Changeset 184


Ignore:
Timestamp:
Oct 6, 2004, 4:18:51 PM (18 years ago)
Author:
Peter
Message:

documentation

File:
1 edited

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  • trunk/src/Alignment.h

    r183 r184  
    1313namespace alignment {
    1414
    15   double NeedlemanWunsch(const gslapi::matrix& dot_matrix,
    16                          const double mismatch);
     15  ///
     16  /// Function calculating the score for the best aligning of two
     17  /// sequences. In the dot_matrix \a A, elament \f$ A_{ij} \f$ is
     18  /// score how well element i in the first sequence match to element
     19  /// j in the other sequence. In the aligning the elements from the
     20  /// two sequences are matched or a gap is added in one of the
     21  /// sequences. The latter is penalized with \a gap, which means if
     22  /// \a gap is large there will be no gaps in the best aligning (if
     23  /// the sequences have the same length).  @return score from the
     24  /// best aligning
     25  ///
     26  double NeedlemanWunsch(const gslapi::matrix& A,
     27                         const double gap);
    1728
    1829}}} // of namespace alignment namespace cpptools and namespace theplu
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