if (!Jalview.isHeadlessMode())
{
progressBar = new ProgressBar(this.statusPanel, this.statusBar);
+ statusPanel.setVisible(Jalview.getInstance().getShowStatus());
+ alignFrameMenuBar.setVisible(Jalview.getInstance().getAllowMenuBar());
}
avc = new jalview.controller.AlignViewController(this, viewport,
{
ap.av.getAlignment().padGaps();
}
- ap.av.updateConservation(ap);
- ap.av.updateConsensus(ap);
- ap.av.updateStrucConsensus(ap);
+ if (Jalview.getInstance().getStartCalculations())
+ {
+ ap.av.updateConservation(ap);
+ ap.av.updateConsensus(ap);
+ ap.av.updateStrucConsensus(ap);
+ }
}
}
applyToAllGroups.setState(av.getColourAppliesToAllGroups());
showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
showDbRefsMenuitem.setSelected(av.isShowDBRefs());
- autoCalculate.setSelected(av.autoCalculateConsensus);
+ autoCalculate.setSelected(av.getAutoCalculateConsensusAndConservation());
sortByTree.setSelected(av.sortByTree);
listenToViewSelections.setSelected(av.followSelection);
Desktop.addInternalFrame(frame, MessageManager
.formatMessage("label.overview_params", new Object[]
{ this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
- true, true);
+ true, true, "overview");
frame.pack();
frame.setLayer(JLayeredPane.PALETTE_LAYER);
frame.addInternalFrameListener(
@Override
public void autoCalculate_actionPerformed(ActionEvent e)
{
- viewport.autoCalculateConsensus = autoCalculate.isSelected();
- if (viewport.autoCalculateConsensus)
+ viewport.setAutoCalculateConsensusAndConservation(autoCalculate.isSelected());
+ if (viewport.getAutoCalculateConsensusAndConservation())
{
viewport.firePropertyChange("alignment", null,
viewport.getAlignment().getSequences());