 Timestamp:
 Sep 18, 2007, 3:14:38 AM (15 years ago)
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trunk/yat/utility/Alignment.h
r869 r873 72 72 whichever maximises the similarity measure. 73 73 74 \param s score matrix in which element $(i,j)$ is the score between75 element $i$ in first sequence vs element $j$ in second sequence.74 \param s score matrix in which element \f$(i,j)\f$ is the score between 75 element \f$i\f$ in first sequence vs element \f$j\f$ in second sequence. 76 76 \param gap cost for having a gap (insertion or deletion) 77 77 \param open_gap cost for open up a gap in sequence, in other words, for a 78 gap of length $l$ the total cost is $open_gap + l*gap$.78 gap of length \f$l\f$ the total cost is \f$open_gap + l*gap\f$. 79 79 */ 80 80 double SmithWaterman(const utility::matrix& s,
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