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");
}
/*
* ukkonenSEA(i, j) performs extension j of phase i of Ukkonen's algorithm.
* This means that we're making sure that array[j,i] (note the inclusivity!)
* is a part of the current suffix tree.
*
* Original Description: pg. 100 of Gusfield
*/
private boolean ukkonenSEA(int i, int j) {
logger.exiting("UkkonenSuffixTree", "ukkonenSEA");
logger.log(Level.FINEST, String.format("j=%d", j));
assert j <= i;
boolean rule3 = false;
TreeNode newRule2Node = null;
EdgeMatch m = extState.matcher;
char lastChar = extState.string.getChar(i);
boolean lastCharIsTerminal = isTerminal(lastChar);
/*
* SEA Step 1:
* "Find the first node v at or above the end of S[j-1,i] that either
* has a suffix link from it or is the root. This requires walking up
* at most one edge from the end of S[j-1,i] in the current tree. Let
* \gamma (possibly empty) denote the string between v and the
* end of S[j-1,i]."
*/
/*
* SEA Step 2:
* "If v is not the root, traverse the suffix link from v to node
* s(v) and then walk down from s(v) following the path for string
* gamma. If v is the root, then follow the path for S[j,i] from the
* root (as in the naive algorithm)."
*/
int gammaEnd = i;
int gammaStart = gammaEnd - extState.gammaLength;
if (extState.nextNode == null || extState.nextNode.isRoot()) {
String beta = extState.string.substring(j, i);
logger.log(Level.FINEST, String.format("beta: %d,%d <%s>%c", j, i, beta, lastChar));
m.reset(j, i);
m.matchFrom(root, true);
} else {
logger.log(Level.FINEST, String.format("gammaLength:%d", extState.gammaLength));
String gamma = extState.string.substring(gammaStart, gammaEnd);
logger.log(
Level.FINEST,
String.format("gamma: %d,%d <%s>%c", gammaStart, gammaEnd, gamma, lastChar));
m.reset(gammaStart, gammaEnd);
m.matchFrom(extState.nextNode, true);
}
/*
* SEA Step 3:
* "Using the extension rules, ensure that the string S[j,i]S(i+1) is
* in the tree."
*
* In our coordinates, this is array[j,i)+array[i]
* \beta = array[j,i)
*
* Rule 1: the path \beta ends at a leaf. (we shouldn't see this case).
* Rule 2: the path \beta is not continued by array[i]. That is, \beta
* ends either at a node (in which case, no child of the node
* starts with array[i]), or in an edge (in which case, the edge
* doesn't continue with array[i]). Either way, we create a new
* edge that is labeled with array[i] (coordinates: [i,i+1) ).
* Rule 3: \beta+array[i] is already in the tree -- either \beta ends in
* an edge that continues with array[i], or at a node that has
* a child under array[i]. Either way, return false (break!).
*/
TreeEdge newEdge = null;
if (m.lastEdge == null) {
logger.log(Level.FINEST, String.format("Found root."));
// the \beta string matched to the root (was empty). So we need
// to simply check the children of the root.
boolean foundLastChar =
!lastCharIsTerminal
? root.childEdges.containsKey(lastChar)
: root.terminalEdges.containsKey(extState.string.getIndex());
if (foundLastChar) {
// Rule 3
rule3 = true;
logger.log(Level.FINEST, "Rule #3, Root");
extState.nextNode = null;
extState.gammaLength = 0;
logger.log(Level.FINEST, String.format("nextGamma: %d", extState.gammaLength));
} else {
// Rule 2
logger.log(Level.FINEST, "Rule #2, Root");
newEdge = new TreeEdge(extState.string, i, null, root);
root.addEdge(newEdge);
extState.nextNode = null;
extState.gammaLength = 0;
logger.log(Level.FINEST, String.format("nextGamma: %d", extState.gammaLength));
}
} else if (m.inEdgeMiddle()) {
int offset = m.lastMatchLength();
logger.log(Level.FINEST, String.format("Found edge middle: %d", offset));
boolean foundLastChar =
!lastCharIsTerminal
? m.lastEdge.getChar(offset) == lastChar
: (m.lastEdge.string.getIndex() == extState.string.getIndex()
&& offset == m.lastEdge.length() - 1);
logger.log(Level.FINEST, String.format("foundLastChar: %s", foundLastChar));
if (foundLastChar) {
// Rule 3
rule3 = true;
logger.log(Level.FINEST, "Rule #3, Edge");
extState.nextNode = m.lastEdge.headNode;
// extState.gammaLength = m.lastMatchLength() + 1;
extState.gammaLength = m.lastMatchLength() + (j == i ? 1 : 0);
assert extState.gammaLength >= 0;
logger.log(Level.FINEST, String.format("nextGamma: %d", extState.gammaLength));
} else {
// Rule 2
logger.log(Level.FINEST, "Rule #2, Edge");
TreeEdge newLowerEdge = m.lastEdge.split(offset);
extState.edgesWithE.add(newLowerEdge);
newEdge = new TreeEdge(extState.string, i, null, m.lastEdge.tailNode);
m.lastEdge.tailNode.addEdge(newEdge);
newRule2Node = m.lastEdge.tailNode;
extState.nextNode = m.lastEdge.headNode;
// extState.gammaLength = m.lastEdge.length() + 1;
extState.gammaLength = m.lastEdge.length() + (j == i ? 1 : 0);
assert extState.gammaLength >= 0;
logger.log(Level.FINEST, String.format("nextGamma: %d", extState.gammaLength));
}
if (extState.nextNode.suffixLink == null && !extState.nextNode.isRoot()) {
logger.log(
Level.FINEST,
String.format("Walking up edge: %d", extState.nextNode.parentEdge.length()));
extState.gammaLength += extState.nextNode.parentEdge.length();
extState.nextNode = extState.nextNode.parentEdge.headNode;
}
} else {
logger.log(Level.FINEST, String.format("Found node."));
boolean foundLastChar =
!lastCharIsTerminal
? m.lastEdge.tailNode.childEdges.containsKey(lastChar)
: m.lastEdge.tailNode.terminalEdges.containsKey(extState.string.getIndex());
logger.log(Level.FINEST, String.format("foundLastChar: %s", foundLastChar));
if (foundLastChar) {
// Rule 3
rule3 = true;
logger.log(Level.FINEST, "Rule #3, Node");
extState.nextNode = m.lastEdge.headNode;
// extState.gammaLength = m.lastEdge.length() + 1;
extState.gammaLength = m.lastEdge.length() + (j == i ? 1 : 0);
assert extState.gammaLength >= 0;
logger.log(Level.FINEST, String.format("nextGamma: %d", extState.gammaLength));
} else {
// Rule 2
logger.log(Level.FINEST, "Rule #2, Node");
newEdge = new TreeEdge(extState.string, i, null, m.lastEdge.tailNode);
m.lastEdge.tailNode.addEdge(newEdge);
extState.nextNode = m.lastEdge.headNode;
// extState.gammaLength = m.lastEdge.length() + 1;
extState.gammaLength = m.lastEdge.length() + (j == i ? 1 : 0);
logger.log(Level.FINEST, String.format("nextGamma: %d", extState.gammaLength));
assert extState.gammaLength >= 0;
}
if (extState.nextNode.suffixLink == null && !extState.nextNode.isRoot()) {
logger.log(
Level.FINEST,
String.format("Walking up edge: %d", extState.nextNode.parentEdge.length()));
extState.gammaLength += extState.nextNode.parentEdge.length();
extState.nextNode = extState.nextNode.parentEdge.headNode;
}
}
if (extState.nextNode != null) {
logger.log(Level.FINEST, "Following suffix link.");
extState.nextNode = extState.nextNode.suffixLink;
} else {
logger.log(Level.FINEST, "Suffix link not found.");
}
if (newEdge != null) {
newEdge.tailNode.suffixes.add(extState.currentSuffix);
extState.nextSuffix();
extState.edgesWithE.add(newEdge);
logger.log(Level.FINEST, String.format("Added suffix: %d", j));
}
/*
* SEA Step 4:
* "If a new internal node w was created in extension j-1 (by extension rule 2)
* then by Lemma 6.1.1 string alpha must end at node s(w), the end node for the
* suffix link from w. Create the suffix link (w, s(w)) from w to s(w)."
*
* This wording is confusing -- is there a typo in Gusfield? I'm not sure where
* the 'w' comes from.
*/
if (extState.rule2Node != null) {
if (m.lastEdge != null) {
extState.rule2Node.suffixLink = m.lastEdge.tailNode;
logger.log(Level.FINEST, "Adding suffix link --> internal node.");
} else {
extState.rule2Node.suffixLink = root;
logger.log(Level.FINEST, "Adding suffix link --> root.");
}
}
/*
* Update any state that will be needed in the next extension.
*/
extState.rule2Node = newRule2Node;
logger.exiting("UkkonenSuffixTree", "ukkonenSEA");
// "Rule 3 is a show stopper" means that, if we encounter rule 3,
// we *don't* continue.
return !rule3;
}
/* 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");
}