- tp = af.showNewickTree(new NewickFile(tree.getNewick()),
- tree.getTitle(), safeInt(tree.getWidth()),
- safeInt(tree.getHeight()), safeInt(tree.getXpos()),
- safeInt(tree.getYpos()));
+ if (tree.isColumnWise())
+ {
+ AlignmentAnnotation aa = (AlignmentAnnotation) annotationIds.get(tree
+ .getColumnReference());
+ if (aa == null)
+ {
+ Console.warn(
+ "Null alignment annotation when restoring columnwise tree");
+ }
+ tp = af.showColumnWiseTree(new NewickFile(tree.getNewick()), aa,
+ tree.getTitle(), safeInt(tree.getWidth()),
+ safeInt(tree.getHeight()), safeInt(tree.getXpos()),
+ safeInt(tree.getYpos()));
+
+ }
+ else
+ {
+ tp = af.showNewickTree(new NewickFile(tree.getNewick()),
+ tree.getTitle(), safeInt(tree.getWidth()),
+ safeInt(tree.getHeight()), safeInt(tree.getXpos()),
+ safeInt(tree.getYpos()));
+ }