--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/egglib/egglib-2.1.5/include/egglib-cpp/SitePolymorphism.hpp	Fri Jul 10 04:39:30 2015 -0400
@@ -0,0 +1,207 @@
+/*
+    Copyright 2008-2009 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_SITEPOLYMORPHISM_HPP
+#define EGGLIB_SITEPOLYMORPHISM_HPP
+
+
+
+namespace egglib {
+
+
+   /** \brief Implements diversity analysis at the site level
+    *
+    * \ingroup polymorphism
+    * 
+    * Data are loaded along with a population index. It is necessary to
+    * set the number of populations prior to use.
+    * 
+    * Outgroup sequence must be loaded separetedly. There can be any
+    * number of outgroups, but they must be all consistent otherwise the
+    * site will be considered as not orientable.
+    * 
+    */
+    class SitePolymorphism {
+
+        public:
+
+           /** \brief Builds an object
+            * 
+            */
+            SitePolymorphism();
+
+
+           /** \brief Builds an object
+            * 
+            * \param npop number of populations
+            * 
+            */
+            SitePolymorphism(unsigned int npop);
+
+
+           /** \brief Destroys an object
+            * 
+            */
+            virtual ~SitePolymorphism();
+
+
+           /** \brief Copy constructor
+            * 
+            */
+            SitePolymorphism(const SitePolymorphism& source);
+
+
+           /** \brief Assignment operator
+            * 
+            */
+            SitePolymorphism& operator=(const SitePolymorphism& source);
+
+
+           /** \brief Sets the number of populations
+            * 
+            * NOTE THAT all previous data is lost.
+            * 
+            */
+            void numberOfPopulations(unsigned int npop);
+
+
+           /** \brief Adds a character
+            * 
+            * \param populationIndex the index of the population from
+            * which is sampled this character (do not use "population
+            * label").
+            * 
+            * \param character the character value (it is assumed it
+            * represents a valid character.
+            * 
+            */
+            void load(unsigned int populationIndex, char character);
+
+
+           /** \brief Loads outgroup state
+            * 
+            * There can be any number of outgroup states. Only
+            * characters that are considered as valid (whatever the list
+            * is) should be loaded.
+            * 
+            */
+            void outgroup(char state);
+
+
+           /** \brief Number of different alleles
+            * 
+            */
+            unsigned int numberOfAlleles() const;
+            
+            
+           /** \brief Gets an allele (unsecure)
+            * 
+            * Assumes that the index provided lies in the valid range
+            * 
+            */
+            char allele(unsigned int index) const;
+
+
+           /** \brief Gets a frequency (unsecure)
+            * 
+            * The sum of of frequencies of the allele over populations
+            * is computed. Not out-of-bounds check is performed.
+            * 
+            */
+            unsigned int alleleFrequency(unsigned int alleleIndex) const;
+
+
+           /** \brief Gets the frequency of an allele in one pop (unsecure)
+            * 
+            * The frequency of the allele in the given population is
+            * returned. Not out-of-bounds check is performed.
+            * 
+            */
+            unsigned int alleleFrequency(unsigned int popIndex, unsigned int alleleIndex) const;
+
+
+           /** \brief Sums the frequency of derived allele(s)
+            * 
+            * This method assumes that the site is orientable. It will
+            * use as outgroup the first outgroup character entered,
+            * assuming at least one was entered and that all (if more
+            * than one) were identical.
+            * 
+            */
+            unsigned int derivedAlleleFrequency() const;
+
+
+           /** \brief Number of sequences that were analyzed
+            * 
+            */
+            unsigned int ns() const;
+
+
+           /** \brief Gets the number of analyzed sequences for a population
+            * 
+            * No out-of-bound check is performed
+            * 
+            */
+            unsigned int ns(unsigned int popIndex) const;
+
+
+           /** \brief Checks if the site can be oriented
+            * 
+            * Returns true if at least one outgroup datum has been
+            * loaded, if all outgroup data are identical (regardless of
+            * their value) and if the outgroup allele is one of the
+            * allele in the sample.
+            * 
+            */
+            bool isOrientable() const;
+
+            bool isPolymorphic(unsigned int popIndex) const;
+            bool hasSpecificAllele(unsigned int popIndex, bool restrictToDerived) const;
+            bool haveFixedDifference(unsigned int pop1, unsigned int pop2) const;
+            bool haveCommonAllele(unsigned int pop1, unsigned int pop2) const;
+            bool haveSharedAllele(unsigned int pop1, unsigned int pop2) const;
+
+
+
+
+        protected:
+
+            // helpers
+            void init();
+            void clear();
+            void copy(const SitePolymorphism& site);
+
+
+            // data
+            unsigned int m_numberOfPopulations;
+            unsigned int m_numberOfStates;
+            char * m_states;
+            unsigned int ** m_frequencies;
+            unsigned int m_numberOfOutgroups;
+            char * m_outgroups;
+            unsigned int m_ns;
+            unsigned int * m_pop_ns;
+            
+            bool m_cache_orientable;
+
+    };
+}
+
+#endif