void insertAnnotationAfter(SequenceAnnotation* upstream, SequenceAnnotation* new_annotation) {
// Update start and end of annotation
int insert_size = strlen(getDNASequenceNucleotides(getDNAComponentSequence(getSequenceAnnotationSubComponent(new_annotation))));
int insertion_site = getPositionProperty(upstream->genbankEnd) + 1;
setSequenceAnnotationStart(new_annotation, insertion_site);
setSequenceAnnotationEnd(new_annotation, insertion_site + insert_size - 1);
// Update precedes relationship of annotations
SequenceAnnotation* downstream = NULL;
if (getNumPointersInArray(upstream->precedes) > 0) {
downstream = getNthPrecedes(upstream, 0);
removePrecedesRelationship(upstream, downstream);
addPrecedesRelationship(upstream, new_annotation);
addPrecedesRelationship(new_annotation, downstream);
upstream = new_annotation;
// Update all start and end indices for annotations downstream from insertion
int old_start, old_end = 0;
int new_start = 0;
int new_end = 0;
while (getNumPointersInArray(upstream->precedes) > 0) {
downstream = getNthPrecedes(upstream, 0);
old_start = getPositionProperty(downstream->genbankStart);
old_end = getPositionProperty(downstream->genbankEnd);
new_start = old_start + insert_size;
new_end = old_end + insert_size;
setPositionProperty(downstream->genbankStart, new_start);
setPositionProperty(downstream->genbankEnd, new_end);
upstream = downstream;
}
}
}
static void writeDNASequence(DNASequence* seq) {
if (!seq)
return;
xmlTextWriterStartElement(WRITER, xmlCharStrdup(NSPREFIX_SBOL ":" NODENAME_DNASEQUENCE));
xmlTextWriterWriteAttribute(WRITER, xmlCharStrdup(NSPREFIX_RDF ":" NODENAME_ABOUT), xmlCharStrdup(getDNASequenceURI(seq)));
// nucleotides
if (!alreadyProcessed((void *)seq)) {
char* nt = getDNASequenceNucleotides(seq);
if (nt) {
xmlTextWriterWriteElement(WRITER, xmlCharStrdup(NSPREFIX_SBOL ":" NODENAME_NUCLEOTIDES), xmlCharStrdup(nt));
markProcessed((void *)seq);
}
free(nt);
}
xmlTextWriterEndElement(WRITER);
}
