org.expasy.mzjava.core.mol

Class Composition.Builder

java.lang.Object

org.expasy.mzjava.core.mol.Composition.Builder

Enclosing class:

Composition

public static final class Composition.Builder
extends Object

Class to build a Composition

Version:

sqrt -1

Author:

Oliver Horlacher

Constructor Summary

Constructors

Constructor and Description
Composition.Builder() Construct a new Builder
Composition.Builder(AtomicSymbol atom) Construct a new Builder and add the atom
Composition.Builder(AtomicSymbol atom, int count) Construct a new Builder and add the atom count times

Method Summary

Methods

Modifier and Type	Method and Description
Composition.Builder	add(AtomicSymbol atom) Add an atom for the specified AtomicSymbol
Composition.Builder	add(AtomicSymbol atom, int count) Add count atoms for the specified AtomicSymbol
Composition.Builder	add(Atom atom, int count) Add the atom count times.
Composition.Builder	addAll(Composition composition) Add all of the atoms in composition to this
Composition.Builder	addIsotope(AtomicSymbol symbol, int isotope) Add an atom for the specified symbol and isotope
Composition.Builder	addIsotope(AtomicSymbol symbol, int isotope, int count) Add an atom count times for the specified symbol and isotope
Composition	build() Build the composition
Composition.Builder	charge(int charge) Set the charge.
boolean	isEmpty() Returns true if there are no atoms in this builder and the charge is 0
static String	makeFormula(gnu.trove.map.TObjectIntMap<Atom> atomCounterMap, int charge) Make the atomic formula given an atomCounterMap and charge
String	toString() Return the atomic composition string defined in AtomicCompositionParser

Methods inherited from class java.lang.Object

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

Constructor Detail

Composition.Builder

public Composition.Builder()

Construct a new Builder

Composition.Builder

public Composition.Builder(AtomicSymbol atom)

Construct a new Builder and add the atom

Parameters:

atom - the first atom to add to the builder

Composition.Builder

public Composition.Builder(AtomicSymbol atom,
                   int count)

Construct a new Builder and add the atom count times

Parameters:

atom - the first atom to add to the builder

count - the number of times to add the atom

Method Detail

charge

public Composition.Builder charge(int charge)

Set the charge.

Returns:

this builder

add

public Composition.Builder add(AtomicSymbol atom)

Add an atom for the specified AtomicSymbol

Parameters:

atom - the symbol of the atom to add

Returns:

this builder

add

public Composition.Builder add(AtomicSymbol atom,
                      int count)

Add count atoms for the specified AtomicSymbol

Parameters:

atom - the symbol of the atom to add

count - the number of times that the atom is to be added

Returns:

this builder

addIsotope

public Composition.Builder addIsotope(AtomicSymbol symbol,
                             int isotope)

Add an atom for the specified symbol and isotope

Parameters:

symbol - the symbol of the atom to add

isotope - the isotope number

Returns:

this builder

addIsotope

public Composition.Builder addIsotope(AtomicSymbol symbol,
                             int isotope,
                             int count)

Add an atom count times for the specified symbol and isotope

Parameters:

symbol - the symbol of the atom to add

isotope - the isotope number

count - the number of times to add the atom

Returns:

this builder

add

public Composition.Builder add(Atom atom,
                      int count)

Add the atom count times.

Parameters:

atom - the atom to add

count - the number of atoms to add

Returns:

this builder

build

public Composition build()

Build the composition

Returns:

the new Composition

toString

public String toString()

Return the atomic composition string defined in AtomicCompositionParser

Overrides:

toString in class Object

Returns:

the formula

See Also:

AtomicCompositionParser

makeFormula

public static String makeFormula(gnu.trove.map.TObjectIntMap<Atom> atomCounterMap,
                 int charge)

Make the atomic formula given an atomCounterMap and charge

Parameters:

atomCounterMap - map containing the counts for the atoms

charge - the charge

Returns:

the formula

addAll

public Composition.Builder addAll(Composition composition)

Add all of the atoms in composition to this

Parameters:

composition - the composition

Returns:

this builder

isEmpty

public boolean isEmpty()

Returns true if there are no atoms in this builder and the charge is 0

Returns:

true if there are no atoms in this builder and the charge is 0