Changeset 2847

Timestamp:

Sep 22, 2012, 12:56:49 PM (11 years ago)

Author:

Peter

Message:

Fixes #724. Adding another test for NeedlemanWunsch?. Fix bug in NW
that score matrix was initialized with smallest positive double rather
than smallest negative value. Also fixed an index error in underlying
Aligner class causing the mess reported in #724.

Location:

branches/0.9-stable

Files:

• test/Makefile.am (modified) (2 diffs)
• test/alignment2.cc (added)
• yat/utility/Aligner.cc (modified) (2 diffs)

branches/0.9-stable/test/Makefile.am

@@ -33 +33 @@
 check_SCRIPTS = test/common_defs.sh
 
-EXTRA_PROGRAMS = test/alignment.test test/averager.test \
+EXTRA_PROGRAMS = test/alignment.test \
+  test/alignment2.test \
+  test/averager.test \
   test/averager1.test \
   test/averager3.test \
@@ -68 +70 @@
 
 # tests not passing through yet
-XFAIL_TESTS = test/alignment.test
+XFAIL_TESTS =
 
 DISTRIBUTED_TESTS = \

branches/0.9-stable/yat/utility/Aligner.cc

@@ -48 +48 @@
   double Aligner::needleman_wunsch(const Matrix& s)
   {
-    Matrix m(s.rows()+1,s.columns()+1, std::numeric_limits<double>::min());
+    Matrix m(s.rows()+1,s.columns()+1, -std::numeric_limits<double>::max());
+    m(0, 0) = 0.0;
     // Init upper and left border of matrix
     for (size_t i=1; i<m.rows(); i++)
@@ -85 +86 @@
 
         if (cigar(i, j-1) == right) {
-          if (x(i-1, j)-horizon_gap_ > x(i,j)) {
+          if (x(i, j-1)-horizon_gap_ > x(i,j)) {
             x(i,j) = x(i,j-1) - horizon_gap_;
             cigar(i,j) = right;