MainFrame aptxApp = Archaeopteryx.createApplication(aptxTree,
APTX_CONFIG, treeTitle);
- adaptAptxGui(aptxApp);
+
LoadedTreeSequenceAssociation bindAptxNodes = new LoadedTreeSequenceAssociation(
jalviewAlignport.getAlignment().getSequencesArray(), aptxTree);
bindAptxNodes.associateLeavesToSequences();
bindAptxNodes.getNodesWithAlignment());
bindTreeViewFrameToJalview(aptxApp);
+ adaptAptxGui(aptxApp);
return aptxApp;
}
else if (menu.getText().contains("View"))
{
menu.addSeparator();
- menu.add(new JMenuItem("Sort alignment by tree"));
+ JMenuItem sortByTree = new JMenuItem("Sort alignment by tree");
+ JMenuItem refreshJalview = new JMenuItem(
+ "Filter alignment to show only currently visible sequences");
+
+ refreshJalview.setFont(menu.getFont());
+
+ menu.add(sortByTree);
+ menu.add(refreshJalview);
+
+ sortByTree.setFont(menu.getFont());
+ sortByTree.setVisible(false); // don't show unless it's actually
+ // possible
+
+ refreshJalview.addActionListener(activeAptx.get(aptxFrame));
+
+
}
}