showTranslation.setVisible(nucleotide);
conservationMenuItem.setEnabled(!nucleotide);
modifyConservation.setEnabled(!nucleotide);
-
+ showGroupConservation.setEnabled(!nucleotide);
// Remember AlignFrame always starts as protein
if (!nucleotide)
{
showUnconservedMenuItem.setSelected(av.showUnconserved);
showGroupConsensus.setSelected(av.showGroupConsensus);
showGroupConservation.setSelected(av.showGroupConservation);
+ showConsensusHistogram.setSelected(av.showConsensusHistogram);
+ showConsensusProfile.setSelected(av.showConsensusProfile);
setColourSelected(ColourSchemeProperty.getColourName(av
.getGlobalColourScheme()));
}
JPanel progressPanel;
+ Long lId=new Long(id);
GridLayout layout = (GridLayout) statusPanel.getLayout();
- if (progressBars.get(new Long(id)) != null)
+ if (progressBars.get(lId) != null)
{
progressPanel = (JPanel) progressBars.get(new Long(id));
statusPanel.remove(progressPanel);
- progressBars.remove(progressPanel);
+ progressBars.remove(lId);
progressPanel = null;
if (message != null)
{
statusBar.setText(message);
}
- if (progressBarHandlers.contains(new Long(id)))
+ if (progressBarHandlers.contains(lId))
{
- progressBarHandlers.remove(new Long(id));
+ progressBarHandlers.remove(lId);
}
layout.setRows(layout.getRows() - 1);
}
layout.setRows(layout.getRows() + 1);
statusPanel.add(progressPanel);
- progressBars.put(new Long(id), progressPanel);
+ progressBars.put(lId, progressPanel);
}
// update GUI
setMenusForViewport();
viewport.historyList.push(command);
viewport.redoList.clear();
updateEditMenuBar();
- viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
+ viewport.hasHiddenColumns = (viewport.colSel!=null && viewport.colSel.getHiddenColumns() != null && viewport.colSel.getHiddenColumns().size()>0);
}
}
if (originalSource != null)
{
- originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
+ originalSource.hasHiddenColumns = (viewport.colSel!=null && viewport.colSel.getHiddenColumns() != null && viewport.colSel.getHiddenColumns().size()>0);
originalSource.firePropertyChange("alignment", null,
originalSource.alignment.getSequences());
}
if (originalSource != null)
{
- originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
+ originalSource.hasHiddenColumns = (viewport.colSel!=null && viewport.colSel.getHiddenColumns() != null && viewport.colSel.getHiddenColumns().size()>0);
originalSource.firePropertyChange("alignment", null,
originalSource.alignment.getSequences());
}
featureSettings.close();
featureSettings = null;
}
+ if (!showSeqFeatures.isSelected())
+ {
+ // make sure features are actually displayed
+ showSeqFeatures.setSelected(true);
+ showSeqFeatures_actionPerformed(null);
+ }
featureSettings = new FeatureSettings(this);
}
{
seqs.setSequences(new SeqCigar[]
{ seqs.getSequences()[0] });
+ // TODO: if seqs.getSequences().length>1 then should really have warned user!
+
}
return seqs;
}
.getServiceClient(sh);
impl.attachWSMenuEntry(seqsrchmenu, this);
}
- // finally, add the whole shebang onto the webservices menu
wsmenu.add(seqsrchmenu);
}
+ // finally, add the whole shebang onto the webservices menu
resetWebServiceMenu();
for (int i = 0, j = wsmenu.size(); i < j; i++)
{
{
webService.removeAll();
build_fetchdbmenu(webService);
+ build_urlServiceMenu(webService);
+ }
+
+ /**
+ * construct any groupURL type service menu entries.
+ * @param webService
+ */
+ private void build_urlServiceMenu(JMenu webService)
+ {
+ jalview.ws.EnfinEnvision2OneWay.getInstance().attachWSMenuEntry(webService, this);
}
/*
protected void showGroupConsensus_actionPerformed(ActionEvent e)
{
viewport.setShowGroupConsensus(showGroupConsensus.getState());
- alignPanel.updateAnnotation();
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
}
protected void showGroupConservation_actionPerformed(ActionEvent e)
{
viewport.setShowGroupConservation(showGroupConservation.getState());
- alignPanel.updateAnnotation();
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+ }
+
+ /* (non-Javadoc)
+ * @see jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt.event.ActionEvent)
+ */
+ protected void showConsensusHistogram_actionPerformed(ActionEvent e)
+ {
+ viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+ }
+
+ /* (non-Javadoc)
+ * @see jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt.event.ActionEvent)
+ */
+ protected void showConsensusProfile_actionPerformed(ActionEvent e)
+ {
+ viewport.setShowConsensusProfile(showConsensusProfile.getState());
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+ }
+ protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
+ {
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
}
/*