QVector<U2Region> MultipleRangeSelector::getSelectedRegions(){
QVector<U2Region> currentRegions;
if(ui->singleButton->isChecked()){
bool ok = false;
int st = ui->startEdit->text().toInt(&ok);
assert(ok);
int en = ui->endEdit->text().toInt(&ok);
assert(ok);
if (isCircular && st > en ) {
currentRegions.append(U2Region(0, en));
currentRegions.append(U2Region(st - 1, seqLen - st + 1));
}
else {
currentRegions.append(U2Region(st - 1, en - st + 1));
}
}else{
QByteArray locEditText = ui->multipleRegionEdit->text().toLatin1();
U2Location currentLocation;
if (isCircular){
Genbank::LocationParser::parseLocation( locEditText.constData(), ui->multipleRegionEdit->text().length(), currentLocation, seqLen);
}else{
Genbank::LocationParser::parseLocation( locEditText.constData(), ui->multipleRegionEdit->text().length(), currentLocation, -1);
}
assert(!currentLocation->isEmpty());
currentRegions = U2Region::join(currentLocation->regions);
}
return currentRegions;
}
void MultipleRangeSelector::accept(){
if(ui->singleButton->isChecked()){
bool ok = false;
int v1 = ui->startEdit->text().toInt(&ok);
if (!ok || v1 < 1 || v1 > seqLen) {
return;
}
int v2 = ui->endEdit->text().toInt(&ok);
if (!ok || (v2 < v1 && !isCircular) || v2 > seqLen) {
return;
}
QDialog::accept();
}else{
QByteArray locEditText = ui->multipleRegionEdit->text().toLatin1();
U2Location currentLocation;
if (isCircular) {
Genbank::LocationParser::parseLocation(locEditText.constData(), ui->multipleRegionEdit->text().length(), currentLocation, seqLen);
} else {
Genbank::LocationParser::parseLocation(locEditText.constData(), ui->multipleRegionEdit->text().length(), currentLocation, -1);
}
if (currentLocation->isEmpty()) {
return;
}
QDialog::accept();
}
}
GeneByGeneCompareResult GeneByGeneComparator::compareGeneAnnotation(const DNASequence& seq, const QList<SharedAnnotationData> &annData,
const QString& annName, float identity)
{
GeneByGeneCompareResult result;
float maxIdentity = -1.0F;
foreach (const SharedAnnotationData &adata, annData) {
if (adata->name == annName) {
U2Location location = adata->location;
if (location->isSingleRegion()) {
int reglen = location->regions.first().length;
float lenRatio = reglen * 100 /static_cast<float>(seq.length());
maxIdentity = qMax(maxIdentity, lenRatio);
if(lenRatio >= identity){ //check length ratio
QString ident = adata->findFirstQualifierValue(BLAST_IDENT);
if (!ident.isEmpty()){
//create BLAST string YES/identity/gaps
float blastIdent = parseBlastQual(ident);
if (blastIdent != -1.0f && blastIdent >= identity){
result.identical = true;
result.identityString = GeneByGeneCompareResult::IDENTICAL_YES;
result.identityString.append(QString("\\%1").arg(blastIdent));
QString gaps = adata->findFirstQualifierValue(BLAST_GAPS);
if (!gaps.isEmpty()){
float blastGaps = parseBlastQual(gaps);
if (blastGaps!=1.0f){
result.identityString.append(QString("\\%1").arg(blastGaps));
}
}else{
result.identityString.append(QString("\\0"));
}
}
}else{ //not a blast annotation
result.identical = true;
result.identityString = GeneByGeneCompareResult::IDENTICAL_YES;
}
}
}
break;
}
}
if (result.identical == false && maxIdentity != -1.0f){
result.identityString.append(QString("\\%1").arg(maxIdentity));
}
return result;
}
QList<Task *> SpideyAlignmentTask::onSubTaskFinished(Task *subTask) {
QList<Task *> res;
propagateSubtaskError();
if (hasError() || isCanceled()) {
return res;
}
if (subTask == prepareDataForSpideyTask) {
SAFE_POINT(!prepareDataForSpideyTask->getResultPath().isEmpty(), "Invalid result path!",
res);
tmpOutputUrl = prepareDataForSpideyTask->getResultPath();
const QStringList &arguments = prepareDataForSpideyTask->getArgumentsList();
spideyTask = new ExternalToolRunTask(ET_SPIDEY, arguments, new SpideyLogParser());
spideyTask->setSubtaskProgressWeight(95);
res.append(spideyTask);
} else if (subTask == spideyTask) {
if (!QFile::exists(tmpOutputUrl)) {
if (AppContext::getExternalToolRegistry()->getByName(ET_SPIDEY)->isValid()) {
stateInfo.setError(tr("Output file not found"));
} else {
ExternalTool *spideyTool = AppContext::getExternalToolRegistry()->getByName(ET_SPIDEY);
SAFE_POINT(NULL != spideyTool, "Invalid Spidey tool!", res);
stateInfo.setError(
tr("Output file not found. May be %1 tool path '%2' not valid?")
.arg(spideyTool->getName()).arg(spideyTool->getPath()));
}
return res;
}
// parse result
QFile resultFile(tmpOutputUrl);
if (!resultFile.open(QFile::ReadOnly)) {
setError(tr("Failed to open result file %1").arg(tmpOutputUrl));
return res;
}
QTextStream inStream(&resultFile);
bool strandDirect = true;
U2Location location;
location->op = U2LocationOperator_Join;
while (!inStream.atEnd()) {
QByteArray buf = inStream.readLine().toLatin1();
if (buf.startsWith("Strand")) {
strandDirect = buf.contains("plus");
}
if (buf.startsWith("Exon")) {
// TODO: better to use reg exp here
int startPos = buf.indexOf(":") + 1;
int endPos = buf.indexOf("(gen)");
if (startPos == -1 || endPos == -1) {
continue;
}
QByteArray loc = buf.mid(startPos, endPos - startPos).trimmed();
QList<QByteArray> loci = loc.split('-');
if (loci.size() < 2) {
continue;
}
int start = QString(loci.at(0)).toInt();
int finish = QString(loci.at(1)).toInt();
if (start == finish) {
continue;
}
location->regions.append(U2Region(start - 1, finish - start + 1));
}
}
if (!location->isEmpty()) {
SharedAnnotationData data(new AnnotationData);
data->location = location;
data->setStrand(U2Strand(strandDirect ? U2Strand::Direct : U2Strand::Complementary));
data->type = U2FeatureTypes::Exon;
data->name = "exon";
U1AnnotationUtils::addDescriptionQualifier(data, annDescription);
resultAnnotations.append(data);
}
}
return res;
}
bool parseLocationDescriptor(U2Location &location, QString& errorReport) {
bool remoteEntry = false;
Token token = lexer.peek();
if (token.getType() == Token::NAME) { // remote entries
remoteEntry = true;
QByteArray accession = lexer.next().getString();
QString data = accession;
if(!match(Token::PERIOD)) {
errorReport = QString("GENBANK LOCATION PARSER: Must be PERIOD instead of %1").arg(lexer.peek().getString().data());
ioLog.trace(errorReport);
return false;
}
qint64 version = 0;
if(!parseNumber(version)) {
errorReport = QString("GENBANK LOCATION PARSER: can't parse Number. Token: %1").arg(lexer.peek().getString().data());
ioLog.trace(errorReport);
return false;
}
if(!match(Token::COLON)) {
errorReport = QString("GENBANK LOCATION PARSER: Must be COLON instead of %1").arg(lexer.peek().getString().data());
ioLog.trace(errorReport);
return false;
}
ioLog.info(LocationParser::tr("Ignoring remote entry: %1.%2").arg(QString(accession)).arg(version));
}
if (token.getType() == Token::COMPLEMENT) {
lexer.next();
return parseComplement(location, errorReport);
}
qint64 firstBase = 0;
bool firstBaseIsFromRange = false;
if(match(Token::LEFT_PARENTHESIS)) { // cases like (1.2)..
firstBaseIsFromRange = true;
if(!parseNumber(firstBase)) { // use the first number as a region boundary
errorReport = QString("GENBANK LOCATION PARSER: can't parse Number. Token: %1").arg(lexer.peek().getString().data());
ioLog.trace(errorReport);
return false;
}
else if(firstBase < 0) {
errorReport = QString("GENBANK LOCATION PARSER: region boundary can not be less then zero. Token: %1%2").arg(firstBase).arg(lexer.peek().getString().data());
ioLog.trace(errorReport);
return false;
}
if(!match(Token::PERIOD)) {
errorReport = QString("GENBANK LOCATION PARSER: Must be PERIOD instead of %1").arg(lexer.peek().getString().data());
ioLog.trace(errorReport);
return false;
}
if(!match(Token::NUMBER)) { // ignore the second number
errorReport = QString("GENBANK LOCATION PARSER: Must be NUMBER instead of %1").arg(lexer.peek().getString().data());
ioLog.trace(errorReport);
return false;
}
if(!match(Token::RIGHT_PARENTHESIS)) {
errorReport = QString("GENBANK LOCATION PARSER: Must be RIGHT_PARENTHESIS instead of %1").arg(lexer.peek().getString().data());
ioLog.trace(errorReport);
return false;
}
ioLog.info(LocationParser::tr("'a single base from a range' in combination with 'sequence span' is not supported"));
} else {
if(match(Token::LESS)) {
ioLog.info(LocationParser::tr("Ignoring '<' at start position"));
}
if(!parseNumber(firstBase)) {
errorReport = QString("GENBANK LOCATION PARSER: can't parse Number. Token: %1").arg(lexer.peek().getString().data());
ioLog.trace(errorReport);
return false;
}
else if(firstBase < 0) {
errorReport = QString("Region boundary can not be less then zero: %1%2").arg(firstBase).arg(lexer.peek().getString().data());
ioLog.trace("GENBANK LOCATION PARSER:" + errorReport);
return false;
}
}
if(match(Token::PERIOD)) {
if(firstBaseIsFromRange) { // ranges are only allowed in spans
errorReport = QString("GENBANK LOCATION PARSER: ranges are only allowed in spans. Token: %1").arg(lexer.peek().getString().data());
ioLog.trace(errorReport);
return false;
}
qint64 secondNumber = 0;
if(!parseNumber(secondNumber)) {
errorReport = QString("GENBANK LOCATION PARSER: can't parse Number. Token: %1").arg(lexer.peek().getString().data());
ioLog.trace(errorReport);
return false;
}
else if(secondNumber < 0) {
errorReport = QString("Region boundary can not be less then zero: %1%2").arg(secondNumber).arg(lexer.peek().getString().data());
ioLog.trace("GENBANK LOCATION PARSER:" + errorReport);
return false;
}
if(!location->isEmpty()) {
errorReport = QString("GENBANK LOCATION PARSER: location is not empty. Token: %1").arg(lexer.peek().getString().data());
ioLog.trace(errorReport);
return false;
}
if(!remoteEntry) { // ignore remote entries
location->regions.append(toRegion(firstBase, secondNumber));
location->regionType = U2LocationRegionType_SingleBase;
}
} else if(match(Token::DOUBLE_PERIOD)) {
qint64 secondNumber = 0;
if(match(Token::LEFT_PARENTHESIS)) { // cases like ..(1.2)
if(!match(Token::NUMBER)) { // ignore the first number
errorReport = QString("GENBANK LOCATION PARSER: Must be NUMBER instead of %1").arg(lexer.peek().getString().data());
ioLog.trace(errorReport);
return false;
}
if(!match(Token::PERIOD)) {
errorReport = QString("GENBANK LOCATION PARSER: Must be PERIOD instead of %1").arg(lexer.peek().getString().data());
ioLog.trace(errorReport);
return false;
}
if(!parseNumber(secondNumber)) { // use the second number as a region boudary
errorReport = QString("GENBANK LOCATION PARSER: can't parse Number. Token: %1").arg(lexer.peek().getString().data());
ioLog.trace(errorReport);
return false;
}
else if(secondNumber < 0) {
errorReport = QString("Region boundary can not be less then zero: %1%2").arg(secondNumber).arg(lexer.peek().getString().data());
ioLog.trace("GENBANK LOCATION PARSER:" + errorReport);
return false;
}
if(!match(Token::RIGHT_PARENTHESIS)) {
errorReport = QString("GENBANK LOCATION PARSER: Must be RIGHT_PARENTHESIS instead of %1").arg(lexer.peek().getString().data());
ioLog.trace(errorReport);
return false;
}
ioLog.info(LocationParser::tr("'a single base from a range' in combination with 'sequence span' is not supported"));
} else {
if(match(Token::GREATER)) {
ioLog.info(LocationParser::tr("Ignoring '>' at end position"));
}
if(!parseNumber(secondNumber)) {
errorReport = QString("GENBANK LOCATION PARSER: can't parse Number. Token: %1").arg(lexer.peek().getString().data());
ioLog.trace(errorReport);
return false;
}
else if(secondNumber < 0) {
errorReport = QString("Region boundary can not be less then zero: %1%2").arg(secondNumber).arg(lexer.peek().getString().data());
ioLog.trace("GENBANK LOCATION PARSER:" + errorReport);
return false;
}
}
if(!remoteEntry) { // ignore remote entries
if(seqLenForCircular != -1 && firstBase > secondNumber){
location->regions.append(toRegion(1, secondNumber));
location->regions.append(toRegion(firstBase, seqLenForCircular));
location->regionType = U2LocationRegionType_Default;
location->op = U2LocationOperator_Join;
}else{
location->regions.append(toRegion(firstBase, secondNumber));
location->regionType = U2LocationRegionType_Default;
}
}
} else if(match(Token::CARET)) {
if(firstBaseIsFromRange) { // ranges are only allowed in spans
return false;
}
qint64 secondBase = 0;
if(!parseNumber(secondBase)) {
return false;
}
if(!location->isEmpty()) {
return false;
}
if(!remoteEntry) { // ignore remote entries
if(seqLenForCircular != -1 && firstBase > secondBase){
location->regions.append(toRegion(1, secondBase));
location->regions.append(toRegion(firstBase, seqLenForCircular));
location->regionType = U2LocationRegionType_Default;
location->op = U2LocationOperator_Join;
}else{
location->regions.append(toRegion(firstBase, secondBase));
location->regionType = U2LocationRegionType_Site;
}
}
} else {
if(firstBaseIsFromRange) { // ranges are only allowed in spans
return false;
}
if(!remoteEntry) { // ignore remote entries
location->regions.append(toRegion(firstBase, firstBase));
location->regionType = U2LocationRegionType_Default;
}
}
return true;
}
