com.hfg.bio.seq

Class ProteinXLink

java.lang.Object

com.hfg.chem.Molecule

com.hfg.bio.seq.ProteinXLink

All Implemented Interfaces:

Matter, HfgXMLSerializable, Cloneable, Comparable

public class ProteinXLink
extends Molecule
implements Cloneable

Biological protein sequence crosslink.

Field Summary

Fields inherited from class com.hfg.chem.Molecule

H2O, mLocked, mName, NaCl, NH3

Constructor Summary

Constructors

Constructor and Description
ProteinXLink(ProteinXLinkType inType, Protein inDonorChain, int inDonorPosition, Protein inAcceptorChain, int inAcceptorPosition)
ProteinXLink(XMLNode inXML)

Method Summary

Modifier and Type	Method and Description
ProteinXLink	clone() Returns an unlocked copy of the Molecule.
int	compareTo(Object inObj)
boolean	equals(Object inObj)
String	getAcceptorChainId()
int	getAcceptorPosition()
Double	getAverageMass()
ProteinXLinkChainLinkage	getChainLinkage()
String	getDonorChainId()
int	getDonorPosition()
Map<Element,Float>	getElementalComposition() Returns an unmodifiable copy of the elemental composition Map.
Double	getMonoisotopicMass()
Double	getOrganicAverageMass()
ProteinXLinkType	getType()
int	hashCode()
protected ProteinXLink	setAcceptorChainId(String inValue)
protected ProteinXLink	setDonorChainId(String inValue)
protected void	setParentProtein(Protein inParentProtein) Sets the protein container to which this x-link belongs.
String	toString()
XMLNode	toXMLNode()
protected void	validate()

Methods inherited from class com.hfg.chem.Molecule

add, add, addAtom, addAtoms, addAtoms, addAtoms, addElementalComposition, addElementalComposition, addElementalComposition, addKa, addKa, calculateMassFromElementalComposition, clearAttributes, clearCalculatedProperties, clearElementalComposition, formatMassString, getAtoms, getAttribute, getAttributeNames, getChemicalFormula, getChemicalFormulaWithSubscripts, 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

Constructor Detail

ProteinXLink

public ProteinXLink(ProteinXLinkType inType,
                    Protein inDonorChain,
                    int inDonorPosition,
                    Protein inAcceptorChain,
                    int inAcceptorPosition)

ProteinXLink

public ProteinXLink(XMLNode inXML)

Method Detail

clone

public ProteinXLink clone()

Description copied from class: Molecule

Returns an unlocked copy of the Molecule.

Overrides:

clone in class Molecule

Returns:

an unlocked copy of the Molecule

getChainLinkage

public ProteinXLinkChainLinkage getChainLinkage()

getType

public ProteinXLinkType getType()

getDonorChainId

public String getDonorChainId()

setDonorChainId

protected ProteinXLink setDonorChainId(String inValue)

getDonorPosition

public int getDonorPosition()

getAcceptorChainId

public String getAcceptorChainId()

setAcceptorChainId

protected ProteinXLink setAcceptorChainId(String inValue)

getAcceptorPosition

public int getAcceptorPosition()

toString

public String toString()

Overrides:

toString in class Molecule

toXMLNode

public XMLNode toXMLNode()

Specified by:

toXMLNode in interface HfgXMLSerializable

Overrides:

toXMLNode in class Molecule

getElementalComposition

public Map<Element,Float> getElementalComposition()

Returns an unmodifiable copy of the elemental composition Map. The keys are Element objects and the values are Floats. Why Floats instead of Integers you ask? Because some amino acid codes such as B and Z are ambiguous averages.

Specified by:

getElementalComposition in interface Matter

Overrides:

getElementalComposition in class Molecule

Returns:

an elemental composition map

getMonoisotopicMass

public Double getMonoisotopicMass()

Specified by:

getMonoisotopicMass in interface Matter

Overrides:

getMonoisotopicMass in class Molecule

getAverageMass

public Double getAverageMass()

Specified by:

getAverageMass in interface Matter

Overrides:

getAverageMass in class Molecule

getOrganicAverageMass

public Double getOrganicAverageMass()

Specified by:

getOrganicAverageMass in interface Matter

Overrides:

getOrganicAverageMass in class Molecule

setParentProtein

protected void setParentProtein(Protein inParentProtein)

Sets the protein container to which this x-link belongs.

Parameters:

inParentProtein - the protein to which this x-link belongs

validate

protected void validate()

equals

public boolean equals(Object inObj)

Overrides:

equals in class Molecule

hashCode

public int hashCode()

Overrides:

hashCode in class Molecule

compareTo

public int compareTo(Object inObj)

Specified by:

compareTo in interface Comparable

Overrides:

compareTo in class Molecule