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>

public class ProteinSequence
extends AbstractSequence<AminoAcidCompound>

The representation of a ProteinSequence

Author:

Scooter Willis, Paolo Pavan

Nested Class Summary

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

AbstractSequence.AnnotationType

Constructor Summary

Constructors

Constructor and Description
ProteinSequence(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.
ProteinSequence(String seqString) Create a protein from a string
ProteinSequence(String seqString, CompoundSet<AminoAcidCompound> compoundSet) Create a protein from a string with a user defined set of amino acids

Method Summary

Modifier and Type	Method and Description
static void	main(String[] args)
void	setParentDNASequence(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, 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 Detail

ProteinSequence

public ProteinSequence(String seqString)
                throws CompoundNotFoundException

Create a protein from a string

Parameters:

seqString -

Throws:

CompoundNotFoundException

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

ProteinSequence

public ProteinSequence(ProxySequenceReader<AminoAcidCompound> proxyLoader)

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 -

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 -

Method Detail

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 -

main

public static void main(String[] args)
                 throws Exception

Throws:

Exception