static void readSequenceAnnotationReferences(xmlNode *node) {
SequenceAnnotation *ann;
xmlChar *path;
xmlChar *ann_uri;
xmlChar *ref_uri;
xmlNode *ref_node;
PointerArray *results;
int n;
// get SequenceAnnotation
ann_uri = getNodeURI(node);
ann = getSequenceAnnotation(DESTINATION, (char *)ann_uri);
xmlFree(ann_uri);
// add subComponent
path = BAD_CAST "./" NSPREFIX_SBOL ":" NODENAME_SUBCOMPONENT
"/" NSPREFIX_SBOL ":" NODENAME_DNACOMPONENT;
if ((ref_uri = getURIOfNodeMatchingXPath(node, path))) {
setSequenceAnnotationSubComponent(ann, getDNAComponent(DESTINATION, (char *)ref_uri));
xmlFree(ref_uri);
}
// add precedes
path = BAD_CAST "./" NSPREFIX_SBOL ":" NODENAME_PRECEDES;
if ((results = getNodesMatchingXPath(node, path))) {
for (n=0; n<getNumPointersInArray(results); n++) {
ref_node = (xmlNode *) getNthPointerInArray(results, n);
ref_uri = getNodeURI(ref_node);
addPrecedesRelationship(ann, getSequenceAnnotation(DESTINATION, (char *)ref_uri));
xmlFree(ref_uri);
}
deletePointerArray(results);
}
}
static void readCollectionReferences(xmlNode *node) {
Collection *col;
xmlChar *path;
xmlChar *col_uri;
xmlChar *ref_uri;
PointerArray *ref_nodes;
xmlNode *ref_node;
int n;
// get Collection
col_uri = getNodeURI(node);
col = getCollection(DESTINATION, (char *)col_uri);
xmlFree(col_uri);
// add components
path = BAD_CAST "./" NSPREFIX_SBOL ":" NODENAME_COMPONENT
"/" NSPREFIX_SBOL ":" NODENAME_DNACOMPONENT;
if ((ref_nodes = getNodesMatchingXPath(node, path))) {
for (n=0; n<getNumPointersInArray(ref_nodes); n++) {
ref_node = (xmlNode *) getNthPointerInArray(ref_nodes, n);
ref_uri = getNodeURI(ref_node);
addDNAComponentToCollection(col, getDNAComponent(DESTINATION, (char *)ref_uri));
xmlFree(ref_uri);
}
deletePointerArray(ref_nodes);
}
}
static xmlNode *getSingleNodeMatchingXPath(xmlNode *node, xmlChar *path) {
PointerArray *results_array = getNodesMatchingXPath(node, path);
if (!results_array)
return NULL;
else if (getNumPointersInArray(results_array) == 0) {
deletePointerArray(results_array);
return NULL;
} else {
if (getNumPointersInArray(results_array) > 1) {
#ifdef SBOL_DEBUG_STATEMENTS
printf("Got too many nodes matching xpath %s\n", (char *)path);
#endif
}
xmlNode *result = getNthPointerInArray(results_array, 0);
deletePointerArray(results_array);
return result;
}
}
static void cleanupSBOLWriter() {
xmlFreeTextWriter(WRITER);
xmlFreeDoc(OUTPUT);
WRITER = NULL;
OUTPUT = NULL;
deletePointerArray(PROCESSED);
PROCESSED = NULL;
xmlCleanupParser();
}
static void applyFunctionToNodesMatchingXPath(void (*fn)(xmlNode *), xmlNode *node, xmlChar *path) {
if (!path)
return;
PointerArray *results = getNodesMatchingXPath(node, path);
if (results) {
if (getNumPointersInArray(results) > 0) {
int n;
for (n=0; n<getNumPointersInArray(results); n++)
fn(getNthPointerInArray(results, n));
}
deletePointerArray(results);
}
}
void deleteSBOLObject(SBOLObject* obj) {
if (obj) {
if (obj->uri) {
deleteURIProperty(obj->uri);
obj->uri = NULL;
}
if (obj->xml_annotations) {
/// @todo free xmlNodes contained in PointerArray
deletePointerArray(obj->xml_annotations);
}
//free(obj); /// @todo what's wrong with this?
obj = NULL;
}
}
void deleteCollection(Collection* col) {
if (col) {
if (col->base) {
deleteSBOLCompoundObject(col->base);
col->base = NULL;
}
if (col->components) {
deletePointerArray(col->components);
col->components = NULL;
}
if (col->doc) {
removeCollection(col->doc, col);
col->doc = NULL;
}
free(col);
col = NULL;
}
}
void deleteSequenceAnnotation(SequenceAnnotation* ann) {
if (ann) {
if (ann->base)
deleteSBOLObject(ann->base);
ann->base = NULL;
if (ann->subComponent)
ann->subComponent = NULL;
if (ann->precedes) {
deletePointerArray(ann->precedes);
ann->precedes = NULL; // TODO needed?
}
if (ann->doc) {
removeSequenceAnnotation(ann->doc, ann);
ann->doc = NULL;
}
free(ann);
ann = NULL;
}
}
static void readDNAComponentReferences(xmlNode *node) {
DNAComponent *com;
xmlChar *path;
xmlChar *com_uri;
xmlChar *ref_uri;
PointerArray *ref_nodes;
xmlNode *ref_node;
int n;
// get DNAComponent
com_uri = getNodeURI(node);
com = getDNAComponent(DESTINATION, (char *)com_uri);
xmlFree(com_uri);
// add sequence
path = BAD_CAST "./" NSPREFIX_SBOL ":" NODENAME_DNASEQUENCE_REF
"/" NSPREFIX_SBOL ":" NODENAME_DNASEQUENCE;
if ((ref_uri = getURIOfNodeMatchingXPath(node, path))) {
setDNAComponentSequence(com, getDNASequence(DESTINATION, (char *)ref_uri));
xmlFree(ref_uri);
}
// add annotations
path = BAD_CAST "./" NSPREFIX_SBOL ":" NODENAME_ANNOTATION
"/" NSPREFIX_SBOL ":" NODENAME_SEQUENCEANNOTATION;
if ((ref_nodes = getNodesMatchingXPath(node, path))) {
for (n=0; n<getNumPointersInArray(ref_nodes); n++) {
ref_node = (xmlNode *) getNthPointerInArray(ref_nodes, n);
ref_uri = getNodeURI(ref_node);
addSequenceAnnotation(com, getSequenceAnnotation(DESTINATION, (char *)ref_uri));
xmlFree(ref_uri);
}
deletePointerArray(ref_nodes);
}
}
static void resetProcessed() {
deletePointerArray(PROCESSED);
PROCESSED = createPointerArray();
}
