bpp-seq  2.2.0
NexusIoSequence.h
Go to the documentation of this file.
1 //
2 // File: NexusIOSequence.h
3 // Created by: Julien Dutheil
4 // Created on: Wed May 27 16:15 2009
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 
19 As a counterpart to the access to the source code and rights to copy,
20 modify and redistribute granted by the license, users are provided only
21 with a limited warranty and the software's author, the holder of the
22 economic rights, and the successive licensors have only limited
23 liability.
24 
25 In this respect, the user's attention is drawn to the risks associated
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
29 therefore means that it is reserved for developers and experienced
30 professionals having in-depth computer knowledge. Users are therefore
31 encouraged to load and test the software's suitability as regards their
32 requirements in conditions enabling the security of their systems and/or
33 data to be ensured and, more generally, to use and operate it in the
34 same conditions as regards security.
35 
36 The fact that you are presently reading this means that you have had
37 knowledge of the CeCILL license and that you accept its terms.
38 */
39 
40 #ifndef _NEXUSIOSEQUENCE_H_
41 #define _NEXUSIOSEQUENCE_H_
42 
43 #include "AbstractIAlignment.h"
44 #include "../Sequence.h"
45 #include "../Container/SequenceContainer.h"
46 #include "../Container/VectorSequenceContainer.h"
47 #include "../Container/AlignedSequenceContainer.h"
48 
49 // From the STL:
50 #include <iostream>
51 
52 namespace bpp
53 {
54 
70  public AbstractIAlignment,
71  public virtual ISequence
72 {
73  protected:
74 
78  unsigned int charsByLine_;
79 
81 
82  public:
89  NexusIOSequence(unsigned int charsByLine = 100, bool checkSequenceNames = true):
90  charsByLine_(charsByLine), checkNames_(checkSequenceNames) {}
91 
92  virtual ~NexusIOSequence() {}
93 
94  public:
95 
101  void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception);
112  virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) {
113  return readAlignment(input, alpha);
114  }
115  virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) {
116  return readAlignment(path, alpha);
117  }
125  const std::string getFormatName() const;
126  const std::string getFormatDescription() const;
132  bool checkNames() const { return checkNames_; }
133 
139  void checkNames(bool yn) { checkNames_ = yn; }
140 
141 
142  private:
143  //Reading tools:
144  const std::vector<std::string> splitNameAndSequence_(const std::string & s) const throw (Exception);
145 };
146 
147 } //end of namespace bpp.
148 
149 #endif //_NEXUSIOSEQUENCE_H_
150 
The SiteContainer interface.
Definition: SiteContainer.h:63
const std::string getFormatName() const
This alphabet is used to deal NumericAlphabet.
Partial implementation of the IAlignment interface, dedicated to alignment readers.
The Alphabet interface.
Definition: Alphabet.h:130
virtual SequenceContainer * readSequences(const std::string &path, const Alphabet *alpha) const
Create a new container from a file.
const std::string getFormatDescription() const
NexusIOSequence(unsigned int charsByLine=100, bool checkSequenceNames=true)
Build a new Phylip file reader.
The Nexus format reader for sequences.
void checkNames(bool yn)
Tell whether the sequence names should be checked when reading from files.
unsigned int charsByLine_
The maximum number of chars to be written on a line.
void appendAlignmentFromStream(std::istream &input, SiteContainer &sc) const
Append sequences to a container from a stream.
const std::vector< std::string > splitNameAndSequence_(const std::string &s) const
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
virtual SequenceContainer * readSequences(std::istream &input, const Alphabet *alpha) const
Create a new container from a stream.