test annotating a sequence with fasta records in a stream

[mussa.git] / alg / sequence.cpp

diff --git a/alg/sequence.cpp b/alg/sequence.cpp
index 1f21bd5edc83e8e66894ffc7ee473c31bfbd170c..521496d3497b2b96d4786819438d170f6ac50ce4 100644 (file)
--- a/alg/sequence.cpp
+++ b/alg/sequence.cpp
@@ -324,6 +324,21 @@ Sequence::load_annot(fs::path file_path, int start_index, int end_index)
     throw mussa_load_error("Error loading annotation file " + file_path.string());
   }
 
+  try {  
+    load_annot(data_stream, start_index, end_index);
+  }  catch(annotation_load_error e) {
+    std::ostringstream msg;
+    msg << file_path.native_file_string()
+        << " "
+        << e.what();
+    throw annotation_load_error(msg.str());
+  }
+  data_stream.close();
+}
+
+void
+Sequence::load_annot(std::istream& data_stream, int start_index, int end_index)
+{
   // so i should probably be passing the parse function some iterators
   // but the annotations files are (currently) small, so i think i can 
   // get away with loading the whole file into memory
@@ -333,17 +348,8 @@ Sequence::load_annot(fs::path file_path, int start_index, int end_index)
     data_stream.get(c);
     data.push_back(c);
   }
-  data_stream.close();
 
-  try {  
-    parse_annot(data, start_index, end_index);
-  } catch(annotation_load_error e) {
-    std::ostringstream msg;
-    msg << file_path.native_file_string()
-        << " "
-        << e.what();
-    throw annotation_load_error(msg.str());
-  }
+  parse_annot(data, start_index, end_index);
 }
 
 /* If this works, yikes, this is some brain hurting code.