bpp-seq  2.2.0
Clustal.h
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1 //
2 // File: Clustal.h
3 // Created by: Julien Dutheil
4 // Created on: ?
5 //
6 
7 /*
8  Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
9 
10  This software is a computer program whose purpose is to provide classes
11  for sequences analysis.
12 
13  This software is governed by the CeCILL license under French law and
14  abiding by the rules of distribution of free software. You can use,
15  modify and/ or redistribute the software under the terms of the CeCILL
16  license as circulated by CEA, CNRS and INRIA at the following URL
17  "http://www.cecill.info".
18 
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20  modify and redistribute granted by the license, users are provided only
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24 
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26  with loading, using, modifying and/or developing or reproducing the
27  software by the user in light of its specific status of free software,
28  that may mean that it is complicated to manipulate, and that also
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38  */
39 
40 #ifndef _CLUSTAL_H_
41 #define _CLUSTAL_H_
42 
43 #include "AbstractIAlignment.h"
44 #include "AbstractOAlignment.h"
45 #include "../Container/SiteContainer.h"
46 
47 // From the STL:
48 #include <iostream>
49 
50 namespace bpp
51 {
57 class Clustal :
58  public AbstractIAlignment,
59  public AbstractOAlignment,
60  public virtual ISequence
61 {
62 private:
64  unsigned int nbSpacesBeforeSeq_;
65  unsigned int charsByLine_;
66 
67 public:
75  Clustal(bool checkSequenceNames = true, unsigned int nbExtraSpacesBeforeSeq = 5, unsigned int charsByLine = 100) throw (Exception) :
76  checkNames_(checkSequenceNames),
77  nbSpacesBeforeSeq_(nbExtraSpacesBeforeSeq + 1),
78  charsByLine_(charsByLine)
79  {}
80 
81  virtual ~Clustal() {}
82 
83 public:
89  void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception);
100  virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) {
101  return readAlignment(input, alpha);
102  }
103  virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) {
104  return readAlignment(path, alpha);
105  }
113  void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception);
114  void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite = true) const throw (Exception)
115  {
116  AbstractOAlignment::writeAlignment(path, sc, overwrite);
117  }
125  const std::string getFormatName() const { return "Clustal"; }
126 
127  const std::string getFormatDescription() const { return "The Clustal alignment tool output format."; }
128 
134  bool checkNames() const { return checkNames_; }
135 
141  void checkNames(bool yn) { checkNames_ = yn; }
142 };
143 } // end of namespace bpp.
144 
145 #endif // _CLUSTAL_H_
146 
unsigned int nbSpacesBeforeSeq_
Definition: Clustal.h:64
virtual SequenceContainer * readSequences(std::istream &input, const Alphabet *alpha) const
Create a new container from a stream.
Definition: Clustal.h:100
The SiteContainer interface.
Definition: SiteContainer.h:63
void checkNames(bool yn)
Tell whether the sequence names should be checked when reading from files.
Definition: Clustal.h:141
This alphabet is used to deal NumericAlphabet.
Partial implementation of the IAlignment interface, dedicated to alignment readers.
The Alphabet interface.
Definition: Alphabet.h:130
const std::string getFormatName() const
Definition: Clustal.h:125
Clustal(bool checkSequenceNames=true, unsigned int nbExtraSpacesBeforeSeq=5, unsigned int charsByLine=100)
Build a new Clustal object.
Definition: Clustal.h:75
The clustal sequence file format.
Definition: Clustal.h:57
void writeAlignment(const std::string &path, const SiteContainer &sc, bool overwrite=true) const
Write a container to a file.
Definition: Clustal.h:114
void appendAlignmentFromStream(std::istream &input, SiteContainer &sc) const
Append sequences to a container from a stream.
Definition: Clustal.cpp:52
bool checkNames_
Definition: Clustal.h:63
bool checkNames() const
Definition: Clustal.h:134
const std::string getFormatDescription() const
Definition: Clustal.h:127
unsigned int charsByLine_
Definition: Clustal.h:65
virtual SequenceContainer * readSequences(const std::string &path, const Alphabet *alpha) const
Create a new container from a file.
Definition: Clustal.h:103
Partial implementation of the OAlignment interface.
The SequenceContainer interface.
virtual void readAlignment(std::istream &input, SiteContainer &sc) const
Add sequences to a container from a stream.
The ISequence interface.
Definition: ISequence.h:64
void writeAlignment(std::ostream &output, const SiteContainer &sc) const
Write a container to a stream.
Definition: Clustal.cpp:114
void writeAlignment(std::ostream &output, const SiteContainer &sc) const =0
Write a container to a stream.
virtual ~Clustal()
Definition: Clustal.h:81