com.hfg.bio.seq

Interface BioSequencePlus

All Superinterfaces:

BioSequence, java.lang.Cloneable

All Known Implementing Classes:

BioSequencePlusImpl, DigestFragment, Intron, NucleicAcid, Protein

public interface BioSequencePlus
extends BioSequence

Interface for an exetended biological protein, DNA, or RNA sequence with support for features, citations, db xrefs, etc.

Method Summary

Modifier and Type	Method and Description
BioSequence	addDbXref(DbXref inValue)
BioSequence	addFeature(SeqFeature inValue)
BioSequence	addKeyword(java.lang.String inValue)
BioSequence	addKeywords(java.util.Collection<java.lang.String> inValues)
BioSequence	addKeywords(java.lang.String[] inValues)
void	addParseException(java.lang.Throwable inException)
BioSequence	addReference(SeqCitation inValue)
void	clearDbXrefs()
void	clearFeatures()
void	clearKeywords()
void	clearParseExceptions()
void	clearReferences()
Clone	getClone()
java.util.List<DbXref>	getDbXrefs()
java.util.List<SeqFeature>	getFeatures()
java.util.List<SeqFeature>	getFeatures(FeatureKey inFeatureKey)
java.util.Set<java.lang.String>	getKeywords()
MolType	getMolType()
NCBITaxon	getNCBITaxon()
java.util.List<java.lang.Throwable>	getParseExceptions()
java.util.List<SeqCitation>	getReferences()
java.util.Date	getRevisionDate()
SeqRepositoryDivision	getSeqRepositoryDivision()
SeqTopology	getSeqTopology()
default boolean	hadParseExceptions()
BioSequencePlusImpl	setClone(Clone inValue)
BioSequencePlusImpl	setMolType(MolType inValue)
BioSequencePlusImpl	setNCBITaxon(NCBITaxon inValue)
BioSequencePlusImpl	setRevisionDate(java.util.Date inValue)
BioSequencePlusImpl	setSeqRepositoryDivision(SeqRepositoryDivision inValue)
BioSequencePlusImpl	setSeqTopology(SeqTopology inValue)

Methods inherited from interface com.hfg.bio.seq.BioSequence

clone, getAttribute, getAttributeNames, getDescription, getID, getMD5Checksum, getSequence, getSequenceReader, getSequenceStream, getSHA1Checksum, getSubSequence, getSubSequenceReader, getType, hasAttribute, instantiate, length, removeAttribute, residueAt, setAttribute, setDescription, setID, setSequence, setSequence, toXMLNode

Method Detail

setSeqRepositoryDivision

BioSequencePlusImpl setSeqRepositoryDivision(SeqRepositoryDivision inValue)

getSeqRepositoryDivision

SeqRepositoryDivision getSeqRepositoryDivision()

setMolType

BioSequencePlusImpl setMolType(MolType inValue)

getMolType

MolType getMolType()

setSeqTopology

BioSequencePlusImpl setSeqTopology(SeqTopology inValue)

getSeqTopology

SeqTopology getSeqTopology()

addFeature

BioSequence addFeature(SeqFeature inValue)

getFeatures

java.util.List<SeqFeature> getFeatures()

getFeatures

java.util.List<SeqFeature> getFeatures(FeatureKey inFeatureKey)

clearFeatures

void clearFeatures()

addReference

BioSequence addReference(SeqCitation inValue)

getReferences

java.util.List<SeqCitation> getReferences()

clearReferences

void clearReferences()

addDbXref

BioSequence addDbXref(DbXref inValue)

getDbXrefs

java.util.List<DbXref> getDbXrefs()

clearDbXrefs

void clearDbXrefs()

addKeyword

BioSequence addKeyword(java.lang.String inValue)

addKeywords

BioSequence addKeywords(java.util.Collection<java.lang.String> inValues)

addKeywords

BioSequence addKeywords(java.lang.String[] inValues)

getKeywords

java.util.Set<java.lang.String> getKeywords()

clearKeywords

void clearKeywords()

setRevisionDate

BioSequencePlusImpl setRevisionDate(java.util.Date inValue)

getRevisionDate

java.util.Date getRevisionDate()

setClone

BioSequencePlusImpl setClone(Clone inValue)

getClone

Clone getClone()

setNCBITaxon

BioSequencePlusImpl setNCBITaxon(NCBITaxon inValue)

getNCBITaxon

NCBITaxon getNCBITaxon()

hadParseExceptions

default boolean hadParseExceptions()

addParseException

void addParseException(java.lang.Throwable inException)

getParseExceptions

java.util.List<java.lang.Throwable> getParseExceptions()

clearParseExceptions

void clearParseExceptions()