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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/egglib/egglib-2.1.5/include/egglib-cpp/DataMatrix.hpp	Fri Jul 10 04:39:30 2015 -0400
@@ -0,0 +1,219 @@
+/*
+    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_DATAMATRIX_HPP
+#define EGGLIB_DATAMATRIX_HPP
+
+
+#include "CharMatrix.hpp"
+
+
+namespace egglib {
+
+    /** \brief Data table
+    *
+    * \ingroup core
+    *
+    * Holds a data matrix representing genotype data from simulations.
+    * Data are stored as integers, to each site is associated a
+    * position, and to each sequence is associated a group index (any
+    * integer labelling, for example, a subpopulation). Supports the
+    * CharMatrix interface with the condition that allele genotype
+    * datum is >=0 and <=9.
+    * 
+    */
+    class DataMatrix : public CharMatrix {
+    
+    public:
+    
+        /** \brief Default constructor
+         *
+         * The data table default dimensions are {0,0}
+         *
+         */
+        DataMatrix();
+
+
+        /** \brief Standard constructor
+         *
+         * The data table dimensions must be given.
+         * Each cell default default is 0, and each site position is 0..
+         *
+         * \param numberOfSequences number of lines of the data table.
+         * \param numberOfSites number of columns of the data table.
+         *
+         */
+        DataMatrix(unsigned int numberOfSequences, unsigned int numberOfSites);
+
+
+        /** \brief Copy constructor
+         * 
+         */
+        DataMatrix(const DataMatrix&);
+
+
+        /** \brief Copy constructor
+         * 
+         */
+        DataMatrix(const CharMatrix&);
+
+        
+        /** \brief Assignment operator
+         * 
+         */
+        virtual DataMatrix& operator=(const DataMatrix&);
+        
+        
+        /** \brief Assignment operator
+         * 
+         */
+        virtual DataMatrix& operator=(const CharMatrix&);
+
+
+        /** \brief Destructor
+         * 
+         */
+        virtual ~DataMatrix();
+        
+        
+        /** \brief Gets number of sites
+         * 
+         */
+        unsigned int numberOfSites() const;
+
+
+        /** \brief Gets number of sequences
+         * 
+         */
+        unsigned int numberOfSequences() const;
+        
+        
+        /** \brief Sets a value of the data table
+         * 
+         */
+        void set(unsigned int sequence, unsigned int site, int value);
+
+
+        /** \brief Gets a value from the data table
+         * 
+         */
+        int get(unsigned int sequence, unsigned int site) const;
+        
+        
+        /** \brief Faster and unsecure version of get
+         * 
+         */
+        inline int fget(unsigned int sequence, unsigned int site) const {
+            return dataMatrix[sequence][site];
+        }
+
+
+        /** \brief Sets the position of a site
+         * 
+         */
+        void sitePosition(unsigned int site, double value);
+
+
+        /** \brief Gets the position of a site
+         * 
+         */
+        double sitePosition(unsigned int site) const;
+
+
+        /** \brief Sets the group label of a sequence
+         * 
+         */
+        void populationLabel(unsigned int sequence, unsigned int value);
+
+
+        /** \brief Gets the group label of a sequence
+         * 
+         */
+        unsigned int populationLabel(unsigned int sequence) const;
+
+
+        /** \brief Removes all information from the object
+         * 
+         */
+        void clear();
+
+
+        /** \brief Resizes the data matrix
+         *
+         * \param newNumberOfSequences number of sequences (rows)
+         * \param newNumberOfSites number of sites (columns)
+         *
+         * If new values are larger, data already set is left unchanged.
+         * New data are set to zero.
+         *
+         */
+        void resize(unsigned int newNumberOfSequences, unsigned int newNumberOfSites);
+
+
+       /** \brief Shifts allele value
+        * 
+        * \param minimum the minimum allele value.
+        * 
+        * Shifts all alleles at all sites to ensure that alleles alleles
+        * are equal to or larger than minimum. The shifting is specific
+        * to each site.
+        * 
+        */
+        void shift(int minimum);
+
+        /** \brief Gets the character at a given position
+         * 
+         * An exception is generated if the allele value at this
+         * position is not >=0 and <=9. Not out-of-bound check is
+         * performed.
+         * 
+         */
+        char character(unsigned int sequence, unsigned int site) const;
+        
+
+
+    private:
+        
+        // Initializes to default values (for empty object)
+        void init();
+        
+        // Copies from a source object
+        virtual void copy(const CharMatrix&);
+
+        // Copies from a source object
+        virtual void copy(const DataMatrix&);
+        
+        // Number of lines of the data matrix
+        unsigned int _numberOfSequences;
+        
+        // Number of columns of the data matrix
+        unsigned int _numberOfSites;
+        
+        // Data matrix
+        int **dataMatrix;
+        
+        // Vector of site positions
+        double *positions;
+        
+        // Vector of group indices
+        unsigned int *groups;
+    };
+}
+
+#endif