diff egglib/egglib-2.1.5/include/egglib-cpp/Current.hpp @ 1:420b57c3c185 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/egglib/egglib-2.1.5/include/egglib-cpp/Current.hpp	Fri Jul 10 04:39:30 2015 -0400
@@ -0,0 +1,128 @@
+/*
+    Copyright 2009-2010 Stéphane De Mita, Mathieu Siol
+
+    This file is part of the EggLib library.
+
+    EggLib 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 3 of the License, or
+    (at your option) any later version.
+
+    EggLib 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 EggLib.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
+#ifndef EGGLIB_CURRENT_HPP
+#define EGGLIB_CURRENT_HPP
+
+
+namespace egglib {
+
+    class Population;
+    class ParamSet;
+
+   /** \brief Represents the current set of populations
+    *
+    * \ingroup coalesce
+    * 
+    */
+    class Current {
+
+        public:
+
+           /** \brief Default constructor
+            * 
+            */
+            Current();
+            
+           /** \brief Standard constructor
+            *
+            * \param paramSet allows to initiate the correct structure
+            * of populations.
+            * 
+            */
+            Current(ParamSet* paramSet);
+
+           /** \brief Rebuilds the object
+            *
+            * \param paramSet allows to initiate the correct structure
+            * of populations.
+            * 
+            */
+            void reset(ParamSet* paramSet);
+            
+           /** \brief Destructor
+            * 
+            */
+            virtual ~Current();
+
+           /** \brief Copy constructor
+            * 
+            */
+            Current(const Current&);
+
+           /** \brief Assignment operator
+            * 
+            */
+            Current& operator=(const Current&);
+
+           /** \brief Gets the current number of populations
+            * 
+            */
+            unsigned int numberOfPopulations() const;
+
+            
+           /** \brief Adds an empty population to the system
+            *
+            */
+            void addPopulation();
+
+            
+           /** \brief Gets the number of lineages contained by a given
+            * population
+            * 
+            */
+            unsigned int populationNumberOfLineages(unsigned int populationIndex) const;
+
+            
+           /** \brief Provides access to a given population
+            * 
+            * The returned pointer can be used to modify the object.
+            * 
+            */
+            Population* population(unsigned int populationIndex);
+            
+            
+           /** \brief Total number of lineages
+            * 
+            */
+            unsigned int totalNumberOfLineages() const;
+
+
+           /** \brief Efficient number of lineages
+            * 
+            * This sums the number of covered segments of each lineage.
+            * 
+            */
+            unsigned int efficientNumberOfLineages() const;
+
+
+        private:
+
+            void setPopulationArray();
+            void copy(const Current&);
+            void clear();
+
+            unsigned int _numberOfPopulations;
+            unsigned int _numberOfSegments;
+            Population** populations;
+    };
+
+}
+
+#endif