[project @ 13]

[mussa.git] / flp_seqcomp.cc

diff --git a/flp_seqcomp.cc b/flp_seqcomp.cc
index d61b55421239aa4a27b5581f700ab3bc26d41c40..e48a3b55372251b0afcb116c8b587f4b405a8d9a 100644 (file)
--- a/flp_seqcomp.cc
+++ b/flp_seqcomp.cc
@@ -1,13 +1,29 @@
+//  This file is part of the Mussa source distribution.
+//  http://mussa.caltech.edu/
+//  Contact author: Tristan  De Buysscher, tristan@caltech.edu
+
+// This program and all associated source code files are Copyright (C) 2005
+// the California Institute of Technology, Pasadena, CA, 91125 USA.  It is
+// under the GNU Public License; please see the included LICENSE.txt
+// file for more information, or contact Tristan directly.
+
+
 //                        ----------------------------------------
 //                         ---------- flp_seqcomp.cc  -----------
 //                        ----------------------------------------
 
 #include "flp.hh"
 
+// Note one recording RC matches.  This version of 'seqcomp' records RC matches
+// as index of the window start in its nonRC form.  However, past versions of
+// the analysis recorded it as the index of the rear of the window, as the
+// following legacy comment indicates.  FR still uses this method
+
 // Titus thinks the start of an RC window should be its "rear" in the
 // normal version of the sequence.  He's wrong, of course, and in the
 // future my followers will annihilate his in the Final Battle, but for
 // now I'll let him have his way.
+
 // note seq2_i is actually the index of the leaving bp, so need to +1
 
 inline void
@@ -45,6 +61,8 @@ FLPs::seqcomp(string sseq1, string sseq2, bool is_RC)
     i2_offset = 0;
 
 
+  // this does the "upper diagonals" of the search 
+
   // loop thru the start positions for sequence 1
   for(start_i = 0; start_i < seq1_win_num; start_i++)
   {
@@ -83,6 +101,9 @@ FLPs::seqcomp(string sseq1, string sseq2, bool is_RC)
     } // end of loop thru the current offset sequence
   } // end of loop thru the start positions of seq1 sequence
 
+
+  // this does the "lower diagonals" of the search
+
   // loop thru the start positions for sequence 1
   for(start_i = 1; start_i < seq2_win_num; start_i++)
   {