Changeset 2738


Ignore:
Timestamp:
May 30, 2012, 10:35:11 AM (9 years ago)
Author:
Peter
Message:

SmithWaterman? improve docs

File:
1 edited

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  • trunk/yat/utility/Alignment.h

    r2717 r2738  
    99  Copyright (C) 2006 Jari Häkkinen
    1010  Copyright (C) 2007, 2008 Jari Häkkinen, Peter Johansson
     11  Copyright (C) 2012 Peter Johansson
    1112
    1213  This file is part of the yat library, http://dev.thep.lu.se/yat
     
    7172     whichever maximises the similarity measure.
    7273
     74     \return the similarity score that maximizes \f$ \sum_{i,j}
     75     A_{ij}s_{ij} - L*gap - N*open\textunderscore gap\f$, where \f$
     76     A_{ij} \f$ is unity if element \a i in first sequence is aligned
     77     against element \a j in second sequence (zero otherwise); \a L is total
     78     length of gaps; and \a N is number of gaps.
     79
    7380     \param s score matrix in which element \f$(i,j)\f$ is the score between
    74      element \f$i\f$ in first sequence vs element \f$j\f$ in second sequence.
     81     element \f$i\f$ in first sequence and element \f$j\f$ in second sequence.
    7582     \param gap cost for having a gap (insertion or deletion)
    7683     \param open_gap cost for open up a gap in sequence, in other words, for a
    77      gap of length \f$l\f$ the total cost is \f$open\textunderscore gap
    78      + l*gap\f$.
     84     gap of length L the total cost is open_gap + L*gap.
    7985   */
    8086  double SmithWaterman(const utility::Matrix& s,
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