com.compomics.util.io

Class MascotEnzymeReader

java.lang.Object

com.compomics.util.io.MascotEnzymeReader

public class MascotEnzymeReader
extends Object

This class will load Enzyme properties from a Mascot (www.matrixscience.com) formatted text file.

Author:

Lennart Martens

Constructor Summary

Constructors

Constructor and Description
MascotEnzymeReader(InputStream aEnzymeStream) The constructor allows you specify to specify an inputstream from which to load the enzyme information.
MascotEnzymeReader(String aEnzymeFile) The constructor requires that you specify the file from which to load the enzyme information.

Method Summary

Methods

Modifier and Type	Method and Description
Enzyme	getEnzyme(String aTitle) This method will return a copy of an Enzyme instance for the given name, or 'null' if the enzyme was not found in the current list.
String[]	getEnzymeNames() This method reports on all the known names for enzymes in this reader.

Methods inherited from class java.lang.Object

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

Constructor Detail

MascotEnzymeReader

public MascotEnzymeReader(String aEnzymeFile)
                   throws IOException

The constructor requires that you specify the file from which to load the enzyme information. Information is immediately loaded upon construction.

Parameters:

aEnzymeFile - String with the filename of the mascot enzyme file.

Throws:

IOException - when the enzyme file could not be read.

MascotEnzymeReader

public MascotEnzymeReader(InputStream aEnzymeStream)
                   throws IOException

The constructor allows you specify to specify an inputstream from which to load the enzyme information. Note that the stream is closed after loading!!! Information is immediately loaded upon construction.

Parameters:

aEnzymeStream - InputStream to the mascot enzyme file.

Throws:

IOException - when the enzyme file could not be read.

Method Detail

getEnzymeNames

public String[] getEnzymeNames()

This method reports on all the known names for enzymes in this reader.

Returns:

String[] with all the names.

getEnzyme

public Enzyme getEnzyme(String aTitle)

This method will return a copy of an Enzyme instance for the given name, or 'null' if the enzyme was not found in the current list.

Parameters:

aTitle - String with the title (name) of the Enzyme to retrieve.

Returns:

Enzyme when the specified enzyme was found, 'null' otherwise!