static PointerArray *getNodesMatchingXPath(xmlNode *node, xmlChar *path) {
if (!path)
return NULL;
xmlXPathObject *results_set;
PointerArray *results_array;
xmlNode *result_node;
int n;
// get results
if (node)
CONTEXT->node = node;
results_set = xmlXPathEvalExpression(path, CONTEXT);
if (!results_set)
return NULL;
// put them in the array
results_array = createPointerArray();
if (results_set->nodesetval && results_set->nodesetval->nodeNr > 0) {
for (n=0; n < results_set->nodesetval->nodeNr; n++) {
result_node = results_set->nodesetval->nodeTab[n];
insertPointerIntoArray(results_array, result_node);
}
}
// finish up
xmlXPathFreeObject(results_set);
CONTEXT->node = NULL;
return results_array;
}
SBOLObject* createSBOLObject(Document* doc, const char* uri) {
if (!doc || !uri || isSBOLObjectURI(doc, uri))
return NULL;
SBOLObject* obj = malloc(sizeof(SBOLObject));
obj->uri = createURIProperty(doc);
obj->xml_annotations = createPointerArray();
setSBOLObjectURI(obj, uri);
return obj;
}
Collection* createCollection(Document* doc, const char* uri) {
if (!doc || !uri || isSBOLObjectURI(doc, uri))
return NULL;
Collection* col = malloc(sizeof(Collection));
col->doc = doc;
col->base = createSBOLCompoundObject(doc, uri);
col->components = createPointerArray();
registerCollection(col);
return col;
}
SequenceAnnotation* createSequenceAnnotation(Document* doc, const char* uri) {
if (!doc || !uri || isSBOLObjectURI(doc, uri))
return NULL;
SequenceAnnotation* ann = malloc(sizeof(SequenceAnnotation));
ann->doc = doc;
ann->base = createSBOLObject(doc, uri);
ann->genbankStart = createPositionProperty();
ann->genbankEnd = createPositionProperty();
//ann->strand = 1;
ann->strand = createPolarityProperty();
ann->subComponent = NULL;
ann->precedes = createPointerArray();
registerSequenceAnnotation(ann);
return ann;
}
SequenceAnnotation* copySequenceAnnotation(SequenceAnnotation* ann, char* id_modifier) {
int i;
char* copy_uri = augmentURI(getSequenceAnnotationURI(ann), id_modifier);
SequenceAnnotation* copy = createSequenceAnnotation(ann->doc, copy_uri);
setSequenceAnnotationStart(copy, getSequenceAnnotationStart(ann));
setSequenceAnnotationEnd(copy, getSequenceAnnotationEnd(ann));
setSequenceAnnotationStrand(copy, getSequenceAnnotationStrand(ann));
// Copy precedes property
copy->precedes = createPointerArray();
char *target_uri;
for (i = 0; i < getNumPointersInArray(ann->precedes); i++) {
target_uri = (char *)getNthPointerInArray(ann->precedes, i);
insertPointerIntoArray(copy->precedes, augmentURI(target_uri, id_modifier));
}
// Copy SubComponent tree recursively
if (ann->subComponent) {
char* sub_com_uri = augmentURI(getDNAComponentURI(ann->subComponent), id_modifier);
DNAComponent* sub_com_copy = createDNAComponent(ann->doc, sub_com_uri);
setSequenceAnnotationSubComponent(copy, sub_com_copy);
}
return (SequenceAnnotation *)copy;
}
static void resetProcessed() {
deletePointerArray(PROCESSED);
PROCESSED = createPointerArray();
}
