////////////////////////////////////////
//MuscleAlignWithExtFileSpecifyDialogController
MuscleAlignWithExtFileSpecifyDialogController::MuscleAlignWithExtFileSpecifyDialogController(QWidget* w, MuscleTaskSettings& _settings)
: QDialog(w),
settings(_settings),
saveController(NULL)
{
setupUi(this);
new HelpButton(this, buttonBox, "17468977");
buttonBox->button(QDialogButtonBox::Ok)->setText(tr("Align"));
buttonBox->button(QDialogButtonBox::Cancel)->setText(tr("Cancel"));
initSaveController();
connect(inputFilePathButton, SIGNAL(clicked()), SLOT(sl_inputPathButtonClicked()));
//we don`t know length of MA, need check this at task
rangeStartSB->setValue(0);
rangeEndSB->setValue(500);
connect(confBox, SIGNAL(currentIndexChanged(int)), SLOT(sl_onPresetChanged(int)));
initPresets();
foreach(const MuscleAlignPreset* p, presets.qlist) {
confBox->addItem(p->name);
}
const DNAAlphabet* al = AppContext::getDNAAlphabetRegistry()->findById(BaseDNAAlphabetIds::NUCL_DNA_DEFAULT());
DNATranslationRegistry* tr = AppContext::getDNATranslationRegistry();
QList<DNATranslation*> aminoTs = tr->lookupTranslation(al, DNATranslationType_NUCL_2_AMINO);
assert(!aminoTs.empty());
foreach(DNATranslation* t, aminoTs) {
translationTableBox->addItem(t->getTranslationName());
}
SequenceObjectContext::SequenceObjectContext (U2SequenceObject* obj, QObject* parent)
: QObject(parent),
seqObj(obj),
aminoTT(NULL),
complTT(NULL),
selection(NULL),
translations(NULL),
visibleFrames(NULL),
rowChoosed(false)
{
selection = new DNASequenceSelection(seqObj, this);
clarifyAminoTT = false;
const DNAAlphabet* al = getAlphabet();
if (al->isNucleic()) {
DNATranslationRegistry* translationRegistry = AppContext::getDNATranslationRegistry();
complTT = GObjectUtils::findComplementTT(seqObj->getAlphabet());
aminoTT = GObjectUtils::findAminoTT(seqObj, true);
clarifyAminoTT = aminoTT == NULL;
QList<DNATranslation*> aminoTs = translationRegistry->lookupTranslation(al, DNATranslationType_NUCL_2_AMINO);
if (!aminoTs.empty()) {
aminoTT = aminoTT == NULL ? translationRegistry->getStandardGeneticCodeTranslation(al) : aminoTT;
translations = new QActionGroup(this);
foreach(DNATranslation* t, aminoTs) {
QAction* a = translations->addAction(t->getTranslationName());
a->setObjectName(t->getTranslationName());
a->setCheckable(true);
a->setChecked(aminoTT == t);
a->setData(QVariant(t->getTranslationId()));
connect(a, SIGNAL(triggered()), SLOT(sl_setAminoTranslation()));
}
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;
}
//KalignAlignWithExtFileSpecifyDialogController
KalignAlignWithExtFileSpecifyDialogController::KalignAlignWithExtFileSpecifyDialogController(QWidget* w, KalignTaskSettings& _settings)
: QDialog(w),
settings(_settings),
saveController(NULL)
{
setupUi(this);
new HelpButton(this, buttonBox, "23331273");
buttonBox->button(QDialogButtonBox::Ok)->setText(tr("Align"));
buttonBox->button(QDialogButtonBox::Cancel)->setText(tr("Cancel"));
initSaveController();
connect(inputFilePathButton, SIGNAL(clicked()), SLOT(sl_inputPathButtonClicked()));
const DNAAlphabet* al = AppContext::getDNAAlphabetRegistry()->findById(BaseDNAAlphabetIds::NUCL_DNA_DEFAULT());
DNATranslationRegistry* tr = AppContext::getDNATranslationRegistry();
QList<DNATranslation*> aminoTs = tr->lookupTranslation(al, DNATranslationType_NUCL_2_AMINO);
assert(!aminoTs.empty());
foreach(DNATranslation* t, aminoTs) {
translationTableBox->addItem(t->getTranslationName());
}
