Serialized Form

Package ubic.gemma.cli.batch

Class ubic.gemma.cli.batch.BatchTaskProcessingResult

class 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

class 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

class 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

class 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

class 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

logTransform

boolean logTransform

If true, perform a log-transformation of the data prior to analysis. The default is to use the data as-is.

If the data is already on a log scale, nothing is done.

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

Exception Class ubic.gemma.core.analysis.expression.coexpression.links.UnsuitableForAnalysisException

class UnsuitableForAnalysisException extends RuntimeException implements Serializable

serialVersionUID:

-4436136164850796179L

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

Exception Class ubic.gemma.core.analysis.expression.diff.AllAnalysesFailedException

class AllAnalysesFailedException extends AnalysisException implements Serializable

Exception Class ubic.gemma.core.analysis.expression.diff.AllSubSetAnalysesFailedException

class AllSubSetAnalysesFailedException extends AllAnalysesFailedException implements Serializable

Exception Class ubic.gemma.core.analysis.expression.diff.AnalysisException

class AnalysisException extends RuntimeException implements Serializable

Serialized Fields

config

DifferentialExpressionAnalysisConfig config

Class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionMetaAnalysisValueObject

class 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

class DiffExpressionSelectedFactorCommand extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

eeId

Long eeId

efId

Long efId

Exception Class ubic.gemma.core.analysis.expression.diff.EbayesFailureException

class EbayesFailureException extends AnalysisException implements Serializable

Exception Class ubic.gemma.core.analysis.expression.diff.FilteringRelatedAnalysisException

class FilteringRelatedAnalysisException extends AnalysisException implements Serializable

Exception Class ubic.gemma.core.analysis.expression.diff.InvalidQuantitationTypeConversionException

class InvalidQuantitationTypeConversionException extends AnalysisException implements Serializable

Exception Class ubic.gemma.core.analysis.expression.diff.NoFactorLeftForAnalysisException

class NoFactorLeftForAnalysisException extends AnalysisException implements Serializable

Package ubic.gemma.core.analysis.preprocess

Exception Class ubic.gemma.core.analysis.preprocess.FilteringRelatedPreprocessingException

class FilteringRelatedPreprocessingException extends PreprocessingException implements Serializable

Serialized Fields

cause

FilteringException cause

Class ubic.gemma.core.analysis.preprocess.OutlierDetails

class OutlierDetails extends Object implements Serializable

Serialized Fields

bioAssayId

Long bioAssayId

firstQuartile

double firstQuartile

medianCorrelation

double medianCorrelation

thirdQuartile

double thirdQuartile

Exception Class ubic.gemma.core.analysis.preprocess.PreprocessingException

class PreprocessingException extends RuntimeException implements Serializable

serialVersionUID:

-8463478950898408838L

Exception Class ubic.gemma.core.analysis.preprocess.QuantitationTypeConversionRelatedPreprocessingException

class QuantitationTypeConversionRelatedPreprocessingException extends PreprocessingException implements Serializable

Serialized Fields

cause

QuantitationTypeConversionException cause

Exception Class ubic.gemma.core.analysis.preprocess.QuantitationTypeDetectionRelatedPreprocessingException

class QuantitationTypeDetectionRelatedPreprocessingException extends PreprocessingException implements Serializable

Serialized Fields

cause

QuantitationTypeDetectionException cause

Exception Class ubic.gemma.core.analysis.preprocess.SampleCoexpressionRelatedPreprocessingException

class SampleCoexpressionRelatedPreprocessingException extends PreprocessingException implements Serializable

Exception Class ubic.gemma.core.analysis.preprocess.SVDRelatedPreprocessingException

class SVDRelatedPreprocessingException extends PreprocessingException implements Serializable

Serialized Fields

cause

SVDException cause

Package ubic.gemma.core.analysis.preprocess.batcheffects

Exception Class ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoMissingException

class BatchInfoMissingException extends BatchInfoPopulationException implements Serializable

Exception Class ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationException

class BatchInfoPopulationException extends PreprocessingException implements Serializable

serialVersionUID:

-1770591991479420212L

Exception Class ubic.gemma.core.analysis.preprocess.batcheffects.FASTQHeadersPresentButNotUsableException

class FASTQHeadersPresentButNotUsableException extends BatchInfoPopulationException implements Serializable

serialVersionUID:

1917074433646650950L

Exception Class ubic.gemma.core.analysis.preprocess.batcheffects.SingletonBatchesException

class SingletonBatchesException extends BatchInfoPopulationException implements Serializable

serialVersionUID:

9088141067684148902L

Exception Class ubic.gemma.core.analysis.preprocess.batcheffects.UnsupportedRawdataFileFormatException

class UnsupportedRawdataFileFormatException extends BatchInfoPopulationException implements Serializable

serialVersionUID:

1L

Package ubic.gemma.core.analysis.preprocess.convert

Exception Class ubic.gemma.core.analysis.preprocess.convert.QuantitationTypeConversionException

class QuantitationTypeConversionException extends Exception implements Serializable

Exception Class ubic.gemma.core.analysis.preprocess.convert.UnsupportedQuantitationRepresentationConversionException

class UnsupportedQuantitationRepresentationConversionException extends UnsupportedQuantitationTypeConversionException implements Serializable

Exception Class ubic.gemma.core.analysis.preprocess.convert.UnsupportedQuantitationScaleConversionException

class UnsupportedQuantitationScaleConversionException extends UnsupportedQuantitationTypeConversionException implements Serializable

Exception Class ubic.gemma.core.analysis.preprocess.convert.UnsupportedQuantitationTypeConversionException

class UnsupportedQuantitationTypeConversionException extends QuantitationTypeConversionException implements Serializable

Package ubic.gemma.core.analysis.preprocess.detect

Exception Class ubic.gemma.core.analysis.preprocess.detect.InferredQuantitationMismatchException

class InferredQuantitationMismatchException extends QuantitationMismatchException implements Serializable

Serialized Fields

inferredQuantitationType

QuantitationType inferredQuantitationType

Exception Class ubic.gemma.core.analysis.preprocess.detect.QuantitationMismatchException

class QuantitationMismatchException extends QuantitationTypeDetectionException implements Serializable

Serialized Fields

quantitationType

QuantitationType quantitationType

Exception Class ubic.gemma.core.analysis.preprocess.detect.QuantitationTypeDetectionException

class QuantitationTypeDetectionException extends Exception implements Serializable

Exception Class ubic.gemma.core.analysis.preprocess.detect.SuspiciousValuesForQuantitationException

class 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

class FilterConfig extends Object implements Serializable

Serialized Fields

highExpressionCut

double highExpressionCut

High cut for expression.

Design elements expressed above the cut will be filtered out.

This threshold applies on the rank of gene expression. A value of 0.1 will drop the bottom 10% of the data.

Set this to zero to disable.

ignoreMinimumRowsThreshold

boolean ignoreMinimumRowsThreshold

If true, the MINIMUM_ROWS_TO_BOTHER is ignored.

ignoreMinimumSampleThreshold

boolean ignoreMinimumSampleThreshold

If true, MINIMUM_SAMPLE is ignored.

lowDistinctValueCut

double lowDistinctValueCut

lowDistinctValueIsSet

boolean lowDistinctValueIsSet

lowExpressionCut

double lowExpressionCut

Low cut for expression.

Design elements expressed below the cut will be filtered out.

This threshold applies on the rank. A value of 0.9 will drop the top 10% of the data.

Set this to one to disable.

lowVarianceCut

double lowVarianceCut

This threshold applies on the variance of the row.

The threshold applies to data on a log2-scale, so a value of 0.01 will retain values with a standard deviation of 0.1.

Set this to zero disable.

minPresentFraction

double minPresentFraction

requireSequences

boolean requireSequences

Set to true if rows lacking associated BioSequences for the element should be removed.

Exception Class ubic.gemma.core.analysis.preprocess.filter.FilteringException

class FilteringException extends Exception implements Serializable

Exception Class ubic.gemma.core.analysis.preprocess.filter.InsufficientDataException

class InsufficientDataException extends FilteringException implements Serializable

Exception Class ubic.gemma.core.analysis.preprocess.filter.InsufficientDesignElementsException

class InsufficientDesignElementsException extends InsufficientDataException implements Serializable

Exception Class ubic.gemma.core.analysis.preprocess.filter.InsufficientSamplesException

class InsufficientSamplesException extends InsufficientDataException implements Serializable

serialVersionUID:

1L

Exception Class ubic.gemma.core.analysis.preprocess.filter.NoDesignElementsException

class NoDesignElementsException extends InsufficientDesignElementsException implements Serializable

Package ubic.gemma.core.analysis.preprocess.svd

Exception Class ubic.gemma.core.analysis.preprocess.svd.SVDException

class SVDException extends Exception implements Serializable

Class ubic.gemma.core.analysis.preprocess.svd.SVDResult

class SVDResult extends Object implements Serializable

Serialized Fields

bioAssays

List<BioAssay> bioAssays

Assays used in the SVD analysis.

In order like the rows of the V matrix.

bioMaterials

List<BioMaterial> bioMaterials

Biomaterials used in the SVD analysis.

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

ExpressionExperiment 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

class 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

class 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

Package ubic.gemma.core.analysis.singleCell.aggregate

Exception Class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellAggregationException

class SingleCellAggregationException extends RuntimeException implements Serializable

Exception Class ubic.gemma.core.analysis.singleCell.aggregate.UnsupportedScaleTypeForSingleCellAggregationException

class UnsupportedScaleTypeForSingleCellAggregationException extends SingleCellAggregationException implements Serializable

Package ubic.gemma.core.job

Class ubic.gemma.core.job.TaskCommand

class TaskCommand extends Object implements Serializable

Serialized Fields

emailAlert

boolean emailAlert

Should an email be sent to the user when the job is done?

maxQueueMillis

long maxQueueMillis

How long we will allow this task to be queued before giving up, or -1 for no limit.

maxRuntimeMillis

long maxRuntimeMillis

How long we will allow this task to run before giving up, or -1 for no limit.

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

Task submitted, if known.

Class ubic.gemma.core.job.TaskResult

class TaskResult extends Object implements Serializable

Serialized Fields

answer

Serializable answer

The actual result object

Package ubic.gemma.core.job.progress

Class ubic.gemma.core.job.progress.ProgressData

class 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

Package ubic.gemma.core.loader.entrez

Exception Class ubic.gemma.core.loader.entrez.EntrezException

class EntrezException extends RuntimeException implements Serializable

Serialized Fields

errors

List<String> errors

Package ubic.gemma.core.loader.expression.arrayDesign

Class ubic.gemma.core.loader.expression.arrayDesign.Reporter

class 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

class 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

class 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

class GeoData extends Object implements Serializable

Serialized Fields

columnDescriptions

List<String> columnDescriptions

columnNames

List<String> columnNames

The column names mean different things in different subclasses. For samples, the column names are the "quantitation types". For platforms, they are descriptor names.

contact

GeoContact contact

geoAccession

String geoAccession

relations

Map<String,Collection<String>> relations

title

String title

Class ubic.gemma.core.loader.expression.geo.model.GeoDataset

class 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

class 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

class 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

class 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

Indicate if the data might be separate, as for some RNA-seq studies.

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

The sample type (ie. DNA, RNA, etc.)

variables

Collection<GeoVariable> variables

warnedAboutGenePix

boolean warnedAboutGenePix

Class ubic.gemma.core.loader.expression.geo.model.GeoSeries

class GeoSeries extends GeoData implements Serializable

Serialized Fields

contributors

Collection<GeoContact> contributors

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

summaries

List<String> summaries

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

class 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

class 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

Exception Class ubic.gemma.core.loader.expression.geo.singleCell.NoSingleCellDataFoundException

class NoSingleCellDataFoundException extends Exception implements Serializable

Package ubic.gemma.core.loader.expression.simple.model

Class ubic.gemma.core.loader.expression.simple.model.SimpleCharacteristic

class 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

class SimpleContactMetadata extends Object implements Serializable

Class ubic.gemma.core.loader.expression.simple.model.SimpleDatabaseEntry

class 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

class 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

String 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

class 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

class 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

class 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

class 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

Exception Class ubic.gemma.core.loader.util.AlreadyExistsInSystemException

class AlreadyExistsInSystemException extends RuntimeException implements Serializable

serialVersionUID:

5677999264920938691L

Serialized Fields

data

Object data

Package ubic.gemma.core.loader.util.anndata

Exception Class ubic.gemma.core.loader.util.anndata.AnnDataException

class AnnDataException extends RuntimeException implements Serializable

Exception Class ubic.gemma.core.loader.util.anndata.InvalidEncodingAttributeException

class InvalidEncodingAttributeException extends AnnDataException implements Serializable

Exception Class ubic.gemma.core.loader.util.anndata.MissingEncodingAttributeException

class MissingEncodingAttributeException extends AnnDataException implements Serializable

Package ubic.gemma.core.loader.util.biomart

Class ubic.gemma.core.loader.util.biomart.Ensembl2NcbiValueObject

class 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

Exception Class ubic.gemma.core.loader.util.hdf5.H5Exception

class H5Exception extends RuntimeException implements Serializable

Serialized Fields

cause

hdf.hdf5lib.exceptions.HDF5Exception cause

Exception Class ubic.gemma.core.loader.util.hdf5.TruncatedH5FileException

class TruncatedH5FileException extends IOException implements Serializable

Package ubic.gemma.core.loader.util.parser

Exception Class ubic.gemma.core.loader.util.parser.FileFormatException

class FileFormatException extends RuntimeException implements Serializable

serialVersionUID:

-1984918923089214361L

Package ubic.gemma.core.search

Exception Class ubic.gemma.core.search.BaseCodeOntologySearchException

class BaseCodeOntologySearchException extends SearchException implements Serializable

Serialized Fields

cause

OntologySearchException cause

Exception Class ubic.gemma.core.search.ParseSearchException

class ParseSearchException extends SearchException implements Serializable

Serialized Fields

originalParseException

ParseSearchException originalParseException

query

String query

Exception Class ubic.gemma.core.search.SearchException

class SearchException extends Exception implements Serializable

Exception Class ubic.gemma.core.search.SearchTimeoutException

class SearchTimeoutException extends SearchException implements Serializable

Serialized Fields

cause

TimeoutException cause

Package ubic.gemma.core.search.lucene

Exception Class ubic.gemma.core.search.lucene.LuceneParseSearchException

class LuceneParseSearchException extends ParseSearchException implements Serializable

Package ubic.gemma.core.search.source

Exception Class ubic.gemma.core.search.source.HibernateSearchException

class HibernateSearchException extends SearchException implements Serializable

Serialized Fields

cause

org.hibernate.search.SearchException cause

Package ubic.gemma.core.tasks

Class ubic.gemma.core.tasks.EntityTaskCommand

class 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

class 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

class DifferentialExpressionAnalysisRemoveTaskCommand extends DifferentialExpressionAnalysisTaskCommand implements Serializable

serialVersionUID:

-6881129987842634598L

Serialized Fields

toRemove

DifferentialExpressionAnalysis toRemove

Class ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisTaskCommand

class 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

class 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

class BatchInfoFetchTaskCommand extends ExpressionExperimentReportTaskCommand implements Serializable

serialVersionUID:

-1901958943061377082L

Class ubic.gemma.core.tasks.analysis.expression.BioAssayOutlierProcessingTaskCommand

class BioAssayOutlierProcessingTaskCommand extends TaskCommand implements Serializable

serialVersionUID:

3083077516188614790L

Serialized Fields

bioAssayIds

Collection<Long> bioAssayIds

revert

boolean revert

Class ubic.gemma.core.tasks.analysis.expression.ExpressionExperimentLoadTaskCommand

class 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

class PreprocessTaskCommand extends TaskCommand implements Serializable

serialVersionUID:

1L

Serialized Fields

diagnosticsOnly

boolean diagnosticsOnly

expressionExperiment

ExpressionExperiment expressionExperiment

Class ubic.gemma.core.tasks.analysis.expression.SvdTaskCommand

class SvdTaskCommand extends TaskCommand implements Serializable

serialVersionUID:

1L

Serialized Fields

expressionExperiment

ExpressionExperiment expressionExperiment

postProcessOnly

boolean postProcessOnly

Class ubic.gemma.core.tasks.analysis.expression.TwoChannelMissingValueTaskCommand

class 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

class 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

class 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

class ArrayDesignProbeMapTaskCommand extends TaskCommand implements Serializable

serialVersionUID:

1L

Serialized Fields

arrayDesign

ArrayDesign arrayDesign

forceAnalysis

boolean forceAnalysis

Class ubic.gemma.core.tasks.analysis.sequence.ArrayDesignRepeatScanTaskCommand

class ArrayDesignRepeatScanTaskCommand extends TaskCommand implements Serializable

serialVersionUID:

1L

Serialized Fields

arrayDesign

ArrayDesign arrayDesign

Package ubic.gemma.core.tasks.maintenance

Class ubic.gemma.core.tasks.maintenance.CharacteristicUpdateCommand

class 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

class ExpressionExperimentReportTaskCommand extends TaskCommand implements Serializable

serialVersionUID:

1L

Serialized Fields

all

boolean all

expressionExperiment

ExpressionExperiment expressionExperiment

Class ubic.gemma.core.tasks.maintenance.IndexerTaskCommand

class 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

class 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

class 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

class 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

Exception Class ubic.gemma.core.util.GemmaRestApiClientException

class GemmaRestApiClientException extends RuntimeException implements Serializable

Package ubic.gemma.core.visualization

Class ubic.gemma.core.visualization.ExpressionDataHeatmap

class ExpressionDataHeatmap extends Object implements Serializable

Serialized Fields

assayIndex

int[] assayIndex

assays

List<BioAssay> assays

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.

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

class 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

class AnalysisResultSetValueObject extends IdentifiableValueObject<R extends AnalysisResultSet<K>> implements Serializable

Class ubic.gemma.model.analysis.AnalysisResultValueObject

class AnalysisResultValueObject extends IdentifiableValueObject<A extends AnalysisResult> implements Serializable

Class ubic.gemma.model.analysis.AnalysisValueObject

class AnalysisValueObject extends IdentifiableValueObject<T extends Analysis> implements Serializable

Serialized Fields

name

String name

protocol

ProtocolValueObject protocol

Class ubic.gemma.model.analysis.CellTypeAssignmentValueObject

class 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

class ProtocolValueObject extends IdentifiableValueObject<Protocol> implements Serializable

Serialized Fields

description

String description

name

String name

Package ubic.gemma.model.analysis.expression.diff

Class ubic.gemma.model.analysis.expression.diff.ContrastResultValueObject

class 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

class ContrastsValueObject extends Object implements Serializable

Serialized Fields

contrasts

List<ContrastVO> contrasts

resultId

Long resultId

Class ubic.gemma.model.analysis.expression.diff.ContrastVO

class ContrastVO extends Object implements Serializable

Serialized Fields

factorValueId

Long factorValueId

id

Long id

logFoldChange

Double logFoldChange

pvalue

Double pvalue

secondFactorValueId

Long secondFactorValueId

Class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResultSetValueObject

class 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

class 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

class 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

class 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

class 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

class 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

class 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

class 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

class IncludedResultSetInfoValueObject extends Object implements Serializable

serialVersionUID:

-4660741839991839187L

Serialized Fields

analysisId

Long analysisId

experimentId

Long experimentId

resultSetId

Long resultSetId

Package ubic.gemma.model.analysis.sequence

Class ubic.gemma.model.analysis.sequence.GeneMappingSummary

class 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.model.association.coexpression

Class ubic.gemma.model.association.coexpression.GeneCoexpressionNodeDegreeValueObject

class 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

class 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

class 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

class IdentifiableValueObject extends Object implements Serializable

Serialized Fields

id

Long id

Package ubic.gemma.model.common.auditAndSecurity

Class ubic.gemma.model.common.auditAndSecurity.AuditEventValueObject

class AuditEventValueObject extends IdentifiableValueObject<AuditEvent> implements Serializable

serialVersionUID:

1L

Serialized Fields

action

String action

date

Date date

detail

String detail

eventType

Class<? extends AuditEventType> eventType

note

String note

performer

String performer

Class ubic.gemma.model.common.auditAndSecurity.GroupAuthority

class 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

class 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

class 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

class 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

class 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

class 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

class DatabaseEntryValueObject extends IdentifiableValueObject<DatabaseEntry> implements Serializable

serialVersionUID:

-527323410580090L

Serialized Fields

accession

String accession

externalDatabase

ExternalDatabaseValueObject externalDatabase

Class ubic.gemma.model.common.description.ExternalDatabaseValueObject

class 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

class 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

class 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

class 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

class 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

class 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

If this BioAssay has a parent via BioMaterial.getSourceBioMaterial(), this is the ID.

This is context-dependent because the parent depends on which BioAssaySet is under consideration. For example, an experiment could have two sets of EE subsets with distinct parents.

userFlaggedOutlier

boolean userFlaggedOutlier

Package ubic.gemma.model.expression.bioAssayData

Class ubic.gemma.model.expression.bioAssayData.BioAssayDimensionValueObject

class 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

class BooleanVectorValueObject extends DataVectorValueObject implements Serializable

Serialized Fields

data

boolean[] data

Class ubic.gemma.model.expression.bioAssayData.CellLevelCharacteristicsValueObject

class 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

class 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

class 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

class ExperimentExpressionLevelsValueObject extends Object implements Serializable

Serialized Fields

datasetId

long datasetId

geneExpressionLevels

LinkedList<ExperimentExpressionLevelsValueObject.GeneElementExpressionsValueObject> geneExpressionLevels

Class ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject.GeneElementExpressionsValueObject

class 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

class VectorElementValueObject extends Object implements Serializable

Serialized Fields

bioAssayExpressionLevels

Map<String,Double> bioAssayExpressionLevels

designElementName

String designElementName

Class ubic.gemma.model.expression.bioAssayData.SingleCellDimensionValueObject

class 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.

numberOfCellIds

int numberOfCellIds

Number of cells.

This is always equal to the length of SingleCellDimensionValueObject.cellIds.

Class ubic.gemma.model.expression.bioAssayData.SlicedDoubleVectorValueObject

class 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

class 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

class 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

class 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

class 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

class ExpressionExperimentDetailsValueObject extends ExpressionExperimentValueObject implements Serializable

serialVersionUID:

-1219449523930648392L

Serialized Fields

arrayDesigns

Collection<ArrayDesignValueObject> arrayDesigns

batchFetchEventType

String batchFetchEventType

cellBrowserDatasetName

String cellBrowserDatasetName

cellBrowserUrl

String cellBrowserUrl

URL for the Cell Browser, if available.

dateArrayDesignLastUpdated

Date dateArrayDesignLastUpdated

The date the platform associated with the experiment was last updated.

If there are multiple platforms this should be the date of the most recent modification of them. This is used to help flag experiments that need re-analysis due to changes in the underlying array design(s).

dateBatchFetch

Date dateBatchFetch

dateCached

Date dateCached

The date this object was generated.

dateDifferentialAnalysis

Date dateDifferentialAnalysis

dateLinkAnalysis

Date dateLinkAnalysis

dateMissingValueAnalysis

Date dateMissingValueAnalysis

datePcaAnalysis

Date datePcaAnalysis

dateProcessedDataVectorComputation

Date dateProcessedDataVectorComputation

differentialExpressionAnalyses

Collection<DifferentialExpressionAnalysisValueObject> differentialExpressionAnalyses

expressionExperimentSets

Collection<ExpressionExperimentSetValueObject> expressionExperimentSets

EE sets this experiment is part of.

font

String font

Font to use when rendering diagnostic plots, etc.

hasBatchInformation

boolean hasBatchInformation

FIXME: rename this to hasUsableBatchInformation

hasBothIntensities

boolean hasBothIntensities

hasCellBrowser

boolean hasCellBrowser

Indicate if this experiment has a Cell Browser associated with it.

hasCoexpressionAnalysis

boolean hasCoexpressionAnalysis

hasDifferentialExpressionAnalysis

boolean hasDifferentialExpressionAnalysis

hasEitherIntensity

boolean hasEitherIntensity

Indicate if the experiment has any intensity information available. Relevant for two-channel studies.

hasMultiplePreferredQuantitationTypes

boolean hasMultiplePreferredQuantitationTypes

hasMultipleTechnologyTypes

boolean hasMultipleTechnologyTypes

isReprocessedFromRawData

boolean isReprocessedFromRawData

isRNASeq

boolean isRNASeq

isSingleCell

boolean isSingleCell

Indicate if this experiment is a single-cell experiment.

lastArrayDesignUpdateDate

String lastArrayDesignUpdateDate

linkAnalysisEventType

String linkAnalysisEventType

missingValueAnalysisEventType

String missingValueAnalysisEventType

numAnnotations

Long numAnnotations

The number of terms (Characteristics) the experiment has to describe it.

numberOfCellIds

Integer numberOfCellIds

The number of cell IDs that the preferred single-cell dimension has.

See Also:

• SingleCellDimension.getNumberOfCellIds()

numberOfCells

Integer numberOfCells

The number of cells this experiment has.

See Also:

• ExpressionExperiment.getNumberOfCells()

numPopulatedFactors

Long numPopulatedFactors

The number of experimental factors the experiment has (counting those that are populated with biomaterials).

originalPlatforms

Collection<ArrayDesignValueObject> originalPlatforms

otherParts

Collection<ExpressionExperimentValueObject> otherParts

Experiments that are related to this one via the splitting of a source experiment.

pcaAnalysisEventType

String pcaAnalysisEventType

primaryCitation

CitationValueObject primaryCitation

processedDataVectorComputationEventType

String processedDataVectorComputationEventType

pubmedId

Integer pubmedId

QChtml

String QChtml

sampleRemovedFlags

Collection<AuditEventValueObject> sampleRemovedFlags

Details of samples that were removed (or marked as outliers). This can happen multiple times in the life of data set, so this is a collection of AuditEvents.

secondaryAccession

String secondaryAccession

Identifier in a second database, if available. For example, if the data are in GEO and in ArrayExpress, this might be a link to the ArrayExpress version.

secondaryExternalDatabase

String secondaryExternalDatabase

secondaryExternalUri

String secondaryExternalUri

Class ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject

class 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

class 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

class 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

class FactorValueBasicValueObject extends AbstractFactorValueValueObject implements Serializable

serialVersionUID:

3378801249808036785L

Serialized Fields

value

String value

Deprecated.

use either AbstractFactorValueValueObject.getCharacteristics() or

invalid reference

#getMeasurement()

Class ubic.gemma.model.expression.experiment.FactorValueValueObject

class 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

class FreeTextExpressionExperimentResultsValueObject extends SessionBoundExpressionExperimentSetValueObject implements Serializable

serialVersionUID:

3557304710219740029L

Serialized Fields

queryString

String queryString

Class ubic.gemma.model.expression.experiment.GeeqAdminValueObject

class 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

class 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

class SessionBoundExpressionExperimentSetValueObject extends ExpressionExperimentSetValueObject implements Serializable

serialVersionUID:

2068650886972222818L

Serialized Fields

modified

boolean modified

Class ubic.gemma.model.expression.experiment.StatementValueObject

class 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

class 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

class 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

class 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

class DatabaseBackedGeneSetValueObject extends GeneSetValueObject implements Serializable

serialVersionUID:

-1360523793656012770L

Class ubic.gemma.model.genome.gene.FreeTextGeneResultsValueObject

class FreeTextGeneResultsValueObject extends SessionBoundGeneSetValueObject implements Serializable

serialVersionUID:

3557304710219740029L

Serialized Fields

queryString

String queryString

Class ubic.gemma.model.genome.gene.GeneProductValueObject

class 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

class 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

class 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

class GOGroupValueObject extends SessionBoundGeneSetValueObject implements Serializable

serialVersionUID:

-185326197992950287L

Serialized Fields

goId

String goId

searchTerm

String searchTerm

Class ubic.gemma.model.genome.gene.SessionBoundGeneSetValueObject

class 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

class 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

class 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

class SequenceTypeValueObject extends Object implements Serializable

Serialized Fields

value

String value

Package ubic.gemma.model.util

Exception Class ubic.gemma.model.util.UninitializedCollectionException

class UninitializedCollectionException extends RuntimeException implements Serializable

Package ubic.gemma.persistence.hibernate

Class ubic.gemma.persistence.hibernate.HibernateTransactionManager

class HibernateTransactionManager extends org.springframework.orm.hibernate4.HibernateTransactionManager implements Serializable

Class ubic.gemma.persistence.hibernate.LocalSessionFactoryBuilder

class LocalSessionFactoryBuilder extends org.springframework.orm.hibernate4.LocalSessionFactoryBuilder implements Serializable

Class ubic.gemma.persistence.hibernate.XSDEntityResolver

class XSDEntityResolver extends DTDEntityResolver implements Serializable

Package ubic.gemma.persistence.service.analysis.expression.diff

Class ubic.gemma.persistence.service.analysis.expression.diff.MissingResult

class MissingResult extends DiffExprGeneSearchResult implements Serializable

serialVersionUID:

-2868418055346274525L

Class ubic.gemma.persistence.service.analysis.expression.diff.NonRetainedResult

class NonRetainedResult extends DiffExprGeneSearchResult implements Serializable

serialVersionUID:

3501605965895623139L

Package ubic.gemma.persistence.service.association.coexpression

Class ubic.gemma.persistence.service.association.coexpression.CoexpressionCacheValueObject

class 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

class 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

Exception Class ubic.gemma.persistence.service.common.quantitationtype.NonUniqueQuantitationTypeByNameException

class NonUniqueQuantitationTypeByNameException extends Exception implements Serializable

Package ubic.gemma.persistence.service.expression.experiment

Exception Class ubic.gemma.persistence.service.expression.experiment.FactorValueMigratorService.MigrationFailedException

class MigrationFailedException extends RuntimeException implements Serializable

Serialized Fields

migration

FactorValueMigratorService.Migration migration

Package ubic.gemma.persistence.service.maintenance

Class ubic.gemma.persistence.service.maintenance.Gene2CsStatus

class 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

class 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

class ArrayDesignWithUsageStatisticsValueObject extends ArrayDesignValueObject implements Serializable

Serialized Fields

numberOfExpressionExperimentsForTechnologyType

Long numberOfExpressionExperimentsForTechnologyType

Class ubic.gemma.rest.DatasetsWebService.DifferentialExpressionAnalysisResultByGeneValueObject

class 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

class ExpressionExperimentSubsetWithFactorValuesObject extends ExpressionExperimentSubsetValueObject implements Serializable

Serialized Fields

factorValues

List<FactorValueBasicValueObject> factorValues

Class ubic.gemma.rest.DatasetsWebService.ExpressionExperimentSubSetWithGroupsValueObject

class ExpressionExperimentSubSetWithGroupsValueObject extends ExpressionExperimentSubsetValueObject implements Serializable

Serialized Fields

subSetGroupIds

List<Long> subSetGroupIds

Class ubic.gemma.rest.DatasetsWebService.ExpressionExperimentWithSearchResultValueObject

class ExpressionExperimentWithSearchResultValueObject extends ExpressionExperimentValueObject implements Serializable

Serialized Fields

searchResult

SearchWebService.SearchResultValueObject<ExpressionExperimentValueObject> searchResult

Class ubic.gemma.rest.DatasetsWebService.TaxonWithUsageStatisticsValueObject

class TaxonWithUsageStatisticsValueObject extends TaxonValueObject implements Serializable

Serialized Fields

numberOfExpressionExperiments

Long numberOfExpressionExperiments

Package ubic.gemma.rest.serializers

Class ubic.gemma.rest.serializers.AbstractFactorValueValueObjectSerializer

class AbstractFactorValueValueObjectSerializer extends com.fasterxml.jackson.databind.ser.std.StdSerializer<T extends AbstractFactorValueValueObject> implements Serializable

Class ubic.gemma.rest.serializers.FactorValueBasicValueObjectSerializer

class FactorValueBasicValueObjectSerializer extends AbstractFactorValueValueObjectSerializer<FactorValueBasicValueObject> implements Serializable

Class ubic.gemma.rest.serializers.FactorValueValueObjectSerializer

class FactorValueValueObjectSerializer extends AbstractFactorValueValueObjectSerializer<FactorValueValueObject> implements Serializable

Package ubic.gemma.rest.util

Exception Class ubic.gemma.rest.util.EntityNotFoundException

class EntityNotFoundException extends Exception implements Serializable

Exception Class ubic.gemma.rest.util.MalformedArgException

class MalformedArgException extends javax.ws.rs.BadRequestException implements Serializable

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

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

class CoexSearchTaskCommand extends TaskCommand implements Serializable

serialVersionUID:

1L

Serialized Fields

searchOptions

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<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 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

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 ExperimentalFactorValueObject implements Serializable

Serialized Fields

bioMaterialCharacteristicCategoryToUse

String bioMaterialCharacteristicCategoryToUse

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

class 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

class 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

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 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.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<GemmaSessionBackedValueObject> allSessionBoundGroups

largestSessionId

Long largestSessionId

sessionBoundModifiedGroups

List<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

QuantitationType quantitationType

searchCriteria

String searchCriteria

searchString

String searchString

viewSampling

boolean viewSampling

Package ubic.gemma.web.taglib

Class ubic.gemma.web.taglib.AbstractHtmlElementTag

class AbstractHtmlElementTag extends org.springframework.web.servlet.tags.HtmlEscapingAwareTag implements Serializable

Serialized Fields

cssClass

String cssClass

cssStyle

String cssStyle

dynamicAttributes

Map<String,Object> dynamicAttributes

title

String title

Class ubic.gemma.web.taglib.AbstractStaticAssetTag

class AbstractStaticAssetTag extends AbstractHtmlElementTag 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

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

DatabaseEntryValueObject databaseEntry

Class ubic.gemma.web.taglib.EntityLinkTag

class EntityLinkTag extends AbstractHtmlElementTag implements Serializable

Serialized Fields

dimension

BioAssayDimension dimension

entity

Identifiable entity

external

boolean external

Class ubic.gemma.web.taglib.FactorValueTag

class FactorValueTag extends org.springframework.web.servlet.tags.HtmlEscapingAwareTag implements Serializable

Serialized Fields

factorValue

FactorValue factorValue

Class ubic.gemma.web.taglib.ImageTag

class ImageTag extends AbstractStaticAssetTag implements Serializable

Serialized Fields

alt

String alt

height

String height

width

String width

Class ubic.gemma.web.taglib.OntologyHierarchyTag

class OntologyHierarchyTag extends AbstractHtmlElementTag implements Serializable

Serialized Fields

ontologyResourceTag

OntologyResourceTag ontologyResourceTag

Class ubic.gemma.web.taglib.OntologyResourceTag

class OntologyResourceTag extends org.springframework.web.servlet.tags.HtmlEscapingAwareTag implements Serializable

Class ubic.gemma.web.taglib.ScriptTag

class ScriptTag extends AbstractStaticAssetTag implements Serializable

Serialized Fields

async

boolean async

defer

boolean defer

Class ubic.gemma.web.taglib.ShortBibliographicReferenceTag

class ShortBibliographicReferenceTag extends javax.servlet.jsp.tagext.TagSupport implements Serializable

serialVersionUID:

-7325678534991860679L

Serialized Fields

citation

BibliographicReference citation

Class ubic.gemma.web.taglib.StyleTag

class StyleTag extends AbstractStaticAssetTag implements Serializable

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<ArrayDesign> subsumees

subsumer

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 AbstractHtmlElementTag implements Serializable

Serialized Fields

alt

String alt

Alternative text to use for the image.

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

class 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

class ExperimentQCTag extends AbstractHtmlElementTag implements Serializable

Serialized Fields

eeManagerId

String eeManagerId

DOM ID of the manager for the experiment.

expressionExperiment

ExpressionExperiment expressionExperiment

Expression experiment to display the QC info for.

font

String font

Font to use for the rendering diagnostic plots.

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

class ExpressionDataHeatmapTag extends AbstractHeatmapTag<ExpressionDataHeatmap> implements Serializable

Class ubic.gemma.web.taglib.expression.experiment.SingleCellSparsityHeatmapTag

class SingleCellSparsityHeatmapTag extends AbstractHeatmapTag<SingleCellSparsityHeatmap> implements Serializable

Serialized Fields

contextPath

String contextPath

htmlEscape

Boolean htmlEscape

type2Alt

Map<SingleCellSparsityHeatmap.SingleCellHeatmapType,String> type2Alt