Serialized Form (Gemma 1.32.0-SNAPSHOT API)

Package ubic.gemma.cli.batch
- Class ubic.gemma.cli.batch.BatchTaskProcessingResult extends Object implements Serializable
  - Serialized Fields
    - message
      
      String message
    - resultType
      
      ubic.gemma.cli.batch.BatchTaskProcessingResult.ResultType resultType
    - source
      
      Serializable source
    - throwable
      
      Throwable throwable
Package ubic.gemma.core.analysis.expression.coexpression
- Class ubic.gemma.core.analysis.expression.coexpression.CoexpressionMetaValueObject extends Object implements Serializable
  - Serialized Fields
    - errorState
      
      String errorState
      
      Error message for the client.
    - maxEdges
      
      int maxEdges
      
      Upper bound on how large we let the graph be from the server side. Can be overridden via the setter.
    - numDatasetsQueried
      
      int numDatasetsQueried
      
      How many data sets were actually used in the query; that is, which had coexpression analysis done.
    - queryGenes
      
      Collection<GeneValueObject> queryGenes
    - queryGenesOnly
      
      boolean queryGenesOnly
      
      if this was a "query genes only" search
    - queryStringency
      
      int queryStringency
      
      The stringency used in the initial query and after 'global' trimming.
    - results
      
      List<CoexpressionValueObjectExt> results
      
      Results for coexpression of the query gene with other 'found' genes (which could potentially include other query genes)
    - searchSettings
      
      CoexpressionSearchCommand searchSettings
      
      The original search settings.
    - summaries
      
      Map<Long,CoexpressionSummaryValueObject> summaries
      
      Summaries of results for each gene (map of gene ids to CoexpressionSummaryValueObject)
- Class ubic.gemma.core.analysis.expression.coexpression.CoexpressionSearchCommand extends Object implements Serializable
  - Serialized Fields
    - dirty
      
      boolean dirty
      
      Set to true to signal that the eeSet has been modified from its stored version.
    - eeIds
      
      Collection<Long> eeIds
    - eeQuery
      
      String eeQuery
      
      we're storing the actual ee ids in the command object; the query string is only here so we can use this object to store the state of the search form between visits...
    - eeSetId
      
      Long eeSetId
    - eeSetName
      
      String eeSetName
    - geneIds
      
      Collection<Long> geneIds
    - geneSetId
      
      Long geneSetId
    - queryGenesOnly
      
      boolean queryGenesOnly
    - quick
      
      boolean quick
      
      if set to true will do a quick coexpression search (without filling in various details)
    - stringency
      
      Integer stringency
    - taxonId
      
      Long taxonId
      
      as eeQuery above, the taxon is only here so we can use this object to store the entire state of the form...
    - useMyDatasets
      
      boolean useMyDatasets
- Class ubic.gemma.core.analysis.expression.coexpression.CoexpressionSummaryValueObject extends Object implements Serializable
  - Serialized Fields
    - coexpNodeDegree
      
      GeneCoexpressionNodeDegreeValueObject coexpNodeDegree
    - datasetsAvailable
      
      int datasetsAvailable
    - datasetsTested
      
      int datasetsTested
    - geneId
      
      long geneId
    - linksFound
      
      int linksFound
Package ubic.gemma.core.analysis.expression.coexpression.links
- Class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - absoluteValue
      
      boolean absoluteValue
    - arrayName
      
      String arrayName
    - cdfCut
      
      double cdfCut
      
      what proportion of links to keep (possibly subject to FWE statistical significance threshold). 1.0 means keep everything. 0.01 means 1%.
    - checkCorrelationDistribution
      
      boolean checkCorrelationDistribution
    - checkForBatchEffect
      
      boolean checkForBatchEffect
    - checkForOutliers
      
      boolean checkForOutliers
    - correlationCacheThreshold
      
      double correlationCacheThreshold
      
      only used for internal cache during calculations.
    - fwe
      
      double fwe
      
      family-wise error rate threshold we use to select links
    - lowerCdfCutUsed
      
      boolean lowerCdfCutUsed
    - lowerTailCut
      
      double lowerTailCut
    - makeSampleCorrMatImages
      
      boolean makeSampleCorrMatImages
    - metric
      
      String metric
    - minNumPresent
      
      int minNumPresent
      
      How many samples must be present in a correlation pair to keep the data, taking into account missing values.
    - normalizationMethod
      
      LinkAnalysisConfig.NormalizationMethod normalizationMethod
    - omitNegLinks
      
      boolean omitNegLinks
      
      Remove negative correlated values at the end.
    - outputFile
      
      File outputFile
      
      Only used if textOut = true; if null, just write to stdout.
    - probeDegreeThreshold
      
      int probeDegreeThreshold
      
      Probes with more than this many links are removed. Zero means no action is taken.
    - singularThreshold
      
      LinkAnalysisConfig.SingularThreshold singularThreshold
    - subset
      
      boolean subset
    - subsetSize
      
      double subsetSize
    - subsetUsed
      
      boolean subsetUsed
    - textOut
      
      boolean textOut
    - upperCdfCutUsed
      
      boolean upperCdfCutUsed
    - upperTailCut
      
      double upperTailCut
    - useDb
      
      boolean useDb
- Class ubic.gemma.core.analysis.expression.coexpression.links.UnsuitableForAnalysisException extends RuntimeException implements Serializable
  
  serialVersionUID:
  
  -4436136164850796179L
Package ubic.gemma.core.analysis.expression.diff
- Class ubic.gemma.core.analysis.expression.diff.AllSubSetAnalysesFailedException extends AnalysisException implements Serializable
  - Serialized Fields
    - subsetExceptions
      
      Collection<AnalysisException> subsetExceptions
- Class ubic.gemma.core.analysis.expression.diff.AnalysisException extends RuntimeException implements Serializable
  - Serialized Fields
    - config
      
      DifferentialExpressionAnalysisConfig config
- Class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionMetaAnalysisValueObject extends Object implements Serializable
  - Serialized Fields
    - activeExperiments
      
      Collection<BioAssaySet> activeExperiments
    - fisherPValue
      
      Double fisherPValue
    - gene
      
      GeneValueObject gene
    - numExperimentsInScope
      
      int numExperimentsInScope
    - numMetThreshold
      
      int numMetThreshold
    - numSearchedExperiments
      
      int numSearchedExperiments
    - probeResults
      
      Collection<DifferentialExpressionValueObject> probeResults
    - sortKey
      
      String sortKey
- Class ubic.gemma.core.analysis.expression.diff.DiffExpressionSelectedFactorCommand extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - eeId
      
      Long eeId
    - efId
      
      Long efId
- Class ubic.gemma.core.analysis.expression.diff.EbayesFailureException extends AnalysisException implements Serializable
- Class ubic.gemma.core.analysis.expression.diff.InvalidQuantitationTypeConversionException extends AnalysisException implements Serializable
- Class ubic.gemma.core.analysis.expression.diff.NoFactorLeftForAnalysisException extends AnalysisException implements Serializable
- Class ubic.gemma.core.analysis.expression.diff.NoSampleLeftForAnalysisException extends AnalysisException implements Serializable
Package ubic.gemma.core.analysis.preprocess
- Class ubic.gemma.core.analysis.preprocess.FilteringRelatedPreprocessingException extends PreprocessingException implements Serializable
  - Serialized Fields
    - cause
      
      FilteringException cause
- 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.QuantitationTypeConversionRelatedPreprocessingException extends PreprocessingException implements Serializable
  - Serialized Fields
    - cause
      
      QuantitationTypeConversionException cause
- Class ubic.gemma.core.analysis.preprocess.QuantitationTypeDetectionRelatedPreprocessingException extends PreprocessingException implements Serializable
  - Serialized Fields
    - cause
      
      QuantitationTypeDetectionException cause
- Class ubic.gemma.core.analysis.preprocess.SampleCoexpressionRelatedPreprocessingException extends PreprocessingException implements Serializable
- Class ubic.gemma.core.analysis.preprocess.SVDRelatedPreprocessingException extends PreprocessingException implements Serializable
  - Serialized Fields
    - cause
      
      SVDException cause
Package ubic.gemma.core.analysis.preprocess.batcheffects
- Class ubic.gemma.core.analysis.preprocess.batcheffects.BatchConfound extends Object implements Serializable
  - Serialized Fields
    - chiSquare
      
      double chiSquare
    - df
      
      int df
    - ee
      
      BioAssaySet ee
    - ef
      
      ExperimentalFactor ef
    - numBatches
      
      int numBatches
    - p
      
      double p
- Class ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoMissingException extends BatchInfoPopulationException implements Serializable
- Class ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationException extends PreprocessingException implements Serializable
  
  serialVersionUID:
  
  -1770591991479420212L
- Class ubic.gemma.core.analysis.preprocess.batcheffects.FASTQHeadersPresentButNotUsableException extends BatchInfoPopulationException implements Serializable
  
  serialVersionUID:
  
  1917074433646650950L
- Class ubic.gemma.core.analysis.preprocess.batcheffects.SingletonBatchesException extends BatchInfoPopulationException implements Serializable
  
  serialVersionUID:
  
  9088141067684148902L
- Class ubic.gemma.core.analysis.preprocess.batcheffects.UnsupportedRawdataFileFormatException extends BatchInfoPopulationException implements Serializable
  
  serialVersionUID:
  
  1L
Package ubic.gemma.core.analysis.preprocess.convert
- Class ubic.gemma.core.analysis.preprocess.convert.QuantitationTypeConversionException extends Exception implements Serializable
- Class ubic.gemma.core.analysis.preprocess.convert.UnsupportedQuantitationScaleConversionException extends QuantitationTypeConversionException implements Serializable
Package ubic.gemma.core.analysis.preprocess.detect
- Class ubic.gemma.core.analysis.preprocess.detect.InferredQuantitationMismatchException extends QuantitationMismatchException implements Serializable
  - Serialized Fields
    - inferredQuantitationType
      
      QuantitationType inferredQuantitationType
- Class ubic.gemma.core.analysis.preprocess.detect.QuantitationMismatchException extends QuantitationTypeDetectionException implements Serializable
  - Serialized Fields
    - quantitationType
      
      QuantitationType quantitationType
- Class ubic.gemma.core.analysis.preprocess.detect.QuantitationTypeDetectionException extends Exception implements Serializable
- Class ubic.gemma.core.analysis.preprocess.detect.SuspiciousValuesForQuantitationException extends QuantitationMismatchException implements Serializable
  - Serialized Fields
    - suspiciousValues
      
      List<SuspiciousValuesForQuantitationException.SuspiciousValueResult> suspiciousValues
Package ubic.gemma.core.analysis.preprocess.filter
- Class ubic.gemma.core.analysis.preprocess.filter.FilterConfig extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - afterDistinctValueCut
      
      int afterDistinctValueCut
    - afterInitialFilter
      
      int afterInitialFilter
    - afterLowExpressionCut
      
      int afterLowExpressionCut
    - afterLowVarianceCut
      
      int afterLowVarianceCut
    - afterMinPresentFilter
      
      int afterMinPresentFilter
    - afterZeroVarianceCut
      
      int afterZeroVarianceCut
    - highExpressionCut
      
      double highExpressionCut
    - ignoreMinimumRowsThreshold
      
      boolean ignoreMinimumRowsThreshold
      
      If true, the MINIMUM_ROWS_TO_BOTHER is ignored.
    - ignoreMinimumSampleThreshold
      
      boolean ignoreMinimumSampleThreshold
      
      If true, MINIMUM_SAMPLE is ignored.
    - logTransform
      
      boolean logTransform
    - lowDistinctValueCut
      
      double lowDistinctValueCut
    - lowDistinctValueIsSet
      
      boolean lowDistinctValueIsSet
    - lowExpressionCut
      
      double lowExpressionCut
    - lowExpressionCutIsSet
      
      boolean lowExpressionCutIsSet
    - lowVarianceCut
      
      double lowVarianceCut
    - lowVarianceCutIsSet
      
      boolean lowVarianceCutIsSet
    - minPresentFraction
      
      double minPresentFraction
    - minPresentFractionIsSet
      
      boolean minPresentFractionIsSet
    - requireSequences
      
      boolean requireSequences
    - startingRows
      
      int startingRows
- Class ubic.gemma.core.analysis.preprocess.filter.FilteringException extends Exception 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.SVDResult extends Object implements Serializable
  - Serialized Fields
    - bioMaterials
      
      List<BioMaterial> bioMaterials
      
      In order like the rows of the v matrix.
    - dateCorrelations
      
      Map<Integer,Double> dateCorrelations
      
      Map of component to correlation that component with "batch/scan date"
      
      See Also:
      
      SVDResult.dates
    - datePVals
      
      Map<Integer,Double> datePVals
      
      P-values associated to the "batch/scan date" component.
      
      See Also:
      
      SVDResult.dates
    - dates
      
      List<Date> dates
      
      Date associated to the SVDResult.bioMaterials.
      Missing values are encoded as null.
    - experimentAnalyzed
      
      BioAssaySet experimentAnalyzed
      
      Experiment or subset this is for.
    - factorCorrelations
      
      Map<Integer,Map<ExperimentalFactor,Double>> factorCorrelations
      
      Map of component to a map of ExperimentalFactor IDs to correlations of that factor with the component.
    - factorPVals
      
      Map<Integer,Map<ExperimentalFactor,Double>> factorPVals
      
      Map of component to map of ExperimentalFactor IDs to P-values for the association of that factor with the component.
      Need to store the correlations of eigengenes with dates of assays, and also with factors. Statistics are rank-based correlations
    - factors
      
      Map<ExperimentalFactor,List<Number>> factors
      
      Map of factors to the double-ized representations of them.
    - variances
      
      double[] variances
      
      An array of values representing the fraction of the variance each component accounts for
    - vMatrix
      
      DoubleMatrix<BioMaterial,Integer> vMatrix
      
      Row names: biomaterials; column names: eigengene number (from 0)
Package ubic.gemma.core.analysis.report
- Class ubic.gemma.core.analysis.report.AuditableObject extends Object implements Serializable
  
  serialVersionUID:
  
  -7862129089784691035L
  - Serialized Fields
    - date
      
      Date date
    - id
      
      Long id
    - type
      
      String type

Package ubic.gemma.core.analysis.sequence

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

Serialized Fields

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

geneProducts

Map<Long,GeneProductValueObject> geneProducts

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

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

serialVersionUID:: 8899320580201273360L

Serialized Fields

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

compositeSequence

CompositeSequenceValueObject compositeSequence

geneProductIdGeneMap

Map<String,GeneValueObject> geneProductIdGeneMap

geneProductIdMap

Map<String,GeneProductValueObject> geneProductIdMap

geneProductMap

Map<GeneProductValueObject,GeneValueObject> geneProductMap

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

Package ubic.gemma.core.analysis.singleCell.aggregate
- Class ubic.gemma.core.analysis.singleCell.aggregate.AggregationException extends RuntimeException implements Serializable
- Class ubic.gemma.core.analysis.singleCell.aggregate.UnsupportedScaleTypeForAggregationException extends AggregationException implements Serializable
Package ubic.gemma.core.datastructure.matrix
- Class ubic.gemma.core.datastructure.matrix.BaseExpressionDataMatrix extends Object implements Serializable
  - Serialized Fields
    - bioAssayDimensions
      
      Map<CompositeSequence,BioAssayDimension> bioAssayDimensions
    - columnAssayMap
      
      Map<BioAssay,Integer> columnAssayMap
    - columnBioAssayMapByInteger
      
      Map<Integer,Collection<BioAssay>> columnBioAssayMapByInteger
    - columnBioMaterialMap
      
      Map<BioMaterial,Integer> columnBioMaterialMap
    - columnBioMaterialMapByInteger
      
      Map<Integer,BioMaterial> columnBioMaterialMapByInteger
    - expressionExperiment
      
      ExpressionExperiment expressionExperiment
    - quantitationTypes
      
      Collection<QuantitationType> quantitationTypes
    - rowDesignElementMapByInteger
      
      Map<Integer,CompositeSequence> rowDesignElementMapByInteger
    - rowElementMap
      
      Map<CompositeSequence,Integer> rowElementMap
    - rowElements
      
      List<ExpressionDataMatrixRowElement> rowElements
- Class ubic.gemma.core.datastructure.matrix.EmptyExpressionMatrix extends BaseExpressionDataMatrix<Object> implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - numCols
      
      int numCols
- Class ubic.gemma.core.datastructure.matrix.ExpressionDataBooleanMatrix extends BaseExpressionDataMatrix<Boolean> implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - matrix
      
      ObjectMatrixImpl<CompositeSequence,Integer,Boolean> matrix
- Class ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix extends BaseExpressionDataMatrix<Double> implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - matrix
      
      DoubleMatrix<CompositeSequence,BioMaterial> matrix
    - ranks
      
      Map<CompositeSequence,Double> ranks
- Class ubic.gemma.core.datastructure.matrix.ExpressionDataIntegerMatrix extends BaseExpressionDataMatrix<Integer> implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - matrix
      
      IntegerMatrix<CompositeSequence,Integer> matrix
- Class ubic.gemma.core.datastructure.matrix.ExpressionDataStringMatrix extends BaseExpressionDataMatrix<String> implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - matrix
      
      StringMatrix<Integer,Integer> matrix
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?
    - maxQueueMinutes
      
      Integer maxQueueMinutes
      
      How long we will allow this task to be queued before giving up.
    - maxRuntime
      
      int maxRuntime
    - persistJobDetails
      
      Boolean persistJobDetails
      
      If true, the jobDetails associated with this task will be persisted in the database. Consider setting to false for test jobs or other super-frequent maintenance tasks.
    - securityContext
      
      org.springframework.security.core.context.SecurityContext securityContext
      
      Used to propagate security to grid workers.
    - submitter
      
      String submitter
    - taskId
      
      String taskId
- Class ubic.gemma.core.job.TaskResult extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - answer
      
      Serializable answer
      
      The actual result object
    - exception
      
      Exception exception
      
      Set if failed.
    - taskId
      
      String taskId
      
      The task id
Package ubic.gemma.core.job.progress
- Class ubic.gemma.core.job.progress.ProgressData extends Object implements Serializable
  
  serialVersionUID:
  
  -4303625064082352461L
  - Serialized Fields
    - description
      
      String description
    - done
      
      boolean done
    - failed
      
      boolean failed
    - forwardingURL
      
      String forwardingURL
    - percent
      
      int percent
    - taskId
      
      String taskId
- Class ubic.gemma.core.job.progress.SubmittedTaskValueObject extends Object implements Serializable
  
  serialVersionUID:
  
  6757089319713433356L
  - Serialized Fields
    - done
      
      boolean done
    - emailAlert
      
      boolean emailAlert
    - finishTime
      
      Date finishTime
    - lastLogMessage
      
      String lastLogMessage
    - logMessages
      
      String logMessages
    - runningRemotely
      
      boolean runningRemotely
    - startTime
      
      Date startTime
    - submissionTime
      
      Date submissionTime
    - submitter
      
      String submitter
    - taskId
      
      String taskId
    - taskStatus
      
      String taskStatus
    - taskType
      
      String taskType
Package ubic.gemma.core.loader.entrez.pubmed
- Class ubic.gemma.core.loader.entrez.pubmed.ESearchException extends Exception implements Serializable
Package ubic.gemma.core.loader.expression.arrayDesign
- Class ubic.gemma.core.loader.expression.arrayDesign.Reporter extends AbstractDescribable implements Serializable
  
  serialVersionUID:
  
  3703827938981026012L
  - Serialized Fields
    - col
      
      Integer col
    - compositeSequence
      
      CompositeSequence compositeSequence
    - immobilizedCharacteristic
      
      BioSequence immobilizedCharacteristic
    - row
      
      Integer row
    - startInBioChar
      
      Long startInBioChar
    - strand
      
      String strand
Package ubic.gemma.core.loader.expression.geo
- Class ubic.gemma.core.loader.expression.geo.GeoSampleCorrespondence extends Object implements Serializable
  
  serialVersionUID:
  
  -5285504953530483114L
  - Serialized Fields
    - accToDataset
      
      Map<String,String> accToDataset
    - accToTitle
      
      Map<String,String> accToTitle
    - sets
      
      Collection<Set<String>> sets
Package ubic.gemma.core.loader.expression.geo.model
- Class ubic.gemma.core.loader.expression.geo.model.GeoContact extends Object implements Serializable
  
  serialVersionUID:
  
  -2042747972349661568L
  - Serialized Fields
    - address
      
      String address
    - city
      
      String city
    - country
      
      String country
    - department
      
      String department
    - email
      
      String email
    - fax
      
      String fax
    - institute
      
      String institute
    - laboratory
      
      String laboratory
    - name
      
      String name
    - phone
      
      String phone
    - postCode
      
      String postCode
    - state
      
      String state
    - webLink
      
      String webLink
- Class ubic.gemma.core.loader.expression.geo.model.GeoData extends Object implements Serializable
  - Serialized Fields
    - columnDescriptions
      
      List<String> columnDescriptions
    - columnNames
      
      List<String> columnNames
    - contact
      
      GeoContact contact
    - geoAccession
      
      String geoAccession
    - title
      
      String title
- Class ubic.gemma.core.loader.expression.geo.model.GeoDataset extends GeoData implements Serializable
  - Serialized Fields
    - completeness
      
      String completeness
    - datasetType
      
      String datasetType
    - description
      
      String description
    - experimentType
      
      GeoDataset.ExperimentType experimentType
    - featureCount
      
      String featureCount
    - numChannels
      
      int numChannels
    - numProbes
      
      int numProbes
    - numSamples
      
      int numSamples
    - order
      
      String order
    - organism
      
      String organism
    - platform
      
      GeoPlatform platform
    - platformType
      
      GeoDataset.PlatformType platformType
    - pubmedId
      
      String pubmedId
    - sampleType
      
      GeoDataset.SampleType sampleType
    - series
      
      Collection<GeoSeries> series
    - subsets
      
      Collection<GeoSubset> subsets
    - updateDate
      
      String updateDate
    - valueType
      
      GeoDataset.ValueType valueType
- Class ubic.gemma.core.loader.expression.geo.model.GeoPlatform extends GeoData implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - catalogNumbers
      
      Collection<String> catalogNumbers
    - coating
      
      String coating
    - contributer
      
      Collection<String> contributer
    - description
      
      String description
    - designElements
      
      Collection<String> designElements
    - distribution
      
      String distribution
    - id
      
      String id
    - lastUpdateDate
      
      String lastUpdateDate
    - manufactureProtocol
      
      String manufactureProtocol
    - manufacturer
      
      String manufacturer
    - organisms
      
      Collection<String> organisms
    - platformData
      
      List<List<String>> platformData
    - platformInformation
      
      Map<String,List<String>> platformInformation
      
      Store information on the platform here. Map of designElements to other information. This has to be lists so the values "line up".
    - probeNamesInGemma
      
      Map<String,String> probeNamesInGemma
      
      Map of original probe names provided by GEO to the names in Gemma (if this platform is already there). This is needed because probe names are sometimes changed after import. This map must be populated prior to import of the data.
    - pubMedIds
      
      Collection<Integer> pubMedIds
    - sample
      
      String sample
    - status
      
      String status
    - submissionDate
      
      String submissionDate
    - supplementaryFile
      
      String supplementaryFile
    - support
      
      String support
    - technology
      
      GeoDataset.PlatformType technology
    - useDataFromGEO
      
      boolean useDataFromGEO
      
      Will be set to false during parsing if data are missing.
    - webLink
      
      String webLink
    - webLinks
      
      Collection<String> webLinks
- Class ubic.gemma.core.loader.expression.geo.model.GeoRecord extends GeoData implements Serializable
  - Serialized Fields
    - contactName
      
      String contactName
    - correspondingExperiments
      
      Collection<Long> correspondingExperiments
    - librarySource
      
      String librarySource
    - libraryStrategy
      
      String libraryStrategy
    - meshHeadings
      
      Collection<String> meshHeadings
      
      MeSh headings, collected from PubMed.
    - numSamples
      
      int numSamples
    - organisms
      
      Collection<String> organisms
    - overallDesign
      
      String overallDesign
    - platform
      
      String platform
    - previousClicks
      
      int previousClicks
      
      How many times a curator has already looked at the details. this helps us track data sets we've already examined for usefulness.
    - pubMedIds
      
      List<String> pubMedIds
    - releaseDate
      
      Date releaseDate
    - sampleDataProcessing
      
      String sampleDataProcessing
    - sampleDescriptions
      
      String sampleDescriptions
    - sampleDetails
      
      String sampleDetails
    - sampleExtractProtocols
      
      String sampleExtractProtocols
    - sampleGEOAccessions
      
      Collection<String> sampleGEOAccessions
    - sampleLabelProtocols
      
      String sampleLabelProtocols
    - sampleLabels
      
      String sampleLabels
    - sampleMolecules
      
      String sampleMolecules
    - seriesType
      
      String seriesType
    - subSeries
      
      boolean subSeries
    - subSeriesOf
      
      String subSeriesOf
    - summary
      
      String summary
    - superSeries
      
      boolean superSeries
    - usable
      
      boolean usable
      
      Curator judgement about whether this is loadable. False indicates a problem.
- Class ubic.gemma.core.loader.expression.geo.model.GeoSample extends GeoData implements Serializable
  - Serialized Fields
    - anchor
      
      String anchor
    - channels
      
      List<GeoChannel> channels
    - dataProcessing
      
      String dataProcessing
    - description
      
      String description
    - hybProtocol
      
      String hybProtocol
    - id
      
      String id
    - isGenePix
      
      boolean isGenePix
    - lastUpdateDate
      
      String lastUpdateDate
    - libSource
      
      GeoLibrarySource libSource
    - libStrategy
      
      GeoLibraryStrategy libStrategy
    - mightNotHaveDataInFile
      
      boolean mightNotHaveDataInFile
    - platforms
      
      Collection<GeoPlatform> platforms
    - replicates
      
      Collection<GeoReplication> replicates
    - scanProtocol
      
      String scanProtocol
    - seriesAppearsIn
      
      Collection<String> seriesAppearsIn
    - status
      
      String status
    - submissionDate
      
      String submissionDate
    - supplementaryFiles
      
      Collection<String> supplementaryFiles
    - 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
      
      GeoSampleType type
    - variables
      
      Collection<GeoVariable> variables
    - warnedAboutGenePix
      
      boolean warnedAboutGenePix
- Class ubic.gemma.core.loader.expression.geo.model.GeoSeries extends GeoData implements Serializable
  - Serialized Fields
    - contributers
      
      Collection<GeoContact> contributers
    - dataSets
      
      Collection<GeoDataset> dataSets
    - isSubSeries
      
      boolean isSubSeries
    - isSuperSeries
      
      boolean isSuperSeries
    - keyWords
      
      Collection<String> keyWords
    - lastUpdateDate
      
      String lastUpdateDate
    - overallDesign
      
      String overallDesign
    - platformId
      
      String platformId
    - pubmedIds
      
      Collection<String> pubmedIds
    - replicates
      
      Map<Integer,GeoReplication> replicates
    - sampleCorrespondence
      
      GeoSampleCorrespondence sampleCorrespondence
    - samples
      
      Collection<GeoSample> samples
    - seriesId
      
      String seriesId
    - seriesTypes
      
      Collection<GeoSeriesType> seriesTypes
    - status
      
      String status
    - submissionDate
      
      String submissionDate
    - subSeries
      
      Collection<String> subSeries
    - summary
      
      String summary
    - supplementaryFiles
      
      Collection<String> supplementaryFiles
    - values
      
      GeoValues values
    - variables
      
      Map<Integer,GeoVariable> variables
    - webLinks
      
      Collection<String> webLinks
- Class ubic.gemma.core.loader.expression.geo.model.GeoSubset extends GeoData implements Serializable
  - Serialized Fields
    - dataSet
      
      String dataSet
    - description
      
      String description
    - owningDataset
      
      GeoDataset owningDataset
    - samples
      
      Collection<GeoSample> samples
    - type
      
      GeoVariable.VariableType type
- Class ubic.gemma.core.loader.expression.geo.model.GeoValues extends Object implements Serializable
  
  serialVersionUID:
  
  3748363645735281578L
  - Serialized Fields
    - data
      
      Map<GeoPlatform,Map<Integer,Map<String,List<String>>>> data
    - quantitationTypeIndexMap
      
      Map<GeoPlatform,Map<Integer,Collection<String>>> quantitationTypeIndexMap
    - quantitationTypeNameMap
      
      Map<GeoPlatform,Map<String,Integer>> quantitationTypeNameMap
    - sampleDimensions
      
      Map<GeoPlatform,Map<Integer,LinkedHashSet<GeoSample>>> sampleDimensions
Package ubic.gemma.core.loader.expression.geo.singleCell
- Class ubic.gemma.core.loader.expression.geo.singleCell.NoSingleCellDataFoundException extends Exception implements Serializable
Package ubic.gemma.core.loader.expression.simple.model
- Class ubic.gemma.core.loader.expression.simple.model.SimpleCharacteristic extends Object implements Serializable
  - Serialized Fields
    - category
      
      String category
    - categoryUri
      
      String categoryUri
    - value
      
      String value
    - valueUri
      
      String valueUri
- Class ubic.gemma.core.loader.expression.simple.model.SimpleContactMetadata extends Object implements Serializable
- Class ubic.gemma.core.loader.expression.simple.model.SimpleDatabaseEntry extends Object implements Serializable
  - Serialized Fields
    - accession
      
      String accession
    - externalDatabaseId
      
      Long externalDatabaseId
    - externalDatabaseName
      
      String externalDatabaseName
- Class ubic.gemma.core.loader.expression.simple.model.SimpleExpressionExperimentMetadata extends Object implements Serializable
  - Serialized Fields
    - accession
      
      SimpleDatabaseEntry accession
    - arrayDesigns
      
      Collection<SimplePlatformMetadata> arrayDesigns
      
      Platforms associated to the experiments.
      Once declared here, they may be referred to in SimpleExpressionExperimentMetadata.samples.
    - description
      
      String description
    - experimentalDesignDescription
      
      String experimentalDesignDescription
    - experimentalDesignName
      
      String experimentalDesignName
    - name
      
      String name
    - probeIdsAreImageClones
      
      boolean probeIdsAreImageClones
      
      If true, biological characteristics imaging the probes will be created.
    - pubMedId
      
      Integer pubMedId
      
      PubMed identifier.
    - quantitationType
      
      SimpleQuantitationTypeMetadata quantitationType
      
      Required if data is provided.
    - samples
      
      Collection<SimpleSampleMetadata> samples
      
      Samples to be associated with this experiment.
      If left unset, the assays will be inferred from the data file.
    - shortName
      
      String shortName
    - source
      
      String source
    - taxon
      
      SimpleTaxonMetadata taxon
- Class ubic.gemma.core.loader.expression.simple.model.SimplePlatformMetadata extends Object implements Serializable
  - Serialized Fields
    - description
      
      String description
    - id
      
      Long id
    - name
      
      String name
    - shortName
      
      String shortName
    - technologyType
      
      TechnologyType technologyType
- Class ubic.gemma.core.loader.expression.simple.model.SimpleQuantitationTypeMetadata extends Object implements Serializable
  - Serialized Fields
    - description
      
      String description
    - generalType
      
      GeneralType generalType
    - isBatchCorrected
      
      Boolean isBatchCorrected
    - isPreferred
      
      Boolean isPreferred
    - isRatio
      
      Boolean isRatio
    - name
      
      String name
    - representation
      
      PrimitiveType representation
    - scale
      
      ScaleType scale
    - type
      
      StandardQuantitationType type
- Class ubic.gemma.core.loader.expression.simple.model.SimpleSampleMetadata extends Object implements Serializable
  - Serialized Fields
    - accession
      
      SimpleDatabaseEntry accession
    - characteristics
      
      Collection<SimpleCharacteristic> characteristics
    - description
      
      String description
    - name
      
      String name
    - platformUsed
      
      SimplePlatformMetadata platformUsed
- Class ubic.gemma.core.loader.expression.simple.model.SimpleTaxonMetadata extends Object implements Serializable
  - Serialized Fields
    - id
      
      Long id
    - name
      
      String name
      
      Taxon name, either common or scientific.
    - ncbiId
      
      Integer ncbiId
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.anndata
- Class ubic.gemma.core.loader.util.anndata.AnnDataException extends RuntimeException implements Serializable
- Class ubic.gemma.core.loader.util.anndata.InvalidEncodingAttributeException extends AnnDataException implements Serializable
- Class ubic.gemma.core.loader.util.anndata.MissingEncodingAttributeException extends AnnDataException implements Serializable
Package ubic.gemma.core.loader.util.biomart
- Class ubic.gemma.core.loader.util.biomart.Ensembl2NcbiValueObject extends Object implements Serializable
  
  serialVersionUID:
  
  -859220901359582113L
  - Serialized Fields
    - enemblTranscriptId
      
      String enemblTranscriptId
    - ensembleGeneId
      
      String ensembleGeneId
    - ensemblPeptideId
      
      String ensemblPeptideId
    - hgcnId
      
      String hgcnId
    - ncbiGenes
      
      Collection<String> ncbiGenes
    - ncbiTaxonId
      
      Integer ncbiTaxonId
Package ubic.gemma.core.loader.util.hdf5
- Class ubic.gemma.core.loader.util.hdf5.H5Exception extends RuntimeException implements Serializable
  - Serialized Fields
    - cause
      
      hdf.hdf5lib.exceptions.HDF5Exception cause
- Class ubic.gemma.core.loader.util.hdf5.TruncatedH5FileException extends IOException implements Serializable
Package ubic.gemma.core.loader.util.parser
- Class ubic.gemma.core.loader.util.parser.FileFormatException extends RuntimeException implements Serializable
  
  serialVersionUID:
  
  -1984918923089214361L
Package ubic.gemma.core.ontology
- Class ubic.gemma.core.ontology.AbstractOntologyResourceSimple extends Object implements Serializable
  - Serialized Fields
    - label
      
      String label
    - uri
      
      String uri
- Class ubic.gemma.core.ontology.OntologyIndividualSimple extends AbstractOntologyResourceSimple implements Serializable
  - Serialized Fields
    - instanceOf
      
      OntologyTermSimple instanceOf
- Class ubic.gemma.core.ontology.OntologyPropertySimple extends AbstractOntologyResourceSimple implements Serializable
Package ubic.gemma.core.search
- Class ubic.gemma.core.search.BaseCodeOntologySearchException extends SearchException implements Serializable
  - Serialized Fields
    - cause
      
      OntologySearchException cause
- Class ubic.gemma.core.search.ParseSearchException extends SearchException implements Serializable
  - Serialized Fields
    - originalParseException
      
      ParseSearchException originalParseException
    - query
      
      String query
- Class ubic.gemma.core.search.SearchException extends Exception implements Serializable
- Class ubic.gemma.core.search.SearchTimeoutException extends SearchException implements Serializable
  - Serialized Fields
    - cause
      
      TimeoutException cause
Package ubic.gemma.core.search.lucene
- Class ubic.gemma.core.search.lucene.LuceneParseSearchException extends ParseSearchException implements Serializable
Package ubic.gemma.core.search.source
- Class ubic.gemma.core.search.source.HibernateSearchException extends SearchException implements Serializable
  - Serialized Fields
    - cause
      
      org.hibernate.search.SearchException cause
Package ubic.gemma.core.tasks
- Class ubic.gemma.core.tasks.EntityTaskCommand extends TaskCommand implements Serializable
  - Serialized Fields
    - entityClass
      
      Class<T extends Identifiable> entityClass
    - entityId
      
      Long entityId
Package ubic.gemma.core.tasks.analysis.coexp
- Class ubic.gemma.core.tasks.analysis.coexp.LinkAnalysisTaskCommand extends TaskCommand implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - expressionExperiment
      
      ExpressionExperiment expressionExperiment
    - filterConfig
      
      FilterConfig filterConfig
    - linkAnalysisConfig
      
      LinkAnalysisConfig linkAnalysisConfig
Package ubic.gemma.core.tasks.analysis.diffex
- Class ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisRemoveTaskCommand extends DifferentialExpressionAnalysisTaskCommand implements Serializable
  
  serialVersionUID:
  
  -6881129987842634598L
  - Serialized Fields
    - toRemove
      
      DifferentialExpressionAnalysis toRemove
- Class ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisTaskCommand extends TaskCommand implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - analysisType
      
      AnalysisType analysisType
      
      Proposed analysis type. If null the system tries to figure it out.
    - expressionExperiment
      
      ExpressionExperiment expressionExperiment
    - factors
      
      Collection<ExperimentalFactor> factors
      
      The factors to actually use in the analysis. If null the system tries to figure it out.
    - forceAnalysis
      
      boolean forceAnalysis
    - includeInteractions
      
      boolean includeInteractions
      
      Whether interactions among the factors should be included. The implementation may limit this to two-way interactions for only up to two factors, so this may not have the effect desired.
    - moderateStatistics
      
      boolean moderateStatistics
      
      Whether to moderate test statistics via empirical Bayes
    - subsetFactor
      
      ExperimentalFactor subsetFactor
    - toRedo
      
      DifferentialExpressionAnalysis toRedo
    - useWeights
      
      boolean useWeights
      
      Whether to use weighted regression based on mean-variance relationships (voom)
- Class ubic.gemma.core.tasks.analysis.diffex.DiffExMetaAnalyzerTaskCommand extends TaskCommand implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - analysisResultSetIds
      
      Collection<Long> analysisResultSetIds
    - description
      
      String description
    - name
      
      String name
    - persist
      
      boolean persist
Package ubic.gemma.core.tasks.analysis.expression
- Class ubic.gemma.core.tasks.analysis.expression.BatchInfoFetchTaskCommand extends ExpressionExperimentReportTaskCommand implements Serializable
  
  serialVersionUID:
  
  -1901958943061377082L
- Class ubic.gemma.core.tasks.analysis.expression.BioAssayOutlierProcessingTaskCommand extends TaskCommand implements Serializable
  
  serialVersionUID:
  
  3083077516188614790L
  - Serialized Fields
    - bioAssayIds
      
      Collection<Long> bioAssayIds
    - revert
      
      boolean revert
- Class ubic.gemma.core.tasks.analysis.expression.ExpressionExperimentLoadTaskCommand extends TaskCommand implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - accession
      
      String accession
    - aggressiveQtRemoval
      
      boolean aggressiveQtRemoval
      
      Set to true to attempt to remove all unneeded quantitation types during parsing.
    - allowArrayExpressDesign
      
      boolean allowArrayExpressDesign
    - allowSubSeriesLoad
      
      boolean allowSubSeriesLoad
    - allowSuperSeriesLoad
      
      boolean allowSuperSeriesLoad
    - arrayDesignName
      
      String arrayDesignName
    - isArrayExpress
      
      boolean isArrayExpress
    - isSplitByPlatform
      
      boolean isSplitByPlatform
    - loadPlatformOnly
      
      boolean loadPlatformOnly
    - suppressMatching
      
      boolean suppressMatching
      
      Used to turn off 'bioassay to biomaterial' matching.
- Class ubic.gemma.core.tasks.analysis.expression.PreprocessTaskCommand extends TaskCommand implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - diagnosticsOnly
      
      boolean diagnosticsOnly
    - expressionExperiment
      
      ExpressionExperiment expressionExperiment
- Class ubic.gemma.core.tasks.analysis.expression.SvdTaskCommand extends TaskCommand implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - expressionExperiment
      
      ExpressionExperiment expressionExperiment
    - postProcessOnly
      
      boolean postProcessOnly
- Class ubic.gemma.core.tasks.analysis.expression.TwoChannelMissingValueTaskCommand extends TaskCommand implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - expressionExperiment
      
      ExpressionExperiment expressionExperiment
    - extraMissingValueIndicators
      
      Collection<Double> extraMissingValueIndicators
    - s2n
      
      double s2n
- Class ubic.gemma.core.tasks.analysis.expression.UpdateEEDetailsCommand extends TaskCommand implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - description
      
      String description
    - entityId
      
      Long entityId
    - name
      
      String name
    - pubMedId
      
      String pubMedId
    - removePrimaryPublication
      
      boolean removePrimaryPublication
    - shortName
      
      String shortName
- Class ubic.gemma.core.tasks.analysis.expression.UpdatePubMedCommand extends TaskCommand implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - entityId
      
      Long entityId
    - pubmedId
      
      String pubmedId
Package ubic.gemma.core.tasks.analysis.sequence
- Class ubic.gemma.core.tasks.analysis.sequence.ArrayDesignProbeMapTaskCommand extends TaskCommand implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - arrayDesign
      
      ArrayDesign arrayDesign
    - forceAnalysis
      
      boolean forceAnalysis
Package ubic.gemma.core.tasks.maintenance
- Class ubic.gemma.core.tasks.maintenance.CharacteristicUpdateCommand extends TaskCommand implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - annotationValueObjects
      
      Collection<AnnotationValueObject> annotationValueObjects
    - remove
      
      boolean remove
      
      If set to true, the annotations passed in will be deleted.
- Class ubic.gemma.core.tasks.maintenance.ExpressionExperimentReportTaskCommand extends TaskCommand implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - all
      
      boolean all
    - expressionExperiment
      
      ExpressionExperiment expressionExperiment
- Class ubic.gemma.core.tasks.maintenance.IndexerTaskCommand extends TaskCommand implements Serializable
  
  serialVersionUID:
  
  -8994831072852393919L
  - Serialized Fields
    - compassOn
      
      boolean compassOn
    - indexAD
      
      boolean indexAD
    - indexBibRef
      
      boolean indexBibRef
    - indexBioSequence
      
      boolean indexBioSequence
    - indexEE
      
      boolean indexEE
    - indexExperimentSet
      
      boolean indexExperimentSet
    - indexGene
      
      boolean indexGene
    - indexGeneSet
      
      boolean indexGeneSet
    - indexOntologies
      
      boolean indexOntologies
    - indexProbe
      
      boolean indexProbe
Package ubic.gemma.core.tasks.visualization
- Class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject extends Object implements Serializable
  - Serialized Fields
    - analysisId
      
      Long analysisId
    - analysisNotRun
      
      boolean analysisNotRun
    - baselineFactorValue
      
      String baselineFactorValue
    - baselineFactorValueId
      
      Long baselineFactorValueId
    - contrastsFactorValueIds
      
      List<Long> contrastsFactorValueIds
    - contrastsFactorValues
      
      Map<Long,String> contrastsFactorValues
    - datasetId
      
      Long datasetId
    - datasetLink
      
      String datasetLink
    - datasetName
      
      String datasetName
    - datasetShortName
      
      String datasetShortName
    - factorCategory
      
      String factorCategory
    - factorDescription
      
      String factorDescription
    - factorId
      
      Long factorId
    - factorName
      
      String factorName
    - numberOfProbes
      
      List<List<Integer>> numberOfProbes
    - numberOfProbesDiffExpressed
      
      int numberOfProbesDiffExpressed
    - numberOfProbesDownRegulated
      
      int numberOfProbesDownRegulated
    - numberOfProbesTotal
      
      int numberOfProbesTotal
    - numberOfProbesUpRegulated
      
      int numberOfProbesUpRegulated
    - qValues
      
      List<List<Double>> qValues
    - resultSetId
      
      Long resultSetId
    - visualizationValues
      
      List<List<Double>> visualizationValues
- Class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject extends Object implements Serializable
  - Serialized Fields
    - cellData
      
      Map<String,Map<Long,DifferentialExpressionGenesConditionsValueObject.Cell>> cellData
      
      Map of Condition IDs to map of Genes to the Cell holding the information for the results for that Gene x Condition combination.
    - conditions
      
      List<DifferentialExpressionGenesConditionsValueObject.Condition> conditions
    - genes
      
      List<DifferentialExpressionGenesConditionsValueObject.DiffExGene> genes
    - resultSetConditions
      
      Map<Long,Collection<DifferentialExpressionGenesConditionsValueObject.Condition>> resultSetConditions
- Class ubic.gemma.core.tasks.visualization.DifferentialExpressionSearchTaskCommand extends TaskCommand implements Serializable
  
  serialVersionUID:
  
  -8510536003059837349L
  - Serialized Fields
    - experimentGroup
      
      Collection<ExpressionExperimentDetailsValueObject> experimentGroup
    - experimentGroupName
      
      String experimentGroupName
    - geneGroup
      
      Collection<GeneValueObject> geneGroup
    - geneGroupName
      
      String geneGroupName
Package ubic.gemma.core.util
- Class ubic.gemma.core.util.GemmaRestApiClientException extends RuntimeException implements Serializable

Package ubic.gemma.core.visualization

Class ubic.gemma.core.visualization.ExpressionDataHeatmap extends Object implements Serializable
- Serialized Fields
  - bioAssaySet
```
BioAssaySet bioAssaySet
```
  - cellLevelCharacteristics
```
CellLevelCharacteristics cellLevelCharacteristics
```
  - cellSize
```
int cellSize
```
  - designElements
```
Slice<CompositeSequence> designElements
```
  - dimension
```
BioAssayDimension dimension
```
  - focusedCellLevelCharacteristic
```
Characteristic focusedCellLevelCharacteristic
```
  - genes
```
List<Gene> genes
```
    List of genes to use for display purposes.
  - sampleIndex
```
int[] sampleIndex
```
  - samples
```
List<BioAssay> samples
```
  - singleCellQuantitationType
```
QuantitationType singleCellQuantitationType
```
    Quantitation type of the single-cell data this heatmap was generated from, if applicable.
  - transpose
```
boolean transpose
```
  - vectors
```
Slice<? extends BulkExpressionDataVector> vectors
```

Class ubic.gemma.core.visualization.SingleCellSparsityHeatmap extends Object implements Serializable

Serialized Fields

cellSize
```
int cellSize
```

designElementsPerSample

Map<BioAssay,Long> designElementsPerSample

dimension
```
BioAssayDimension dimension
```

expressionExperiment

ExpressionExperiment expressionExperiment

samples
```
List<BioAssay> samples
```
singleCellDimension
```
SingleCellDimension singleCellDimension
```

subSets

List<ExpressionExperimentSubSet> subSets

transpose
```
boolean transpose
```

type

SingleCellSparsityHeatmap.SingleCellHeatmapType type

Package ubic.gemma.model.analysis
- Class ubic.gemma.model.analysis.AnalysisResultSetValueObject 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
  - Serialized Fields
    - name
      
      String name
    - protocol
      
      ProtocolValueObject protocol
- Class ubic.gemma.model.analysis.CellTypeAssignmentValueObject extends AnalysisValueObject<CellTypeAssignment> implements Serializable
  - Serialized Fields
    - cellTypeIds
      
      List<Long> cellTypeIds
      
      A list of IDs, one-per-cell, that refers to one of the cell type labels in CellTypeAssignmentValueObject.cellTypes.
      null is used to indicate an unknown cell type.
    - cellTypes
      
      Set<CharacteristicValueObject> cellTypes
      
      A set of cell types that are assigned to individual cells.
    - isPreferred
      
      boolean isPreferred
      
      Indicate if this assignment is the preferred one.
    - numberOfAssignedCells
      
      Integer numberOfAssignedCells
      
      Indicate how many cells have an assigned cell type, or null if this information is not available.
- Class ubic.gemma.model.analysis.ProtocolValueObject extends IdentifiableValueObject<Protocol> implements Serializable
  - Serialized Fields
    - characteristics
      
      Set<CharacteristicValueObject> characteristics
    - description
      
      String description
    - name
      
      String name
Package ubic.gemma.model.analysis.expression.diff
- Class ubic.gemma.model.analysis.expression.diff.ContrastResultValueObject extends IdentifiableValueObject<ContrastResult> implements Serializable
  - Serialized Fields
    - coefficient
      
      Double coefficient
    - factorValue
      
      FactorValueBasicValueObject factorValue
    - factorValueId
      
      Long factorValueId
    - logFoldChange
      
      Double logFoldChange
    - pvalue
      
      Double pvalue
    - secondFactorValue
      
      FactorValueBasicValueObject secondFactorValue
    - secondFactorValueId
      
      Long secondFactorValueId
    - tStat
      
      Double tStat
- Class ubic.gemma.model.analysis.expression.diff.ContrastsValueObject extends Object implements Serializable
  - Serialized Fields
    - contrasts
      
      List<ContrastVO> contrasts
    - resultId
      
      Long resultId
- Class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResultSetValueObject extends AnalysisResultSetValueObject<DifferentialExpressionAnalysisResult,ExpressionAnalysisResultSet> implements Serializable
  - Serialized Fields
    - analysis
      
      DifferentialExpressionAnalysisValueObject analysis
    - baselineGroup
      
      FactorValueBasicValueObject baselineGroup
    - experimentalFactors
      
      Collection<ExperimentalFactorValueObject> experimentalFactors
    - results
      
      Collection<DifferentialExpressionAnalysisResultValueObject> results
      
      Related analysis results.
      Note that this field is excluded from the JSON serialization if left unset.
    - secondBaselineGroup
      
      FactorValueBasicValueObject secondBaselineGroup
    - taxa
      
      Set<TaxonValueObject> taxa
      
      When genes are included, this field is populated.
- Class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResultValueObject extends AnalysisResultValueObject<DifferentialExpressionAnalysisResult> implements Serializable
  - Serialized Fields
    - contrasts
      
      List<ContrastResultValueObject> contrasts
    - correctedPvalue
      
      Double correctedPvalue
    - genes
      
      List<GeneValueObject> genes
    - probeId
      
      Long probeId
    - probeName
      
      String probeName
    - pValue
      
      Double pValue
    - rank
      
      Double rank
- Class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisValueObject extends AnalysisValueObject<DifferentialExpressionAnalysis> implements Serializable
  
  serialVersionUID:
  
  622877438067070041L
  - Serialized Fields
    - arrayDesignsUsed
      
      Collection<Long> arrayDesignsUsed
    - experimentAnalyzedId
      
      Long experimentAnalyzedId
    - factorValuesUsed
      
      Map<Long,Collection<FactorValueValueObject>> factorValuesUsed
    - resultSets
      
      Collection<DiffExResultSetSummaryValueObject> resultSets
    - sourceExperimentId
      
      Long sourceExperimentId
    - subsetFactor
      
      ExperimentalFactorValueObject subsetFactor
    - subsetFactorId
      
      Long subsetFactorId
    - subsetFactorValue
      
      FactorValueValueObject subsetFactorValue
    - subsetFactorValueId
      
      Long subsetFactorValueId
- Class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionValueObject extends Object implements Serializable
  - Serialized Fields
    - contrasts
      
      ContrastsValueObject contrasts
    - corrP
      
      Double corrP
    - direction
      
      Direction direction
    - experimentalFactors
      
      Collection<ExperimentalFactorValueObject> experimentalFactors
    - expressionExperiment
      
      BioAssaySetValueObject expressionExperiment
    - fisherContribution
      
      Boolean fisherContribution
    - gene
      
      GeneValueObject gene
    - id
      
      Long id
    - metThreshold
      
      Boolean metThreshold
    - p
      
      Double p
    - probe
      
      String probe
    - probeId
      
      Long probeId
    - resultSetId
      
      Long resultSetId
    - sortKey
      
      String sortKey
- Class ubic.gemma.model.analysis.expression.diff.DiffExprGeneSearchResult extends Object implements Serializable
  
  serialVersionUID:
  
  -6199218806972657112L
  - Serialized Fields
    - analysisResultId
      
      Long analysisResultId
    - correctedPvalue
      
      Double correctedPvalue
    - geneId
      
      Long geneId
    - numberOfProbes
      
      int numberOfProbes
    - numberOfProbesDiffExpressed
      
      int numberOfProbesDiffExpressed
    - pvalue
      
      Double pvalue
    - resultSetId
      
      Long resultSetId
    - score
      
      Double score
- Class ubic.gemma.model.analysis.expression.diff.DiffExResultSetSummaryValueObject extends Object implements Serializable
  
  serialVersionUID:
  
  2063274043081170625L
  - Serialized Fields
    - analysisId
      
      Long analysisId
    - arrayDesignsUsed
      
      Collection<Long> arrayDesignsUsed
    - baselineGroup
      
      FactorValueValueObject baselineGroup
    - bioAssaySetAnalyzedId
      
      Long bioAssaySetAnalyzedId
      
      Analyzed BioAssaySet ID.
      This is redundant because of DifferentialExpressionAnalysisValueObject#getExperimentAnalyzedId(), and always displayed in that context in the RESTful API.
    - downregulatedCount
      
      Integer downregulatedCount
      
      Number of diffex probes in the Direction.DOWN hit list if available.
    - experimentalFactors
      
      Collection<ExperimentalFactorValueObject> experimentalFactors
    - factorIds
      
      Collection<Long> factorIds
    - id
      
      Long id
    - numberOfDiffExpressedProbes
      
      Integer numberOfDiffExpressedProbes
      
      Number of diffex probes in the Direction.EITHER hit list if available.
    - numberOfGenesAnalyzed
      
      Integer numberOfGenesAnalyzed
    - numberOfProbesAnalyzed
      
      Integer numberOfProbesAnalyzed
    - qValue
      
      Double qValue
      
      This is used once in the frontend, but never filled, so please ignore.
    - threshold
      
      Double threshold
      
      Threshold applied to the hitlist.
    - upregulatedCount
      
      Integer upregulatedCount
      
      Number of diffex probes in the Direction.UP hit list if available.
- Class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisDetailValueObject extends Object implements Serializable
  
  serialVersionUID:
  
  3868004995989355452L
  - Serialized Fields
    - includedResultSetsInfo
      
      Collection<IncludedResultSetInfoValueObject> includedResultSetsInfo
    - numGenesAnalyzed
      
      Integer numGenesAnalyzed
    - results
      
      Collection<GeneDifferentialExpressionMetaAnalysisResultValueObject> results
- Class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisResultValueObject extends Object implements Serializable
  
  serialVersionUID:
  
  6099286095885830140L
  - Serialized Fields
    - geneName
      
      String geneName
    - geneSymbol
      
      String geneSymbol
    - metaPvalue
      
      Double metaPvalue
    - metaQvalue
      
      Double metaQvalue
    - upperTail
      
      Boolean upperTail
- Class ubic.gemma.model.analysis.expression.diff.IncludedResultSetInfoValueObject extends Object implements Serializable
  
  serialVersionUID:
  
  -4660741839991839187L
  - Serialized Fields
    - analysisId
      
      Long analysisId
    - experimentId
      
      Long experimentId
    - resultSetId
      
      Long resultSetId
Package ubic.gemma.model.association.coexpression
- Class ubic.gemma.model.association.coexpression.GeneCoexpressionNodeDegreeValueObject extends Object implements Serializable
  - Serialized Fields
    - geneId
      
      Long geneId
    - nodeDegreesNeg
      
      TreeMap<Integer,Integer> nodeDegreesNeg
    - nodeDegreesPos
      
      TreeMap<Integer,Integer> nodeDegreesPos
    - relDegreesNeg
      
      TreeMap<Integer,Double> relDegreesNeg
    - relDegreesPos
      
      TreeMap<Integer,Double> relDegreesPos
Package ubic.gemma.model.blacklist
- Class ubic.gemma.model.blacklist.BlacklistedValueObject extends IdentifiableValueObject<BlacklistedEntity> implements Serializable
  
  serialVersionUID:
  
  -4817418347388923905L
  - Serialized Fields
    - accession
      
      String accession
    - externalDatabase
      
      ExternalDatabaseValueObject externalDatabase
    - name
      
      String name
    - reason
      
      String reason
    - shortName
      
      String shortName
    - type
      
      String type
Package ubic.gemma.model.common
- Class ubic.gemma.model.common.BaseValueObject extends Object implements Serializable
  
  serialVersionUID:
  
  -5290562301261202171L
  - Serialized Fields
    - accessDenied
      
      boolean accessDenied
    - errorFound
      
      boolean errorFound
    - objectAlreadyRemoved
      
      boolean objectAlreadyRemoved
    - userNotLoggedIn
      
      boolean userNotLoggedIn
    - valueObject
      
      Serializable valueObject
- Class ubic.gemma.model.common.IdentifiableValueObject extends Object implements Serializable
  - Serialized Fields
    - id
      
      Long id
Package ubic.gemma.model.common.auditAndSecurity
- Class ubic.gemma.model.common.auditAndSecurity.AuditEventValueObject extends IdentifiableValueObject<AuditEvent> implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - action
      
      String action
    - date
      
      Date date
    - detail
      
      String detail
    - eventType
      
      AuditEventType eventType
    - note
      
      String note
    - performer
      
      String performer
- Class ubic.gemma.model.common.auditAndSecurity.GroupAuthority extends AbstractIdentifiable implements Serializable
  - Serialized Fields
    - authority
      
      String authority
Package ubic.gemma.model.common.auditAndSecurity.curation
- Class ubic.gemma.model.common.auditAndSecurity.curation.AbstractCuratableValueObject extends IdentifiableValueObject<C extends Curatable> implements Serializable
  - Serialized Fields
    - curationNote
      
      String curationNote
    - lastNeedsAttentionEvent
      
      AuditEventValueObject lastNeedsAttentionEvent
    - lastNoteUpdateEvent
      
      AuditEventValueObject lastNoteUpdateEvent
    - lastTroubledEvent
      
      AuditEventValueObject lastTroubledEvent
    - lastUpdated
      
      Date lastUpdated
    - needsAttention
      
      Boolean needsAttention
    - troubled
      
      Boolean troubled
Package ubic.gemma.model.common.description
- Class ubic.gemma.model.common.description.AnnotationValueObject extends IdentifiableValueObject<Characteristic> implements Serializable
  - Serialized Fields
    - className
      
      String className
    - classUri
      
      String classUri
    - description
      
      String description
    - evidenceCode
      
      String evidenceCode
    - objectClass
      
      String objectClass
    - parentDescription
      
      String parentDescription
    - parentLink
      
      String parentLink
    - parentName
      
      String parentName
    - parentOfParentDescription
      
      String parentOfParentDescription
    - parentOfParentLink
      
      String parentOfParentLink
    - parentOfParentName
      
      String parentOfParentName
    - termName
      
      String termName
    - termUri
      
      String termUri
- Class ubic.gemma.model.common.description.BibliographicReferenceValueObject extends IdentifiableValueObject<BibliographicReference> implements Serializable
  - Serialized Fields
    - abstractText
      
      String abstractText
    - authorList
      
      String authorList
    - chemicalsTerms
      
      Collection<String> chemicalsTerms
    - citation
      
      CitationValueObject citation
    - experiments
      
      Collection<ExpressionExperimentValueObject> experiments
    - issue
      
      String issue
    - meshTerms
      
      Collection<String> meshTerms
    - pages
      
      String pages
    - pubAccession
      
      String pubAccession
    - publication
      
      String publication
    - publicationDate
      
      Date publicationDate
    - publisher
      
      String publisher
    - retracted
      
      boolean retracted
    - title
      
      String title
    - volume
      
      String volume
- Class ubic.gemma.model.common.description.CharacteristicValueObject extends IdentifiableValueObject<Characteristic> implements Serializable
  - Serialized Fields
    - alreadyPresentInDatabase
      
      boolean alreadyPresentInDatabase
    - alreadyPresentOnGene
      
      boolean alreadyPresentOnGene
    - category
      
      String category
    - categoryUri
      
      String categoryUri
    - child
      
      boolean child
      
      child term from a root
    - numTimesUsed
      
      int numTimesUsed
    - ontologyUsed
      
      String ontologyUsed
      
      what Ontology uses this term
    - originalValue
      
      String originalValue
    - privateGeneCount
      
      long privateGeneCount
    - publicGeneCount
      
      long publicGeneCount
      
      number of occurrences in all genes
    - root
      
      boolean root
      
      root of a query
    - taxon
      
      String taxon
    - urlId
      
      String urlId
      
      id used by url on the client side
    - value
      
      String value
    - valueDefinition
      
      String valueDefinition
      
      The definition of the value, if it is an ontology term, as supplied by the ontology. If the value is free text, this will be empty
    - valueId
      
      String valueId
      
      A unique ontology identifier (i.e. IRI) for this characteristic.
    - valueUri
      
      String valueUri
- Class ubic.gemma.model.common.description.CitationValueObject extends Object implements Serializable
  - Serialized Fields
    - citation
      
      String citation
    - id
      
      Long id
      
      the DB id of the BibliographicReference being represented
    - pubmedAccession
      
      String pubmedAccession
    - pubmedURL
      
      String pubmedURL
    - retracted
      
      boolean retracted
- Class ubic.gemma.model.common.description.DatabaseEntryValueObject extends IdentifiableValueObject<DatabaseEntry> implements Serializable
  
  serialVersionUID:
  
  -527323410580090L
  - Serialized Fields
    - accession
      
      String accession
    - externalDatabase
      
      ExternalDatabaseValueObject externalDatabase
- Class ubic.gemma.model.common.description.ExternalDatabaseValueObject extends IdentifiableValueObject<ExternalDatabase> implements Serializable
  
  serialVersionUID:
  
  -1714429166594162374L
  - Serialized Fields
    - checked
      
      boolean checked
    - description
      
      String description
    - externalDatabases
      
      Set<ExternalDatabaseValueObject> externalDatabases
    - lastUpdated
      
      Date lastUpdated
    - name
      
      String name
    - releaseUrl
      
      URL releaseUrl
    - releaseVersion
      
      String releaseVersion
    - uri
      
      String uri
Package ubic.gemma.model.common.measurement
- Class ubic.gemma.model.common.measurement.MeasurementValueObject extends IdentifiableValueObject<Measurement> implements Serializable
  - Serialized Fields
    - representation
      
      String representation
    - type
      
      String type
    - unit
      
      String unit
    - unitId
      
      Long unitId
    - value
      
      String value
Package ubic.gemma.model.common.quantitationtype
- Class ubic.gemma.model.common.quantitationtype.QuantitationTypeValueObject extends IdentifiableValueObject<QuantitationType> implements Serializable
  
  serialVersionUID:
  
  7537853492100102404L
  - Serialized Fields
    - description
      
      String description
    - expressionExperimentId
      
      Long expressionExperimentId
      
      Associated expression experiment ID.
      This is unnecessary in the context of the RESTful API because vector types are always retrieved when the associated ExpressionExperiment is known.
    - generalType
      
      String generalType
    - isBackground
      
      boolean isBackground
    - isBackgroundSubtracted
      
      boolean isBackgroundSubtracted
    - isBatchCorrected
      
      boolean isBatchCorrected
    - isMaskedPreferred
      
      boolean isMaskedPreferred
      
      Deprecated.
    - isNormalized
      
      boolean isNormalized
    - isPreferred
      
      boolean isPreferred
    - isRatio
      
      boolean isRatio
    - isRecomputedFromRawData
      
      boolean isRecomputedFromRawData
    - name
      
      String name
    - representation
      
      String representation
    - scale
      
      String scale
    - type
      
      String type
    - vectorType
      
      String vectorType
      
      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.SearchSettingsValueObject extends Object implements Serializable
  
  serialVersionUID:
  
  -934534534L
  - Serialized Fields
    - maxResults
      
      Integer maxResults
    - platformConstraint
      
      ArrayDesign platformConstraint
    - query
      
      String query
    - searchBibrefs
      
      Boolean searchBibrefs
    - searchBioSequences
      
      Boolean searchBioSequences
    - searchExperiments
      
      Boolean searchExperiments
    - searchExperimentSets
      
      Boolean searchExperimentSets
    - searchGenes
      
      Boolean searchGenes
    - searchGeneSets
      
      Boolean searchGeneSets
    - searchPlatforms
      
      Boolean searchPlatforms
    - searchProbes
      
      Boolean searchProbes
    - taxon
      
      Taxon taxon
    - termUri
      
      String termUri
    - useCharacteristics
      
      Boolean useCharacteristics
    - useDatabase
      
      Boolean useDatabase
    - useGo
      
      Boolean useGo
    - useIndices
      
      Boolean useIndices
Package ubic.gemma.model.expression.arrayDesign
- Class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject extends AbstractCuratableValueObject<ArrayDesign> implements Serializable
  
  serialVersionUID:
  
  -8259245319391937522L
  - Serialized Fields
    - blackListed
      
      Boolean blackListed
    - color
      
      String color
      
      Deprecated.
    - createDate
      
      Date createDate
    - dateCached
      
      String dateCached
    - description
      
      String description
    - designElementCount
      
      Integer designElementCount
    - expressionExperimentCount
      
      Long expressionExperimentCount
    - externalReferences
      
      Set<DatabaseEntryValueObject> externalReferences
      
      Main external reference.
    - hasBlatAssociations
      
      Boolean hasBlatAssociations
    - hasGeneAssociations
      
      Boolean hasGeneAssociations
    - hasSequenceAssociations
      
      Boolean hasSequenceAssociations
    - isAffymetrixAltCdf
      
      Boolean isAffymetrixAltCdf
    - isMerged
      
      Boolean isMerged
      
      Indicates this array design is the merger of other array designs.
    - isMergee
      
      Boolean isMergee
      
      Indicates that this array design has been merged into another.
    - isSubsumed
      
      Boolean isSubsumed
      
      Indicate if this array design is subsumed by some other array design.
    - isSubsumer
      
      Boolean isSubsumer
      
      Indicates if this array design subsumes some other array design(s)
    - lastGeneMapping
      
      Date lastGeneMapping
    - lastRepeatMask
      
      Date lastRepeatMask
    - lastSequenceAnalysis
      
      Date lastSequenceAnalysis
    - lastSequenceUpdate
      
      Date lastSequenceUpdate
    - name
      
      String name
    - numGenes
      
      String numGenes
      
      The number of unique genes that this array design maps to.
    - numProbeAlignments
      
      String numProbeAlignments
      
      The number of probes that have BLAT alignments.
    - numProbeSequences
      
      String numProbeSequences
      
      The number of probes that map to bioSequences.
    - numProbesToGenes
      
      String numProbesToGenes
      
      The number of probes that map to genes. This count includes probe-aligned regions, predicted genes, and known genes.
    - releaseUrl
      
      URL releaseUrl
    - releaseVersion
      
      String releaseVersion
    - shortName
      
      String shortName
    - switchedExpressionExperimentCount
      
      Long switchedExpressionExperimentCount
    - taxonObject
      
      TaxonValueObject taxonObject
    - technologyType
      
      String technologyType
Package ubic.gemma.model.expression.bioAssay
- Class ubic.gemma.model.expression.bioAssay.BioAssayValueObject extends IdentifiableValueObject<BioAssay> implements Serializable
  
  serialVersionUID:
  
  9164284536309673585L
  - Serialized Fields
    - accession
      
      DatabaseEntryValueObject accession
    - arrayDesign
      
      ArrayDesignValueObject arrayDesign
    - description
      
      String description
    - metadata
      
      String metadata
    - name
      
      String name
    - originalPlatform
      
      ArrayDesignValueObject originalPlatform
    - outlier
      
      Boolean outlier
    - predictedOutlier
      
      Boolean predictedOutlier
    - processingDate
      
      Date processingDate
    - sample
      
      BioMaterialValueObject sample
    - sequencePairedReads
      
      Boolean sequencePairedReads
    - sequenceReadCount
      
      Long sequenceReadCount
    - sequenceReadLength
      
      Integer sequenceReadLength
    - shortName
      
      String shortName
    - sourceBioAssayId
      
      Long sourceBioAssayId
    - userFlaggedOutlier
      
      Boolean userFlaggedOutlier
Package ubic.gemma.model.expression.bioAssayData
- Class ubic.gemma.model.expression.bioAssayData.BioAssayDimensionValueObject extends IdentifiableValueObject<BioAssayDimension> implements Serializable
  
  serialVersionUID:
  
  -8686807689616396835L
  - Serialized Fields
    - bioAssays
      
      List<BioAssayValueObject> bioAssays
    - description
      
      String description
      
      Deprecated.
    - isReordered
      
      boolean isReordered
    - isSubset
      
      boolean isSubset
    - name
      
      String name
      
      Deprecated.
    - sourceBioAssayDimension
      
      BioAssayDimensionValueObject sourceBioAssayDimension
      
      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
  - Serialized Fields
    - data
      
      boolean[] data
- Class ubic.gemma.model.expression.bioAssayData.CellLevelCharacteristicsValueObject extends IdentifiableValueObject<CellLevelCharacteristics> implements Serializable
  - Serialized Fields
    - characteristicIds
      
      List<Long> characteristicIds
    - characteristics
      
      Set<CharacteristicValueObject> characteristics
    - numberOfAssignedCells
      
      Integer numberOfAssignedCells
      
      Indicate how many cells have an assigned characteristic, or null if this information is not available.
- Class ubic.gemma.model.expression.bioAssayData.DataVectorValueObject extends IdentifiableValueObject<DataVector> implements Serializable
  - Serialized Fields
    - bioAssayDimension
      
      BioAssayDimensionValueObject bioAssayDimension
      
      Represents the order of the bioassays for this. It might not be a real (persistent) BioAssayDimension: it might be a subset, or a "padded" one.
    - designElement
      
      CompositeSequenceValueObject designElement
    - expressionExperiment
      
      BioAssaySetValueObject expressionExperiment
    - genes
      
      Collection<Long> genes
    - quantitationType
      
      QuantitationTypeValueObject quantitationType
- Class ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject extends DataVectorValueObject implements Serializable
  - Serialized Fields
    - data
      
      double[] data
      
      The data of this vector.
    - masked
      
      boolean masked
      
      Indicate if this vector is "masked", i.e. it is processed.
    - pvalue
      
      Double pvalue
      
      If this vector is associated to a statistical test (i.e. from a DE analysis), this is the P-value.
    - rank
      
      Double rank
    - rankByMax
      
      Double rankByMax
    - rankByMean
      
      Double rankByMean
    - reorganized
      
      boolean reorganized
      
      True if the data has been rearranged relative to the bioassay dimension (as a matter of practice the bioassay dimension should be set to null if it is not valid; this boolean is an additional check)
- Class ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject extends Object implements Serializable
  - Serialized Fields
    - datasetId
      
      long datasetId
    - geneExpressionLevels
      
      LinkedList<ExperimentExpressionLevelsValueObject.GeneElementExpressionsValueObject> geneExpressionLevels
- Class ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject.GeneElementExpressionsValueObject extends Object implements Serializable
  - Serialized Fields
    - elements
      
      List<ExperimentExpressionLevelsValueObject.VectorElementValueObject> elements
    - geneNcbiId
      
      Integer geneNcbiId
    - geneOfficialSymbol
      
      String geneOfficialSymbol
- Class ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject.VectorElementValueObject extends Object implements Serializable
  - Serialized Fields
    - bioAssayExpressionLevels
      
      Map<String,Double> bioAssayExpressionLevels
    - designElementName
      
      String designElementName
- Class ubic.gemma.model.expression.bioAssayData.SingleCellDimensionValueObject extends IdentifiableValueObject<SingleCellDimension> implements Serializable
  - Serialized Fields
    - bioAssayIds
      
      List<Long> bioAssayIds
      
      A list of BioAssay IDs that are applicable to the cells.
    - cellIds
      
      List<String> cellIds
      
      Cell identifiers.
      This may be null if cell IDs are explicitly omitted (i.e. ExpressionExperimentDao.getPreferredSingleCellDimensionWithoutCellIds(ExpressionExperiment)), in which case it will not be serialized in JSON.
    - cellLevelCharacteristics
      
      Set<CellLevelCharacteristicsValueObject> cellLevelCharacteristics
      
      All the other cell-level characteristics.
    - cellTypeAssignments
      
      Set<CellTypeAssignmentValueObject> cellTypeAssignments
      
      All the cell type assignments.
    - numberOfCells
      
      int numberOfCells
      
      Number of cells.
      This is always equal to the length of SingleCellDimensionValueObject.cellIds.
- Class ubic.gemma.model.expression.bioAssayData.SlicedDoubleVectorValueObject extends DoubleVectorValueObject implements Serializable
  - Serialized Fields
    - sourceVectorId
      
      Long sourceVectorId
      
      Obtain the ID of the vector from which this slice is derived from.
Package ubic.gemma.model.expression.biomaterial
- Class ubic.gemma.model.expression.biomaterial.BioMaterialValueObject extends IdentifiableValueObject<BioMaterial> implements Serializable
  
  serialVersionUID:
  
  -145137827948521045L
  - Serialized Fields
    - assayDescription
      
      String assayDescription
    - assayName
      
      String assayName
    - assayProcessingDate
      
      Date assayProcessingDate
    - basicFVs
      
      boolean basicFVs
      
      Indicate if this is using the BioMaterialValueObject.fVBasicVOs or BioMaterialValueObject.factorValueObjects for representing factor values.
    - bioAssayIds
      
      Collection<Long> bioAssayIds
      
      Related BioAssay IDs.
    - characteristicOriginalValues
      
      Map<String,String> characteristicOriginalValues
      
      Map of categories to original text values (for this biomaterial). This is only used for display and will only be populated if the original value is different from the value.
    - characteristics
      
      Collection<CharacteristicValueObject> characteristics
    - characteristicValues
      
      Map<String,String> characteristicValues
    - description
      
      String description
    - factorIdToFactorValueId
      
      Map<String,String> factorIdToFactorValueId
      
      Map of factor ids (factor232) to factor value (id or the actual value) for this biomaterial.
    - factors
      
      Map<String,String> factors
      
      Deprecated.
      
      Map of ids (factor232) to a representation of the factor (e.g., the name).
    - factorValueObjects
      
      Collection<FactorValueValueObject> factorValueObjects
    - factorValues
      
      Map<String,String> factorValues
      
      Map of ids (fv133) to a representation of the value (for this biomaterial.)
    - fastqHeaders
      
      String fastqHeaders
    - fVBasicVOs
      
      Collection<FactorValueBasicValueObject> fVBasicVOs
    - name
      
      String name
    - sourceBioMaterialId
      
      Long sourceBioMaterialId
Package ubic.gemma.model.expression.designElement
- Class ubic.gemma.model.expression.designElement.CompositeSequenceValueObject extends IdentifiableValueObject<CompositeSequence> implements Serializable
  
  serialVersionUID:
  
  4915680501039784666L
  - Serialized Fields
    - arrayDesign
      
      ArrayDesignValueObject arrayDesign
    - description
      
      String description
    - geneMappingSummaries
      
      Collection<GeneMappingSummary> geneMappingSummaries
    - name
      
      String name
Package ubic.gemma.model.expression.experiment
- Class ubic.gemma.model.expression.experiment.AbstractFactorValueValueObject extends IdentifiableValueObject<FactorValue> implements Serializable
  - Serialized Fields
    - characteristics
      
      List<CharacteristicValueObject> characteristics
      
      The characteristics associated with this factor value.
    - experimentalFactorCategory
      
      CharacteristicValueObject experimentalFactorCategory
      
      The experiment factor category.
    - experimentalFactorId
      
      Long experimentalFactorId
      
      The ID of the experimental factor this factor value belongs to.
    - experimentalFactorType
      
      String experimentalFactorType
      
      The experimental factor type.
    - measurementObject
      
      MeasurementValueObject measurementObject
      
      The measurement associated with this factor value.
      This is named as such to avoid conflict with AbstractFactorValueValueObject.isMeasurement().
    - ontologyId
      
      String ontologyId
      
      A unique ontology identifier (i.e. IRI) for this factor value.
    - statements
      
      List<StatementValueObject> statements
      
      The statements associated with this factor value.
    - summary
      
      String summary
      
      Human-readable summary of the factor value.
- Class ubic.gemma.model.expression.experiment.ExperimentalFactorValueObject extends IdentifiableValueObject<ExperimentalFactor> implements Serializable
  
  serialVersionUID:
  
  -2615804031123874251L
  - Serialized Fields
    - category
      
      String category
    - categoryUri
      
      String categoryUri
    - description
      
      String description
    - factorValues
      
      String factorValues
      
      Deprecated.
    - name
      
      String name
    - type
      
      String type
    - values
      
      Collection<FactorValueValueObject> values
- Class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject extends ExpressionExperimentValueObject implements Serializable
  
  serialVersionUID:
  
  -1219449523930648392L
  - Serialized Fields
    - arrayDesigns
      
      Collection<ArrayDesignValueObject> arrayDesigns
    - batchFetchEventType
      
      String batchFetchEventType
    - dateArrayDesignLastUpdated
      
      Date dateArrayDesignLastUpdated
    - dateBatchFetch
      
      Date dateBatchFetch
    - dateCached
      
      Date dateCached
    - dateDifferentialAnalysis
      
      Date dateDifferentialAnalysis
    - dateLinkAnalysis
      
      Date dateLinkAnalysis
    - dateMissingValueAnalysis
      
      Date dateMissingValueAnalysis
    - datePcaAnalysis
      
      Date datePcaAnalysis
    - dateProcessedDataVectorComputation
      
      Date dateProcessedDataVectorComputation
    - differentialExpressionAnalyses
      
      Collection<DifferentialExpressionAnalysisValueObject> differentialExpressionAnalyses
    - expressionExperimentSets
      
      Collection<ExpressionExperimentSetValueObject> expressionExperimentSets
    - hasBatchInformation
      
      boolean hasBatchInformation
      
      FIXME: rename this to hasUsableBatchInformation
    - hasBothIntensities
      
      Boolean hasBothIntensities
    - hasCoexpressionAnalysis
      
      Boolean hasCoexpressionAnalysis
    - hasDifferentialExpressionAnalysis
      
      Boolean hasDifferentialExpressionAnalysis
    - hasEitherIntensity
      
      Boolean hasEitherIntensity
    - hasMultiplePreferredQuantitationTypes
      
      Boolean hasMultiplePreferredQuantitationTypes
    - hasMultipleTechnologyTypes
      
      Boolean hasMultipleTechnologyTypes
    - isRNASeq
      
      Boolean isRNASeq
    - lastArrayDesignUpdateDate
      
      String lastArrayDesignUpdateDate
    - linkAnalysisEventType
      
      String linkAnalysisEventType
    - missingValueAnalysisEventType
      
      String missingValueAnalysisEventType
    - numAnnotations
      
      Long numAnnotations
    - numPopulatedFactors
      
      Long numPopulatedFactors
    - originalPlatforms
      
      Collection<ArrayDesignValueObject> originalPlatforms
    - otherParts
      
      Collection<ExpressionExperimentValueObject> otherParts
    - pcaAnalysisEventType
      
      String pcaAnalysisEventType
    - primaryCitation
      
      CitationValueObject primaryCitation
    - processedDataVectorComputationEventType
      
      String processedDataVectorComputationEventType
    - pubmedId
      
      Integer pubmedId
    - QChtml
      
      String QChtml
    - reprocessedFromRawData
      
      boolean reprocessedFromRawData
    - sampleRemovedFlags
      
      Collection<AuditEventValueObject> sampleRemovedFlags
    - secondaryAccession
      
      String secondaryAccession
    - secondaryExternalDatabase
      
      String secondaryExternalDatabase
    - secondaryExternalUri
      
      String secondaryExternalUri
- Class ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject extends IdentifiableValueObject<ExpressionExperimentSet> implements Serializable
  
  serialVersionUID:
  
  -6852364688337216390L
  - Serialized Fields
    - description
      
      String description
    - expressionExperimentIds
      
      Collection<Long> expressionExperimentIds
    - isPublic
      
      boolean isPublic
    - modifiable
      
      boolean modifiable
      
      If modifying the set is constrained by existing analyses.
    - name
      
      String name
    - numWithCoexpressionAnalysis
      
      Integer numWithCoexpressionAnalysis
    - numWithDifferentialExpressionAnalysis
      
      Integer numWithDifferentialExpressionAnalysis
    - shared
      
      boolean shared
    - size
      
      Integer size
    - taxonId
      
      Long taxonId
    - taxonName
      
      String taxonName
    - userCanWrite
      
      boolean userCanWrite
    - userOwned
      
      boolean userOwned
- Class ubic.gemma.model.expression.experiment.ExpressionExperimentSubsetValueObject extends IdentifiableValueObject<ExpressionExperimentSubSet> implements Serializable
  - Serialized Fields
    - accession
      
      String accession
      
      Deprecated.
      Do not use, there's never been an accession field in the data model.
    - bioAssays
      
      Collection<BioAssayValueObject> bioAssays
    - characteristics
      
      Collection<CharacteristicValueObject> characteristics
    - description
      
      String description
    - isPublic
      
      boolean isPublic
    - isShared
      
      boolean isShared
    - minPvalue
      
      Double minPvalue
    - name
      
      String name
    - numberOfBioAssays
      
      Integer numberOfBioAssays
    - sourceExperimentId
      
      Long sourceExperimentId
      
      The ID of the ExpressionExperiment this is a subset of.
    - sourceExperimentShortName
      
      String sourceExperimentShortName
      
      The short name of the ExpressionExperiment this is a subset of.
    - userCanWrite
      
      boolean userCanWrite
    - userOwned
      
      boolean userOwned
- Class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject extends AbstractCuratableValueObject<ExpressionExperiment> implements Serializable
  
  serialVersionUID:
  
  -6861385216096602508L
  - Serialized Fields
    - accession
      
      String accession
    - arrayDesignCount
      
      Long arrayDesignCount
    - batchConfound
      
      String batchConfound
    - batchEffect
      
      String batchEffect
      
      Batch effect type. See BatchEffectType enum for possible values.
    - batchEffectStatistics
      
      String batchEffectStatistics
      
      Summary statistics of a batch effect is present.
    - bioMaterialCount
      
      Integer bioMaterialCount
    - characteristics
      
      Set<CharacteristicValueObject> characteristics
    - description
      
      String description
    - experimentalDesign
      
      Long experimentalDesign
    - externalDatabase
      
      String externalDatabase
    - externalDatabaseUri
      
      String externalDatabaseUri
    - externalUri
      
      String externalUri
    - geeq
      
      GeeqValueObject geeq
    - isPublic
      
      boolean isPublic
    - isShared
      
      boolean isShared
    - metadata
      
      String metadata
    - minPvalue
      
      Double minPvalue
    - name
      
      String name
    - numberOfBioAssays
      
      Integer numberOfBioAssays
    - processedExpressionVectorCount
      
      Integer processedExpressionVectorCount
    - shortName
      
      String shortName
    - source
      
      String source
    - suitableForDEA
      
      Boolean suitableForDEA
    - taxonObject
      
      TaxonValueObject taxonObject
      
      FIXME: this should be named simply "taxon", but that field is already taken for Gemma Web, see ExpressionExperimentValueObject.getTaxon().
    - technologyType
      
      String technologyType
    - userCanWrite
      
      boolean userCanWrite
    - userOwned
      
      boolean userOwned
- Class ubic.gemma.model.expression.experiment.FactorValueBasicValueObject extends AbstractFactorValueValueObject implements Serializable
  
  serialVersionUID:
  
  3378801249808036785L
  - Serialized Fields
    - value
      
      String value
      
      Deprecated.
      use either #getCharacteristics() or #getMeasurement()
- Class ubic.gemma.model.expression.experiment.FactorValueValueObject extends AbstractFactorValueValueObject implements Serializable
  
  serialVersionUID:
  
  3378801249808036785L
  - Serialized Fields
    - category
      
      String category
      
      Deprecated.
    - categoryUri
      
      String categoryUri
      
      Deprecated.
    - charId
      
      Long charId
      
      Deprecated.
      
      It could be the id of the measurement if there is no characteristic.
    - factorId
      
      Long factorId
      
      Deprecated.
      
      ID of the experimental factor this FV belongs to.
    - needsAttention
      
      Boolean needsAttention
      
      Deprecated.
    - object
      
      String object
      
      Deprecated.
    - objectUri
      
      String objectUri
      
      Deprecated.
    - predicate
      
      String predicate
      
      Deprecated.
    - predicateUri
      
      String predicateUri
      
      Deprecated.
    - secondObject
      
      String secondObject
      
      Deprecated.
    - secondObjectUri
      
      String secondObjectUri
      
      Deprecated.
    - secondPredicate
      
      String secondPredicate
      
      Deprecated.
    - secondPredicateUri
      
      String secondPredicateUri
      
      Deprecated.
    - value
      
      String value
      
      Deprecated.
    - valueUri
      
      String valueUri
      
      Deprecated.
- Class ubic.gemma.model.expression.experiment.FreeTextExpressionExperimentResultsValueObject extends SessionBoundExpressionExperimentSetValueObject implements Serializable
  
  serialVersionUID:
  
  3557304710219740029L
  - Serialized Fields
    - queryString
      
      String queryString
- Class ubic.gemma.model.expression.experiment.GeeqAdminValueObject extends GeeqValueObject implements Serializable
  - Serialized Fields
    - detectedQualityScore
      
      double detectedQualityScore
    - detectedSuitabilityScore
      
      double detectedSuitabilityScore
    - manualBatchConfoundActive
      
      boolean manualBatchConfoundActive
    - manualBatchEffectActive
      
      boolean manualBatchEffectActive
    - manualHasBatchConfound
      
      boolean manualHasBatchConfound
    - manualHasNoBatchEffect
      
      boolean manualHasNoBatchEffect
    - manualHasStrongBatchEffect
      
      boolean manualHasStrongBatchEffect
    - manualQualityOverride
      
      boolean manualQualityOverride
    - manualQualityScore
      
      double manualQualityScore
    - manualSuitabilityOverride
      
      boolean manualSuitabilityOverride
    - manualSuitabilityScore
      
      double manualSuitabilityScore
    - otherIssues
      
      String otherIssues
    - qScoreBatchConfound
      
      double qScoreBatchConfound
    - qScoreBatchEffect
      
      double qScoreBatchEffect
- Class ubic.gemma.model.expression.experiment.GeeqValueObject extends IdentifiableValueObject<Geeq> implements Serializable
  - Serialized Fields
    - batchCorrected
      
      boolean batchCorrected
    - corrMatIssues
      
      byte corrMatIssues
    - noVectors
      
      boolean noVectors
    - publicQualityScore
      
      double publicQualityScore
    - publicSuitabilityScore
      
      double publicSuitabilityScore
    - qScoreBatchInfo
      
      double qScoreBatchInfo
    - qScoreOutliers
      
      double qScoreOutliers
    - qScorePlatformsTech
      
      double qScorePlatformsTech
    - qScorePublicBatchConfound
      
      double qScorePublicBatchConfound
    - qScorePublicBatchEffect
      
      double qScorePublicBatchEffect
    - qScoreReplicates
      
      double qScoreReplicates
    - qScoreSampleCorrelationVariance
      
      double qScoreSampleCorrelationVariance
    - qScoreSampleMeanCorrelation
      
      double qScoreSampleMeanCorrelation
    - qScoreSampleMedianCorrelation
      
      double qScoreSampleMedianCorrelation
    - replicatesIssues
      
      byte replicatesIssues
    - sScoreAvgPlatformPopularity
      
      double sScoreAvgPlatformPopularity
    - sScoreAvgPlatformSize
      
      double sScoreAvgPlatformSize
    - sScoreMissingValues
      
      double sScoreMissingValues
    - sScorePlatformAmount
      
      double sScorePlatformAmount
    - sScorePlatformsTechMulti
      
      double sScorePlatformsTechMulti
    - sScorePublication
      
      double sScorePublication
    - sScoreRawData
      
      double sScoreRawData
    - sScoreSampleSize
      
      double sScoreSampleSize
- Class ubic.gemma.model.expression.experiment.SessionBoundExpressionExperimentSetValueObject extends ExpressionExperimentSetValueObject implements Serializable
  
  serialVersionUID:
  
  2068650886972222818L
  - Serialized Fields
    - modified
      
      boolean modified
- Class ubic.gemma.model.expression.experiment.StatementValueObject extends IdentifiableValueObject<Statement> implements Serializable
  - Serialized Fields
    - category
      
      String category
    - categoryUri
      
      String categoryUri
    - object
      
      String object
    - objectId
      
      String objectId
      
      A unique ontology identifier (i.e. IRI) for this object.
    - objectUri
      
      String objectUri
    - predicate
      
      String predicate
    - predicateUri
      
      String predicateUri
    - secondObject
      
      String secondObject
    - secondObjectUri
      
      String secondObjectUri
    - secondPredicate
      
      String secondPredicate
    - secondPredicateUri
      
      String secondPredicateUri
    - subject
      
      String subject
    - subjectId
      
      String subjectId
      
      A unique ontology identifier (i.e. IRI) for this subject.
    - subjectUri
      
      String subjectUri
Package ubic.gemma.model.genome
- Class ubic.gemma.model.genome.GeneOntologyTermValueObject extends Object implements Serializable
  - Serialized Fields
    - comment
      
      String comment
    - goId
      
      String goId
    - isObsolete
      
      boolean isObsolete
    - label
      
      String label
    - localName
      
      String localName
    - term
      
      String term
    - uri
      
      String uri
- Class ubic.gemma.model.genome.PhysicalLocationValueObject extends IdentifiableValueObject<PhysicalLocation> implements Serializable
  - Serialized Fields
    - bin
      
      Integer bin
    - chromosome
      
      String chromosome
    - nucleotide
      
      Long nucleotide
    - nucleotideLength
      
      Integer nucleotideLength
    - strand
      
      String strand
    - taxon
      
      TaxonValueObject taxon
- Class ubic.gemma.model.genome.TaxonValueObject extends IdentifiableValueObject<Taxon> implements Serializable
  - Serialized Fields
    - commonName
      
      String commonName
    - externalDatabase
      
      ExternalDatabaseValueObject externalDatabase
    - isGenesUsable
      
      Boolean isGenesUsable
    - isSpecies
      
      Boolean isSpecies
    - ncbiId
      
      Integer ncbiId
    - scientificName
      
      String scientificName
Package ubic.gemma.model.genome.gene
- Class ubic.gemma.model.genome.gene.DatabaseBackedGeneSetValueObject extends GeneSetValueObject implements Serializable
  
  serialVersionUID:
  
  -1360523793656012770L
- Class ubic.gemma.model.genome.gene.FreeTextGeneResultsValueObject extends SessionBoundGeneSetValueObject implements Serializable
  
  serialVersionUID:
  
  3557304710219740029L
  - Serialized Fields
    - queryString
      
      String queryString
- Class ubic.gemma.model.genome.gene.GeneProductValueObject extends IdentifiableValueObject<GeneProduct> implements Serializable
  
  serialVersionUID:
  
  1156628868995566223L
  - Serialized Fields
    - chromosome
      
      String chromosome
    - geneId
      
      Long geneId
    - name
      
      String name
    - ncbiId
      
      String ncbiId
    - nucleotideEnd
      
      Long nucleotideEnd
      
      Deprecated.
    - nucleotideStart
      
      Long nucleotideStart
    - strand
      
      String strand
- Class ubic.gemma.model.genome.gene.GeneSetValueObject extends IdentifiableValueObject<GeneSet> implements Serializable
  
  serialVersionUID:
  
  6212231006289412683L
  - Serialized Fields
    - description
      
      String description
    - geneIds
      
      Collection<Long> geneIds
      
      Gene IDs part of this gene set.
    - isPublic
      
      boolean isPublic
    - isShared
      
      boolean isShared
    - name
      
      String name
    - size
      
      Long size
    - taxon
      
      TaxonValueObject taxon
    - userOwned
      
      boolean userOwned
- Class ubic.gemma.model.genome.gene.GeneValueObject extends IdentifiableValueObject<Gene> implements Serializable
  
  serialVersionUID:
  
  -7098036090107647318L
  - Serialized Fields
    - accessions
      
      Set<DatabaseEntryValueObject> accessions
    - aliases
      
      SortedSet<String> aliases
      
      Gene aliases, sorted alphabetically.
    - associatedExperimentCount
      
      Integer associatedExperimentCount
      
      How many experiments "involve" (manipulate, etc.) this gene
    - compositeSequenceCount
      
      Integer compositeSequenceCount
    - description
      
      String description
    - ensemblId
      
      String ensemblId
    - geneSets
      
      Collection<GeneSetValueObject> geneSets
    - homologues
      
      Collection<GeneValueObject> homologues
    - includeTaxon
      
      boolean includeTaxon
    - isQuery
      
      Boolean isQuery
      
      Was this gene directly used in a query? Or is it inferred somehow. The default is true, use this when you need to differentiate
    - multifunctionalityRank
      
      Double multifunctionalityRank
    - name
      
      String name
    - ncbiId
      
      Integer ncbiId
    - nodeDegreeNegRanks
      
      double[] nodeDegreeNegRanks
    - nodeDegreePosRanks
      
      double[] nodeDegreePosRanks
    - nodeDegreesNeg
      
      int[] nodeDegreesNeg
      
      Array containing number of links supported by 0,1,2, .... data sets (value in first index is always 0) for negative correlation coexpression
    - nodeDegreesPos
      
      int[] nodeDegreesPos
      
      Array containing number of links supported by 0,1,2, .... data sets (value in first index is always 0) for positive coexpression
    - numGoTerms
      
      Integer numGoTerms
    - officialName
      
      String officialName
    - officialSymbol
      
      String officialSymbol
    - platformCount
      
      Integer platformCount
    - score
      
      Double score
    - taxon
      
      TaxonValueObject taxon
- Class ubic.gemma.model.genome.gene.GOGroupValueObject extends SessionBoundGeneSetValueObject implements Serializable
  
  serialVersionUID:
  
  -185326197992950287L
  - Serialized Fields
    - goId
      
      String goId
    - searchTerm
      
      String searchTerm
- Class ubic.gemma.model.genome.gene.SessionBoundGeneSetValueObject extends GeneSetValueObject implements Serializable
  
  serialVersionUID:
  
  5073203626044664184L
  - Serialized Fields
    - modified
      
      boolean modified
Package ubic.gemma.model.genome.sequenceAnalysis
- 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.BlatResultValueObject extends IdentifiableValueObject<BlatResult> implements Serializable
  - Serialized Fields
    - blockCount
      
      Integer blockCount
    - blockSizes
      
      String blockSizes
    - identity
      
      Double identity
    - matches
      
      Integer matches
    - mismatches
      
      Integer mismatches
    - ns
      
      Integer ns
    - queryEnd
      
      Integer queryEnd
    - queryGapBases
      
      Integer queryGapBases
    - queryGapCount
      
      Integer queryGapCount
    - querySequence
      
      BioSequenceValueObject querySequence
    - queryStart
      
      Integer queryStart
    - queryStarts
      
      String queryStarts
    - repMatches
      
      Integer repMatches
    - score
      
      Double score
    - strand
      
      String strand
    - targetChromosomeName
      
      String targetChromosomeName
    - targetDatabase
      
      String targetDatabase
    - targetEnd
      
      Long targetEnd
    - targetGapBases
      
      Integer targetGapBases
    - targetGapCount
      
      Integer targetGapCount
    - targetStart
      
      Long targetStart
    - targetStarts
      
      String targetStarts
    - taxon
      
      TaxonValueObject taxon
- Class ubic.gemma.model.genome.sequenceAnalysis.SequenceTypeValueObject extends Object implements Serializable
  - Serialized Fields
    - value
      
      String value
Package ubic.gemma.model.util
- Class ubic.gemma.model.util.UninitializedCollectionException extends RuntimeException implements Serializable
Package ubic.gemma.persistence.hibernate
- Class ubic.gemma.persistence.hibernate.HibernateTransactionManager extends org.springframework.orm.hibernate4.HibernateTransactionManager implements Serializable
- Class ubic.gemma.persistence.hibernate.LocalSessionFactoryBuilder extends org.springframework.orm.hibernate4.LocalSessionFactoryBuilder implements Serializable
- Class ubic.gemma.persistence.hibernate.XSDEntityResolver extends DTDEntityResolver implements Serializable
Package ubic.gemma.persistence.service.analysis.expression.diff
- Class ubic.gemma.persistence.service.analysis.expression.diff.MissingResult extends DiffExprGeneSearchResult implements Serializable
  
  serialVersionUID:
  
  -2868418055346274525L
- Class ubic.gemma.persistence.service.analysis.expression.diff.NonRetainedResult extends DiffExprGeneSearchResult implements Serializable
  
  serialVersionUID:
  
  3501605965895623139L
Package ubic.gemma.persistence.service.association.coexpression
- Class ubic.gemma.persistence.service.association.coexpression.CoexpressionCacheValueObject extends Object implements Serializable
  
  serialVersionUID:
  
  184287422449009209L
  - Serialized Fields
    - coexGeneSymbol
      
      String coexGeneSymbol
    - coexpGene
      
      Long coexpGene
    - positiveCorrelation
      
      boolean positiveCorrelation
    - queryGene
      
      Long queryGene
    - queryGeneSymbol
      
      String queryGeneSymbol
    - support
      
      int support
    - supportDetailsId
      
      Long supportDetailsId
    - supportingDatasets
      
      Collection<Long> supportingDatasets
    - testedInDatasets
      
      ubic.gemma.persistence.service.association.coexpression.CompressedLongSet testedInDatasets
- Class ubic.gemma.persistence.service.association.coexpression.CoexpressionValueObject extends Object implements Serializable
  - Serialized Fields
    - coexGeneId
      
      Long coexGeneId
    - coexGeneSymbol
      
      String coexGeneSymbol
    - eeConstraint
      
      boolean eeConstraint
      
      If true, this means the results were trimmed to a subset.
    - fromCache
      
      boolean fromCache
      
      True if these data were pulled from the cache, or if they were put in the cache (so future queries will find them); false otherwise.
    - interQueryLink
      
      boolean interQueryLink
    - maxResults
      
      int maxResults
      
      the max results limit used in the query; 0 means no limit.
    - positiveCorrelation
      
      boolean positiveCorrelation
    - queryGeneId
      
      Long queryGeneId
    - queryGeneSymbol
      
      String queryGeneSymbol
    - queryStringency
      
      int queryStringency
      
      The stringency used in the query (will be 1 by default)
    - support
      
      Integer support
    - supportDetailsId
      
      Long supportDetailsId
    - supportingDatasets
      
      Set<Long> supportingDatasets
      
      The data sets which supported the link. If eeConstraint = true, this reflects only data sets which were in the query.
    - testedInDatasets
      
      Set<Long> testedInDatasets
      
      The data sets in which the link was tested. If eeConstraint = true, this reflects only data sets which were in the query.
Package ubic.gemma.persistence.service.common.quantitationtype
- Class ubic.gemma.persistence.service.common.quantitationtype.NonUniqueQuantitationTypeByNameException extends Exception implements Serializable
Package ubic.gemma.persistence.service.expression.experiment
- Class ubic.gemma.persistence.service.expression.experiment.FactorValueMigratorService.MigrationFailedException extends RuntimeException implements Serializable
  - Serialized Fields
    - migration
      
      FactorValueMigratorService.Migration migration
Package ubic.gemma.persistence.service.maintenance
- Class ubic.gemma.persistence.service.maintenance.Gene2CsStatus extends Object implements Serializable
  
  serialVersionUID:
  
  1956861185764899312L
  - Serialized Fields
    - annotation
      
      String annotation
    - error
      
      Exception error
    - lastUpdate
      
      Date lastUpdate
Package ubic.gemma.rest
- Class ubic.gemma.rest.DatasetsWebService.AnnotationWithUsageStatisticsValueObject extends AnnotationValueObject implements Serializable
  - Serialized Fields
    - numberOfExpressionExperiments
      
      Long numberOfExpressionExperiments
      
      Number of times the characteristic is mentioned among matching datasets.
    - parentTerms
      
      Set<DatasetsWebService.OntologyTermValueObject> parentTerms
      
      URIs of parent terms, or null if excluded.
- Class ubic.gemma.rest.DatasetsWebService.ArrayDesignWithUsageStatisticsValueObject extends ArrayDesignValueObject implements Serializable
  - Serialized Fields
    - numberOfExpressionExperimentsForTechnologyType
      
      Long numberOfExpressionExperimentsForTechnologyType
- Class ubic.gemma.rest.DatasetsWebService.DifferentialExpressionAnalysisResultByGeneValueObject extends DifferentialExpressionAnalysisResultValueObject implements Serializable
  - Serialized Fields
    - baseline
      
      FactorValueBasicValueObject baseline
    - experimentAnalyzedId
      
      Long experimentAnalyzedId
      
      The ID of the experiment analyzed which is either an ExpressionExperiment or an ExpressionExperimentSubSet.
    - resultSetId
      
      Long resultSetId
      
      The result set ID to which this result belong.
    - secondBaseline
      
      FactorValueBasicValueObject secondBaseline
    - sourceExperimentId
      
      Long sourceExperimentId
      
      The ID of the source experiment, which differs only if this result is from a subset. This is always referring to an ExpressionExperiment.
- Class ubic.gemma.rest.DatasetsWebService.ExpressionExperimentSubsetWithFactorValuesObject extends ExpressionExperimentSubsetValueObject implements Serializable
  - Serialized Fields
    - factorValues
      
      List<FactorValueBasicValueObject> factorValues
- Class ubic.gemma.rest.DatasetsWebService.ExpressionExperimentSubSetWithGroupsValueObject extends ExpressionExperimentSubsetValueObject implements Serializable
  - Serialized Fields
    - subSetGroupIds
      
      List<Long> subSetGroupIds
- Class ubic.gemma.rest.DatasetsWebService.ExpressionExperimentWithSearchResultValueObject extends ExpressionExperimentValueObject implements Serializable
  - Serialized Fields
    - searchResult
      
      SearchWebService.SearchResultValueObject<ExpressionExperimentValueObject> searchResult
- Class ubic.gemma.rest.DatasetsWebService.TaxonWithUsageStatisticsValueObject extends TaxonValueObject implements Serializable
  - Serialized Fields
    - numberOfExpressionExperiments
      
      Long numberOfExpressionExperiments
Package ubic.gemma.rest.serializers
- Class ubic.gemma.rest.serializers.AbstractFactorValueValueObjectSerializer extends com.fasterxml.jackson.databind.ser.std.StdSerializer<T extends AbstractFactorValueValueObject> implements Serializable
- Class ubic.gemma.rest.serializers.FactorValueBasicValueObjectSerializer extends AbstractFactorValueValueObjectSerializer<FactorValueBasicValueObject> implements Serializable
- Class ubic.gemma.rest.serializers.FactorValueValueObjectSerializer extends AbstractFactorValueValueObjectSerializer<FactorValueValueObject> implements Serializable
Package ubic.gemma.rest.util
- Class ubic.gemma.rest.util.EntityNotFoundException extends Exception implements Serializable
- Class ubic.gemma.rest.util.MalformedArgException extends javax.ws.rs.BadRequestException implements Serializable
Package ubic.gemma.web.controller.coexpressionSearch
- Class ubic.gemma.web.controller.coexpressionSearch.CoexSearchTaskCommand extends TaskCommand implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - searchOptions
      
      CoexpressionSearchCommand searchOptions
Package ubic.gemma.web.controller.common.auditAndSecurity
- Class ubic.gemma.web.controller.common.auditAndSecurity.FileUpload extends Object implements Serializable
  
  serialVersionUID:
  
  537156568346654834L
  - Serialized Fields
    - file
      
      byte[] file
    - localPath
      
      String localPath
- Class ubic.gemma.web.controller.common.auditAndSecurity.SidValueObject extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - authority
      
      String authority
    - principal
      
      boolean principal
Package ubic.gemma.web.controller.common.auditAndSecurity.recaptcha
- Class ubic.gemma.web.controller.common.auditAndSecurity.recaptcha.ReCaptchaException extends RuntimeException implements Serializable
Package ubic.gemma.web.controller.diff
- Class ubic.gemma.web.controller.diff.DiffExpressionSearchCommand extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - dirty
      
      boolean dirty
    - eeIds
      
      Collection<Long> eeIds
    - eeQuery
      
      String eeQuery
    - eeSetId
      
      Long eeSetId
    - eeSetName
      
      String eeSetName
    - geneIds
      
      Collection<Long> geneIds
    - selectedFactors
      
      Collection<DiffExpressionSelectedFactorCommand> selectedFactors
    - taxonId
      
      Long taxonId
    - threshold
      
      Double threshold
Package ubic.gemma.web.controller.expression.arrayDesign
- Class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignValueObjectExt extends ArrayDesignValueObject implements Serializable
  
  serialVersionUID:
  
  218696698777199533L
  - Serialized Fields
    - additionalTaxa
      
      Set<String> additionalTaxa
    - allParentsAnnotationLink
      
      String allParentsAnnotationLink
    - alternateNames
      
      Collection<String> alternateNames
    - alternative
      
      ArrayDesignValueObject alternative
    - bioProcessAnnotationLink
      
      String bioProcessAnnotationLink
    - colorString
      
      String colorString
    - mergees
      
      Collection<ArrayDesignValueObject> mergees
    - merger
      
      ArrayDesignValueObject merger
    - noParentsAnnotationLink
      
      String noParentsAnnotationLink
    - subsumees
      
      Collection<ArrayDesignValueObject> subsumees
    - subsumer
      
      ArrayDesignValueObject subsumer
Package ubic.gemma.web.controller.expression.experiment
- Class ubic.gemma.web.controller.expression.experiment.DesignMatrixRowValueObject extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - count
      
      int count
    - factors
      
      List<String> factors
    - factorTypes
      
      List<String> factorTypes
    - factorValueMap
      
      Map<String,String> factorValueMap
- Class ubic.gemma.web.controller.expression.experiment.ExperimentalFactorValueWebUIObject extends ExperimentalFactorValueObject implements Serializable
  - Serialized Fields
    - bioMaterialCharacteristicCategoryToUse
      
      String bioMaterialCharacteristicCategoryToUse
- Class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentDataFetchCommand extends TaskCommand implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - analysisId
      
      Long analysisId
    - experimentalDesignId
      
      Long experimentalDesignId
    - expressionExperimentId
      
      Long expressionExperimentId
    - filter
      
      boolean filter
    - forceRewrite
      
      boolean forceRewrite
    - format
      
      String format
    - quantitationTypeId
      
      Long quantitationTypeId
- Class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditValueObject extends ExpressionExperimentDetailsValueObject implements Serializable
  
  serialVersionUID:
  
  1630521876359566915L
  - Serialized Fields
    - bioAssays
      
      Collection<BioAssayValueObject> bioAssays
    - quantitationTypes
      
      Collection<QuantitationTypeValueObject> quantitationTypes
- Class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentUploadResponse extends Object implements Serializable
  - Serialized Fields
    - error
      
      boolean error
    - errorMessage
      
      String errorMessage
    - taskId
      
      Long taskId
- Class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentCommandValidation extends Object implements Serializable
  - Serialized Fields
    - arrayDesignMatchesDataFile
      
      boolean arrayDesignMatchesDataFile
    - arrayDesignMismatchProblemMessage
      
      String arrayDesignMismatchProblemMessage
    - dataFileFormatProblemMessage
      
      String dataFileFormatProblemMessage
    - dataFileIsValidFormat
      
      boolean dataFileIsValidFormat
    - isValid
      
      boolean isValid
    - nonMatchingProbeNameExamples
      
      Collection<String> nonMatchingProbeNameExamples
    - numberMatchingProbes
      
      int numberMatchingProbes
    - numberOfNonMatchingProbes
      
      int numberOfNonMatchingProbes
    - numColumns
      
      int numColumns
    - numRows
      
      int numRows
    - otherProblemsMessage
      
      String otherProblemsMessage
    - quantitationTypeIsValid
      
      boolean quantitationTypeIsValid
    - quantitationTypeProblemMessage
      
      String quantitationTypeProblemMessage
    - shortNameIsUnique
      
      boolean shortNameIsUnique
- Class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentLoadTaskCommand extends TaskCommand implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - arrayDesignIds
      
      Collection<Long> arrayDesignIds
    - description
      
      String description
    - isRatio
      
      Boolean isRatio
    - name
      
      String name
    - originalFileName
      
      String originalFileName
    - pubMedId
      
      Integer pubMedId
    - quantitationTypeDescription
      
      String quantitationTypeDescription
    - quantitationTypeName
      
      String quantitationTypeName
    - scale
      
      ScaleType scale
    - serverFilePath
      
      String serverFilePath
    - shortName
      
      String shortName
    - taxonId
      
      Long taxonId
    - validateOnly
      
      boolean validateOnly
Package ubic.gemma.web.controller.visualization
- Class ubic.gemma.web.controller.visualization.ExpressionExperimentVisualizationCommand extends Object implements Serializable
  
  serialVersionUID:
  
  2166768356457316142L
  - Serialized Fields
    - expressionExperimentId
      
      Long expressionExperimentId
    - maskMissing
      
      boolean maskMissing
    - name
      
      String name
    - quantitationType
      
      QuantitationType quantitationType
    - searchCriteria
      
      String searchCriteria
    - searchString
      
      String searchString
    - viewSampling
      
      boolean viewSampling
Package ubic.gemma.web.persistence
- Class ubic.gemma.web.persistence.AbstractSetListContainer extends Object implements Serializable
  
  serialVersionUID:
  
  -7207696842986893748L
  - Serialized Fields
    - allSessionBoundGroups
      
      List<GemmaSessionBackedValueObject> allSessionBoundGroups
    - largestSessionId
      
      Long largestSessionId
    - sessionBoundModifiedGroups
      
      List<GemmaSessionBackedValueObject> sessionBoundModifiedGroups
- Class ubic.gemma.web.persistence.ExperimentSetListContainer extends AbstractSetListContainer implements Serializable
  
  serialVersionUID:
  
  2031936160381488016L
- Class ubic.gemma.web.persistence.GeneSetListContainer extends AbstractSetListContainer implements Serializable
  
  serialVersionUID:
  
  2163440335723257830L
Package ubic.gemma.web.taglib
- Class ubic.gemma.web.taglib.AbstractStaticAssetTag extends org.springframework.web.servlet.tags.HtmlEscapingAwareTag implements Serializable
  - Serialized Fields
    - src
      
      String src
    - srcAttributeName
      
      String srcAttributeName
- Class ubic.gemma.web.taglib.CharacteristicTag extends org.springframework.web.servlet.tags.HtmlEscapingAwareTag implements Serializable
  - Serialized Fields
    - category
      
      boolean category
      
      Only render the category part of the characteristic.
    - characteristic
      
      Characteristic characteristic
      
      Characteristic to generate the tag for.
    - external
      
      boolean external
      
      Generate an external link.
      The default is to generate an internal link.
- 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.EntityLinkTag extends org.springframework.web.servlet.tags.HtmlEscapingAwareTag implements Serializable
  - Serialized Fields
    - dimension
      
      BioAssayDimension dimension
    - dynamicAttributes
      
      Map<String,Object> dynamicAttributes
    - entity
      
      Identifiable entity
    - external
      
      boolean external
    - title
      
      String title
- Class ubic.gemma.web.taglib.FactorValueTag extends org.springframework.web.servlet.tags.HtmlEscapingAwareTag implements Serializable
  - Serialized Fields
    - factorValue
      
      FactorValue factorValue
- Class ubic.gemma.web.taglib.ImageTag extends AbstractStaticAssetTag implements Serializable
  - Serialized Fields
    - alt
      
      String alt
    - cssClass
      
      String cssClass
    - cssStyle
      
      String cssStyle
    - dynamicAttributes
      
      Map<String,Object> dynamicAttributes
    - height
      
      String height
    - width
      
      String width
- Class ubic.gemma.web.taglib.ScriptTag extends AbstractStaticAssetTag implements Serializable
  - Serialized Fields
    - async
      
      boolean async
    - defer
      
      boolean defer
    - dynamicAttributes
      
      Map<String,Object> dynamicAttributes
- Class ubic.gemma.web.taglib.ShortBibliographicReferenceTag extends javax.servlet.jsp.tagext.TagSupport implements Serializable
  
  serialVersionUID:
  
  -7325678534991860679L
  - Serialized Fields
    - citation
      
      BibliographicReference citation
- Class ubic.gemma.web.taglib.StyleTag extends AbstractStaticAssetTag implements Serializable
  - Serialized Fields
    - dynamicAttributes
      
      Map<String,Object> dynamicAttributes
Package ubic.gemma.web.taglib.arrayDesign
- Class ubic.gemma.web.taglib.arrayDesign.ArrayDesignGroupingTag extends javax.servlet.jsp.tagext.TagSupport implements Serializable
  
  serialVersionUID:
  
  -5646614364631502667L
  - Serialized Fields
    - subsumees
      
      Collection<ArrayDesign> subsumees
    - subsumer
      
      ArrayDesign subsumer
Package ubic.gemma.web.taglib.common.auditAndSecurity
- Class ubic.gemma.web.taglib.common.auditAndSecurity.ExceptionTag extends org.springframework.web.servlet.tags.RequestContextAwareTag implements Serializable
  
  serialVersionUID:
  
  4323477499674966726L
  - Serialized Fields
    - exception
      
      Exception exception
      
      Exception to display.
    - showStackTrace
      
      boolean showStackTrace
      
      Display the stacktrace.
      Note: the stack trace is never display to non-administrators.
Package ubic.gemma.web.taglib.expression.experiment
- Class ubic.gemma.web.taglib.expression.experiment.AbstractHeatmapTag extends org.springframework.web.servlet.tags.HtmlEscapingAwareTag implements Serializable
  - Serialized Fields
    - alt
      
      String alt
      
      Alternative text to use for the image.
    - dynamicAttributes
      
      Map<String,Object> dynamicAttributes
    - heatmap
      
      T extends Heatmap heatmap
      
      Heatmap to render.
    - maxHeight
      
      int maxHeight
      
      Maximum height of the heatmap in pixels.
    - maxWidth
      
      int maxWidth
      
      Maximum width of the heatmap in pixels.
    - showXLabels
      
      boolean showXLabels
      
      Display row labels.
    - showYLabels
      
      boolean showYLabels
      
      Display column labels.
    - useResizeTrick
      
      boolean useResizeTrick
      
      Use the resize trick to render the heatmap by generating one pixel per cell and scaling it with CSS.
- Class ubic.gemma.web.taglib.expression.experiment.AssayViewTag extends org.springframework.web.servlet.tags.HtmlEscapingAwareTag implements Serializable
  - Serialized Fields
    - bioAssays
      
      Collection<BioAssayValueObject> bioAssays
    - currentRow
      
      int currentRow
    - edit
      
      boolean edit
    - emptyAssays
      
      int emptyAssays
    - expressionExperimentId
      
      Long expressionExperimentId
- Class ubic.gemma.web.taglib.expression.experiment.ExperimentQCTag extends org.springframework.web.servlet.tags.HtmlEscapingAwareTag implements Serializable
  - Serialized Fields
    - dynamicAttributes
      
      Map<String,Object> dynamicAttributes
    - eeManagerId
      
      String eeManagerId
      
      DOM ID of the manager for the experiment.
    - expressionExperiment
      
      ExpressionExperiment expressionExperiment
      
      Expression experiment to display the QC info for.
    - hasCorrMat
      
      boolean hasCorrMat
      
      Indicate if there is a correlation matrix.
    - hasMeanVariance
      
      boolean hasMeanVariance
      
      Indicate if there is a mean-variance relation.
    - hasPCA
      
      boolean hasPCA
      
      Indicate if there is a PCA.
    - hasSingleCellData
      
      boolean hasSingleCellData
      
      Indicate if the experiment has single-cell data.
    - htmlEscape
      
      Boolean htmlEscape
    - numFactors
      
      int numFactors
      
      How many factors (including batch etc) are available for PCA display?
    - numOutliersRemoved
      
      int numOutliersRemoved
      
      Number of outliers removed.
    - numPcsToDisplay
      
      int numPcsToDisplay
      
      Number of principal components to display.
    - numPossibleOutliers
      
      int numPossibleOutliers
      
      Number of possible outliers.
    - singleCellSparsityHeatmap
      
      SingleCellSparsityHeatmap singleCellSparsityHeatmap
      
      Heatmap for single-cell data.
      This heatmap might not be present if the experiment has not been aggregated.
- Class ubic.gemma.web.taglib.expression.experiment.ExpressionDataHeatmapTag extends AbstractHeatmapTag<ExpressionDataHeatmap> implements Serializable
- Class ubic.gemma.web.taglib.expression.experiment.SingleCellSparsityHeatmapTag extends AbstractHeatmapTag<SingleCellSparsityHeatmap> implements Serializable
  - Serialized Fields
    - contextPath
      
      String contextPath
    - htmlEscape
      
      Boolean htmlEscape
    - type2Alt
      
      Map<SingleCellSparsityHeatmap.SingleCellHeatmapType,String> type2Alt
Package ubic.gemma.web.tasks.analysis.sequence
- Class ubic.gemma.web.tasks.analysis.sequence.ArrayDesignRepeatScanTaskCommand extends TaskCommand implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - arrayDesign
      
      ArrayDesign arrayDesign
Package ubic.gemma.web.util
- Class ubic.gemma.web.util.ConfigurationCookie extends javax.servlet.http.Cookie implements Serializable
  - Serialized Fields
    - configuration
      
      org.apache.commons.configuration2.PropertiesConfiguration configuration
- Class ubic.gemma.web.util.EntityNotFoundException extends RuntimeException implements Serializable
  
  serialVersionUID:
  
  -4361183252269974819L
- Class ubic.gemma.web.util.LabelValue extends Object implements Serializable
  
  serialVersionUID:
  
  3485837885293359602L
  - Serialized Fields
    - label
      
      String label
      
      The property which supplies the option label visible to the end user.
    - value
      
      String value
      
      The property which supplies the value returned to the server.
- Class ubic.gemma.web.util.ServiceUnavailableException extends RuntimeException implements Serializable
Package ubic.gemma.web.util.upload
- Class ubic.gemma.web.util.upload.CommonsMultipartFile extends Object implements Serializable
  
  serialVersionUID:
  
  6483196912349343465L
  - Serialized Fields
    - fileItem
      
      org.apache.commons.fileupload.FileItem fileItem
      
      Deprecated.
    - size
      
      long size
      
      Deprecated.
- Class ubic.gemma.web.util.upload.UploadInfo extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - bytesRead
      
      long bytesRead
    - fileIndex
      
      int fileIndex
    - status
      
      String status
    - totalSize
      
      long totalSize

Serialized Form

Package ubic.gemma.cli.batch

Class ubic.gemma.cli.batch.BatchTaskProcessingResult extends Object implements Serializable

Serialized Fields

message

resultType

source

throwable

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

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

Serialized Fields

errorState

maxEdges

numDatasetsQueried

queryGenes

queryGenesOnly

queryStringency

results

searchSettings

summaries

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

Serialized Fields

dirty

eeIds

eeQuery

eeSetId

eeSetName

geneIds

geneSetId

queryGenesOnly

quick

stringency

taxonId

useMyDatasets

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

Serialized Fields

coexpNodeDegree

datasetsAvailable

datasetsTested

geneId

linksFound

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

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

Serialized Fields

absoluteValue

arrayName

cdfCut

checkCorrelationDistribution

checkForBatchEffect

checkForOutliers

correlationCacheThreshold

fwe

lowerCdfCutUsed

lowerTailCut

makeSampleCorrMatImages

metric

minNumPresent

normalizationMethod

omitNegLinks

outputFile

probeDegreeThreshold

singularThreshold

subset

subsetSize

subsetUsed

textOut

upperCdfCutUsed

upperTailCut

useDb

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

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

Class ubic.gemma.core.analysis.expression.diff.AllSubSetAnalysesFailedException extends AnalysisException implements Serializable

Serialized Fields

subsetExceptions

Class ubic.gemma.core.analysis.expression.diff.AnalysisException extends RuntimeException implements Serializable

Serialized Fields

config

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

Serialized Fields

activeExperiments