Ensembl Datasource Aware Module v1.09
© Roslin Institute 2010. GNU General Public License, version3
uk.ac.roslin.ensembl.datasourceaware.core
Class DAEnsemblDNASequenceReader
java.lang.Object
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
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
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
DAEnsemblDNASequenceReader
public DAEnsemblDNASequenceReader()
DAEnsemblDNASequenceReader
public DAEnsemblDNASequenceReader(Integer coordSystemID,
Integer seqRegionID,
Integer length,
String name,
uk.ac.roslin.ensembl.dao.factory.DAOCoreFactory factory)
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
© Roslin Institute 2010. GNU General Public License, version3