Task::ReportResult GTest_DNAcompareSequencesInTwoObjects::report() {
Document* doc = getContext<Document>(this, docContextName);
if (doc == NULL) {
stateInfo.setError(QString("document not found %1").arg(docContextName));
return ReportResult_Finished;
}
Document* doc2 = getContext<Document>(this, secondDocContextName);
if (doc2 == NULL) {
stateInfo.setError(QString("document not found %1").arg(secondDocContextName));
return ReportResult_Finished;
}
const QList<GObject*>& objs = doc->getObjects();
const QList<GObject*>& objs2 = doc2->getObjects();
GObject*obj=NULL;
GObject*obj2=NULL;
U2SequenceObject * mySequence;
U2SequenceObject * mySequence2;
for(int i=0;(i!=objs.size())&&(i!=objs2.size());i++){
obj = objs.at(i);
obj2 = objs2.at(i);
if((obj->getGObjectType()== GObjectTypes::SEQUENCE)&&(obj2->getGObjectType()== GObjectTypes::SEQUENCE)){
mySequence = qobject_cast<U2SequenceObject*>(obj);
if(mySequence==NULL){
stateInfo.setError(QString("can't cast to sequence from: %1 in position %2").arg(obj->getGObjectName()).arg(i));
return ReportResult_Finished;
}
mySequence2 = qobject_cast<U2SequenceObject*>(obj2);
if(mySequence2==NULL){
stateInfo.setError(QString("can't cast to sequence from: %1 in position %2").arg(obj2->getGObjectName()).arg(i));
return ReportResult_Finished;
}
if(mySequence->getWholeSequenceData(stateInfo) != mySequence2->getWholeSequenceData(stateInfo)){
CHECK_OP(stateInfo, ReportResult_Finished);
stateInfo.setError(QString("Sequences of object in position %1 not matched").arg(i));
return ReportResult_Finished;
}
CHECK_OP(stateInfo, ReportResult_Finished);
}
}
if (objs.size() != objs2.size()) {
QString error("Number of objects in doc mismatches: [%1=%2] vs [%3=%4]");
error = error.arg(docContextName).arg(objs.size())
.arg(secondDocContextName).arg(objs2.size());
if (obj) {
error += QString("\nLast good object: %1").arg(obj->getGObjectName());
}
stateInfo.setError(error);
}
return ReportResult_Finished;
}
void GTest_SecStructPredictTask::prepare()
{
U2SequenceObject * mySequence = getContext<U2SequenceObject>(this, seqName);
if(mySequence==NULL){
stateInfo.setError( QString("error can't cast to sequence from GObject"));
return;
}
SecStructPredictAlgRegistry* sspr = AppContext::getSecStructPredictAlgRegistry();
if (!sspr->hadRegistered(algName)) {
stateInfo.setError( QString(tr("Algorithm named %1 not found")).arg(algName));
return;
}
SecStructPredictTaskFactory* factory = sspr->getAlgorithm(algName);
QByteArray seqData = mySequence->getWholeSequenceData(stateInfo);
task = factory->createTaskInstance(seqData);
CHECK_OP(stateInfo, );
addSubTask(task);
}
MAlignment Kalign_Load_Align_Compare_Task::dna_to_ma(QList<GObject*> dnaSeqs) {
int seqCount = dnaSeqs.count();
U2SequenceObject *seq = qobject_cast<U2SequenceObject *>(dnaSeqs[0]);
MAlignment ma("Alignment",seq->getAlphabet());
for(int i=0; i<seqCount; i++) {
seq = qobject_cast<U2SequenceObject *>(dnaSeqs[i]);
if(seq == NULL) {
stateInfo.setError( QString("Can't cast GObject to U2SequenceObject") );
return ma;
}
QByteArray seqData = seq->getWholeSequenceData(stateInfo);
SAFE_POINT_OP(stateInfo, MAlignment());
ma.addRow(seq->getSequenceName(), seqData, stateInfo);
SAFE_POINT_OP(stateInfo, MAlignment());
}
return ma;
}
