com.compomics.util.experiment.biology

Class EnzymeFactory

java.lang.Object

com.compomics.util.experiment.biology.EnzymeFactory

public class EnzymeFactory
extends Object

This factory will provide the implemented enzymes.

Author:

Marc Vaudel

Method Summary

Methods

Modifier and Type	Method and Description
void	addEnzyme(Enzyme enzyme) Adds an enzyme in the factory.
boolean	enzymeLoaded(String enzyme) Indicates whether an enzyme is loaded in the factory.
Enzyme	getEnzyme(String enzymeName) Returns the enzyme corresponding to the given name.
static CvTerm	getEnzymeCvTerm(Enzyme enzyme) Tries to convert the given enzyme to a CvTerm for use in mzIdentML etc.
ArrayList<Enzyme>	getEnzymes() Get the imported enzymes.
static EnzymeFactory	getInstance() Static method to get an instance of the factory.
static Enzyme	getUtilitiesEnzyme(String prideEnzymeName) Tries to map the enzyme name given in the PRIDE file a utilities/OMSSA enzyme.
void	importEnzymes(File enzymeFile) Import enzymes.
void	writeMsAmandaEnzymeFile(File file) Creates the MS Amanda enzyme settings file corresponding to the enzymes loaded in the factory to the given file.

Methods inherited from class java.lang.Object

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

Method Detail

getInstance

public static EnzymeFactory getInstance()

Static method to get an instance of the factory.

Returns:

the factory instance

getEnzymes

public ArrayList<Enzyme> getEnzymes()

Get the imported enzymes.

Returns:

The enzymes as ArrayList

getEnzyme

public Enzyme getEnzyme(String enzymeName)

Returns the enzyme corresponding to the given name. Null if not found.

Parameters:

enzymeName - the name of the desired enzyme

Returns:

the corresponding enzyme

addEnzyme

public void addEnzyme(Enzyme enzyme)

Adds an enzyme in the factory.

Parameters:

enzyme - the new enzyme to add

enzymeLoaded

public boolean enzymeLoaded(String enzyme)

Indicates whether an enzyme is loaded in the factory.

Parameters:

enzyme - the name of the enzyme

Returns:

a boolean indicating whether an enzyme is loaded in the factory

importEnzymes

public void importEnzymes(File enzymeFile)
                   throws org.xmlpull.v1.XmlPullParserException,
                          IOException

Import enzymes.

Parameters:

enzymeFile - XML file containing the enzymes

Throws:

org.xmlpull.v1.XmlPullParserException - when the parser failed

IOException - when reading the corresponding file failed

getUtilitiesEnzyme

public static Enzyme getUtilitiesEnzyme(String prideEnzymeName)

Tries to map the enzyme name given in the PRIDE file a utilities/OMSSA enzyme.

Parameters:

prideEnzymeName - the PRIDE enzyme name

Returns:

the Enzyme object, or null if not mapping is found

writeMsAmandaEnzymeFile

public void writeMsAmandaEnzymeFile(File file)
                             throws IOException

Creates the MS Amanda enzyme settings file corresponding to the enzymes loaded in the factory to the given file.

Parameters:

file - the file

Throws:

IOException - exception thrown whenever an error occurred while writing the file

getEnzymeCvTerm

public static CvTerm getEnzymeCvTerm(Enzyme enzyme)

Tries to convert the given enzyme to a CvTerm for use in mzIdentML etc.

Parameters:

enzyme - the enzyme to convert

Returns:

the enzyme as a CvTerm