Package 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>
RNASequence where RNACompoundSet are the allowed values
- Author:
- Scooter Willis
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Nested Class Summary
Nested classes/interfaces inherited from class org.biojava.nbio.core.sequence.template.AbstractSequence
AbstractSequence.AnnotationType -
Constructor Summary
ConstructorsConstructorDescriptionRNASequence(String seqString) Create a RNA sequence from a StringRNASequence(String seqString, CompoundSet<NucleotideCompound> compoundSet) Create a RNA sequence from a string with a user defined RNA compound setRNASequence(ProxySequenceReader<NucleotideCompound> proxyLoader) Create a RNA aequence from a proxy readerRNASequence(ProxySequenceReader<NucleotideCompound> proxyLoader, CompoundSet<NucleotideCompound> compoundSet) Create a RNA sequence from a proxy reader and user defined RNA compound set -
Method Summary
Modifier and TypeMethodDescriptionGet the complement view of the RNA sequencedoublegetGC()Get the inverse view of the sequence.Get the ProteinSequence from the RNA sequenceGet the ProteinSequene from the RNA sequence with user defined transcription engineGet reverse complement view of the sequenceMethods 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, toStringMethods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, waitMethods inherited from interface java.lang.Iterable
forEach, spliterator
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Constructor Details
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RNASequence
Create a RNA sequence from a String- Parameters:
seqString-- Throws:
CompoundNotFoundException
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RNASequence
Create a RNA aequence from a proxy reader- Parameters:
proxyLoader-
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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
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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-
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Method Details
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getReverseComplement
Get reverse complement view of the sequence- Returns:
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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:
getInversein interfaceSequence<NucleotideCompound>- Overrides:
getInversein classAbstractSequence<NucleotideCompound>- Returns:
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getComplement
Get the complement view of the RNA sequence- Returns:
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getProteinSequence
Get the ProteinSequence from the RNA sequence- Returns:
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getProteinSequence
Get the ProteinSequene from the RNA sequence with user defined transcription engine- Parameters:
engine-- Returns:
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getGC
public double getGC()
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