static void sequenceSetup() {
metaSequence = metaSequence_construct(0, 10, "ACTGACTGAC", ">one",
event_getName(eventTree_getRootEvent(eventTree)), cactusDisk);
sequence = sequence_construct(metaSequence, flower);
metaSequence2 = metaSequence_construct(0, 10, "ACTGACTGAC", ">two",
event_getName(eventTree_getRootEvent(eventTree)), cactusDisk);
sequence2 = sequence_construct(metaSequence2, flower);
}
static int64_t setCoordinates(Flower *flower, MetaSequence *metaSequence, Cap *cap, int64_t coordinate) {
/*
* Sets the coordinates of the reference thread and sets the bases of the actual sequence
* that of the consensus.
*/
Sequence *sequence = flower_getSequence(flower, metaSequence_getName(metaSequence));
if (sequence == NULL) {
sequence = sequence_construct(metaSequence, flower);
}
while (1) {
assert(cap_getStrand(cap));
assert(!cap_getSide(cap));
Cap *adjacentCap = cap_getAdjacency(cap);
assert(adjacentCap != NULL);
assert(cap_getStrand(adjacentCap));
assert(cap_getSide(adjacentCap));
int64_t adjacencyLength = cap_getCoordinate(cap);
assert(adjacencyLength == cap_getCoordinate(adjacentCap));
assert(adjacencyLength != INT64_MAX);
assert(adjacencyLength >= 0);
cap_setCoordinates(cap, coordinate, 1, sequence);
coordinate += adjacencyLength + 1;
cap_setCoordinates(adjacentCap, coordinate, 1, sequence);
//Traverse any block..
if ((cap = cap_getOtherSegmentCap(adjacentCap)) == NULL) {
break;
}
coordinate += segment_getLength(cap_getSegment(adjacentCap)) - 1;
}
return coordinate;
}
Sequence *sequence_loadFromBinaryRepresentation(void **binaryString, Flower *flower) {
Sequence *sequence;
sequence = NULL;
if(binaryRepresentation_peekNextElementType(*binaryString) == CODE_SEQUENCE) {
binaryRepresentation_popNextElementType(binaryString);
sequence = sequence_construct(cactusDisk_getMetaSequence(flower_getCactusDisk(flower), binaryRepresentation_getName(binaryString)), flower);
}
return sequence;
}
void testEnd_getGroup(CuTest* testCase) {
cactusEndTestSetup();
Flower *flower2 = flower_construct(cactusDisk);
eventTree_copyConstruct(eventTree, flower2, testEnd_copyConstructP);
sequence_construct(metaSequence, flower2);
End *end2 = end_copyConstruct(end, flower2);
CuAssertTrue(testCase, end_getGroup(end) == NULL);
Group *group = group_construct(flower, flower2);
CuAssertTrue(testCase, end_getGroup(end) == group);
CuAssertTrue(testCase, end_getGroup(end2) == NULL);
cactusEndTestTeardown();
}
void testEnd_copyConstruct(CuTest* testCase) {
cactusEndTestSetup();
Flower *flower2 = flower_construct(cactusDisk);
eventTree_copyConstruct(eventTree, flower2, testEnd_copyConstructP);
sequence_construct(metaSequence, flower2);
End *end2 = end_copyConstruct(end, flower2);
CuAssertTrue(testCase, end_getName(end2) != NULL_NAME);
CuAssertTrue(testCase, end_getName(end2) == end_getName(end));
CuAssertTrue(testCase, flower_getEnd(flower2, end_getName(end2)) == end2);
CuAssertTrue(testCase, cap_getName(end_getInstance(end2, cap_getName(rootCap))) == cap_getName(rootCap));
CuAssertTrue(testCase, cap_getName(end_getInstance(end2, cap_getName(leaf1Cap))) == cap_getName(leaf1Cap));
CuAssertTrue(testCase, cap_getName(end_getInstance(end2, cap_getName(leaf2Cap))) == cap_getName(leaf2Cap));
cactusEndTestTeardown();
}
void processSequence(const char *fastaHeader, const char *string, int64_t length) {
/*
* Processes a sequence by adding it to the flower disk.
*/
End *end1;
End *end2;
Cap *cap1;
Cap *cap2;
MetaSequence *metaSequence;
Sequence *sequence;
//Now put the details in a flower.
metaSequence = metaSequence_construct(2, length, string, fastaHeader, event_getName(event), cactusDisk);
sequence = sequence_construct(metaSequence, flower);
end1 = end_construct2(0, isComplete, flower);
end2 = end_construct2(1, isComplete, flower);
cap1 = cap_construct2(end1, 1, 1, sequence);
cap2 = cap_construct2(end2, length + 2, 1, sequence);
cap_makeAdjacent(cap1, cap2);
totalSequenceNumber++;
}
