bpp-seq  2.2.0
SymbolListTools.h
Go to the documentation of this file.
1 //
2 // File: SymbolListTools.h
3 // Created by: Julien Dutheil
4 // Created on: Wed Apr 9 2004
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 _SYMBOLLISTTOOLS_H_
41 #define _SYMBOLLISTTOOLS_H_
42 
43 #include "SymbolList.h"
45 #include <Bpp/Numeric/VectorExceptions.h>
46 
47 // From the STL:
48 #include <map>
49 
50 namespace bpp
51 {
52 
57 {
58  public:
60  virtual ~SymbolListTools() {}
61 
62  public:
70  static void getCounts(const SymbolList& list, std::map<int, size_t>& counts)
71  {
72  for(std::vector<int>::const_iterator seqit = list.getContent().begin();
73  seqit != list.getContent().end();
74  seqit++)
75  counts[*seqit]++;
76  }
77 
90  static void getCounts(const SymbolList& list1, const SymbolList& list2, std::map<int, std::map<int, size_t> >& counts) throw (DimensionException)
91  {
92  if(list1.size() != list2.size()) throw DimensionException("SymbolListTools::getCounts: the two sites must have the same size.", list1.size(), list2.size());
93  for(size_t i = 0; i < list1.size(); i++)
94  counts[list1[i]][list2[i]]++;
95  }
96 
109  static void getCounts(const SymbolList& list, std::map<int, double>& counts, bool resolveUnknowns);
110 
128  static void getCounts(const SymbolList& list1, const SymbolList& list2, std::map< int, std::map<int, double> >& counts, bool resolveUnknowns) throw (DimensionException);
129 
139  static void getFrequencies(const SymbolList& list, std::map<int, double>& frequencies, bool resolveUnknowns = false);
140 
151  static void getFrequencies(const SymbolList& list1, const SymbolList& list2, std::map<int, std::map<int, double> >& frequencies, bool resolveUnknowns = false) throw (DimensionException);
152 
162  static double getGCContent(const SymbolList& list, bool ignoreUnresolved = true, bool ignoreGap = true) throw (AlphabetException);
163 
174  static size_t getNumberOfDistinctPositions(const SymbolList& l1, const SymbolList& l2) throw (AlphabetMismatchException);
175 
186  static size_t getNumberOfPositionsWithoutGap(const SymbolList& l1, const SymbolList& l2) throw (AlphabetMismatchException);
187 
194 
201 
202 };
203 
204 } //end of namespace bpp.
205 
206 #endif // _SYMBOLLISTTOOLS_H_
207 
static void changeUnresolvedCharactersToGaps(SymbolList &l)
Change all unknown characters to gap elements.
static void getCounts(const SymbolList &list, std::map< int, size_t > &counts)
Count all states in the list.
static size_t getNumberOfDistinctPositions(const SymbolList &l1, const SymbolList &l2)
Get the number of distinct positions.
The SymbolList interface.
Definition: SymbolList.h:60
This alphabet is used to deal NumericAlphabet.
static void getFrequencies(const SymbolList &list, std::map< int, double > &frequencies, bool resolveUnknowns=false)
Get all states frequencies in the list.
Utilitary functions dealing with both sites and sequences.
The alphabet exception base class.
static double getGCContent(const SymbolList &list, bool ignoreUnresolved=true, bool ignoreGap=true)
Get the GC content of a symbol list.
static size_t getNumberOfPositionsWithoutGap(const SymbolList &l1, const SymbolList &l2)
Get the number of positions without gap.
virtual const std::vector< int > & getContent() const =0
Get the whole content of the list as a vector of int.
static void getCounts(const SymbolList &list1, const SymbolList &list2, std::map< int, std::map< int, size_t > > &counts)
Count all pair of states for two lists of the same size.
Exception thrown when two alphabets do not match.
static void changeGapsToUnknownCharacters(SymbolList &l)
Change all gap elements to unknown characters.