/* ukkonenSPA(i) performs phase i of Ukkonen's algorithm. This
* means that we're making sure that array[0,i] (note the inclusivity!)
* is a part of the current suffix tree.
*
* Original Description: pg. 106 of Gusfield
*/
private void ukkonenSPA(int i) {
logger.entering("UkkonenSuffixTree", "ukkonenSPA");
logger.log(Level.FINEST, String.format("i=%d", i));
assert i >= 0;
/*
* SPA Step 1:
* "Increment index e to i+1"
*
* The equivalent of Gusfield's i+1 is, in our situation, just i.
* However, the coordinates are inclusive in Gusfield,
* and exclusive in our case (along the tree edges). Therefore,
* lastE should be updated to be i+1, exactly.
*/
extState.lastE = i + 1;
logger.log(Level.FINEST, String.format("e=%d", extState.lastE));
/*
* SPA Step 2:
* "Explicitly compute successive extensions, using the SEA algorithm,
* starting at j_i + 1 until reaching the first extension j* where rule3
* applies or until all extensions are done in this phase."
*
* extState.nextExtStart encodes the (j_i)+1 value. We start there, and
* iterate forward until all extensions have been performed, or until
* ukkonenSEA returns false (ukkonenSEA returns a true if rule 1 or rule 2
* applies in its extension).
*
* We extend until j==i, because the last extension of each phase is
* the extension that *just* adds the new character into the tree.
*/
logger.log(Level.FINEST, String.format("jstart=%d", extState.nextExtStart));
boolean keepExtending = true;
int j = extState.nextExtStart;
while (keepExtending && j <= i) {
if (ukkonenSEA(i, j)) {
j++;
// we don't want to just put in the terminal character.
if (i == extState.string.length() - 1 && j == i) {
keepExtending = false;
}
} else {
keepExtending = false;
}
System.out.println(String.format("Phase %d, Extension %d tree: ", i, j));
print(System.out);
System.out.println();
System.out.flush();
System.err.println();
System.err.flush();
}
/*
* SPA Step 3:
* "Set j_{i+1} to j*-1, to prepare for the next phase."
*/
extState.nextExtStart = j;
logger.log(Level.FINEST, String.format("j*=%d", extState.nextExtStart));
logger.exiting("UkkonenSuffixTree", "ukkonenSPA");
}
