serialized Fields
    - ncbiId
```
String ncbiId
```
    - name
```
String name
```
    - geneId
```
Long geneId
```
    - chromosome
```
String chromosome
```
    - strand
```
String strand
```
    - nucleotideStart
```
Long nucleotideStart
```
    - nucleotideEnd
```
Long nucleotideEnd
```
      Deprecated.
- Class ubic.gemma.model.genome.gene.GeneSet extends AbstractAuditable implements Serializable
  
  serialVersionUID:
  
  4357218100681569138L
  - Serialized Fields
    - characteristics
```
Set<E> characteristics
```
    - sourceAccession
```
DatabaseEntry sourceAccession
```
    - literatureSources
```
Set<E> literatureSources
```
    - members
```
Set<E> members
```
- Class ubic.gemma.model.genome.gene.GeneSetMember extends Object implements Serializable
  
  serialVersionUID:
  
  -926690781193097196L
  - Serialized Fields
    - score
```
Double score
```
    - id
```
Long id
```
    - gene
```
Gene gene
```
- Class ubic.gemma.model.genome.gene.GeneSetValueObject extends IdentifiableValueObject<GeneSet> implements Serializable
  
  serialVersionUID:
  
  6212231006289412683L
  - Serialized Fields
    - name
```
String name
```
    - description
```
String description
```
    - geneIds
```
Collection<E> geneIds
```
      Gene IDs part of this gene set.
      This is currently not populated, but we might consider it, see #445.
    - size
```
Integer size
```
    - taxon
```
TaxonValueObject taxon
```
    - userOwned
```
boolean userOwned
```
    - isPublic
```
boolean isPublic
```
    - isShared
```
boolean isShared
```
- Class ubic.gemma.model.genome.gene.GeneValueObject extends IdentifiableValueObject<Gene> implements Serializable
  
  serialVersionUID:
  
  -7098036090107647318L
  - Serialized Fields
    - aliases
```
SortedSet<E> aliases
```
      Gene aliases, sorted alphabetically.
    - associatedExperimentCount
```
Integer associatedExperimentCount
```
      How many experiments "involve" (manipulate, etc.) this gene
    - compositeSequenceCount
```
Integer compositeSequenceCount
```
    - description
```
String description
```
    - geneSets
```
Collection<E> geneSets
```
    - homologues
```
Collection<E> homologues
```
    - 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
```
    - ensemblId
```
String ensemblId
```
    - accessions
```
Set<E> accessions
```
    - 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<E> phenotypes
```
    - platformCount
```
Integer platformCount
```
    - score
```
Double score
```
    - taxon
```
TaxonValueObject taxon
```
- Class ubic.gemma.model.genome.gene.Multifunctionality extends Object implements Serializable
  
  serialVersionUID:
  
  1842256912459855071L
  - Serialized Fields
    - score
```
Double score
```
    - rank
```
Double rank
```
    - numGoTerms
```
Integer numGoTerms
```
    - id
```
Long id
```
Package ubic.gemma.model.genome.gene.phenotype.valueObject
- Class ubic.gemma.model.genome.gene.phenotype.valueObject.BibliographicPhenotypesValueObject extends Object implements Serializable
  - Serialized Fields
    - geneNCBI
```
Integer geneNCBI
```
    - geneName
```
String geneName
```
    - evidenceId
```
Long evidenceId
```
    - phenotypesValues
```
Set<E> phenotypesValues
```
- Class ubic.gemma.model.genome.gene.phenotype.valueObject.CharacteristicBasicValueObject extends IdentifiableValueObject<Characteristic> implements Serializable
  - Serialized Fields
    - value
```
String value
```
    - valueUri
```
String valueUri
```
    - category
```
String category
```
    - categoryUri
```
String categoryUri
```
- Class ubic.gemma.model.genome.gene.phenotype.valueObject.CharacteristicValueObject extends IdentifiableValueObject<Characteristic> implements Serializable
  - Serialized Fields
    - urlId
```
String urlId
```
      id used by url on the client side
    - 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
    - privateGeneCount
```
long privateGeneCount
```
    - publicGeneCount
```
long publicGeneCount
```
      number of occurrences in all genes
    - root
```
boolean root
```
      root of a query
    - taxon
```
String taxon
```
    - value
```
String value
```
    - valueUri
```
String valueUri
```
- Class ubic.gemma.model.genome.gene.phenotype.valueObject.DiffExpressionEvidenceValueObject extends EvidenceValueObject<DifferentialExpressionEvidence> implements Serializable
  
  serialVersionUID:
  
  7262262666070114995L
  - Serialized Fields
    - selectionThreshold
```
Double selectionThreshold
```
    - metaPvalue
```
Double metaPvalue
```
    - metaQvalue
```
Double metaQvalue
```
    - meanLogFoldChange
```
Double meanLogFoldChange
```
    - metaPvalueRank
```
Double metaPvalueRank
```
    - upperTail
```
Boolean upperTail
```
    - geneDifferentialExpressionMetaAnalysisId
```
Long geneDifferentialExpressionMetaAnalysisId
```
    - geneDifferentialExpressionMetaAnalysisResultId
```
Long geneDifferentialExpressionMetaAnalysisResultId
```
    - geneDifferentialExpressionMetaAnalysisSummaryValueObject
```
GeneDifferentialExpressionMetaAnalysisSummaryValueObject geneDifferentialExpressionMetaAnalysisSummaryValueObject
```
    - numEvidenceFromSameMetaAnalysis
```
Long numEvidenceFromSameMetaAnalysis
```
- Class ubic.gemma.model.genome.gene.phenotype.valueObject.DumpsValueObject extends Object implements Serializable
  - Serialized Fields
    - name
```
String name
```
    - url
```
String url
```
    - lastModified
```
String lastModified
```
- 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
    - description
```
String description
```
    - evidenceCode
```
String evidenceCode
```
    - isNegativeEvidence
```
boolean isNegativeEvidence
```
    - className
```
String className
```
    - phenotypes
```
Set<E> phenotypes
```
    - evidenceSource
```
EvidenceSourceValueObject evidenceSource
```
    - externalUrl
```
String externalUrl
```
    - lastUpdated
```
Long lastUpdated
```
    - evidenceSecurityValueObject
```
EvidenceSecurityValueObject evidenceSecurityValueObject
```
    - geneId
```
Long geneId
```
    - geneNCBI
```
Integer geneNCBI
```
    - geneOfficialSymbol
```
String geneOfficialSymbol
```
    - geneOfficialName
```
String geneOfficialName
```
    - taxonCommonName
```
String taxonCommonName
```
    - relationship
```
String relationship
```
    - isHomologueEvidence
```
boolean isHomologueEvidence
```
    - containQueryPhenotype
```
boolean containQueryPhenotype
```
    - originalPhenotype
```
String originalPhenotype
```
    - phenotypeMapping
```
String phenotypeMapping
```
    - phenotypeAssPubVO
```
Set<E> phenotypeAssPubVO
```
    - scoreValueObject
```
ScoreValueObject scoreValueObject
```
- Class ubic.gemma.model.genome.gene.phenotype.valueObject.ExperimentalEvidenceValueObject extends EvidenceValueObject<ExperimentalEvidence> implements Serializable
  
  serialVersionUID:
  
  4243531745086284715L
  - Serialized Fields
    - experimentCharacteristics
```
Collection<E> experimentCharacteristics
```
- Class ubic.gemma.model.genome.gene.phenotype.valueObject.ExternalDatabaseStatisticsValueObject extends Object implements Serializable
  - Serialized Fields
    - name
```
String name
```
    - description
```
String description
```
    - webUri
```
String webUri
```
    - numEvidence
```
Long numEvidence
```
    - numGenes
```
Long numGenes
```
    - numPhenotypes
```
Long numPhenotypes
```
    - numPublications
```
Long numPublications
```
    - lastUpdateDate
```
Date lastUpdateDate
```
    - pathToDownloadFile
```
String pathToDownloadFile
```
- Class ubic.gemma.model.genome.gene.phenotype.valueObject.GeneEvidenceValueObject extends GeneValueObject implements Serializable
  
  serialVersionUID:
  
  -3484291071757959936L
  - Serialized Fields
    - evidence
```
Collection<E> evidence
```
      Deprecated.
      
      Added field for the Candidate Gene Management System
    - phenotypesValueUri
```
Set<E> 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
    - type
```
String type
```
    - citationValueObject
```
CitationValueObject citationValueObject
```
- 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
    - strength
```
Double strength
```
    - scoreValue
```
String scoreValue
```
    - scoreName
```
String scoreName
```
- Class ubic.gemma.model.genome.gene.phenotype.valueObject.SimpleTreeValueObject extends Object implements Serializable
  - Serialized Fields
    - _parent
```
String _parent
```
    - _is_leaf
```
boolean _is_leaf
```
    - value
```
String value
```
    - valueUri
```
String valueUri
```
    - publicGeneCount
```
long publicGeneCount
```
    - privateGeneCount
```
long privateGeneCount
```
    - urlId
```
String urlId
```
    - dbPhenotype
```
boolean dbPhenotype
```
    - children
```
List<E> children
```
- Class ubic.gemma.model.genome.gene.phenotype.valueObject.TreeCharacteristicValueObject extends CharacteristicValueObject implements Serializable
  - Serialized Fields
    - _id
```
String _id
```
    - children
```
TreeSet<E> children
```
    - dbPhenotype
```
boolean dbPhenotype
```
      phenotype present in the database
    - publicGenesNBCI
```
HashSet<E> publicGenesNBCI
```
    - rootOfTree
```
String rootOfTree
```
- Class ubic.gemma.model.genome.gene.phenotype.valueObject.ValidateEvidenceValueObject extends Object implements Serializable
  - Serialized Fields
    - sameGeneAnnotated
```
boolean sameGeneAnnotated
```
    - lastUpdateDifferent
```
boolean lastUpdateDifferent
```
    - sameGeneAndOnePhenotypeAnnotated
```
boolean sameGeneAndOnePhenotypeAnnotated
```
    - sameGeneAndPhenotypesAnnotated
```
boolean sameGeneAndPhenotypesAnnotated
```
    - sameGeneAndPhenotypeChildOrParentAnnotated
```
boolean sameGeneAndPhenotypeChildOrParentAnnotated
```
    - pubmedIdInvalid
```
boolean pubmedIdInvalid
```
    - evidenceNotFound
```
boolean evidenceNotFound
```
    - accessDenied
```
boolean accessDenied
```
    - userNotLoggedIn
```
boolean userNotLoggedIn
```
    - sameEvidenceFound
```
boolean sameEvidenceFound
```
    - descriptionInvalidSymbol
```
boolean descriptionInvalidSymbol
```
    - problematicEvidenceIds
```
Set<E> problematicEvidenceIds
```
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
```
    - taxon
```
TaxonValueObject taxon
```
    - targetEnd
```
Long targetEnd
```
    - targetGapBases
```
Integer targetGapBases
```
    - targetGapCount
```
Integer targetGapCount
```
    - targetStart
```
Long targetStart
```
    - targetStarts
```
String targetStarts
```
- Class ubic.gemma.model.genome.sequenceAnalysis.SequenceSimilaritySearchResult extends Object implements Serializable
  
  serialVersionUID:
  
  -7196820023599562042L
  - Serialized Fields
    - id
```
Long id
```
    - querySequence
```
BioSequence querySequence
```
    - targetSequence
```
BioSequence targetSequence
```
    - targetChromosome
```
Chromosome targetChromosome
```
    - searchedDatabase
```
ExternalDatabase searchedDatabase
```
    - targetAlignedRegion
```
PhysicalLocation targetAlignedRegion
```
- Class ubic.gemma.model.genome.sequenceAnalysis.SequenceTypeValueObject extends Object implements Serializable
  - Serialized Fields
    - value
```
String value
```
Package ubic.gemma.persistence.model
- Class ubic.gemma.persistence.model.Gene2CsStatus extends Object implements Serializable
  
  serialVersionUID:
  
  1956861185764899312L
  - Serialized Fields
    - lastUpdate
```
Date lastUpdate
```
    - error
```
Exception error
```
    - annotation
```
String annotation
```
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
    - queryGene
```
Long queryGene
```
    - coexpGene
```
Long coexpGene
```
    - support
```
int support
```
    - positiveCorrelation
```
boolean positiveCorrelation
```
    - coexGeneSymbol
```
String coexGeneSymbol
```
    - queryGeneSymbol
```
String queryGeneSymbol
```
    - supportDetailsId
```
Long supportDetailsId
```
    - supportingDatasets
```
Collection<E> 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
```
    - positiveCorrelation
```
boolean positiveCorrelation
```
    - queryGeneId
```
Long queryGeneId
```
    - 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.
    - 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<E> supportingDatasets
```
      The data sets which supported the link. If eeConstraint = true, this reflects only data sets which were in the query.
    - testedInDatasets
```
Set<E> 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.util
- Class ubic.gemma.persistence.util.TaskCancelledException extends RuntimeException implements Serializable
  
  serialVersionUID:
  
  7343146551545342910L
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
    - geneIds
```
Collection<E> geneIds
```
    - threshold
```
Double threshold
```
    - taxonId
```
Long taxonId
```
    - selectedFactors
```
Collection<E> selectedFactors
```
    - eeQuery
```
String eeQuery
```
    - eeSetId
```
Long eeSetId
```
    - eeSetName
```
String eeSetName
```
    - eeIds
```
Collection<E> eeIds
```
    - dirty
```
boolean dirty
```
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<E> additionalTaxa
```
    - allParentsAnnotationLink
```
String allParentsAnnotationLink
```
    - alternateNames
```
Collection<E> alternateNames
```
    - alternative
```
ArrayDesignValueObject alternative
```
    - bioProcessAnnotationLink
```
String bioProcessAnnotationLink
```
    - colorString
```
String colorString
```
    - mergees
```
Collection<E> mergees
```
    - merger
```
ArrayDesignValueObject merger
```
    - noParentsAnnotationLink
```
String noParentsAnnotationLink
```
    - subsumees
```
Collection<E> 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<E> factors
```
    - factorTypes
```
List<E> factorTypes
```
    - factorValueMap
```
Map<K,V> factorValueMap
```
- Class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentDataFetchCommand extends TaskCommand implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - quantitationTypeId
```
Long quantitationTypeId
```
    - expressionExperimentId
```
Long expressionExperimentId
```
    - filter
```
boolean filter
```
    - experimentalDesignId
```
Long experimentalDesignId
```
    - format
```
String format
```
    - forceRewrite
```
boolean forceRewrite
```
    - analysisId
```
Long analysisId
```
- Class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditValueObject extends ExpressionExperimentDetailsValueObject implements Serializable
  
  serialVersionUID:
  
  1630521876359566915L
  - Serialized Fields
    - quantitationTypes
```
Collection<E> quantitationTypes
```
    - bioAssays
```
Collection<E> bioAssays
```
- Class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentLoadTaskCommand extends SimpleExpressionExperimentMetaData implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - validateOnly
```
boolean validateOnly
```
    - serverFilePath
```
String serverFilePath
```
    - originalFileName
```
String originalFileName
```
    - arrayDesignName
```
String arrayDesignName
```
    - taxonName
```
String taxonName
```
Package ubic.gemma.web.controller.visualization
- Class ubic.gemma.web.controller.visualization.ExpressionExperimentVisualizationCommand extends Object implements Serializable
  
  serialVersionUID:
  
  2166768356457316142L
  - Serialized Fields
    - searchCriteria
```
String searchCriteria
```
    - name
```
String name
```
    - expressionExperimentId
```
Long expressionExperimentId
```
    - searchString
```
String searchString
```
    - viewSampling
```
boolean viewSampling
```
    - maskMissing
```
boolean maskMissing
```
    - quantitationType
```
QuantitationType quantitationType
```
Package ubic.gemma.web.persistence
- Class ubic.gemma.web.persistence.AbstractSetListContainer extends Object implements Serializable
  
  serialVersionUID:
  
  -7207696842986893748L
  - Serialized Fields
    - allSessionBoundGroups
```
List<E> allSessionBoundGroups
```
    - sessionBoundModifiedGroups
```
List<E> sessionBoundModifiedGroups
```
    - largestSessionId
```
Long largestSessionId
```
- 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.services.rest.util
- Class ubic.gemma.web.services.rest.util.MalformedArgException extends javax.ws.rs.BadRequestException implements Serializable
Package ubic.gemma.web.services.rest.util.args
- Class ubic.gemma.web.services.rest.util.args.FilterArgParseException extends Exception implements Serializable
  - Serialized Fields
    - part
```
Integer part
```
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
    - subsumer
```
ArrayDesign subsumer
```
    - subsumees
```
Collection<E> subsumees
```
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
    - edit
```
boolean edit
```
    - bioAssays
```
Collection<E> bioAssays
```
    - 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
```
    - hasCorrMat
```
boolean hasCorrMat
```
    - hasCorrDist
```
boolean hasCorrDist
```
    - hasPCA
```
boolean hasPCA
```
    - hasMeanVariance
```
boolean hasMeanVariance
```
    - eeManagerId
```
String eeManagerId
```
    - hasNodeDegreeDist
```
boolean hasNodeDegreeDist
```
    - 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.
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
    - totalSize
```
long totalSize
```
    - bytesRead
```
long bytesRead
```
    - status
```
String status
```
    - fileIndex
```
int fileIndex
```

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

quick

eeIds

eeQuery

eeSetId

eeSetName

geneSetId

geneIds

queryGenesOnly

stringency

useMyDatasets

taxonId

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

Serialized Fields

geneId

coexpNodeDegree

datasetsAvailable

datasetsTested

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

correlationCacheThreshold

checkForBatchEffect

checkForOutliers

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

persist

subsetFactor

subsetFactorValue

useWeights

makeArchiveFile

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

Serialized Fields

gene

sortKey