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 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);
}
}
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 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 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;
}
}
void removePrecedesRelationship(SequenceAnnotation* upstream, SequenceAnnotation* downstream) {
if (upstream && downstream) {
char *target_uri = getSequenceAnnotationURI(downstream);
char *query_uri;
int FOUND = 0; // found URI in list of URIs
int EOL = 0; // end of list
int i_uri = 0; // index of URI in list
while (!FOUND && !EOL) {
query_uri = (char *)getNthPointerInArray(upstream->precedes, i_uri);
if (strcmp(query_uri, target_uri) == 0) {
FOUND++;
removePointerFromArray(upstream->precedes, i_uri);
}
i_uri++;
if (i_uri == getNumPointersInArray(upstream->precedes)) {
EOL++;
}
}
}
return;
}
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 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);
}
}
int getNumPrecedes(const SequenceAnnotation* ann) {
if (ann && ann->precedes)
return getNumPointersInArray(ann->precedes);
else
return 0;
}
int getNumDNAComponentsIn(const Collection* col) {
if (col)
return getNumPointersInArray(col->components);
else
return -1;
}
int getNumStructuredAnnotations(SBOLObject* obj) {
return getNumPointersInArray(obj->xml_annotations);
}
