--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/egglib/egglib-2.1.5/include/egglib-cpp/Container.hpp	Fri Jul 10 04:39:30 2015 -0400
@@ -0,0 +1,326 @@
+/*
+    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_CONTAINER_HPP
+#define EGGLIB_CONTAINER_HPP
+
+
+namespace egglib {
+
+   /** \brief Handles a set of sequence alignment (aligned or not)
+    *
+    * \ingroup core
+    * 
+    * Creation from a file or string stream should be performed using
+    * the class Fasta.
+    *
+    * 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 Container
+    * was a list of triplets (name, sequence, group).
+    *
+    * The data matrix is implemented as continuous arrays (char**) and
+    * allows efficient access and modification of data. For very large
+    * data matrices you might claim immediately the required memory
+    * using the constructor Container(unsigned int, char**).
+    *
+    */
+    class Container {
+    
+        public:
+      
+          /** \brief Creates an empty object
+            * 
+            */
+            Container();
+        
+        
+           /** \brief Copy constructor
+            * 
+            */
+            Container(const Container& source);
+        
+        
+           /** \brief Assignment operator
+            * 
+            */
+            Container& operator= (const Container& source);
+
+
+           /** \brief Creates an object from a data matrix
+            * 
+            * Allows you to create an object from data stored in a char*
+            * array. The array's size must be passed to the constructor.
+            * Since sequences can have different lengths, you need to
+            * terminate each sequence by a NULL character. This constructor
+            * is dedicated to very performance-critical tasks. For usual
+            * tasks, using the default constructor and subsequently adding
+            * sequences with addSeq should be enough.
+            * 
+            * \param number_of_sequences the number of sequences (the length
+            * of the first dimension of the array).
+            * 
+            * \param cstring_array the pointer to the data matrix.
+            * 
+            */
+            Container(unsigned int number_of_sequences, char const* const* const cstring_array);
+
+
+           /** \brief Destructor
+            * 
+            */
+            virtual ~Container();
+
+        
+           /** \brief Clears all content of the object
+            * 
+            */
+            virtual void clear();
+
+
+           /** \brief Adds a sequence to the object
+            *
+            * \param name the name of the sequence, as a c-string.
+            * \param sequence the sequence string, as a c-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 sequence from the object
+            *
+            * \param pos the index of the sequence to remove.
+            * 
+            * \return The new number of sequences.
+            */
+            virtual unsigned int remove(unsigned int pos);
+
+
+           /** \brief Changes the name of a given sequence
+            * 
+            * \param pos the sequence index.
+            * \param name the new name as a C-like string.
+            * 
+            */
+            virtual void name(unsigned int pos, const char* name);
+
+
+           /** \brief Changes the sequence string of a given sequence
+            * 
+            * \param pos the sequence index.
+            * \param sequence the new sequence as a C-like string.
+            * 
+            */
+            virtual void sequence(unsigned int pos, const char* sequence);
+
+
+           /** \brief Appends a string to the a given sequence
+            * 
+            * \param pos the sequence index.
+            * \param sequence the sequence to append at the end of the
+            * current one.
+            * 
+            */
+            virtual void appendSequence(unsigned int pos, const char* sequence);
+
+
+           /** \brief Changes a character
+            * 
+            * \param sequence the sequence index.
+            * \param position the character index.
+            * \param ch the new character value.
+            * 
+            * The positions must fit in the current ranges.
+            * 
+            */
+            virtual void set(unsigned int sequence, unsigned position, char ch);
+
+
+           /** \brief Gets a given character
+            * 
+            * \param s the sequence index.
+            * \param p the character index.
+            * 
+            * \return the character value.
+            * 
+            * The positions must fit in the current ranges.
+            * 
+            */
+            virtual char get(unsigned int s, unsigned int p) const;
+
+
+           /** \brief Changes the group index of a given sequence
+            * 
+            * \param pos the sequence index.
+            * \param group the new group index value.
+            * 
+            */
+            virtual void group(unsigned int pos, unsigned int group);
+
+        
+           /** \brief Extracts a range of sequences
+            * 
+            * \param a the index of the first sequence.
+            * 
+            * \param b the index immediately passed the last sequence to
+            * extract.
+            * 
+            * \return A copy of the object containing the specified
+            * range of sequences.
+            * 
+            * Sequences a to b-1 are extracted, provided that the
+            * indices fit in the current number of sequences. To extract
+            * all sequences, use container.hslice(0, container.ns()).
+            * 
+            * 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.
+            * 
+            */
+            Container hslice(unsigned int a, unsigned int b) const;
+
+
+           /** \brief Gets the number of sequences
+            * 
+            */
+            unsigned int ns() const;
+        
+        
+           /** \brief Gets the length of a given sequence
+            * 
+            * \param pos the index of the sequence.
+            * 
+            * \return The length of that particular sequence.
+            * 
+            */
+            virtual unsigned int ls(unsigned int pos) const ;
+        
+        
+           /** \brief Gets the name of the a given sequence
+            * 
+            * \param pos the index of the sequence.
+            * 
+            * \return The name of that particular sequence.
+            * 
+            */
+            virtual const char* name(unsigned int pos) const;
+
+        
+           /** \brief Gets the name of a given sequence
+            * 
+            * \param pos the index of the sequence.
+            * 
+            * \return The sequence string for that particular sequence.
+            * 
+            */
+            virtual const char* sequence(unsigned int pos) const;
+
+
+
+           /** \brief Gets the group index of a given sequence
+            * 
+            * \param pos the index of the sequence.
+            * 
+            * \return The group index of that particular sequence.
+            * 
+            */
+            virtual unsigned int group(unsigned int pos) const;
+        
+        
+           /** \brief Checks if all lengths are equal
+            * 
+            * Returns true if the length of all sequences are equal or
+            * if there is less thant two sequences.
+            * 
+            */
+            bool isEqual() const;
+
+
+           /** \brief Equalizes sequence lengths
+            *
+            * Extends sequences as need to ensure that all sequences
+            * have the same length.
+            *
+            * \param ch the character to use for padding.
+            * 
+            * \return The final length obtained, which is the length of
+            * the longest sequence before the operation.
+            * 
+            */
+            unsigned int equalize(char ch='?');
+
+        
+           /** \brief Finds a sequence by its name
+            * 
+            * Gets the position of the first sequence with the specified
+            * name.
+            * 
+            * \param string a sequence name.
+            * 
+            * \param strict if true, seeks an exact match. If false,
+            * compares only until the end of the requested name (for
+            * example: ATCFF will match ATCFF_01 if strict is false).
+            * 
+            * \return The lowest index where the name matches, -1 if no
+            * sequence has such name.
+            * 
+            */
+            int find(const char* string, bool strict=true) const;
+
+
+        protected:
+            // The number of sequences
+            unsigned int _ns;
+        
+            // The array of name lengths
+            unsigned int* lnames;
+    
+            // The array of names
+            char** names;
+        
+            // The array of sequences (as c-strings)
+            char** sequences;
+        
+            // The array of groups
+            unsigned int* groups;
+        
+            // Imports an array of c-strings
+            virtual void setFromSource(unsigned int number_of_sequences, const char* const* const cstring_array);
+        
+            // Constructor helper
+            virtual void copyObject(const Container&);
+        
+            // Constructor partial helper
+            virtual void getNamesAndGroups(const Container&);
+        
+        private:
+       
+            // The array of sequence lengths
+            unsigned int* lsequences;
+        
+            // Setup a valid empty object
+            virtual void init();
+    };
+}
+    
+#endif