com.hfg.chem

Interface Matter

All Known Subinterfaces:

BioSequence, BioSequencePlus

All Known Implementing Classes:

AminoAcid, BioSequenceImpl, BioSequencePlusImpl, CTerminalGroup, DigestFragment, Element, Glycan, Intron, Isotope, Molecule, Monosaccharide, NTerminalGroup, NucleicAcid, Nucleotide, Protein, ProteinXLink, ProteinXLinkType

public interface Matter

Interface for an elemental composition and mass tracking object. All matter has mass and an elemental composition.

Method Summary

Modifier and Type	Method and Description
Double	getAverageMass()
String	getChemicalFormula()
Map<Element,Float>	getElementalComposition() Returns an unmodifiable copy of the elemental composition Map.
Double	getMonoisotopicMass()
Double	getOrganicAverageMass()

Method Detail

getElementalComposition

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.

Returns:

Map containing the elemental composition

getMonoisotopicMass

Double getMonoisotopicMass()

getAverageMass

Double getAverageMass()

getOrganicAverageMass

Double getOrganicAverageMass()

getChemicalFormula

String getChemicalFormula()