Package eu.isas.peptideshaker.cmd

Class FollowUpCLI

java.lang.Object

eu.isas.peptideshaker.preferences.UserPreferencesParent

eu.isas.peptideshaker.utils.PsdbParent

eu.isas.peptideshaker.cmd.FollowUpCLI

All Implemented Interfaces:

AutoCloseable

public class FollowUpCLI
extends PsdbParent

Command line interface to run follow-up analysis on psdb files.

Author:

Marc Vaudel, Harald Barsnes

Field Summary

Fields inherited from class eu.isas.peptideshaker.utils.PsdbParent

dbFolder, displayParameters, filterParameters, geneMaps, identification, identificationFeaturesGenerator, identificationParameters, metrics, msFileHandler, projectDetails, projectParameters, projectType, proteinDetailsProvider, psdbFile, sequenceProvider, spectrumCountingParameters

Fields inherited from class eu.isas.peptideshaker.preferences.UserPreferencesParent

userPreferences

Constructor Summary

Constructors

Constructor	Description
FollowUpCLI(FollowUpCLIInputBean followUpCLIInputBean)	Construct a new FollowUpCLI runnable from a FollowUpCLI Bean.

Method Summary

Modifier and Type	Method	Description
Object	call()	Calling this method will run the configured PeptideShaker process.
static void	main(String[] args)	Starts the launcher by calling the launch method.
String	toString()

Methods inherited from class eu.isas.peptideshaker.utils.PsdbParent

close, getDbFolder, getDisplayParameters, getExtendedProjectReport, getFilterParameters, getGeneMaps, getIdentification, getIdentificationFeaturesGenerator, getIdentificationParameters, getMetrics, getProjectDetails, getProjectParameters, getProjectType, getProteinDetailsProvider, getPsdbFile, getPsdbImportFromZip, getSequenceProvider, getSpectrumCountingParameters, getSpectrumProvider, getUserParameters, loadFastaFile, loadPsdbFile, loadPsdbFromZipFile, loadSpectrumFile, loadSpectrumFile, loadSpectrumFiles, loadSpectrumFiles, resetIdentificationFeaturesGenerator, saveProject, setDbFolder, setDefaultParameters, setDisplayParameters, setFilterParameters, setGeneMaps, setIdentification, setIdentificationFeaturesGenerator, setIdentificationParameters, setMetrics, setMsFileHandler, setProject, setProjectDetails, setProjectType, setProteinDetailsProvider, setPsdbFile, setPsdbImportFromZip, setSequenceProvider, setSpectrumCountingParameters

Methods inherited from class eu.isas.peptideshaker.preferences.UserPreferencesParent

loadUserParameters, saveUserParameters

Methods inherited from class java.lang.Object

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

Constructor Details

FollowUpCLI

public FollowUpCLI(FollowUpCLIInputBean followUpCLIInputBean)

Construct a new FollowUpCLI runnable from a FollowUpCLI Bean. When initialization is successful, calling "run" will open the PeptideShaker project and write the desired output files.

Parameters:

followUpCLIInputBean - the follow-up options

Method Details

call

public Object call()

Calling this method will run the configured PeptideShaker process.

Returns:

returns 1 if the process was canceled

main

public static void main(String[] args)

Starts the launcher by calling the launch method. Use this as the main class in the jar file.

Parameters:

args - the command line arguments

toString

public String toString()

Overrides:

toString in class Object