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Ensembl Datasource Aware Module v1.09 |
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java.lang.Objectorg.biojava3.core.sequence.template.AbstractSequence<org.biojava3.core.sequence.compound.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
public class DAChromosome
Nested Class Summary |
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Nested classes/interfaces inherited from class org.biojava3.core.sequence.DNASequence |
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org.biojava3.core.sequence.DNASequence.DNAType |
Nested classes/interfaces inherited from class org.biojava3.core.sequence.template.AbstractSequence |
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org.biojava3.core.sequence.template.AbstractSequence.AnnotationType |
Field Summary |
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Fields inherited from class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence |
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comparaFactories, coordSystem, daoFactory, DBSeqLength, dbSpeciesName, dbVersion, id, mappedRegions, mappings, name, objectTypeMappings, registry, schemaVersion, seqRegionID, species |
Constructor Summary | |
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DAChromosome()
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DAChromosome(uk.ac.roslin.ensembl.dao.factory.DAOCoreFactory factory)
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Method Summary | |
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String |
getChromosomeName()
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HashMap<DADNASequence,uk.ac.roslin.ensembl.model.MappingSet> |
getRegionsOfConservedSynteny(uk.ac.roslin.ensembl.model.Coordinate range,
uk.ac.roslin.ensembl.model.core.Species target)
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void |
setChromosomeName(String name)
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String |
toString()
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Methods inherited from class uk.ac.roslin.ensembl.datasourceaware.core.DAAssembledDNASequence |
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getCompleteAssembly, getReverseComplementSequenceAsString, getReverseComplementSequenceAsString, getSequenceAsString, getSequenceAsString, getSequenceAsString |
Methods inherited from class uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence |
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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 |
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getComplement, getDNAType, getGCCount, getReverse, getReverseComplement, getRNASequence, getRNASequence, getRNASequence, getRNASequence, main, setDNAType |
Methods inherited from class org.biojava3.core.sequence.template.AbstractSequence |
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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 |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Methods inherited from interface uk.ac.roslin.ensembl.model.core.AssembledDNASequence |
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getCompleteAssembly |
Methods inherited from interface uk.ac.roslin.ensembl.model.core.DNASequence |
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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 |
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getAssembly, getSpecies, setSpecies |
Methods inherited from interface uk.ac.roslin.ensembl.model.MappableObject |
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addMapping, clearAllMappings, getMappings, getMappings |
Methods inherited from interface uk.ac.roslin.ensembl.model.IdentifiableObject |
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getDBVersion, getHashID, getId, getSchemaVersion, getType, setId |
Methods inherited from interface org.biojava3.core.sequence.template.Sequence |
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countCompounds, getAsList, getCompoundAt, getCompoundSet, getIndexOf, getInverse, getLastIndexOf, getLength, getSequenceAsString, getSubSequence |
Methods inherited from interface java.lang.Iterable |
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iterator |
Methods inherited from interface org.biojava3.core.sequence.template.Accessioned |
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getAccession |
Constructor Detail |
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public DAChromosome()
public DAChromosome(uk.ac.roslin.ensembl.dao.factory.DAOCoreFactory factory)
Method Detail |
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public String getChromosomeName()
getChromosomeName
in interface uk.ac.roslin.ensembl.model.core.Chromosome
public void setChromosomeName(String name)
setChromosomeName
in interface uk.ac.roslin.ensembl.model.core.Chromosome
public String toString()
toString
in class DADNASequence
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
getRegionsOfConservedSynteny
in interface uk.ac.roslin.ensembl.model.core.Chromosome
uk.ac.roslin.ensembl.exception.DAOException
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Ensembl Datasource Aware Module v1.09 |
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