public static double TCSValue( int[][] alignmentInstance, AlignmentMaker am, Configuration config) { String filename = config.temporaryFileDirectory + "tmp" + alignmentInstance.hashCode() + "_" + am.hashCode() + "_" + config.hashCode() + "_" + am.in.hashCode(); int oldVerbosity = am.in.verbosity; am.in.verbosity = -1; am.printOutput(alignmentInstance, filename); am.in.verbosity = oldVerbosity; String command = config.tcoffeeDirectory + "t_coffee -infile " + filename + " -evaluate -method proba_pair -output score_ascii -outfile=stdout"; String result = "-1"; try { result = execCmd(command); execCmd("rm " + filename); } catch (NumberFormatException e) { // TODO Auto-generated catch block e.printStackTrace(); } catch (IOException e) { // TODO Auto-generated catch block e.printStackTrace(); } // System.err.println("Command: \""+command+"\"\nPre Parse Line: \""+result+"\""); return Double.parseDouble(result) / 100.0; }