void testEnd_isAttachedOrFree(CuTest* testCase) {
cactusEndTestSetup();
End *end2 = end_construct(1, flower);
End *end3 = end_construct(0, flower);
Block *block = block_construct(2, flower);
End *end4 = block_get5End(block);
End *end5 = block_get3End(block);
CuAssertTrue(testCase, end_isAttached(end2));
CuAssertTrue(testCase, !end_isAttached(end3));
CuAssertTrue(testCase, !end_isFree(end2));
CuAssertTrue(testCase, end_isFree(end3));
CuAssertTrue(testCase, !end_isAttached(end4));
CuAssertTrue(testCase, !end_isAttached(end5));
CuAssertTrue(testCase, end_isFree(end4));
CuAssertTrue(testCase, end_isFree(end5));
cactusEndTestTeardown();
}
int64_t flower_getFreeStubEndNumber(Flower *flower) {
End *end;
Flower_EndIterator *iterator = flower_getEndIterator(flower);
int64_t i = 0;
while ((end = flower_getNextEnd(iterator)) != NULL) {
if (end_isStubEnd(end) && end_isFree(end)) {
i++;
}
}
flower_destructEndIterator(iterator);
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;
}
