From 431b44bc25f290de99d6edd1f7f22c28f0f4d467 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Mon, 1 Jun 2009 15:52:28 +0000
Subject: [PATCH] prototype function for relabelling treenodes with different
 accession/labels

---
 src/jalview/gui/TreePanel.java |   60 +++++++++++++++++++++++++++++++++++++++-
 1 file changed, 59 insertions(+), 1 deletion(-)

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index 0c937dd..eef07fa 100755
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -690,4 +690,62 @@ public class TreePanel extends GTreePanel
       ex.printStackTrace();
     }
   }
-}
+  /**
+   * change node labels to the annotation referred to by labelClass
+   * TODO: promote to a datamodel modification that can be undone
+   * TODO: make argument one case of a generic transformation function ie { undoStep = apply(Tree, TransformFunction)};
+   * @param labelClass
+   */
+  public void changeNames(final String labelClass)
+  {
+    tree.applyToNodes(new NodeTransformI() {
+
+      public void transform(BinaryNode node)
+      {
+        if (node instanceof SequenceNode && !((SequenceNode) node).isPlaceholder() && !((SequenceNode) node).isDummy())
+        {
+          String newname=null;
+          SequenceI sq = (SequenceI) ((SequenceNode) node).element();
+          if (sq!=null)
+          {
+            // search dbrefs, features and annotation
+            DBRefEntry[] refs = jalview.util.DBRefUtils.selectRefs(sq.getDBRef(), new String[] {labelClass.toUpperCase()});
+            if (refs!=null)
+            {
+              for (int i=0; i<refs.length;i++)
+              {
+                if (newname == null) {
+                    newname = new String(refs[i].getAccessionId());
+                } else {
+                  newname = newname +"; "+refs[i].getAccessionId();
+                }
+              }
+            }
+            if (newname==null)
+            {
+              SequenceFeature sf[] = sq.getSequenceFeatures();
+              for (int i=0;sf!=null && i<sf.length; i++)
+              {
+                if (sf[i].getType().equals(labelClass))
+                {
+                  if (newname==null)
+                  {
+                    newname = new String(sf[i].getDescription());
+                  } else {
+                    newname = newname + "; "+sf[i].getDescription();
+                  }
+                }
+              }
+            }
+        }
+          if (newname!=null)
+          {
+            String oldname = ((SequenceNode) node).getName();
+            // TODO : save in the undo object for this modification.
+            ((SequenceNode) node).setName(newname);
+          }
+        }
+      }
+    });
+  }
+}
\ No newline at end of file
-- 
1.7.10.2