Package com.compomics.cli.peptide_mapper

Class PeptideMapperCLI

java.lang.Object

com.compomics.cli.peptide_mapper.PeptideMapperCLI

public class PeptideMapperCLI
extends Object

Command line peptide mapping.

Author:

Dominik Kopczynski

Field Summary

Fields

Modifier and Type	Field	Description
static int	TIMEOUT_DAYS

Constructor Summary

Constructors

Constructor	Description
PeptideMapperCLI()

Method Summary

Modifier and Type	Method	Description
static void	convertSearchGUIFile(String[] args)
static void	handleError(String outputFileName, String errorMessage, Throwable e)
static void	handleParameters(String[] args)
static void	main(String[] args)	Main class.
static void	printHelp()
static void	runMapping(File fastaFile, WaitingHandlerCLIImpl waitingHandlerCLIImpl, IdentificationParameters identificationParameters, String inputFilePath, String outputFilePath, int nCores, boolean peptideMapping)
static String	tagToString(Tag tag)

Methods inherited from class java.lang.Object

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

Field Details

TIMEOUT_DAYS

public static int TIMEOUT_DAYS

Constructor Details

PeptideMapperCLI

public PeptideMapperCLI()

Method Details

printHelp

public static void printHelp()

main

public static void main(String[] args)

Main class.

Parameters:

args - command line arguments

tagToString

public static String tagToString(Tag tag)

convertSearchGUIFile

public static void convertSearchGUIFile(String[] args)

handleParameters

public static void handleParameters(String[] args)

handleError

public static void handleError(String outputFileName,
 String errorMessage,
 Throwable e)

runMapping

public static void runMapping(File fastaFile,
 WaitingHandlerCLIImpl waitingHandlerCLIImpl,
 IdentificationParameters identificationParameters,
 String inputFilePath,
 String outputFilePath,
 int nCores,
 boolean peptideMapping)