org.biojava.nbio.core.sequence.views

Class RnaSequenceView

java.lang.Object

org.biojava.nbio.core.sequence.template.SequenceProxyView<NucleotideCompound>

org.biojava.nbio.core.sequence.views.RnaSequenceView

All Implemented Interfaces:

Iterable<NucleotideCompound>, Accessioned, ProxySequenceReader<NucleotideCompound>, Sequence<NucleotideCompound>, SequenceReader<NucleotideCompound>, SequenceView<NucleotideCompound>

public class RnaSequenceView
extends SequenceProxyView<NucleotideCompound>
implements ProxySequenceReader<NucleotideCompound>

Attempts to do on the fly translation of RNA by not requesting the compounds until asked.

Author:

ayates

Constructor Summary

Constructors

Constructor and Description
RnaSequenceView(Sequence<NucleotideCompound> sourceDna)
RnaSequenceView(Sequence<NucleotideCompound> sourceDna, CompoundSet<NucleotideCompound> rnaCompounds)

Method Summary

Methods

Modifier and Type	Method and Description
protected void	buildTranslators()
NucleotideCompound	getCompoundAt(int position) Returns the Compound at the given biological index
Map<NucleotideCompound,NucleotideCompound>	getDnaToRna()
int	getIndexOf(NucleotideCompound compound) Scans through the Sequence looking for the first occurrence of the given compound
int	getLastIndexOf(NucleotideCompound compound) Scans through the Sequence looking for the last occurrence of the given compound
Map<NucleotideCompound,NucleotideCompound>	getRnaToDna()
String	getSequenceAsString() Returns the String representation of the Sequence
void	setCompoundSet(CompoundSet<NucleotideCompound> compoundSet)
void	setContents(String sequence)

Methods inherited from class org.biojava.nbio.core.sequence.template.SequenceProxyView

countCompounds, getAccession, getAsList, getBioEnd, getBioStart, getCompoundSet, getInverse, getLength, getSubSequence, getViewedSequence, iterator, setBioEnd, setBioStart

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.biojava.nbio.core.sequence.template.Sequence

countCompounds, getAsList, getCompoundSet, getInverse, getLength, getSubSequence

Methods inherited from interface java.lang.Iterable

iterator

Methods inherited from interface org.biojava.nbio.core.sequence.template.Accessioned

getAccession

Constructor Detail

RnaSequenceView

public RnaSequenceView(Sequence<NucleotideCompound> sourceDna)

RnaSequenceView

public RnaSequenceView(Sequence<NucleotideCompound> sourceDna,
               CompoundSet<NucleotideCompound> rnaCompounds)

Method Detail

getSequenceAsString

public String getSequenceAsString()

Description copied from interface: Sequence

Returns the String representation of the Sequence

Specified by:

getSequenceAsString in interface Sequence<NucleotideCompound>

Overrides:

getSequenceAsString in class SequenceProxyView<NucleotideCompound>

getCompoundAt

public NucleotideCompound getCompoundAt(int position)

Description copied from interface: Sequence

Returns the Compound at the given biological index

Specified by:

getCompoundAt in interface Sequence<NucleotideCompound>

Overrides:

getCompoundAt in class SequenceProxyView<NucleotideCompound>

Parameters:

position - Biological index (1 to n)

Returns:

Compound at the specified position

getIndexOf

public int getIndexOf(NucleotideCompound compound)

Description copied from interface: Sequence

Scans through the Sequence looking for the first occurrence of the given compound

Specified by:

getIndexOf in interface Sequence<NucleotideCompound>

Overrides:

getIndexOf in class SequenceProxyView<NucleotideCompound>

Parameters:

compound - Compounds to look for

Returns:

Index of the first position of the compound in the sequence (1 to n)

getLastIndexOf

public int getLastIndexOf(NucleotideCompound compound)

Description copied from interface: Sequence

Scans through the Sequence looking for the last occurrence of the given compound

Specified by:

getLastIndexOf in interface Sequence<NucleotideCompound>

Overrides:

getLastIndexOf in class SequenceProxyView<NucleotideCompound>

Parameters:

compound - Compounds to look for

Returns:

Index of the last position of the compound in the sequence (1 to n)

getRnaToDna

public Map<NucleotideCompound,NucleotideCompound> getRnaToDna()

getDnaToRna

public Map<NucleotideCompound,NucleotideCompound> getDnaToRna()

buildTranslators

protected void buildTranslators()

setCompoundSet

public void setCompoundSet(CompoundSet<NucleotideCompound> compoundSet)

Specified by:

setCompoundSet in interface SequenceReader<NucleotideCompound>

setContents

public void setContents(String sequence)
                 throws CompoundNotFoundException

Specified by:

setContents in interface SequenceReader<NucleotideCompound>

Throws:

CompoundNotFoundException