SharedAnnotationData FindAlgorithmResult::toAnnotation(const QString &name, bool splitCircular, int seqLen) const {
SAFE_POINT(!splitCircular || (seqLen != -1), "Sequence length is not set!", SharedAnnotationData());
SharedAnnotationData data(new AnnotationData);
data->name = name;
if (splitCircular && (region.endPos() > seqLen) ) {
if (region.startPos >= seqLen) {
data->location->regions << U2Region(region.startPos - seqLen, region.length);
} else {
SAFE_POINT(region.startPos < seqLen, "Region is not correct", SharedAnnotationData());
data->location->regions << U2Region(region.startPos, seqLen - region.startPos);
data->location->regions << U2Region(0, region.length - (seqLen - region.startPos));
}
} else {
data->location->regions << region;
}
data->setStrand(strand);
data->qualifiers.append(U2Qualifier("mismatches", QString::number(err)));
return data;
}
SharedAnnotationData SwissProtPlainTextFormat::readAnnotation(IOAdapter* io, char* cbuff, int len, int READ_BUFF_SIZE, U2OpStatus& si, int offset, int seqLen){
Q_UNUSED(seqLen);
AnnotationData* a = new AnnotationData();
SharedAnnotationData f(a);
QString key = QString::fromLatin1(cbuff+5, 10).trimmed();
if (key.isEmpty()) {
si.setError(EMBLGenbankAbstractDocument::tr("Annotation name is empty"));
return SharedAnnotationData();
}
a->name = key;
if(key == "STRAND" || key == "HELIX" || key == "TURN"){
a->qualifiers.append(U2Qualifier(GBFeatureUtils::QUALIFIER_GROUP, "Secondary structure"));
}
QString start= QString::fromLatin1(cbuff+15, 5).trimmed();
if(start.isEmpty()){
si.setError(EMBLGenbankAbstractDocument::tr("Annotation start position is empty"));
return SharedAnnotationData();
}
QString end= QString::fromLatin1(cbuff+22, 5).trimmed();
if(end.isEmpty()){
si.setError(EMBLGenbankAbstractDocument::tr("Annotation end position is empty"));
return SharedAnnotationData();
}
a->location->reset();
if(key == "DISULFID" && start != end){
a->location->op=U2LocationOperator_Order;
U2Region reg1(start.toInt()-1,1);
U2Region reg2(end.toInt()-1,1);
a->location->regions.append(reg1);
a->location->regions.append(reg2);
}else{
U2Region reg(start.toInt()-1,end.toInt() - start.toInt()+1);
a->location->regions.append(reg);
}
if (offset!=0) {
U2Region::shift(offset, a->location->regions);
}
QString valQStr = QString::fromLatin1(cbuff).split(QRegExp("\\n")).first().mid(34);
QString nameQStr = "Description";
bool isDescription=true;
const QByteArray& aminoQ = GBFeatureUtils::QUALIFIER_AMINO_STRAND;
const QByteArray& nameQ = GBFeatureUtils::QUALIFIER_NAME;
//here we have valid key and location;
//reading qualifiers
bool lineOk = true;
while ((len = io->readUntil(cbuff, READ_BUFF_SIZE, TextUtils::LINE_BREAKS, IOAdapter::Term_Include, &lineOk) ) > 0) {
if (len == 0 || len < QN_COL+1 || cbuff[K_COL]!=' ' || cbuff[0]!=fPrefix[0] || cbuff[1]!=fPrefix[1]) {
io->skip(-len);
if(isDescription && !valQStr.isEmpty()){
isDescription=false;
a->qualifiers.append(U2Qualifier(nameQStr, valQStr));
}
break;
}
if (!lineOk) {
si.setError(EMBLGenbankAbstractDocument::tr("Unexpected line format"));
break;
}
//parse line
if(cbuff[A_COL] != '/'){//continue of description
valQStr.append(" ");
valQStr.append(QString::fromLatin1(cbuff).split(QRegExp("\\n")).takeAt(0).mid(34));
}else{
for (; QN_COL < len && TextUtils::LINE_BREAKS[(uchar)cbuff[len-1]]; len--){}; //remove line breaks
int flen = len + readMultilineQualifier(io, cbuff, READ_BUFF_SIZE-len, len == maxAnnotationLineLen, len, si);
//now the whole feature is in cbuff
int valStart = A_COL + 1;
for (; valStart < flen && cbuff[valStart] != '='; valStart++){}; //find '==' and valStart
if (valStart < flen) {
valStart++; //skip '=' char
}
const QBitArray& WHITE_SPACES = TextUtils::WHITES;
for (; valStart < flen && WHITE_SPACES[(uchar)cbuff[flen-1]]; flen--){}; //trim value
const char* qname = cbuff + QN_COL;
int qnameLen = valStart - (QN_COL + 1);
const char* qval = cbuff + valStart;
int qvalLen = flen - valStart;
if (qnameLen == aminoQ.length() && TextUtils::equals(qname, aminoQ.constData(), qnameLen)) {
//a->aminoFrame = qvalLen == aminoQYes.length() && TextUtils::equals(qval, aminoQYes.constData(), qvalLen) ? TriState_Yes
// : (qvalLen == aminoQNo.length() && TextUtils::equals(qval, aminoQNo.constData(), qvalLen) ? TriState_No : TriState_Unknown);
} else if (qnameLen == nameQ.length() && TextUtils::equals(qname, nameQ.constData(), qnameLen)) {
a->name = QString::fromLocal8Bit(qval, qvalLen);
} else {
QString nameQStr = QString::fromLocal8Bit(qname, qnameLen);
QString valQStr = QString::fromLocal8Bit(qval, qvalLen);
a->qualifiers.append(U2Qualifier(nameQStr, valQStr));
}
}
}
return f;
}