javadoc

[jalview.git] / src / jalview / gui / TreePanel.java

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index d179355..c6d87d7 100755 (executable)
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
+ * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -30,6 +30,7 @@ import javax.swing.*;
 
 import org.jibble.epsgraphics.*;
 import jalview.analysis.*;
+import jalview.commands.OrderCommand;
 import jalview.datamodel.*;
 import jalview.io.*;
 import jalview.jbgui.*;
@@ -56,17 +57,17 @@ public class TreePanel extends GTreePanel
    * Creates a new TreePanel object.
    * 
    * @param av
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param seqVector
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param type
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param pwtype
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param s
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public TreePanel(AlignmentPanel ap, String type, String pwtype)
   {
@@ -82,15 +83,15 @@ public class TreePanel extends GTreePanel
    * Creates a new TreePanel object.
    * 
    * @param av
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param seqVector
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param newtree
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param type
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param pwtype
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public TreePanel(AlignmentPanel ap, String type, String pwtype,
           NewickFile newtree)
@@ -149,7 +150,7 @@ public class TreePanel extends GTreePanel
 
           tree.UpdatePlaceHolders((Vector) evt.getNewValue());
           treeCanvas.nameHash.clear(); // reset the mapping between canvas
-                                        // rectangles and leafnodes
+          // rectangles and leafnodes
           repaint();
         }
       }
@@ -290,7 +291,10 @@ public class TreePanel extends GTreePanel
       treeCanvas.setTree(tree);
       treeCanvas.repaint();
       av.setCurrentTree(tree);
-
+      if (av.getSortByTree())
+      {
+        sortByTree_actionPerformed(null);
+      }
     }
   }
 
@@ -331,7 +335,7 @@ public class TreePanel extends GTreePanel
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void textbox_actionPerformed(ActionEvent e)
   {
@@ -369,7 +373,7 @@ public class TreePanel extends GTreePanel
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void saveAsNewick_actionPerformed(ActionEvent e)
   {
@@ -408,7 +412,7 @@ public class TreePanel extends GTreePanel
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void printMenu_actionPerformed(ActionEvent e)
   {
@@ -479,7 +483,7 @@ public class TreePanel extends GTreePanel
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void fitToWindow_actionPerformed(ActionEvent e)
   {
@@ -488,10 +492,28 @@ public class TreePanel extends GTreePanel
   }
 
   /**
+   * sort the associated alignment view by the current tree.
+   * @param e
+   */
+  public void sortByTree_actionPerformed(ActionEvent e)
+  {
+    AlignmentPanel ap = av.getAlignPanel();
+    SequenceI[] oldOrder = av.getAlignment().getSequencesArray();
+    AlignmentSorter.sortByTree(av.getAlignment(), tree);
+
+    ap.alignFrame
+            .addHistoryItem(new OrderCommand("Tree Sort", oldOrder,
+                    av.alignment));
+
+    ap.paintAlignment(true);
+
+  }
+
+  /**
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void font_actionPerformed(ActionEvent e)
   {
@@ -520,7 +542,7 @@ public class TreePanel extends GTreePanel
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void distanceMenu_actionPerformed(ActionEvent e)
   {
@@ -531,7 +553,7 @@ public class TreePanel extends GTreePanel
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void bootstrapMenu_actionPerformed(ActionEvent e)
   {
@@ -542,7 +564,7 @@ public class TreePanel extends GTreePanel
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void placeholdersMenu_actionPerformed(ActionEvent e)
   {
@@ -553,7 +575,7 @@ public class TreePanel extends GTreePanel
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void epsTree_actionPerformed(ActionEvent e)
   {
@@ -625,7 +647,7 @@ public class TreePanel extends GTreePanel
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void pngTree_actionPerformed(ActionEvent e)
   {
@@ -668,4 +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);
+          }
+        }
+      }
+    });
+  }
 }