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java.lang.Objectcom.compomics.util.experiment.biology.EnzymeFactory
public class EnzymeFactory
This factory will provide the implemented enzymes.
Method Summary | |
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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. |
ArrayList<Enzyme> |
getEnzymes()
Get the imported enzymes. |
static EnzymeFactory |
getInstance()
Static method to get an instance of the factory. |
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. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Method Detail |
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public static EnzymeFactory getInstance()
public ArrayList<Enzyme> getEnzymes()
public Enzyme getEnzyme(String enzymeName)
enzymeName
- the name of the desired enzyme
public void addEnzyme(Enzyme enzyme)
enzyme
- the new enzyme to addpublic boolean enzymeLoaded(String enzyme)
enzyme
- the name of the enzyme
public void importEnzymes(File enzymeFile) throws org.xmlpull.v1.XmlPullParserException, IOException
enzymeFile
- xml file containing the enzymes
org.xmlpull.v1.XmlPullParserException
- when the parser failed
IOException
- when reading the corresponding file failedpublic Enzyme getUtilitiesEnzyme(String prideEnzymeName)
prideEnzymeName
- the PRIDE enzyme name
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