com.compomics.util.experiment.biology

Class AtomChain

java.lang.Object

com.compomics.util.experiment.biology.AtomChain

All Implemented Interfaces:

Serializable

public class AtomChain
extends Object
implements Serializable

A chain of atoms.

Author:

Marc Vaudel

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
AtomChain() Creates an empty atom chain.
AtomChain(boolean addition) Creates an empty atom chain.
AtomChain(String chain) Constructor for a monoisotopic chain as a string of additions, e.g.
AtomChain(String chain, boolean addition) Constructor for a monoisotopic chain as a string, e.g.

Method Summary

Modifier and Type	Method and Description
void	append(AtomImpl atom) Appends an atom to the chain of atoms.
void	append(AtomImpl atom, int occurrence) Appends an atom to the chain of atoms.
AtomChain	clone()
Boolean	getAddition() Returns true of the given atomic chain consists of additions, i.e., all atoms are added when calculating the mass, false, means that all atoms are subtracted.
ArrayList<AtomImpl>	getAtomChain() Returns the atom chain as a list of AtomImpl.
Double	getMass() Returns the mass of the atomic chain as sum of the individual atoms.
int	getOccurrence(Atom atom, Integer isotope) Returns the occurrence of a given atom in the chain.
boolean	isSameCompositionAs(AtomChain anotherChain) Indicates whether two atom chains are of the same composition by comparing their string and type.
void	remove(Atom atom, Integer isotope) Removes all the occurrences of the given atom.
void	setAddition(Boolean addition) Set if the given atomic chain consists of additions, i.e., all atoms are added when calculating the mass, false, means that all atoms are subtracted.
void	setOccurrence(Atom atom, Integer isotope, Integer occurrence) Sets the occurrence of a given atom.
int	size() Returns the number of atoms in this atom chain.
String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

AtomChain

public AtomChain()

Creates an empty atom chain.

AtomChain

public AtomChain(boolean addition)

Creates an empty atom chain.

Parameters:

addition - if the atom chain consists of additions

AtomChain

public AtomChain(String chain)
          throws IllegalArgumentException

Constructor for a monoisotopic chain as a string of additions, e.g. C3PO which is interpreted as three C's, one P and one O.

Parameters:

chain - the atomic chain as a string

Throws:

IllegalArgumentException - if an illegal atom is used

AtomChain

public AtomChain(String chain,
                 boolean addition)
          throws IllegalArgumentException

Constructor for a monoisotopic chain as a string, e.g. C3PO which is interpreted as three C's, one P and one O.

Parameters:

chain - the atomic chain as a string

addition - if the atom chain consists of additions

Throws:

IllegalArgumentException - if an illegal atom is used

Method Detail

append

public void append(AtomImpl atom)

Appends an atom to the chain of atoms.

Parameters:

atom - a new atom

append

public void append(AtomImpl atom,
                   int occurrence)

Appends an atom to the chain of atoms.

Parameters:

atom - a new atom

occurrence - the number of times this atom should be added

getAtomChain

public ArrayList<AtomImpl> getAtomChain()

Returns the atom chain as a list of AtomImpl.

Returns:

the atom chain as a list of AtomImpl

getMass

public Double getMass()

Returns the mass of the atomic chain as sum of the individual atoms.

Returns:

the mass of the atomic chain as sum of the individual atoms

size

public int size()

Returns the number of atoms in this atom chain.

Returns:

the number of atoms in this atom chain

getOccurrence

public int getOccurrence(Atom atom,
                         Integer isotope)

Returns the occurrence of a given atom in the chain.

Parameters:

atom - the atom of interest

isotope - the isotope to look for

Returns:

the occurrence of the atom in this atom chain

remove

public void remove(Atom atom,
                   Integer isotope)

Removes all the occurrences of the given atom.

Parameters:

atom - the atom

isotope - the isotope

setOccurrence

public void setOccurrence(Atom atom,
                          Integer isotope,
                          Integer occurrence)

Sets the occurrence of a given atom.

Parameters:

atom - the atom

isotope - the isotope number

occurrence - the occurrence

isSameCompositionAs

public boolean isSameCompositionAs(AtomChain anotherChain)

Indicates whether two atom chains are of the same composition by comparing their string and type. An empty chain is considered to be the same composition as a null chain.

Parameters:

anotherChain - another atom chain

Returns:

a boolean indicating whether two atom chains are of the same composition

toString

public String toString()

Overrides:

toString in class Object

clone

public AtomChain clone()

Overrides:

clone in class Object

getAddition

public Boolean getAddition()

Returns true of the given atomic chain consists of additions, i.e., all atoms are added when calculating the mass, false, means that all atoms are subtracted.

Returns:

true of the given atomic consists of additions

setAddition

public void setAddition(Boolean addition)

Set if the given atomic chain consists of additions, i.e., all atoms are added when calculating the mass, false, means that all atoms are subtracted.

Parameters:

addition - true if the given atomic chain consists of additions