void block_setRootInstance(Block *block, Segment *segment) {
block = block_getPositiveOrientation(block);
segment = segment_getPositiveOrientation(segment);
assert(block_getInstance(block, segment_getName(segment)) == segment);
end_setRootInstance(block_get5End(block), segment_get5Cap(segment));
end_setRootInstance(block_get3End(block), segment_get3Cap(segment));
}
void testBlock_serialisation(CuTest* testCase) {
cactusBlockTestSetup();
Name rootInstanceName = segment_getName(rootSegment);
Name leaf1InstanceName = segment_getName(leaf1Segment);
Name leaf2InstanceName = segment_getName(leaf2Segment);
int64_t i;
void
*vA =
binaryRepresentation_makeBinaryRepresentation(block,
(void(*)(void *, void(*)(const void *, size_t,
size_t))) block_writeBinaryRepresentation,
&i);
CuAssertTrue(testCase, i > 0);
block_destruct(block);
void *vA2 = vA;
block = block_loadFromBinaryRepresentation(&vA2, flower);
rootSegment
= segment_getReverse(block_getInstance(block, rootInstanceName));
leaf1Segment = block_getInstance(block, leaf1InstanceName);
leaf2Segment = segment_getReverse(block_getInstance(block,
leaf2InstanceName));
free(vA);
nestedTest = 1;
testBlock_getName(testCase);
testBlock_getOrientation(testCase);
testBlock_getReverse(testCase);
testBlock_getLength(testCase);
testBlock_getFlower(testCase);
testBlock_getLeftEnd(testCase);
testBlock_getRightEnd(testCase);
testBlock_getSetRootInstance(testCase);
testBlock_getInstanceNumber(testCase);
testBlock_getInstance(testCase);
testBlock_getFirst(testCase);
testBlock_instanceIterator(testCase);
testBlock_makeNewickString(testCase);
testBlock_getChain(testCase);
testBlock_getSegmentForEvent(testCase);
nestedTest = 0;
cactusBlockTestTeardown();
}
void testBlock_getInstance(CuTest* testCase) {
cactusBlockTestSetup();
CuAssertTrue(testCase, block_getInstance(block, segment_getName(rootSegment)) == segment_getReverse(rootSegment));
CuAssertTrue(testCase, block_getInstance(block, segment_getName(leaf1Segment)) == leaf1Segment);
CuAssertTrue(testCase, block_getInstance(block, segment_getName(leaf2Segment)) == segment_getReverse(leaf2Segment));
CuAssertTrue(testCase, block_getInstance(block_getReverse(block), segment_getName(rootSegment)) == rootSegment);
CuAssertTrue(testCase, block_getInstance(block_getReverse(block), segment_getName(leaf1Segment)) == segment_getReverse(leaf1Segment));
CuAssertTrue(testCase, block_getInstance(block_getReverse(block), segment_getName(leaf2Segment)) == leaf2Segment);
cactusBlockTestTeardown();
}
char *block_makeNewickStringP(Segment *segment, bool includeInternalNames, bool includeUnaryEvents) {
if(!includeUnaryEvents && segment_getChildNumber(segment) == 1) {
return block_makeNewickStringP(segment_getChild(segment, 0), includeInternalNames, includeUnaryEvents);
}
if(segment_getChildNumber(segment) > 0) {
char *left = stString_print("(");
int64_t i;
bool comma = 0;
for(i=0; i<segment_getChildNumber(segment); i++) {
Segment *childSegment = segment_getChild(segment, i);
char *cA = block_makeNewickStringP(childSegment, includeInternalNames, includeUnaryEvents);
char *cA2 = stString_print(comma ? "%s,%s" : "%s%s", left, cA);
free(cA);
left = cA2;
comma = 1;
}
char *final = includeInternalNames ?
stString_print("%s)%s", left, cactusMisc_nameToStringStatic(segment_getName(segment))) :
stString_print("%s)", left);
free(left);
return final;
}
int blockConstruct_constructP(const void *o1, const void *o2) {
return cactusMisc_nameCompare(segment_getName((Segment *)o1), segment_getName((Segment *)o2));
}
static int flower_constructSegmentsP(const void *o1, const void *o2) {
return cactusMisc_nameCompare(segment_getName((Segment *) o1), segment_getName((Segment *) o2));
}
