org.openscience.cdk.debug

Class DebugAdductFormula

java.lang.Object

org.openscience.cdk.formula.AdductFormula

org.openscience.cdk.debug.DebugAdductFormula

All Implemented Interfaces:

Cloneable, Iterable<IMolecularFormula>, IAdductFormula, ICDKObject, IMolecularFormulaSet

public class DebugAdductFormula
extends AdductFormula
implements IAdductFormula

Debugging implementation of IAdductFormula.

Source code:

master

Belongs to CDK module:

datadebug

Constructor Summary

Constructors

Constructor and Description
DebugAdductFormula()
DebugAdductFormula(IMolecularFormula formula)

Method Summary

Modifier and Type	Method and Description
void	add(IMolecularFormulaSet formulaSet) Adds all molecularFormulas in the AdductFormula to this chemObject.
void	addMolecularFormula(IMolecularFormula formula) Adds an molecularFormula to this chemObject.
boolean	contains(IIsotope isotope) True, if the AdductFormula contains the given IIsotope object and not the instance.
boolean	contains(IMolecularFormula formula) True, if the AdductFormula contains the given IMolecularFormula object.
IChemObjectBuilder	getBuilder() Returns a IChemObjectBuilder for the data classes that extend this class.
Integer	getCharge() Returns the partial charge of this Adduct.
int	getIsotopeCount() Checks a set of Nodes for the number of different isotopes in the adduct formula.
int	getIsotopeCount(IIsotope isotope) Checks a set of Nodes for the occurrence of the isotope in the adduct formula from a particular isotope.
IMolecularFormula	getMolecularFormula(int position) Returns the MolecularFormula at position number in the chemObject.
Iterable<IIsotope>	isotopes() Returns an Iterator for looping over all isotopes in this adduct formula.
Iterator<IMolecularFormula>	iterator() Returns an Iterator for looping over all IMolecularFormula in this adduct formula.
Iterable<IMolecularFormula>	molecularFormulas() Returns an Iterable for looping over all IMolecularFormula in this adduct formula.
void	removeAllMolecularFormulas() Removes all IMolecularFormula from this chemObject.
void	removeMolecularFormula(IMolecularFormula formula) Removes an IMolecularFormula from this chemObject.
void	removeMolecularFormula(int position) Removes an MolecularFormula from this chemObject.
void	setCharge(Integer charge) No use this method.
int	size() Returns the number of MolecularFormulas in this AdductFormula.

Methods inherited from class org.openscience.cdk.formula.AdductFormula

clone

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.openscience.cdk.interfaces.IAdductFormula

clone

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Constructor Detail

DebugAdductFormula

public DebugAdductFormula()

DebugAdductFormula

public DebugAdductFormula(IMolecularFormula formula)

Method Detail

contains

public boolean contains(IIsotope isotope)

True, if the AdductFormula contains the given IIsotope object and not the instance. The method looks for other isotopes which has the same symbol, natural abundance and exact mass.

Specified by:

contains in interface IAdductFormula

Overrides:

contains in class AdductFormula

Parameters:

isotope - The IIsotope this AdductFormula is searched for

Returns:

True, if the AdductFormula contains the given isotope object

getCharge

public Integer getCharge()

Returns the partial charge of this Adduct. If the charge has not been set the return value is Double.NaN.

Specified by:

getCharge in interface IAdductFormula

Overrides:

getCharge in class AdductFormula

Returns:

the charge of this Adduct

See Also:

AdductFormula.setCharge(java.lang.Integer)

getIsotopeCount

public int getIsotopeCount(IIsotope isotope)

Checks a set of Nodes for the occurrence of the isotope in the adduct formula from a particular isotope. It returns 0 if the does not exist.

Specified by:

getIsotopeCount in interface IAdductFormula

Overrides:

getIsotopeCount in class AdductFormula

Parameters:

isotope - The IIsotope to look for

Returns:

The occurrence of this isotope in this adduct

See Also:

AdductFormula.getIsotopeCount()

getIsotopeCount

public int getIsotopeCount()

Checks a set of Nodes for the number of different isotopes in the adduct formula.

Specified by:

getIsotopeCount in interface IAdductFormula

Overrides:

getIsotopeCount in class AdductFormula

Returns:

The the number of different isotopes in this adduct formula

See Also:

AdductFormula.getIsotopeCount(IIsotope)

isotopes

public Iterable<IIsotope> isotopes()

Returns an Iterator for looping over all isotopes in this adduct formula.

Specified by:

isotopes in interface IAdductFormula

Overrides:

isotopes in class AdductFormula

Returns:

An Iterator with the isotopes in this adduct formula

setCharge

public void setCharge(Integer charge)

No use this method. The charge is defined in each IMolecularFormula.

Specified by:

setCharge in interface IAdductFormula

Overrides:

setCharge in class AdductFormula

Parameters:

charge - The partial charge

See Also:

AdductFormula.getCharge()

add

public void add(IMolecularFormulaSet formulaSet)

Adds all molecularFormulas in the AdductFormula to this chemObject.

Specified by:

add in interface IMolecularFormulaSet

Overrides:

add in class AdductFormula

Parameters:

formulaSet - The MolecularFormulaSet

addMolecularFormula

public void addMolecularFormula(IMolecularFormula formula)

Adds an molecularFormula to this chemObject.

Specified by:

addMolecularFormula in interface IMolecularFormulaSet

Overrides:

addMolecularFormula in class AdductFormula

Parameters:

formula - The molecularFormula to be added to this chemObject

contains

public boolean contains(IMolecularFormula formula)

True, if the AdductFormula contains the given IMolecularFormula object.

Specified by:

contains in interface IMolecularFormulaSet

Overrides:

contains in class AdductFormula

Parameters:

formula - The IMolecularFormula this AdductFormula is searched for

Returns:

True, if the AdductFormula contains the given IMolecularFormula object

getMolecularFormula

public IMolecularFormula getMolecularFormula(int position)

Returns the MolecularFormula at position number in the chemObject.

Specified by:

getMolecularFormula in interface IMolecularFormulaSet

Overrides:

getMolecularFormula in class AdductFormula

Parameters:

position - The position of the IMolecularFormula to be returned.

Returns:

The IMolecularFormula at position number .

iterator

public Iterator<IMolecularFormula> iterator()

Returns an Iterator for looping over all IMolecularFormula in this adduct formula.

Specified by:

iterator in interface Iterable<IMolecularFormula>

Overrides:

iterator in class AdductFormula

Returns:

An Iterator with the IMolecularFormula in this adduct formula

molecularFormulas

public Iterable<IMolecularFormula> molecularFormulas()

Returns an Iterable for looping over all IMolecularFormula in this adduct formula.

Specified by:

molecularFormulas in interface IMolecularFormulaSet

Overrides:

molecularFormulas in class AdductFormula

Returns:

An Iterable with the IMolecularFormula in this adduct formula

See Also:

IMolecularFormulaSet.addMolecularFormula(IMolecularFormula)

removeAllMolecularFormulas

public void removeAllMolecularFormulas()

Removes all IMolecularFormula from this chemObject.

Specified by:

removeAllMolecularFormulas in interface IMolecularFormulaSet

Overrides:

removeAllMolecularFormulas in class AdductFormula

removeMolecularFormula

public void removeMolecularFormula(IMolecularFormula formula)

Removes an IMolecularFormula from this chemObject.

Specified by:

removeMolecularFormula in interface IMolecularFormulaSet

Overrides:

removeMolecularFormula in class AdductFormula

Parameters:

formula - The IMolecularFormula to be removed from this chemObject

removeMolecularFormula

public void removeMolecularFormula(int position)

Removes an MolecularFormula from this chemObject.

Specified by:

removeMolecularFormula in interface IMolecularFormulaSet

Overrides:

removeMolecularFormula in class AdductFormula

Parameters:

position - The position of the MolecularFormula to be removed from this chemObject

size

public int size()

Returns the number of MolecularFormulas in this AdductFormula.

Specified by:

size in interface IMolecularFormulaSet

Overrides:

size in class AdductFormula

Returns:

The number of MolecularFormulas in this AdductFormula

getBuilder

public IChemObjectBuilder getBuilder()

Returns a IChemObjectBuilder for the data classes that extend this class.

Specified by:

getBuilder in interface ICDKObject

Overrides:

getBuilder in class AdductFormula

Returns:

The IChemObjectBuilder matching this ICDKObject