From: Diane Trout <diane@caltech.edu>
Date: Wed, 8 Mar 2006 06:57:29 +0000 (+0000)
Subject: fix segfault when changing soft threshold when no analysis is loaded
X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=mussa.git;a=commitdiff_plain;h=263c577e74c6a9d986ea02dc6f2a41ac965d488f

fix segfault when changing soft threshold when no analysis is loaded
somehow the trans_path_search tweaked things so that it when it was
called again it'd seg fault.
---

diff --git a/alg/nway_other.cxx b/alg/nway_other.cxx
index 94df136..b788d6e 100644
--- a/alg/nway_other.cxx
+++ b/alg/nway_other.cxx
@@ -210,6 +210,8 @@ bool is_transitive_path(const vector<int>& path,
 void
 NwayPaths::trans_path_search(vector<vector<FLPs> > all_comparisons)
 {
+  if (all_comparisons.size() == 0 or all_comparisons[0].size() == 0)
+    return;
   vector<int> path;
   int win_i, window_num;
   bool still_paths;
@@ -227,7 +229,7 @@ NwayPaths::trans_path_search(vector<vector<FLPs> > all_comparisons)
   cout << "window number = " << window_num << endl;   // just a sanity check
   cout << "trans: comparison size= " << all_comparisons.size() << endl;
   // loop thru all windows in first species
-  for (win_i = 0; win_i < window_num; win_i++)
+  for (win_i = 0; win_i != window_num; win_i++)
   {
     // if 1st seq has a match to all the others for this window,
     // then make all possible paths out of all these matches (in all_matches)
diff --git a/alg/test/test_mussa.cxx b/alg/test/test_mussa.cxx
index a55b8b5..00cae24 100644
--- a/alg/test/test_mussa.cxx
+++ b/alg/test/test_mussa.cxx
@@ -58,6 +58,19 @@ BOOST_AUTO_TEST_CASE( mussa_sequences )
   BOOST_CHECK_EQUAL( analysis.sequences()[2].get_seq(), s2);
 }
 
+// for some reason we can call nway once safely but it
+// somehow changed things and caused a segfault
+// fixed by adding a return statement in trans_path_search 
+BOOST_AUTO_TEST_CASE ( empty_mussa_set_threshold )
+{
+  Mussa m;
+  m.set_soft_thres(15);
+  m.nway();
+
+  m.set_soft_thres(25);
+  m.nway();
+}
+
 #include <unistd.h>
 BOOST_AUTO_TEST_CASE( mussa_load_mupa )
 {
diff --git a/py/getm.py b/py/getm.py
index be5be65..e11d0c3 100644
--- a/py/getm.py
+++ b/py/getm.py
@@ -4,7 +4,7 @@ import mussa
 m = mussa.Mussa()
 #m.load_mupa("examples/mck3test.mupa")
 #m.analyze(0, 0, mussa.analysis_modes.TransitiveNway, 0)
-m.load("../mussa_analyses/land/myogenin_w30_t21")
+m.load("../../mussa_analyses/land/myogenin_w30_t21")
 path = m.paths()
 
 count = 0