java.lang.Iterable<AminoAcidCompound>
, Accessioned
, Sequence<AminoAcidCompound>
public class ProteinSequence extends AbstractSequence<AminoAcidCompound>
AbstractSequence.AnnotationType
Constructor | Description |
---|---|
ProteinSequence(java.lang.String seqString) |
Create a protein from a string
|
ProteinSequence(java.lang.String seqString,
CompoundSet<AminoAcidCompound> compoundSet) |
Create a protein from a string with a user defined set of amino acids
|
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.
|
Modifier and Type | Method | Description |
---|---|---|
static void |
main(java.lang.String[] args) |
|
void |
setParentDNASequence(AbstractSequence<NucleotideCompound> parentDNASequence,
java.lang.Integer begin,
java.lang.Integer end) |
A Protein sequence can be stand alone or loaded from a transcript
sequence.
|
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
public ProteinSequence(java.lang.String seqString) throws CompoundNotFoundException
seqString
- CompoundNotFoundException
public ProteinSequence(java.lang.String seqString, CompoundSet<AminoAcidCompound> compoundSet) throws CompoundNotFoundException
seqString
- compoundSet
- CompoundNotFoundException
public ProteinSequence(ProxySequenceReader<AminoAcidCompound> proxyLoader)
proxyLoader
- public ProteinSequence(ProxySequenceReader<AminoAcidCompound> proxyLoader, CompoundSet<AminoAcidCompound> compoundSet)
proxyLoader
- compoundSet
- public void setParentDNASequence(AbstractSequence<NucleotideCompound> parentDNASequence, java.lang.Integer begin, java.lang.Integer end)
parentDNASequence
- begin
- end
- public static void main(java.lang.String[] args) throws java.lang.Exception
java.lang.Exception