void EnzymesPlugin::sl_onOpenCreateFragmentDialog() {
GObjectViewWindow* w = GObjectViewUtils::getActiveObjectViewWindow();
if (w == NULL) {
QMessageBox::information(QApplication::activeWindow(), openCreateFragmentDialog->text(),
tr("There is no active sequence object.\nTo create fragment open sequence document."));
return;
}
AnnotatedDNAView* view = qobject_cast<AnnotatedDNAView*>(w->getObjectView());
if (view == NULL) {
QMessageBox::information(QApplication::activeWindow(), openCreateFragmentDialog->text(),
tr("There is no active sequence object.\nTo create fragment open sequence document."));
return;
}
U2SequenceObject* dnaObj = view->getSequenceInFocus()->getSequenceObject();
assert(dnaObj != NULL);
if (!dnaObj->getAlphabet()->isNucleic()) {
QMessageBox::information(QApplication::activeWindow(), openCreateFragmentDialog->text(),
tr("The sequence doesn't have nucleic alphabet, it can not be used in cloning."));
return;
}
QObjectScopedPointer<CreateFragmentDialog> dlg = new CreateFragmentDialog(view->getSequenceInFocus(), QApplication::activeWindow());
dlg->exec();
}
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 EnzymesPlugin::sl_onOpenDigestSequenceDialog() {
GObjectViewWindow* w = GObjectViewUtils::getActiveObjectViewWindow();
if (w == NULL) {
QMessageBox::information(QApplication::activeWindow(), openDigestSequenceDialog->text(),
tr("There is no active sequence object.\nTo start partition open sequence document."));
return;
}
AnnotatedDNAView* view = qobject_cast<AnnotatedDNAView*>(w->getObjectView());
if (view == NULL) {
QMessageBox::information(QApplication::activeWindow(), openDigestSequenceDialog->text(),
tr("There is no active sequence object.\nTo start partition open sequence document."));
return;
}
if (!view->getSequenceInFocus()->getSequenceObject()->getAlphabet()->isNucleic()) {
QMessageBox::information(QApplication::activeWindow(), openDigestSequenceDialog->text(),
tr("Can not digest into fragments non-nucleic sequence."));
return;
}
QObjectScopedPointer<DigestSequenceDialog> dlg = new DigestSequenceDialog(view->getSequenceInFocus(), QApplication::activeWindow());
dlg->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();
}
bool PcrOptionsPanelSavableTab::childValueIsAcceptable(const QString &childId, const QVariant &value) const {
if (PCR_PRODUCTS_TABLE_NAME == childId) {
const AdvContextPcrProductPair data = value.value<AdvContextPcrProductPair>();
AnnotatedDNAView *dnaView = originalWrappedWidget->getDnaView();
SAFE_POINT(NULL != dnaView, "Invalid sequence view detected", false);
return dnaView->getSequenceContexts().contains(data.first);
} else {
return U2SavableWidget::childValueIsAcceptable(childId, value);
}
}
void ADVGlobalAction::updateState() {
AnnotatedDNAView* av = qobject_cast<AnnotatedDNAView*>(getObjectView());
ADVSequenceWidget* w = av->getSequenceWidgetInFocus();
bool enabled = w!=NULL;
if (enabled && flags.testFlag(ADVGlobalActionFlag_SingleSequenceOnly) && qobject_cast<ADVSingleSequenceWidget*>(w) == NULL) {
enabled = false;
}
if (enabled && !alphabetFilter.isEmpty()) {
DNAAlphabetType t = w->getActiveSequenceContext()->getAlphabet()->getType();
enabled = alphabetFilter.contains(t);
}
setEnabled(enabled);
}
void ChromaViewContext::sl_showChromatogram() {
ChromaViewAction* a = qobject_cast<ChromaViewAction*>(sender());
CHECK(a!=NULL, );
ADVSingleSequenceWidget* sw = qobject_cast<ADVSingleSequenceWidget*>(a->seqWidget);
DNAChromatogramObject* chromaObj = findChromaObj(sw);
CHECK(sw->getSequenceContext(), );
AnnotatedDNAView *adv = sw->getSequenceContext()->getAnnotatedDNAView();
CHECK(adv, );
if (a->isChecked()) {
CHECK(a->view == NULL, );
CHECK(chromaObj!=NULL, );
adv->addObject(chromaObj);
a->view = new ChromatogramView(sw, sw->getSequenceContext(), sw->getPanGSLView(), chromaObj->getChromatogram());
sw->addSequenceView(a->view);
} else {
void uHMMPlugin::sl_search() {
//to select a sequence
//1. check that annotated DNA view is active
//2. if not -> check that DNASequence object is selected in project view
U2SequenceObject* obj = NULL;
MWMDIWindow* w = AppContext::getMainWindow()->getMDIManager()->getActiveWindow();
if (w!=NULL) {
GObjectViewWindow* ow = qobject_cast<GObjectViewWindow*>(w);
if (ow!=NULL) {
GObjectView* ov = ow->getObjectView();
AnnotatedDNAView* av = qobject_cast<AnnotatedDNAView*>(ov);
if (av!=NULL) {
ADVSequenceObjectContext* seqCtx = av->getSequenceInFocus();
obj = seqCtx->getSequenceObject();
}
}
}
if (obj == NULL) {
ProjectView* pv = AppContext::getProjectView();
if (pv!=NULL) {
const GObjectSelection* sel = pv->getGObjectSelection();
GObject* o = sel->getSelectedObjects().size() == 1 ? sel->getSelectedObjects().first() : NULL;
obj = qobject_cast<U2SequenceObject*>(o);
}
}
QWidget *p = (QWidget*)AppContext::getMainWindow()->getQMainWindow();
if (obj == NULL) {
QMessageBox::critical(p, tr("Error"), tr("Error! Select sequence in Project view or open sequence view."));
return;
}
U2OpStatusImpl os;
DNASequence sequence = obj->getWholeSequence(os);
CHECK_OP_EXT(os, QMessageBox::critical(QApplication::activeWindow(), L10N::errorTitle(), os.getError()), );
QObjectScopedPointer<HMMSearchDialogController> d = new HMMSearchDialogController(sequence, obj, p);
d->exec();
}
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();
}
void EnzymesADVContext::buildMenu(GObjectView *v, QMenu *m) {
AnnotatedDNAView *av = qobject_cast<AnnotatedDNAView *>(v);
SAFE_POINT(NULL != av, "Invalid sequence view",);
CHECK(av->getSequenceInFocus()->getAlphabet()->isNucleic(),);
QMenu *cloningMenu = new QMenu(tr("Cloning"), m);
cloningMenu->menuAction()->setObjectName("Cloning");
cloningMenu->addActions(cloningActions);
QAction *exportMenuAction = GUIUtils::findAction(m->actions(), ADV_MENU_EXPORT);
m->insertMenu(exportMenuAction, cloningMenu);
if (!av->getAnnotationsSelection()->getSelection().isEmpty()) {
Annotation *a = av->getAnnotationsSelection()->getSelection().first().annotation;
const QString annName = a->getName();
const QString groupName = a->getGroup()->getName();
const int annCount = a->getGroup()->getAnnotations().size();
if (annName == PRIMER_ANNOTATION_NAME && groupName.startsWith(PRIMER_ANNOTATION_GROUP_NAME) && 2 == annCount) {
QAction *a = findViewAction(v, CREATE_PCR_PRODUCT_ACTION_NAME);
SAFE_POINT(NULL != a, "Invalid menu action",);
cloningMenu->addAction(a);
}