add --motifs

ticket:143 this patch allows one to specify a motifs file to annotate
an analysis with.

diff --git a/alg/parse_options.cpp b/alg/parse_options.cpp
index 489fbfe32fd7ba24730a9189166e1f095ada4741..b0d10626b2963692c66fb2947083fa29291bd26c 100644 (file)
--- a/alg/parse_options.cpp
+++ b/alg/parse_options.cpp
@@ -25,6 +25,8 @@ void initialize_mussa(MussaOptions& opts, int argc, char **argv)
      "run an analysis defined by the mussa parameter file")
     ("view-analysis", po::value<std::string>(),
      "load a previously run analysis")
+    ("motifs", po::value<std::string>(),
+     "annotate analysis with motifs from this file")
     ("no-gui", "terminate without running an analysis")
     ("python", "launch as a python interpreter")
   ;
@@ -54,6 +56,9 @@ void initialize_mussa(MussaOptions& opts, int argc, char **argv)
   else if (vm.count("view-analysis")) {
     opts.analysis->load( vm["view-analysis"].as< std::string >() );
   }
+  if (vm.count("motifs") and opts.analysis) {
+    opts.analysis->load_motifs( vm["motifs"].as< std::string >() );
+  }
   if (vm.count("no-gui")) {
     opts.useGUI=false;
   }