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 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 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);
}