com.hfg.bio

Class DigestFragment

java.lang.Object

com.hfg.chem.Molecule

com.hfg.bio.seq.BioSequenceImpl

com.hfg.bio.seq.BioSequencePlusImpl

com.hfg.bio.seq.Protein

com.hfg.bio.DigestFragment

All Implemented Interfaces:

BioSequence, BioSequencePlus, Matter, HfgXMLSerializable, Cloneable, Comparable

public class DigestFragment
extends Protein

Product of a proteolytic digest.

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
DigestFragment()

Method Summary

Modifier and Type	Method and Description
int	getBegin()
int	getBeginFragIndex()
int	getEnd()
int	getEndFragIndex()
String	getFragIndexString()
int	getNumUncleavedSites()
Character	getPrecedingResidue()
SeqLocation	getSeqLocation()
String	getSrcChainId()
Character	getTrailingResidue()
void	setBegin(int inValue)
void	setBeginFragIndex(int inValue)
void	setEnd(int inValue)
void	setEndFragIndex(int inValue)
void	setNumUncleavedSites(int inValue)
void	setPrecedingResidue(Character inValue)
DigestFragment	setSrcChainId(String inValue)
void	setTrailingResidue(Character inValue)
String	toString()

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

addChain, addChains, addChains, addGlycan, addGlycans, addXLink, aminoAcidAt, clearCalculatedProperties, clearElementalCompositionAndCalculatedProperties, clone, compareTo, countGaps, createNTerminalPyroGlu, findNLinkedSites, getAminoAcidComposition, getAminoAcidSet, getAverageMass, getAverageMass, getChain, getChainIds, getChains, getChainStoichiometryGroups, getComposition, getDistinctChains, getElementalComposition, getExtinctionCoeff, getGlycans, getIsoelectricPoint, getIsoelectricPoint, getIsoelectricPoint, getMD5Checksum, getMillimolarConcFromAbsorbance280, getMonoisotopicMass, getMonoisotopicMass, getNetCharge, getNetCharge, getNumChains, getOrganicAverageMass, getOrganicAverageMass, getParent, getPercentExtinctionCoeff, getResidueComposition, getSHA1Checksum, getTerminiComposition, getTotalNumDisulfideBonds, getTotalNumFreeCysteines, getType, getXLinkComposition, getXLinks, getXLinks, hasChains, hashCode, length, recalculateElementalComposition, removeXLink, removeXLinks, removeXLinks, setAminoAcidSet, setChains, setDescription, setID, setNCBITaxon, setNumDisulfideBonds, setSequence, setSequence, toXMLNode, treatWithPNGaseF

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

addDbXref, addFeature, addKeyword, addKeywords, addKeywords, addParseException, addReference, clearDbXrefs, clearFeatures, clearKeywords, clearParseExceptions, clearReferences, getClone, getDbXrefs, getFeatures, getFeatures, getKeywords, getMolType, getNCBITaxon, getParseExceptions, getReferences, getRevisionDate, getSeqRepositoryDivision, getSeqTopology, setClone, setMolType, setReferences, setRevisionDate, setSeqRepositoryDivision, setSeqTopology

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

containsGaps, equals, getChemicalFormula, getChemicalFormulaWithSubscripts, getDescription, getElementalComposition, getID, getNumGaps, getReverseSequenceStream, getSequence, getSequenceReader, getSequenceStream, getSubSequence, getSubSequenceReader, getTotalGapLength, residueAt, setCompressionThreshold, setNumGaps, setResidueAt, setTotalGapLength

Methods inherited from class com.hfg.chem.Molecule

add, add, addAtom, addAtoms, addAtoms, addAtoms, addElementalComposition, addElementalComposition, addElementalComposition, addKa, addKa, calculateMassFromElementalComposition, clearAttributes, clearElementalComposition, formatMassString, getAtoms, getAttribute, getAttributeNames, getKas, getLastAtom, getPhysicalProperty, hasAttribute, hasAttributes, 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, getSequence, getSequenceReader, getSequenceStream, getSubSequence, getSubSequenceReader, hasAttribute, instantiate, removeAttribute, residueAt, setAttribute

Methods inherited from interface com.hfg.chem.Matter

getChemicalFormula, getElementalComposition

Constructor Detail

DigestFragment

public DigestFragment()

Method Detail

setSrcChainId

public DigestFragment setSrcChainId(String inValue)

getSrcChainId

public String getSrcChainId()

setBegin

public void setBegin(int inValue)

getBegin

public int getBegin()

setEnd

public void setEnd(int inValue)

getEnd

public int getEnd()

getSeqLocation

public SeqLocation getSeqLocation()

setPrecedingResidue

public void setPrecedingResidue(Character inValue)

getPrecedingResidue

public Character getPrecedingResidue()

setTrailingResidue

public void setTrailingResidue(Character inValue)

getTrailingResidue

public Character getTrailingResidue()

setNumUncleavedSites

public void setNumUncleavedSites(int inValue)

getNumUncleavedSites

public int getNumUncleavedSites()

setBeginFragIndex

public void setBeginFragIndex(int inValue)

getBeginFragIndex

public int getBeginFragIndex()

setEndFragIndex

public void setEndFragIndex(int inValue)

getEndFragIndex

public int getEndFragIndex()

getFragIndexString

public String getFragIndexString()

toString

public String toString()

Overrides:

toString in class BioSequenceImpl