uk.ac.roslin.ensembl.datasourceaware.core

Class DAEnsemblDNASequenceReader

java.lang.Object

uk.ac.roslin.ensembl.datasourceaware.core.DAEnsemblDNASequenceReader

All Implemented Interfaces:

Serializable, Iterable<NucleotideCompound>, Accessioned, ProxySequenceReader<NucleotideCompound>, Sequence<NucleotideCompound>, SequenceReader<NucleotideCompound>, EnsemblDNASequenceReader

public class DAEnsemblDNASequenceReader
extends Object
implements EnsemblDNASequenceReader

Author:

paterson

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	DAEnsemblDNASequenceReader.EmptyIterator<NucleotideCompound>

Field Summary

Fields

Modifier and Type	Field and Description
protected EnsemblDNACompoundSet	compoundSet
protected Integer	coordSystemID
protected DADNASequence	dASequence
protected DAOCoreFactory	factory
protected Integer	length
protected String	name
protected DADNASequence	parent
protected Integer	seqRegionID
protected String	sequence

Constructor Summary

Constructors

Constructor and Description
DAEnsemblDNASequenceReader()
DAEnsemblDNASequenceReader(Integer coordSystemID, Integer seqRegionID, Integer length, String name, DAOCoreFactory factory)

Method Summary

Methods

Modifier and Type	Method and Description
int	countCompounds(NucleotideCompound... compounds)
AccessionID	getAccession()
List<NucleotideCompound>	getAsList()
NucleotideCompound	getCompoundAt(int position)
CompoundSet<NucleotideCompound>	getCompoundSet()
Integer	getCoordSystemID()
DAOCoreFactory	getFactory()
int	getIndexOf(NucleotideCompound compound)
SequenceView<NucleotideCompound>	getInverse()
int	getLastIndexOf(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, Strand strand)
SequenceView<NucleotideCompound>	getSubSequence(Integer start, Integer end)
Iterator<NucleotideCompound>	iterator()
void	setCompoundSet(CompoundSet compoundSet)
void	setContents(String sequence)
void	setCoordSystemID(Integer coordSystemID)
void	setFactory(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 EnsemblDNACompoundSet compoundSet

dASequence

protected DADNASequence dASequence

coordSystemID

protected Integer coordSystemID

seqRegionID

protected Integer seqRegionID

length

protected Integer length

name

protected String name

factory

protected DAOCoreFactory factory

parent

protected DADNASequence parent

Constructor Detail

DAEnsemblDNASequenceReader

public DAEnsemblDNASequenceReader()

DAEnsemblDNASequenceReader

public DAEnsemblDNASequenceReader(Integer coordSystemID,
                          Integer seqRegionID,
                          Integer length,
                          String name,
                          DAOCoreFactory factory)

Method Detail

getParent

public DADNASequence getParent()

setParent

public void setParent(DADNASequence parent)

getFactory

public DAOCoreFactory getFactory()

setFactory

public void setFactory(DAOCoreFactory factory)

getName

public String getName()

Specified by:

getName in interface EnsemblDNASequenceReader

setName

public void setName(String name)

Specified by:

setName in interface EnsemblDNASequenceReader

getCoordSystemID

public Integer getCoordSystemID()

Specified by:

getCoordSystemID in interface EnsemblDNASequenceReader

setCoordSystemID

public void setCoordSystemID(Integer coordSystemID)

Specified by:

setCoordSystemID in interface EnsemblDNASequenceReader

getLength

public int getLength()

Specified by:

getLength in interface Sequence<NucleotideCompound>

getLengthInteger

public Integer getLengthInteger()

Specified by:

getLengthInteger in interface EnsemblDNASequenceReader

setLength

public void setLength(Integer length)

Specified by:

setLength in interface EnsemblDNASequenceReader

getSeqRegionID

public Integer getSeqRegionID()

Specified by:

getSeqRegionID in interface EnsemblDNASequenceReader

setSeqRegionID

public void setSeqRegionID(Integer seqRegionID)

Specified by:

setSeqRegionID in interface EnsemblDNASequenceReader

setCompoundSet

public void setCompoundSet(CompoundSet compoundSet)

Specified by:

setCompoundSet in interface SequenceReader<NucleotideCompound>

setContents

public void setContents(String sequence)

Specified by:

setContents in interface SequenceReader<NucleotideCompound>

getCompoundAt

public NucleotideCompound getCompoundAt(int position)

Specified by:

getCompoundAt in interface Sequence<NucleotideCompound>

getIndexOf

public int getIndexOf(NucleotideCompound compound)

Specified by:

getIndexOf in interface Sequence<NucleotideCompound>

getLastIndexOf

public int getLastIndexOf(NucleotideCompound compound)

Specified by:

getLastIndexOf in interface Sequence<NucleotideCompound>

getSequenceAsString

public String getSequenceAsString()

Specified by:

getSequenceAsString in interface Sequence<NucleotideCompound>

getSequenceAsString

public String getSequenceAsString(Integer start,
                         Integer end,
                         Strand strand)

getReverseComplementSequenceAsString

public String getReverseComplementSequenceAsString(Integer start,
                                          Integer end)

Specified by:

getReverseComplementSequenceAsString in interface EnsemblDNASequenceReader

getAsList

public List<NucleotideCompound> getAsList()

Specified by:

getAsList in interface Sequence<NucleotideCompound>

getSubSequence

public SequenceView<NucleotideCompound> getSubSequence(Integer start,
                                              Integer end)

Specified by:

getSubSequence in interface Sequence<NucleotideCompound>

getCompoundSet

public CompoundSet<NucleotideCompound> getCompoundSet()

Specified by:

getCompoundSet in interface Sequence<NucleotideCompound>

getAccession

public AccessionID getAccession()

Specified by:

getAccession in interface Accessioned

countCompounds

public int countCompounds(NucleotideCompound... compounds)

Specified by:

countCompounds in interface Sequence<NucleotideCompound>

iterator

public Iterator<NucleotideCompound> iterator()

Specified by:

iterator in interface Iterable<NucleotideCompound>

getInverse

public SequenceView<NucleotideCompound> getInverse()

Specified by:

getInverse in interface Sequence<NucleotideCompound>