Task::ReportResult GTest_DNASequencePart::report() {
GObject *obj = getContext<GObject>(this,objContextName);
if (obj==NULL) {
stateInfo.setError(QString("wrong value: %1").arg(OBJ_ATTR));
return ReportResult_Finished;
}
U2SequenceObject * objSequence = qobject_cast<U2SequenceObject*>(obj);
if (objSequence==NULL) {
stateInfo.setError(QString("can't cast to sequence from: %1").arg(obj->getGObjectName()));
return ReportResult_Finished;
}
if (objSequence->getSequenceLength() < startPos + subseq.length()) {
stateInfo.setError(QString("sequence size is less that region end: size=%1, region-end=%2, objectName=%3").arg(objSequence->getSequenceLength()).arg(startPos + subseq.length()).arg(obj->getGObjectName()));
return ReportResult_Finished;
}
QByteArray objSubSeq = objSequence->getSequenceData(U2Region(startPos, subseq.length()));
if (!objSequence->getAlphabet()->isCaseSensitive()) {
subseq = subseq.toUpper();
}
if (objSubSeq != subseq){
stateInfo.setError(QString("region not matched: %1, expected %2").arg(objSubSeq.constData()).arg(subseq.constData()));
return ReportResult_Finished;
}
return ReportResult_Finished;
}
Task::ReportResult GTest_DNATranslation3to1Test::report() {
GObject *obj = getContext<GObject>(this, objContextName);
if (obj==NULL){
stateInfo.setError(QString("wrong value: %1").arg(OBJ_ATTR));
return ReportResult_Finished;
}
U2SequenceObject * mySequence = qobject_cast<U2SequenceObject*>(obj);
if(mySequence==NULL){
stateInfo.setError(QString("error can't cast to sequence from: %1").arg(obj->getGObjectName()));
return ReportResult_Finished;
}
if(!(mySequence->getAlphabet()->isNucleic())){
stateInfo.setError(QString("error Alphabet is not Nucleic: %1").arg(mySequence->getAlphabet()->getId()));
return ReportResult_Finished;
}
DNATranslation* aminoTransl = 0;
DNATranslationRegistry* tr = AppContext::getDNATranslationRegistry();
QList<DNATranslation*> aminoTs = tr->lookupTranslation(mySequence->getAlphabet(), DNATranslationType_NUCL_2_AMINO);
if (!aminoTs.empty()) {
aminoTransl = tr->getStandardGeneticCodeTranslation(mySequence->getAlphabet());
}
int tempValue;
if(strTo == -1){
tempValue=-1;
} else{
tempValue=(strTo-strFrom+1);
}
QByteArray myByteArray = mySequence->getSequenceData(U2Region(strFrom,tempValue));
QByteArray rezult(myByteArray.length() / 3, 0);
int n = aminoTransl->translate(myByteArray, myByteArray.length(), rezult.data(), rezult.length());
assert(n == rezult.length()); Q_UNUSED(n);
if(rezult != stringValue.toLatin1()){
stateInfo.setError(QString("translated sequence not matched: %1, expected %2 ").arg(rezult.data()).arg(stringValue));
return ReportResult_Finished;
}
return ReportResult_Finished;
}
