source: trunk/src/Alignment.h @ 185

Last change on this file since 185 was 185, checked in by Jari Häkkinen, 17 years ago

Added namespace documentation.

  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 1.1 KB
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1// $Id: Alignment.h 185 2004-10-07 07:36:10Z jari $
2
3#ifndef _theplu_cpptools_alignment_
4#define _theplu_cpptools_alignment_
5
6namespace theplu {
7
8namespace gslapi {
9  class matrix;
10}
11
12namespace cpptools {
13// Jari, this should probably go somewhere else for doxygen to process.
14///
15/// All alignment algorithm should go into the aligment namespace
16///
17/// \brief Container for alignment algorithms
18///
19namespace alignment {
20
21  ///
22  /// Function calculating the score for the best aligning of two
23  /// sequences. In the dot_matrix \a A, elament \f$ A_{ij} \f$ is
24  /// score how well element i in the first sequence match to element
25  /// j in the other sequence. In the aligning the elements from the
26  /// two sequences are matched or a gap is added in one of the
27  /// sequences. The latter is penalized with \a gap, which means if
28  /// \a gap is large there will be no gaps in the best aligning (if
29  /// the sequences have the same length).  @return score from the
30  /// best aligning
31  ///
32  double NeedlemanWunsch(const gslapi::matrix& A,
33                         const double gap);
34
35}}} // of namespace alignment namespace cpptools and namespace theplu
36
37#endif
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