void block_check(Block *block) {
//Check is connected to flower properly
cactusCheck(flower_getBlock(block_getFlower(block), block_getName(block)) == block_getPositiveOrientation(block));
//Check we have actually set built blocks for the flower..
cactusCheck(flower_builtBlocks(block_getFlower(block)));
//Checks the two ends are block ends.
End *_5End = block_get5End(block);
End *_3End = block_get3End(block);
cactusCheck(end_isBlockEnd(_5End));
cactusCheck(end_isBlockEnd(_3End));
cactusCheck(end_getOrientation(_5End) == block_getOrientation(block));
cactusCheck(end_getOrientation(_3End) == block_getOrientation(block));
cactusCheck(end_getBlock(_5End) == block);
cactusCheck(end_getBlock(_3End) == block);
cactusCheck(end_getSide(_5End)); //Check the sides of the ends are consistent.
cactusCheck(!end_getSide(_3End));
cactusCheck(block_getLength(block) > 0); //check block has non-zero length
//Check reverse
Block *rBlock = block_getReverse(block);
cactusCheck(rBlock != NULL);
cactusCheck(block_getReverse(block) == rBlock);
cactusCheck(block_getOrientation(block) == !block_getOrientation(rBlock));
cactusCheck(block_getLength(block) == block_getLength(rBlock));
cactusCheck(block_get5End(block) == end_getReverse(block_get3End(rBlock)));
cactusCheck(block_get3End(block) == end_getReverse(block_get5End(rBlock)));
cactusCheck(block_getInstanceNumber(block) == block_getInstanceNumber(rBlock));
if(block_getInstanceNumber(block) > 0) {
cactusCheck(block_getFirst(block) == segment_getReverse(block_getFirst(rBlock)));
if(block_getRootInstance(block) == NULL) {
cactusCheck(block_getRootInstance(rBlock) == NULL);
}
else {
cactusCheck(block_getRootInstance(block) == segment_getReverse(block_getRootInstance(rBlock)));
}
}
//For each segment calls segment_check.
Block_InstanceIterator *iterator = block_getInstanceIterator(block);
Segment *segment;
while((segment = block_getNext(iterator)) != NULL) {
segment_check(segment);
}
block_destructInstanceIterator(iterator);
}
void testBlock_getRightEnd(CuTest* testCase) {
cactusBlockTestSetup();
End *rightEnd = block_get3End(block);
CuAssertTrue(testCase, rightEnd != NULL);
CuAssertTrue(testCase, end_getBlock(rightEnd) == block);
CuAssertTrue(testCase, block_getOrientation(block) == end_getOrientation(rightEnd));
cactusBlockTestTeardown();
}
void testBlock_getLeftEnd(CuTest* testCase) {
cactusBlockTestSetup();
End *leftEnd = block_get5End(block);
CuAssertTrue(testCase, leftEnd != NULL);
CuAssertTrue(testCase, end_getBlock(leftEnd) == block);
CuAssertTrue(testCase, block_getOrientation(block) == end_getOrientation(leftEnd));
cactusBlockTestTeardown();
}
void testEnd_getBlock(CuTest* testCase) {
cactusEndTestSetup();
Block *block = block_construct(10, flower);
End *leftEnd = block_get5End(block);
End *rightEnd = block_get3End(block);
CuAssertTrue(testCase, end_getBlock(end) == NULL);
CuAssertTrue(testCase, end_getBlock(end_getReverse(end)) == NULL);
CuAssertTrue(testCase, end_getBlock(leftEnd) == block);
CuAssertTrue(testCase, end_getBlock(end_getReverse(leftEnd)) == block_getReverse(block));
CuAssertTrue(testCase, block_getOrientation(block) == end_getOrientation(leftEnd));
CuAssertTrue(testCase, end_getBlock(rightEnd) == block);
CuAssertTrue(testCase, end_getBlock(end_getReverse(rightEnd)) == block_getReverse(block));
CuAssertTrue(testCase, block_getOrientation(block) == end_getOrientation(rightEnd));
cactusEndTestTeardown();
}
void testCap_getOrientation(CuTest* testCase) {
cactusCapTestSetup();
CuAssertTrue(testCase, cap_getOrientation(rootCap) == end_getOrientation(cap_getEnd(rootCap)));
CuAssertTrue(testCase, cap_getOrientation(leaf1Cap) == end_getOrientation(cap_getEnd(leaf1Cap)));
CuAssertTrue(testCase, cap_getOrientation(leaf2Cap) == end_getOrientation(cap_getEnd(leaf2Cap)));
CuAssertTrue(testCase, cap_getOrientation(cap_getReverse(rootCap)) == end_getOrientation(end_getReverse(cap_getEnd(rootCap))));
CuAssertTrue(testCase, cap_getOrientation(cap_getReverse(leaf1Cap)) == end_getOrientation(end_getReverse(cap_getEnd(leaf1Cap))));
CuAssertTrue(testCase, cap_getOrientation(cap_getReverse(leaf2Cap)) == end_getOrientation(end_getReverse(cap_getEnd(leaf2Cap))));
CuAssertTrue(testCase, cap_getOrientation(leaf1Cap) == cap_getOrientation(rootCap));
CuAssertTrue(testCase, cap_getOrientation(leaf1Cap) != cap_getOrientation(leaf2Cap));
cactusCapTestTeardown();
}
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;
}
void testEnd_getOrientation(CuTest* testCase) {
cactusEndTestSetup();
CuAssertTrue(testCase, end_getOrientation(end));
CuAssertTrue(testCase, !end_getOrientation(end_getReverse(end)));
cactusEndTestTeardown();
}