public void addString(String str) {
char[] array = str.toCharArray();
strings.add(new TreeString(strings.size(), array));
logger.log(Level.INFO, String.format("Adding string \"%s\"", str));
ukkonenExtendSuffixTree(strings.size() - 1);
// naiveExtendSuffixTree(strings.size()-1);
}
// Returns boolean values: PASSED or FAILED
private static boolean checkNames(
Vector<String> expNames, Vector<String> retNames, String failMsg) {
boolean status = PASSED;
if (expNames.size() != retNames.size()) {
status = FAILED;
} else {
boolean checked[] = new boolean[retNames.size()];
for (int i = 0; i < expNames.size(); i++) {
int j = 0;
for (; j < retNames.size(); j++) {
if (!checked[j] && expNames.elementAt(i).equals(retNames.elementAt(j))) {
checked[j] = true;
break;
}
}
if (j >= retNames.size()) {
status = FAILED;
break;
}
}
}
if (!status) {
printFailMsg(expNames, retNames, failMsg);
}
return status;
}
public synchronized TaskReport[] getReduceTaskReports(String jobid) {
JobInProgress job = (JobInProgress) jobs.get(jobid);
if (job == null) {
return new TaskReport[0];
} else {
Vector reports = new Vector();
Vector completeReduceTasks = job.reportTasksInProgress(false, true);
for (Iterator it = completeReduceTasks.iterator(); it.hasNext(); ) {
TaskInProgress tip = (TaskInProgress) it.next();
reports.add(tip.generateSingleReport());
}
Vector incompleteReduceTasks = job.reportTasksInProgress(false, false);
for (Iterator it = incompleteReduceTasks.iterator(); it.hasNext(); ) {
TaskInProgress tip = (TaskInProgress) it.next();
reports.add(tip.generateSingleReport());
}
return (TaskReport[]) reports.toArray(new TaskReport[reports.size()]);
}
}
public void loadNetwork() throws IOException {
logger.log(Level.INFO, "Loading metabolism network...");
File file = props.getNetworkFile();
Mapper<String, MetabolicEntry> entryMapper = new MetabolicEntry.MetabolicMapper();
Parser<MetabolicEntry> parser = new Parser<MetabolicEntry>(file, entryMapper);
while (parser.hasNext()) {
MetabolicEntry entry = parser.next();
entries.add(entry);
Rxn rxn =
new Rxn(
props,
entry.getReaction(),
entry.getAbbreviation(),
entry.getReactionName(),
entry.getORF());
reactions.put(entry.getAbbreviation(), rxn);
locations.add(rxn.getLocation());
LogicalORFTree lot = new LogicalORFTree(entry.getORF());
ORFSet os = new ORFSet(entry.getORF());
totalORFs.addAll(os.getORFs());
orfSets.put(entry.getAbbreviation(), lot);
}
logger.log(Level.FINE, String.format("Loaded %d entries.", entries.size()));
abbrevs = new MetabolismAbbreviations(props);
abbrevs.loadAbbreviations();
logger.log(Level.FINEST, "Loaded abbrevations.");
}
private static void printFailMsg(
Vector<String> expNames, Vector<String> retNames, String failMsg) {
out.println();
out.println(failMsg);
if (expNames.size() == 0) {
out.println("# there are NO expected logger names");
} else {
out.println("# expected logger names (" + expNames.size() + "):");
for (int i = 0; i < expNames.size(); i++) {
out.println(" expNames[" + i + "] = " + expNames.elementAt(i));
}
}
if (retNames.size() == 0) {
out.println("# there are NO returned logger names");
} else {
out.println("# returned logger names (" + retNames.size() + "):");
for (int i = 0; i < retNames.size(); i++) {
out.println(" retNames[" + i + "] = " + retNames.elementAt(i));
}
}
}
public int size() {
return strings.size();
}