bpp-seq  2.2.0
MaseTools.h
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1 //
2 // File: MaseTools.h
3 // Created by: Julien Dutheil
4 // Created on: Tue Apr 1 09:16:59 2003
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
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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 _MASETOOLS_H_
41 #define _MASETOOLS_H_
42 
43 #include "../Container/SequenceContainer.h"
44 #include "../Container/OrderedSequenceContainer.h"
45 #include "../Container/SequenceContainerTools.h"
46 #include "../Container/SiteContainer.h"
47 #include "../Container/SiteContainerTools.h"
48 #include <Bpp/Exceptions.h>
49 
50 namespace bpp
51 {
52 
63  class MaseTools
64  {
65  public:
66 
74  static SiteSelection getSiteSet(const Comments& maseFileHeader, const std::string& setName) throw (IOException);
75 
83  static SequenceSelection getSequenceSet(const Comments& maseFileHeader, const std::string& setName) throw (IOException);
84 
97  static SiteContainer* getSelectedSites(const SiteContainer& sequences, const std::string& setName) throw (IOException);
98 
111  static SequenceContainer* getSelectedSequences(const OrderedSequenceContainer& sequences, const std::string & setName) throw (IOException);
112 
119  static std::map<std::string, size_t> getAvailableSiteSelections(const Comments & maseHeader);
120 
127  static std::map<std::string, size_t> getAvailableSequenceSelections(const Comments & maseHeader);
128 
139  static size_t getPhase(const Comments & maseFileHeader, const std::string &setName) throw (Exception);
140 
141  };
142 
143 } //end of namespace bpp.
144 
145 #endif //_MASETOOLS_H_
146 
std::vector< size_t > SiteSelection
static size_t getPhase(const Comments &maseFileHeader, const std::string &setName)
Get the phase of a given coding region from a mase+ header.
Definition: MaseTools.cpp:269
std::vector< std::string > Comments
Declaration of Comments type.
Definition: Sequence.h:60
The SiteContainer interface.
Definition: SiteContainer.h:63
The OrderedSequenceContainer interface.
This alphabet is used to deal NumericAlphabet.
static std::map< std::string, size_t > getAvailableSequenceSelections(const Comments &maseHeader)
Get a list of all available sequences selections.
Definition: MaseTools.cpp:243
std::vector< size_t > SequenceSelection
static SequenceSelection getSequenceSet(const Comments &maseFileHeader, const std::string &setName)
Get a sequence selection from a Mase+ header file.
Definition: MaseTools.cpp:104
Utilitary methods that deal with the Mase format.
Definition: MaseTools.h:63
static SiteSelection getSiteSet(const Comments &maseFileHeader, const std::string &setName)
Get a site selection from a Mase+ header file.
Definition: MaseTools.cpp:52
static std::map< std::string, size_t > getAvailableSiteSelections(const Comments &maseHeader)
Get a list of all available site selections.
Definition: MaseTools.cpp:196
static SequenceContainer * getSelectedSequences(const OrderedSequenceContainer &sequences, const std::string &setName)
Create a new container corresponding to a site set given in the mase+ format.
Definition: MaseTools.cpp:184
static SiteContainer * getSelectedSites(const SiteContainer &sequences, const std::string &setName)
Create a new container corresponding to a site set given in the mase+ format.
Definition: MaseTools.cpp:151
The SequenceContainer interface.