void PairAlign::connectSignals() {
connect(showHideSequenceWidget, SIGNAL(si_subgroupStateChanged(QString)), SLOT(sl_subwidgetStateChanged(QString)));
connect(showHideSettingsWidget, SIGNAL(si_subgroupStateChanged(QString)), SLOT(sl_subwidgetStateChanged(QString)));
connect(showHideOutputWidget, SIGNAL(si_subgroupStateChanged(QString)), SLOT(sl_subwidgetStateChanged(QString)));
connect(algorithmListComboBox, SIGNAL(currentIndexChanged(QString)), SLOT(sl_algorithmSelected(QString)));
connect(inNewWindowCheckBox, SIGNAL(clicked(bool)), SLOT(sl_inNewWindowCheckBoxChangeState(bool)));
connect(alignButton, SIGNAL(clicked()), SLOT(sl_alignButtonPressed()));
connect(outputFileSelectButton, SIGNAL(clicked()), SLOT(sl_checkState()));
connect(outputFileLineEdit, SIGNAL(textChanged(QString)), SLOT(sl_outputFileChanged()));
connect(firstSeqSelectorWC, SIGNAL(si_selectionChanged()), SLOT(sl_selectorTextChanged()));
connect(secondSeqSelectorWC, SIGNAL(si_selectionChanged()), SLOT(sl_selectorTextChanged()));
connect(msa->getMaObject(), SIGNAL(si_lockedStateChanged()), SLOT(sl_checkState()));
connect(msa->getMaObject(), SIGNAL(si_alignmentChanged(const MultipleAlignment&, const MaModificationInfo&)), SLOT(sl_alignmentChanged()));
}
void LRegionsSelection::clear() {
QVector<U2Region> tmpRemoved = regions;
regions.clear();
if (!tmpRemoved.isEmpty()) {
emit si_selectionChanged(this, emptyLRegions, tmpRemoved);
}
}
void LRegionsSelection::removeRegion(const U2Region& r) {
int idx = regions.indexOf(r);
if (idx == -1) {
return;
}
regions.remove(idx);
QVector<U2Region> tmpRemoved; tmpRemoved.append(r);
emit si_selectionChanged(this, emptyLRegions, tmpRemoved);
}
void LRegionsSelection::addRegion(const U2Region& r) {
assert(r.length > 0);
if (regions.contains(r)) {
return;
}
regions.append(r);
QVector<U2Region> tmpAdded; tmpAdded.append(r);
emit si_selectionChanged(this, tmpAdded, emptyLRegions);
}
MSAOverview::MSAOverview(MSAEditorUI *_ui)
: editor(_ui->getEditor()),
ui(_ui),
sequenceArea(_ui->getSequenceArea())
{
connect(sequenceArea, SIGNAL(si_visibleRangeChanged()), this, SLOT(sl_visibleRangeChanged()));
connect(sequenceArea, SIGNAL(si_selectionChanged(MSAEditorSelection,MSAEditorSelection)),
SLOT(sl_selectionChanged()));
connect(editor->getMSAObject(), SIGNAL(si_alignmentChanged(MAlignment,MAlignmentModInfo)),
SLOT(sl_redraw()));
}
McaEditorReferenceArea::McaEditorReferenceArea(McaEditorWgt *ui, SequenceObjectContext *ctx)
: PanView(ui, ctx, McaEditorReferenceRenderAreaFactory(ui, NULL != ui ? ui->getEditor() : NULL)),
editor(NULL != ui ? ui->getEditor() : NULL),
ui(ui),
renderer(dynamic_cast<McaReferenceAreaRenderer *>(getRenderArea()->getRenderer()))
{
SAFE_POINT(NULL != renderer, "Renderer is NULL", );
singleBaseSelection = true;
setLocalToolbarVisible(false);
settings->showMainRuler = false;
scrollBar->hide();
rowBar->hide();
connect(ui->getEditor()->getMaObject(), SIGNAL(si_alignmentChanged(MultipleAlignment,MaModificationInfo)),
SLOT(sl_update()));
connect(ui->getScrollController(), SIGNAL(si_visibleAreaChanged()), SLOT(sl_visibleRangeChanged()));
connect(ui->getSequenceArea(), SIGNAL(si_selectionChanged(MaEditorSelection,MaEditorSelection)),
SLOT(sl_selectionChanged(MaEditorSelection,MaEditorSelection)));
connect(ui, SIGNAL(si_clearSelection()), SLOT(sl_clearSelection()));
connect(ui->getSequenceArea(), SIGNAL(si_clearReferenceSelection()),
SLOT(sl_clearSelection()));
connect(ctx->getSequenceSelection(),
SIGNAL(si_selectionChanged(LRegionsSelection*, const QVector<U2Region>&, const QVector<U2Region>&)),
SLOT(sl_onSelectionChanged(LRegionsSelection*, const QVector<U2Region>&, const QVector<U2Region>&)));
connect(this, SIGNAL(si_selectionChanged()),
ui->getSequenceArea(), SLOT(sl_backgroundSelectionChanged()));
connect(editor, SIGNAL(si_fontChanged(const QFont &)), SLOT(sl_fontChanged(const QFont &)));
connect(ui->getConsensusArea(), SIGNAL(si_mismatchRedrawRequired()), SLOT(completeUpdate()));
connect(scrollBar, SIGNAL(valueChanged(int)), ui->getScrollController()->getHorizontalScrollBar(), SLOT(setValue(int)));
sl_fontChanged(editor->getFont());
}
MaOverview::MaOverview(MaEditorWgt *ui)
: QWidget(ui),
editor(ui->getEditor()),
ui(ui),
sequenceArea(ui->getSequenceArea()),
stepX(0),
stepY(0)
{
connect(sequenceArea, SIGNAL(si_visibleRangeChanged()), this, SLOT(sl_visibleRangeChanged()));
connect(sequenceArea, SIGNAL(si_selectionChanged(MaEditorSelection,MaEditorSelection)),
SLOT(sl_selectionChanged()));
connect(editor->getMaObject(), SIGNAL(si_alignmentChanged(MultipleAlignment,MaModificationInfo)),
SLOT(sl_redraw()));
connect(ui->getScrollController(), SIGNAL(si_visibleAreaChanged()), SLOT(sl_redraw()));
connect(ui->getCollapseModel(), SIGNAL(si_toggled()), SLOT(sl_redraw()));
}
QWidget* RefSeqCommonWidget::createReferenceGroup(){
QWidget *group = new QWidget(this);
QVBoxLayout *layout = new QVBoxLayout;
layout->setContentsMargins(0, 0, 0, 0);
layout->setSpacing(5);
layout->setAlignment(Qt::AlignTop);
reSeqSelector = new SequenceSelectorWidgetController(msaEditor);
connect(reSeqSelector, SIGNAL(si_selectionChanged()), SLOT(sl_textControllerChanged()));
layout->addWidget(reSeqSelector);
group->setLayout(layout);
return group;
}
McaEditorWgt::McaEditorWgt(McaEditor *editor)
: MaEditorWgt(editor)
{
rowHeightController = new McaRowHeightController(this);
refCharController = new McaReferenceCharController(this, editor);
initActions();
initWidgets();
refArea = new McaEditorReferenceArea(this, getEditor()->getReferenceContext());
connect(refArea, SIGNAL(si_selectionChanged()), statusBar, SLOT(sl_update()));
seqAreaHeaderLayout->insertWidget(0, refArea);
MaEditorConsensusAreaSettings consSettings;
consSettings.visibleElements = MSAEditorConsElement_CONSENSUS_TEXT | MSAEditorConsElement_RULER;
consSettings.highlightMismatches = true;
consArea->setDrawSettings(consSettings);
MSAConsensusAlgorithmFactory* algoFactory = AppContext::getMSAConsensusAlgorithmRegistry()->getAlgorithmFactory(BuiltInConsensusAlgorithms::SIMPLE_EXTENDED_ALGO);
consArea->setConsensusAlgorithm(algoFactory);
QString name = getEditor()->getReferenceContext()->getSequenceObject()->getSequenceName();
QWidget *refName = createHeaderLabelWidget(tr("Reference %1:").arg(name),
Qt::Alignment(Qt::AlignRight | Qt::AlignVCenter), refArea);
refName->setObjectName("reference label container widget");
nameAreaLayout->insertWidget(0, refName);
QVector<U2Region> itemRegions;
for (int i = 0; i < editor->getNumSequences(); i++) {
itemRegions << U2Region(i, 1);
}
collapseModel->setTrivialGroupsPolicy(MSACollapsibleItemModel::Allow);
collapseModel->reset(itemRegions);
collapseModel->collapseAll(false);
collapseModel->setFakeCollapsibleModel(true);
collapsibleMode = true;
McaEditorConsensusArea* mcaConsArea = qobject_cast<McaEditorConsensusArea*>(consArea);
SAFE_POINT(mcaConsArea != NULL, "Failed to cast consensus area to MCA consensus area", );
connect(mcaConsArea->getMismatchController(), SIGNAL(si_selectMismatch(int)), refArea, SLOT(sl_selectMismatch(int)));
}
void McaEditorReferenceArea::sl_onSelectionChanged(LRegionsSelection * /*selection*/, const QVector<U2Region> &addedRegions, const QVector<U2Region> &removedRegions) {
if (addedRegions.size() == 1) {
const U2Region addedRegion = addedRegions.first();
qint64 baseToScrollTo = -1;
if (removedRegions.size() == 1) {
const U2Region removedRegion = removedRegions.first();
if (addedRegion.startPos < removedRegion.startPos && addedRegion.endPos() == removedRegion.endPos()) {
baseToScrollTo = addedRegion.startPos;
} else if (addedRegion.startPos == removedRegion.startPos && addedRegion.endPos() > removedRegion.endPos()) {
baseToScrollTo = addedRegion.endPos() - 1;
} else {
baseToScrollTo = addedRegion.startPos;
}
} else {
baseToScrollTo = addedRegion.startPos;
}
ui->getScrollController()->scrollToBase(static_cast<int>(baseToScrollTo), width());
}
emit si_selectionChanged();
}
void LRegionsSelection::setSelectedRegions(const QVector<U2Region>& newSelection) {
QVector<U2Region> tmpRemoved = regions;
regions = newSelection;
emit si_selectionChanged(this, newSelection, tmpRemoved);
}