static void cactusGroupTestSetup() {
cactusGroupTestTeardown();
cactusDisk = testCommon_getTemporaryCactusDisk();
flower = flower_construct(cactusDisk);
nestedFlower = flower_construct(cactusDisk);
end1 = end_construct2(0, 0, flower);
end2 = end_construct(0, flower);
end3 = end_construct(0, flower);
nestedEnd1 = end_copyConstruct(end1, nestedFlower);
nestedEnd2 = end_copyConstruct(end2, nestedFlower);
group = group_construct(flower, nestedFlower);
group2 = group_construct2(flower);
end4 = end_construct(0, flower);
}
void testBlock_getChain(CuTest* testCase) {
cactusBlockTestSetup();
Block *block2 = block_construct(2, flower);
Flower *flower2 = flower_construct(cactusDisk);
eventTree_copyConstruct(flower_getEventTree(flower), flower2, NULL);
end_copyConstruct(block_get3End(block), flower2);
end_copyConstruct(block_get5End(block2), flower2);
Group *group = group_construct(flower, flower2);
Chain *chain = chain_construct(flower);
link_construct(block_get3End(block), block_get5End(block2), group, chain);
CuAssertTrue(testCase, block_getChain(block_construct(2, flower)) == NULL);
CuAssertTrue(testCase, block_getChain(block) == chain);
CuAssertTrue(testCase, block_getChain(block2) == chain);
cactusBlockTestTeardown();
}
void testGroup_updateContainedEnds(CuTest* testCase) {
cactusGroupTestSetup();
end_copyConstruct(end3, nestedFlower);
CuAssertTrue(testCase, group_getEndNumber(group) == 2);
group_updateContainedEnds(group);
CuAssertTrue(testCase, group_getEndNumber(group) == 3);
CuAssertTrue(testCase, group_getEnd(group, end_getName(end1)) == end1);
CuAssertTrue(testCase, group_getEnd(group, end_getName(end2)) == end2);
CuAssertTrue(testCase, group_getEnd(group, end_getName(end3)) == end3);
cactusGroupTestTeardown();
}
void testEnd_getGroup(CuTest* testCase) {
cactusEndTestSetup();
Flower *flower2 = flower_construct(cactusDisk);
eventTree_copyConstruct(eventTree, flower2, testEnd_copyConstructP);
sequence_construct(metaSequence, flower2);
End *end2 = end_copyConstruct(end, flower2);
CuAssertTrue(testCase, end_getGroup(end) == NULL);
Group *group = group_construct(flower, flower2);
CuAssertTrue(testCase, end_getGroup(end) == group);
CuAssertTrue(testCase, end_getGroup(end2) == NULL);
cactusEndTestTeardown();
}
void testEnd_copyConstruct(CuTest* testCase) {
cactusEndTestSetup();
Flower *flower2 = flower_construct(cactusDisk);
eventTree_copyConstruct(eventTree, flower2, testEnd_copyConstructP);
sequence_construct(metaSequence, flower2);
End *end2 = end_copyConstruct(end, flower2);
CuAssertTrue(testCase, end_getName(end2) != NULL_NAME);
CuAssertTrue(testCase, end_getName(end2) == end_getName(end));
CuAssertTrue(testCase, flower_getEnd(flower2, end_getName(end2)) == end2);
CuAssertTrue(testCase, cap_getName(end_getInstance(end2, cap_getName(rootCap))) == cap_getName(rootCap));
CuAssertTrue(testCase, cap_getName(end_getInstance(end2, cap_getName(leaf1Cap))) == cap_getName(leaf1Cap));
CuAssertTrue(testCase, cap_getName(end_getInstance(end2, cap_getName(leaf2Cap))) == cap_getName(leaf2Cap));
cactusEndTestTeardown();
}
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;
}
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();
}
