static void comparePaths_local(Node * destination, Node * origin)
{
IDnum slowLength, fastLength;
Node *fastNode, *slowNode;
IDnum i;
PassageMarkerI marker;
//Measure lengths
slowLength = fastLength = 0;
fastNode = destination;
slowNode = origin;
//velvetLog("Looking into separate paths\n");
while (fastNode != slowNode) {
//velvetLog("Fast node %li Slow node %li\n", getNodeID(fastNode), getNodeID(slowNode));
if (getNodeTime(fastNode) > getNodeTime(slowNode)) {
fastLength++;
fastNode = getNodePrevious(fastNode);
} else if (getNodeTime(fastNode) < getNodeTime(slowNode)) {
slowLength++;
slowNode = getNodePrevious(slowNode);
} else if (isPreviousToNode(slowNode, fastNode)) {
while (fastNode != slowNode) {
fastLength++;
fastNode = getNodePrevious(fastNode);
}
} else if (isPreviousToNode(fastNode, slowNode)) {
while (slowNode != fastNode) {
slowLength++;
slowNode = getNodePrevious(slowNode);
}
} else {
fastLength++;
fastNode = getNodePrevious(fastNode);
slowLength++;
slowNode = getNodePrevious(slowNode);
}
if (slowLength > MAXNODELENGTH
|| fastLength > MAXNODELENGTH) {
//velvetLog("Paths too fragmented %li %li\n", slowLength, fastLength);
return;
}
}
if (fastLength == 0)
return;
//Backtracking to record actual paths
fastPath = addUncertainPassageMarker(1, destination);
setPassageMarkerStatus(fastPath, true);
for (i = 0; i < fastLength; i++) {
marker =
addUncertainPassageMarker(1,
getNodePrevious(getNode
(fastPath)));
setPassageMarkerStatus(marker, true);
connectPassageMarkers(marker, fastPath, graph);
fastPath = marker;
}
slowPath = addUncertainPassageMarker(2, destination);
setPassageMarkerStatus(slowPath, true);
marker = addUncertainPassageMarker(2, origin);
setPassageMarkerStatus(marker, true);
connectPassageMarkers(marker, slowPath, graph);
slowPath = marker;
for (i = 0; i < slowLength; i++) {
marker =
addUncertainPassageMarker(2,
getNodePrevious(getNode
(slowPath)));
setPassageMarkerStatus(marker, true);
connectPassageMarkers(marker, slowPath, graph);
slowPath = marker;
}
//Extract sequences
if (!extractSequence(fastPath, fastSequence)
|| !extractSequence(slowPath, slowSequence)) {
//velvetLog("Paths too long\n");
destroyPaths();
return;
}
//Compare sequences
if (compareSequences(fastSequence, slowSequence)) {
//velvetLog("Correcting discrepancy\n");
cleanUpRedundancy_local();
return;
}
//velvetLog("\tFinished comparing paths, changes made\n");
destroyPaths();
}
int
findTarget(HashMMData *mmData, unsigned char *target, int targetLen, unsigned char *extract, unsigned char *originalTarget, int eAllowed, int eAdded, unsigned int id, int outputP)
{
int count;
int hash;
int i;
unsigned int leftHigh, leftLow;
int offset;
unsigned int *offsetTable = mmData->offsetTable;
unsigned int *posTable = mmData->posTable;
unsigned int rightHigh, rightLow;
unsigned char *stop = target + targetLen - MerSize;
count = 0;
hash = 0;
for (i = 0; i < MerSize; ++i) {
int code = codings[target[i]];
hash = ((hash << 2) | code) & MerHashMask;
}
leftLow = offsetTable[hash];
leftHigh = offsetTable[hash+1];
if (leftLow == leftHigh) return 0;
offset = targetLen - MerSize;
if (offset) {
hash = 0;
for (i = offset; i < (offset+MerSize); ++i) {
int code = codings[target[i]];
if (code < 0) return 0;
hash = ((hash << 2) | code) & MerHashMask;
}
rightLow = offsetTable[hash];
rightHigh = offsetTable[hash+1];
if (rightLow == rightHigh) return 0;
while (1) {
if (posTable[leftLow]+offset > posTable[rightLow]) {
++rightLow;
}
else if (posTable[leftLow]+offset < posTable[rightLow]) {
++leftLow;
}
else {
int eSeen = 0;
// We know that the ends of extract and target agree for MerSize nts.
unsigned char *ep = extract+MerSize;
unsigned char *tp = target+MerSize;
if ((tp < stop) || outputP)
extractSequence(mmData, posTable[leftLow], targetLen, extract);
while (tp < stop) {
// Ignore case by mapping to lower.
if (((*tp++)|32) != ((*ep++)|32))
if (++eSeen > eAllowed) break;
}
if (eSeen <= eAllowed) {
++count;
if (outputP) {
printf("%u\t%d\t%d\t%.*s\t%.*s\n", id, eSeen+eAdded, posTable[leftLow], targetLen, originalTarget, targetLen, extract);
}
}
++leftLow;
++rightLow;
}
if (rightLow == rightHigh) break;
if (leftLow == leftHigh) break;
}
}
else {
for (i = leftLow; i < leftHigh; ++i) {
++count;
if (outputP) {
extractSequence(mmData, posTable[i], targetLen, extract);
printf("%u\t%d\t%d\t%.*s\t%.*s\n", id, eAdded, posTable[i], targetLen, originalTarget, targetLen, extract);
}
}
}
return count;
}
