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 DAEnsemblDNASequenceReader

java.lang.Object
  extended by uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader
All Implemented Interfaces:
Serializable, Iterable<org.biojava3.core.sequence.compound.NucleotideCompound>, org.biojava3.core.sequence.template.Accessioned, org.biojava3.core.sequence.template.ProxySequenceReader<org.biojava3.core.sequence.compound.NucleotideCompound>, org.biojava3.core.sequence.template.Sequence<org.biojava3.core.sequence.compound.NucleotideCompound>, org.biojava3.core.sequence.template.SequenceReader<org.biojava3.core.sequence.compound.NucleotideCompound>, uk.ac.roslin.ensembl.biojava3.EnsemblDNASequenceReader

public class DAEnsemblDNASequenceReader
extends Object
implements uk.ac.roslin.ensembl.biojava3.EnsemblDNASequenceReader

Author:
paterson
See Also:
Serialized Form

Nested Class Summary
static class DAEnsemblDNASequenceReader.EmptyIterator<NucleotideCompound>
           
 
Field Summary
protected  uk.ac.roslin.ensembl.biojava3.EnsemblDNACompoundSet compoundSet
           
protected  Integer coordSystemID
           
protected  DADNASequence dASequence
           
protected  uk.ac.roslin.ensembl.dao.factory.DAOCoreFactory factory
           
protected  Integer length
           
protected  String name
           
protected  DADNASequence parent
           
protected  Integer seqRegionID
           
protected  String sequence
           
 
Constructor Summary
DAEnsemblDNASequenceReader()
           
DAEnsemblDNASequenceReader(Integer coordSystemID, Integer seqRegionID, Integer length, String name, uk.ac.roslin.ensembl.dao.factory.DAOCoreFactory factory)
           
 
Method Summary
 int countCompounds(org.biojava3.core.sequence.compound.NucleotideCompound... compounds)
           
 org.biojava3.core.sequence.AccessionID getAccession()
           
 List<org.biojava3.core.sequence.compound.NucleotideCompound> getAsList()
           
 org.biojava3.core.sequence.compound.NucleotideCompound getCompoundAt(int position)
           
 org.biojava3.core.sequence.template.CompoundSet<org.biojava3.core.sequence.compound.NucleotideCompound> getCompoundSet()
           
 Integer getCoordSystemID()
           
 uk.ac.roslin.ensembl.dao.factory.DAOCoreFactory getFactory()
           
 int getIndexOf(org.biojava3.core.sequence.compound.NucleotideCompound compound)
           
 org.biojava3.core.sequence.template.SequenceView<org.biojava3.core.sequence.compound.NucleotideCompound> getInverse()
           
 int getLastIndexOf(org.biojava3.core.sequence.compound.NucleotideCompound compound)
           
 int getLength()
           
 Integer getLengthInteger()
           
 String getName()
           
 DADNASequence getParent()
           
 String getReverseComplementSequenceAsString(Integer start, Integer end)
           
 Integer getSeqRegionID()
           
 String getSequenceAsString()
           
 String getSequenceAsString(Integer start, Integer end, org.biojava3.core.sequence.Strand strand)
           
 org.biojava3.core.sequence.template.SequenceView<org.biojava3.core.sequence.compound.NucleotideCompound> getSubSequence(Integer start, Integer end)
           
 Iterator<org.biojava3.core.sequence.compound.NucleotideCompound> iterator()
           
 void setCompoundSet(org.biojava3.core.sequence.template.CompoundSet compoundSet)
           
 void setContents(String sequence)
           
 void setCoordSystemID(Integer coordSystemID)
           
 void setFactory(uk.ac.roslin.ensembl.dao.factory.DAOCoreFactory factory)
           
 void setLength(Integer length)
           
 void setName(String name)
           
 void setParent(DADNASequence parent)
           
 void setSeqRegionID(Integer seqRegionID)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

sequence

protected String sequence

compoundSet

protected uk.ac.roslin.ensembl.biojava3.EnsemblDNACompoundSet compoundSet

dASequence

protected DADNASequence dASequence

coordSystemID

protected Integer coordSystemID

seqRegionID

protected Integer seqRegionID

length

protected Integer length

name

protected String name

factory

protected uk.ac.roslin.ensembl.dao.factory.DAOCoreFactory factory

parent

protected DADNASequence parent
Constructor Detail

DAEnsemblDNASequenceReader

public DAEnsemblDNASequenceReader()

DAEnsemblDNASequenceReader

public DAEnsemblDNASequenceReader(Integer coordSystemID,
                                  Integer seqRegionID,
                                  Integer length,
                                  String name,
                                  uk.ac.roslin.ensembl.dao.factory.DAOCoreFactory factory)
Method Detail

getParent

public DADNASequence getParent()

setParent

public void setParent(DADNASequence parent)

getFactory

public uk.ac.roslin.ensembl.dao.factory.DAOCoreFactory getFactory()

setFactory

public void setFactory(uk.ac.roslin.ensembl.dao.factory.DAOCoreFactory factory)

getName

public String getName()
Specified by:
getName in interface uk.ac.roslin.ensembl.biojava3.EnsemblDNASequenceReader

setName

public void setName(String name)
Specified by:
setName in interface uk.ac.roslin.ensembl.biojava3.EnsemblDNASequenceReader

getCoordSystemID

public Integer getCoordSystemID()
Specified by:
getCoordSystemID in interface uk.ac.roslin.ensembl.biojava3.EnsemblDNASequenceReader

setCoordSystemID

public void setCoordSystemID(Integer coordSystemID)
Specified by:
setCoordSystemID in interface uk.ac.roslin.ensembl.biojava3.EnsemblDNASequenceReader

getLength

public int getLength()
Specified by:
getLength in interface org.biojava3.core.sequence.template.Sequence<org.biojava3.core.sequence.compound.NucleotideCompound>

getLengthInteger

public Integer getLengthInteger()
Specified by:
getLengthInteger in interface uk.ac.roslin.ensembl.biojava3.EnsemblDNASequenceReader

setLength

public void setLength(Integer length)
Specified by:
setLength in interface uk.ac.roslin.ensembl.biojava3.EnsemblDNASequenceReader

getSeqRegionID

public Integer getSeqRegionID()
Specified by:
getSeqRegionID in interface uk.ac.roslin.ensembl.biojava3.EnsemblDNASequenceReader

setSeqRegionID

public void setSeqRegionID(Integer seqRegionID)
Specified by:
setSeqRegionID in interface uk.ac.roslin.ensembl.biojava3.EnsemblDNASequenceReader

setCompoundSet

public void setCompoundSet(org.biojava3.core.sequence.template.CompoundSet compoundSet)
Specified by:
setCompoundSet in interface org.biojava3.core.sequence.template.SequenceReader<org.biojava3.core.sequence.compound.NucleotideCompound>

setContents

public void setContents(String sequence)
Specified by:
setContents in interface org.biojava3.core.sequence.template.SequenceReader<org.biojava3.core.sequence.compound.NucleotideCompound>

getCompoundAt

public org.biojava3.core.sequence.compound.NucleotideCompound getCompoundAt(int position)
Specified by:
getCompoundAt in interface org.biojava3.core.sequence.template.Sequence<org.biojava3.core.sequence.compound.NucleotideCompound>

getIndexOf

public int getIndexOf(org.biojava3.core.sequence.compound.NucleotideCompound compound)
Specified by:
getIndexOf in interface org.biojava3.core.sequence.template.Sequence<org.biojava3.core.sequence.compound.NucleotideCompound>

getLastIndexOf

public int getLastIndexOf(org.biojava3.core.sequence.compound.NucleotideCompound compound)
Specified by:
getLastIndexOf in interface org.biojava3.core.sequence.template.Sequence<org.biojava3.core.sequence.compound.NucleotideCompound>

getSequenceAsString

public String getSequenceAsString()
Specified by:
getSequenceAsString in interface org.biojava3.core.sequence.template.Sequence<org.biojava3.core.sequence.compound.NucleotideCompound>

getSequenceAsString

public String getSequenceAsString(Integer start,
                                  Integer end,
                                  org.biojava3.core.sequence.Strand strand)

getReverseComplementSequenceAsString

public String getReverseComplementSequenceAsString(Integer start,
                                                   Integer end)
Specified by:
getReverseComplementSequenceAsString in interface uk.ac.roslin.ensembl.biojava3.EnsemblDNASequenceReader

getAsList

public List<org.biojava3.core.sequence.compound.NucleotideCompound> getAsList()
Specified by:
getAsList in interface org.biojava3.core.sequence.template.Sequence<org.biojava3.core.sequence.compound.NucleotideCompound>

getSubSequence

public org.biojava3.core.sequence.template.SequenceView<org.biojava3.core.sequence.compound.NucleotideCompound> getSubSequence(Integer start,
                                                                                                                               Integer end)
Specified by:
getSubSequence in interface org.biojava3.core.sequence.template.Sequence<org.biojava3.core.sequence.compound.NucleotideCompound>

getCompoundSet

public org.biojava3.core.sequence.template.CompoundSet<org.biojava3.core.sequence.compound.NucleotideCompound> getCompoundSet()
Specified by:
getCompoundSet in interface org.biojava3.core.sequence.template.Sequence<org.biojava3.core.sequence.compound.NucleotideCompound>

getAccession

public org.biojava3.core.sequence.AccessionID getAccession()
Specified by:
getAccession in interface org.biojava3.core.sequence.template.Accessioned

countCompounds

public int countCompounds(org.biojava3.core.sequence.compound.NucleotideCompound... compounds)
Specified by:
countCompounds in interface org.biojava3.core.sequence.template.Sequence<org.biojava3.core.sequence.compound.NucleotideCompound>

iterator

public Iterator<org.biojava3.core.sequence.compound.NucleotideCompound> iterator()
Specified by:
iterator in interface Iterable<org.biojava3.core.sequence.compound.NucleotideCompound>

getInverse

public org.biojava3.core.sequence.template.SequenceView<org.biojava3.core.sequence.compound.NucleotideCompound> getInverse()
Specified by:
getInverse in interface org.biojava3.core.sequence.template.Sequence<org.biojava3.core.sequence.compound.NucleotideCompound>

Ensembl Datasource Aware Module
v1.09

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