void SecStructPredictViewAction::sl_execute() {
QAction *a = dynamic_cast<QAction*>(sender());
GObjectViewAction *viewAction = dynamic_cast<GObjectViewAction*>(a);
SAFE_POINT(NULL != viewAction, "NULL action",);
AnnotatedDNAView *av = qobject_cast<AnnotatedDNAView*>(viewAction->getObjectView());
SAFE_POINT(NULL != av, "NULL dna view",);
SecStructPredictAlgRegistry *sspar = AppContext::getSecStructPredictAlgRegistry();
SAFE_POINT(NULL != sspar, "NULL SecStructPredictAlgRegistry",);
if (sspar->getAlgNameList().isEmpty()) {
QMessageBox::information(av->getWidget(),
tr("Secondary Structure Prediction"),
tr("No algorithms for secondary structure prediction are available.\nPlease, load the corresponding plugins."));
return;
}
ADVSequenceObjectContext *seqCtx = av->getSequenceInFocus();
SAFE_POINT(NULL != seqCtx, "NULL sequence context",);
SAFE_POINT(NULL != seqCtx->getAlphabet(), "NULL alphabet",);
SAFE_POINT(seqCtx->getAlphabet()->isAmino(), "Wrong alphabet",);
QObjectScopedPointer<SecStructDialog> secStructDialog = new SecStructDialog(seqCtx, av->getWidget());
secStructDialog->exec();
}
void EnzymesADVContext::sl_search() {
GObjectViewAction* action = qobject_cast<GObjectViewAction*>(sender());
assert(action!=NULL);
AnnotatedDNAView* av = qobject_cast<AnnotatedDNAView*>(action->getObjectView());
assert(av!=NULL);
ADVSequenceObjectContext* seqCtx = av->getSequenceInFocus();
assert(seqCtx->getAlphabet()->isNucleic());
QObjectScopedPointer<FindEnzymesDialog> d = new FindEnzymesDialog(seqCtx);
d->exec();
}
void EnzymesADVContext::initViewContext(GObjectView* view) {
AnnotatedDNAView* av = qobject_cast<AnnotatedDNAView*>(view);
ADVGlobalAction* a = new ADVGlobalAction(av, QIcon(":enzymes/images/enzymes.png"), tr("Find restriction sites..."), 50);
a->setObjectName("Find restriction sites");
a->addAlphabetFilter(DNAAlphabet_NUCL);
connect(a, SIGNAL(triggered()), SLOT(sl_search()));
GObjectViewAction *createPCRProductAction = new GObjectViewAction(av, av, tr("Create PCR product..."));
createPCRProductAction->setObjectName(CREATE_PCR_PRODUCT_ACTION_NAME);
connect(createPCRProductAction, SIGNAL(triggered()), SLOT(sl_createPCRProduct()));
addViewAction(createPCRProductAction);
}
void HMMMSAEditorContext::initViewContext(GObjectView* view) {
MSAEditor* msaed = qobject_cast<MSAEditor*>(view);
assert(msaed!=NULL);
if (msaed->getMSAObject() == NULL)
return;
GObjectViewAction* a = new GObjectViewAction(this, view, tr("Build HMMER2 profile"));
a->setObjectName("Build HMMER2 profile");
a->setIcon(QIcon(":/hmm2/images/hmmer_16.png"));
connect(a, SIGNAL(triggered()), SLOT(sl_build()));
addViewAction(a);
}
void HMMMSAEditorContext::sl_build() {
GObjectViewAction* action = qobject_cast<GObjectViewAction*>(sender());
assert(action!=NULL);
MSAEditor* ed = qobject_cast<MSAEditor*>(action->getObjectView());
assert(ed!=NULL);
MAlignmentObject* obj = ed->getMSAObject();
if (obj) {
QString profileName = obj->getGObjectName() == MA_OBJECT_NAME ? obj->getDocument()->getName() : obj->getGObjectName();
QObjectScopedPointer<HMMBuildDialogController> d = new HMMBuildDialogController(profileName, obj->getMAlignment());
d->exec();
CHECK(!d.isNull(), );
}
}
void HMMADVContext::sl_search() {
GObjectViewAction* action = qobject_cast<GObjectViewAction*>(sender());
assert(action!=NULL);
AnnotatedDNAView* av = qobject_cast<AnnotatedDNAView*>(action->getObjectView());
assert(av!=NULL);
QWidget *p;
if (av->getWidget()){
p = av->getWidget();
}else{
p = (QWidget*)AppContext::getMainWindow()->getQMainWindow();
}
ADVSequenceObjectContext* seqCtx = av->getSequenceInFocus();
if(seqCtx == NULL) {
QMessageBox::critical(p, tr("Error"), tr("No sequences found"));
return;
}
U2OpStatusImpl os;
DNASequence sequence = seqCtx->getSequenceObject()->getWholeSequence(os);
CHECK_OP_EXT(os, QMessageBox::critical(QApplication::activeWindow(), L10N::errorTitle(), os.getError()), );
QObjectScopedPointer<HMMSearchDialogController> d = new HMMSearchDialogController(sequence, seqCtx->getSequenceObject(), p);
d->exec();
}