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CoordinateLogProcess.cpp

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+//::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
+//
+//        This file is part of E-Cell Simulation Environment package
+//
+//                Copyright (C) 2006-2009 Keio University
+//
+//::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
+//
+//
+// E-Cell 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; either
+// version 2 of the License, or (at your option) any later version.
+// 
+// E-Cell 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 General Public License for more details.
+// 
+// You should have received a copy of the GNU General Public
+// License along with E-Cell -- see the file COPYING.
+// If not, write to the Free Software Foundation, Inc.,
+// 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+// 
+//END_HEADER
+//
+// written by Satya Arjunan <satya.arjunan@gmail.com>
+// E-Cell Project, Institute for Advanced Biosciences, Keio University.
+//
+
+#include "CoordinateLogProcess.hpp"
+
+LIBECS_DM_INIT(CoordinateLogProcess, Process); 

CoordinateLogProcess.hpp

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+//::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
+//
+//        This file is part of E-Cell Simulation Environment package
+//
+//                Copyright (C) 2006-2009 Keio University
+//
+//::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
+//
+//
+// E-Cell 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; either
+// version 2 of the License, or (at your option) any later version.
+// 
+// E-Cell 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 General Public License for more details.
+// 
+// You should have received a copy of the GNU General Public
+// License along with E-Cell -- see the file COPYING.
+// If not, write to the Free Software Foundation, Inc.,
+// 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+// 
+//END_HEADER
+//
+// written by Satya Arjunan <satya.arjunan@gmail.com>
+// E-Cell Project, Institute for Advanced Biosciences, Keio University.
+//
+
+
+#ifndef __CoordinateLogProcess_hpp
+#define __CoordinateLogProcess_hpp
+
+#include <fstream> //provides ofstream
+#include <MethodProxy.hpp>
+#include "IteratingLogProcess.hpp"
+#include "SpatiocyteSpecies.hpp"
+
+LIBECS_DM_CLASS(CoordinateLogProcess, IteratingLogProcess)
+{ 
+public:
+  LIBECS_DM_OBJECT(CoordinateLogProcess, Process)
+    {
+      INHERIT_PROPERTIES(IteratingLogProcess);
+    }
+  CoordinateLogProcess():
+    theMoleculeSize(0) {}
+  virtual ~CoordinateLogProcess() {}
+  virtual void initializeLastOnce()
+    {
+      for(unsigned int i(0); i != theProcessSpecies.size(); ++i)
+        {
+          theMoleculeSize += theProcessSpecies[i]->size();
+        }
+      theLogFile.open(FileName.c_str(), ios::trunc);
+      initializeLog();
+      logSpecies();
+    }
+  virtual void fire()
+    {
+      if(theTime <= LogDuration)
+        {
+          logSpecies();
+          theTime += theStepInterval;
+        }
+      else
+        {
+          theTime = libecs::INF;
+          theLogFile.flush();
+          theLogFile.close();
+        }
+      thePriorityQueue->moveTop();
+    }
+  void logSpecies()
+    {
+      for(unsigned int i(0); i != theProcessSpecies.size(); ++i)
+        {
+          logMolecules(i);
+        }
+      theLogFile << endl;
+    }
+protected:
+  void initializeLog()
+    {
+      Point aCenterPoint(theSpatiocyteStepper->getCenterPoint());
+      theLogFile
+        << "startCoord:" << theSpatiocyteStepper->getStartCoord()
+        << " rowSize:" << theSpatiocyteStepper->getRowSize() 
+        << " layerSize:" << theSpatiocyteStepper->getLayerSize()
+        << " colSize:" << theSpatiocyteStepper->getColSize()
+        << " width:" << aCenterPoint.z*2
+        << " height:" << aCenterPoint.y*2
+        << " length:" <<  aCenterPoint.x*2
+        << " voxelRadius:" << theSpatiocyteStepper->getVoxelRadius()
+        << " moleculeSize:" << theMoleculeSize << endl;
+    }
+  void logMolecules(int anIndex)
+    {
+      Species* aSpecies(theProcessSpecies[anIndex]);
+      for(unsigned int i(0); i != aSpecies->size(); ++i)
+        {
+          theLogFile << ", " << aSpecies->getCoord(i);
+        }
+    }
+private:
+  double theMoleculeSize;
+};
+
+#endif /* __CoordinateLogProcess_hpp */