org.expasy.mzjava.core.mol

Class Composition

java.lang.Object

org.expasy.mzjava.core.mol.Mass

org.expasy.mzjava.core.mol.Composition

All Implemented Interfaces:

Weighable

Direct Known Subclasses:

NeutralLoss

public class Composition
extends Mass

A collection of atoms and charge

Version:

1.0

Author:

Oliver Horlacher, nikitin

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	Composition.Builder Class to build a Composition

Field Summary

Fields

Modifier and Type	Field and Description
protected gnu.trove.map.TObjectIntMap<Atom>	atomCounterMap
protected int	charge

Fields inherited from class org.expasy.mzjava.core.mol.Mass

ZERO

Constructor Summary

Constructors

Modifier	Constructor and Description
	Composition(Composition... compositions) Constructs a composition that is the sum of the compositions
protected	Composition(String formula, gnu.trove.map.TObjectIntMap<Atom> atomCountMap, int charge)
	Composition(gnu.trove.map.TObjectIntMap<Atom> atomCounterMap, int charge) Construct a new composition that contains the charge and the atoms in the atomCounterMap.

Method Summary

Methods

Modifier and Type	Method and Description
boolean	equals(Object o)
Set<Atom>	getAtoms() Returns a set containing all the Atoms in this composition.
int	getCharge() Return the charge for this composition.
int	getCount(Atom atom) Counts the number of times atom occurs in this Composition
String	getFormula() Return the formula for this composition.
double	getMassDefect() The amount by which the mass of all atomic nuclei in this composition differs from the sum of the masses of its constituent protons, neutrons and electrons.
double	getMolecularMass() Returns the monoisotopic molecular mass of this composition.
int	hashCode()
boolean	isEmpty() Returns true if this composition contains no atoms or charge, false otherwise.
static Composition	parseComposition(String s) Creates a Composition by parsing the given string.
int	size() Returns the number of atoms in this composition
static Composition	subtractCompositions(Composition composition1, Composition composition2)
String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

charge

protected final int charge

atomCounterMap

protected final gnu.trove.map.TObjectIntMap<Atom> atomCounterMap

Constructor Detail

Composition

public Composition(gnu.trove.map.TObjectIntMap<Atom> atomCounterMap,
           int charge)

Construct a new composition that contains the charge and the atoms in the atomCounterMap.

Parameters:

atomCounterMap - the atoms to include in the composition

charge - the charge of the composition

Composition

protected Composition(String formula,
           gnu.trove.map.TObjectIntMap<Atom> atomCountMap,
           int charge)

Composition

public Composition(Composition... compositions)

Constructs a composition that is the sum of the compositions

Parameters:

compositions - the Compositions to sum

Method Detail

getAtoms

public Set<Atom> getAtoms()

Returns a set containing all the Atoms in this composition.

Returns:

a set containing all the Atoms in this composition.

getMolecularMass

public double getMolecularMass()

Returns the monoisotopic molecular mass of this composition.

Roundoff error and error propagation

At rare occasion, masses of different instances with exact same composition may slightly differ.

This is due to the fact that as our composition is a Map of unsorted atoms the same atoms traversing order is not garantied.

As each instance mass is calculated by traversing atomic masses and that mass are unexactly represented in the standard binary floating point, these roundoff errors
can propagate through the calculation in non-intuitive ways and may lead to teany tiny different results.

Returns:

the monoisotopic molecular mass of this composition

getFormula

public String getFormula()

Return the formula for this composition.

Specified by:

getFormula in class Mass

Returns:

the formula for this composition

See Also:

AtomicCompositionParser

getMassDefect

public double getMassDefect()

Description copied from class: Mass

The amount by which the mass of all atomic nuclei in this composition differs from the sum of the masses of its constituent protons, neutrons and electrons. This is the mass equivalent of the energy released in the formation of the nucleus.

Specified by:

getMassDefect in class Mass

Returns:

the mass defect

getCharge

public int getCharge()

Return the charge for this composition.

Returns:

the charge for this composition

getCount

public int getCount(Atom atom)

Counts the number of times atom occurs in this Composition

Parameters:

atom - the atom

Returns:

the number of times atom occurs in this Composition

size

public int size()

Returns the number of atoms in this composition

Returns:

the number of atoms in this composition

isEmpty

public boolean isEmpty()

Returns true if this composition contains no atoms or charge, false otherwise.

Returns:

true if this composition contains no atoms or charge, false otherwise

equals

public boolean equals(Object o)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object

toString

public String toString()

Overrides:

toString in class Object

parseComposition

public static Composition parseComposition(String s)

Creates a Composition by parsing the given string. For the format that is allowed see AtomicCompositionParser

Parameters:

s - the string to parse

Returns:

the new Composition

See Also:

AtomicCompositionParser

subtractCompositions

public static Composition subtractCompositions(Composition composition1,
                               Composition composition2)