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comparison egglib/egglib-2.1.5/include/egglib-cpp/Align.hpp @ 1:420b57c3c185 draft

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author	dereeper
date	Fri, 10 Jul 2015 04:39:30 -0400
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+/*
+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

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comparison egglib/egglib-2.1.5/include/egglib-cpp/Align.hpp @ 1:420b57c3c185 draft