org.biojava3.core.sequence
Class ProteinSequence

java.lang.Object
  extended by org.biojava3.core.sequence.template.AbstractSequence<AminoAcidCompound>
      extended by org.biojava3.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

Nested Class Summary
 
Nested classes/interfaces inherited from class org.biojava3.core.sequence.template.AbstractSequence
AbstractSequence.AnnotationType
 
Constructor Summary
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
static void main(String[] args)
           
 void setParentDNASequence(AbstractSequence parentDNASequence, Integer begin, Integer end)
          A Protein sequence can be stand alone or loaded from a transcript 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, getInverse, 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

ProteinSequence

public ProteinSequence(String seqString)
Create a protein from a string

Parameters:
seqString -

ProteinSequence

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

Parameters:
seqString -
compoundSet -

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 -
Method Detail

setParentDNASequence

public void setParentDNASequence(AbstractSequence 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)