com.hfg.bio.seq

Class BioSequencePlusImpl

java.lang.Object

com.hfg.chem.Molecule

com.hfg.bio.seq.BioSequenceImpl

com.hfg.bio.seq.BioSequencePlusImpl

All Implemented Interfaces:

BioSequence, BioSequencePlus, Matter, HfgXMLSerializable, Cloneable, Comparable

Direct Known Subclasses:

NucleicAcid, Protein

public abstract class BioSequencePlusImpl
extends BioSequenceImpl
implements BioSequencePlus

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

Nested Class Summary

Nested classes/interfaces inherited from class com.hfg.bio.seq.BioSequenceImpl

BioSequenceImpl.SeqFilterReader

Field Summary

Fields inherited from class com.hfg.bio.seq.BioSequenceImpl

GAP_PATTERN

Fields inherited from class com.hfg.chem.Molecule

H2O, mLocked, mName, NaCl, NH3

Constructor Summary

Constructors

Constructor and Description
BioSequencePlusImpl()
BioSequencePlusImpl(XMLNode inXML)

Method Summary

Modifier and Type	Method and Description
BioSequenceImpl	addDbXref(DbXref inValue)
BioSequenceImpl	addFeature(SeqFeature inValue)
BioSequenceImpl	addKeyword(String inValue)
BioSequenceImpl	addKeywords(Collection<String> inValues)
BioSequenceImpl	addKeywords(String[] inValues)
void	addParseException(Throwable inException)
BioSequenceImpl	addReference(SeqCitation inValue)
void	clearDbXrefs()
void	clearFeatures()
void	clearKeywords()
void	clearParseExceptions()
void	clearReferences()
BioSequencePlusImpl	clone() Returns an unlocked copy of the Molecule.
Clone	getClone()
List<DbXref>	getDbXrefs()
List<SeqFeature>	getFeatures()
List<SeqFeature>	getFeatures(FeatureKey inFeatureKey)
Set<String>	getKeywords()
MolType	getMolType()
NCBITaxon	getNCBITaxon()
List<Throwable>	getParseExceptions()
List<SeqCitation>	getReferences()
Date	getRevisionDate()
SeqRepositoryDivision	getSeqRepositoryDivision()
SeqTopology	getSeqTopology()
BioSequencePlusImpl	setClone(Clone inValue)
BioSequencePlusImpl	setMolType(MolType inValue)
BioSequencePlusImpl	setNCBITaxon(NCBITaxon inValue)
BioSequenceImpl	setReferences(List<SeqCitation> inValues)
BioSequencePlusImpl	setRevisionDate(Date inValue)
BioSequencePlusImpl	setSeqRepositoryDivision(SeqRepositoryDivision inValue)
BioSequencePlusImpl	setSeqTopology(SeqTopology inValue)
XMLNode	toXMLNode()

Methods inherited from class com.hfg.bio.seq.BioSequenceImpl

clearCalculatedProperties, clearElementalCompositionAndCalculatedProperties, containsGaps, countGaps, equals, getAverageMass, getChemicalFormula, getChemicalFormulaWithSubscripts, getComposition, getDescription, getElementalComposition, getID, getMD5Checksum, getMonoisotopicMass, getNumGaps, getOrganicAverageMass, getResidueComposition, getReverseSequenceStream, getSequence, getSequenceReader, getSequenceStream, getSHA1Checksum, getSubSequence, getSubSequenceReader, getTerminiComposition, getTotalGapLength, getType, getXLinkComposition, length, recalculateElementalComposition, residueAt, setCompressionThreshold, setDescription, setID, setNumGaps, setResidueAt, setSequence, setSequence, setTotalGapLength, toString

Methods inherited from class com.hfg.chem.Molecule

add, add, addAtom, addAtoms, addAtoms, addAtoms, addElementalComposition, addElementalComposition, addElementalComposition, addKa, addKa, calculateMassFromElementalComposition, clearAttributes, clearElementalComposition, compareTo, formatMassString, getAtoms, getAttribute, getAttributeNames, getKas, getLastAtom, getPhysicalProperty, hasAttribute, hasAttributes, hashCode, isLocked, lock, massesAreUserSet, name, remove, remove, removeAttribute, setAttribute, setAverageMass, setChemicalFormula, setElementalComposition, setMonoisotopicMass, setName, setOrganicAverageMass, setPhysicalProperty

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

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

hadParseExceptions

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

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

Methods inherited from interface java.lang.Comparable

compareTo

Methods inherited from interface com.hfg.chem.Matter

getAverageMass, getChemicalFormula, getElementalComposition, getMonoisotopicMass, getOrganicAverageMass

Constructor Detail

BioSequencePlusImpl

public BioSequencePlusImpl()

BioSequencePlusImpl

public BioSequencePlusImpl(XMLNode inXML)

Method Detail

toXMLNode

public XMLNode toXMLNode()

Specified by:

toXMLNode in interface BioSequence

Specified by:

toXMLNode in interface HfgXMLSerializable

Overrides:

toXMLNode in class BioSequenceImpl

clone

public BioSequencePlusImpl clone()

Description copied from class: Molecule

Returns an unlocked copy of the Molecule.

Specified by:

clone in interface BioSequence

Overrides:

clone in class BioSequenceImpl

Returns:

an unlocked copy of the Molecule

addFeature

public BioSequenceImpl addFeature(SeqFeature inValue)

Specified by:

addFeature in interface BioSequencePlus

getFeatures

public List<SeqFeature> getFeatures()

Specified by:

getFeatures in interface BioSequencePlus

getFeatures

public List<SeqFeature> getFeatures(FeatureKey inFeatureKey)

Specified by:

getFeatures in interface BioSequencePlus

clearFeatures

public void clearFeatures()

Specified by:

clearFeatures in interface BioSequencePlus

setReferences

public BioSequenceImpl setReferences(List<SeqCitation> inValues)

addReference

public BioSequenceImpl addReference(SeqCitation inValue)

Specified by:

addReference in interface BioSequencePlus

getReferences

public List<SeqCitation> getReferences()

Specified by:

getReferences in interface BioSequencePlus

clearReferences

public void clearReferences()

Specified by:

clearReferences in interface BioSequencePlus

addDbXref

public BioSequenceImpl addDbXref(DbXref inValue)

Specified by:

addDbXref in interface BioSequencePlus

getDbXrefs

public List<DbXref> getDbXrefs()

Specified by:

getDbXrefs in interface BioSequencePlus

clearDbXrefs

public void clearDbXrefs()

Specified by:

clearDbXrefs in interface BioSequencePlus

addKeyword

public BioSequenceImpl addKeyword(String inValue)

Specified by:

addKeyword in interface BioSequencePlus

addKeywords

public BioSequenceImpl addKeywords(Collection<String> inValues)

Specified by:

addKeywords in interface BioSequencePlus

addKeywords

public BioSequenceImpl addKeywords(String[] inValues)

Specified by:

addKeywords in interface BioSequencePlus

getKeywords

public Set<String> getKeywords()

Specified by:

getKeywords in interface BioSequencePlus

clearKeywords

public void clearKeywords()

Specified by:

clearKeywords in interface BioSequencePlus

setSeqRepositoryDivision

public BioSequencePlusImpl setSeqRepositoryDivision(SeqRepositoryDivision inValue)

Specified by:

setSeqRepositoryDivision in interface BioSequencePlus

getSeqRepositoryDivision

public SeqRepositoryDivision getSeqRepositoryDivision()

Specified by:

getSeqRepositoryDivision in interface BioSequencePlus

setMolType

public BioSequencePlusImpl setMolType(MolType inValue)

Specified by:

setMolType in interface BioSequencePlus

getMolType

public MolType getMolType()

Specified by:

getMolType in interface BioSequencePlus

setSeqTopology

public BioSequencePlusImpl setSeqTopology(SeqTopology inValue)

Specified by:

setSeqTopology in interface BioSequencePlus

getSeqTopology

public SeqTopology getSeqTopology()

Specified by:

getSeqTopology in interface BioSequencePlus

setRevisionDate

public BioSequencePlusImpl setRevisionDate(Date inValue)

Specified by:

setRevisionDate in interface BioSequencePlus

getRevisionDate

public Date getRevisionDate()

Specified by:

getRevisionDate in interface BioSequencePlus

setClone

public BioSequencePlusImpl setClone(Clone inValue)

Specified by:

setClone in interface BioSequencePlus

getClone

public Clone getClone()

Specified by:

getClone in interface BioSequencePlus

setNCBITaxon

public BioSequencePlusImpl setNCBITaxon(NCBITaxon inValue)

Specified by:

setNCBITaxon in interface BioSequencePlus

getNCBITaxon

public NCBITaxon getNCBITaxon()

Specified by:

getNCBITaxon in interface BioSequencePlus

addParseException

public void addParseException(Throwable inException)

Specified by:

addParseException in interface BioSequencePlus

clearParseExceptions

public void clearParseExceptions()

Specified by:

clearParseExceptions in interface BioSequencePlus

getParseExceptions

public List<Throwable> getParseExceptions()

Specified by:

getParseExceptions in interface BioSequencePlus