static stList *getSubstringsForFlowerSegments(stList *flowers) {
/*
* Get the set of substrings representing the strings in the segments of the given flowers.
*/
stList *substrings = stList_construct3(0, (void (*)(void *)) substring_destruct);
for (int64_t i = 0; i < stList_length(flowers); i++) {
Flower *flower = stList_get(flowers, i);
Flower_EndIterator *blockIt = flower_getBlockIterator(flower);
Block *block;
while ((block = flower_getNextBlock(blockIt)) != NULL) {
Block_InstanceIterator *instanceIt = block_getInstanceIterator(block);
Segment *segment;
while ((segment = block_getNext(instanceIt)) != NULL) {
Sequence *sequence;
if ((sequence = segment_getSequence(segment)) != NULL) {
segment = segment_getStrand(segment) ? segment : segment_getReverse(segment);
assert(segment_getLength(segment) > 0);
stList_append(substrings,
substring_construct(sequence_getMetaSequence(sequence)->stringName,
segment_getStart(segment) - sequence_getStart(sequence),
segment_getLength(segment)));
}
}
block_destructInstanceIterator(instanceIt);
}
flower_destructBlockIterator(blockIt);
}
return substrings;
}
static void getReferenceSequences(FILE *fileHandle, Flower *flower, char *referenceEventString){
//get names of all the sequences in 'flower' for event with name 'referenceEventString'
Sequence *sequence;
Flower_SequenceIterator * seqIterator = flower_getSequenceIterator(flower);
while((sequence = flower_getNextSequence(seqIterator)) != NULL)
{
Event* event = sequence_getEvent(sequence);
const char* eventName = event_getHeader(event);
if (strcmp(eventName, referenceEventString) == 0 &&
sequence_getLength(sequence) > 0 &&
!metaSequence_isTrivialSequence(sequence_getMetaSequence(sequence))) {
const char *sequenceHeader = formatSequenceHeader(sequence);
st_logInfo("Sequence %s\n", sequenceHeader);
char *string = sequence_getString(sequence, sequence_getStart(sequence), sequence_getLength(sequence), 1);
fastaWrite(string, (char *)sequenceHeader, fileHandle);
free(string);
}
}
flower_destructSequenceIterator(seqIterator);
return;
}
static stList *getSubstringsForFlowers(stList *flowers) {
/*
* Get the set of substrings for sequence intervals in the given set of flowers.
*/
stList *substrings = stList_construct3(0, (void (*)(void *)) substring_destruct);
for (int64_t i = 0; i < stList_length(flowers); i++) {
Flower *flower = stList_get(flowers, i);
Flower_EndIterator *endIt = flower_getEndIterator(flower);
End *end;
while ((end = flower_getNextEnd(endIt)) != NULL) {
if (end_isStubEnd(end)) {
End_InstanceIterator *instanceIt = end_getInstanceIterator(end);
Cap *cap;
while ((cap = end_getNext(instanceIt)) != NULL) {
Sequence *sequence;
if ((sequence = cap_getSequence(cap)) != NULL) {
cap = cap_getStrand(cap) ? cap : cap_getReverse(cap);
if (!cap_getSide(cap)) { //We have a sequence interval of interest
Cap *adjacentCap = cap_getAdjacency(cap);
assert(adjacentCap != NULL);
int64_t length = cap_getCoordinate(adjacentCap) - cap_getCoordinate(cap) - 1;
assert(length >= 0);
if (length > 0) {
stList_append(substrings,
substring_construct(sequence_getMetaSequence(sequence)->stringName,
cap_getCoordinate(cap) + 1 - sequence_getStart(sequence), length));
}
}
}
}
end_destructInstanceIterator(instanceIt);
}
}
flower_destructEndIterator(endIt);
}
return substrings;
}
