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| author | dereeper |
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| date | Fri, 20 Apr 2018 09:04:25 -0400 |
| parents | 420b57c3c185 |
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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_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