void testGroup_serialisation(CuTest* testCase) {
cactusGroupTestSetup();
int64_t i;
Name name = group_getName(group);
void
*vA =
binaryRepresentation_makeBinaryRepresentation(group,
(void(*)(void *, void(*)(const void *, size_t,
size_t))) group_writeBinaryRepresentation,
&i);
CuAssertTrue(testCase, i > 0);
group_destruct(group);
void *vA2 = vA;
group = group_loadFromBinaryRepresentation(&vA2, flower);
free(vA);
CuAssertTrue(testCase, group_getName(group) == name);
CuAssertTrue(testCase, group_getFlower(group) == flower);
CuAssertTrue(testCase, group_getNestedFlower(group) == nestedFlower);
Group_EndIterator *iterator = group_getEndIterator(group);
CuAssertTrue(testCase, group_getNextEnd(iterator) == end1);
CuAssertTrue(testCase, group_getNextEnd(iterator) == end2);
CuAssertTrue(testCase, group_getNextEnd(iterator) == NULL);
group_destructEndIterator(iterator);
cactusGroupTestTeardown();
}
void sequence_check(Sequence *sequence) {
Flower *flower = sequence_getFlower(sequence);
cactusCheck(flower_getSequence(flower, sequence_getName(sequence)) == sequence); //properly connected to the flower..
Group *parentGroup = flower_getParentGroup(flower);
if(parentGroup != NULL) {
Flower *parentFlower = group_getFlower(parentGroup);
Sequence *parentSequence = flower_getSequence(parentFlower, sequence_getName(sequence));
if(parentSequence != NULL) {
cactusCheck(event_getName(sequence_getEvent(sequence)) == event_getName(sequence_getEvent(parentSequence)));
}
}
}
bool flower_removeIfRedundant(Flower *flower) {
if (!flower_isLeaf(flower) && flower_getParentGroup(flower) != NULL && flower_getBlockNumber(flower) == 0) { //We will remove this flower..
Group *parentGroup = flower_getParentGroup(flower); //This group will be destructed
//Deal with any parent chain..
if (group_isLink(parentGroup)) {
link_split(group_getLink(parentGroup));
}
Flower *parentFlower = group_getFlower(parentGroup); //We will add the groups in the flower to the parent
/*
* For each group in the flower we take its nested flower and attach it to the parent.
*/
Group *group;
Flower_GroupIterator *groupIt = flower_getGroupIterator(flower);
while ((group = flower_getNextGroup(groupIt)) != NULL) {
if (!group_isLeaf(group)) {
//Copy the group into the parent..
Flower *nestedFlower = group_getNestedFlower(group);
assert(nestedFlower != NULL);
Group *newParentGroup = group_construct(parentFlower, nestedFlower);
flower_setParentGroup(nestedFlower, newParentGroup);
group_constructChainForLink(newParentGroup);
} else {
Group *newParentGroup = group_construct2(parentFlower);
End *end;
Group_EndIterator *endIt = group_getEndIterator(group);
while ((end = group_getNextEnd(endIt)) != NULL) {
End *parentEnd = flower_getEnd(parentFlower, end_getName(end));
assert(parentEnd != NULL);
end_setGroup(parentEnd, newParentGroup);
}
group_destructEndIterator(endIt);
group_constructChainForLink(newParentGroup);
}
}
flower_destructGroupIterator(groupIt);
//The group attached to the flower should now be empty
assert(group_getEndNumber(parentGroup) == 0);
group_destruct(parentGroup);
//Now wipe the flower out..
cactusDisk_deleteFlowerFromDisk(flower_getCactusDisk(flower), flower);
flower_destruct(flower, 0);
return 1;
}
return 0;
}
void event_check(Event *event) {
EventTree *eventTree = event_getEventTree(event);
Event *ancestorEvent = event_getParent(event);
//Check event and eventree properly linked
cactusCheck(eventTree_getEvent(event_getEventTree(event), event_getName(event)) == event);
//Event has parent, unless it is root.
if (eventTree_getRootEvent(eventTree) == event) {
cactusCheck(ancestorEvent == NULL);
} else { //not root, so must have ancestor.
cactusCheck(ancestorEvent != NULL);
}
//Each child event has event as parent.
int64_t i = 0;
for (i = 0; i < event_getChildNumber(event); i++) {
Event *childEvent = event_getChild(event, i);
cactusCheck(event_getParent(childEvent) == event);
}
//Ancestor-event --> event edge is consistent with any event tree that is in the parent of the containing flower.
Group *parentGroup = flower_getParentGroup(eventTree_getFlower(
event_getEventTree(event)));
if (parentGroup != NULL) {
EventTree *parentEventTree = flower_getEventTree(group_getFlower(
parentGroup));
Event *parentEvent = eventTree_getEvent(parentEventTree, event_getName(
event));
if (parentEvent != NULL) {
if (ancestorEvent == NULL) { //the case where they are both root.
cactusCheck(eventTree_getRootEvent(parentEventTree) == parentEvent);
} else {
//Check edge ancestorEvent --> event is in parent event tree.
while (1) {
Event *parentAncestorEvent = eventTree_getEvent(
parentEventTree, event_getName(ancestorEvent));
if (parentAncestorEvent != NULL) {
cactusCheck(event_isAncestor(parentEvent, parentAncestorEvent));
break;
}
ancestorEvent = event_getParent(ancestorEvent);
cactusCheck(ancestorEvent != NULL);
}
}
}
}
}
static Cap *copyCapToParent(Cap *cap, stList *recoveredCaps) {
/*
* Get the adjacent stub end by looking at the reference adjacency in the parent.
*/
End *end = cap_getEnd(cap);
assert(end != NULL);
Group *parentGroup = flower_getParentGroup(end_getFlower(end));
assert(parentGroup != NULL);
End *copiedEnd = end_copyConstruct(end, group_getFlower(parentGroup));
end_setGroup(copiedEnd, parentGroup); //Set group
Cap *copiedCap = end_getInstance(copiedEnd, cap_getName(cap));
assert(copiedCap != NULL);
copiedCap = cap_getStrand(copiedCap) ? copiedCap : cap_getReverse(copiedCap);
if (!cap_getSide(copiedCap)) {
stList_append(recoveredCaps, copiedCap);
}
return copiedCap;
}
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;
}
void testGroup_getFlower(CuTest* testCase) {
cactusGroupTestSetup();
CuAssertTrue(testCase, group_getFlower(group) == flower);
cactusGroupTestTeardown();
}
void flower_setParentGroup(Flower *flower, Group *group) {
//assert(flower->parentFlowerName == NULL_NAME); we can change this if merging the parent flowers, so this no longer applies.
flower->parentFlowerName = flower_getName(group_getFlower(group));
}
void testFlower_removeIfRedundant(CuTest *testCase) {
/*
* Do a simple test to see if function can remove a redundant flower.
*/
cactusFlowerTestSetup();
endsSetup();
//First construct a redundant flower from the root.
Flower *flower2 = flower_construct(cactusDisk);
Group *group = group_construct(flower, flower2);
end_setGroup(end, group);
end_setGroup(end2, group);
//Now hang another couple of flowers of that.
Flower *flower3 = flower_construct(cactusDisk);
group_construct(flower2, flower3);
//Now hang another flower of that.
Group *group3b = group_construct2(flower2);
//Finally hang one more flower on the end..
Flower *flower4 = flower_construct(cactusDisk);
group_construct(flower3, flower4);
//Copy the ends into the flowers.
end_copyConstruct(end, flower2);
end_copyConstruct(end2, flower2);
end_copyConstruct(end, flower3);
end_setGroup(flower_getEnd(flower2, end_getName(end2)), group3b);
end_copyConstruct(end, flower4);
//st_uglyf("I got %" PRIi64 " %" PRIi64 " %" PRIi64 " %" PRIi64 "\n", flower_getName(flower), flower_getName(flower2), flower_getName(flower3), flower_getName(flower4));
//Write the mess to disk.
cactusDisk_write(cactusDisk);
//Now test the removal function (check we get a negative on this leaf).
CuAssertTrue(testCase, !flower_removeIfRedundant(flower4));
//Check we can't remove the root..
CuAssertTrue(testCase, !flower_removeIfRedundant(flower));
//We will remove flower2
//Before
CuAssertTrue(testCase, flower_getGroupNumber(flower) == 1);
CuAssertTrue(testCase, group_getFlower(flower_getParentGroup(flower2)) == flower);
CuAssertTrue(testCase, flower_removeIfRedundant(flower2));
//After, check the flower/group connections
CuAssertTrue(testCase, flower_getGroupNumber(flower) == 2);
CuAssertTrue(testCase, !flower_isLeaf(flower));
CuAssertTrue(testCase, group_getFlower(flower_getParentGroup(flower3)) == flower);
group3b = end_getGroup(end2);
CuAssertTrue(testCase, group_getFlower(group3b) == flower);
CuAssertTrue(testCase, group_isLeaf(group3b));
CuAssertTrue(testCase, flower_getGroup(flower, flower_getName(flower3)) == flower_getParentGroup(flower3));
//Check the ends..
CuAssertTrue(testCase, flower_getEndNumber(flower) == 2);
CuAssertTrue(testCase, flower_getEndNumber(flower3) == 1);
CuAssertTrue(testCase, group_getEndNumber(group3b) == 1);
CuAssertTrue(testCase, end_getGroup(end) == flower_getParentGroup(flower3));
CuAssertTrue(testCase, end_getGroup(end2) == group3b);
CuAssertTrue(testCase, flower_getEnd(flower3, end_getName(end)) != NULL);
//Check the child of 3 is still okay..
CuAssertTrue(testCase, group_getFlower(flower_getParentGroup(flower4)) == flower3);
//Now do removal of flower3
CuAssertTrue(testCase, !flower_removeIfRedundant(flower));
CuAssertTrue(testCase, !flower_removeIfRedundant(flower4));
CuAssertTrue(testCase, flower_removeIfRedundant(flower3));
//Check groups again
CuAssertTrue(testCase, flower_getGroupNumber(flower) == 2);
CuAssertTrue(testCase, !flower_isLeaf(flower));
CuAssertTrue(testCase, group_getFlower(flower_getParentGroup(flower4)) == flower);
CuAssertTrue(testCase, group_getFlower(group3b) == flower);
CuAssertTrue(testCase, flower_getGroup(flower, flower_getName(flower4)) == flower_getParentGroup(flower4));
//Check the ends again..
CuAssertTrue(testCase, flower_getEndNumber(flower) == 2);
CuAssertTrue(testCase, flower_getEndNumber(flower4) == 1);
CuAssertTrue(testCase, group_getEndNumber(group3b) == 1);
CuAssertTrue(testCase, end_getGroup(end) == flower_getParentGroup(flower4));
CuAssertTrue(testCase, end_getGroup(end2) == group3b);
CuAssertTrue(testCase, flower_getEnd(flower4, end_getName(end)) != NULL);
cactusFlowerTestTeardown();
}
