Serialized Form (JEnsembl: A Java API for Ensembl Data Access 1.78 API)

Package uk.ac.roslin.ensembl.biojava3
- Class uk.ac.roslin.ensembl.biojava3.EnsemblDNACompoundSet extends AmbiguityDNACompoundSet implements Serializable
Package uk.ac.roslin.ensembl.config
- Class uk.ac.roslin.ensembl.config.AssemblyExceptionType extends EnsemblType implements Serializable
- Class uk.ac.roslin.ensembl.config.CodonTable extends EnsemblType implements Serializable
- Class uk.ac.roslin.ensembl.config.EnsemblComparaDivision extends EnsemblType implements Serializable
- Class uk.ac.roslin.ensembl.config.EnsemblCoordSystemType extends EnsemblType implements Serializable
- Class uk.ac.roslin.ensembl.config.EnsemblCoreObjectType extends EnsemblType implements Serializable
- Class uk.ac.roslin.ensembl.config.EnsemblDBType extends EnsemblType implements Serializable
  - Serialization Methods
    - readResolve
```
private Object readResolve()
                    throws ObjectStreamException
```
      Ensure Singleton class
      
      Throws:
      
      ObjectStreamException
  - Serialized Fields
    - databaseType
```
uk.ac.roslin.ensembl.config.EnsemblDBType.SpecificDBType databaseType
```
      The SpecificDBType of a given EnsemblDBType Object i.e. CORE, COMPARA etc.
    - ENSEMBL_TYPE
```
uk.ac.roslin.ensembl.config.EnsemblDBType.GenericDBType ENSEMBL_TYPE
```
      The GenericDBType of a given EnsemblDBType Object i.e. SINGLE_SPECIES, SPECIES_COMPARISON etc.
- Class uk.ac.roslin.ensembl.config.EnsemblType extends Object implements Serializable
  - Serialized Fields
    - label
```
String label
```
- Class uk.ac.roslin.ensembl.config.ExternalDBType extends EnsemblType implements Serializable
- Class uk.ac.roslin.ensembl.config.FeatureType extends EnsemblType implements Serializable
Package uk.ac.roslin.ensembl.datasourceaware
- Class uk.ac.roslin.ensembl.datasourceaware.DAAnalysis extends DAObject implements Serializable
  - Serialized Fields
    - creationDate
```
Date creationDate
```
    - logicalName
```
String logicalName
```
    - description
```
String description
```
    - displayLabel
```
String displayLabel
```
    - externalDatabaseName
```
String externalDatabaseName
```
    - externalDatabaseVersion
```
String externalDatabaseVersion
```
    - moduleName
```
String moduleName
```
    - moduleVersion
```
String moduleVersion
```
    - programName
```
String programName
```
    - programVersion
```
String programVersion
```
    - programParameters
```
String programParameters
```
    - gffSource
```
String gffSource
```
    - gffFeature
```
String gffFeature
```
- Class uk.ac.roslin.ensembl.datasourceaware.DAObject extends Object implements Serializable
  - Serialized Fields
    - daoFactory
```
DAOFactory daoFactory
```
    - schemaVersion
```
String schemaVersion
```
    - dbVersion
```
String dbVersion
```
    - registry
```
Registry registry
```
    - id
```
Integer id
```
    - lazyloadAllowed
```
boolean lazyloadAllowed
```
- 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
```
ExternalDB dB
```
    - version
```
String version
```
    - description
```
String description
```
    - infoType
```
String infoType
```
    - info
```
String info
```
    - displayID
```
String displayID
```
    - primaryAccession
```
String primaryAccession
```
    - initialized
```
boolean initialized
```
    - synonyms
```
TreeSet<E> synonyms
```
    - evidence
```
Evidence evidence
```
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
```
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
```
HomologyAlignmentProperties targetProperties
```
- Class uk.ac.roslin.ensembl.datasourceaware.compara.DAHomologyRelationship extends DAObject implements Serializable
  - Serialized Fields
    - type
```
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.DAAnalyzedFeature extends DAFeature implements Serializable
  - Serialized Fields
    - analysisID
```
Integer analysisID
```
- 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
  - Serialized Fields
    - pseudoAutosomalRegion
```
MappingSet pseudoAutosomalRegion
```
    - parChromosome
```
DAChromosome parChromosome
```
    - PAR
```
boolean PAR
```
    - exceptions
```
HashMap<K,V> exceptions
```
- Class uk.ac.roslin.ensembl.datasourceaware.core.DACoordinateSystem extends Object implements Serializable
  - Serialized Fields
    - id
```
Integer id
```
    - speciesID
```
Integer speciesID
```
    - type
```
EnsemblCoordSystemType type
```
    - rank
```
Integer rank
```
    - version
```
String version
```
    - defaultVersion
```
Boolean defaultVersion
```
    - sequenceLevel
```
Boolean sequenceLevel
```
    - topLevel
```
Boolean topLevel
```
- Class uk.ac.roslin.ensembl.datasourceaware.core.DACoreObject extends DAObject implements Serializable
  - Serialized Fields
    - species
```
Species species
```
    - stableID
```
String stableID
```
    - version
```
Integer version
```
    - modificationDate
```
Date modificationDate
```
    - creationDate
```
Date creationDate
```
    - comparaFactories
```
HashMap<K,V> comparaFactories
```
- Class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence extends DNASequence implements Serializable
  - Serialized Fields
    - daoFactory
```
DAOFactory daoFactory
```
    - schemaVersion
```
String schemaVersion
```
    - dbVersion
```
String dbVersion
```
    - registry
```
Registry registry
```
    - id
```
Integer id
```
    - seqRegionID
```
Integer seqRegionID
```
    - name
```
String name
```
    - dbSpeciesName
```
String dbSpeciesName
```
    - species
```
Species species
```
    - DBSeqLength
```
Integer DBSeqLength
```
    - coordSystem
```
CoordinateSystem coordSystem
```
    - mappings
```
MappingSet mappings
```
    - mappedRegions
```
HashMap<K,V> mappedRegions
```
    - objectTypeMappings
```
HashMap<K,V> objectTypeMappings
```
    - comparaFactories
```
HashMap<K,V> comparaFactories
```
    - codonTableID
```
Integer codonTableID
```
    - lazyLoaded
```
boolean lazyLoaded
```
    - adhocAttributes
```
HashMap<K,V> adhocAttributes
```
    - csID
```
Integer csID
```
- Class uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader extends Object implements Serializable
  - Serialized Fields
    - sequence
```
String sequence
```
    - compoundSet
```
EnsemblDNACompoundSet compoundSet
```
    - dASequence
```
DADNASequence dASequence
```
    - coordSystemID
```
Integer coordSystemID
```
    - seqRegionID
```
Integer seqRegionID
```
    - length
```
Integer length
```
    - name
```
String name
```
    - factory
```
DAOCoreFactory factory
```
    - parent
```
DADNASequence parent
```
    - cache
```
LinkedHashMap<K,V> cache
```
    - chunkSize
```
Integer chunkSize
```
    - usesCache
```
boolean usesCache
```
    - nonCacheLazyLoaded
```
boolean nonCacheLazyLoaded
```
    - chunks
```
Integer chunks
```
    - sequenceReader
```
SequenceReader<C extends Compound> sequenceReader
```
- Class uk.ac.roslin.ensembl.datasourceaware.core.DAExon extends DAFeature implements Serializable
  - Serialized Fields
    - transcript
```
DATranscript transcript
```
    - transcriptID
```
Integer transcriptID
```
    - rank
```
Integer rank
```
    - phase
```
int phase
```
    - endPhase
```
int endPhase
```
    - constitutive
```
Boolean constitutive
```
    - targetCoordinates
```
Coordinate targetCoordinates
```
    - target
```
DNASequence target
```
- Class uk.ac.roslin.ensembl.datasourceaware.core.DAFeature extends DACoreObject implements Serializable
  - Serialized Fields
    - mappings
```
MappingSet mappings
```
    - objectTypeMappings
```
HashMap<K,V> objectTypeMappings
```
    - mappedObjectTypes
```
Set<E> mappedObjectTypes
```
    - description
```
String description
```
    - displayXRef
```
DAXRef displayXRef
```
    - displayName
```
String displayName
```
    - status
```
DAFeature.Status status
```
    - current
```
Boolean current
```
    - topLevelTargetCoordinates
```
Coordinate topLevelTargetCoordinates
```
    - topLevelTargetSequence
```
DADNASequence topLevelTargetSequence
```
    - thisSequence
```
DADNASequence thisSequence
```
    - topLevelCS
```
CoordinateSystem topLevelCS
```
    - length
```
Integer length
```
    - initialized
```
boolean initialized
```
- Class uk.ac.roslin.ensembl.datasourceaware.core.DAGene extends DAAnalyzedFeature implements Serializable
  - Serialized Fields
    - biotype
```
String biotype
```
    - canonicalTranscriptID
```
Integer canonicalTranscriptID
```
    - canonicalTranscript
```
DATranscript canonicalTranscript
```
    - transcriptHash
```
TreeMap<K,V> transcriptHash
```
    - homologies
```
HashMap<K,V> homologies
```
    - homologySearchesPerformed
```
TreeSet<E> homologySearchesPerformed
```
    - synonyms
```
TreeSet<E> synonyms
```
    - xrefs
```
Set<E> xrefs
```
    - typedXRefs
```
HashMap<K,V> typedXRefs
```
    - xrefsInitialized
```
boolean xrefsInitialized
```
    - orthologueCount
```
Integer orthologueCount
```
    - paralogueCount
```
Integer paralogueCount
```
    - homoeologueCount
```
Integer homoeologueCount
```
    - vegaGeneID
```
String vegaGeneID
```
- 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
```
Integer analysisID
```
    - score
```
Double score
```
    - eValue
```
Double eValue
```
    - percentIdentity
```
Double percentIdentity
```
- Class uk.ac.roslin.ensembl.datasourceaware.core.DATranscript extends DAAnalyzedFeature implements Serializable
  - Serialized Fields
    - canonicalTranslationID
```
Integer canonicalTranslationID
```
    - canonicalTranslation
```
DATranslation canonicalTranslation
```
    - translationHash
```
TreeMap<K,V> translationHash
```
    - biotype
```
String biotype
```
    - gene
```
DAGene gene
```
    - canonical
```
boolean canonical
```
    - geneID
```
Integer geneID
```
    - exonHash
```
TreeMap<K,V> exonHash
```
    - primaryTranscriptExonMappings
```
MappingSet primaryTranscriptExonMappings
```
    - processedTranscriptExonMappings
```
MappingSet processedTranscriptExonMappings
```
    - processedTranscriptLength
```
Integer processedTranscriptLength
```
    - processedTranscript
```
DADNASequence processedTranscript
```
    - synonyms
```
TreeSet<E> synonyms
```
    - xrefs
```
Set<E> xrefs
```
    - typedXRefs
```
HashMap<K,V> typedXRefs
```
    - xrefsInitialized
```
boolean xrefsInitialized
```
    - vegaTranscriptID
```
String vegaTranscriptID
```
    - ccdsID
```
String ccdsID
```
- Class uk.ac.roslin.ensembl.datasourceaware.core.DATranslation extends DACoreObject implements Serializable
  - Serialized Fields
    - transcript
```
DATranscript transcript
```
    - proteinFeatures
```
List<E> proteinFeatures
```
    - canonical
```
boolean canonical
```
    - firstExon
```
DAExon firstExon
```
    - firstExonID
```
Integer firstExonID
```
    - lastExon
```
DAExon lastExon
```
    - lastExonID
```
Integer lastExonID
```
    - firstExonStart
```
Integer firstExonStart
```
    - lastExonEnd
```
Integer lastExonEnd
```
    - transcriptID
```
Integer transcriptID
```
    - translatedSequence
```
DNASequence translatedSequence
```
    - translationMappings
```
MappingSet translationMappings
```
      Each Mapping in this TreeSet has source: null (implicitly the translated sequence) sourceCoordinates: the coordinate on the translated sequence - including any 1 or 2 residue shift due to Exon1 phase issues. target: the (unprocessed) primaryTranscript specifying this Translation targetCoordinates: the coordinates on the (unprocessed) pimaryTranscript
    - vegaProteinID
```
String vegaProteinID
```
    - xrefs
```
Set<E> xrefs
```
    - typedXRefs
```
HashMap<K,V> typedXRefs
```
    - xrefsInitialized
```
boolean xrefsInitialized
```
    - initialized
```
boolean initialized
```
    - synonyms
```
TreeSet<E> synonyms
```
- Class uk.ac.roslin.ensembl.datasourceaware.core.GapSequence extends DADNASequence implements Serializable
  - Serialized Fields
    - seq
```
StringBuffer seq
```
Package uk.ac.roslin.ensembl.datasourceaware.variation
- Class uk.ac.roslin.ensembl.datasourceaware.variation.DAVariation extends DAObject implements Serializable
  - Serialized Fields
    - mappings
```
MappingSet mappings
```
    - objectTypeMappings
```
HashMap<K,V> objectTypeMappings
```
    - mappedObjectTypes
```
Set<E> mappedObjectTypes
```
    - name
```
String name
```
    - synonym
```
String synonym
```
    - synonyms
```
List<E> synonyms
```
    - ancestralAllele
```
String ancestralAllele
```
    - xref
```
DAVariationXRef xref
```
    - varType
```
VariationType varType
```
    - somatic
```
Boolean somatic
```
    - flipped
```
Boolean flipped
```
    - occurrences
```
int occurrences
```
    - initOK
```
Boolean initOK
```
- Class uk.ac.roslin.ensembl.datasourceaware.variation.DAVariationXRef extends DAXRef implements Serializable
  - Serialized Fields
    - url
```
String url
```
    - assayType
```
String assayType
```
    - tissueSource
```
String tissueSource
```
    - dBName
```
String dBName
```
- Class uk.ac.roslin.ensembl.datasourceaware.variation.VariationMapping extends Mapping implements Serializable
  - Serialized Fields
    - consequences
```
List<E> consequences
```
    - alleleString
```
String alleleString
```
    - id
```
Integer id
```
Package uk.ac.roslin.ensembl.exception
- Class uk.ac.roslin.ensembl.exception.BacterialCollectionException extends EnsemblRuntimeException implements Serializable
- Class uk.ac.roslin.ensembl.exception.ConfigurationException extends EnsemblException implements Serializable
  
  serialVersionUID:
  
  1L
- Class uk.ac.roslin.ensembl.exception.DAOException extends EnsemblException implements Serializable
  
  serialVersionUID:
  
  1L
- Class uk.ac.roslin.ensembl.exception.EnsemblException extends Exception implements Serializable
- Class uk.ac.roslin.ensembl.exception.EnsemblRuntimeException extends RuntimeException implements Serializable
- Class uk.ac.roslin.ensembl.exception.NonUniqueException extends EnsemblException implements Serializable
  - Serialized Fields
    - allHits
```
Collection<E> allHits
```
- Class uk.ac.roslin.ensembl.exception.RangeException extends EnsemblRuntimeException implements Serializable
Package uk.ac.roslin.ensembl.mapper.handler
- Class uk.ac.roslin.ensembl.mapper.handler.HashMapHolder extends Object implements Serializable
  - Serialized Fields
    - fakeid
```
String fakeid
```
    - map
```
HashMap<K,V> map
```
Package uk.ac.roslin.ensembl.model
- Class uk.ac.roslin.ensembl.model.Coordinate extends Object implements Serializable
  - Serialized Fields
    - start
```
Integer start
```
    - end
```
Integer end
```
    - strand
```
Coordinate.Strand strand
```
    - strandInt
```
Integer strandInt
```
- Class uk.ac.roslin.ensembl.model.CoordinateSet extends TreeSet<Coordinate> implements Serializable
- Class uk.ac.roslin.ensembl.model.Evidence extends Object implements Serializable
  - Serialized Fields
    - label
```
String label
```
- Class uk.ac.roslin.ensembl.model.ExternalDB extends Object implements Serializable
  - Serialized Fields
    - dBName
```
String dBName
```
    - dBDisplayName
```
String dBDisplayName
```
    - dBRelease
```
String dBRelease
```
    - dBStatus
```
String dBStatus
```
    - dBType
```
String dBType
```
    - dBDescription
```
String dBDescription
```
    - id
```
Integer id
```
- Class uk.ac.roslin.ensembl.model.GoEvidence extends Evidence implements Serializable
  - Serialized Fields
    - code
```
String code
```
    - value
```
String value
```
- Class uk.ac.roslin.ensembl.model.Mapping extends Object implements Serializable
  - Serialized Fields
    - source
```
MappableObject source
```
    - target
```
MappableObject target
```
    - sourceCoordinates
```
Coordinate sourceCoordinates
```
    - targetCoordinates
```
Coordinate targetCoordinates
```
    - sourceCoordSystem
```
CoordinateSystem sourceCoordSystem
```
    - targetCoordSystem
```
CoordinateSystem targetCoordSystem
```
    - reverseMapping
```
Mapping reverseMapping
```
- Class uk.ac.roslin.ensembl.model.MappingSet extends TreeSet<Mapping> implements Serializable
Package uk.ac.roslin.ensembl.model.compara
- Class uk.ac.roslin.ensembl.model.compara.HomologyAlignmentProperties extends Object implements Serializable
  - Serialized Fields
    - cigarLine
```
String cigarLine
```
    - peptideID
```
String peptideID
```
    - geneID
```
String geneID
```
    - speciesName
```
String speciesName
```
    - percentCovered
```
Integer percentCovered
```
    - percentIdentity
```
Integer percentIdentity
```
    - percentSimilar
```
Integer percentSimilar
```
    - coords
```
Coordinate coords
```
    - sequenceName
```
String sequenceName
```
- Class uk.ac.roslin.ensembl.model.compara.HomologyType extends RelationshipType implements Serializable
  - Serialization Methods
    - readResolve
```
private Object readResolve()
                    throws ObjectStreamException
```
      Ensure Singleton class
      
      Throws:
      
      ObjectStreamException
Package uk.ac.roslin.ensembl.model.core
Package uk.ac.roslin.ensembl.model.database
Package uk.ac.roslin.ensembl.model.relationship
- Class uk.ac.roslin.ensembl.model.relationship.RelationshipType extends EnsemblType implements Serializable
  - Serialization Methods
    - readResolve
```
private Object readResolve()
                    throws ObjectStreamException
```
      Ensure Singleton class
      
      Throws:
      
      ObjectStreamException
Package uk.ac.roslin.ensembl.model.variation
- Class uk.ac.roslin.ensembl.model.variation.VariationType extends EnsemblType implements Serializable
  - Serialized Fields
    - setID
```
Integer setID
```
    - SOTerm
```
String SOTerm
```
    - DisplayTerm
```
String DisplayTerm
```
    - SOAccession
```
String SOAccession
```

Serialized Form

Package uk.ac.roslin.ensembl.biojava3

Class uk.ac.roslin.ensembl.biojava3.EnsemblDNACompoundSet extends AmbiguityDNACompoundSet implements Serializable

Package uk.ac.roslin.ensembl.config

Class uk.ac.roslin.ensembl.config.AssemblyExceptionType extends EnsemblType implements Serializable

Class uk.ac.roslin.ensembl.config.CodonTable extends EnsemblType implements Serializable

Class uk.ac.roslin.ensembl.config.EnsemblComparaDivision extends EnsemblType implements Serializable

Class uk.ac.roslin.ensembl.config.EnsemblCoordSystemType extends EnsemblType implements Serializable

Class uk.ac.roslin.ensembl.config.EnsemblCoreObjectType extends EnsemblType implements Serializable

Class uk.ac.roslin.ensembl.config.EnsemblDBType extends EnsemblType implements Serializable

Serialization Methods

readResolve

Serialized Fields

databaseType

ENSEMBL_TYPE

Class uk.ac.roslin.ensembl.config.EnsemblType extends Object implements Serializable

Serialized Fields

label

Class uk.ac.roslin.ensembl.config.ExternalDBType extends EnsemblType implements Serializable

Class uk.ac.roslin.ensembl.config.FeatureType extends EnsemblType implements Serializable

Package uk.ac.roslin.ensembl.datasourceaware

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

Serialized Fields

creationDate

logicalName

description

displayLabel

externalDatabaseName

externalDatabaseVersion

moduleName

moduleVersion

programName

programVersion

programParameters

gffSource

gffFeature

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

Serialized Fields

daoFactory

schemaVersion

dbVersion

registry

id

lazyloadAllowed

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

version

description

infoType

info

displayID

primaryAccession

initialized

synonyms

evidence

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

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

Serialized Fields

source

target

sourceProperties

targetProperties

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

Serialized Fields

type

lastCommonAncestor

members

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

Serialized Fields

originalHPR

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

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

Serialized Fields

analysisID

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

Serialized Fields

completeAssembly

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