Package de.isas.lipidomics.palinom.cli

Class CmdLineParser

java.lang.Object

de.isas.lipidomics.palinom.cli.CmdLineParser

public class CmdLineParser
extends Object

Create a new command line parser for parsing of lipid names.

Author:

nils.hoffmann

Field Summary

Fields

Modifier and Type	Field	Description
static String	LIPIDMAPS_CLASS_REGEXP

Constructor Summary

Constructors

Constructor	Description
CmdLineParser()

Method Summary

Modifier and Type	Method	Description
protected static String	addGrammarOption(org.apache.commons.cli.Options options)
protected static String	addHelpOption(org.apache.commons.cli.Options options)
protected static String	addLipidFileInputOption(org.apache.commons.cli.Options options)
protected static String	addLipidNameInputOption(org.apache.commons.cli.Options options)
protected static String	addOutputToFileOption(org.apache.commons.cli.Options options)
protected static String	addVersionOption(org.apache.commons.cli.Options options)
static void	main(String[] args)	Runs the command line parser for jgoslin, including validation.
protected static org.apache.commons.lang3.tuple.Pair<String,List<de.isas.lipidomics.palinom.cli.CmdLineParser.ValidationResult>>	parseName(String lipidName)
protected static List<org.apache.commons.lang3.tuple.Pair<String,List<de.isas.lipidomics.palinom.cli.CmdLineParser.ValidationResult>>>	parseNames(Stream<String> lipidNames)
protected static List<org.apache.commons.lang3.tuple.Pair<String,List<de.isas.lipidomics.palinom.cli.CmdLineParser.ValidationResult>>>	parseNamesWith(Stream<String> lipidNames, CmdLineParser.ValidationResult.Grammar grammar)
protected static org.apache.commons.lang3.tuple.Pair<String,de.isas.lipidomics.palinom.cli.CmdLineParser.ValidationResult>	parseNameWith(String lipidName, CmdLineParser.ValidationResult.Grammar grammar)
protected static String	toTable(List<org.apache.commons.lang3.tuple.Pair<String,List<de.isas.lipidomics.palinom.cli.CmdLineParser.ValidationResult>>> results)
protected static boolean	writeToFile(File f, List<org.apache.commons.lang3.tuple.Pair<String,List<de.isas.lipidomics.palinom.cli.CmdLineParser.ValidationResult>>> results)
protected static boolean	writeToStdOut(List<org.apache.commons.lang3.tuple.Pair<String,List<de.isas.lipidomics.palinom.cli.CmdLineParser.ValidationResult>>> results)
protected static void	writeToWriter(BufferedWriter bw, List<org.apache.commons.lang3.tuple.Pair<String,List<de.isas.lipidomics.palinom.cli.CmdLineParser.ValidationResult>>> results)

Methods inherited from class java.lang.Object

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

Field Detail

LIPIDMAPS_CLASS_REGEXP

public static final String LIPIDMAPS_CLASS_REGEXP

See Also:

Constant Field Values

Constructor Detail

CmdLineParser

public CmdLineParser()

Method Detail

main

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

Runs the command line parser for jgoslin, including validation.

Parameters:

args - an array of String lipid names.

Throws:

Exception - if any unexpected errors occur.

writeToStdOut

protected static boolean writeToStdOut(List<org.apache.commons.lang3.tuple.Pair<String,List<de.isas.lipidomics.palinom.cli.CmdLineParser.ValidationResult>>> results)

writeToFile

protected static boolean writeToFile(File f,
                                     List<org.apache.commons.lang3.tuple.Pair<String,List<de.isas.lipidomics.palinom.cli.CmdLineParser.ValidationResult>>> results)

toTable

protected static String toTable(List<org.apache.commons.lang3.tuple.Pair<String,List<de.isas.lipidomics.palinom.cli.CmdLineParser.ValidationResult>>> results)

writeToWriter

protected static void writeToWriter(BufferedWriter bw,
                                    List<org.apache.commons.lang3.tuple.Pair<String,List<de.isas.lipidomics.palinom.cli.CmdLineParser.ValidationResult>>> results)

parseNames

protected static List<org.apache.commons.lang3.tuple.Pair<String,List<de.isas.lipidomics.palinom.cli.CmdLineParser.ValidationResult>>> parseNames(Stream<String> lipidNames)

parseNamesWith

protected static List<org.apache.commons.lang3.tuple.Pair<String,List<de.isas.lipidomics.palinom.cli.CmdLineParser.ValidationResult>>> parseNamesWith(Stream<String> lipidNames,
                                                                                                                                                            CmdLineParser.ValidationResult.Grammar grammar)

parseNameWith

protected static org.apache.commons.lang3.tuple.Pair<String,de.isas.lipidomics.palinom.cli.CmdLineParser.ValidationResult> parseNameWith(String lipidName,
                                                                                                                                               CmdLineParser.ValidationResult.Grammar grammar)

parseName

protected static org.apache.commons.lang3.tuple.Pair<String,List<de.isas.lipidomics.palinom.cli.CmdLineParser.ValidationResult>> parseName(String lipidName)

addLipidFileInputOption

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

addLipidNameInputOption

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

addVersionOption

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

addHelpOption

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

addOutputToFileOption

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

addGrammarOption

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