bool capsAreAdjacent(Cap *cap1, Cap *cap2, int64_t *separationDistance) {
if (cap_getName(cap2) != cap_getName(cap1) && cap_getCoordinate(cap1) != cap_getCoordinate(cap2)) { //This can happen if end1 == end2
if (sequence_getMetaSequence(cap_getSequence(cap1)) == sequence_getMetaSequence(cap_getSequence(cap2))) {
assert(strcmp(event_getHeader(cap_getEvent(cap1)), event_getHeader(
cap_getEvent(cap2))) == 0);
assert(cap_getPositiveOrientation(cap1)
!= cap_getPositiveOrientation(cap2));
assert(cap_getName(cap1) != cap_getName(cap2));
assert(sequence_getMetaSequence(cap_getSequence(cap1))
== sequence_getMetaSequence(cap_getSequence(cap2)));
if (!cap_getStrand(cap1)) {
cap1 = cap_getReverse(cap1);
}
if (!cap_getStrand(cap2)) {
cap2 = cap_getReverse(cap2);
}
assert(cap_getStrand(cap1));
assert(cap_getStrand(cap2));
if (cap_getCoordinate(cap1) < cap_getCoordinate(cap2)) {
if (!cap_getSide(cap1) && cap_getSide(cap2)) {
*separationDistance = cap_getCoordinate(cap2) - cap_getCoordinate(cap1) - 1; //The minus 1, to give the length of the sequence between the two caps.
return 1;
}
} else {
if (cap_getSide(cap1) && !cap_getSide(cap2)) {
*separationDistance = cap_getCoordinate(cap1) - cap_getCoordinate(cap2) - 1;
return 1;
}
}
}
}
return 0;
}
/*
* Constructs a face from a given Cap
*/
static void buildFaces_constructFromCap(Cap * startingCap,
stHash *liftedEdgesTable, Flower * flower) {
Face *face = face_construct(flower);
stList *topNodes = stList_construct3(16, NULL);
stList *liftedEdges;
Cap *cap, *bottomNode, *ancestor;
int64_t index, index2;
printf("Constructing new face");
// Establishlist of top nodes
buildFaces_fillTopNodeList(startingCap, topNodes, liftedEdgesTable);
#ifndef NDEBUG
// What, no top nodes!?
if (stList_length(topNodes) == 0)
abort();
#endif
// Initialize data structure
face_allocateSpace(face, stList_length(topNodes));
// For every top node
for (index = 0; index < stList_length(topNodes); index++) {
cap = stList_get(topNodes, index);
face_setTopNode(face, index, cap);
liftedEdges = stHash_search(liftedEdgesTable, cap);
if (!liftedEdges) {
face_setBottomNodeNumber(face, index, 0);
continue;
}
face_setBottomNodeNumber(face, index, stList_length(liftedEdges));
// For every bottom node of that top node
for (index2 = 0; index2 < stList_length(liftedEdges); index2++) {
bottomNode
= ((LiftedEdge *) stList_get(liftedEdges, index2))->bottomNode;
face_addBottomNode(face, index, bottomNode);
ancestor = cap_getTopCap(cap_getPositiveOrientation(
cap_getAdjacency(bottomNode)));
if (cap_getAdjacency(cap) != ancestor)
face_setDerivedDestination(face, index, index2, ancestor);
else
face_setDerivedDestination(face, index, index2, NULL);
#ifndef NDEBUG
// If bottom nodes part of top nodes
assert(!stList_contains(topNodes, cap_getPositiveOrientation(
((LiftedEdge*) stList_get(liftedEdges, index2))->bottomNode)));
#endif
}
}
// Clean up
stList_destruct(topNodes);
}
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;
}
}
}
/*
* Fill uplist with bottom nodes for top node
*/
static void buildFaces_computeLiftedEdgesAtTopNode(Cap * cap, stList * liftedEdges) {
int64_t childIndex;
LiftedEdge * liftedEdge;
// Termination
if (cap_getAdjacency(cap)) {
liftedEdge = st_malloc(sizeof(LiftedEdge));
liftedEdge->bottomNode = cap_getPositiveOrientation(cap);
liftedEdge->destination = cap_getPositiveOrientation(cap_getTopCap(cap_getAdjacency(cap)));
stList_append(liftedEdges, liftedEdge);
return;
}
// Recursion through children
for (childIndex = 0; childIndex < cap_getChildNumber(cap); childIndex++)
buildFaces_computeLiftedEdgesAtTopNode(cap_getChild(cap, childIndex), liftedEdges);
}
/*
* Fill in a hashtable which to every node associates
* alist of lifted edges
*/
static stHash *buildFaces_computeLiftedEdges(Flower * flower) {
stHash *liftedEdgesTable = stHash_construct3(buildFaces_hashfunction,
buildFaces_key_eq_fn, NULL, buildFaces_destructValue);
Flower_CapIterator *iter = flower_getCapIterator(flower);
Cap *cap, *attachedAncestor;
Cap *adjacency, *adjacencyAncestor;
stList *liftedEdges;
LiftedEdge *liftedEdge;
// Iterate through potential bottom nodes
while ((cap = flower_getNextCap(iter))) {
// ... check if connected
if ((adjacency = cap_getAdjacency(cap))) {
// ... lift
attachedAncestor = cap_getTopCap(cap);
adjacencyAncestor = cap_getTopCap(cap_getPositiveOrientation(
adjacency));
#ifndef NDEBUG
assert((attachedAncestor && adjacencyAncestor) || (!attachedAncestor && !adjacencyAncestor));
#endif
// If root node
if (attachedAncestor == NULL)
continue;
// ... create lifted edge
liftedEdge = st_malloc(sizeof(LiftedEdge));
liftedEdge->destination = adjacencyAncestor;
liftedEdge->bottomNode = cap;
#ifndef NDEBUG
// Self loop
if (adjacencyAncestor == attachedAncestor)
abort();
#endif
// ... add it to the hashtable
if ((liftedEdges
= stHash_search(liftedEdgesTable, attachedAncestor))) {
stList_append(liftedEdges, liftedEdge);
} else {
liftedEdges = stList_construct3(2,
buildFaces_stList_destructElem);
stList_append(liftedEdges, liftedEdge);
stHash_insert(liftedEdgesTable, attachedAncestor, liftedEdges);
}
}
}
flower_destructCapIterator(iter);
return liftedEdgesTable;
}
bool endsAreConnected(End *end1, End *end2, stList *eventStrings) {
if (end_getName(end1) == end_getName(end2)) { //Then the ends are the same and are part of the same chromosome by definition.
End_InstanceIterator *instanceIterator = end_getInstanceIterator(end1);
Cap *cap1;
while ((cap1 = end_getNext(instanceIterator)) != NULL) {
if (capHasGivenEvents(cap1, eventStrings)) {
end_destructInstanceIterator(instanceIterator);
return 1;
}
}
return 0;
}
End_InstanceIterator *instanceIterator = end_getInstanceIterator(end1);
Cap *cap1;
while ((cap1 = end_getNext(instanceIterator)) != NULL) {
if (capHasGivenEvents(cap1, eventStrings)) {
End_InstanceIterator *instanceIterator2 = end_getInstanceIterator(end2);
Cap *cap2;
while ((cap2 = end_getNext(instanceIterator2)) != NULL) {
assert(cap_getName(cap2) != cap_getName(cap1)); //This could only happen if end1 == end2
if (sequence_getMetaSequence(cap_getSequence(cap1)) == sequence_getMetaSequence(cap_getSequence(cap2))) {
assert(strcmp(event_getHeader(cap_getEvent(cap1)),
event_getHeader(cap_getEvent(cap2))) == 0);
assert(cap_getPositiveOrientation(cap1)
!= cap_getPositiveOrientation(cap2));
assert(cap_getName(cap1) != cap_getName(cap2));
//they could have the same coordinate if they represent two ends of a block of length 1.
end_destructInstanceIterator(instanceIterator);
end_destructInstanceIterator(instanceIterator2);
return 1;
}
}
end_destructInstanceIterator(instanceIterator2);
}
}
end_destructInstanceIterator(instanceIterator);
return 0;
}
/*
* Recursive function which fills a givenlist with the
* connected nodes within a module and fills their lifted
* edges in the same pass
*/
static void buildFaces_fillTopNodeList2(Cap * cap, stList *list,
stHash *liftedEdgesTable) {
stList *liftedEdges = stList_construct3(2,
buildFaces_stList_destructElem);
int64_t index;
// Orientation check
cap = cap_getPositiveOrientation(cap);
// Limit of recursion
if (stList_contains(list, cap))
return;
// Actual filling
st_logInfo("Adding cap %p to face\n", cap);
stList_append(list, cap);
// Compute lifted edges
for (index = 0; index < cap_getChildNumber(cap); index++)
buildFaces_computeLiftedEdgesAtTopNode(cap_getChild(cap, index), liftedEdges);
// If emptylist...
if (stList_length(liftedEdges) == 0)
stList_destruct(liftedEdges);
// Recursion through lifted edges
else {
stHash_insert(liftedEdgesTable, cap, liftedEdges);
for (index = 0; index < stList_length(liftedEdges); index++)
buildFaces_fillTopNodeList2(
((LiftedEdge *) stList_get(liftedEdges, index))->destination,
list, liftedEdgesTable);
}
// Recursion through adjacency
if (cap_getAdjacency(cap))
buildFaces_fillTopNodeList2(cap_getAdjacency(cap),list,
liftedEdgesTable);
}
void flower_removeCap(Flower *flower, Cap *cap) {
cap = cap_getPositiveOrientation(cap);
assert(stSortedSet_search(flower->caps, cap) != NULL);
stSortedSet_remove(flower->caps, cap);
}
void flower_addCap(Flower *flower, Cap *cap) {
cap = cap_getPositiveOrientation(cap);
assert(stSortedSet_search(flower->caps, cap) == NULL);
stSortedSet_insert(flower->caps, cap);
}
