bpp-phyl  2.1.0
 All Classes Namespaces Files Functions Variables Friends Pages
SubstitutionMappingTools.h
Go to the documentation of this file.
1 //
2 // File: SubstitutionMappingTools.h
3 // Created by: Julien Dutheil
4 // Created on: Wed Apr 5 13:04 2006
5 //
6 
7 /*
8 Copyright or © or Copr. Bio++ Development Team, (November 16, 2004, 2005, 2006)
9 
10 This software is a computer program whose purpose is to provide classes
11 for phylogenetic data 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 _SUBSTITUTIONMAPPINGTOOLS_H_
41 #define _SUBSTITUTIONMAPPINGTOOLS_H_
42 
44 #include "SubstitutionCount.h"
46 #include "../Likelihood/DRTreeLikelihood.h"
47 
48 namespace bpp
49 {
50 
64 {
65  public:
68 
69  public:
70 
82  const DRTreeLikelihood& drtl,
83  SubstitutionCount& substitutionCount,
84  bool verbose = true) throw (Exception);
85 
107  const DRTreeLikelihood& drtl,
108  SubstitutionCount& substitutionCount,
109  bool verbose = true) throw (Exception);
110 
130  const DRTreeLikelihood& drtl,
131  SubstitutionCount& substitutionCount,
132  bool verbose = true) throw (Exception);
133 
150  const DRTreeLikelihood& drtl,
151  SubstitutionCount& substitutionCount,
152  bool verbose = true) throw (Exception);
153 
154 
163  const DRTreeLikelihood& drtl,
164  bool verbose = true) throw (Exception)
165  {
166  OneJumpSubstitutionCount ojsm(0);
167  return computeSubstitutionVectors(drtl, ojsm, 0);
168  }
169 
181  static void writeToStream(
182  const ProbabilisticSubstitutionMapping& substitutions,
183  const SiteContainer& sites,
184  size_t type,
185  std::ostream& out)
186  throw (IOException);
187 
196  static void readFromStream(std::istream& in, ProbabilisticSubstitutionMapping& substitutions, size_t type)
197  throw (IOException);
198 
206  static std::vector<double> computeTotalSubstitutionVectorForSite(const SubstitutionMapping& smap, size_t siteIndex);
207 
219  static double computeNormForSite(const SubstitutionMapping& smap, size_t siteIndex);
220 
228  static std::vector<double> computeSumForBranch(const SubstitutionMapping& smap, size_t branchIndex);
229 
237  static std::vector<double> computeSumForSite(const SubstitutionMapping& smap, size_t siteIndex);
238  };
239 
240 } //end of namespace bpp.
241 
242 #endif //_SUBSTITUTIONMAPPINGTOOLS_H_
243