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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/egglib/egglib-2.1.5/include/egglib-cpp/MicrosatelliteDiversity.hpp	Fri Jul 10 04:39:30 2015 -0400
@@ -0,0 +1,120 @@
+/*
+    Copyright 2008-2010 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_MICROSATELLITEDIVERSITY_HPP
+#define EGGLIB_MICROSATELLITEDIVERSITY_HPP
+
+#include "DataMatrix.hpp"
+#include <cstdlib>
+
+namespace egglib {
+
+   /** \brief Analyzes microsatellite data
+    *
+    * \ingroup polymorphism
+    * 
+    * Use the load() method to analyze data. All sites will be analyzed
+    * and accessors allow to access the value of a given statistics for
+    * a given site. There is no out-of-bound checking implemented in
+    * accessors.
+    * 
+    */
+    class MicrosatelliteDiversity {
+        
+          public:
+            
+           /** \brief Creates an object
+            * 
+            */
+            MicrosatelliteDiversity();
+            
+            
+           /** \brief Destroys an object
+            * 
+            */
+            virtual ~MicrosatelliteDiversity();
+
+
+           /** \brief Performs the analysis
+            *
+            * \param dataMatrix the object to analyze.
+            * 
+            * \param missingData the integer identifying missing data.
+            * 
+            * \param noMissingData if true, no allele will be
+            * excluded (including the one identified by the argument
+            * missingData).
+            * 
+            */
+            void load(const DataMatrix& dataMatrix,
+                    int missingData=999, bool noMissingData=false);
+            
+            
+            /// Number of sites (or markers)
+            unsigned int numberOfSites() const;
+            
+            /// Heterozygosity
+            double He(unsigned int siteIndex) const;
+            
+            /// Number of alleles
+            unsigned int numberOfAlleles(unsigned int siteIndex) const;
+            
+            /// Variance of allele size
+            double sizeVariance(unsigned int siteIndex) const;
+            
+            /// IAM-based estimator of theta
+            double thetaAssumingIAM(unsigned int siteIndex) const;
+            
+            /// SMM-based estimator of theta, calculated from He
+            double thetaAssumingSMMfromHe(unsigned int siteIndex) const;
+
+            /// SMM-based estimator of theta, calculated from VarSize
+            double thetaAssumingSMMfromSizeVariance(unsigned int siteIndex) const;
+            
+            
+        protected:
+        
+            unsigned int  v_numberOfSites;
+            double       *v_He;
+            unsigned int *v_numberOfAlleles;
+            double       *v_sizeVariance;
+            double       *v_thetaAssumingIAM;
+            double       *v_thetaAssumingSMMfromHe;
+            double       *v_thetaAssumingSMMfromSizeVariance;
+            
+            void init();
+            void clear();
+        
+        
+        private:
+        
+        
+            /// No copy allowed
+            MicrosatelliteDiversity(const MicrosatelliteDiversity& source) {
+            }
+            
+            /// No copy allowed
+            MicrosatelliteDiversity& operator=(const MicrosatelliteDiversity& source) {
+                return *this;
+            }
+        
+    };
+}
+
+#endif