Index: trunk/yat/utility/Alignment.h
===================================================================
--- trunk/yat/utility/Alignment.h (revision 872)
+++ trunk/yat/utility/Alignment.h (revision 873)
@@ -72,9 +72,9 @@
whichever maximises the similarity measure.
- \param s score matrix in which element $(i,j)$ is the score between
- element $i$ in first sequence vs element $j$ in second sequence.
+ \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.
\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 $l$ the total cost is $open_gap + l*gap$.
+ gap of length \f$l\f$ the total cost is \f$open_gap + l*gap\f$.
*/
double SmithWaterman(const utility::matrix& s,