public Object tryArgument(String arg) throws Exception {
try {
ArrayList<Object> retval = new ArrayList<Object>();
String[] values = arg.split(separator);
if (values.length == 0) {
throw new Exception("Invalid argument");
}
if (values.length == 1) {
return handler.tryArgument(values[0]);
}
if (values.length > maxEntries) {
throw new Exception(String.format("Cannot exceed %d entries", maxEntries));
}
for (String v : values) {
Object param = handler.tryArgument(v);
if (param == null) {
throw new Exception(String.format("Invalid member of list: %s", v));
}
retval.add(param);
}
return retval;
} catch (Exception e) {
throw e;
}
}
public String toUsageString(String prepend) {
StringBuilder builder = new StringBuilder();
builder.append(prepend);
builder.append(String.format("%s: %s", name, description));
builder.append("\n");
if (defaultValue != null) {
builder.append(prepend);
builder.append(String.format("\tDefault: %s", defaultValue.toString()));
builder.append("\n");
}
String handlerUsage = handler.toUsageString(prepend);
if (handlerUsage != null && handlerUsage.length() > 0) {
builder.append("\t");
builder.append(handlerUsage);
builder.append("\n");
}
return builder.toString();
}
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);
}