Changeset 2738

Timestamp:

May 30, 2012, 10:35:11 AM (10 years ago)

Author:

Peter

Message:

SmithWaterman? improve docs

File:

• trunk/yat/utility/Alignment.h (modified) (2 diffs)

trunk/yat/utility/Alignment.h

@@ -9 +9 @@
   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
@@ -71 +72 @@
      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,