sniplay: egglib/egglib-2.1.5/include/egglib-cpp/Container.hpp comparison

comparison egglib/egglib-2.1.5/include/egglib-cpp/Container.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_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

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