Package org.biojava.nbio.core.sequence

Class DNASequence

java.lang.Object

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

org.biojava.nbio.core.sequence.DNASequence

All Implemented Interfaces:

Iterable<NucleotideCompound>, Accessioned, Sequence<NucleotideCompound>

Direct Known Subclasses:

CDSSequence, ChromosomeSequence, ExonSequence, GeneSequence, IntronSequence, StartCodonSequence, StopCodonSequence, TranscriptSequence

public class DNASequence
extends AbstractSequence<NucleotideCompound>

This is class should model the attributes associated with a DNA sequence

Author:

Scooter Willis

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	DNASequence.DNAType	The type of DNA sequence

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

AbstractSequence.AnnotationType

Constructor Summary

Constructors

Constructor	Description
DNASequence()	Shouldn't be used but makes it bean happy
DNASequence(String seqString)	String is king and create a sequence from DNA with default DNA compound set
DNASequence(String seqString, CompoundSet<NucleotideCompound> compoundSet)	Create a sequence from a string with user defined compound set
DNASequence(SequenceReader<NucleotideCompound> proxyLoader)	Create a sequence where the actual storage of the sequence data is somewhere else
DNASequence(SequenceReader<NucleotideCompound> proxyLoader, CompoundSet<NucleotideCompound> compoundSet)	Create a sequence from a ProxySequencereader and user defined compound set

Method Summary

Modifier and Type	Method	Description
SequenceView<NucleotideCompound>	getComplement()	Returns a Sequence which will complement every base
DNASequence.DNAType	getDNAType()
int	getGCCount()	Get the GC count in the DNA Sequence
SequenceView<NucleotideCompound>	getReverse()	Returns a Sequence which runs in the current reverse order
SequenceView<NucleotideCompound>	getReverseComplement()	Delegates to AbstractSequence.getInverse() for the reverse complement
RNASequence	getRNASequence()	Return the RNASequence equivalent of the DNASequence using default Transcription Engine.
RNASequence	getRNASequence(Frame frame)	Allows the user to pass in the Frame shift.
RNASequence	getRNASequence(TranscriptionEngine engine)	Allow a user to pass in a rules engine to do the DNA to RNA translation
RNASequence	getRNASequence(TranscriptionEngine engine, Frame frame)
void	setDNAType(DNASequence.DNAType dnaType)

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

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

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Constructor Detail

DNASequence

public DNASequence()

Shouldn't be used but makes it bean happy

DNASequence

public DNASequence(String seqString)
            throws CompoundNotFoundException

String is king and create a sequence from DNA with default DNA compound set

Parameters:

seqString -

Throws:

CompoundNotFoundException

DNASequence

public DNASequence(SequenceReader<NucleotideCompound> proxyLoader)

Create a sequence where the actual storage of the sequence data is somewhere else

Parameters:

proxyLoader -

DNASequence

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

Create a sequence from a string with user defined compound set

Parameters:

seqString -

compoundSet -

Throws:

CompoundNotFoundException

DNASequence

public DNASequence(SequenceReader<NucleotideCompound> proxyLoader,
                   CompoundSet<NucleotideCompound> compoundSet)

Create a sequence from a ProxySequencereader and user defined compound set

Parameters:

proxyLoader -

compoundSet -

Method Detail

getRNASequence

public RNASequence getRNASequence()

Return the RNASequence equivalent of the DNASequence using default Transcription Engine. Not all species follow the same rules. If you don't know better use this method

Returns:

RNA sequence

getRNASequence

public RNASequence getRNASequence(TranscriptionEngine engine)

Allow a user to pass in a rules engine to do the DNA to RNA translation

Parameters:

engine -

Returns:

RNA sequence

getRNASequence

public RNASequence getRNASequence(Frame frame)

Allows the user to pass in the Frame shift.

Parameters:

frame -

Returns:

rna sequence

getRNASequence

public RNASequence getRNASequence(TranscriptionEngine engine,
                                  Frame frame)

getGCCount

public int getGCCount()

Get the GC count in the DNA Sequence

Returns:

GC count

getReverse

public SequenceView<NucleotideCompound> getReverse()

Returns a Sequence which runs in the current reverse order

getComplement

public SequenceView<NucleotideCompound> getComplement()

Returns a Sequence which will complement every base

getReverseComplement

public SequenceView<NucleotideCompound> getReverseComplement()

Delegates to AbstractSequence.getInverse() for the reverse complement

getDNAType

public DNASequence.DNAType getDNAType()

Returns:

the dnaType

setDNAType

public void setDNAType(DNASequence.DNAType dnaType)

Parameters:

dnaType - the dnaType to set