sortbytree view setting and action added - setting is not yet stored in the jalview xml

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index b90d89b..19ec9e0 100755 (executable)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -184,6 +184,8 @@ public class AlignViewport implements SelectionSource
 
   Hashtable hiddenRepSequences;
 
+  boolean sortByTree;
+
   /**
    * Creates a new AlignViewport object.
    * 
@@ -374,13 +376,14 @@ public class AlignViewport implements SelectionSource
 
     wrapAlignment = jalview.bin.Cache.getDefault("WRAP_ALIGNMENT", false);
     showUnconserved = jalview.bin.Cache.getDefault("SHOW_UNCONSERVED", false);
+    sortByTree = jalview.bin.Cache.getDefault("SORT_BY_TREE", false);
   }
 
   /**
-   * DOCUMENT ME!
+   * set the flag
    * 
    * @param b
-   *                DOCUMENT ME!
+   *             features are displayed if true
    */
   public void setShowSequenceFeatures(boolean b)
   {
@@ -2207,4 +2210,30 @@ public class AlignViewport implements SelectionSource
   {
     showUnconserved=showunconserved;
   }
+  /**
+   * return the alignPanel containing the given viewport. Use this to get the
+   * components currently handling the given viewport.
+   * @param av
+   * @return null or an alignPanel guaranteed to have non-null alignFrame reference
+   */
+  public AlignmentPanel getAlignPanel()
+  {
+    AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(this.getSequenceSetId());
+    AlignmentPanel ap=null;
+    for (int p=0;aps!=null && p<aps.length; p++)
+    {
+      if (aps[p].av == this)
+      {
+        return aps[p];
+      }
+    }
+    return null;
+  }
+  public boolean getSortByTree()
+  {
+    return sortByTree;
+  }
+  public void setSortByTree(boolean sort) {
+    sortByTree = sort;
+  }
 }

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index d179355..0c937dd 100755 (executable)
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -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)
   {