First commit of PhyloMOEO files with some additions to Paradiseo-MOEO

git-svn-id: svn://scm.gforge.inria.fr/svnroot/paradiseo@1335 331e1502-861f-0410-8da2-ba01fb791d7f

contribution/branches/PhyloMOEA/PhyloMOEA/probmatrixcontainer.h

@@ -0,0 +1,93 @@
+/***************************************************************************
+ *   Copyright (C) 2005 by Waldo Cancino                                   *
+ *   wcancino@icmc.usp.br                                                  *
+ *                                                                         *
+ *   This program 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.                                   *
+ *                                                                         *
+ *   This program 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 this program; if not, write to the                         *
+ *   Free Software Foundation, Inc.,                                       *
+ *   59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.             *
+ ***************************************************************************/
+#ifndef PROBMATRIXCONTAINER_H
+#define PROBMATRIXCONTAINER_H
+#include "ProbMatrix.h"
+#include <map>
+/**
+@author Waldo Cancino
+*/
+// container for an arbitrary number of Probmatrix under certain
+// evolution model
+
+
+class ProbMatrixContainer{
+
+private:
+	SubstModel *model;
+	// contains the probamatirx
+	std::map<double, ProbMatrix *> container;
+public:
+	ProbMatrix &operator[] (double branchlength)
+	{
+		if (container.find(branchlength)!=container.end() )
+		{
+			return *container[branchlength];
+		}
+		else
+		{
+			ProbMatrix *new_prob_matrix = new ProbMatrix(model, branchlength);
+			new_prob_matrix->init();
+			container[branchlength] = new_prob_matrix;
+			return *new_prob_matrix;
+		}
+	}
+	
+	ProbMatrixContainer( SubstModel &m )
+	{
+		model = &m;
+	}
+
+	void change_matrix(double bl_old, double bl_new)
+	{
+		ProbMatrix &p = (*this)[bl_old];
+		p.set_branch_length(bl_new);
+		std::map<double, ProbMatrix *>::iterator it = container.find(bl_old);
+		container.erase(it);
+		it = container.find(bl_new);
+		// prevent duplication
+		if(it!=container.end()) delete (*it).second;
+		/*{
+			std::cout << " duplication " << bl_new << std::endl;
+			container.erase(it);
+		}*/
+		// replace the container
+		container[bl_new] = &p;
+	}
+	
+	void clear()
+	{
+		std::map<double, ProbMatrix *>::iterator it = container.begin();
+		std::map<double, ProbMatrix *>::iterator end = container.end();
+		while(it!=end)
+		{
+			delete (*it).second;
+			it++;
+		}
+		container.clear();
+	}
+
+	~ProbMatrixContainer() { 
+		//std::cout << "limpando ..." << container.size() <<  " matrizes alocadas\n"; 
+		clear(); }
+
+};
+
+#endif