static int64_t traceThreadLength(Cap *cap, Cap **terminatingCap) {
/*
* Gets the length in bases of the thread in the flower, starting from a given attached stub cap.
* The thread length includes the lengths of adjacencies that it contains.
*
* Terminating cap is initialised with the final cap on the thread from cap.
*/
assert(end_isStubEnd(cap_getEnd(cap)));
int64_t threadLength = 0;
while (1) {
assert(cap_getCoordinate(cap) != INT64_MAX);
int64_t adjacencyLength = cap_getCoordinate(cap);
threadLength += adjacencyLength;
Cap *adjacentCap = cap_getAdjacency(cap);
assert(adjacentCap != NULL);
assert(adjacencyLength == cap_getCoordinate(adjacentCap));
//Traverse any block..
if (cap_getSegment(adjacentCap) != NULL) {
threadLength += segment_getLength(cap_getSegment(adjacentCap));
cap = cap_getOtherSegmentCap(adjacentCap);
assert(cap != NULL);
} else {
assert(end_isStubEnd(cap_getEnd(adjacentCap)));
*terminatingCap = adjacentCap;
return threadLength;
}
}
return 1;
}
void testCap_getSegment(CuTest* testCase) {
cactusCapTestSetup();
Block *block = block_construct(2, flower);
Segment *segment = segment_construct(block, rootEvent);
CuAssertTrue(testCase, cap_getSegment(segment_get5Cap(segment)) == segment);
CuAssertTrue(testCase, cap_getSegment(segment_get3Cap(segment)) == segment);
CuAssertTrue(testCase, cap_getOrientation(segment_get5Cap(segment)) == segment_getOrientation(segment));
CuAssertTrue(testCase, cap_getOrientation(segment_get3Cap(segment)) == segment_getOrientation(segment));
CuAssertTrue(testCase, cap_getSegment(cap_getReverse(segment_get5Cap(segment))) == segment_getReverse(segment));
CuAssertTrue(testCase, cap_getSegment(cap_getReverse(segment_get3Cap(segment))) == segment_getReverse(segment));
cactusCapTestTeardown();
}
static int64_t setCoordinates(Flower *flower, MetaSequence *metaSequence, Cap *cap, int64_t coordinate) {
/*
* Sets the coordinates of the reference thread and sets the bases of the actual sequence
* that of the consensus.
*/
Sequence *sequence = flower_getSequence(flower, metaSequence_getName(metaSequence));
if (sequence == NULL) {
sequence = sequence_construct(metaSequence, flower);
}
while (1) {
assert(cap_getStrand(cap));
assert(!cap_getSide(cap));
Cap *adjacentCap = cap_getAdjacency(cap);
assert(adjacentCap != NULL);
assert(cap_getStrand(adjacentCap));
assert(cap_getSide(adjacentCap));
int64_t adjacencyLength = cap_getCoordinate(cap);
assert(adjacencyLength == cap_getCoordinate(adjacentCap));
assert(adjacencyLength != INT64_MAX);
assert(adjacencyLength >= 0);
cap_setCoordinates(cap, coordinate, 1, sequence);
coordinate += adjacencyLength + 1;
cap_setCoordinates(adjacentCap, coordinate, 1, sequence);
//Traverse any block..
if ((cap = cap_getOtherSegmentCap(adjacentCap)) == NULL) {
break;
}
coordinate += segment_getLength(cap_getSegment(adjacentCap)) - 1;
}
return coordinate;
}
static int addAdjacenciesPP(Cap *cap1, Cap *cap2) {
assert(cap_getStrand(cap1) && cap_getStrand(cap2));
Sequence *sequence1 = cap_getSequence(cap1);
Sequence *sequence2 = cap_getSequence(cap2);
int64_t i = cactusMisc_nameCompare(sequence_getName(sequence1), sequence_getName(sequence2));
if (i == 0) {
int64_t j = cap_getCoordinate(cap1);
int64_t k = cap_getCoordinate(cap2);
i = j > k ? 1 : (j < k ? -1 : 0);
if (i == 0) {
assert(cap_getSegment(cap1) == cap_getSegment(cap2));
j = cap_getSide(cap1);
k = cap_getSide(cap2);
assert((j && !k) || (!j && k));
i = j ? -1 : 1;
}
}
return i;
}
Segment *getCapsSegment(Cap *cap) {
if (cap_getSegment(cap) != NULL) {
return cap_getSegment(cap);
}
assert(!end_isBlockEnd(cap_getEnd(cap)));
assert(end_isStubEnd(cap_getEnd(cap)));
//Walk up to get the next adjacency.
Group *parentGroup = flower_getParentGroup(end_getFlower(cap_getEnd(cap)));
if (parentGroup != NULL) {
Cap *parentCap = flower_getCap(group_getFlower(parentGroup), cap_getName(cap));
if (parentCap != NULL) {
assert(cap_getOrientation(parentCap));
if (!cap_getOrientation(cap)) {
parentCap = cap_getReverse(parentCap);
}
return getCapsSegment(parentCap);
} else { //Cap must be a free stub end.
assert(0); //Not in the current alignments.
assert(end_isFree(cap_getEnd(cap)));
}
}
return NULL;
}
static void block_splitP2(Segment *segment,
Segment *parentLeftSegment,
Segment *parentRightSegment,
Block *leftBlock, Block *rightBlock) {
Segment *leftSegment = block_splitP(segment, leftBlock, rightBlock);
Segment *rightSegment = cap_getSegment(cap_getAdjacency(segment_get3Cap(leftSegment)));
if(parentLeftSegment != NULL) {
assert(parentRightSegment != NULL);
segment_makeParentAndChild(parentLeftSegment, leftSegment);
segment_makeParentAndChild(parentRightSegment, rightSegment);
}
else {
assert(parentRightSegment == NULL);
block_setRootInstance(leftBlock, leftSegment);
block_setRootInstance(rightBlock, rightSegment);
}
int64_t i;
for(i=0; i<segment_getChildNumber(segment); i++) {
block_splitP2(segment_getChild(segment, i), leftSegment, rightSegment, leftBlock, rightBlock);
}
}
int64_t flower_getTotalBaseLength(Flower *flower) {
/*
* The implementation of this function is very like that in group_getTotalBaseLength, with a few differences. Consider merging them.
*/
Flower_EndIterator *endIterator = flower_getEndIterator(flower);
End *end;
int64_t totalLength = 0;
while ((end = flower_getNextEnd(endIterator)) != NULL) {
if (!end_isBlockEnd(end)) {
End_InstanceIterator *instanceIterator = end_getInstanceIterator(end);
Cap *cap;
while ((cap = end_getNext(instanceIterator)) != NULL) {
cap = cap_getStrand(cap) ? cap : cap_getReverse(cap);
if (!cap_getSide(cap) && cap_getSequence(cap) != NULL) {
Cap *cap2 = cap_getAdjacency(cap);
assert(cap2 != NULL);
while (end_isBlockEnd(cap_getEnd(cap2))) {
Segment *segment = cap_getSegment(cap2);
assert(segment != NULL);
assert(segment_get5Cap(segment) == cap2);
cap2 = cap_getAdjacency(segment_get3Cap(segment));
assert(cap2 != NULL);
assert(cap_getStrand(cap2));
assert(cap_getSide(cap2));
}
assert(cap_getStrand(cap2));
assert(cap_getSide(cap2));
int64_t length = cap_getCoordinate(cap2) - cap_getCoordinate(cap) - 1;
assert(length >= 0);
totalLength += length;
}
}
end_destructInstanceIterator(instanceIterator);
}
}
flower_destructEndIterator(endIterator);
return totalLength;
}
Segment *block_getRootInstance(Block *block) {
Cap *cap = end_getRootInstance(block_get5End(block));
return cap != NULL ? cap_getSegment(cap) : NULL;
}