void printSequenceAnnotation(const SequenceAnnotation* ann, int tabs) {
if (!ann)
return;
indent(tabs); printf("%s\n", getSequenceAnnotationURI(ann));
//int start = ann->genbankStart;
int start = getSequenceAnnotationStart(ann);
//int end = ann->genbankEnd;
int end = getSequenceAnnotationEnd(ann);
if (start != -1 || end != -1) { /// @todo is 0 valid?
indent(tabs+1); printf("%i --> %i\n", start, end);
}
char strand = polarityToChar( getPolarityProperty(ann->strand) );
indent(tabs+1); printf("strand: %c\n", strand);
if (ann->subComponent) {
indent(tabs+1); printf("subComponent: %s\n", getDNAComponentURI(ann->subComponent));
}
int num = getNumPrecedes(ann);
if (num > 0) {
indent(tabs+1); printf("%i precedes:\n", num);
int i;
for (i=0; i<num; i++) {
indent(tabs+2); printf("%s\n", getSequenceAnnotationURI(getNthPrecedes(ann, i)));
}
}
}
static void writeSequenceAnnotation(SequenceAnnotation* ann) {
if (!ann)
return;
markProcessed((void *)ann);
xmlTextWriterStartElement(WRITER, xmlCharStrdup(NSPREFIX_SBOL ":" NODENAME_SEQUENCEANNOTATION));
xmlTextWriterWriteAttribute(WRITER, xmlCharStrdup(NSPREFIX_RDF ":" NODENAME_ABOUT), xmlCharStrdup(getSequenceAnnotationURI(ann)));
// precedes
int n;
SequenceAnnotation* ann2;
indentMore();
for (n=0; n<getNumPrecedes(ann); n++) {
ann2 = getNthPrecedes(ann, n);
xmlTextWriterStartElement(WRITER, xmlCharStrdup(NSPREFIX_SBOL ":" NODENAME_PRECEDES));
xmlTextWriterWriteAttribute(WRITER, xmlCharStrdup(NSPREFIX_RDF ":" NODENAME_RESOURCE), xmlCharStrdup(getSequenceAnnotationURI(ann2)));
xmlTextWriterEndElement(WRITER);
}
indentLess();
// start, end
int start = getSequenceAnnotationStart(ann);
int end = getSequenceAnnotationEnd(ann);
if (start>0)
xmlTextWriterWriteElement(WRITER, xmlCharStrdup(NSPREFIX_SBOL ":" NODENAME_BIOSTART), xmlCharStrdup(intToStr(start)));
if (end>0)
xmlTextWriterWriteElement(WRITER, xmlCharStrdup(NSPREFIX_SBOL ":" NODENAME_BIOEND), xmlCharStrdup(intToStr(end)));
// subComponent
char* uri;
indentMore();
if (ann->subComponent) {
uri = getDNAComponentURI(ann->subComponent);
xmlTextWriterStartElement(WRITER, xmlCharStrdup(NSPREFIX_SBOL ":" NODENAME_SUBCOMPONENT));
if (alreadyProcessed((void *)(ann->subComponent)))
xmlTextWriterWriteAttribute(WRITER, xmlCharStrdup(NSPREFIX_RDF ":" NODENAME_RESOURCE), xmlCharStrdup(uri));
else {
indentMore();
writeDNAComponent(ann->subComponent);
indentLess();
}
xmlTextWriterEndElement(WRITER);
}
indentLess();
xmlTextWriterEndElement(WRITER);
}
void printCollection(const Collection* col, int tabs) {
if (!col)
return;
indent(tabs); printf("%s\n", getCollectionURI(col));
indent(tabs+1); printf("name: %s\n", getCollectionName(col));
indent(tabs+1); printf("description: %s\n", getCollectionDescription(col));
int i;
int num;
if (col->components) {
DNAComponent* com;
num = getNumDNAComponentsIn(col);
if (num > 0) {
indent(tabs+1); printf("%i components:\n", num);
for (i=0; i<num; i++) {
com = getNthDNAComponentIn(col, i);
indent(tabs+2); printf("%s\n", getDNAComponentURI(com));
}
}
}
}
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 writeDNAComponent(DNAComponent* com) {
if (!com)
return;
xmlTextWriterStartElement(WRITER, xmlCharStrdup(NSPREFIX_SBOL ":" NODENAME_DNACOMPONENT));
if (!alreadyProcessed((void *)com)) {
markProcessed((void *)com);
xmlTextWriterWriteAttribute(WRITER, xmlCharStrdup(NSPREFIX_RDF ":" NODENAME_ABOUT), xmlCharStrdup(getDNAComponentURI(com)));
// properties
char* data;
data = getDNAComponentDisplayID(com);
if (data)
xmlTextWriterWriteElement(WRITER, xmlCharStrdup(NSPREFIX_SBOL ":" NODENAME_DISPLAYID), xmlCharStrdup(data));
data = getDNAComponentName(com);
if (data)
xmlTextWriterWriteElement(WRITER, xmlCharStrdup(NSPREFIX_SBOL ":" NODENAME_NAME), xmlCharStrdup(data));
data = getDNAComponentDescription(com);
if (data)
xmlTextWriterWriteElement(WRITER, xmlCharStrdup(NSPREFIX_SBOL ":" NODENAME_DESCRIPTION), xmlCharStrdup(data));
data = getDNAComponentType(com);
if (data) {
xmlTextWriterStartElement(WRITER, xmlCharStrdup(NSPREFIX_RDF ":" NODENAME_TYPE));
xmlTextWriterWriteAttribute(WRITER, xmlCharStrdup(NSPREFIX_RDF ":" NODENAME_RESOURCE), xmlCharStrdup(data));
xmlTextWriterEndElement(WRITER);
}
// sequence
if (com->dnaSequence) {
xmlTextWriterStartElement(WRITER, xmlCharStrdup(NSPREFIX_SBOL ":" NODENAME_DNASEQUENCE_REF));
indentMore();
/// @todo sometimes no contents?
writeDNASequence(com->dnaSequence);
markProcessed(com->dnaSequence);
indentLess();
xmlTextWriterEndElement(WRITER);
}
// annotations
int n;
int num = getNumSequenceAnnotationsFor(com);
SequenceAnnotation* ann;
indentMore();
if (num>0) {
for (n=0; n<num; n++) {
ann = getNthSequenceAnnotationFor(com, n);
indentMore();
xmlTextWriterStartElement(WRITER, xmlCharStrdup(NSPREFIX_SBOL ":" NODENAME_ANNOTATION));
writeSequenceAnnotation(ann);
xmlTextWriterEndElement(WRITER);
indentLess();
}
}
indentLess();
} else
xmlTextWriterWriteAttribute(WRITER, xmlCharStrdup(NSPREFIX_RDF ":" NODENAME_RESOURCE), xmlCharStrdup(getDNAComponentURI(com)));
xmlTextWriterEndElement(WRITER);
}
