public boolean printBestIncludePreRealignment() {
if (facetScore > preRealignmentFacetScore) {
if (in.verbosity > -1) {
System.err.printf("\nbest facet value -- %.6f (%s)", facetScore, conf);
}
return am.printOutput(alignmentInstance, in.bestOutputFileIncludePreRealignment);
} else {
if (in.verbosity > 0 && facetScore > -1) {
System.err.printf("\npre-realignment facet score: %.6f", preRealignmentFacetScore);
}
return am.printOutput(
preRealignmentAlignmentInstance, in.bestOutputFileIncludePreRealignment, false);
}
}
public boolean printBest() {
if (facetScore != -1 && in.verbosity > -1) {
System.err.printf("\nbest facet value -- %.6f (%s)", facetScore, conf);
}
return am.printOutput(alignmentInstance, in.bestOutputFile);
}
public boolean printBestPreRealignment() {
if (in.verbosity > -1) {
System.err.printf(
"\nbest pre-realignment facet value -- %.6f (%s)", preRealignmentFacetScore, conf);
}
return am.printOutput(preRealignmentAlignmentInstance, in.bestPreRealignmentOutputFile, false);
}
public boolean printPreRealignment() {
if (in.verbosity > 0 && facetScore > -1) {
System.err.printf("\npre-realignment facet score: %.6f", preRealignmentFacetScore);
}
if (in.preRealignmentOutputFile != null) {
String fname = in.preRealignmentOutputFile.replace("__CONFIG__", conf.toString());
if (conf.repetition >= 0)
fname = fname.replace("__ITTERATION__", Integer.toString(conf.repetition));
if (facetScore >= 0)
fname =
fname.replace(
"__FACETSCORE__", "facetScore" + Double.toString(preRealignmentFacetScore));
return am.printOutput(preRealignmentAlignmentInstance, fname, false);
} else {
return am.printOutput(preRealignmentAlignmentInstance, null, false);
}
}
public boolean print() {
// if(facetScore==-1){
// am = null;
// }
if (in.verbosity > 0 && facetScore > -1) {
System.err.printf("\nfacet score: %.6f", facetScore);
}
if (in.configOutputFile != null) {
String fname = in.configOutputFile.replace("__CONFIG__", conf.toString());
if (conf.repetition >= 0)
fname = fname.replace("__ITTERATION__", Integer.toString(conf.repetition));
if (facetScore >= 0)
fname = fname.replace("__FACETSCORE__", "facetScore" + Double.toString(facetScore));
return am.printOutput(alignmentInstance, fname);
} else return am.printOutput(alignmentInstance, null);
}
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;
}