Serialized Form (Gemma Web 1.32.0-SNAPSHOT API)

Package ubic.gemma.web.controller.coexpressionSearch
- Class ubic.gemma.web.controller.coexpressionSearch.CoexSearchTaskCommand extends ubic.gemma.core.job.TaskCommand implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - searchOptions
      
      ubic.gemma.core.analysis.expression.coexpression.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<ubic.gemma.core.analysis.expression.diff.DiffExpressionSelectedFactorCommand> selectedFactors
    - taxonId
      
      Long taxonId
    - threshold
      
      Double threshold

Package ubic.gemma.web.controller.expression.arrayDesign

Class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignValueObjectExt extends ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject implements Serializable

serialVersionUID:: 218696698777199533L

Serialized Fields

additionalTaxa
```
Set<String> additionalTaxa
```
allParentsAnnotationLink
```
String allParentsAnnotationLink
```
alternateNames
```
Collection<String> alternateNames
```

alternative

ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject alternative

bioProcessAnnotationLink
```
String bioProcessAnnotationLink
```
colorString
```
String colorString
```

mergees

Collection<ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject> mergees

merger

ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject merger

noParentsAnnotationLink
```
String noParentsAnnotationLink
```

subsumees

Collection<ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject> subsumees

subsumer

ubic.gemma.model.expression.arrayDesign.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 ubic.gemma.model.expression.experiment.ExperimentalFactorValueObject implements Serializable
  - Serialized Fields
    - bioMaterialCharacteristicCategoryToUse
      
      String bioMaterialCharacteristicCategoryToUse
- Class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentDataFetchCommand extends ubic.gemma.core.job.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 ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject implements Serializable
  
  serialVersionUID:
  
  1630521876359566915L
  - Serialized Fields
    - bioAssays
      
      Collection<ubic.gemma.model.expression.bioAssay.BioAssayValueObject> bioAssays
    - quantitationTypes
      
      Collection<ubic.gemma.model.common.quantitationtype.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 ubic.gemma.core.job.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
      
      ubic.gemma.model.common.quantitationtype.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
      
      ubic.gemma.model.common.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<ubic.gemma.model.common.GemmaSessionBackedValueObject> allSessionBoundGroups
    - largestSessionId
      
      Long largestSessionId
    - sessionBoundModifiedGroups
      
      List<ubic.gemma.model.common.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
      
      ubic.gemma.model.common.description.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
      
      ubic.gemma.model.common.description.DatabaseEntryValueObject databaseEntry
- Class ubic.gemma.web.taglib.EntityLinkTag extends org.springframework.web.servlet.tags.HtmlEscapingAwareTag implements Serializable
  - Serialized Fields
    - dimension
      
      ubic.gemma.model.expression.bioAssayData.BioAssayDimension dimension
    - dynamicAttributes
      
      Map<String,Object> dynamicAttributes
    - entity
      
      ubic.gemma.model.common.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
      
      ubic.gemma.model.expression.experiment.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
      
      ubic.gemma.model.common.description.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<ubic.gemma.model.expression.arrayDesign.ArrayDesign> subsumees
    - subsumer
      
      ubic.gemma.model.expression.arrayDesign.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 ubic.gemma.core.visualization.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<ubic.gemma.model.expression.bioAssay.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
      
      ubic.gemma.model.expression.experiment.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
      
      ubic.gemma.core.visualization.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<ubic.gemma.core.visualization.ExpressionDataHeatmap> implements Serializable
- Class ubic.gemma.web.taglib.expression.experiment.SingleCellSparsityHeatmapTag extends AbstractHeatmapTag<ubic.gemma.core.visualization.SingleCellSparsityHeatmap> implements Serializable
  - Serialized Fields
    - contextPath
      
      String contextPath
    - htmlEscape
      
      Boolean htmlEscape
    - type2Alt
      
      Map<ubic.gemma.core.visualization.SingleCellSparsityHeatmap.SingleCellHeatmapType,String> type2Alt
Package ubic.gemma.web.tasks.analysis.sequence
- Class ubic.gemma.web.tasks.analysis.sequence.ArrayDesignRepeatScanTaskCommand extends ubic.gemma.core.job.TaskCommand implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - arrayDesign
      
      ubic.gemma.model.expression.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.web.controller.coexpressionSearch

Class ubic.gemma.web.controller.coexpressionSearch.CoexSearchTaskCommand extends ubic.gemma.core.job.TaskCommand implements Serializable

Serialized Fields

searchOptions

Package ubic.gemma.web.controller.common.auditAndSecurity

Class ubic.gemma.web.controller.common.auditAndSecurity.FileUpload extends Object implements Serializable

Serialized Fields

file

localPath

Class ubic.gemma.web.controller.common.auditAndSecurity.SidValueObject extends Object implements Serializable

Serialized Fields

authority

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

Serialized Fields

dirty

eeIds

eeQuery

eeSetId

eeSetName

geneIds

selectedFactors

taxonId

threshold

Package ubic.gemma.web.controller.expression.arrayDesign

Class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignValueObjectExt extends ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject implements Serializable

Serialized Fields

additionalTaxa

allParentsAnnotationLink

alternateNames

alternative

bioProcessAnnotationLink

colorString

mergees

merger

noParentsAnnotationLink

subsumees

subsumer

Package ubic.gemma.web.controller.expression.experiment

Class ubic.gemma.web.controller.expression.experiment.DesignMatrixRowValueObject extends Object implements Serializable

Serialized Fields

count

factors

factorTypes

factorValueMap

Class ubic.gemma.web.controller.expression.experiment.ExperimentalFactorValueWebUIObject extends ubic.gemma.model.expression.experiment.ExperimentalFactorValueObject implements Serializable

Serialized Fields

bioMaterialCharacteristicCategoryToUse

Class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentDataFetchCommand extends ubic.gemma.core.job.TaskCommand implements Serializable

Serialized Fields

analysisId

experimentalDesignId

expressionExperimentId

filter

forceRewrite

format

quantitationTypeId

Class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditValueObject extends ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject implements Serializable

Serialized Fields

bioAssays

quantitationTypes

Class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentUploadResponse extends Object implements Serializable

Serialized Fields

error

errorMessage

taskId

Class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentCommandValidation extends Object implements Serializable

Serialized Fields

arrayDesignMatchesDataFile

arrayDesignMismatchProblemMessage

dataFileFormatProblemMessage

dataFileIsValidFormat

isValid

nonMatchingProbeNameExamples

numberMatchingProbes

numberOfNonMatchingProbes