Serialized Form


Package edu.georgetown.pir

Class edu.georgetown.pir.AdditionalOrganismName extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

id

java.lang.Long id

source

java.lang.String source

value

java.lang.String value

comment

java.lang.String comment

organismCollection

java.util.Set<E> organismCollection

Class edu.georgetown.pir.Organism extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

id

java.lang.Long id

ncbiTaxonomyId

java.lang.Long ncbiTaxonomyId

scientificName

java.lang.String scientificName

commonName

java.lang.String commonName

taxonomyRank

java.lang.String taxonomyRank

ethnicityStrain

java.lang.String ethnicityStrain

termSource

TermSource termSource

additionalOrganismNameCollection

java.util.Set<E> additionalOrganismNameCollection

Package gov.nih.nci.caarray.domain

Class gov.nih.nci.caarray.domain.AbstractCaArrayEntity extends AbstractCaArrayObject implements Serializable

serialVersionUID: 2732929116326299995L

Serialized Fields

lsidAuthority

java.lang.String lsidAuthority

lsidNamespace

java.lang.String lsidNamespace

lsidObjectId

java.lang.String lsidObjectId

Class gov.nih.nci.caarray.domain.AbstractCaArrayObject extends java.lang.Object implements Serializable

serialVersionUID: 2732929116326299995L

Serialized Fields

id

java.lang.Long id

caBigId

java.lang.String caBigId

Class gov.nih.nci.caarray.domain.AbstractUnitableValue extends AbstractCaArrayEntity implements Serializable

serialVersionUID: 1L

Class gov.nih.nci.caarray.domain.BlobHolder extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

id

java.lang.Long id

contents

java.sql.Blob contents

Class gov.nih.nci.caarray.domain.LSID extends java.lang.Object implements Serializable

serialVersionUID: 3343197687318404334L

Serialized Fields

authority

java.lang.String authority

namespace

java.lang.String namespace

objectId

java.lang.String objectId

Class gov.nih.nci.caarray.domain.MultiPartBlob extends java.lang.Object implements Serializable

serialVersionUID: -2527332971292994350L

Serialized Fields

id

java.lang.Long id

creationTimestamp

java.util.Date creationTimestamp

uncompressedSize

long uncompressedSize

compressedSize

long compressedSize

blobParts

java.util.List<E> blobParts

Package gov.nih.nci.caarray.domain.array

Class gov.nih.nci.caarray.domain.array.AbstractDesignElement extends AbstractCaArrayObject implements Serializable

Class gov.nih.nci.caarray.domain.array.AbstractProbe extends AbstractDesignElement implements Serializable

Serialized Fields

annotation

AbstractProbeAnnotation annotation

name

java.lang.String name

Class gov.nih.nci.caarray.domain.array.AbstractProbeAnnotation extends AbstractCaArrayEntity implements Serializable

Class gov.nih.nci.caarray.domain.array.Accession extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

databaseName

java.lang.String databaseName

accessionNumber

java.lang.String accessionNumber

Class gov.nih.nci.caarray.domain.array.Array extends AbstractCaArrayEntity implements Serializable

serialVersionUID: 1234567890L

Serialized Fields

batch

java.lang.String batch

serialNumber

java.lang.String serialNumber

production

ProtocolApplication production

design

ArrayDesign design

arrayGroup

ArrayGroup arrayGroup

Class gov.nih.nci.caarray.domain.array.ArrayDesign extends AbstractCaArrayEntity implements Serializable

serialVersionUID: 1234567890L

Serialized Fields

name

java.lang.String name

description

java.lang.String description

assayTypes

java.util.SortedSet<E> assayTypes

printing

ProtocolApplication printing

polymerType

Term polymerType

numberOfFeatures

java.lang.Integer numberOfFeatures

substrateType

Term substrateType

surfaceType

Term surfaceType

technologyType

Term technologyType

organism

Organism organism

version

java.lang.String version

annotationFile

CaArrayFile annotationFile

designFiles

java.util.Set<E> designFiles

provider

Organization provider

designDetails

ArrayDesignDetails designDetails

geoAccession

java.lang.String geoAccession

Class gov.nih.nci.caarray.domain.array.ArrayDesignDetails extends AbstractCaArrayObject implements Serializable

serialVersionUID: -4810002388725364910L

Serialized Fields

features

java.util.Set<E> features

probeGroups

java.util.Set<E> probeGroups

probes

java.util.Set<E> probes

logicalProbes

java.util.Set<E> logicalProbes

Class gov.nih.nci.caarray.domain.array.ArrayGroup extends AbstractCaArrayObject implements Serializable

serialVersionUID: 697901960168637674L

Serialized Fields

name

java.lang.String name

arrays

java.util.Set<E> arrays

Class gov.nih.nci.caarray.domain.array.ExonProbeAnnotation extends AbstractProbeAnnotation implements Serializable

serialVersionUID: 1L

Serialized Fields

start

java.lang.Long start

stop

java.lang.Long stop

strand

java.lang.String strand

uniprotId

java.lang.String uniprotId

exonArrayReporter

ExonArrayReporter exonArrayReporter

gene

Gene gene

Class gov.nih.nci.caarray.domain.array.ExpressionProbeAnnotation extends AbstractProbeAnnotation implements Serializable

serialVersionUID: 1L

Serialized Fields

gene

Gene gene

expressionArrayReporter

ExpressionArrayReporter expressionArrayReporter

chromosomeName

java.lang.String chromosomeName

chromosomeStartPosition

java.lang.Long chromosomeStartPosition

chromosomeEndPosition

java.lang.Long chromosomeEndPosition

Class gov.nih.nci.caarray.domain.array.Feature extends AbstractDesignElement implements Serializable

serialVersionUID: -6319120292398781186L

Serialized Fields

blockColumn

short blockColumn

blockRow

short blockRow

column

short column

row

short row

featureNumber

java.lang.Integer featureNumber

x_Coordinate

java.lang.Double x_Coordinate

y_Coordinate

java.lang.Double y_Coordinate

coordinateUnits

Term coordinateUnits

arrayDesignDetails

ArrayDesignDetails arrayDesignDetails

Class gov.nih.nci.caarray.domain.array.Gene extends AbstractCaArrayEntity implements Serializable

serialVersionUID: 1L

Serialized Fields

fullName

java.lang.String fullName

symbol

java.lang.String symbol

genbankAccession

java.lang.String genbankAccession

genbankAccessionVersion

java.lang.String genbankAccessionVersion

ensemblgeneID

java.lang.String ensemblgeneID

unigeneclusterID

java.lang.String unigeneclusterID

entrezgeneID

java.lang.String entrezgeneID

refseqAccession

java.lang.String refseqAccession

thcAccession

java.lang.String thcAccession

additonalAccessions

java.util.Set<E> additonalAccessions

Class gov.nih.nci.caarray.domain.array.LogicalProbe extends AbstractProbe implements Serializable

serialVersionUID: 4406463229622624441L

Serialized Fields

probes

java.util.Set<E> probes

arrayDesignDetails

ArrayDesignDetails arrayDesignDetails

Class gov.nih.nci.caarray.domain.array.MiRNAProbeAnnotation extends AbstractProbeAnnotation implements Serializable

serialVersionUID: 1L

Serialized Fields

accessions

java.util.Set<E> accessions

Class gov.nih.nci.caarray.domain.array.PhysicalProbe extends AbstractProbe implements Serializable

serialVersionUID: -7343503650075935784L

Serialized Fields

probeGroup

ProbeGroup probeGroup

features

java.util.Set<E> features

arrayDesignDetails

ArrayDesignDetails arrayDesignDetails

controlType

Term controlType

Class gov.nih.nci.caarray.domain.array.ProbeGroup extends AbstractCaArrayEntity implements Serializable

serialVersionUID: -7001732731586530134L

Serialized Fields

probes

java.util.Set<E> probes

name

java.lang.String name

arrayDesignDetails

ArrayDesignDetails arrayDesignDetails

Class gov.nih.nci.caarray.domain.array.SNPProbeAnnotation extends AbstractProbeAnnotation implements Serializable

serialVersionUID: 1L

Serialized Fields

dbSNPId

java.lang.String dbSNPId

dbSNPVersion

java.lang.Integer dbSNPVersion

alleleA

java.lang.String alleleA

alleleB

java.lang.String alleleB

chromosome

java.lang.Integer chromosome

physicalPosition

java.lang.Long physicalPosition

flank

java.lang.String flank

snpArrayReporter

SNPArrayReporter snpArrayReporter

Package gov.nih.nci.caarray.domain.contact

Class gov.nih.nci.caarray.domain.contact.AbstractContact extends AbstractCaArrayEntity implements Serializable

serialVersionUID: 1234567890L

Serialized Fields

email

java.lang.String email

fax

java.lang.String fax

phone

java.lang.String phone

url

java.lang.String url

address

Address address

Class gov.nih.nci.caarray.domain.contact.Address extends AbstractCaArrayEntity implements Serializable

serialVersionUID: 1234567890L

Serialized Fields

street1

java.lang.String street1

street2

java.lang.String street2

city

java.lang.String city

state

java.lang.String state

zipCode

java.lang.String zipCode

Class gov.nih.nci.caarray.domain.contact.Organization extends AbstractContact implements Serializable

serialVersionUID: 1234567890L

Serialized Fields

name

java.lang.String name

provider

boolean provider

Class gov.nih.nci.caarray.domain.contact.Person extends AbstractContact implements Serializable

serialVersionUID: 1234567890L

Serialized Fields

firstName

java.lang.String firstName

middleInitials

java.lang.String middleInitials

lastName

java.lang.String lastName

affiliations

java.util.Set<E> affiliations

Package gov.nih.nci.caarray.domain.country

Class gov.nih.nci.caarray.domain.country.Country extends AbstractCaArrayEntity implements Serializable

serialVersionUID: 3434506314749437341L

Serialized Fields

code

java.lang.String code

name

java.lang.String name

printableName

java.lang.String printableName

iso3

java.lang.String iso3

numcode

java.lang.String numcode

Package gov.nih.nci.caarray.domain.data

Class gov.nih.nci.caarray.domain.data.AbstractArrayData extends AbstractCaArrayEntity implements Serializable

serialVersionUID: 1234567890L

Serialized Fields

name

java.lang.String name

dataFile

CaArrayFile dataFile

type

ArrayDataType type

protocolApplications

java.util.Set<E> protocolApplications

dataSet

DataSet dataSet

hybridizations

java.util.Set<E> hybridizations

Class gov.nih.nci.caarray.domain.data.AbstractDataColumn extends AbstractCaArrayObject implements Serializable

serialVersionUID: 1L

Serialized Fields

hybridizationData

HybridizationData hybridizationData

quantitationType

QuantitationType quantitationType

dataHandle

java.net.URI dataHandle

Class gov.nih.nci.caarray.domain.data.ArrayDataType extends AbstractCaArrayObject implements Serializable

serialVersionUID: -192577620722459309L

Serialized Fields

name

java.lang.String name

version

java.lang.String version

quantitationTypes

java.util.Set<E> quantitationTypes

Class gov.nih.nci.caarray.domain.data.BooleanColumn extends AbstractDataColumn implements Serializable

serialVersionUID: 1L

Serialized Fields

values

boolean[] values

Class gov.nih.nci.caarray.domain.data.DataRetrievalRequest extends java.lang.Object implements Serializable

serialVersionUID: 408918013610243473L

Serialized Fields

id

java.lang.Long id

designElements

java.util.List<E> designElements

hybridizations

java.util.List<E> hybridizations

quantitationTypes

java.util.List<E> quantitationTypes

Class gov.nih.nci.caarray.domain.data.DataSet extends AbstractCaArrayObject implements Serializable

serialVersionUID: 4430513886275629776L

Serialized Fields

arrayData

AbstractArrayData arrayData

hybridizationDataList

java.util.List<E> hybridizationDataList

quantitationTypes

java.util.List<E> quantitationTypes

designElementList

DesignElementList designElementList

Class gov.nih.nci.caarray.domain.data.DerivedArrayData extends AbstractArrayData implements Serializable

serialVersionUID: 1234567890L

Serialized Fields

derivedFromArrayDataCollection

java.util.Set<E> derivedFromArrayDataCollection

Class gov.nih.nci.caarray.domain.data.DesignElementList extends AbstractCaArrayEntity implements Serializable

serialVersionUID: 4430513886275629776L

Serialized Fields

designElementReferences

java.util.List<E> designElementReferences

designElements

java.util.List<E> designElements

designElementType

java.lang.String designElementType

Class gov.nih.nci.caarray.domain.data.DesignElementReference extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

designElement

AbstractDesignElement designElement

index

int index

designElementList

DesignElementList designElementList

id

java.lang.Long id

Class gov.nih.nci.caarray.domain.data.DoubleColumn extends AbstractDataColumn implements Serializable

serialVersionUID: 1L

Serialized Fields

values

double[] values

Class gov.nih.nci.caarray.domain.data.FloatColumn extends AbstractDataColumn implements Serializable

serialVersionUID: 1L

Serialized Fields

values

float[] values

Class gov.nih.nci.caarray.domain.data.HybridizationData extends AbstractCaArrayObject implements Serializable

serialVersionUID: 8804648118447372387L

Serialized Fields

dataSet

DataSet dataSet

hybridization

Hybridization hybridization

labeledExtract

LabeledExtract labeledExtract

columns

java.util.List<E> columns

Class gov.nih.nci.caarray.domain.data.Image extends AbstractCaArrayEntity implements Serializable

serialVersionUID: 1234567890L

Serialized Fields

name

java.lang.String name

protocolApplications

java.util.Set<E> protocolApplications

imageFile

CaArrayFile imageFile

hybridization

Hybridization hybridization

rawArrayData

RawArrayData rawArrayData

Class gov.nih.nci.caarray.domain.data.IntegerColumn extends AbstractDataColumn implements Serializable

serialVersionUID: 1L

Serialized Fields

values

int[] values

Class gov.nih.nci.caarray.domain.data.LongColumn extends AbstractDataColumn implements Serializable

serialVersionUID: 1L

Serialized Fields

values

long[] values

Class gov.nih.nci.caarray.domain.data.QuantitationType extends AbstractCaArrayObject implements Serializable

serialVersionUID: 7207891070185665511L

Serialized Fields

name

java.lang.String name

type

java.lang.String type

arrayDataTypes

java.util.Set<E> arrayDataTypes

Class gov.nih.nci.caarray.domain.data.RawArrayData extends AbstractArrayData implements Serializable

serialVersionUID: 1234567890L

Serialized Fields

sourceImages

java.util.Set<E> sourceImages

Class gov.nih.nci.caarray.domain.data.ShortColumn extends AbstractDataColumn implements Serializable

serialVersionUID: 1L

Serialized Fields

values

short[] values

Class gov.nih.nci.caarray.domain.data.StringColumn extends AbstractDataColumn implements Serializable

serialVersionUID: 1L

Serialized Fields

values

java.lang.String[] values

Package gov.nih.nci.caarray.domain.file

Class gov.nih.nci.caarray.domain.file.CaArrayFile extends AbstractCaArrayEntity implements Serializable

serialVersionUID: 1234567890L

Serialized Fields

name

java.lang.String name

type

java.lang.String type

status

java.lang.String status

project

Project project

validationResult

gov.nih.nci.caarray.validation.FileValidationResult validationResult

uncompressedSize

long uncompressedSize

compressedSize

long compressedSize

partialSize

long partialSize

dataHandle

java.net.URI dataHandle

parent

CaArrayFile parent

children

java.util.Set<E> children

uniqueNameProject

java.lang.Boolean uniqueNameProject

Class gov.nih.nci.caarray.domain.file.CaArrayFileSet extends java.lang.Object implements Serializable

serialVersionUID: -831461553674445009L

Serialized Fields

files

java.util.Set<E> files

projectId

java.lang.Long projectId

Package gov.nih.nci.caarray.domain.hybridization

Class gov.nih.nci.caarray.domain.hybridization.Hybridization extends AbstractExperimentDesignNode implements Serializable

serialVersionUID: 1234567890L

Serialized Fields

name

java.lang.String name

description

java.lang.String description

amountOfMaterial

float amountOfMaterial

amountOfMaterialUnit

Term amountOfMaterialUnit

rawDataCollection

java.util.Set<E> rawDataCollection

array

Array array

images

java.util.Set<E> images

derivedDataCollection

java.util.Set<E> derivedDataCollection

protocolApplications

java.util.List<E> protocolApplications

labeledExtract

java.util.Set<E> labeledExtract

factorValues

java.util.Set<E> factorValues

experiment

Experiment experiment

hybridizationData

java.util.Set<E> hybridizationData

Package gov.nih.nci.caarray.domain.permissions

Class gov.nih.nci.caarray.domain.permissions.AccessProfile extends java.lang.Object implements Serializable

serialVersionUID: -7994016784349522735L

Serialized Fields

id

java.lang.Long id

securityLevel

SecurityLevel securityLevel

sampleSecurityLevels

java.util.Map<K,V> sampleSecurityLevels

projectForPublicProfile

Project projectForPublicProfile

projectForGroupProfile

Project projectForGroupProfile

group

CollaboratorGroup group

Class gov.nih.nci.caarray.domain.permissions.CollaboratorGroup extends java.lang.Object implements Serializable

serialVersionUID: -7566813289284832301L

Serialized Fields

id

java.lang.Long id

group

gov.nih.nci.security.authorization.domainobjects.Group group

owner

gov.nih.nci.security.authorization.domainobjects.User owner

accessProfiles

java.util.Set<E> accessProfiles

Package gov.nih.nci.caarray.domain.project

Class gov.nih.nci.caarray.domain.project.AbstractExperimentDesignNode extends AbstractCaArrayEntity implements Serializable

serialVersionUID: 1L

Class gov.nih.nci.caarray.domain.project.AbstractFactorValue extends AbstractUnitableValue implements Serializable

serialVersionUID: 1234567890L

Serialized Fields

factor

Factor factor

hybridization

Hybridization hybridization

unit

Term unit

Class gov.nih.nci.caarray.domain.project.AssayType extends AbstractCaArrayEntity implements Serializable

serialVersionUID: 68829322193456517L

Serialized Fields

name

java.lang.String name

Class gov.nih.nci.caarray.domain.project.Experiment extends AbstractCaArrayEntity implements Serializable

serialVersionUID: 1234567890L

Serialized Fields

title

java.lang.String title

description

java.lang.String description

date

java.util.Date date

publicReleaseDate

java.util.Date publicReleaseDate

assayTypes

java.util.SortedSet<E> assayTypes

manufacturer

Organization manufacturer

organism

Organism organism

factors

java.util.Set<E> factors

experimentContacts

java.util.List<E> experimentContacts

experimentDesignTypes

java.util.Set<E> experimentDesignTypes

designDescription

java.lang.String designDescription

qualityControlDescription

java.lang.String qualityControlDescription

qualityControlTypes

java.util.Set<E> qualityControlTypes

replicateDescription

java.lang.String replicateDescription

replicateTypes

java.util.Set<E> replicateTypes

normalizationTypes

java.util.Set<E> normalizationTypes

publications

java.util.Set<E> publications

arrayDesigns

java.util.Set<E> arrayDesigns

biomaterials

java.util.Set<E> biomaterials

sources

java.util.Set<E> sources

samples

java.util.Set<E> samples

extracts

java.util.Set<E> extracts

labeledExtracts

java.util.Set<E> labeledExtracts

hybridizations

java.util.Set<E> hybridizations

publicIdentifier

java.lang.String publicIdentifier

project

Project project

lastDataModificationDate

java.util.Date lastDataModificationDate

Class gov.nih.nci.caarray.domain.project.ExperimentContact extends AbstractCaArrayEntity implements Serializable

serialVersionUID: 1234567890L

Serialized Fields

contact

Person contact

roles

java.util.Set<E> roles

experiment

Experiment experiment

Class gov.nih.nci.caarray.domain.project.Factor extends AbstractCaArrayEntity implements Serializable

serialVersionUID: 1234567890L

Serialized Fields

name

java.lang.String name

description

java.lang.String description

type

Term type

factorValues

java.util.Set<E> factorValues

experiment

Experiment experiment

Class gov.nih.nci.caarray.domain.project.MeasurementFactorValue extends AbstractFactorValue implements Serializable

serialVersionUID: 1L

Serialized Fields

value

java.lang.Float value

Class gov.nih.nci.caarray.domain.project.Project extends AbstractCaArrayEntity implements Serializable

serialVersionUID: 1234567890L

Serialized Fields

locked

boolean locked

experiment

Experiment experiment

files

java.util.SortedSet<E> files

importedFiles

java.util.SortedSet<E> importedFiles

importingFiles

java.util.SortedSet<E> importingFiles

supplementalFiles

java.util.SortedSet<E> supplementalFiles

unImportedFiles

java.util.SortedSet<E> unImportedFiles

publicProfile

AccessProfile publicProfile

groupProfiles

java.util.Map<K,V> groupProfiles

lastUpdated

java.util.Date lastUpdated

importDescription

java.lang.String importDescription

Class gov.nih.nci.caarray.domain.project.TermBasedFactorValue extends AbstractFactorValue implements Serializable

serialVersionUID: 1L

Serialized Fields

term

Term term

Class gov.nih.nci.caarray.domain.project.UserDefinedFactorValue extends AbstractFactorValue implements Serializable

serialVersionUID: 1L

Serialized Fields

value

java.lang.String value

Package gov.nih.nci.caarray.domain.protocol

Class gov.nih.nci.caarray.domain.protocol.AbstractParameterValue extends AbstractUnitableValue implements Serializable

serialVersionUID: 1234567890L

Serialized Fields

parameter

Parameter parameter

protocolApplication

ProtocolApplication protocolApplication

unit

Term unit

Class gov.nih.nci.caarray.domain.protocol.MeasurementParameterValue extends AbstractParameterValue implements Serializable

serialVersionUID: 1L

Serialized Fields

value

java.lang.Float value

Class gov.nih.nci.caarray.domain.protocol.Parameter extends AbstractCaArrayEntity implements Serializable

serialVersionUID: 1234567890L

Serialized Fields

name

java.lang.String name

defaultValue

AbstractParameterValue defaultValue

protocol

Protocol protocol

Class gov.nih.nci.caarray.domain.protocol.Protocol extends AbstractCaArrayEntity implements Serializable

serialVersionUID: 1234567890L

Serialized Fields

contact

java.lang.String contact

description

java.lang.String description

hardware

java.lang.String hardware

name

java.lang.String name

software

java.lang.String software

type

Term type

source

TermSource source

url

java.lang.String url

parameters

java.util.Set<E> parameters

Class gov.nih.nci.caarray.domain.protocol.ProtocolApplication extends AbstractCaArrayEntity implements Serializable

serialVersionUID: 1234567890L

Serialized Fields

protocol

Protocol protocol

notes

java.lang.String notes

values

java.util.Set<E> values

Class gov.nih.nci.caarray.domain.protocol.TermBasedParameterValue extends AbstractParameterValue implements Serializable

serialVersionUID: 1L

Serialized Fields

term

Term term

Class gov.nih.nci.caarray.domain.protocol.UserDefinedParameterValue extends AbstractParameterValue implements Serializable

serialVersionUID: 1L

Serialized Fields

value

java.lang.String value

Package gov.nih.nci.caarray.domain.publication

Class gov.nih.nci.caarray.domain.publication.Publication extends AbstractCaArrayEntity implements Serializable

serialVersionUID: 1234567890L

Serialized Fields

authors

java.lang.String authors

doi

java.lang.String doi

editor

java.lang.String editor

issue

java.lang.String issue

pages

java.lang.String pages

publisher

java.lang.String publisher

pubMedId

java.lang.String pubMedId

title

java.lang.String title

uri

java.lang.String uri

volume

java.lang.String volume

year

java.lang.String year

status

Term status

type

Term type

publication

java.lang.String publication

Package gov.nih.nci.caarray.domain.register

Class gov.nih.nci.caarray.domain.register.RegistrationRequest extends java.lang.Object implements Serializable

serialVersionUID: -9198769730580475043L

Serialized Fields

loginName

java.lang.String loginName

firstName

java.lang.String firstName

middleInitial

java.lang.String middleInitial

lastName

java.lang.String lastName

email

java.lang.String email

phone

java.lang.String phone

fax

java.lang.String fax

organization

java.lang.String organization

address1

java.lang.String address1

address2

java.lang.String address2

city

java.lang.String city

state

State state

province

java.lang.String province

country

Country country

zip

java.lang.String zip

role

java.lang.String role

id

java.lang.Long id

Package gov.nih.nci.caarray.domain.sample

Class gov.nih.nci.caarray.domain.sample.AbstractBioMaterial extends AbstractExperimentDesignNode implements Serializable

serialVersionUID: 1234567890L

Serialized Fields

tissueSite

Term tissueSite

materialType

Term materialType

cellType

Term cellType

diseaseState

Term diseaseState

name

java.lang.String name

description

java.lang.String description

externalId

java.lang.String externalId

characteristics

java.util.Set<E> characteristics

protocolApplications

java.util.List<E> protocolApplications

organism

Organism organism

experiment

Experiment experiment

lastModifiedDataTime

java.util.Date lastModifiedDataTime

Class gov.nih.nci.caarray.domain.sample.AbstractCharacteristic extends AbstractUnitableValue implements Serializable

serialVersionUID: 1L

Serialized Fields

bioMaterial

AbstractBioMaterial bioMaterial

category

Category category

unit

Term unit

Class gov.nih.nci.caarray.domain.sample.Extract extends AbstractBioMaterial implements Serializable

serialVersionUID: 1234567890L

Serialized Fields

samples

java.util.Set<E> samples

labeledExtracts

java.util.Set<E> labeledExtracts

Class gov.nih.nci.caarray.domain.sample.LabeledExtract extends AbstractBioMaterial implements Serializable

serialVersionUID: 1234567890L

Serialized Fields

label

Term label

extracts

java.util.Set<E> extracts

hybridizations

java.util.Set<E> hybridizations

Class gov.nih.nci.caarray.domain.sample.MeasurementCharacteristic extends AbstractCharacteristic implements Serializable

serialVersionUID: 1L

Serialized Fields

value

java.lang.Float value

Class gov.nih.nci.caarray.domain.sample.Sample extends AbstractBioMaterial implements Serializable

serialVersionUID: 1234567890L

Serialized Fields

sources

java.util.Set<E> sources

extracts

java.util.Set<E> extracts

Class gov.nih.nci.caarray.domain.sample.Source extends AbstractBioMaterial implements Serializable

serialVersionUID: 1234567890L

Serialized Fields

samples

java.util.Set<E> samples

providers

java.util.Set<E> providers

Class gov.nih.nci.caarray.domain.sample.TermBasedCharacteristic extends AbstractCharacteristic implements Serializable

serialVersionUID: 1L

Serialized Fields

term

Term term

Class gov.nih.nci.caarray.domain.sample.UserDefinedCharacteristic extends AbstractCharacteristic implements Serializable

serialVersionUID: 1L

Serialized Fields

value

java.lang.String value

Package gov.nih.nci.caarray.domain.state

Class gov.nih.nci.caarray.domain.state.State extends AbstractCaArrayEntity implements Serializable

serialVersionUID: 5622159437616247967L

Serialized Fields

code

java.lang.String code

name

java.lang.String name

Package gov.nih.nci.caarray.domain.vocabulary

Class gov.nih.nci.caarray.domain.vocabulary.Category extends AbstractCaArrayEntity implements Serializable

serialVersionUID: 1234567890L

Serialized Fields

name

java.lang.String name

accession

java.lang.String accession

url

java.lang.String url

source

TermSource source

parents

java.util.Set<E> parents

children

java.util.Set<E> children

Class gov.nih.nci.caarray.domain.vocabulary.Term extends AbstractCaArrayEntity implements Serializable

serialVersionUID: 1234567890L

Serialized Fields

value

java.lang.String value

accession

java.lang.String accession

url

java.lang.String url

description

java.lang.String description

categories

java.util.Set<E> categories

source

TermSource source

Class gov.nih.nci.caarray.domain.vocabulary.TermSource extends AbstractCaArrayEntity implements Serializable

serialVersionUID: 1234567890L

Serialized Fields

name

java.lang.String name

url

java.lang.String url

version

java.lang.String version

Package gov.nih.nci.caarray.services

Class gov.nih.nci.caarray.services.EntityPruner.MaxCollectionSizeExceeededException extends java.lang.Exception implements Serializable

serialVersionUID: 1L

Class gov.nih.nci.caarray.services.ServerConnectionException extends java.lang.Exception implements Serializable

serialVersionUID: 4865588860956168307L


Package gov.nih.nci.caarray.services.external.v1_0

Class gov.nih.nci.caarray.services.external.v1_0.ApiException extends java.lang.Exception implements Serializable

serialVersionUID: 1L

Class gov.nih.nci.caarray.services.external.v1_0.IncorrectEntityTypeException extends gov.nih.nci.caarray.services.external.v1_0.InvalidReferenceException implements Serializable

serialVersionUID: 1L

Class gov.nih.nci.caarray.services.external.v1_0.InvalidInputException extends gov.nih.nci.caarray.services.external.v1_0.ApiException implements Serializable

serialVersionUID: 1L

Class gov.nih.nci.caarray.services.external.v1_0.InvalidReferenceException extends gov.nih.nci.caarray.services.external.v1_0.InvalidInputException implements Serializable

serialVersionUID: 1L

Serialized Fields

reference

gov.nih.nci.caarray.external.v1_0.CaArrayEntityReference reference

Class gov.nih.nci.caarray.services.external.v1_0.NoEntityMatchingReferenceException extends gov.nih.nci.caarray.services.external.v1_0.InvalidReferenceException implements Serializable

serialVersionUID: 1L

Class gov.nih.nci.caarray.services.external.v1_0.UnsupportedCategoryException extends gov.nih.nci.caarray.services.external.v1_0.InvalidInputException implements Serializable

serialVersionUID: 1L

Serialized Fields

category

gov.nih.nci.caarray.external.v1_0.CaArrayEntityReference category

Package gov.nih.nci.caarray.util

Class gov.nih.nci.caarray.util.CaArrayAuditLogInterceptor extends com.fiveamsolutions.nci.commons.audit.AuditLogInterceptor implements Serializable

serialVersionUID: 1L

Serialized Fields

hibernateHelper

com.fiveamsolutions.nci.commons.util.HibernateHelper hibernateHelper

processor

com.fiveamsolutions.nci.commons.audit.DefaultProcessor processor

dialect

org.hibernate.dialect.Dialect dialect
For getting sequence numbers.


idGenerator

gov.nih.nci.caarray.util.CaArrayAuditLogInterceptor.TxIdGenerator idGenerator

Class gov.nih.nci.caarray.util.LabelValue extends java.lang.Object implements Serializable

serialVersionUID: 3689355407466181430L

Serialized Fields

label

java.lang.String label
The property which supplies the option label visible to the end user.


value

java.lang.String value
The property which supplies the value returned to the server.

Class gov.nih.nci.caarray.util.NamingStrategy extends org.hibernate.cfg.ImprovedNamingStrategy implements Serializable

serialVersionUID: -2556633166307295370L


Package gov.nih.nci.caarray.util.owlparser

Class gov.nih.nci.caarray.util.owlparser.ParseException extends java.lang.Exception implements Serializable

serialVersionUID: 1L


Package gov.nih.nci.cabio.domain

Class gov.nih.nci.cabio.domain.ArrayReporter extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

id

java.lang.Long id

name

java.lang.String name

bigid

java.lang.String bigid

Class gov.nih.nci.cabio.domain.ExonArrayReporter extends TranscriptArrayReporter implements Serializable

serialVersionUID: 1L

Serialized Fields

probeSelectionRegionId

java.lang.Long probeSelectionRegionId

probeCount

java.lang.Long probeCount

strand

java.lang.String strand

Class gov.nih.nci.cabio.domain.ExpressionArrayReporter extends TranscriptArrayReporter implements Serializable

serialVersionUID: 1L

Serialized Fields

sequenceSource

java.lang.String sequenceSource

sequenceType

java.lang.String sequenceType

targetDescription

java.lang.String targetDescription

targetId

java.lang.String targetId

Class gov.nih.nci.cabio.domain.SNPArrayReporter extends ArrayReporter implements Serializable

serialVersionUID: 1L

Serialized Fields

phastConservation

java.lang.String phastConservation

Class gov.nih.nci.cabio.domain.TranscriptArrayReporter extends ArrayReporter implements Serializable

serialVersionUID: 1L


Package gov.nih.nci.cagrid.caarray.service.globus

Class gov.nih.nci.cagrid.caarray.service.globus.CaArraySvcAuthorization extends java.lang.Object implements Serializable


Package gov.nih.nci.cagrid.caarray.util

Class gov.nih.nci.cagrid.caarray.util.CaArrayDeserializer extends gov.nih.nci.cagrid.encoding.SDKDeserializer implements Serializable

Class gov.nih.nci.cagrid.caarray.util.CaArraySerializer extends gov.nih.nci.cagrid.encoding.SDKSerializer implements Serializable

Class gov.nih.nci.cagrid.caarray.util.DeserializationFactory extends org.apache.axis.encoding.ser.BaseDeserializerFactory implements Serializable

Class gov.nih.nci.cagrid.caarray.util.SerializationFactory extends org.apache.axis.encoding.ser.BaseSerializerFactory implements Serializable