void testBlock_getName(CuTest* testCase) {
cactusBlockTestSetup();
CuAssertTrue(testCase, block_getName(block) != NULL_NAME);
CuAssertTrue(testCase, flower_getBlock(flower, block_getName(block)) == block);
CuAssertTrue(testCase, block_getName(block) == block_getName(block_getReverse(block)));
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 int flower_constructBlocksP(const void *o1, const void *o2) {
return cactusMisc_nameCompare(block_getName((Block *) o1), block_getName((Block *) o2));
}
void mapBlockToExon(Cap *cap, int level, FILE *fileHandle){
fprintf(fileHandle, "\t\t\t<block>\n");
Block *block = end_getBlock(cap_getEnd(cap));
Chain *chain = block_getChain(block);
int start = cap_getCoordinate(cap);
int end = cap_getCoordinate(cap_getOtherSegmentCap(cap)) +1;
fprintf(fileHandle, "\t\t\t\t<blockName>%s</blockName>\n", cactusMisc_nameToString(block_getName(block)));
if(chain != NULL){
fprintf(fileHandle, "\t\t\t\t<chainName>%s</chainName>\n", cactusMisc_nameToString(chain_getName(chain)));
}else{
fprintf(fileHandle, "\t\t\t\t<chainName>NA</chainName>\n");
}
fprintf(fileHandle, "\t\t\t\t<level>%d</level>\n", level);
fprintf(fileHandle, "\t\t\t\t<start>%d</start>\n", start);
fprintf(fileHandle, "\t\t\t\t<end>%d</end>\n", end);
fprintf(fileHandle, "\t\t\t</block>\n");
st_logInfo("mapBlockToExon: start: %d, end: %d\n", start, end);
}
