Ensembl Datasource Aware Module v1.09
© Roslin Institute 2010. GNU General Public License, version3
Ensembl Datasource Aware Module
v1.09

Serialized Form


Package uk.ac.roslin.ensembl.datasourceaware

Class uk.ac.roslin.ensembl.datasourceaware.DAExternalDB extends DAObject implements Serializable

Serialized Fields

dBName

String dBName

dBDisplayName

String dBDisplayName

dBRelease

String dBRelease

dBStatus

String dBStatus

dBType

String dBType

Class uk.ac.roslin.ensembl.datasourceaware.DAObject extends Object implements Serializable

Serialized Fields

daoFactory

uk.ac.roslin.ensembl.dao.factory.DAOFactory daoFactory

schemaVersion

String schemaVersion

dbVersion

String dbVersion

registry

uk.ac.roslin.ensembl.model.database.Registry registry

id

Integer id

Class uk.ac.roslin.ensembl.datasourceaware.DAObject.DAComparator extends Object implements Serializable

Class uk.ac.roslin.ensembl.datasourceaware.DAXRef extends DAObject implements Serializable

Serialized Fields

dB

DAExternalDB dB

dBName

String dBName

version

String version

description

String description

infoType

String infoType

info

String info

displayID

String displayID

Package uk.ac.roslin.ensembl.datasourceaware.compara

Class uk.ac.roslin.ensembl.datasourceaware.compara.DAHomologyPairRelationship extends DAHomologyRelationship implements Serializable

Serialized Fields

source

DAGene source

target

DAGene target

sourceProperties

uk.ac.roslin.ensembl.model.compara.HomologyAlignmentProperties sourceProperties
Because a DAHomologyPairRelationship is tyeically instantiated from the compara databases - the target gene in particular is likely to not be a core-datasource aware object, and therefore species & and mapping details are only simple fields grabbed from compara: these are held in properties objects


targetProperties

uk.ac.roslin.ensembl.model.compara.HomologyAlignmentProperties targetProperties

Class uk.ac.roslin.ensembl.datasourceaware.compara.DAHomologyRelationship extends DAObject implements Serializable

Serialized Fields

type

uk.ac.roslin.ensembl.model.compara.HomologyType type

lastCommonAncestor

String lastCommonAncestor

members

TreeSet<E> members

Class uk.ac.roslin.ensembl.datasourceaware.compara.InverseHomologyPairRelationshipView extends DAHomologyPairRelationship implements Serializable

Serialized Fields

originalHPR

DAHomologyPairRelationship originalHPR

Package uk.ac.roslin.ensembl.datasourceaware.core

Class uk.ac.roslin.ensembl.datasourceaware.core.DAAnalysis extends DACoreObject implements Serializable

Class uk.ac.roslin.ensembl.datasourceaware.core.DAAssembledDNASequence extends DADNASequence implements Serializable

Serialized Fields

completeAssembly

DAAssembly completeAssembly

Class uk.ac.roslin.ensembl.datasourceaware.core.DAChromosome extends DAAssembledDNASequence implements Serializable

Class uk.ac.roslin.ensembl.datasourceaware.core.DACoordinateSystem extends Object implements Serializable

Serialized Fields

id

Integer id

speciesID

Integer speciesID

type

uk.ac.roslin.ensembl.config.EnsemblCoordSystemType type

rank

Integer rank

version

String version

defaultVersion

Boolean defaultVersion

sequenceLevel

Boolean sequenceLevel

Class uk.ac.roslin.ensembl.datasourceaware.core.DACoreObject extends DAObject implements Serializable

Serialized Fields

species

uk.ac.roslin.ensembl.model.core.Species species

comparaFactories

HashMap<K,V> comparaFactories

Class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence extends org.biojava3.core.sequence.DNASequence implements Serializable

Serialized Fields

daoFactory

uk.ac.roslin.ensembl.dao.factory.DAOFactory daoFactory

schemaVersion

String schemaVersion

dbVersion

String dbVersion

registry

uk.ac.roslin.ensembl.model.database.Registry registry

id

Integer id

seqRegionID

Integer seqRegionID

name

String name

dbSpeciesName

String dbSpeciesName

species

uk.ac.roslin.ensembl.model.core.Species species

DBSeqLength

Integer DBSeqLength

coordSystem

uk.ac.roslin.ensembl.model.core.CoordinateSystem coordSystem

mappings

uk.ac.roslin.ensembl.model.MappingSet mappings

mappedRegions

HashMap<K,V> mappedRegions

objectTypeMappings

HashMap<K,V> objectTypeMappings

comparaFactories

HashMap<K,V> comparaFactories

Class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader extends Object implements Serializable

Serialized Fields

sequence

String sequence

compoundSet

uk.ac.roslin.ensembl.biojava3.EnsemblDNACompoundSet compoundSet

dASequence

DADNASequence dASequence

coordSystemID

Integer coordSystemID

seqRegionID

Integer seqRegionID

length

Integer length

name

String name

factory

uk.ac.roslin.ensembl.dao.factory.DAOCoreFactory factory

parent

DADNASequence parent

cache

LinkedHashMap<K,V> cache

chunkSize

Integer chunkSize

usesCache

boolean usesCache

nonCacheLazyLoaded

boolean nonCacheLazyLoaded

chunks

Integer chunks

sequenceReader

org.biojava3.core.sequence.template.SequenceReader<C extends org.biojava3.core.sequence.template.Compound> sequenceReader

Class uk.ac.roslin.ensembl.datasourceaware.core.DAExon extends DAFeature implements Serializable

Serialized Fields

stableID

String stableID

transcript

DATranscript transcript

transcriptID

Integer transcriptID

rank

Integer rank

phase

int phase

endPhase

int endPhase

constitutive

Boolean constitutive

Class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature extends DACoreObject implements Serializable

Serialized Fields

mappings

uk.ac.roslin.ensembl.model.MappingSet mappings

objectTypeMappings

HashMap<K,V> objectTypeMappings

mappedObjectTypes

Set<E> mappedObjectTypes

creationDate

Date creationDate

modificationDate

Date modificationDate

description

String description

displayXRef

DAXRef displayXRef

xrefs

List<E> xrefs

displayName

String displayName

status

DAFeature.Status status

current

Boolean current

Class uk.ac.roslin.ensembl.datasourceaware.core.DAGene extends DAFeature implements Serializable

Serialized Fields

biotype

String biotype

analysis

DAAnalysis analysis

canonicalTranscriptID

Integer canonicalTranscriptID

stableID

String stableID

transcriptHash

TreeMap<K,V> transcriptHash

homologies

HashMap<K,V> homologies

homologySearchesPerformed

TreeSet<E> homologySearchesPerformed

Class uk.ac.roslin.ensembl.datasourceaware.core.DAProteinFeature extends DACoreObject implements Serializable

Serialized Fields

translationID

int translationID

sourceStart

int sourceStart

sourceEnd

int sourceEnd

targetName

String targetName

targetStart

int targetStart

targetEnd

int targetEnd

analysisID

int analysisID

score

Double score

eValue

Double eValue

percentIdentity

Double percentIdentity

Class uk.ac.roslin.ensembl.datasourceaware.core.DATranscript extends DAFeature implements Serializable

Serialized Fields

translation

DATranslation translation

stableID

String stableID

biotype

String biotype

gene

DAGene gene

canonical

boolean canonical

geneID

Integer geneID

exonHash

TreeMap<K,V> exonHash

Class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation extends DACoreObject implements Serializable

Serialized Fields

transcript

DATranscript transcript

proteinFeatures

List<E> proteinFeatures

Class uk.ac.roslin.ensembl.datasourceaware.core.GapSequence extends DADNASequence implements Serializable

Serialized Fields

seq

StringBuffer seq


Ensembl Datasource Aware Module
v1.09

Ensembl Datasource Aware Module v1.09
© Roslin Institute 2010. GNU General Public License, version3