Package org.biojava.nbio.core.sequence
Class ProteinSequence
java.lang.Object
org.biojava.nbio.core.sequence.template.AbstractSequence<AminoAcidCompound>
org.biojava.nbio.core.sequence.ProteinSequence
- All Implemented Interfaces:
Iterable<AminoAcidCompound>,Accessioned,Sequence<AminoAcidCompound>
The representation of a ProteinSequence
- Author:
- Scooter Willis, Paolo Pavan
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Nested Class Summary
Nested classes/interfaces inherited from class org.biojava.nbio.core.sequence.template.AbstractSequence
AbstractSequence.AnnotationType -
Constructor Summary
ConstructorsConstructorDescriptionProteinSequence(String seqString) Create a protein from a stringProteinSequence(String seqString, CompoundSet<AminoAcidCompound> compoundSet) Create a protein from a string with a user defined set of amino acidsProteinSequence(ProxySequenceReader<AminoAcidCompound> proxyLoader) A protein sequence where the storage of the sequence is somewhere else.ProteinSequence(ProxySequenceReader<AminoAcidCompound> proxyLoader, CompoundSet<AminoAcidCompound> compoundSet) A protein sequence where the storage of the sequence is somewhere else with user defined set of amino acids. -
Method Summary
Modifier and TypeMethodDescriptionstatic voidvoidsetParentDNASequence(AbstractSequence<NucleotideCompound> parentDNASequence, Integer begin, Integer end) A Protein sequence can be stand alone or loaded from a transcript 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, 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, 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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ProteinSequence
Create a protein from a string- Parameters:
seqString-- Throws:
CompoundNotFoundException
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ProteinSequence
public ProteinSequence(String seqString, CompoundSet<AminoAcidCompound> compoundSet) throws CompoundNotFoundException Create a protein from a string with a user defined set of amino acids- Parameters:
seqString-compoundSet-- Throws:
CompoundNotFoundException
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ProteinSequence
A protein sequence where the storage of the sequence is somewhere else. Could be loaded from a large Fasta file or via a Uniprot Proxy reader via Uniprot ID- Parameters:
proxyLoader-
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ProteinSequence
public ProteinSequence(ProxySequenceReader<AminoAcidCompound> proxyLoader, CompoundSet<AminoAcidCompound> compoundSet) A protein sequence where the storage of the sequence is somewhere else with user defined set of amino acids. Could be loaded from a large Fasta file or via a Uniprot Proxy reader via Uniprot ID- Parameters:
proxyLoader-compoundSet-
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Method Details
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setParentDNASequence
public void setParentDNASequence(AbstractSequence<NucleotideCompound> parentDNASequence, Integer begin, Integer end) A Protein sequence can be stand alone or loaded from a transcript sequence. The design goal is to allow the creation of a Protein sequence from a Uniprot ID or some other Protein ID that based on cross reference you should be able to get the GeneSequence that codes for the protein if the CDS/Gene region is known. From the GeneSequence you should then be able to get the ChromosomeSequence which then allows you explore flaning regions of the gene sequences. The framework is in place to do this but currently hasn't been implement in the reverse direction starting from the Protein sequence.- Parameters:
parentDNASequence-begin-end-
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main
- Throws:
Exception
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