static void setAdjacencyLengthsAndRecoverNewCapsAndBrokenAdjacencies(Cap *cap, stList *recoveredCaps) {
/*
* Sets the coordinates of the caps to be equal to the length of the adjacency sequence between them.
* Used to build the reference sequence bottom up.
*
* One complexity is that a reference thread between the two caps
* in each flower f may be broken into two in the children of f.
* Therefore, for each flower f first identify attached stub ends present in the children of f that are
* not present in f and copy them into f, reattaching the reference caps as needed.
*/
while (1) {
Cap *adjacentCap = cap_getAdjacency(cap);
assert(adjacentCap != NULL);
assert(cap_getCoordinate(cap) == INT64_MAX);
assert(cap_getCoordinate(adjacentCap) == INT64_MAX);
assert(cap_getStrand(cap) == cap_getStrand(adjacentCap));
assert(cap_getSide(cap) != cap_getSide(adjacentCap));
Group *group = end_getGroup(cap_getEnd(cap));
assert(group != NULL);
if (!group_isLeaf(group)) { //Adjacency is not terminal, so establish its sequence.
Flower *nestedFlower = group_getNestedFlower(group);
Cap *nestedCap = flower_getCap(nestedFlower, cap_getName(cap));
assert(nestedCap != NULL);
Cap *nestedAdjacentCap = flower_getCap(nestedFlower, cap_getName(adjacentCap));
assert(nestedAdjacentCap != NULL);
Cap *breakerCap;
int64_t adjacencyLength = traceThreadLength(nestedCap, &breakerCap);
assert(cap_getOrientation(nestedAdjacentCap));
if (cap_getPositiveOrientation(breakerCap) != nestedAdjacentCap) { //The thread is broken at the lower level.
//Copy cap into higher level graph.
breakerCap = copyCapToParent(breakerCap, recoveredCaps);
assert(cap_getSide(breakerCap));
cap_makeAdjacent(cap, breakerCap);
setAdjacencyLength(cap, breakerCap, adjacencyLength);
adjacencyLength = traceThreadLength(nestedAdjacentCap, &breakerCap);
assert(cap_getPositiveOrientation(breakerCap) != cap);
breakerCap = copyCapToParent(breakerCap, recoveredCaps);
assert(!cap_getSide(breakerCap));
cap_makeAdjacent(breakerCap, adjacentCap);
setAdjacencyLength(adjacentCap, breakerCap, adjacencyLength);
} else { //The thread is not broken at the lower level
setAdjacencyLength(cap, adjacentCap, adjacencyLength);
}
} else {
//Set the coordinates of the caps to the adjacency size
setAdjacencyLength(cap, adjacentCap, 0);
}
if ((cap = cap_getOtherSegmentCap(adjacentCap)) == NULL) {
break;
}
}
}
void testCap_getTopCap(CuTest* testCase) {
cactusCapTestSetup();
End *end1 = end_construct(0, flower);
End *end2 = end_construct(0, flower);
End *end3 = end_construct(0, flower);
Event *intermediateEvent = event_construct4(NULL, 0.0, rootEvent, leafEvent, eventTree);
Cap *cap1T = cap_construct(end1, rootEvent);
Cap *cap1I = cap_construct(end1, intermediateEvent);
Cap *cap1L1 = cap_construct(end1, leafEvent);
Cap *cap1L2 = cap_construct(end1, leafEvent);
cap_makeParentAndChild(cap1I, cap1L1);
cap_makeParentAndChild(cap1I, cap1L2);
cap_makeParentAndChild(cap1T, cap1I);
end_setRootInstance(end1, cap1T);
assert(end_getRootInstance(end1) == cap1T);
CuAssertTrue(testCase, cap_getTopCap(cap1L1) == NULL);
CuAssertTrue(testCase, cap_getTopCap(cap_getReverse(cap1L1)) == NULL);
CuAssertTrue(testCase, cap_getTopCap(cap1L2) == NULL);
CuAssertTrue(testCase, cap_getTopCap(cap1I) == NULL);
Cap *cap2T = cap_construct(end2, rootEvent);
Cap *cap2L = cap_construct(end2, leafEvent);
cap_makeParentAndChild(cap2T, cap2L);
end_setRootInstance(end2, cap2T);
cap_makeAdjacent(cap1L1, cap2L);
CuAssertTrue(testCase, cap_getTopCap(cap1L1) == cap1T);
CuAssertTrue(testCase, cap_getTopCap(cap_getReverse(cap1L1)) == cap_getReverse(cap1T));
CuAssertTrue(testCase, cap_getTopCap(cap1I) == NULL);
Cap *cap3T = cap_construct(end3, rootEvent);
Cap *cap3I = cap_construct(end3, intermediateEvent);
cap_makeParentAndChild(cap3T, cap3I);
end_setRootInstance(end3, cap3T);
cap_makeAdjacent(cap1I, cap3I);
cap_makeAdjacent(cap1T, cap3T);
CuAssertTrue(testCase, cap_getTopCap(cap1L1) == cap1I);
CuAssertTrue(testCase, cap_getTopCap(cap_getReverse(cap1L1)) == cap_getReverse(cap1I));
CuAssertTrue(testCase, cap_getTopCap(cap1I) == cap1T);
CuAssertTrue(testCase, cap_getTopCap(cap_getReverse(cap1I)) == cap_getReverse(cap1T));
CuAssertTrue(testCase, cap_getTopCap(cap1T) == NULL);
cactusCapTestTeardown();
}
static void recoverBrokenAdjacencies(Flower *flower, stList *recoveredCaps, Name referenceEventName) {
/*
* Find reference intervals that are book-ended by stubs created in a child flower.
*/
Flower_GroupIterator *groupIt = flower_getGroupIterator(flower);
Group *group;
while((group = flower_getNextGroup(groupIt)) != NULL) {
Flower *nestedFlower;
if((nestedFlower = group_getNestedFlower(group)) != NULL) {
Flower_EndIterator *endIt = flower_getEndIterator(nestedFlower);
End *childEnd;
while((childEnd = flower_getNextEnd(endIt)) != NULL) {
if(end_isStubEnd(childEnd) && flower_getEnd(flower, end_getName(childEnd)) == NULL) { //We have a thread we need to promote
Cap *childCap = getCapForReferenceEvent(childEnd, referenceEventName); //The cap in the reference
assert(childCap != NULL);
assert(!end_isAttached(childEnd));
childCap = cap_getStrand(childCap) ? childCap : cap_getReverse(childCap);
if (!cap_getSide(childCap)) {
Cap *adjacentChildCap = NULL;
int64_t adjacencyLength = traceThreadLength(childCap, &adjacentChildCap);
Cap *cap = copyCapToParent(childCap, recoveredCaps);
assert(adjacentChildCap != NULL);
assert(!end_isAttached(cap_getEnd(adjacentChildCap)));
assert(!cap_getSide(cap));
Cap *adjacentCap = copyCapToParent(adjacentChildCap, recoveredCaps);
cap_makeAdjacent(cap, adjacentCap);
setAdjacencyLength(cap, adjacentCap, adjacencyLength);
}
}
}
flower_destructEndIterator(endIt);
}
}
flower_destructGroupIterator(groupIt);
}
void stCaf_addAdjacencies(Flower *flower) {
//Build a list of caps.
stList *list = stList_construct();
Flower_EndIterator *endIterator = flower_getEndIterator(flower);
End *end;
while ((end = flower_getNextEnd(endIterator)) != NULL) {
End_InstanceIterator *instanceIterator = end_getInstanceIterator(end);
Cap *cap;
while ((cap = end_getNext(instanceIterator)) != NULL) {
if (!cap_getStrand(cap)) {
cap = cap_getReverse(cap);
}
stList_append(list, cap);
}
end_destructInstanceIterator(instanceIterator);
}
flower_destructEndIterator(endIterator);
assert(stList_length(list) % 2 == 0);
//Sort the list of caps.
stList_sort(list, (int(*)(const void *, const void *)) addAdjacenciesPP);
//Now make the adjacencies.
for (int64_t i = 1; i < stList_length(list); i += 2) {
Cap *cap = stList_get(list, i - 1);
Cap *cap2 = stList_get(list, i);
cap_makeAdjacent(cap, cap2);
}
//Clean up.
stList_destruct(list);
}
void testCap_getBottomAndTopFaceEnd(CuTest* testCase) {
cactusCapTestSetup();
End *end1 = end_construct(0, flower);
Cap *cap1T = cap_construct(end1, rootEvent);
Cap *cap1L = cap_construct(end1, leafEvent);
cap_makeParentAndChild(cap1T, cap1L);
end_setRootInstance(end1, cap1T);
End *end2 = end_construct(0, flower);
Cap *cap2T = cap_construct(end2, rootEvent);
Cap *cap2L = cap_construct(end2, leafEvent);
cap_makeParentAndChild(cap2T, cap2L);
end_setRootInstance(end2, cap2T);
CuAssertTrue(testCase, cap_getBottomFaceEnd(cap1T) == NULL);
CuAssertTrue(testCase, cap_getBottomFaceEnd(cap1L) == NULL);
CuAssertTrue(testCase, cap_getTopFaceEnd(cap1T) == NULL);
CuAssertTrue(testCase, cap_getTopFaceEnd(cap1L) == NULL);
cap_makeAdjacent(cap1L, cap2L);
cap_makeAdjacent(cap1T, cap2T);
//Now make the face
Face *face = face_construct(flower);
face_allocateSpace(face, 2);
face_setTopNode(face, 0, cap1T);
face_setTopNode(face, 1, cap2T);
face_setBottomNodeNumber(face, 0, 1);
face_setBottomNodeNumber(face, 1, 1);
face_addBottomNode(face, 0, cap1L);
face_addBottomNode(face, 1, cap2L);
CuAssertTrue(testCase, cap_getTopFaceEnd(cap1L) == NULL);
CuAssertTrue(testCase, cap_getTopFaceEnd(cap2L) == NULL);
FaceEnd *faceEnd1 = cap_getTopFaceEnd(cap1T);
FaceEnd *faceEnd2 = cap_getTopFaceEnd(cap2T);
CuAssertTrue(testCase, faceEnd_getTopNode(faceEnd1) == cap1T);
CuAssertTrue(testCase, faceEnd_getTopNode(faceEnd2) == cap2T);
CuAssertTrue(testCase, cap_getBottomFaceEnd(cap1T) == NULL);
CuAssertTrue(testCase, cap_getBottomFaceEnd(cap2T) == NULL);
CuAssertTrue(testCase, cap_getBottomFaceEnd(cap1L) == faceEnd1);
CuAssertTrue(testCase, cap_getBottomFaceEnd(cap2L) == faceEnd2);
cactusCapTestTeardown();
}
void testCap_adjacent(CuTest* testCase) {
cactusCapTestSetup();
CuAssertTrue(testCase, cap_getAdjacency(leaf1Cap) == NULL);
CuAssertTrue(testCase, cap_getAdjacency(leaf3Cap) == NULL);
cap_makeAdjacent(leaf1Cap, leaf3Cap);
CuAssertTrue(testCase, cap_getAdjacency(leaf1Cap) == cap_getReverse(leaf3Cap));
CuAssertTrue(testCase, cap_getAdjacency(leaf3Cap) == cap_getReverse(leaf1Cap));
CuAssertTrue(testCase, cap_getAdjacency(cap_getReverse(leaf1Cap)) == leaf3Cap);
CuAssertTrue(testCase, cap_getAdjacency(cap_getReverse(leaf3Cap)) == leaf1Cap);
cactusCapTestTeardown();
}
Segment *block_splitP(Segment *segment,
Block *leftBlock, Block *rightBlock) {
Segment *leftSegment = segment_getSequence(segment) != NULL
? segment_construct2(leftBlock, segment_getStart(segment), segment_getStrand(segment), segment_getSequence(segment))
: segment_construct(leftBlock, segment_getEvent(segment));
Segment *rightSegment = segment_getSequence(segment) != NULL
? segment_construct2(rightBlock, segment_getStart(segment) + block_getLength(leftBlock), segment_getStrand(segment), segment_getSequence(segment))
: segment_construct(rightBlock, segment_getEvent(segment));
//link together.
cap_makeAdjacent(segment_get3Cap(leftSegment), segment_get5Cap(rightSegment));
//update adjacencies.
Cap *_5Cap = segment_get5Cap(segment);
Cap *new5Cap = segment_get5Cap(leftSegment);
Cap *_3Cap = segment_get3Cap(segment);
Cap *new3Cap = segment_get3Cap(rightSegment);
if(cap_getAdjacency(_5Cap) != NULL) {
cap_makeAdjacent(cap_getAdjacency(_5Cap), new5Cap);
}
if(cap_getAdjacency(_3Cap) != NULL) {
cap_makeAdjacent(cap_getAdjacency(_3Cap), new3Cap);
}
return leftSegment;
}
void processSequence(const char *fastaHeader, const char *string, int64_t length) {
/*
* Processes a sequence by adding it to the flower disk.
*/
End *end1;
End *end2;
Cap *cap1;
Cap *cap2;
MetaSequence *metaSequence;
Sequence *sequence;
//Now put the details in a flower.
metaSequence = metaSequence_construct(2, length, string, fastaHeader, event_getName(event), cactusDisk);
sequence = sequence_construct(metaSequence, flower);
end1 = end_construct2(0, isComplete, flower);
end2 = end_construct2(1, isComplete, flower);
cap1 = cap_construct2(end1, 1, 1, sequence);
cap2 = cap_construct2(end2, length + 2, 1, sequence);
cap_makeAdjacent(cap1, cap2);
totalSequenceNumber++;
}