/usr/include/Bpp/Seq/Io/Clustal.h is in libbpp-seq-dev 2.1.0-1ubuntu3.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 | //
// File: Clustal.h
// Created by: Julien Dutheil
// Created on: ?
//
/*
Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
This software is a computer program whose purpose is to provide classes
for sequences analysis.
This software is governed by the CeCILL license under French law and
abiding by the rules of distribution of free software. You can use,
modify and/ or redistribute the software under the terms of the CeCILL
license as circulated by CEA, CNRS and INRIA at the following URL
"http://www.cecill.info".
As a counterpart to the access to the source code and rights to copy,
modify and redistribute granted by the license, users are provided only
with a limited warranty and the software's author, the holder of the
economic rights, and the successive licensors have only limited
liability.
In this respect, the user's attention is drawn to the risks associated
with loading, using, modifying and/or developing or reproducing the
software by the user in light of its specific status of free software,
that may mean that it is complicated to manipulate, and that also
therefore means that it is reserved for developers and experienced
professionals having in-depth computer knowledge. Users are therefore
encouraged to load and test the software's suitability as regards their
requirements in conditions enabling the security of their systems and/or
data to be ensured and, more generally, to use and operate it in the
same conditions as regards security.
The fact that you are presently reading this means that you have had
knowledge of the CeCILL license and that you accept its terms.
*/
#ifndef _CLUSTAL_H_
#define _CLUSTAL_H_
#include "AbstractIAlignment.h"
#include "AbstractOAlignment.h"
#include "../Container/SiteContainer.h"
// From the STL:
#include <iostream>
namespace bpp
{
/**
* @brief The clustal sequence file format.
*
* An AlignedSequenceContainer object is used instead of a VectorSequenceContainer.
*/
class Clustal :
public AbstractIAlignment,
public AbstractOAlignment,
public virtual ISequence
{
private:
bool checkNames_;
unsigned int nbSpacesBeforeSeq_;
unsigned int charsByLine_;
public:
/**
* @brief Build a new Clustal object.
*
* @param checkSequenceNames Tell if the names in the file should be checked for unicity (slower, in o(n*n) where n is the number of sequences).
* @param nbExtraSpacesBeforeSeq Specify the number of extra space characters separating the sequence name form content. The default is 5 (hence 6 spaces in total) for backward compatibility, using 0 will not allow for any space in the sequence names.
* @param charsByLine Number of character per line when writing file.
*/
Clustal(bool checkSequenceNames = true, unsigned int nbExtraSpacesBeforeSeq = 5, unsigned int charsByLine = 100) throw (Exception) :
checkNames_(checkSequenceNames),
nbSpacesBeforeSeq_(nbExtraSpacesBeforeSeq + 1),
charsByLine_(charsByLine)
{}
virtual ~Clustal() {}
public:
/**
* @name The AbstractIAlignment interface.
*
* @{
*/
void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception);
/** @} */
/**
* @name The ISequence interface.
*
* As a SiteContainer is a subclass of SequenceContainer, we hereby implement the ISequence
* interface by downcasting the interface.
*
* @{
*/
virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) {
return readAlignment(input, alpha);
}
virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) {
return readAlignment(path, alpha);
}
/** @} */
/**
* @name The AbstractOAlignment interface.
*
* @{
*/
void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception);
void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite = true) const throw (Exception)
{
AbstractOAlignment::writeAlignment(path, sc, overwrite);
}
/** @} */
/**
* @name The IOSequence interface.
*
* @{
*/
const std::string getFormatName() const { return "Clustal"; }
const std::string getFormatDescription() const { return "The Clustal alignment tool output format."; }
/** @} */
/**
* @return true if the names are to be checked when reading sequences from files.
*/
bool checkNames() const { return checkNames_; }
/**
* @brief Tell whether the sequence names should be checked when reading from files.
*
* @param yn whether the sequence names should be checked when reading from files.
*/
void checkNames(bool yn) { checkNames_ = yn; }
};
} // end of namespace bpp.
#endif // _CLUSTAL_H_
|