com.compomics.util.experiment.identification.search_parameters_cli

Class IdentificationParametersInputBean

java.lang.Object

com.compomics.util.experiment.identification.search_parameters_cli.IdentificationParametersInputBean

public class IdentificationParametersInputBean
extends java.lang.Object

This class contains the parses parameters from a command line and stores them in a SearchParameters object.

Author:

Marc Vaudel, Harald Barsnes

Constructor Summary

Constructors

Constructor and Description
IdentificationParametersInputBean(org.apache.commons.cli.CommandLine aLine) Takes all the arguments from a command line.

Method Summary

Methods

Modifier and Type	Method and Description
java.io.File	getDestinationFile() Returns the file where to save the identification parameters.
SearchParameters	getSearchParameters() Returns the search parameters.
java.lang.Boolean	isListMods() Indicates whether the modifications should be printed on the screen.
static boolean	isValidModifications(org.apache.commons.cli.CommandLine aLine) Verifies that modifications are correctly recognized.
static boolean	isValidStartup(org.apache.commons.cli.CommandLine aLine) Verifies the command line start parameters.

Methods inherited from class java.lang.Object

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

Constructor Detail

IdentificationParametersInputBean

public IdentificationParametersInputBean(org.apache.commons.cli.CommandLine aLine)
                                  throws java.io.FileNotFoundException,
                                         java.io.IOException,
                                         java.lang.ClassNotFoundException

Takes all the arguments from a command line.

Parameters:

aLine - the command line

Throws:

java.io.FileNotFoundException

java.io.IOException

java.lang.ClassNotFoundException

Method Detail

getSearchParameters

public SearchParameters getSearchParameters()

Returns the search parameters.

Returns:

the search parameters

getDestinationFile

public java.io.File getDestinationFile()

Returns the file where to save the identification parameters.

Returns:

the file where to save the identification parameters

isListMods

public java.lang.Boolean isListMods()

Indicates whether the modifications should be printed on the screen.

Returns:

true if the modifications should be printed on the screen

isValidModifications

public static boolean isValidModifications(org.apache.commons.cli.CommandLine aLine)
                                    throws java.io.IOException

Verifies that modifications are correctly recognized.

Parameters:

aLine - the command line to validate

Returns:

true if the startup was valid

Throws:

java.io.IOException

isValidStartup

public static boolean isValidStartup(org.apache.commons.cli.CommandLine aLine)
                              throws java.io.IOException

Verifies the command line start parameters.

Parameters:

aLine - the command line to validate

Returns:

true if the startup was valid

Throws:

java.io.IOException