Package de.isas.mztab2.cli

Class MZTabCommandLine

java.lang.Object

de.isas.mztab2.cli.MZTabCommandLine

public class MZTabCommandLine
extends Object

MZTabCommandLine class.

Since:

17/09/13

Author:

qingwei, nilshoffmann

Constructor Summary

Constructors

Constructor	Description
MZTabCommandLine()

Method Summary

Modifier and Type	Method	Description
protected static String	addCheckOption(org.apache.commons.cli.Options options)
protected static String	addCheckSemanticOption(org.apache.commons.cli.Options options)
protected static String	addDeserializeOption(org.apache.commons.cli.Options options)
protected static String	addHelpOption(org.apache.commons.cli.Options options)
protected static String	addLevelOption(org.apache.commons.cli.Options options)
protected static String	addMessageOption(org.apache.commons.cli.Options options)
protected static String	addOutFileOption(org.apache.commons.cli.Options options)
protected static String	addSerializeOption(org.apache.commons.cli.Options options)
protected static String	addVersionOption(org.apache.commons.cli.Options options)
protected static void	handleMsgOption(org.apache.commons.cli.CommandLine line, String msgOpt, uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorTypeMap typeMap)
protected static boolean	handleSemanticValidation(org.apache.commons.cli.CommandLine line, String checkSemanticOpt, File inFile, PrintStream outFile, de.isas.mztab2.io.MzTabFileParser mzTabParser, uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorType.Level level)
protected static boolean	handleValidation(org.apache.commons.cli.CommandLine line, String checkOpt, PrintStream outFile, uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorType.Level level, String checkSemanticOpt, boolean toJson, boolean fromJson)
protected static boolean	handleValidationOptions(org.apache.commons.cli.CommandLine line, String outOpt, String levelOpt, String serializeOpt, String deserializeOpt, String checkOpt, String checkSemanticOpt)
static void	main(String[] args)	Runs the command line parser for mzTab, including validation.

Methods inherited from class java.lang.Object

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

Constructor Detail

MZTabCommandLine

public MZTabCommandLine()

Method Detail

main

public static void main(String[] args)
                 throws Exception

Runs the command line parser for mzTab, including validation.

Parameters:

args - an array of String objects.

Throws:

Exception - if any.

addVersionOption

protected static String addVersionOption(org.apache.commons.cli.Options options)

addHelpOption

protected static String addHelpOption(org.apache.commons.cli.Options options)

addCheckSemanticOption

protected static String addCheckSemanticOption(org.apache.commons.cli.Options options)
                                        throws IllegalArgumentException

Throws:

IllegalArgumentException

addDeserializeOption

protected static String addDeserializeOption(org.apache.commons.cli.Options options)

addSerializeOption

protected static String addSerializeOption(org.apache.commons.cli.Options options)

addLevelOption

protected static String addLevelOption(org.apache.commons.cli.Options options)

addCheckOption

protected static String addCheckOption(org.apache.commons.cli.Options options)
                                throws IllegalArgumentException

Throws:

IllegalArgumentException

addOutFileOption

protected static String addOutFileOption(org.apache.commons.cli.Options options)

addMessageOption

protected static String addMessageOption(org.apache.commons.cli.Options options)
                                  throws IllegalArgumentException

Throws:

IllegalArgumentException

handleValidationOptions

protected static boolean handleValidationOptions(org.apache.commons.cli.CommandLine line,
                                                 String outOpt,
                                                 String levelOpt,
                                                 String serializeOpt,
                                                 String deserializeOpt,
                                                 String checkOpt,
                                                 String checkSemanticOpt)
                                          throws JAXBException,
                                                 IllegalArgumentException,
                                                 URISyntaxException

Throws:

JAXBException

IllegalArgumentException

URISyntaxException

handleMsgOption

protected static void handleMsgOption(org.apache.commons.cli.CommandLine line,
                                      String msgOpt,
                                      uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorTypeMap typeMap)
                               throws NumberFormatException

Throws:

NumberFormatException

handleValidation

protected static boolean handleValidation(org.apache.commons.cli.CommandLine line,
                                          String checkOpt,
                                          PrintStream outFile,
                                          uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorType.Level level,
                                          String checkSemanticOpt,
                                          boolean toJson,
                                          boolean fromJson)
                                   throws URISyntaxException,
                                          JAXBException,
                                          IllegalArgumentException,
                                          IOException

Throws:

URISyntaxException

JAXBException

IllegalArgumentException

IOException

handleSemanticValidation

protected static boolean handleSemanticValidation(org.apache.commons.cli.CommandLine line,
                                                  String checkSemanticOpt,
                                                  File inFile,
                                                  PrintStream outFile,
                                                  de.isas.mztab2.io.MzTabFileParser mzTabParser,
                                                  uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorType.Level level)
                                           throws JAXBException,
                                                  MalformedURLException,
                                                  URISyntaxException

Throws:

JAXBException

MalformedURLException

URISyntaxException