import jalview.structures.models.AAStructureBindingModel;
import jalview.util.MappingUtils;
import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
public class AlignFrame extends EmbmenuFrame implements ActionListener,
ItemListener, KeyListener, AlignViewControllerGuiI
public AlignFrame(AlignmentI al, JalviewLite applet,
String title, boolean embedded, boolean addToDisplay)
{
+ this(al, null, null, applet, title, embedded, addToDisplay);
+ }
+
+ public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
+ ColumnSelection columnSelection, JalviewLite applet,
+ String title, boolean embedded)
+ {
+ this(al, hiddenSeqs, columnSelection, applet, title, embedded, true);
+ }
+
+ public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
+ ColumnSelection columnSelection, JalviewLite applet,
+ String title, boolean embedded, boolean addToDisplay)
+ {
if (applet != null)
{
jalviewServletURL = applet.getParameter("APPLICATION_URL");
}
}
viewport = new AlignViewport(al, applet);
+
+ if (hiddenSeqs != null && hiddenSeqs.length > 0)
+ {
+ viewport.hideSequence(hiddenSeqs);
+ viewport.setHasHiddenRows(true);
+ }
+ if (columnSelection != null)
+ {
+ viewport.setColumnSelection(columnSelection);
+ }
+
alignPanel = new AlignmentPanel(this, viewport);
avc = new jalview.controller.AlignViewController(this, viewport,
alignPanel);
viewport.updateConsensus(alignPanel);
displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
- followMouseOverFlag.setState(viewport.getFollowHighlight());
+ followMouseOverFlag.setState(viewport.isFollowHighlight());
showGroupConsensus.setState(viewport.isShowGroupConsensus());
showGroupConservation.setState(viewport.isShowGroupConservation());
showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
private void mouseOverFlag_stateChanged()
{
- viewport.followHighlight = followMouseOverFlag.getState();
+ viewport.setFollowHighlight(followMouseOverFlag.getState());
// TODO: could kick the scrollTo mechanism to reset view for current
// searchresults.
}
jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
"label.alignment_output_command", new Object[]
{ e.getActionCommand() }), 600, 500);
- cap.setText(new AppletFormatAdapter().formatSequences(
+
+ FeatureRenderer fr = this.alignPanel.cloneFeatureRenderer();
+ viewport.setFeatureRenderer(fr);
+ cap.setText(new AppletFormatAdapter(viewport).formatSequences(
e.getActionCommand(), viewport.getAlignment(),
viewport.getShowJVSuffix()));
}
viewport.addToRedoList(command);
command.undoCommand(null);
- AlignViewport originalSource = getOriginatingSource(command);
+ AlignmentViewport originalSource = getOriginatingSource(command);
// JBPNote Test
if (originalSource != viewport)
{
viewport.addToHistoryList(command);
command.doCommand(null);
- AlignViewport originalSource = getOriginatingSource(command);
+ AlignmentViewport originalSource = getOriginatingSource(command);
// JBPNote Test
if (originalSource != viewport)
{
.getAlignment().getSequences());
}
- AlignViewport getOriginatingSource(CommandI command)
+ AlignmentViewport getOriginatingSource(CommandI command)
{
- AlignViewport originalSource = null;
+ AlignmentViewport originalSource = null;
// For sequence removal and addition, we need to fire
// the property change event FROM the viewport where the
// original alignment was altered
}
- void changeColour(ColourSchemeI cs)
+ public void changeColour(ColourSchemeI cs)
{
int threshold = 0;
private CheckboxMenuItem showAutoLast;
+ private SplitFrame splitFrame;
+
/**
* Attach the alignFrame panels after embedding menus, if necessary. This used
* to be called setEmbedded, but is now creates the dropdown menus in a
return false;
}
+ public SplitFrame getSplitFrame()
+ {
+ return this.splitFrame;
+ }
+
+ public void setSplitFrame(SplitFrame sf)
+ {
+ this.splitFrame = sf;
+ }
}