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 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 OpenMaEditorTask::updateTitle(MSAEditor* msaEd) {
const QString& oldViewName = msaEd->getName();
GObjectViewWindow* w = GObjectViewUtils::findViewByName(oldViewName);
if (w != NULL) {
MultipleAlignmentObject* msaObject = msaEd->getMaObject();
QString newViewName = GObjectViewUtils::genUniqueViewName(msaObject->getDocument(), msaObject);
msaEd->setName(newViewName);
w->setWindowTitle(newViewName);
}
}
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 uHMMPlugin::sl_build() {
MAlignment ma;
//try to find alignment check that MSA Editor is active
QString profileName;
MWMDIWindow* w = AppContext::getMainWindow()->getMDIManager()->getActiveWindow();
if (w!=NULL) {
GObjectViewWindow* ow = qobject_cast<GObjectViewWindow*>(w);
if (ow!=NULL) {
GObjectView* ov = ow->getObjectView();
MSAEditor* av = qobject_cast<MSAEditor*>(ov);
if (av!=NULL) {
MAlignmentObject* maObj = av->getMSAObject();
if (maObj!=NULL) {
ma = maObj->getMAlignment();
profileName = maObj->getGObjectName() == MA_OBJECT_NAME ? maObj->getDocument()->getName() : maObj->getGObjectName();
}
}
}
}
QWidget *p = (QWidget*)AppContext::getMainWindow()->getQMainWindow();
QObjectScopedPointer<HMMBuildDialogController> d = new HMMBuildDialogController(profileName, ma, p);
d->exec();
}
