QStringList GTUtilsMSAEditorSequenceArea::getNameList(HI::GUITestOpStatus &os) {
QMainWindow* mw = AppContext::getMainWindow()->getQMainWindow();
MSAEditor* editor = mw->findChild<MSAEditor*>();
CHECK_SET_ERR_RESULT(editor != NULL, "MsaEditor not found", QStringList());
QStringList result = editor->getMSAObject()->getMAlignment().getRowNames();
return result;
}
void DNAStatMSAEditorContext::buildMenu(GObjectView* v, QMenu* m) {
MSAEditor* msaed = qobject_cast<MSAEditor*>(v);
if (msaed != NULL && !msaed->getMaObject())
return;
QList<GObjectViewAction *> actions = getViewActions(v);
QMenu* statMenu = GUIUtils::findSubMenu(m, MSAE_MENU_STATISTICS);
SAFE_POINT(statMenu != NULL, "statMenu", );
foreach(GObjectViewAction* a, actions) {
statMenu->addAction(a);
}
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 HMMMSAEditorContext::buildMenu(GObjectView* v, QMenu* m) {
MSAEditor* msaed = qobject_cast<MSAEditor*>(v);
assert( NULL != msaed && NULL != m );
if (msaed->getMSAObject() == NULL)
return;
QList<GObjectViewAction*> list = getViewActions(v);
assert(list.size()==1);
GObjectViewAction* a = list.first();
QMenu* aMenu = GUIUtils::findSubMenu(m, MSAE_MENU_ADVANCED);
SAFE_POINT(aMenu != NULL, "aMenu", );
aMenu->addAction(a);
}
bool GTUtilsMSAEditorSequenceArea::isSequenceSelected(HI::GUITestOpStatus &os, const QString &seqName) {
MSAEditorSequenceArea *msaEditArea = qobject_cast<MSAEditorSequenceArea*>
(GTWidget::findWidget(os, "msa_editor_sequence_area"));
CHECK_SET_ERR_RESULT(msaEditArea != NULL, "MsaEditorSequenceArea not found", false);
QMainWindow* mw = AppContext::getMainWindow()->getQMainWindow();
MSAEditor* editor = mw->findChild<MSAEditor*>();
CHECK_SET_ERR_RESULT(editor != NULL, "MsaEditor not found", false);
//Seq names are drawn on widget, so this hack is needed
U2Region selectedRowsRegion = msaEditArea->getSelectedRows();
QStringList selectedRowNames;
for(int x = selectedRowsRegion.startPos; x < selectedRowsRegion.endPos(); x++)
selectedRowNames.append(editor->getMSAObject()->getRow(x).getName());
if (selectedRowNames.contains(seqName)) {
return true;
}
return false;
}
QStringList GTUtilsMSAEditorSequenceArea::getVisibleNames(HI::GUITestOpStatus &os){
Q_UNUSED(os);
QMainWindow* mw = AppContext::getMainWindow()->getQMainWindow();
MSAEditor* editor = mw->findChild<MSAEditor*>();
CHECK_SET_ERR_RESULT(editor != NULL, "MsaEditor not found", QStringList());
MSAEditorSequenceArea* seqArea = editor->getUI()->getSequenceArea();
CHECK_SET_ERR_RESULT(NULL != seqArea, "MSA Editor sequence area is NULL", QStringList());
int startSeq = seqArea->getFirstVisibleSequence();
int lastSeq = seqArea->getLastVisibleSequence(true);
QVector<U2Region> rows;
editor->getUI()->getCollapseModel()->getVisibleRows(startSeq, lastSeq, rows);
QStringList visiableRowNames;
foreach(U2Region region, rows){
for(int x = region.startPos; x < region.endPos(); x++)
visiableRowNames.append(editor->getMSAObject()->getRow(x).getName());
}
return visiableRowNames;
}
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();
}