void testBlock_getInstanceNumber(CuTest* testCase) {
cactusBlockTestSetup();
CuAssertTrue(testCase, block_getInstanceNumber(block) == 3);
Block *block2 = block_construct(1, flower);
CuAssertTrue(testCase, block_getInstanceNumber(block2) == 0);
cactusBlockTestTeardown();
}
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);
}
static char *segmentWriteFn(Segment *segment) {
stTree *phylogeneticTree = stHash_search(segmentWriteFn_flowerToPhylogeneticTreeHash, block_getFlower(segment_getBlock(segment)));
assert(phylogeneticTree != NULL);
char *segmentString = getMaximumLikelihoodString(phylogeneticTree, segment_getBlock(segment));
//We append a zero to a segment string if it is part of block containing only a reference segment, else we append a 1.
//We use these boolean values to determine if a sequence contains only these trivial strings, and is therefore trivial.
char *appendedSegmentString = stString_print("%s%c ", segmentString, block_getInstanceNumber(segment_getBlock(segment)) == 1 ? '0' : '1');
free(segmentString);
return appendedSegmentString;
}
void testBlock_splitBlock(CuTest* testCase) {
cactusBlockTestSetup();
Block *leftBlock, *rightBlock;
block_split(block, 2, &leftBlock, &rightBlock);
CuAssertIntEquals(testCase, 2, block_getLength(leftBlock));
CuAssertIntEquals(testCase, 1, block_getLength(rightBlock));
CuAssertIntEquals(testCase, 3, block_getInstanceNumber(leftBlock));
CuAssertIntEquals(testCase, 3, block_getInstanceNumber(rightBlock));
Block *leftLeftBlock, *leftRightBlock;
block_split(leftBlock, 1, &leftLeftBlock, &leftRightBlock);
CuAssertIntEquals(testCase, 1, block_getLength(leftLeftBlock));
CuAssertIntEquals(testCase, 1, block_getLength(leftRightBlock));
CuAssertIntEquals(testCase, 3, block_getInstanceNumber(leftLeftBlock));
CuAssertIntEquals(testCase, 3, block_getInstanceNumber(leftRightBlock));
//doesn't currently check the instances.
cactusBlockTestTeardown();
}
