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);
}*/
}
public static void main(String[] argv) {
OpalLogWriter.setLogger(new DefaultLogger());
ArgumentHandler argHandler = new ArgumentHandler(argv);
if (argHandler.getVerbosity() > 0) {
OpalLogWriter.printVersion();
OpalLogWriter.stdErrLogln("");
}
/*String fileA = argHandler.getFileA();
String fileB = argHandler.getFileB();
String structFileA = argHandler.getStructFileA();
String structFileB = argHandler.getStructFileB();
String costName = argHandler.getCostName();
int gamma = argHandler.getGamma();
int lambda = argHandler.getLambda();
int gammaTerm = argHandler.getGammaTerm();
int lambdaTerm = argHandler.getLambdaTerm();
int verbosity = argHandler.getVerbosity();
boolean toUpper = argHandler.isToUpper();
boolean justDoConvert= argHandler.isJustDoConvert();
boolean justDoSubOpt= argHandler.isJustDoSubOpt();
boolean justTree= argHandler.isJustTree();*/
Date start = new Date();
Configuration[] advising_config = argHandler.getAdvisingConfigs();
Configuration[] realignment_config = argHandler.getRealignmentConfigs();
Inputs input = argHandler.getInputs();
runAlignment[] thread = new runAlignment[advising_config.length];
int last_joined = -1;
int max_threads = Runtime.getRuntime().availableProcessors();
if (argHandler.getMaxThreads() > -1) max_threads = argHandler.getMaxThreads();
if (input.verbosity > 0) {
OpalLogWriter.stdErrLogln(
"The number of available threads is "
+ Runtime.getRuntime().availableProcessors()
+ ", Opal will use "
+ max_threads);
}
int maxIndex = 0;
int maxPreRealignmentIndex = 0;
for (int i = 0; i < advising_config.length; i++) {
thread[i] = new runAlignment(advising_config[i], input, realignment_config);
// thread[i] = new printLine(config[i],i);
thread[i].start();
if (i - last_joined >= max_threads) {
last_joined++;
try {
thread[last_joined].join();
if (input.configOutputFile != null) thread[last_joined].print();
if (input.configOutputFile != null && realignment_config != null)
thread[last_joined].printPreRealignment();
if (thread[last_joined].facetScore > thread[maxIndex].facetScore) {
if (maxPreRealignmentIndex != maxIndex) thread[maxIndex] = null;
maxIndex = last_joined;
}
if (thread[last_joined].preRealignmentFacetScore
> thread[maxPreRealignmentIndex].preRealignmentFacetScore) {
if (maxPreRealignmentIndex != maxIndex) thread[maxPreRealignmentIndex] = null;
maxPreRealignmentIndex = last_joined;
}
if (last_joined != maxIndex && last_joined != maxPreRealignmentIndex)
thread[last_joined] = null;
} catch (InterruptedException e) {
OpalLogWriter.stdErrLogln("InterruptedException " + e.toString());
throw new GenericOpalException("InterruptedException " + e.toString());
}
}
}
for (last_joined++; last_joined < advising_config.length; last_joined++) {
try {
thread[last_joined].join();
if (input.configOutputFile != null) thread[last_joined].print();
if (input.configOutputFile != null && realignment_config != null)
thread[last_joined].printPreRealignment();
if (thread[last_joined].facetScore > thread[maxIndex].facetScore) {
if (maxPreRealignmentIndex != maxIndex) thread[maxIndex] = null;
maxIndex = last_joined;
}
if (thread[last_joined].preRealignmentFacetScore
> thread[maxPreRealignmentIndex].preRealignmentFacetScore) {
if (maxPreRealignmentIndex != maxIndex) thread[maxPreRealignmentIndex] = null;
maxPreRealignmentIndex = last_joined;
}
if (last_joined != maxIndex && last_joined != maxPreRealignmentIndex)
thread[last_joined] = null;
} catch (InterruptedException e) {
OpalLogWriter.stdErrLogln("InterruptedException " + e.toString());
throw new GenericOpalException("InterruptedException " + e.toString());
}
}
// if(advising_config.length>1 && thread[maxIndex]!=null && thread[maxIndex].facetScore>=0)
if (!thread[maxIndex].printBest()) System.err.println("Print returned false");
if (advising_config.length > 1
&& realignment_config != null
&& thread[maxPreRealignmentIndex] != null
&& thread[maxPreRealignmentIndex].facetScore >= 0) {
if (input.bestPreRealignmentOutputFile != null)
if (!thread[maxPreRealignmentIndex].printBestPreRealignment())
System.err.println("Print returned false");
if (input.bestPreRealignmentsRealignmentOutputFile != null)
if (!thread[maxPreRealignmentIndex].printBestPreRealignmentsRealignment())
System.err.println("Print returned false");
if (input.bestPreRealignmentsRealignmentOutputFileIncludePreRealignment != null)
if (!thread[maxPreRealignmentIndex]
.printBestPreRealignmentsRealignmentIncludePreRealignment())
System.err.println("Print returned false");
}
if (advising_config.length > 1
&& realignment_config != null
&& thread[maxIndex] != null
&& thread[maxIndex].facetScore >= 0
&& thread[maxPreRealignmentIndex] != null
&& thread[maxPreRealignmentIndex].facetScore >= 0
&& thread[maxPreRealignmentIndex].preRealignmentFacetScore < thread[maxIndex].facetScore) {
if (input.bestOutputFileIncludePreRealignment != null)
if (!thread[maxIndex].printBestIncludePreRealignment())
System.err.println("Print returned false");
} else if (advising_config.length > 1
&& thread[maxPreRealignmentIndex] != null
&& thread[maxPreRealignmentIndex].facetScore >= 0) {
if (input.bestOutputFileIncludePreRealignment != null)
if (!thread[maxPreRealignmentIndex].printBestIncludePreRealignment())
System.err.println("Print returned false");
}
if (input.verbosity > 0) {
Date now = new Date();
long diff = now.getTime() - start.getTime();
System.err.printf("Total time for job: %.1f seconds\n\n", ((float) diff / 1000 + .05));
}
System.exit(0);
}