Package eu.isas.peptideshaker.cmd

Class ReportCLI

java.lang.Object

eu.isas.peptideshaker.preferences.UserPreferencesParent

eu.isas.peptideshaker.utils.PsdbParent

eu.isas.peptideshaker.cmd.ReportCLI

All Implemented Interfaces:

AutoCloseable

public class ReportCLI
extends PsdbParent

This class performs the command line export of reports in command line.

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
ReportCLI(ReportCLIInputBean reportCLIInputBean)	Construct a new ReportCLI runnable from a ReportCLI Bean.

Method Summary

Modifier and Type	Method	Description
Object	call()	Calling this method will run the configured PeptideShaker process.
void	closePeptideShaker()	Close the PeptideShaker instance by clearing up factories and cache.
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

ReportCLI

public ReportCLI(ReportCLIInputBean reportCLIInputBean)

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

Parameters:

reportCLIInputBean - the input bean

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

closePeptideShaker

public void closePeptideShaker()
                        throws IOException,
SQLException,
InterruptedException,
ClassNotFoundException

Close the PeptideShaker instance by clearing up factories and cache.

Throws:

IOException - thrown if an exception occurred while closing the connection to a file

SQLException - thrown if an exception occurred while closing the connection to a database

InterruptedException - if a thread was interrupted when closing the database

ClassNotFoundException - if a class was not found when emptying the cache