Serialized Form

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.SimpleExpressionExperimentLoadTaskCommand extends ubic.gemma.core.loader.expression.simple.model.SimpleExpressionExperimentMetaData implements Serializable

serialVersionUID:

1L

Serialized Fields

arrayDesignName

String arrayDesignName

originalFileName

String originalFileName

serverFilePath

String serverFilePath

taxonName

String taxonName

validateOnly

boolean validateOnly

Package ubic.gemma.web.controller.visualization

Class ubic.gemma.web.controller.visualization.ExpressionExperimentVisualizationCommand extends Object implements Serializable

serialVersionUID:

2166768356457316142L

Serialized Fields

expressionExperimentId

Long expressionExperimentId

maskMissing

boolean maskMissing

name

String name

quantitationType

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.GemmaSessionBackedValueObject> allSessionBoundGroups

largestSessionId

Long largestSessionId

sessionBoundModifiedGroups

List<ubic.gemma.model.GemmaSessionBackedValueObject> sessionBoundModifiedGroups

Class ubic.gemma.web.persistence.ExperimentSetListContainer extends AbstractSetListContainer implements Serializable

serialVersionUID:

2031936160381488016L

Class ubic.gemma.web.persistence.GeneSetListContainer extends AbstractSetListContainer implements Serializable

serialVersionUID:

2163440335723257830L

Package ubic.gemma.web.taglib

Class ubic.gemma.web.taglib.ConstantsTag extends javax.servlet.jsp.tagext.TagSupport implements Serializable

serialVersionUID:

4937929483183805421L

Serialized Fields

clazz

String clazz

The class to expose the variables from.

scope

String scope

The scope to be put the variable in.

var

String var

The single variable to expose.

Class ubic.gemma.web.taglib.DatabaseEntryTag extends javax.servlet.jsp.tagext.TagSupport implements Serializable

serialVersionUID:

-8225561718129593445L

Serialized Fields

databaseEntry

ubic.gemma.model.common.description.DatabaseEntryValueObject databaseEntry

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

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 javax.servlet.jsp.tagext.TagSupport implements Serializable

serialVersionUID:

4323477499674966726L

Serialized Fields

exception

Exception exception

showStackTrace

Boolean showStackTrace

Package ubic.gemma.web.taglib.expression.experiment

Class ubic.gemma.web.taglib.expression.experiment.AssayViewTag extends javax.servlet.jsp.tagext.TagSupport implements Serializable

serialVersionUID:

8754490187937841260L

Serialized Fields

bioAssays

Collection<ubic.gemma.model.expression.bioAssay.BioAssayValueObject> bioAssays

edit

boolean edit

objectMapper

com.fasterxml.jackson.databind.ObjectMapper objectMapper

Jackson serializer to map objects to JSON.

Class ubic.gemma.web.taglib.expression.experiment.ExperimentQCTag extends javax.servlet.jsp.tagext.TagSupport implements Serializable

serialVersionUID:

-466958848014180520L

Serialized Fields

eeid

Long eeid

eeManagerId

String eeManagerId

hasCorrDist

boolean hasCorrDist

hasCorrMat

boolean hasCorrMat

hasMeanVariance

boolean hasMeanVariance

hasNodeDegreeDist

boolean hasNodeDegreeDist

hasPCA

boolean hasPCA

numFactors

int numFactors

numOutliersRemoved

int numOutliersRemoved

numPossibleOutliers

int numPossibleOutliers

Package ubic.gemma.web.tasks.analysis.sequence

Class ubic.gemma.web.tasks.analysis.sequence.ArrayDesignRepeatScanTaskCommand extends 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