uk.ac.roslin.ensembl.datasourceaware.core

Class DAChromosome

java.lang.Object

org.biojava3.core.sequence.template.AbstractSequence<NucleotideCompound>

org.biojava3.core.sequence.DNASequence

uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

uk.ac.roslin.ensembl.datasourceaware.core.DAAssembledDNASequence

uk.ac.roslin.ensembl.datasourceaware.core.DAChromosome

All Implemented Interfaces:

Serializable, Iterable<NucleotideCompound>, Accessioned, Sequence<NucleotideCompound>, AssembledDNASequence, Chromosome, CoreObject, DNASequence, IdentifiableObject, MappableObject

public class DAChromosome
extends DAAssembledDNASequence
implements Chromosome

A DAChromosome is a particular type of DAAssembledDNASequence for representing whole chromosomes.

Author:

paterson

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class org.biojava3.core.sequence.DNASequence

DNASequence.DNAType

Nested classes/interfaces inherited from class org.biojava3.core.sequence.template.AbstractSequence

AbstractSequence.AnnotationType

Field Summary

Fields inherited from class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

codonTableID, comparaFactories, coordSystem, csID, daoFactory, DBSeqLength, dbSpeciesName, dbVersion, id, lazyLoaded, mappedRegions, mappings, name, objectTypeMappings, registry, schemaVersion, seqRegionID, species

Constructor Summary

Constructors

Constructor and Description
DAChromosome()
DAChromosome(DAOCoreFactory factory)

Method Summary

Methods

Modifier and Type	Method and Description
void	addException(AssemblyExceptionType type, Mapping mapping) public method called by the DA infrastructure when adding an AssemblyException mapping of the indicated type.
MappingSet	getAssemblyExceptions(AssemblyExceptionType type) Returns a MappingSet of AssemblyExceptions of the indicated AssemblyExceptionType.
String	getChromosomeName()
DAChromosome	getParChromosome() Returns the sex-linked 'PAR' chromosome associated with this Chromosome.
MappingSet	getPseudoAutosomalRegion()
ObjectType	getType()
boolean	hasExceptions() Returns whether this chromosome has any AssemblyExceptions.
boolean	isPAR()
void	setChromosomeName(String name)
void	setExceptions(boolean set) flag method to create the 'exceptions' HashMap for this chromosome if necessary.
void	setPAR(boolean hasPAR)
String	toString()

Methods inherited from class uk.ac.roslin.ensembl.datasourceaware.core.DAAssembledDNASequence

getCompleteAssembly, getPaddedReverseComplementSequenceAsString, getPaddedSequenceAsString, getReverseComplementSequenceAsString, getReverseComplementSequenceAsString, getSequenceAsString, getSequenceAsString, getSequenceAsString

Methods inherited from class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence

addAttribute, addMapping, clearAllMappings, getAssembly, getAttribute, getAttributes, getBioEnd, getCodonTableID, getComparaDivision, getComparaFactory, getComparaFactory, getCoordSystem, getCsID, getDaoFactory, getDBName, getDBSeqLength, getDBVersion, getGenesOnRegion, getGenesOnRegion, getGenesOnRegion, getHashID, getId, getLength, getLoadedMappings, getLoadedMappings, getMappedRegions, getName, getObjectTypeMappings, getRegionsOfConservedSynteny, getRegionsOfConservedSynteny, getRegistry, getSchemaVersion, getSpecies, getVariationMappingsOnRegion, getVariationMappingsOnRegion, getVariationsOnRegion, getVariationsOnRegion, setAttributes, setCodonTableID, setCoordSystem, setCsID, setDaoFactory, setDBSeqLength, setId, setLazyLoaded, setName, setRegistry, setSequenceStorage, setSpecies

Methods inherited from class org.biojava3.core.sequence.DNASequence

getComplement, getDNAType, getGCCount, getReverse, getReverseComplement, getRNASequence, getRNASequence, getRNASequence, getRNASequence, main, setDNAType

Methods inherited from class org.biojava3.core.sequence.template.AbstractSequence

addFeature, addFeature, addNote, countCompounds, getAccession, getAnnotationType, getAsList, getBioBegin, getCompoundAt, getCompoundSet, getDatabaseReferences, getDescription, getFeatures, getFeatures, getFeatures, getFeaturesByType, getFeaturesKeyWord, getIndexOf, getInverse, getLastIndexOf, getNotesList, getOriginalHeader, getParentSequence, getProxySequenceReader, getSequenceScore, getSource, getSubSequence, getTaxonomy, getUserCollection, iterator, removeFeature, removeNote, setAccession, setAnnotationType, setBioBegin, setBioEnd, setCompoundSet, setDatabaseReferences, setDescription, setFeaturesKeyWord, setNotesList, setOriginalHeader, setParentSequence, setProxySequenceReader, setSequenceScore, setSource, setTaxonomy, setUserCollection

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface uk.ac.roslin.ensembl.model.core.AssembledDNASequence

getCompleteAssembly

Methods inherited from interface uk.ac.roslin.ensembl.model.core.DNASequence

getCodonTableID, getCoordSystem, getDBSeqLength, getGenesOnRegion, getGenesOnRegion, getGenesOnRegion, getMappedRegions, getName, getObjectTypeMappings, getPaddedReverseComplementSequenceAsString, getPaddedSequenceAsString, getRegionsOfConservedSynteny, getRegionsOfConservedSynteny, getReverseComplementSequenceAsString, getReverseComplementSequenceAsString, getSequenceAsString, getVariationMappingsOnRegion, getVariationMappingsOnRegion, getVariationsOnRegion, getVariationsOnRegion, setCoordSystem, setDBSeqLength, setName

Methods inherited from interface uk.ac.roslin.ensembl.model.core.CoreObject

getAssembly, getSpecies, setSpecies

Methods inherited from interface uk.ac.roslin.ensembl.model.MappableObject

addMapping, clearAllMappings, getLoadedMappings, getLoadedMappings

Methods inherited from interface uk.ac.roslin.ensembl.model.IdentifiableObject

getDBVersion, getHashID, getId, getSchemaVersion, setId

Methods inherited from interface org.biojava3.core.sequence.template.Sequence

countCompounds, getAsList, getCompoundAt, getCompoundSet, getIndexOf, getInverse, getLastIndexOf, getLength, getSequenceAsString, getSubSequence

Methods inherited from interface java.lang.Iterable

iterator

Methods inherited from interface org.biojava3.core.sequence.template.Accessioned

getAccession

Constructor Detail

DAChromosome

public DAChromosome()

DAChromosome

public DAChromosome(DAOCoreFactory factory)

Method Detail

getChromosomeName

public String getChromosomeName()

Specified by:

getChromosomeName in interface Chromosome

setChromosomeName

public void setChromosomeName(String name)

Specified by:

setChromosomeName in interface Chromosome

toString

public String toString()

Overrides:

toString in class DADNASequence

getType

public ObjectType getType()

Specified by:

getType in interface IdentifiableObject

Overrides:

getType in class DADNASequence

getPseudoAutosomalRegion

public MappingSet getPseudoAutosomalRegion()

Specified by:

getPseudoAutosomalRegion in interface Chromosome

isPAR

public boolean isPAR()

Specified by:

isPAR in interface Chromosome

setPAR

public void setPAR(boolean hasPAR)

getParChromosome

public DAChromosome getParChromosome()

Returns the sex-linked 'PAR' chromosome associated with this Chromosome. Null if this chromsome is not flagged as a PAR/Sex-linked chromosome. Triggers lazy loading when not set.

Specified by:

getParChromosome in interface Chromosome

getAssemblyExceptions

public MappingSet getAssemblyExceptions(AssemblyExceptionType type)
                                 throws DAOException

Returns a MappingSet of AssemblyExceptions of the indicated AssemblyExceptionType. Triggers lazy load on this Species to retrieve AssemblyExceptions if necessary.

Parameters:

type -

Throws:

DAOException

hasExceptions

public boolean hasExceptions()

Returns whether this chromosome has any AssemblyExceptions. Triggers lazy load on this Species to retrieve AssemblyExceptions if necessary.

addException

public void addException(AssemblyExceptionType type,
                Mapping mapping)

public method called by the DA infrastructure when adding an AssemblyException mapping of the indicated type.

Parameters:

type -

mapping -

setExceptions

public void setExceptions(boolean set)

flag method to create the 'exceptions' HashMap for this chromosome if necessary.

Parameters:

set -