org.openscience.cdk.formula.rules

Class MMElementRule

java.lang.Object

org.openscience.cdk.formula.rules.MMElementRule

All Implemented Interfaces:

IRule

public class MMElementRule
extends Object
implements IRule

This class validate if the occurrence of the IElements in the IMolecularFormula, for metabolites, are into a maximal limit according paper: . The study is from 2 different mass spectral databases and according different mass of the metabolites. The analysis don't take account if the IElement is not contained in the matrix. It will be jumped.

The rules is based from Tobias Kind paper with the title "Seven Golden Rules for heuristic filtering of molecular formula" [Kind, Tobias and Fiehn, Oliver, Seven Golden Rules for heuristic filtering of molecular formulas obtained by accurate mass spectrometry, BMC Bioinformatics, 2007, 8:?-?, doi:10.1186/1471-2105-8-105].

Table 1: Parameters set by this rule.

Name	Default	Description
database	willey	Mass spectral databases extraction
massRange	< 500	Mass to take account

Author:

miguelrojasch

Source code:

master

Belongs to CDK module:

formula

Created on:

2007-11-20

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	MMElementRule.Database A enumeration of the possible databases according the rules.
static class	MMElementRule.RangeMass A enumeration of the possible mass range according the rules.

Constructor Summary

Constructors

Constructor and Description
MMElementRule() Constructor for the MMElementRule object.

Method Summary

Methods

Modifier and Type	Method and Description
Object[]	getParameters() Gets the parameters attribute of the MMElementRule object.
void	setParameters(Object[] params) Sets the parameters attribute of the MMElementRule object.
double	validate(IMolecularFormula formula) Validate the occurrence of this IMolecularFormula.

Methods inherited from class java.lang.Object

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

Constructor Detail

MMElementRule

public MMElementRule()

Constructor for the MMElementRule object.

Method Detail

setParameters

public void setParameters(Object[] params)
                   throws CDKException

Sets the parameters attribute of the MMElementRule object.

Specified by:

setParameters in interface IRule

Parameters:

params - The new parameters value

Throws:

CDKException - Description of the Exception

See Also:

getParameters()

getParameters

public Object[] getParameters()

Gets the parameters attribute of the MMElementRule object.

Specified by:

getParameters in interface IRule

Returns:

The parameters value

See Also:

setParameters(java.lang.Object[])

validate

public double validate(IMolecularFormula formula)
                throws CDKException

Validate the occurrence of this IMolecularFormula.

Specified by:

validate in interface IRule

Parameters:

formula - Parameter is the IMolecularFormula

Returns:

An ArrayList containing 9 elements in the order described above

Throws:

CDKException - if an error occurs during the validation. See documentation for individual rules