introducing qcommandlineparser

src/masschroq_cli.cpp

@@ -20,6 +20,7 @@
 #include "masschroq_cli.h"
 
 #include <QDebug>
+#include <QCommandLineParser>
 
 
 
@@ -84,6 +85,12 @@ void masschroqCli::run()
     const QDateTime dt_begin = QDateTime::currentDateTime();
     const QString masschroq_dir_path(QCoreApplication::applicationDirPath());
 
+    QCommandLineParser parser;
+    parser.setApplicationDescription("Perform Mass Chromatogram Quantification as indicated in the XML input FILE.");
+    parser.addHelpOption();
+    parser.addVersionOption();
+
+
     QStringList arguments = app->arguments();
     QString fileName;
     /// by default, temporary files go in the temporary directory of the system
@@ -103,7 +110,7 @@ void masschroqCli::run()
     switch (args_number) {
 
     case 2 :
-      qDebug() << "masschroqml cli case 2";
+        qDebug() << "masschroqml cli case 2";
         first = arguments.at(1);
         if ( (first == "--help") ||
                 (first == "-h") )
@@ -129,7 +136,7 @@ void masschroqCli::run()
         break;
 
     case 3 :
-      qDebug() << "masschroqml cli case 3";
+        qDebug() << "masschroqml cli case 3";
         fileName = arguments.at(2);
         option = arguments.at(1);
         if ( (option == "--parse-peptides") ||
@@ -152,7 +159,7 @@ void masschroqCli::run()
         }
         break;
     case 4 :
-      qDebug() << "masschroqml cli case 4";
+        qDebug() << "masschroqml cli case 4";
         option = arguments.at(1);
         fileName = arguments.at(3);
 
@@ -180,8 +187,8 @@ void masschroqCli::run()
         break;
 
     case 6 :
-        	  qDebug() << "masschroqml cli case 6";
-       option = arguments.at(1);
+        qDebug() << "masschroqml cli case 6";
+        option = arguments.at(1);
         fileName = arguments.at(5);
 
         if ( (option == "--tmpdir") ||
@@ -229,14 +236,14 @@ void masschroqCli::run()
         }
         break;
     case 1 :
-       	  qDebug() << "masschroqml cli case 1";
-       mcqerr() << "masschroq : missing input filename." << endl;
+        qDebug() << "masschroqml cli case 1";
+        mcqerr() << "masschroq : missing input filename." << endl;
         mcqerr() << "Try 'masschroq --help' for more information." << endl;
         windaube_exit();
         app->exit(1);
         break;
     default :
-      	  qDebug() << "masschroqml cli default";
+        qDebug() << "masschroqml cli default";
 
         mcqerr() << "masschroq : invalid use." << endl;
         mcqerr() << "Try 'masschroq --help' for more information." << endl;
@@ -256,14 +263,14 @@ void masschroqCli::run()
         mass_chroq_engine.setXmlFilename(fileName);
 
         if (masschroqml_validation == true) {
-	  qDebug() << "masschroqml_validation == true";
+            qDebug() << "masschroqml_validation == true";
             mass_chroq_engine.validateXmlFile();
 // you must call quit when complete or the program will stay in the
             // messaging loop
-           // quit();
+            // quit();
         }
         else {
-	  qDebug() << "masschroqml_validation == false";
+            qDebug() << "masschroqml_validation == false";
 
             mass_chroq_engine.setTmpDir(tmpDirName);
 
@@ -304,10 +311,10 @@ void masschroqCli::run()
         mcqerr() << error.qwhat() << endl;
 
         windaube_exit();
-	exit(1);
+        exit(1);
         app->exit(1);
     }
-qDebug() << "before final quit()";
+    qDebug() << "before final quit()";
 
     // you must call quit when complete or the program will stay in the
     // messaging loop