initial pass at cleanup

Code/Shape/cli_code/parseCommandLine.h

@@ -0,0 +1,54 @@
+/*******************************************************************************
+parseCommandLine.h - Shape-it
+ 
+Copyright 2012 by Silicos-it, a division of Imacosi BVBA
+ 
+This file is part of Shape-it.
+
+	Shape-it is free software: you can redistribute it and/or modify
+	it under the terms of the GNU Lesser General Public License as published 
+	by the Free Software Foundation, either version 3 of the License, or
+	(at your option) any later version.
+
+	Shape-it is distributed in the hope that it will be useful,
+	but WITHOUT ANY WARRANTY; without even the implied warranty of
+	MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+	GNU Lesser General Public License for more details.
+
+	You should have received a copy of the GNU Lesser General Public License
+	along with Shape-it.  If not, see <http://www.gnu.org/licenses/>.
+
+Shape-it is linked against OpenBabel version 2.
+
+	OpenBabel is free software; you can redistribute it and/or modify
+	it under the terms of the GNU General Public License as published by
+	the Free Software Foundation version 2 of the License.
+
+***********************************************************************/
+
+
+
+#ifndef __SILICOSIT_SHAPEIT_PARSECOMMANDLINE_H__
+#define __SILICOSIT_SHAPEIT_PARSECOMMANDLINE_H__
+
+
+
+// General
+#include <getopt.h>
+#include <stdlib.h>
+#include <algorithm>
+
+// OpenBabel
+
+// Shape-it
+#include <Shape/options.h>
+#include <Shape/mainErr.h>
+
+
+
+Options parseCommandLine(int argc, char* argv[]);
+
+
+
+
+#endif