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 enum

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)

static void

main(String[] args)

void

setDNAType(DNASequence.DNAType dnaType)

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, getInverse, 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

Methods inherited from interface java.lang.Iterable
forEach, spliterator

Constructor Details
- 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 Details
- 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
- main
  
  public static void main(String[] args) throws Exception
  
  Throws:
  
  Exception

Class DNASequence

Nested Class Summary

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

Constructor Summary

Method Summary

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

Methods inherited from class java.lang.Object

Methods inherited from interface java.lang.Iterable

Constructor Details

DNASequence

DNASequence

DNASequence

DNASequence

DNASequence

Method Details

getRNASequence

getRNASequence

getRNASequence

getRNASequence

getGCCount

getReverse

getComplement

getReverseComplement

getDNAType

setDNAType

main