initial pass at cleanup

Code/Shape/cli_code/options.cpp

@@ -0,0 +1,180 @@
+/*******************************************************************************
+options.cpp - 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.
+
+***********************************************************************/
+
+
+
+#include <Shape/options.h>
+
+      
+
+Options::Options(void)
+{
+   refInpFile = "";
+   refInpStream = NULL;
+   refInpReader = NULL;
+
+   dbInpFile = "";
+   dbInpStream = NULL;
+	 dbInpReader = NULL;
+   
+   molOutFile = "";
+   molOutStream = NULL;
+   molOutWriter = NULL;
+
+   scoreOutFile = "";
+   scoreOutStream = NULL;
+
+   bestHits = 0;
+   cutOff = 0.0;
+   maxIter = 0;
+   
+   whichScore = tanimoto;
+   
+   scoreOnly = false;
+   showRef = true;
+   
+   version = false;
+   help = false;
+}
+
+
+
+
+Options::~Options(void)
+{
+   // reference input
+   if (!refInpFile.empty())
+   {
+      refInpFile = "";
+   };
+   if (refInpStream)
+   {
+      delete refInpStream;
+      refInpStream = NULL;
+   };
+   if (refInpReader)
+   {
+      delete refInpReader;
+      refInpReader = NULL;
+   };
+
+
+   // Database input
+   if (!dbInpFile.empty())
+   {
+      dbInpFile = "";
+   };
+   if (dbInpStream)
+   {
+      delete dbInpStream;
+      dbInpStream = NULL;
+   };
+   if (dbInpReader)
+   {
+      delete dbInpReader;
+      dbInpReader = NULL;
+   };
+
+
+   // Molecule output
+   if (!molOutFile.empty())
+   {
+      molOutFile = "";
+   };
+   if (molOutStream)
+   {
+      delete molOutStream;
+      molOutStream = NULL;
+   };
+   if (molOutWriter)
+   {
+      delete molOutWriter;
+      molOutWriter = NULL;
+   };
+   
+   
+   // Score output
+   if (!scoreOutFile.empty())
+   {
+      scoreOutFile = "";
+   };
+   if (scoreOutStream)
+   {
+      delete scoreOutStream;
+      scoreOutStream = NULL;
+   };
+}
+
+
+
+std::string
+Options::print(void) const
+{
+   std::ostringstream os;
+   os << std::endl;
+   os << "COMMAND_LINE OPTIONS:" << std::endl;
+   os << std::endl;
+   os << "  -> Reference file:    " << refInpFile << std::endl;
+   os << "  -> Database file:     " << dbInpFile << std::endl;
+   os << "  -> Output file:       " << (molOutFile.empty() ? "no" : molOutFile) << std::endl;
+   os << "  -> Scores file:       " << (scoreOutFile.empty() ? "no" : scoreOutFile) << std::endl;
+   os << "  -> Best hits:         ";
+   if (bestHits)
+   {
+      os << bestHits << std::endl;
+   }
+   else
+   {
+      os << "no" << std::endl;
+   }
+   os << "  -> Scoring only:      " << (scoreOnly ? "yes" : "no") << std::endl;
+   os << "  -> Extra iterations:  ";
+   if (maxIter)
+   {
+      os << maxIter << std::endl;
+   }
+   else
+   {
+      os << "no" << std::endl;
+   }
+   os << "  -> Rank by:           " << whichScore << std::endl;
+   os << "  -> Cutoff:            ";
+   if (cutOff)
+   {
+      os << cutOff << std::endl;
+   }
+   else
+   {
+      os << "no" << std::endl;
+   }
+   os << "  -> Output reference   " << (showRef ? "yes" : "no") << std::endl;
+   
+   os << std::endl;   
+   std::string r = os.str();
+   return r;
+}