Serialized Form


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

Class gov.nih.nci.caarray.external.v1_0.AbstractCaArrayEntity extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

id

java.lang.String id

Class gov.nih.nci.caarray.external.v1_0.CaArrayEntityReference extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

id

java.lang.String id

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

Class gov.nih.nci.caarray.external.v1_0.array.ArrayDesign extends AbstractCaArrayEntity implements Serializable

serialVersionUID: 1L

Serialized Fields

name

java.lang.String name

lsid

java.lang.String lsid

version

java.lang.String version

arrayProvider

ArrayProvider arrayProvider

technologyType

Term technologyType

organism

Organism organism

assayTypes

java.util.Set<E> assayTypes

files

java.util.Set<E> files

Class gov.nih.nci.caarray.external.v1_0.array.ArrayProvider extends AbstractCaArrayEntity implements Serializable

serialVersionUID: 1L

Serialized Fields

name

java.lang.String name

Class gov.nih.nci.caarray.external.v1_0.array.AssayType extends AbstractCaArrayEntity implements Serializable

serialVersionUID: 1L

Serialized Fields

name

java.lang.String name

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

Class gov.nih.nci.caarray.external.v1_0.data.AbstractDataColumn extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialization Methods

readExternal

public void readExternal(java.io.ObjectInput oi)
                  throws java.io.IOException,
                         java.lang.ClassNotFoundException
Optimizes the serialized form of this class by compressing the values array.

Throws:
java.io.IOException
java.lang.ClassNotFoundException

writeExternal

public void writeExternal(java.io.ObjectOutput oo)
                   throws java.io.IOException
Optimizes the serialized form of this class by compressing the values array.

Throws:
java.io.IOException

Class gov.nih.nci.caarray.external.v1_0.data.ArrayDataType extends AbstractCaArrayEntity implements Serializable

serialVersionUID: 1L

Serialized Fields

name

java.lang.String name

version

java.lang.String version

quantitationTypes

java.util.Set<E> quantitationTypes

Class gov.nih.nci.caarray.external.v1_0.data.BooleanColumn extends AbstractDataColumn implements Serializable

serialVersionUID: 1L

Serialization Methods

readExternal

public void readExternal(java.io.ObjectInput oi)
                  throws java.io.IOException,
                         java.lang.ClassNotFoundException
Optimizes the serialized form of this class by compressing the values array.

Throws:
java.io.IOException
java.lang.ClassNotFoundException

writeExternal

public void writeExternal(java.io.ObjectOutput oo)
                   throws java.io.IOException
Optimizes the serialized form of this class by compressing the values array.

Throws:
java.io.IOException

Class gov.nih.nci.caarray.external.v1_0.data.DataSet extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

designElements

java.util.List<E> designElements

datas

java.util.List<E> datas

quantitationTypes

java.util.List<E> quantitationTypes

Class gov.nih.nci.caarray.external.v1_0.data.DesignElement extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

name

java.lang.String name

Class gov.nih.nci.caarray.external.v1_0.data.DoubleColumn extends AbstractDataColumn implements Serializable

serialVersionUID: 1L

Serialization Methods

readExternal

public void readExternal(java.io.ObjectInput oi)
                  throws java.io.IOException,
                         java.lang.ClassNotFoundException
Optimizes the serialized form of this class by compressing the values array.

Throws:
java.io.IOException
java.lang.ClassNotFoundException

writeExternal

public void writeExternal(java.io.ObjectOutput oo)
                   throws java.io.IOException
Optimizes the serialized form of this class by compressing the values array.

Throws:
java.io.IOException

Class gov.nih.nci.caarray.external.v1_0.data.File extends AbstractCaArrayEntity implements Serializable

serialVersionUID: 1L

Serialized Fields

metadata

FileMetadata metadata

Class gov.nih.nci.caarray.external.v1_0.data.FileContents extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

metadata

FileMetadata metadata

contents

byte[] contents

compressed

boolean compressed

Class gov.nih.nci.caarray.external.v1_0.data.FileMetadata extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

compressedSize

long compressedSize

uncompressedSize

long uncompressedSize

name

java.lang.String name

fileType

FileType fileType

Class gov.nih.nci.caarray.external.v1_0.data.FileStreamableContents extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

metadata

FileMetadata metadata

contentStream

com.healthmarketscience.rmiio.RemoteInputStream contentStream

compressed

boolean compressed

Class gov.nih.nci.caarray.external.v1_0.data.FileType extends AbstractCaArrayEntity implements Serializable

serialVersionUID: 1L

Serialized Fields

name

java.lang.String name

Class gov.nih.nci.caarray.external.v1_0.data.FloatColumn extends AbstractDataColumn implements Serializable

serialVersionUID: 1L

Serialization Methods

readExternal

public void readExternal(java.io.ObjectInput oi)
                  throws java.io.IOException,
                         java.lang.ClassNotFoundException
Optimizes the serialized form of this class by compressing the values array.

Throws:
java.io.IOException
java.lang.ClassNotFoundException

writeExternal

public void writeExternal(java.io.ObjectOutput oo)
                   throws java.io.IOException
Optimizes the serialized form of this class by compressing the values array.

Throws:
java.io.IOException

Class gov.nih.nci.caarray.external.v1_0.data.HybridizationData extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

dataColumns

java.util.List<E> dataColumns

hybridization

Hybridization hybridization

Class gov.nih.nci.caarray.external.v1_0.data.IntegerColumn extends AbstractDataColumn implements Serializable

serialVersionUID: 1L

Serialization Methods

readExternal

public void readExternal(java.io.ObjectInput oi)
                  throws java.io.IOException,
                         java.lang.ClassNotFoundException
Optimizes the serialized form of this class by compressing the values array.

Throws:
java.io.IOException
java.lang.ClassNotFoundException

writeExternal

public void writeExternal(java.io.ObjectOutput oo)
                   throws java.io.IOException
Optimizes the serialized form of this class by compressing the values array.

Throws:
java.io.IOException

Class gov.nih.nci.caarray.external.v1_0.data.LongColumn extends AbstractDataColumn implements Serializable

serialVersionUID: 1L

Serialization Methods

readExternal

public void readExternal(java.io.ObjectInput oi)
                  throws java.io.IOException,
                         java.lang.ClassNotFoundException
Optimizes the serialized form of this class by compressing the values array.

Throws:
java.io.IOException
java.lang.ClassNotFoundException

writeExternal

public void writeExternal(java.io.ObjectOutput oo)
                   throws java.io.IOException
Optimizes the serialized form of this class by compressing the values array.

Throws:
java.io.IOException

Class gov.nih.nci.caarray.external.v1_0.data.MageTabFileSet extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

idf

FileContents idf

sdrf

FileContents sdrf

dataFiles

java.util.Set<E> dataFiles

Class gov.nih.nci.caarray.external.v1_0.data.QuantitationType extends AbstractCaArrayEntity implements Serializable

serialVersionUID: 1L

Serialized Fields

name

java.lang.String name

dataType

DataType dataType

Class gov.nih.nci.caarray.external.v1_0.data.ShortColumn extends AbstractDataColumn implements Serializable

serialVersionUID: 1L

Serialization Methods

readExternal

public void readExternal(java.io.ObjectInput oi)
                  throws java.io.IOException,
                         java.lang.ClassNotFoundException
Optimizes the serialized form of this class by compressing the values array.

Throws:
java.io.IOException
java.lang.ClassNotFoundException

writeExternal

public void writeExternal(java.io.ObjectOutput oo)
                   throws java.io.IOException
Optimizes the serialized form of this class by compressing the values array.

Throws:
java.io.IOException

Class gov.nih.nci.caarray.external.v1_0.data.StringColumn extends AbstractDataColumn implements Serializable

serialVersionUID: 1L

Serialization Methods

readExternal

public void readExternal(java.io.ObjectInput oi)
                  throws java.io.IOException,
                         java.lang.ClassNotFoundException
Optimizes the serialized form of this class by compressing the values array.

Throws:
java.io.IOException
java.lang.ClassNotFoundException

writeExternal

public void writeExternal(java.io.ObjectOutput oo)
                   throws java.io.IOException
Optimizes the serialized form of this class by compressing the values array.

Throws:
java.io.IOException

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

Class gov.nih.nci.caarray.external.v1_0.experiment.Experiment extends AbstractCaArrayEntity implements Serializable

serialVersionUID: 1L

Serialized Fields

publicIdentifier

java.lang.String publicIdentifier

title

java.lang.String title

description

java.lang.String description

organism

Organism organism

contacts

java.util.Set<E> contacts

experimentalDesigns

java.util.Set<E> experimentalDesigns

replicateTypes

java.util.Set<E> replicateTypes

normalizationTypes

java.util.Set<E> normalizationTypes

qualityControlTypes

java.util.Set<E> qualityControlTypes

arrayProvider

ArrayProvider arrayProvider

assayTypes

java.util.Set<E> assayTypes

factors

java.util.Set<E> factors

arrayDesigns

java.util.Set<E> arrayDesigns

lastDataModificationDate

java.util.Date lastDataModificationDate

Class gov.nih.nci.caarray.external.v1_0.experiment.ExperimentalContact extends AbstractCaArrayEntity implements Serializable

serialVersionUID: 1L

Serialized Fields

person

Person person

roles

java.util.Set<E> roles

Class gov.nih.nci.caarray.external.v1_0.experiment.Organism extends Term implements Serializable

serialVersionUID: 1L

Serialized Fields

commonName

java.lang.String commonName

scientificName

java.lang.String scientificName

Class gov.nih.nci.caarray.external.v1_0.experiment.Person extends AbstractCaArrayEntity implements Serializable

serialVersionUID: 1L

Serialized Fields

firstName

java.lang.String firstName

lastName

java.lang.String lastName

middleInitials

java.lang.String middleInitials

emailAddress

java.lang.String emailAddress

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

Class gov.nih.nci.caarray.external.v1_0.factor.Factor extends AbstractCaArrayEntity implements Serializable

serialVersionUID: 1L

Serialized Fields

name

java.lang.String name

description

java.lang.String description

type

Term type

Class gov.nih.nci.caarray.external.v1_0.factor.FactorValue extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

factor

Factor factor

value

AbstractValue value

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

Class gov.nih.nci.caarray.external.v1_0.query.AnnotationCriterion extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

value

java.lang.String value

category

CaArrayEntityReference category

Class gov.nih.nci.caarray.external.v1_0.query.AnnotationSetRequest extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

experimentGraphNodes

java.util.List<E> experimentGraphNodes

categories

java.util.List<E> categories

Class gov.nih.nci.caarray.external.v1_0.query.BiomaterialKeywordSearchCriteria extends KeywordSearchCriteria implements Serializable

serialVersionUID: 1L

Serialized Fields

types

java.util.Set<E> types

Class gov.nih.nci.caarray.external.v1_0.query.BiomaterialSearchCriteria extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

experiment

CaArrayEntityReference experiment

names

java.util.Set<E> names

externalIds

java.util.Set<E> externalIds

annotationCriterions

java.util.Set<E> annotationCriterions

types

java.util.Set<E> types

Class gov.nih.nci.caarray.external.v1_0.query.DataSetRequest extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

quantitationTypes

java.util.Set<E> quantitationTypes

dataFiles

java.util.Set<E> dataFiles

hybridizations

java.util.Set<E> hybridizations

Class gov.nih.nci.caarray.external.v1_0.query.ExampleSearchCriteria extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

example

AbstractCaArrayEntity example

matchMode

MatchMode matchMode

excludeNulls

boolean excludeNulls

excludeZeroes

boolean excludeZeroes

Class gov.nih.nci.caarray.external.v1_0.query.ExperimentSearchCriteria extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

title

java.lang.String title

publicIdentifier

java.lang.String publicIdentifier

organism

CaArrayEntityReference organism

arrayProvider

CaArrayEntityReference arrayProvider

assayType

CaArrayEntityReference assayType

principalInvestigators

java.util.Set<E> principalInvestigators

annotationCriterions

java.util.Set<E> annotationCriterions

Class gov.nih.nci.caarray.external.v1_0.query.FileSearchCriteria extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

experiment

CaArrayEntityReference experiment

extension

java.lang.String extension

types

java.util.Set<E> types

categories

java.util.Set<E> categories

experimentGraphNodes

java.util.Set<E> experimentGraphNodes

Class gov.nih.nci.caarray.external.v1_0.query.HybridizationSearchCriteria extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

experiment

CaArrayEntityReference experiment

names

java.util.Set<E> names

biomaterials

java.util.Set<E> biomaterials

Class gov.nih.nci.caarray.external.v1_0.query.KeywordSearchCriteria extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

keyword

java.lang.String keyword

Class gov.nih.nci.caarray.external.v1_0.query.LimitOffset extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

limit

int limit

offset

int offset

Class gov.nih.nci.caarray.external.v1_0.query.QuantitationTypeSearchCriteria extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

fileTypes

java.util.Set<E> fileTypes

fileCategories

java.util.Set<E> fileCategories

arrayDataTypes

java.util.Set<E> arrayDataTypes

hybridization

CaArrayEntityReference hybridization

Class gov.nih.nci.caarray.external.v1_0.query.SearchResult extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

results

java.util.List<E> results

maxAllowedResults

int maxAllowedResults

firstResultOffset

int firstResultOffset

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

Class gov.nih.nci.caarray.external.v1_0.sample.AbstractExperimentGraphNode extends AbstractCaArrayEntity implements Serializable

serialVersionUID: 1L

Serialized Fields

name

java.lang.String name

experiment

CaArrayEntityReference experiment

Class gov.nih.nci.caarray.external.v1_0.sample.AnnotationColumn extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

node

AbstractExperimentGraphNode node

valueSets

java.util.List<E> valueSets

Class gov.nih.nci.caarray.external.v1_0.sample.AnnotationSet extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

categories

java.util.List<E> categories

columns

java.util.List<E> columns

Class gov.nih.nci.caarray.external.v1_0.sample.AnnotationValueSet extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

values

java.util.Set<E> values

category

Category category

Class gov.nih.nci.caarray.external.v1_0.sample.Biomaterial extends AbstractExperimentGraphNode implements Serializable

serialVersionUID: 1L

Serialized Fields

description

java.lang.String description

externalId

java.lang.String externalId

diseaseState

TermValue diseaseState

tissueSite

TermValue tissueSite

materialType

TermValue materialType

cellType

TermValue cellType

organism

Organism organism

characteristics

java.util.Set<E> characteristics

type

BiomaterialType type

lastModifiedDataTime

java.util.Date lastModifiedDataTime

Class gov.nih.nci.caarray.external.v1_0.sample.Characteristic extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

category

Category category

value

AbstractValue value

Class gov.nih.nci.caarray.external.v1_0.sample.Hybridization extends AbstractExperimentGraphNode implements Serializable

serialVersionUID: 1L

Serialized Fields

factorValues

java.util.Set<E> factorValues

arrayDesign

ArrayDesign arrayDesign

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

Class gov.nih.nci.caarray.external.v1_0.value.AbstractValue extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

unit

Term unit

Class gov.nih.nci.caarray.external.v1_0.value.MeasurementValue extends AbstractValue implements Serializable

serialVersionUID: 1L

Serialized Fields

measurement

java.lang.Float measurement

Class gov.nih.nci.caarray.external.v1_0.value.TermValue extends AbstractValue implements Serializable

serialVersionUID: 1L

Serialized Fields

term

Term term

Class gov.nih.nci.caarray.external.v1_0.value.UserDefinedValue extends AbstractValue implements Serializable

serialVersionUID: 1L

Serialized Fields

value

java.lang.String value

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

Class gov.nih.nci.caarray.external.v1_0.vocabulary.Category extends AbstractCaArrayEntity implements Serializable

serialVersionUID: 1L

Serialized Fields

name

java.lang.String name

accession

java.lang.String accession

url

java.lang.String url

termSource

TermSource termSource

Class gov.nih.nci.caarray.external.v1_0.vocabulary.Term extends AbstractCaArrayEntity implements Serializable

serialVersionUID: 1L

Serialized Fields

accession

java.lang.String accession

url

java.lang.String url

termSource

TermSource termSource

value

java.lang.String value

Class gov.nih.nci.caarray.external.v1_0.vocabulary.TermSource extends AbstractCaArrayEntity implements Serializable

serialVersionUID: 1L

Serialized Fields

name

java.lang.String name

version

java.lang.String version

url

java.lang.String url

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 InvalidReferenceException implements Serializable

serialVersionUID: 1L

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

serialVersionUID: 1L

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

serialVersionUID: 1L

Serialized Fields

reference

CaArrayEntityReference reference

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

serialVersionUID: 1L

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

serialVersionUID: 1L

Serialized Fields

category

CaArrayEntityReference category

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

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

serialVersionUID: 1L

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

serialVersionUID: 1L


Package gov.nih.nci.caarray.services.external.v1_0.grid.service.globus

Class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.CaArraySvc_v1_0Authorization extends java.lang.Object implements Serializable

Serialized Fields

authorizationClassMap

java.util.Map<K,V> authorizationClassMap

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

Class gov.nih.nci.caarray.services.external.v1_0.search.SearchApiUtils.WrapperException extends java.lang.RuntimeException implements Serializable

serialVersionUID: 1L


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.cagrid.enumeration.service.globus

Class gov.nih.nci.cagrid.enumeration.service.globus.CaGridEnumerationAuthorization extends java.lang.Object implements Serializable

Serialized Fields

authorizationClassMap

java.util.Map<K,V> authorizationClassMap