setColourSelected(ColourSchemeProperty.getColourName(av
.getGlobalColourScheme()));
- showSeqFeatures.setSelected(av.showSequenceFeatures);
+ showSeqFeatures.setSelected(av.isShowSequenceFeatures());
hiddenMarkers.setState(av.showHiddenMarkers);
applyToAllGroups.setState(av.getColourAppliesToAllGroups());
showNpFeatsMenuitem.setSelected(av.isShowNpFeats());
@Override
public void exportAnnotations_actionPerformed(ActionEvent e)
{
- new AnnotationExporter().exportAnnotations(alignPanel,
- viewport.isShowAnnotation() ? viewport.getAlignment()
- .getAlignmentAnnotation() : null, viewport
- .getAlignment().getGroups(), ((Alignment) viewport
- .getAlignment()).alignmentProperties);
+ new AnnotationExporter().exportAnnotations(alignPanel);
}
@Override
return;
}
- Vector hiddenColumns = null;
+ ArrayList<int[]> hiddenColumns = null;
if (viewport.hasHiddenColumns())
{
- hiddenColumns = new Vector();
+ hiddenColumns = new ArrayList<int[]>();
int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
.getSelectionGroup().getEndRes();
- for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
- .size(); i++)
+ for (int[] region : viewport.getColumnSelection().getHiddenColumns())
{
- int[] region = (int[]) viewport.getColumnSelection()
- .getHiddenColumns().elementAt(i);
if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
{
- hiddenColumns.addElement(new int[]
+ hiddenColumns.add(new int[]
{ region[0] - hiddenOffset, region[1] - hiddenOffset });
}
}
if (Desktop.jalviewClipboard != null
&& Desktop.jalviewClipboard[2] != null)
{
- Vector hc = (Vector) Desktop.jalviewClipboard[2];
- for (int i = 0; i < hc.size(); i++)
+ List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
+ for (int[] region : hc)
{
- int[] region = (int[]) hc.elementAt(i);
af.viewport.hideColumns(region[0], region[1]);
}
}
if (Desktop.jalviewClipboard != null
&& Desktop.jalviewClipboard[2] != null)
{
- Vector hc = (Vector) Desktop.jalviewClipboard[2];
- for (int i = 0; i < hc.size(); i++)
+ List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
+ for (int region[] : hc)
{
- int[] region = (int[]) hc.elementAt(i);
af.viewport.hideColumns(region[0], region[1]);
}
}
{
viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
.isSelected());
- if (viewport.getShowSequenceFeaturesHeight())
+ if (viewport.isShowSequenceFeaturesHeight())
{
// ensure we're actually displaying features
viewport.setShowSequenceFeatures(true);
}
@Override
+ public void annotationColumn_actionPerformed(ActionEvent e)
+ {
+ new AnnotationColumnChooser(viewport, alignPanel);
+ }
+
+ @Override
public void rnahelicesColour_actionPerformed(ActionEvent e)
{
new RNAHelicesColourChooser(viewport, alignPanel);
{
featuresFile = new FeaturesFile(file, type).parse(viewport
.getAlignment().getDataset(), alignPanel.getSeqPanel().seqCanvas
- .getFeatureRenderer().featureColours, false,
+ .getFeatureRenderer().getFeatureColours(), false,
jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
} catch (Exception ex)
{
if (featuresFile)
{
- viewport.showSequenceFeatures = true;
+ viewport.setShowSequenceFeatures(true);
showSeqFeatures.setSelected(true);
if (alignPanel.getSeqPanel().seqCanvas.fr != null)
{
// try to parse as annotation.
boolean isAnnotation = (format == null || format
.equalsIgnoreCase("PFAM")) ? new AnnotationFile()
- .readAnnotationFile(viewport.getAlignment(), file, protocol)
+ .annotateAlignmentView(viewport, file, protocol)
: false;
if (!isAnnotation)
alignPanel.paintAlignment(true);
}
}
+ public void clearAlignmentSeqRep()
+ {
+ // TODO refactor alignmentseqrep to controller
+ if (viewport.getAlignment().hasSeqrep()) {
+ viewport.getAlignment().setSeqrep(null);
+ PaintRefresher.Refresh(this, viewport.getSequenceSetId());
+ alignPanel.updateAnnotation();
+ alignPanel.paintAlignment(true);
+ }
+ }
@Override
protected void createGroup_actionPerformed(ActionEvent e)