allow to best match files

src/radiant.cpp

@@ -288,11 +288,12 @@ main(int argc, char const *argv[])
 		fs::path detailedFile;
 		po::options_description hiddenO("Hidden options");
 		int w;//, m;
-		fs::path m;
+		fs::path m, m2;
 		hiddenO.add_options()
 			("detailed", po::value<fs::path>(&detailedFile), "The output file for the detailed results")
 			("window_size", po::value<int>(&w), "The window size")
 			("match", po::value<fs::path>(&m), "The number of matches required")
+			("match2", po::value<fs::path>(&m2), "The number of matches required")
 		;
 
 		allOpts.add(general).add(outputO).add(translateO).add(hiddenO);
@@ -385,28 +386,34 @@ main(int argc, char const *argv[])
 			//fs::path tmp = outFile;
 		//	tmp += to_string(max_dist) + "_" + to_string(min_count) + ".txt";
 		//
-		map<unsigned short, int> domain2match;
+		map<unsigned short, int> domain2match, domain2match2;
 		std::ifstream file(m.string());
 		unsigned short p_id;
 		int threshold;
 		while(!file.eof())
 		{
-
 		    file >> p_id >> threshold; // extracts 2 floating point values seperated by whitespace
 			domain2match[p_id] = threshold;
-		    // do something with them
 		}
-		//
-			AlgorithmPack::Output out(outFile);
+		file.close();
+
+		file.open(m2.string());
+		while(!file.eof())
+		{
+			file >> p_id >> threshold; // extracts 2 floating point values seperated by whitespace
+			domain2match2[p_id] = threshold;
+		}
+		file.close();
+
+		AlgorithmPack::Output out(outFile);
 		if (!noHeader)
 			printHeader(radiantVersion, pfamLike, translate, inFile, databaseFile, out);
 		for (size_t i = 0; i< seqSet.size(); ++i)
 		{
 			auto &assignment = assignments[i];
-		//	auto da = words2arrangement(assignment, m, w);
 			auto da = words2arrangement(assignment, domain2match, 10);
-			//if (da.size() == 0)
-			//	da = words2arrangement(assignment, 3, 5);
+			if (da.size() == 0)
+				da = words2arrangement(assignment, domain2match2, 5);
 
 			if (pfamLike)
 			{