package jalview.ext.archaeopteryx;
import jalview.bin.Cache;
-import jalview.ext.treeviewer.ExternalTreeControlsI;
-import jalview.ext.treeviewer.ExternalTreeFrame;
-import jalview.ext.treeviewer.ExternalTreeI;
-import jalview.ext.treeviewer.ExternalTreePanel;
+import jalview.ext.treeviewer.TreeControlsI;
+import jalview.ext.treeviewer.TreeFrameI;
+import jalview.ext.treeviewer.TreeI;
+import jalview.ext.treeviewer.TreePanelI;
+import jalview.ext.treeviewer.TreeViewerBindingI;
+import jalview.ext.treeviewer.TreeViewerUtils;
import jalview.gui.Desktop;
import jalview.gui.EPSOptions;
import jalview.io.JalviewFileChooser;
import org.forester.phylogeny.Phylogeny;
import org.jibble.epsgraphics.EpsGraphics2D;
-public class AptxFrame implements ExternalTreeFrame
+public class AptxFrame implements TreeFrameI
{
private final MainFrame aptxFrame;
- private ExternalTreePanel aptxPanel;
+ private TreeViewerBindingI viewBinding;
- private ExternalTreeControlsI aptxControls;
+ private TreePanelI aptxPanel;
+
+ private TreeControlsI aptxControls;
public AptxFrame(Phylogeny tree, Configuration aptxConfig,
else if (menu.getText().contains("View"))
{
menu.addSeparator();
+
JMenuItem sortByTree = new JMenuItem("Sort alignment by tree");
JMenuItem refreshJalview = new JMenuItem(
"Filter alignment to show only currently visible sequences");
+ JMenuItem hideCollapsed = new JMenuItem(
+ "Hide sequences of collapsed nodes");
refreshJalview.setFont(menu.getFont());
+ refreshJalview.addActionListener(new ActionListener() {
+
+ @Override
+ public void actionPerformed(ActionEvent e) {
+ TreeViewerBindingI bindingManager = TreeViewerUtils
+ .getActiveTreeViews().get(AptxFrame.this);
+ bindingManager.actionPerformed(e);
+ }
+ });
+
+ sortByTree.addActionListener(new ActionListener()
+ {
- menu.add(sortByTree);
- menu.add(refreshJalview);
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ TreeViewerBindingI bindingManager = TreeViewerUtils
+ .getActiveTreeViews().get(AptxFrame.this);
+ bindingManager.sortByTree_actionPerformed();
- sortByTree.setFont(menu.getFont());
- refreshJalview.addActionListener(new ActionListener()
+ }
+
+ });
+
+ hideCollapsed.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- // TODO Auto-generated method stub
-
+ TreeViewerBindingI bindingManager = TreeViewerUtils
+ .getActiveTreeViews().get(AptxFrame.this);
+ bindingManager.hideCollapsedSequences_actionPerformed();
+
}
});
+ menu.add(sortByTree);
+ menu.add(refreshJalview);
+ menu.add(hideCollapsed);
+
+ sortByTree.setFont(menu.getFont());
+
+
}
}
}
@Override
- public ExternalTreePanel getTreePanel()
+ public TreePanelI getTreePanel()
{
return aptxPanel;
}
@Override
- public ExternalTreeI getTree()
+ public TreeI getTree()
{
return aptxPanel.getTree();
}
@Override
- public void checkMultipleTrees()
+ public void enableMultipleTrees()
{
aptxFrame.activateSaveAllIfNeeded();
}
@Override
- public ExternalTreeControlsI getTreeControls()
+ public TreeControlsI getTreeControls()
{
return aptxControls;
}
}
+ @Override
+ public TreeViewerBindingI getViewBinding()
+ {
+ return viewBinding;
+ }
+
+ @Override
+ public void setViewBinding(TreeViewerBindingI alignmentBinding)
+ {
+ viewBinding = alignmentBinding;
+ }
+
+
+ @Override
+ public void setMaximumSize(Dimension maximumSize)
+ {
+ aptxFrame.setMaximumSize(maximumSize);
+
+ }
+
+ @Override
+ public void setPreferredSize(Dimension preferredSize)
+ {
+ aptxFrame.setPreferredSize(preferredSize);
+
+ }
+
}
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