Serialized Form (Gemma Web 1.33.0-SNAPSHOT API)

Package ubic.gemma.web.controller.analysis.expression.coexpression
- Class ubic.gemma.web.controller.analysis.expression.coexpression.CoexSearchTaskCommand
  
  class 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.analysis.expression.diff
- Class ubic.gemma.web.controller.analysis.expression.diff.DiffExpressionSearchCommand
  
  class 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.common.auditAndSecurity
- Class ubic.gemma.web.controller.common.auditAndSecurity.FileUpload
  
  class FileUpload extends Object implements Serializable
  
  serialVersionUID:
  
  537156568346654834L
  - Serialized Fields
    
    file
    
    byte[] file
    
    localPath
    
    String localPath
- Class ubic.gemma.web.controller.common.auditAndSecurity.SidValueObject
  
  class SidValueObject extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    
    authority
    
    String authority
    
    principal
    
    boolean principal
Package ubic.gemma.web.controller.common.auditAndSecurity.recaptcha
- Exception Class ubic.gemma.web.controller.common.auditAndSecurity.recaptcha.ReCaptchaException
  
  class ReCaptchaException extends RuntimeException implements Serializable

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

Class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignValueObjectExt

class 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
  
  class 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
  
  class ExperimentalFactorValueWebUIObject extends ubic.gemma.model.expression.experiment.ExperimentalFactorValueObject implements Serializable
  - Serialized Fields
    
    bioMaterialCharacteristicCategoryToUse
    
    String bioMaterialCharacteristicCategoryToUse
- Class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentDataFetchCommand
  
  class 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
  
  class 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
  
  class ExpressionExperimentUploadResponse extends Object implements Serializable
  - Serialized Fields
    
    error
    
    boolean error
    
    errorMessage
    
    String errorMessage
    
    taskId
    
    Long taskId
- Class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentCommandValidation
  
  class 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
  
  class 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.job
- Class ubic.gemma.web.controller.job.SubmittedTaskValueObject
  
  class 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.web.controller.persistence
- Class ubic.gemma.web.controller.persistence.AbstractSetListContainer
  
  class 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.controller.persistence.ExperimentSetListContainer
  
  class ExperimentSetListContainer extends AbstractSetListContainer implements Serializable
  
  serialVersionUID:
  
  2031936160381488016L
- Class ubic.gemma.web.controller.persistence.GeneSetListContainer
  
  class GeneSetListContainer extends AbstractSetListContainer implements Serializable
  
  serialVersionUID:
  
  2163440335723257830L
Package ubic.gemma.web.controller.util
- Exception Class ubic.gemma.web.controller.util.EntityNotFoundException
  
  class EntityNotFoundException extends RuntimeException implements Serializable
  
  serialVersionUID:
  
  -4361183252269974819L
- Exception Class ubic.gemma.web.controller.util.ServiceUnavailableException
  
  class ServiceUnavailableException extends RuntimeException implements Serializable
Package ubic.gemma.web.controller.util.upload
- Class ubic.gemma.web.controller.util.upload.CommonsMultipartFile
  
  class 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.controller.util.upload.UploadInfo
  
  class UploadInfo extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    
    bytesRead
    
    long bytesRead
    
    fileIndex
    
    int fileIndex
    
    status
    
    String status
    
    totalSize
    
    long totalSize
Package ubic.gemma.web.controller.visualization
- Class ubic.gemma.web.controller.visualization.ExpressionExperimentVisualizationCommand
  
  class 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.taglib
- Class ubic.gemma.web.taglib.AbstractStaticAssetTag
  
  class AbstractStaticAssetTag extends org.springframework.web.servlet.tags.HtmlEscapingAwareTag implements Serializable
  - Serialized Fields
    
    src
    
    String src
    
    srcAttributeName
    
    String srcAttributeName
- Class ubic.gemma.web.taglib.CharacteristicTag
  
  class 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
  
  class 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
  
  class 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
  
  class 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
  
  class 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
  
  class 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
  
  class ScriptTag extends AbstractStaticAssetTag implements Serializable
  - Serialized Fields
    
    async
    
    boolean async
    
    defer
    
    boolean defer
    
    dynamicAttributes
    
    Map<String,Object> dynamicAttributes
- Class ubic.gemma.web.taglib.ShortBibliographicReferenceTag
  
  class 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
  
  class 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
  
  class 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
  
  class 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
  
  class 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
  
  class 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
  
  class 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
  
  class ExpressionDataHeatmapTag extends AbstractHeatmapTag<ubic.gemma.core.visualization.ExpressionDataHeatmap> implements Serializable
- Class ubic.gemma.web.taglib.expression.experiment.SingleCellSparsityHeatmapTag
  
  class 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

Serialized Form

Package ubic.gemma.web.controller.analysis.expression.coexpression

Class ubic.gemma.web.controller.analysis.expression.coexpression.CoexSearchTaskCommand

Serialized Fields

searchOptions

Package ubic.gemma.web.controller.analysis.expression.diff

Class ubic.gemma.web.controller.analysis.expression.diff.DiffExpressionSearchCommand

Serialized Fields

dirty

eeIds

eeQuery

eeSetId

eeSetName

geneIds

selectedFactors

taxonId

threshold

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

Class ubic.gemma.web.controller.common.auditAndSecurity.FileUpload

Serialized Fields

file

localPath

Class ubic.gemma.web.controller.common.auditAndSecurity.SidValueObject

Serialized Fields

authority

principal

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

Exception Class ubic.gemma.web.controller.common.auditAndSecurity.recaptcha.ReCaptchaException

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

Class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignValueObjectExt

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

Serialized Fields

count

factors

factorTypes

factorValueMap

Class ubic.gemma.web.controller.expression.experiment.ExperimentalFactorValueWebUIObject

Serialized Fields

bioMaterialCharacteristicCategoryToUse

Class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentDataFetchCommand

Serialized Fields

analysisId

experimentalDesignId

expressionExperimentId

filter

forceRewrite

format

quantitationTypeId

Class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditValueObject

Serialized Fields

bioAssays

quantitationTypes

Class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentUploadResponse

Serialized Fields

error

errorMessage

taskId

Class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentCommandValidation

Serialized Fields

arrayDesignMatchesDataFile

arrayDesignMismatchProblemMessage

dataFileFormatProblemMessage

dataFileIsValidFormat

isValid

nonMatchingProbeNameExamples

numberMatchingProbes

numberOfNonMatchingProbes