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 and 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 and 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 Detail

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 Detail

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.