org.biojava.nbio.core.sequence

Class RNASequence

java.lang.Object

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

org.biojava.nbio.core.sequence.RNASequence

All Implemented Interfaces:

Iterable<NucleotideCompound>, Accessioned, Sequence<NucleotideCompound>

public class RNASequence
extends AbstractSequence<NucleotideCompound>

RNASequence where RNACompoundSet are the allowed values

Author:

Scooter Willis

Nested Class Summary

Nested classes/interfaces inherited from class org.biojava.nbio.core.sequence.template.AbstractSequence

AbstractSequence.AnnotationType

Constructor Summary

Constructors

Constructor and Description
RNASequence(ProxySequenceReader<NucleotideCompound> proxyLoader) Create a RNA aequence from a proxy reader
RNASequence(ProxySequenceReader<NucleotideCompound> proxyLoader, CompoundSet<NucleotideCompound> compoundSet) Create a RNA sequence from a proxy reader and user defined RNA compound set
RNASequence(String seqString) Create a RNA sequence from a String
RNASequence(String seqString, CompoundSet<NucleotideCompound> compoundSet) Create a RNA sequence from a string with a user defined RNA compound set

Method Summary

Methods

Modifier and Type	Method and Description
SequenceView<NucleotideCompound>	getComplement() Get the complement view of the RNA sequence
double	getGC()
SequenceView<NucleotideCompound>	getInverse() Get the inverse view of the sequence.
ProteinSequence	getProteinSequence() Get the ProteinSequence from the RNA sequence
ProteinSequence	getProteinSequence(TranscriptionEngine engine) Get the ProteinSequene from the RNA sequence with user defined transcription engine
SequenceView<NucleotideCompound>	getReverseComplement() Get reverse complement view of the sequence

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

addFeature, addFeature, addNote, countCompounds, getAccession, getAnnotationType, getAsList, getBioBegin, getBioEnd, getCompoundAt, getCompoundSet, getDatabaseReferences, getDescription, getFeatureRetriever, getFeatures, getFeatures, getFeatures, getFeaturesByType, getFeaturesKeyWord, getIndexOf, getLastIndexOf, getLength, getNotesList, getOriginalHeader, getParentSequence, getProxySequenceReader, getSequenceAsString, getSequenceAsString, getSequenceScore, getSource, getSubSequence, getTaxonomy, getUserCollection, iterator, removeFeature, removeNote, setAccession, setAnnotationType, setBioBegin, setBioEnd, setCompoundSet, setDatabaseReferences, setDescription, setFeatureRetriever, setFeaturesKeyWord, setNotesList, setOriginalHeader, setParentSequence, setProxySequenceReader, setSequenceScore, setSource, setTaxonomy, setUserCollection, toString

Methods inherited from class java.lang.Object

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

Constructor Detail

RNASequence

public RNASequence(String seqString)
            throws CompoundNotFoundException

Create a RNA sequence from a String

Parameters:

seqString -

Throws:

CompoundNotFoundException

RNASequence

public RNASequence(ProxySequenceReader<NucleotideCompound> proxyLoader)

Create a RNA aequence from a proxy reader

Parameters:

proxyLoader -

RNASequence

public RNASequence(String seqString,
           CompoundSet<NucleotideCompound> compoundSet)
            throws CompoundNotFoundException

Create a RNA sequence from a string with a user defined RNA compound set

Parameters:

seqString -

compoundSet -

Throws:

CompoundNotFoundException

RNASequence

public RNASequence(ProxySequenceReader<NucleotideCompound> proxyLoader,
           CompoundSet<NucleotideCompound> compoundSet)

Create a RNA sequence from a proxy reader and user defined RNA compound set

Parameters:

proxyLoader -

compoundSet -

Method Detail

getReverseComplement

public SequenceView<NucleotideCompound> getReverseComplement()

Get reverse complement view of the sequence

Returns:

getInverse

public SequenceView<NucleotideCompound> getInverse()

Get the inverse view of the sequence. It is the reverse sequence from end to begin where use reverse could imply complement. Called getInverse() in the hopes of making less confusing.

Specified by:

getInverse in interface Sequence<NucleotideCompound>

Overrides:

getInverse in class AbstractSequence<NucleotideCompound>

Returns:

getComplement

public SequenceView<NucleotideCompound> getComplement()

Get the complement view of the RNA sequence

Returns:

getProteinSequence

public ProteinSequence getProteinSequence()

Get the ProteinSequence from the RNA sequence

Returns:

getProteinSequence

public ProteinSequence getProteinSequence(TranscriptionEngine engine)

Get the ProteinSequene from the RNA sequence with user defined transcription engine

Parameters:

engine -

Returns:

getGC

public double getGC()