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;
}
