# Changeset 2738

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

SmithWaterman? improve docs

File:
1 edited

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