bool AbstractTwoLevelAgreement::readAnnotations() {
annotatedGraph=newGraph(true);
if (!readAnnotation(fileName+".tags",tags,annotatedGraph)){
_error << "Annotation File does not exist\n";
QFile file(QString("%1.tags").arg(fileName).toStdString().data());
if (file.open(QIODevice::WriteOnly)) {
QDataStream out(&file); // we will serialize the data into the file
out << outputList;
generatedGraph->writeToStream(out);;
file.close();
_error << "Annotation File has been written from current detected expressions, Correct it before use.\n";
}
return false;
}
return true;
}
unique_ptr<SpanTree> AnnotationDeserializer::readSpanTree() {
VespaDocumentDeserializer deserializer(_repo, _stream, _version);
StringFieldValue tree_name;
deserializer.read(tree_name);
_nodes.clear();
SpanNode::UP root = readSpanNode();
unique_ptr<SpanTree> span_tree(new SpanTree(tree_name.getValue(), std::move(root)));
uint32_t annotation_count = getInt1_2_4Bytes(_stream);
span_tree->reserveAnnotations(annotation_count);
for (uint32_t i = 0; i < annotation_count; ++i) {
readAnnotation(span_tree->annotation(i));
}
return span_tree;
}
void SwissProtPlainTextFormat::readAnnotations(ParserState *st, int offset){
st->si.setDescription(tr("Reading annotations %1").arg(st->entry->name));
st->entry->hasAnnotationObjectFlag = true;
do {
int fplen = fPrefix.length();
if (st->len >= 6 && TextUtils::equals(fPrefix.data(), st->buff, fplen)) {
while (fplen < 5) {
if (st->buff[fplen++] != ' ') {
st->si.setError(tr("Invalid format of feature table"));
break;
}
}
} else {
// end of feature table
break;
}
//parsing feature;
SharedAnnotationData f = readAnnotation(st->io, st->buff, st->len, READ_BUFF_SIZE, st->si, offset);
st->entry->features.push_back(f);
} while (st->readNextLine());
}