Ensembl Datasource Aware Module v1.09
© Roslin Institute 2010. GNU General Public License, version3
Serialized Form
Package uk.ac.roslin.ensembl.datasourceaware |
dBName
String dBName
dBDisplayName
String dBDisplayName
dBRelease
String dBRelease
dBStatus
String dBStatus
dBType
String dBType
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
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 |
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
type
uk.ac.roslin.ensembl.model.compara.HomologyType type
lastCommonAncestor
String lastCommonAncestor
members
TreeSet<E> members
originalHPR
DAHomologyPairRelationship originalHPR
Package uk.ac.roslin.ensembl.datasourceaware.core |
completeAssembly
DAAssembly completeAssembly
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
species
uk.ac.roslin.ensembl.model.core.Species species
comparaFactories
HashMap<K,V> comparaFactories
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
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
stableID
String stableID
transcript
DATranscript transcript
transcriptID
Integer transcriptID
rank
Integer rank
phase
int phase
endPhase
int endPhase
constitutive
Boolean constitutive
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
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
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
translation
DATranslation translation
stableID
String stableID
biotype
String biotype
gene
DAGene gene
canonical
boolean canonical
geneID
Integer geneID
exonHash
TreeMap<K,V> exonHash
transcript
DATranscript transcript
proteinFeatures
List<E> proteinFeatures
seq
StringBuffer seq
Ensembl Datasource Aware Module v1.09
© Roslin Institute 2010. GNU General Public License, version3