--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/egglib/egglib-2.1.5/include/egglib-cpp/Align.hpp	Fri Jul 10 04:39:30 2015 -0400
@@ -0,0 +1,378 @@
+/*
+    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_ALIGN_HPP
+#define EGGLIB_ALIGN_HPP
+
+#include "Container.hpp"
+#include "CharMatrix.hpp"
+#include <vector>
+
+/** \mainpage Summary
+ * 
+ * This is the automatically-generated reference manual of the C++
+ * egglib-cpp library. The library is presented as several modules, but
+ * note that they are only used to structure the documentation.
+ * 
+ * There is a single namespace (egglib) in which all classes are
+ * defined. See an example of programming with egglib-cpp in the
+ * EggLib package main documentation. Use "Modules" or "Classes" above
+ * to navigate in the library reference manual.
+ * 
+ */
+
+
+/** \defgroup core core
+ *
+ * \brief Central core of the C++ library of Egglib
+ *
+ * Data storage classes, parsers/formatters and tools, plus exception
+ * types.
+ * 
+ */
+
+namespace egglib {
+
+
+   /** \brief Handles a sequence alignment
+    *
+    * \ingroup core
+    * 
+    * Creation from a file or string stream should be performed using
+    * the class Fasta. Align objects can be created by deep copy from
+    * both Align and Container type. In the latter case, the length are
+    * artificially equalized by "?" characters. Align objects can be
+    * created from a DataMatrix object (and all the way arround) using
+    * the specific class DMAConverter.
+    *
+    * Sequences are represented by two strings (name and sequence) and
+    * an integer (group) that can be accessed or modified by index.The
+    * order of sequences is guaranteed to be conserved, as if Align was
+    * a list of triplets (name, sequence, group).
+    *
+    * The data matrix is implemented as continuous array (char**) and
+    * allows efficient access and modification of data. For very large
+    * data matrices you might claim immediately the required memory
+    * using the constructor Align(unsigned int, char**).
+    * 
+    */
+    class Align : public Container, public CharMatrix {
+        public:
+        
+           /** \brief Creates an empty alignment
+            * 
+            */
+            Align();
+
+
+           /** \brief Creates an alignment from a data matrix.
+            * 
+            * Allows you to create an object from data stored in a char*
+            * array. The array's dimensions must be passed to the
+            * constructor, and as a result there is not need to
+            * terminate each sequence by a NULL character.
+            * 
+            * \param number_of_sequences the number of sequences (the
+            * length of the first dimension of the array).
+            * 
+            * \param alignment_length the length of sequences (the
+            * length of all lines of the array).
+            * 
+            * \param cstring_array the pointer to the data matrix.
+            * 
+            */
+            Align(unsigned int number_of_sequences, unsigned int alignment_length, char const * const * const cstring_array);
+
+
+            /** \brief Creates an alignment with given dimensions
+             * 
+             * Allows you to allocate directly a data matrix of a given
+             * size. Names are empty strings, groups 0, and all
+             * characters are ?.
+             * 
+            * \param number_of_sequences the number of sequences (the
+            * length of the first dimension of the array).
+            * 
+            * \param alignment_length the length of sequences (the
+            * length of all lines of the array).
+            * 
+            */
+            Align(unsigned int number_of_sequences, unsigned int alignment_length);
+
+
+           /** \brief Copy constructor
+            * 
+            */
+            Align(const Align& align);
+
+
+           /** \brief Copy constructor accepting a Container object
+            * 
+            * All but the longest sequences are padded with ? to match
+            * the longest sequence's length.
+            * 
+            */
+            Align(const Container& container);
+
+
+           /** \brief Copy operator
+            * 
+            */
+            Align& operator=(const Align& align);
+
+
+           /** \brief Copy operator accepting a Container object
+            * 
+            * All but the longest sequences are padded with ? to match
+            * the longest sequence's length.
+            * 
+            */
+            Align& operator=(const Container& container);
+
+
+           /** \brief Destructor
+            * 
+            */
+            virtual ~Align();
+
+
+           /** \brief Adds a sequence
+            *
+            * If the object already contains at least one sequence, the
+            * new sequence must have the same length. Otherwise, a
+            * EggUnalignedError is raised.
+            *
+            * \param name the name of the sequence.
+            * \param sequence the sequence string.
+            * \param group the group index of the sequence.
+            * \return The new number of sequences.
+            * 
+            */
+            virtual unsigned int append(const char* name, const char* sequence, unsigned int group=0);
+
+
+           /** \brief Removes a position (column) of the alignment
+            *
+            * \param pos the position to remove in the alignment.
+            * \return The new length of the alignment.
+            *
+            */
+            virtual unsigned int removePosition(unsigned int pos);
+
+
+           /** \brief Removes a sequence from the alignment
+            *
+            * \param pos the index of the sequence to remove.
+            * \return The new number of sequences.
+            * 
+            */
+            virtual unsigned int remove(unsigned int pos);
+
+
+           /** \brief Replace a sequence string
+            * 
+            * The new sequence must have the same length than the
+            * alignment. Otherwise, a EggUnalignedError is raised.
+            * 
+            * \param seq the index of the sequence to change.
+            * \param sequence the new sequence.
+            * 
+            */
+            virtual void sequence(unsigned int seq, const char* sequence);
+
+
+           /** \brief Gets the name of a given sequence
+            * 
+            * \param pos the index of the sequence.
+            * 
+            * \return The sequence string for that particular sequence.
+            * 
+            */
+            virtual inline const char* sequence(unsigned int pos) const { return Container::sequence(pos); }
+            
+            
+           /** \brief Alignment length
+            * 
+            * Returns 0 if the alignment is empty.
+            * 
+            */
+            virtual  unsigned int ls() const;
+
+
+           /** \brief Length of a given sequence
+            * 
+            * Calling this function is exactly the same as calling ls()
+            * (without arguments), regardless of the index provided,
+            * except that an exception is thrown if the index is out of
+            * bounds. Provided for compatibility with Container.
+            * 
+            * \param pos the index of the sequence.
+            * \return the length of the alignment.
+            * 
+            */
+            virtual unsigned int ls(unsigned int pos) const;
+
+
+           /** \brief Fast and unsecure accessor
+            * 
+            * This accessor doesn't perform out-of-bound checking!
+            * 
+            * \param s the index of the sequence (line).
+            * \param p the position in the alignment (column).
+            * \return The character at the given position.
+            * 
+            */
+            inline char character(unsigned int s, unsigned int p) const { return sequences[s][p]; }
+
+
+           /** \brief Gets a nucleotide
+            * 
+            * This modifier does perform out-of-bound checking.
+            * The specified position must exist.
+            * 
+            * \param sequence the index of the sequence (line).
+            * \param position the position in the alignment (column).
+            * \return the character at the given position.
+            * 
+            */
+            virtual char get(unsigned int sequence, unsigned int position) const;
+
+
+           /** \brief Sets a matrix position to a new character
+            * 
+            * This modifier does perform out-of-bound checking.
+            * The specified position must exist.
+            * 
+            * \param sequence the index of the sequence (line).
+            * \param position the position in the alignment (column).
+            * \param ch the new character value.
+            */
+            virtual void set(unsigned int sequence, unsigned position, char ch);
+
+
+           /** \brief Reverse a given column in binary data
+            *
+            * The specified column must contain only "0" ans "1" characters.
+            * "0" is replaced by "1" and all the way around
+            * 
+            */
+            void binSwitch(unsigned int pos);
+
+
+           /** \brief Extracts specified positions (columns) of the alignment
+            *
+            * All the specified sites are extracted in the specified
+            * order. This function is suitable for bootstrap (resample
+            * allowing redrawing the same site) and permutations.
+            * 
+            * This function doesn't perform out-of-bound checking.
+            * 
+            * \param list_of_sites a vector containing alignment
+            * positions.
+            * 
+            * \return A copy of the object containing the specified
+            * set of positions.
+            * 
+            */
+            Align vslice(std::vector<unsigned int> list_of_sites);
+
+
+           /** \brief Extracts a range of positions (columns)
+            * 
+            * \param a the first position.
+            * 
+            * \param b the index immediately passed the last sequence to
+            * extract.
+            * 
+            * \return A copy of the object containing the specified
+            * range of sequences.
+            * 
+            * Positions a to b-1 are extracted, provided that the
+            * indices fit in the current length of sequences. To extract
+            * all sequences, use align.vslice(0, align.ls()).
+            * 
+            * Note: invalid ranges will be silently supported. If
+            * a>=ls or b<=a, an empty object is returned. If b>ns,
+            * ls will be substituted to a.
+            */
+            Align vslice(unsigned int a, unsigned int b);
+
+
+           /** \brief Deletes all the content of the object
+            * 
+            */
+            virtual void clear();
+
+
+           /** \brief Same as ns()
+            * 
+            */
+            inline unsigned int numberOfSequences() const {
+                return _ns;
+            }
+
+
+           /** \brief Same as ls()
+            * 
+            */
+            inline unsigned int numberOfSites() const {
+                return _ls;
+            }
+
+
+           /** \brief Gets a group label (insecure)
+            * 
+            */
+            inline unsigned int populationLabel(unsigned int sequenceIndex) const {
+                return groups[sequenceIndex];
+            }
+            
+            
+           /** \brief Just return the passed value
+            *
+            */
+            inline double sitePosition(unsigned int position) const {
+                return (double) position;
+            }
+
+
+        protected:
+        
+            /// This function is not available for alignments
+            virtual void appendSequence(unsigned int pos, const char* sequence) {}
+
+            // Initializer (creates a valid empty alignment)
+            virtual void init();
+        
+            // Makes a deep copy of the specified data matrix - if cstring_array is NULL, then ignores it and pads with ?'s
+            virtual void setFromSource(unsigned int number_of_sequences, unsigned int alignment_length, const char* const * const cstring_array);
+
+            // Copies from a Container
+            virtual void copyObject(const Container&);
+            
+            // Copies from an Align
+            virtual void copyObject(const Align&);
+            
+            // Alignment length
+            unsigned int _ls;
+    };
+}
+
+#endif