void testGroup_getChain(CuTest* testCase) {
cactusGroupTestSetup();
CuAssertTrue(testCase, group_getLink(group) == NULL);
Chain *chain = chain_construct(flower);
link_construct(end1, end2, group, chain);
CuAssertTrue(testCase, group_getLink(group) == chain_getFirst(chain));
cactusGroupTestTeardown();
}
void testGroup_getLink(CuTest *testCase) {
cactusGroupTestSetup();
CuAssertTrue(testCase, group_getLink(group2) == NULL);
Chain *chain = setupChain();
CuAssertTrue(testCase, group_getLink(group2) == chain_getFirst(chain));
chain_destruct(chain);
CuAssertTrue(testCase, group_getLink(group2) == NULL);
cactusGroupTestTeardown();
}
Chain *block_getChain(Block *block) {
Link *link;
Chain *chain1, *chain2;
Group *group = end_getGroup(block_get5End(block));
chain1 = (group != NULL && (link = group_getLink(group)) != NULL) ? link_getChain(link) : NULL;
group = end_getGroup(block_get3End(block));
chain2 = (group != NULL && (link = group_getLink(group)) != NULL) ? link_getChain(link) : NULL;
if(chain1 != NULL && chain2 != NULL) {
assert(chain1 == chain2); //block should not be in more than one chain!
}
return chain1 != NULL ? chain1 : chain2;
}
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 testGroup_constructChainForLink(CuTest *testCase) {
cactusGroupTestSetup();
//Create a link group and test function works!
Group *group3 = group_construct2(flower);
End *_5End = end_construct2(1, 1, flower);
End *_3End = end_construct2(0, 1, flower);
End *stubEnd = end_construct2(1, 0, flower);
end_setGroup(_5End, group3);
end_setGroup(_3End, group3);
end_setGroup(stubEnd, group3);
CuAssertTrue(testCase, group_isTangle(group3));
CuAssertTrue(testCase, group_getEndNumber(group3) == 3);
group_constructChainForLink(group3);
CuAssertTrue(testCase, group_isLink(group3));
Link *link = group_getLink(group3);
CuAssertTrue(testCase, link_get5End(link) == _5End);
CuAssertTrue(testCase, link_get3End(link) == _3End);
cactusGroupTestTeardown();
}
int main(int argc, char *argv[]) {
st_setLogLevelFromString(argv[1]);
st_logDebug("Set up logging\n");
stKVDatabaseConf *kvDatabaseConf = stKVDatabaseConf_constructFromString(argv[2]);
CactusDisk *cactusDisk = cactusDisk_construct(kvDatabaseConf, 0);
stKVDatabaseConf_destruct(kvDatabaseConf);
st_logDebug("Set up the flower disk\n");
Name flowerName = cactusMisc_stringToName(argv[3]);
Flower *flower = cactusDisk_getFlower(cactusDisk, flowerName);
int64_t totalBases = flower_getTotalBaseLength(flower);
int64_t totalEnds = flower_getEndNumber(flower);
int64_t totalFreeEnds = flower_getFreeStubEndNumber(flower);
int64_t totalAttachedEnds = flower_getAttachedStubEndNumber(flower);
int64_t totalCaps = flower_getCapNumber(flower);
int64_t totalBlocks = flower_getBlockNumber(flower);
int64_t totalGroups = flower_getGroupNumber(flower);
int64_t totalChains = flower_getChainNumber(flower);
int64_t totalLinkGroups = 0;
int64_t maxEndDegree = 0;
int64_t maxAdjacencyLength = 0;
int64_t totalEdges = 0;
Flower_EndIterator *endIt = flower_getEndIterator(flower);
End *end;
while((end = flower_getNextEnd(endIt)) != NULL) {
assert(end_getOrientation(end));
if(end_getInstanceNumber(end) > maxEndDegree) {
maxEndDegree = end_getInstanceNumber(end);
}
stSortedSet *ends = stSortedSet_construct();
End_InstanceIterator *capIt = end_getInstanceIterator(end);
Cap *cap;
while((cap = end_getNext(capIt)) != NULL) {
if(cap_getSequence(cap) != NULL) {
Cap *adjacentCap = cap_getAdjacency(cap);
assert(adjacentCap != NULL);
End *adjacentEnd = end_getPositiveOrientation(cap_getEnd(adjacentCap));
stSortedSet_insert(ends, adjacentEnd);
int64_t adjacencyLength = cap_getCoordinate(cap) - cap_getCoordinate(adjacentCap);
if(adjacencyLength < 0) {
adjacencyLength *= -1;
}
assert(adjacencyLength >= 1);
if(adjacencyLength >= maxAdjacencyLength) {
maxAdjacencyLength = adjacencyLength;
}
}
}
end_destructInstanceIterator(capIt);
totalEdges += stSortedSet_size(ends);
if(stSortedSet_search(ends, end) != NULL) { //This ensures we count self edges twice, so that the division works.
totalEdges += 1;
}
stSortedSet_destruct(ends);
}
assert(totalEdges % 2 == 0);
flower_destructEndIterator(endIt);
Flower_GroupIterator *groupIt = flower_getGroupIterator(flower);
Group *group;
while((group = flower_getNextGroup(groupIt)) != NULL) {
if(group_getLink(group) != NULL) {
totalLinkGroups++;
}
}
flower_destructGroupIterator(groupIt);
printf("flower name: %" PRIi64 " total bases: %" PRIi64 " total-ends: %" PRIi64 " total-caps: %" PRIi64 " max-end-degree: %" PRIi64 " max-adjacency-length: %" PRIi64 " total-blocks: %" PRIi64 " total-groups: %" PRIi64 " total-edges: %" PRIi64 " total-free-ends: %" PRIi64 " total-attached-ends: %" PRIi64 " total-chains: %" PRIi64 " total-link groups: %" PRIi64 "\n",
flower_getName(flower), totalBases, totalEnds, totalCaps, maxEndDegree, maxAdjacencyLength, totalBlocks, totalGroups, totalEdges/2, totalFreeEnds, totalAttachedEnds, totalChains, totalLinkGroups);
return 0;
}
