org.biojava3.core.sequence
Class RNASequence

java.lang.Object
  extended by org.biojava3.core.sequence.template.AbstractSequence<NucleotideCompound>
      extended by org.biojava3.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.biojava3.core.sequence.template.AbstractSequence
AbstractSequence.AnnotationType
 
Constructor Summary
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
 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.biojava3.core.sequence.template.AbstractSequence
addFeature, addFeature, addNote, countCompounds, getAccession, getAnnotationType, getAsList, getBioBegin, getBioEnd, getCompoundAt, getCompoundSet, getDatabaseReferences, getDescription, 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, 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)
Create a RNA sequence from a String

Parameters:
seqString -

RNASequence

public RNASequence(ProxySequenceReader<NucleotideCompound> proxyLoader)
Create a RNA aequence from a proxy reader

Parameters:
proxyLoader -

RNASequence

public RNASequence(String seqString,
                   CompoundSet<NucleotideCompound> compoundSet)
Create a RNA sequence from a string with a user defined RNA compound set

Parameters:
seqString -
compoundSet -

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()