import jalview.commands.CommandI;
import jalview.commands.OrderCommand;
import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.BinaryNode;
initTreePanel(alignPanel, null, null, newtree, inputData);
}
+ /**
+ * columnwise tree associated with positions in aa
+ *
+ * @param alignPanel
+ * @param fin
+ * @param title
+ * @param aa
+ */
+ public TreePanel(AlignmentPanel alignPanel, NewickFile fin,
+ AlignmentAnnotation aa, String title)
+ {
+ super();
+ columnWise=true;
+ assocAnnotation = aa;
+ this.setFrameIcon(null);
+ this.treeTitle = title;
+ initTreePanel(alignPanel, null, null, fin, null);
+ }
+
+ boolean columnWise=false;
+ AlignmentAnnotation assocAnnotation=null;
+ public boolean isColumnWise()
+ {
+ return columnWise;
+ }
+ public AlignmentAnnotation getAssocAnnotation() {
+ return assocAnnotation;
+ }
+
public AlignmentI getAlignment()
{
return getTreeCanvas().getViewport().getAlignment();
this.treeType = type;
this.scoreModelName = modelName;
+ if (columnWise)
+ {
+ bootstrapMenu.setVisible(false);
+ placeholdersMenu.setSelected(false);
+ placeholdersMenu.setVisible(false);
+ fitToWindow.setSelected(false);
+ sortAssocViews.setVisible(false);
+ }
+
treeCanvas = new TreeCanvas(this, ap, scrollPane);
scrollPane.setViewportView(treeCanvas);
&& !((SequenceNode) node).isDummy())
{
String newname = null;
- SequenceI sq = (SequenceI) ((SequenceNode) node).element();
+ SequenceI sq = (SequenceI) ((BinaryNode) node).element();
if (sq != null)
{
// search dbrefs, features and annotation
{
// String oldname = ((SequenceNode) node).getName();
// TODO : save oldname in the undo object for this modification.
- ((SequenceNode) node).setName(newname);
+ ((BinaryNode) node).setName(newname);
}
}
}