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 DADNASequence

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
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 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
protected  HashMap<uk.ac.roslin.ensembl.config.EnsemblComparaDivision,uk.ac.roslin.ensembl.dao.factory.DAOComparaFactory> comparaFactories
           
protected  uk.ac.roslin.ensembl.model.core.CoordinateSystem coordSystem
           
protected  uk.ac.roslin.ensembl.dao.factory.DAOFactory daoFactory
           
protected  Integer DBSeqLength
           
protected  String dbSpeciesName
           
protected  String dbVersion
           
protected  Integer id
           
protected  HashMap<uk.ac.roslin.ensembl.model.ObjectType,uk.ac.roslin.ensembl.model.CoordinateSet> mappedRegions
           
protected  uk.ac.roslin.ensembl.model.MappingSet mappings
           
protected  String name
           
protected  HashMap<uk.ac.roslin.ensembl.model.ObjectType,uk.ac.roslin.ensembl.model.MappingSet> objectTypeMappings
           
protected  uk.ac.roslin.ensembl.model.database.Registry registry
           
protected  String schemaVersion
           
protected  Integer seqRegionID
           
protected  uk.ac.roslin.ensembl.model.core.Species species
           
 
Constructor Summary
DADNASequence()
           
DADNASequence(DAEnsemblDNASequenceReader proxyLoader)
           
DADNASequence(uk.ac.roslin.ensembl.dao.factory.DAOCoreFactory factory)
           
DADNASequence(String sequence)
           
 
Method Summary
 Boolean addMapping(uk.ac.roslin.ensembl.model.Mapping mapping)
           
 void clearAllMappings()
           
 String getAssembly()
           
 Integer getBioEnd()
           
 uk.ac.roslin.ensembl.config.EnsemblComparaDivision getComparaDivision()
           
 uk.ac.roslin.ensembl.dao.factory.DAOComparaFactory getComparaFactory()
           
 uk.ac.roslin.ensembl.dao.factory.DAOComparaFactory getComparaFactory(uk.ac.roslin.ensembl.config.EnsemblComparaDivision comparaDivision)
           
 uk.ac.roslin.ensembl.model.core.CoordinateSystem getCoordSystem()
           
 uk.ac.roslin.ensembl.dao.factory.DAOCoreFactory getDaoFactory()
           
 String getDBName()
           
 Integer getDBSeqLength()
           
 String getDBVersion()
           
 List<DAGene> getGenesOnRegion(uk.ac.roslin.ensembl.model.Coordinate coord)
           
 List<DAGene> getGenesOnRegion(Integer start, Integer stop)
           
 List<DAGene> getGenesOnRegion(Integer start, Integer stop, uk.ac.roslin.ensembl.model.Coordinate.Strand strand)
           
 String getHashID()
           
 Integer getId()
           
 int getLength()
           
 HashMap<uk.ac.roslin.ensembl.model.ObjectType,uk.ac.roslin.ensembl.model.CoordinateSet> getMappedRegions()
           
 uk.ac.roslin.ensembl.model.MappingSet getMappings()
           
 uk.ac.roslin.ensembl.model.MappingSet getMappings(uk.ac.roslin.ensembl.model.ObjectType targetType)
           
 String getName()
           
 HashMap<uk.ac.roslin.ensembl.model.ObjectType,uk.ac.roslin.ensembl.model.MappingSet> getObjectTypeMappings()
           
 uk.ac.roslin.ensembl.model.database.Registry getRegistry()
           
 String getReverseComplementSequenceAsString()
           
 String getReverseComplementSequenceAsString(Integer begin, Integer end)
           
 String getSchemaVersion()
           
 String getSequenceAsString(Integer begin, Integer end)
           
 uk.ac.roslin.ensembl.model.core.Species getSpecies()
           
 uk.ac.roslin.ensembl.model.ObjectType getType()
           
 void setCoordSystem(uk.ac.roslin.ensembl.model.core.CoordinateSystem coordSystem)
           
 void setDaoFactory(uk.ac.roslin.ensembl.dao.factory.DAOFactory daoFactory)
           
 void setDBSeqLength(Integer seqLength)
           
 void setId(Integer id)
           
 void setName(String name)
           
 void setRegistry(uk.ac.roslin.ensembl.model.database.Registry datasource)
           
 void setSequenceStorage(DAEnsemblDNASequenceReader proxyLoader)
           
 void setSpecies(uk.ac.roslin.ensembl.model.core.Species species)
           
 String toString()
           
 
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 class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 
Methods inherited from interface org.biojava3.core.sequence.template.Sequence
countCompounds, getAsList, getCompoundAt, getCompoundSet, getIndexOf, getInverse, getLastIndexOf, getSequenceAsString, getSubSequence
 
Methods inherited from interface java.lang.Iterable
iterator
 
Methods inherited from interface org.biojava3.core.sequence.template.Accessioned
getAccession
 

Field Detail

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
Constructor Detail

DADNASequence

public DADNASequence()

DADNASequence

public DADNASequence(DAEnsemblDNASequenceReader proxyLoader)

DADNASequence

public DADNASequence(String sequence)

DADNASequence

public DADNASequence(uk.ac.roslin.ensembl.dao.factory.DAOCoreFactory factory)
Method Detail

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

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