Package eu.isas.peptideshaker.cmd

Class PeptideShakerCLI

java.lang.Object

eu.isas.peptideshaker.preferences.UserPreferencesParent

eu.isas.peptideshaker.utils.PsdbParent

eu.isas.peptideshaker.cmd.PeptideShakerCLI

All Implemented Interfaces:

AutoCloseable, Callable

public class PeptideShakerCLI
extends PsdbParent
implements Callable

A command line interface to run PeptideShaker.

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
PeptideShakerCLI()	Construct a new PeptideShakerCLI runnable.

Method Summary

Modifier and Type	Method	Description
Object	call()
static void	closePeptideShaker(com.compomics.util.experiment.identification.Identification identification)	Close the PeptideShaker instance.
void	createProject()	Creates the PeptideShaker project based on the identification files provided in the command line input
static String	getLogFileMessage()	Returns the "see the log file" message.
static void	main(String[] args)	Starts the launcher by calling the launch method.
static void	redirectErrorStream(File aLogFolder)	Redirects the error stream to the PeptideShaker.log of a given folder.
void	setPeptideShakerCLIInputBean(PeptideShakerCLIInputBean cliInputBean)	Set the PeptideShakerCLIInputBean.
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

PeptideShakerCLI

public PeptideShakerCLI()

Construct a new PeptideShakerCLI runnable. When initialization is successful and the PeptideShakerCLIInputBean is set, calling "run" will start PeptideShaker and write the output files when finished.

Method Details

setPeptideShakerCLIInputBean

public void setPeptideShakerCLIInputBean(PeptideShakerCLIInputBean cliInputBean)

Set the PeptideShakerCLIInputBean.

Parameters:

cliInputBean - the PeptideShakerCLIInputBean

call

public Object call()

Specified by:

call in interface Callable

createProject

public void createProject()
                   throws IOException,
InterruptedException,
TimeoutException

Creates the PeptideShaker project based on the identification files provided in the command line input

Throws:

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

InterruptedException - exception thrown if a thread is interrupted

TimeoutException - exception thrown if a process times out

closePeptideShaker

public static void closePeptideShaker(com.compomics.util.experiment.identification.Identification identification)
                               throws IOException,
SQLException

Close the PeptideShaker instance. Closes file connections and deletes temporary files.

Parameters:

identification - the identification to close

Throws:

IOException - exception thrown whenever an error occurred while writing the object

SQLException - exception thrown whenever an error occurred while closing the database connection

redirectErrorStream

public static void redirectErrorStream(File aLogFolder)

Redirects the error stream to the PeptideShaker.log of a given folder.

Parameters:

aLogFolder - the folder where to save the log

getLogFileMessage

public static String getLogFileMessage()

Returns the "see the log file" message. With the path if available.

Returns:

the "see the log file" message

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