#include <boost/program_options.hpp>
namespace po = boost::program_options;
+#include <boost/filesystem/path.hpp>
+namespace fs = boost::filesystem;
#include <string>
#include <iostream>
#include "alg/parse_options.hpp"
MussaOptions::MussaOptions()
- : analysis(0),
- useGUI(true),
+ : useGUI(true),
runAsPythonInterpeter(false)
{
}
"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")
;
std::cout << options << std::endl;
return;
}
-
- opts.analysis = new Mussa();
+
+ opts.analysis = Mussa::init();
// currently we can only have one analysis loaded, so
// running trumps viewing.
if (vm.count("run-analysis")) {
- opts.analysis->load_mupa_file( vm["run-analysis"].as< std::string >() );
+ fs::path analysis_path(vm["run-analysis"].as< std::string >(), fs::native);
+ opts.analysis->load_mupa_file( analysis_path );
std::cout << "I apologize for blocking the gui while running the analysis"
<< std::endl;
opts.analysis->analyze();
+ if (opts.analysis->is_dirty())
+ opts.analysis->save();
}
else if (vm.count("view-analysis")) {
- opts.analysis->load( vm["view-analysis"].as< std::string >() );
+ fs::path analysis_path(vm["view-analysis"].as< std::string >(), fs::native);
+ opts.analysis->load( analysis_path );
+ }
+ if (vm.count("motifs") and opts.analysis) {
+ fs::path motif_path(vm["motifs"].as< std::string >(), fs::native);
+ opts.analysis->load_motifs( motif_path );
}
if (vm.count("no-gui")) {
opts.useGUI=false;