Package org.biojava.nbio.aaproperties.xml

Class AminoAcidCompositionTable

java.lang.Object

org.biojava.nbio.aaproperties.xml.AminoAcidCompositionTable

public class AminoAcidCompositionTable
extends Object

Constructor Summary

Constructors

Constructor	Description
AminoAcidCompositionTable()
AminoAcidCompositionTable(List<AminoAcidComposition> aaList)

Method Summary

Modifier and Type	Method	Description
void	computeMolecularWeight(ElementTable eTable)	Computes and store the molecular weight of each amino acid by its symbol in aaSymbol2MolecularWeight.
List<AminoAcidComposition>	getAminoacid()
ModifiedAminoAcidCompoundSet	getAminoAcidCompoundSet()
double	getMolecularWeight(Character aaSymbol)
Set<Character>	getSymbolSet()
void	setAminoacid(List<AminoAcidComposition> aminoacid)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

AminoAcidCompositionTable

public AminoAcidCompositionTable()

AminoAcidCompositionTable

public AminoAcidCompositionTable(List<AminoAcidComposition> aaList)

Method Details

getAminoAcidCompoundSet

public ModifiedAminoAcidCompoundSet getAminoAcidCompoundSet()

getAminoacid

public List<AminoAcidComposition> getAminoacid()

setAminoacid

public void setAminoacid(List<AminoAcidComposition> aminoacid)

getSymbolSet

public Set<Character> getSymbolSet()

computeMolecularWeight

public void computeMolecularWeight(ElementTable eTable)

Computes and store the molecular weight of each amino acid by its symbol in aaSymbol2MolecularWeight.

Parameters:

eTable - Stores the mass of elements and isotopes

getMolecularWeight

public double getMolecularWeight(Character aaSymbol)

Parameters:

aaSymbol - Standard symbol of Amino Acid

Returns:

the molecular weight given its symbol

Throws:

NullPointerException - thrown if AminoAcidCompositionTable.computeMolecularWeight(ElementTable) is not called before this method