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;
}
public void run() {
if (in.verbosity > 1) System.err.println("Config : " + conf);
try {
if (AlignmentMaker_SingleSequences.consistency) {
int increase = AlignmentMaker_SingleSequences.consistency_subs_increase;
conf.cost.increaseCosts(
increase); // arbitrary number ... just trying to make w-w identities non-zero cost, and
// high enough to avoid rounding effects
conf.cost.multiplyCosts(2);
conf.increaseGapCosts(increase / 2);
conf.multiplyGapCosts(2);
}
if (Tree.treeType == Tree.TreeType.entered) {
Tree.iterations = 1;
}
FacetAlignment fa = null;
if (in.justDoSubOpt) {
am = new AlignmentMaker_SuboptimalityTester();
// am.initialize(in.fileA, in.structFileA);
am.initialize(conf, in);
alignmentInstance = am.buildAlignment();
if (in.structFileA != null) {
fa =
new FacetAlignment(
conf.sc.convertIntsToSeqs(alignmentInstance), in.structure.structure);
}
} else if (in.justDoConvert) {
am = new AlignmentMaker_Converter();
// am.initialize(in.fileA, in.structFileA);
am.initialize(conf, in);
alignmentInstance = am.buildAlignment();
if (in.structFileA != null) {
fa =
new FacetAlignment(
conf.sc.convertIntsToSeqs(alignmentInstance), in.structure.structure);
}
} else if (in.fileB != null) { // alignalign call
am = new AlignmentMaker_TwoAlignments();
// am.initialize(in.fileA, in.fileB);
// Aligner.useStructure = false;
am.initialize(conf, in);
alignmentInstance = am.buildAlignment();
if (in.structFileA != null) {
fa =
new FacetAlignment(
((AlignmentMaker_TwoAlignments) am).result, in.structure.structure);
}
} else if (in.justTree || Tree.justPWDists) { //
am = new AlignmentMaker_SingleSequences();
// am.initialize(in.fileA, in.structFileA);
am.initialize(conf, in);
((AlignmentMaker_SingleSequences) am).buildTree(conf, in);
} else { // multiple alignment call
am = new AlignmentMaker_SingleSequences();
// am.initialize(in.fileA, in.structFileA);
am.initialize(conf, in);
// final Timer queueRunner = new Timer();
// ShutdownHandler sh = new ShutdownHandler(queueRunner,
// (AlignmentMaker_SingleSequences)am);
// Runtime.getRuntime().addShutdownHook(sh);
// Thread.setDefaultUncaughtExceptionHandler(sh); // this should be available for all calls
// ... but this is the one I use a lot, so it's all I've implemented it for
alignmentInstance = am.buildAlignment();
if (in.structFileA != null) {
if (realignmentConfigList != null) {
Configuration newRealignmentConfigList[] =
new Configuration[realignmentConfigList.length];
for (int rNum = 0; rNum < realignmentConfigList.length; rNum++) {
newRealignmentConfigList[rNum] = new Configuration(realignmentConfigList[rNum]);
}
preRealignmentAlignmentInstance = alignmentInstance.clone();
preRealignmentFacetScore =
Facet.defaultValue(
new FacetAlignment(
conf.sc.convertIntsToSeqs(preRealignmentAlignmentInstance),
in.structure.structure),
conf.useLegacyFacetFunction);
if (conf.useTCSforAdvising)
preRealignmentFacetScore = TCS.TCSValue(preRealignmentAlignmentInstance, am, conf);
realignmentDriver realigner =
new realignmentDriver(
conf.sc.convertIntsToSeqs(preRealignmentAlignmentInstance),
in.structure.structure,
newRealignmentConfigList,
conf,
(float) preRealignmentFacetScore,
am);
if (conf.realignment_window_type == Configuration.WINDOW_SIZE.VALUE)
realigner.simpleRealignment((int) conf.realignment_window_value);
else if (conf.realignment_window_type == Configuration.WINDOW_SIZE.PERCENTAGE) {
int window_size =
(int)
(conf.realignment_window_value
* (float) preRealignmentAlignmentInstance[0].length);
if (window_size > conf.maximum_realignment_window_value)
window_size = (int) conf.maximum_realignment_window_value;
if (window_size < conf.minimum_realignment_window_value)
window_size = (int) conf.minimum_realignment_window_value;
realigner.simpleRealignment(window_size);
}
alignmentInstance = realigner.newAlignment();
newRealignmentConfigList = null;
}
fa =
new FacetAlignment(
conf.sc.convertIntsToSeqs(alignmentInstance), in.structure.structure);
}
}
if (fa != null) {
if (in.featureOutputFile != null) {
String fname = in.featureOutputFile.replace("__CONFIG__", conf.toString());
if (conf.repetition >= 0)
fname = fname.replace("__ITTERATION__", Integer.toString(conf.repetition));
Facet.outputDefaultFeatures(fname, fa);
}
facetScore = Facet.defaultValue(fa, conf.useLegacyFacetFunction);
if (conf.useTCSforAdvising) facetScore = TCS.TCSValue(alignmentInstance, am, conf);
}
// in.structFileA = "";
// System.err.println("File: " + in.structFileA);
// System.err.printf("facet value -- %.6f\n\n",facetScore);
} catch (GenericOpalException e) {
System.exit(1);
} /*catch (FileNotFoundException e){
System.err.println("File Error:" + e.toString());
System.exit(15);
}*/
}