Package eu.isas.peptideshaker.cmd

Class StirredOptionsBean

java.lang.Object

eu.isas.peptideshaker.cmd.StirredOptionsBean

public class StirredOptionsBean
extends Object

This class parses the parameters from an ModificationsCLI.

Author:

Marc Vaudel, Harald Barsnes

Field Summary

Fields

Modifier and Type	Field	Description
String	contactAddress	The address of the contact to annotate in the mzIdentML file.
String	contactEmail	The email of the contact to annotate in the mzIdentML file.
String	contactFirstName	The first name of the contact to annotate in the mzIdentML file.
String	contactLastName	The last name of the contact to annotate in the mzIdentML file.
String	contactOrganizationAddress	The address of the organization of the contact to annotate in the mzIdentML file.
String	contactOrganizationEmail	The email of the organization of the contact to annotate in the mzIdentML file.
String	contactOrganizationName	The name of the organization of the contact to annotate in the mzIdentML file.
File	fastaFile	The fasta file.
File	identificationParametersFile	The identification parameters file.
File	inputFile	The input file.
File	logFile	The log file.
int	nThreads	The number of threads to use.
File	outputFolder	The output folder.
File	spectrumFile	The spectrum file.
File	tempFolder	The temp folder to use for temp files.
int	timeOutDays	The timeout time in days.

Constructor Summary

Constructors

Constructor	Description
StirredOptionsBean(org.apache.commons.cli.CommandLine aLine)	Parses all the arguments from a command line.

Method Summary

Methods inherited from class java.lang.Object

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

Field Details

inputFile

public final File inputFile

The input file.

spectrumFile

public File spectrumFile

The spectrum file.

fastaFile

public File fastaFile

The fasta file.

identificationParametersFile

public File identificationParametersFile

The identification parameters file.

tempFolder

public final File tempFolder

The temp folder to use for temp files.

logFile

public final File logFile

The log file.

nThreads

public int nThreads

The number of threads to use.

timeOutDays

public int timeOutDays

The timeout time in days.

outputFolder

public final File outputFolder

The output folder.

contactFirstName

public String contactFirstName

The first name of the contact to annotate in the mzIdentML file.

contactLastName

public String contactLastName

The last name of the contact to annotate in the mzIdentML file.

contactAddress

public String contactAddress

The address of the contact to annotate in the mzIdentML file.

contactEmail

public String contactEmail

The email of the contact to annotate in the mzIdentML file.

contactOrganizationName

public String contactOrganizationName

The name of the organization of the contact to annotate in the mzIdentML file.

contactOrganizationAddress

public String contactOrganizationAddress

The address of the organization of the contact to annotate in the mzIdentML file.

contactOrganizationEmail

public String contactOrganizationEmail

The email of the organization of the contact to annotate in the mzIdentML file.

Constructor Details

StirredOptionsBean

public StirredOptionsBean(org.apache.commons.cli.CommandLine aLine) throws IOException

Parses all the arguments from a command line.

Parameters:

aLine - the command line

Throws:

IOException - if an error occurs while reading or writing a file.