Ensembl Datasource Aware Module v1.09
© Roslin Institute 2010. GNU General Public License, version3
uk.ac.roslin.ensembl.datasourceaware.core
Class DADNASequence
java.lang.Object
org.biojava3.core.sequence.template.AbstractSequence<org.biojava3.core.sequence.compound.NucleotideCompound>
org.biojava3.core.sequence.DNASequence
uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence
- 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.CoreObject, uk.ac.roslin.ensembl.model.core.DNASequence, uk.ac.roslin.ensembl.model.IdentifiableObject, uk.ac.roslin.ensembl.model.MappableObject
- Direct Known Subclasses:
- DAAssembledDNASequence, GapSequence
public class DADNASequence
- extends org.biojava3.core.sequence.DNASequence
- implements uk.ac.roslin.ensembl.model.core.CoreObject, uk.ac.roslin.ensembl.model.core.DNASequence
- Author:
- paterson
- See Also:
- Serialized Form
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 |
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, getSequenceAsString, getSequenceAsString, 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 interface org.biojava3.core.sequence.template.Sequence |
countCompounds, getAsList, getCompoundAt, getCompoundSet, getIndexOf, getInverse, getLastIndexOf, getSequenceAsString, getSubSequence |
Methods inherited from interface org.biojava3.core.sequence.template.Accessioned |
getAccession |
daoFactory
protected uk.ac.roslin.ensembl.dao.factory.DAOFactory daoFactory
schemaVersion
protected String schemaVersion
dbVersion
protected String dbVersion
registry
protected uk.ac.roslin.ensembl.model.database.Registry registry
id
protected Integer id
seqRegionID
protected Integer seqRegionID
name
protected String name
dbSpeciesName
protected String dbSpeciesName
species
protected uk.ac.roslin.ensembl.model.core.Species species
DBSeqLength
protected Integer DBSeqLength
coordSystem
protected uk.ac.roslin.ensembl.model.core.CoordinateSystem coordSystem
mappings
protected uk.ac.roslin.ensembl.model.MappingSet mappings
mappedRegions
protected HashMap<uk.ac.roslin.ensembl.model.ObjectType,uk.ac.roslin.ensembl.model.CoordinateSet> mappedRegions
objectTypeMappings
protected HashMap<uk.ac.roslin.ensembl.model.ObjectType,uk.ac.roslin.ensembl.model.MappingSet> objectTypeMappings
comparaFactories
protected HashMap<uk.ac.roslin.ensembl.config.EnsemblComparaDivision,uk.ac.roslin.ensembl.dao.factory.DAOComparaFactory> comparaFactories
DADNASequence
public DADNASequence()
DADNASequence
public DADNASequence(DAEnsemblDNASequenceReader proxyLoader)
DADNASequence
public DADNASequence(String sequence)
DADNASequence
public DADNASequence(uk.ac.roslin.ensembl.dao.factory.DAOCoreFactory factory)
setSequenceStorage
public void setSequenceStorage(DAEnsemblDNASequenceReader proxyLoader)
getDaoFactory
public uk.ac.roslin.ensembl.dao.factory.DAOCoreFactory getDaoFactory()
setDaoFactory
public void setDaoFactory(uk.ac.roslin.ensembl.dao.factory.DAOFactory daoFactory)
getSchemaVersion
public String getSchemaVersion()
- Specified by:
getSchemaVersion
in interface uk.ac.roslin.ensembl.model.IdentifiableObject
getDBVersion
public String getDBVersion()
- Specified by:
getDBVersion
in interface uk.ac.roslin.ensembl.model.IdentifiableObject
getRegistry
public uk.ac.roslin.ensembl.model.database.Registry getRegistry()
setRegistry
public void setRegistry(uk.ac.roslin.ensembl.model.database.Registry datasource)
getId
public Integer getId()
- Specified by:
getId
in interface uk.ac.roslin.ensembl.model.IdentifiableObject
setId
public void setId(Integer id)
- Specified by:
setId
in interface uk.ac.roslin.ensembl.model.IdentifiableObject
getDBName
public String getDBName()
getSpecies
public uk.ac.roslin.ensembl.model.core.Species getSpecies()
- Specified by:
getSpecies
in interface uk.ac.roslin.ensembl.model.core.CoreObject
setSpecies
public void setSpecies(uk.ac.roslin.ensembl.model.core.Species species)
- Specified by:
setSpecies
in interface uk.ac.roslin.ensembl.model.core.CoreObject
getType
public uk.ac.roslin.ensembl.model.ObjectType getType()
- Specified by:
getType
in interface uk.ac.roslin.ensembl.model.IdentifiableObject
getDBSeqLength
public Integer getDBSeqLength()
- Specified by:
getDBSeqLength
in interface uk.ac.roslin.ensembl.model.core.DNASequence
setDBSeqLength
public void setDBSeqLength(Integer seqLength)
- Specified by:
setDBSeqLength
in interface uk.ac.roslin.ensembl.model.core.DNASequence
getBioEnd
public Integer getBioEnd()
- Overrides:
getBioEnd
in class org.biojava3.core.sequence.template.AbstractSequence<org.biojava3.core.sequence.compound.NucleotideCompound>
getLength
public int getLength()
- Specified by:
getLength
in interface org.biojava3.core.sequence.template.Sequence<org.biojava3.core.sequence.compound.NucleotideCompound>
- Overrides:
getLength
in class org.biojava3.core.sequence.template.AbstractSequence<org.biojava3.core.sequence.compound.NucleotideCompound>
getName
public String getName()
- Specified by:
getName
in interface uk.ac.roslin.ensembl.model.core.DNASequence
setName
public void setName(String name)
- Specified by:
setName
in interface uk.ac.roslin.ensembl.model.core.DNASequence
getCoordSystem
public uk.ac.roslin.ensembl.model.core.CoordinateSystem getCoordSystem()
- Specified by:
getCoordSystem
in interface uk.ac.roslin.ensembl.model.core.DNASequence
setCoordSystem
public void setCoordSystem(uk.ac.roslin.ensembl.model.core.CoordinateSystem coordSystem)
- Specified by:
setCoordSystem
in interface uk.ac.roslin.ensembl.model.core.DNASequence
getMappings
public uk.ac.roslin.ensembl.model.MappingSet getMappings()
- Specified by:
getMappings
in interface uk.ac.roslin.ensembl.model.MappableObject
getMappings
public uk.ac.roslin.ensembl.model.MappingSet getMappings(uk.ac.roslin.ensembl.model.ObjectType targetType)
- Specified by:
getMappings
in interface uk.ac.roslin.ensembl.model.MappableObject
addMapping
public Boolean addMapping(uk.ac.roslin.ensembl.model.Mapping mapping)
- Specified by:
addMapping
in interface uk.ac.roslin.ensembl.model.MappableObject
getGenesOnRegion
public List<DAGene> getGenesOnRegion(uk.ac.roslin.ensembl.model.Coordinate coord)
throws uk.ac.roslin.ensembl.exception.DAOException
- Specified by:
getGenesOnRegion
in interface uk.ac.roslin.ensembl.model.core.DNASequence
- Throws:
uk.ac.roslin.ensembl.exception.DAOException
getGenesOnRegion
public List<DAGene> getGenesOnRegion(Integer start,
Integer stop,
uk.ac.roslin.ensembl.model.Coordinate.Strand strand)
throws uk.ac.roslin.ensembl.exception.DAOException
- Specified by:
getGenesOnRegion
in interface uk.ac.roslin.ensembl.model.core.DNASequence
- Throws:
uk.ac.roslin.ensembl.exception.DAOException
getGenesOnRegion
public List<DAGene> getGenesOnRegion(Integer start,
Integer stop)
throws uk.ac.roslin.ensembl.exception.DAOException
- Specified by:
getGenesOnRegion
in interface uk.ac.roslin.ensembl.model.core.DNASequence
- Throws:
uk.ac.roslin.ensembl.exception.DAOException
getSequenceAsString
public String getSequenceAsString(Integer begin,
Integer end)
- Specified by:
getSequenceAsString
in interface uk.ac.roslin.ensembl.model.core.DNASequence
getReverseComplementSequenceAsString
public String getReverseComplementSequenceAsString(Integer begin,
Integer end)
- Specified by:
getReverseComplementSequenceAsString
in interface uk.ac.roslin.ensembl.model.core.DNASequence
getReverseComplementSequenceAsString
public String getReverseComplementSequenceAsString()
- Specified by:
getReverseComplementSequenceAsString
in interface uk.ac.roslin.ensembl.model.core.DNASequence
getObjectTypeMappings
public HashMap<uk.ac.roslin.ensembl.model.ObjectType,uk.ac.roslin.ensembl.model.MappingSet> getObjectTypeMappings()
- Specified by:
getObjectTypeMappings
in interface uk.ac.roslin.ensembl.model.core.DNASequence
getMappedRegions
public HashMap<uk.ac.roslin.ensembl.model.ObjectType,uk.ac.roslin.ensembl.model.CoordinateSet> getMappedRegions()
- Specified by:
getMappedRegions
in interface uk.ac.roslin.ensembl.model.core.DNASequence
getHashID
public String getHashID()
- Specified by:
getHashID
in interface uk.ac.roslin.ensembl.model.IdentifiableObject
toString
public String toString()
- Overrides:
toString
in class org.biojava3.core.sequence.template.AbstractSequence<org.biojava3.core.sequence.compound.NucleotideCompound>
clearAllMappings
public void clearAllMappings()
- Specified by:
clearAllMappings
in interface uk.ac.roslin.ensembl.model.MappableObject
getComparaDivision
public uk.ac.roslin.ensembl.config.EnsemblComparaDivision getComparaDivision()
getComparaFactory
public uk.ac.roslin.ensembl.dao.factory.DAOComparaFactory getComparaFactory(uk.ac.roslin.ensembl.config.EnsemblComparaDivision comparaDivision)
getComparaFactory
public uk.ac.roslin.ensembl.dao.factory.DAOComparaFactory getComparaFactory()
getAssembly
public String getAssembly()
- Specified by:
getAssembly
in interface uk.ac.roslin.ensembl.model.core.CoreObject
Ensembl Datasource Aware Module v1.09
© Roslin Institute 2010. GNU General Public License, version3