private void ukkonenExtendSuffixTree(int arrayIdx) {
logger.entering("UkkonenSuffixTree", "ukkonenExtendSuffixTree");
logger.log(Level.FINEST, String.format("Ukkonen Algorithm String #%d", arrayIdx));
TreeString string = strings.get(arrayIdx);
extState = new UkkonenState(string);
logger.log(
Level.FINEST,
String.format("Ukkonen: (%d,%d)", extState.nextPhaseStart, extState.string.length()));
for (int phase = extState.nextPhaseStart; phase < extState.string.length(); phase++) {
ukkonenSPA(phase);
System.err.println(String.format("Phase %d results: ", phase));
print(System.err);
System.err.println();
System.err.flush();
}
logger.log(Level.FINEST, String.format("Finishing edges: %d", extState.lastE));
extState.finishFinalEdges();
System.err.println(String.format("Finished results: "));
print(System.err);
System.err.println();
System.err.flush();
logger.exiting("UkkonenSuffixTree", "ukkonenExtendSuffixTree");
}
private void naiveExtendSuffixTree(int arrayIdx) {
TreeString string = strings.get(arrayIdx);
// the array.length-1 constraint, instead of array.length, is because
// we assume that the terminal character has already been added to the
// string, and we don't want to *just* add the suffix that is that
// character.
for (int i = 0; i <= string.length(); i++) {
logger.log(
Level.FINEST,
String.format("Naive Extension: \"%s\"", string.substring(i, string.length() + 1)));
naiveExtendSuffix(string, i);
}
}
public TreeString getString(int i) {
return strings.get(i);
}