Changeset 2738
 Timestamp:
 May 30, 2012, 10:35:11 AM (10 years ago)
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trunk/yat/utility/Alignment.h
r2717 r2738 9 9 Copyright (C) 2006 Jari Häkkinen 10 10 Copyright (C) 2007, 2008 Jari Häkkinen, Peter Johansson 11 Copyright (C) 2012 Peter Johansson 11 12 12 13 This file is part of the yat library, http://dev.thep.lu.se/yat … … 71 72 whichever maximises the similarity measure. 72 73 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 73 80 \param s score matrix in which element \f$(i,j)\f$ is the score between 74 element \f$i\f$ in first sequence vselement \f$j\f$ in second sequence.81 element \f$i\f$ in first sequence and element \f$j\f$ in second sequence. 75 82 \param gap cost for having a gap (insertion or deletion) 76 83 \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. 79 85 */ 80 86 double SmithWaterman(const utility::Matrix& s,
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