From 03d92f51588c1cd45178321a86cb3aacb80a0f33 Mon Sep 17 00:00:00 2001
From: Diane Trout <diane@caltech.edu>
Date: Thu, 19 Apr 2007 23:12:35 +0000
Subject: [PATCH] improve mupa comment character parsing ticket:261 It also
 makes sure that load_mupa throws an exception when it loads a file it doesn't
 understand.

I wonder if the GUI knows to catch this?
---
 alg/mussa.cpp           |  8 +++++++-
 alg/test/test_mussa.cpp | 33 +++++++++++++++++++++++++++++++++
 2 files changed, 40 insertions(+), 1 deletion(-)

diff --git a/alg/mussa.cpp b/alg/mussa.cpp
index 9a5935e..2fb639b 100644
--- a/alg/mussa.cpp
+++ b/alg/mussa.cpp
@@ -381,6 +381,7 @@ Mussa::load_mupa_file(fs::path para_file_path)
 void
 Mussa::load_mupa_stream(std::istream& para_file, fs::path& file_path_base)
 {
+  bool error_occured = false;
   string file_data_line;
   string param, value; 
   fs::path annot_file;
@@ -454,11 +455,13 @@ Mussa::load_mupa_stream(std::istream& para_file, fs::path& file_path_base)
       did_seq = true;
     }
     //ignore empty lines or that start with '#'
-    else if ((param == "") || (param == "#")) {}
+    else if ( (param.size() == 0) || (param[0] == '#')) 
+    {} // pass
     else
     {
       clog << "Illegal/misplaced mussa parameter in file\n";
       clog << param << "\n";
+      error_occured = true;
     }
 
     if (!did_seq)
@@ -471,6 +474,9 @@ Mussa::load_mupa_stream(std::istream& para_file, fs::path& file_path_base)
     }
   }
 
+  if (error_occured) {
+    throw mussa_load_error("Error parsing MUPA file");
+  }
   soft_thres = threshold;
   // no file was loaded, signal error
   set_dirty(true);
diff --git a/alg/test/test_mussa.cpp b/alg/test/test_mussa.cpp
index e1cef22..9f11a5e 100644
--- a/alg/test/test_mussa.cpp
+++ b/alg/test/test_mussa.cpp
@@ -129,6 +129,39 @@ BOOST_AUTO_TEST_CASE( mussa_load_mupa_crlf )
   // Should run with no exceptions
 }
 
+BOOST_AUTO_TEST_CASE( mussa_load_mupa_comment_character )
+{
+  fs::path mupa_path(EXAMPLE_DIR, fs::native);
+  fs::path seq_path = fs::initial_path() / "seq" / "mouse_mck_pro.fa";
+  fs::path annot_path = fs::initial_path() / "mm_mck3test.annot";
+
+  std::string mupa(
+    "# hello\015\012"
+    "ANA_NAME load_mupa_crlf\015\012");
+  mupa += "#SEQUENCE " + seq_path.native_file_string() + "\015\012";
+  mupa += "#ANNOTATION " + annot_path.native_file_string() + "\015\012";
+  
+  istringstream mupa_stream(mupa);
+  Mussa m;
+  fs::path base;
+  m.load_mupa_stream( mupa_stream, base );
+  // Should run with no exceptions
+}
+
+BOOST_AUTO_TEST_CASE( mussa_load_mupa_exception )
+{
+  std::string mupa(
+    "# hello\015\012"
+    "ANA_NAME load_mupa_crlf\015\012"
+    "mwahhaha I broke you!\n"
+  );
+  
+  istringstream mupa_stream(mupa);
+  Mussa m;
+  fs::path base;
+  BOOST_CHECK_THROW(m.load_mupa_stream( mupa_stream, base ), mussa_load_error);
+}
+
 BOOST_AUTO_TEST_CASE( mussa_load_mupa )
 {
   fs::path mupa_path(EXAMPLE_DIR, fs::native);
-- 
2.30.2