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);
}
void ExportContext::endElement() {
if(!m_objectStack.size()) {
reportError("endElement(): no object being written.\n");
return;
}
ASSERT(m_elementStack.size());
element_entry& entry = m_elementStack.back();
if(m_state != WRITE_END && m_state != WRITE_CONTENT) {
reportError("endElement(): not allowed.\n");
return;
}
indentLess();
BString out;
// write closing tag
if(!entry.hasContent)
out << "/>";
else
out << "\n" << indentString() << "</" << entry.name.String() << ">";
writeString(out);
// pop element off stack
m_elementStack.pop_back();
}
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);
}
static void writeCollection(Collection* col) {
if (!col)
return;
xmlTextWriterStartElement(WRITER, xmlCharStrdup(NSPREFIX_SBOL ":" NODENAME_COLLECTION));
if (!alreadyProcessed((void *)col)) {
markProcessed((void *)col);
int n;
int num;
// properties
if (getCollectionURI(col))
xmlTextWriterWriteAttribute(WRITER, xmlCharStrdup(NSPREFIX_RDF ":" NODENAME_ABOUT), xmlCharStrdup(getCollectionURI(col)));
if(getCollectionDisplayID(col))
xmlTextWriterWriteElement(WRITER, xmlCharStrdup(NSPREFIX_SBOL ":" NODENAME_DISPLAYID), xmlCharStrdup(getCollectionDisplayID(col)));
if (getCollectionName(col))
xmlTextWriterWriteElement(WRITER, xmlCharStrdup(NSPREFIX_SBOL ":" NODENAME_NAME), xmlCharStrdup(getCollectionName(col)));
if (getCollectionDescription(col))
xmlTextWriterWriteElement(WRITER, xmlCharStrdup(NSPREFIX_SBOL ":" NODENAME_DESCRIPTION), xmlCharStrdup(getCollectionDescription(col)));
// components
DNAComponent* com;
num = getNumDNAComponentsIn(col);
if (num>0) {
indentMore();
for (n=0; n<num; n++) {
xmlTextWriterStartElement(WRITER, xmlCharStrdup(NSPREFIX_SBOL ":" NODENAME_COMPONENT));
com = getNthDNAComponentIn(col, n);
indentMore();
writeDNAComponent(com);
indentLess();
xmlTextWriterEndElement(WRITER);
}
indentLess();
}
} else
xmlTextWriterWriteAttribute(WRITER, xmlCharStrdup(NSPREFIX_RDF ":" NODENAME_RESOURCE), xmlCharStrdup(getCollectionURI(col)));
xmlTextWriterEndElement(WRITER);
}
static void endSBOLDocument() {
indentLess();
xmlTextWriterEndElement(WRITER);
xmlTextWriterEndDocument(WRITER);
}
