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

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

java.lang.Object
  extended by org.biojava3.core.sequence.template.AbstractSequence<org.biojava3.core.sequence.compound.NucleotideCompound>
      extended by org.biojava3.core.sequence.DNASequence
          extended by uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence
              extended by uk.ac.roslin.ensembl.datasourceaware.core.DAAssembledDNASequence
                  extended by uk.ac.roslin.ensembl.datasourceaware.core.DAChromosome
All Implemented Interfaces:
Serializable, Iterable<org.biojava3.core.sequence.compound.NucleotideCompound>, org.biojava3.core.sequence.template.Accessioned, org.biojava3.core.sequence.template.Sequence<org.biojava3.core.sequence.compound.NucleotideCompound>, uk.ac.roslin.ensembl.model.core.AssembledDNASequence, uk.ac.roslin.ensembl.model.core.Chromosome, uk.ac.roslin.ensembl.model.core.CoreObject, uk.ac.roslin.ensembl.model.core.DNASequence, uk.ac.roslin.ensembl.model.IdentifiableObject, uk.ac.roslin.ensembl.model.MappableObject

public class DAChromosome
extends DAAssembledDNASequence
implements uk.ac.roslin.ensembl.model.core.Chromosome

Author:
paterson
See Also:
Serialized Form

Nested Class Summary
 
Nested classes/interfaces inherited from class org.biojava3.core.sequence.DNASequence
org.biojava3.core.sequence.DNASequence.DNAType
 
Nested classes/interfaces inherited from class org.biojava3.core.sequence.template.AbstractSequence
org.biojava3.core.sequence.template.AbstractSequence.AnnotationType
 
Field Summary
 
Fields inherited from class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence
comparaFactories, coordSystem, daoFactory, DBSeqLength, dbSpeciesName, dbVersion, id, mappedRegions, mappings, name, objectTypeMappings, registry, schemaVersion, seqRegionID, species
 
Constructor Summary
DAChromosome()
           
DAChromosome(uk.ac.roslin.ensembl.dao.factory.DAOCoreFactory factory)
           
 
Method Summary
 String getChromosomeName()
           
 HashMap<DADNASequence,uk.ac.roslin.ensembl.model.MappingSet> getRegionsOfConservedSynteny(uk.ac.roslin.ensembl.model.Coordinate range, uk.ac.roslin.ensembl.model.core.Species target)
           
 void setChromosomeName(String name)
           
 String toString()
           
 
Methods inherited from class uk.ac.roslin.ensembl.datasourceaware.core.DAAssembledDNASequence
getCompleteAssembly, getReverseComplementSequenceAsString, getReverseComplementSequenceAsString, getSequenceAsString, getSequenceAsString, getSequenceAsString
 
Methods inherited from class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence
addMapping, clearAllMappings, getAssembly, getBioEnd, getComparaDivision, getComparaFactory, getComparaFactory, getCoordSystem, getDaoFactory, getDBName, getDBSeqLength, getDBVersion, getGenesOnRegion, getGenesOnRegion, getGenesOnRegion, getHashID, getId, getLength, getMappedRegions, getMappings, getMappings, getName, getObjectTypeMappings, getRegistry, getSchemaVersion, getSpecies, getType, setCoordSystem, setDaoFactory, setDBSeqLength, setId, 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
getCoordSystem, getDBSeqLength, getGenesOnRegion, getGenesOnRegion, getGenesOnRegion, getMappedRegions, getName, getObjectTypeMappings, getReverseComplementSequenceAsString, getReverseComplementSequenceAsString, getSequenceAsString, 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, getMappings, getMappings
 
Methods inherited from interface uk.ac.roslin.ensembl.model.IdentifiableObject
getDBVersion, getHashID, getId, getSchemaVersion, getType, 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(uk.ac.roslin.ensembl.dao.factory.DAOCoreFactory factory)
Method Detail

getChromosomeName

public String getChromosomeName()
Specified by:
getChromosomeName in interface uk.ac.roslin.ensembl.model.core.Chromosome

setChromosomeName

public void setChromosomeName(String name)
Specified by:
setChromosomeName in interface uk.ac.roslin.ensembl.model.core.Chromosome

toString

public String toString()
Overrides:
toString in class DADNASequence

getRegionsOfConservedSynteny

public HashMap<DADNASequence,uk.ac.roslin.ensembl.model.MappingSet> getRegionsOfConservedSynteny(uk.ac.roslin.ensembl.model.Coordinate range,
                                                                                                 uk.ac.roslin.ensembl.model.core.Species target)
                                                                                          throws uk.ac.roslin.ensembl.exception.DAOException
Specified by:
getRegionsOfConservedSynteny in interface uk.ac.roslin.ensembl.model.core.Chromosome
Throws:
uk.ac.roslin.ensembl.exception.DAOException

Ensembl Datasource Aware Module
v1.09

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