X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreePanel.java;h=e67365e677f9597de1bd72533668f5b10a5c130a;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=d179355ade6c4639d958677b22bb4ea5fa71b279;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index d179355..e67365e 100755
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -1,26 +1,30 @@
 /*
- * 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 (Version 2.8.2b1)
+ * Copyright (C) 2014 The Jalview Authors
  * 
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
  * 
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
  * 
  * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.gui;
 
 import java.beans.*;
 import java.io.*;
 import java.util.*;
+import java.util.List;
+
 import javax.imageio.*;
 
 import java.awt.*;
@@ -30,9 +34,12 @@ import javax.swing.*;
 
 import org.jibble.epsgraphics.*;
 import jalview.analysis.*;
+import jalview.commands.CommandI;
+import jalview.commands.OrderCommand;
 import jalview.datamodel.*;
 import jalview.io.*;
 import jalview.jbgui.*;
+import jalview.util.MessageManager;
 
 /**
  * DOCUMENT ME!
@@ -56,17 +63,17 @@ 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 +89,15 @@ 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)
@@ -140,6 +147,10 @@ public class TreePanel extends GTreePanel
           if (tree == null)
           {
             System.out.println("tree is null");
+            // TODO: deal with case when a change event is received whilst a
+            // tree is still being calculated - should save reference for
+            // processing message later.
+            return;
           }
           if (evt.getNewValue() == null)
           {
@@ -147,9 +158,9 @@ public class TreePanel extends GTreePanel
                     .println("new alignment sequences vector value is null");
           }
 
-          tree.UpdatePlaceHolders((Vector) evt.getNewValue());
+          tree.UpdatePlaceHolders((List<SequenceI>) evt.getNewValue());
           treeCanvas.nameHash.clear(); // reset the mapping between canvas
-                                        // rectangles and leafnodes
+          // rectangles and leafnodes
           repaint();
         }
       }
@@ -250,11 +261,11 @@ public class TreePanel extends GTreePanel
       {
         if (odata == null)
         {
-          tree = new NJTree(av.alignment.getSequencesArray(), newtree);
+          tree = new NJTree(av.getAlignment().getSequencesArray(), newtree);
         }
         else
         {
-          tree = new NJTree(av.alignment.getSequencesArray(), odata,
+          tree = new NJTree(av.getAlignment().getSequencesArray(), odata,
                   newtree);
         }
         if (!tree.hasOriginalSequenceData())
@@ -266,19 +277,21 @@ public class TreePanel extends GTreePanel
       {
         int start, end;
         SequenceI[] seqs;
-        AlignmentView seqStrings = av.getAlignmentView(av
-                .getSelectionGroup() != null);
-        if (av.getSelectionGroup() == null)
+        boolean selview = av.getSelectionGroup() != null
+                && av.getSelectionGroup().getSize() > 1;
+        AlignmentView seqStrings = av.getAlignmentView(selview);
+        if (!selview)
         {
           start = 0;
-          end = av.alignment.getWidth();
-          seqs = av.alignment.getSequencesArray();
+          end = av.getAlignment().getWidth();
+          seqs = av.getAlignment().getSequencesArray();
         }
         else
         {
           start = av.getSelectionGroup().getStartRes();
           end = av.getSelectionGroup().getEndRes() + 1;
-          seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
+          seqs = av.getSelectionGroup().getSequencesInOrder(
+                  av.getAlignment());
         }
 
         tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);
@@ -290,7 +303,10 @@ public class TreePanel extends GTreePanel
       treeCanvas.setTree(tree);
       treeCanvas.repaint();
       av.setCurrentTree(tree);
-
+      if (av.getSortByTree())
+      {
+        sortByTree_actionPerformed(null);
+      }
     }
   }
 
@@ -331,7 +347,7 @@ public class TreePanel extends GTreePanel
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void textbox_actionPerformed(ActionEvent e)
   {
@@ -357,27 +373,34 @@ public class TreePanel extends GTreePanel
       buffer.append("PID");
     }
 
-    Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);
+    jalview.io.NewickFile fout = new jalview.io.NewickFile(
+            tree.getTopNode());
+    try
+    {
+      cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(),
+              tree.isHasRootDistance()));
+      Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);
+    } catch (OutOfMemoryError oom)
+    {
+      new OOMWarning("generating newick tree file", oom);
+      cap.dispose();
+    }
 
-    jalview.io.NewickFile fout = new jalview.io.NewickFile(tree
-            .getTopNode());
-    cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(),
-            tree.isHasRootDistance()));
   }
 
   /**
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void saveAsNewick_actionPerformed(ActionEvent e)
   {
-    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
-            .getProperty("LAST_DIRECTORY"));
+    JalviewFileChooser chooser = new JalviewFileChooser(
+            jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
     chooser.setFileView(new JalviewFileView());
-    chooser.setDialogTitle("Save tree as newick file");
-    chooser.setToolTipText("Save");
+    chooser.setDialogTitle(MessageManager.getString("label.save_tree_as_newick"));
+    chooser.setToolTipText(MessageManager.getString("action.save"));
 
     int value = chooser.showSaveDialog(null);
 
@@ -389,10 +412,10 @@ public class TreePanel extends GTreePanel
 
       try
       {
-        jalview.io.NewickFile fout = new jalview.io.NewickFile(tree
-                .getTopNode());
-        String output = fout.print(tree.isHasBootstrap(), tree
-                .isHasDistances(), tree.isHasRootDistance());
+        jalview.io.NewickFile fout = new jalview.io.NewickFile(
+                tree.getTopNode());
+        String output = fout.print(tree.isHasBootstrap(),
+                tree.isHasDistances(), tree.isHasRootDistance());
         java.io.PrintWriter out = new java.io.PrintWriter(
                 new java.io.FileWriter(choice));
         out.println(output);
@@ -408,7 +431,7 @@ public class TreePanel extends GTreePanel
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void printMenu_actionPerformed(ActionEvent e)
   {
@@ -469,8 +492,10 @@ public class TreePanel extends GTreePanel
         // af.addSortByOrderMenuItem(ServiceName + " Ordering",
         // msaorder);
 
-        Desktop.addInternalFrame(af, "Original Data for " + this.title,
-                AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+        Desktop.addInternalFrame(af, MessageManager.formatMessage(
+                "label.original_data_for_params", new String[]
+                { this.title }), AlignFrame.DEFAULT_WIDTH,
+                AlignFrame.DEFAULT_HEIGHT);
       }
     }
   }
@@ -479,7 +504,7 @@ public class TreePanel extends GTreePanel
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void fitToWindow_actionPerformed(ActionEvent e)
   {
@@ -488,10 +513,87 @@ public class TreePanel extends GTreePanel
   }
 
   /**
+   * sort the associated alignment view by the current tree.
+   * 
+   * @param e
+   */
+  public void sortByTree_actionPerformed(ActionEvent e)
+  {
+
+    if (treeCanvas.applyToAllViews)
+    {
+      final ArrayList<CommandI> commands = new ArrayList<CommandI>();
+      for (AlignmentPanel ap : PaintRefresher.getAssociatedPanels(av
+              .getSequenceSetId()))
+      {
+        commands.add(sortAlignmentIn(ap.av.getAlignPanel()));
+      }
+      av.getAlignPanel().alignFrame.addHistoryItem(new CommandI()
+      {
+
+        @Override
+        public void undoCommand(AlignmentI[] views)
+        {
+          for (CommandI tsort : commands)
+          {
+            tsort.undoCommand(views);
+          }
+        }
+
+        @Override
+        public int getSize()
+        {
+          return commands.size();
+        }
+
+        @Override
+        public String getDescription()
+        {
+          return "Tree Sort (many views)";
+        }
+
+        @Override
+        public void doCommand(AlignmentI[] views)
+        {
+
+          for (CommandI tsort : commands)
+          {
+            tsort.doCommand(views);
+          }
+        }
+      });
+      for (AlignmentPanel ap : PaintRefresher.getAssociatedPanels(av
+              .getSequenceSetId()))
+      {
+        // ensure all the alignFrames refresh their GI after adding an undo item
+        ap.alignFrame.updateEditMenuBar();
+      }
+    }
+    else
+    {
+      treeCanvas.ap.alignFrame
+              .addHistoryItem(sortAlignmentIn(treeCanvas.ap));
+    }
+
+  }
+
+  public CommandI sortAlignmentIn(AlignmentPanel ap)
+  {
+    AlignViewport av = ap.av;
+    SequenceI[] oldOrder = av.getAlignment().getSequencesArray();
+    AlignmentSorter.sortByTree(av.getAlignment(), tree);
+    CommandI undo;
+    undo = new OrderCommand("Tree Sort", oldOrder, av.getAlignment());
+
+    ap.paintAlignment(true);
+    return undo;
+  }
+
+  /**
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void font_actionPerformed(ActionEvent e)
   {
@@ -520,7 +622,7 @@ public class TreePanel extends GTreePanel
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void distanceMenu_actionPerformed(ActionEvent e)
   {
@@ -531,7 +633,7 @@ public class TreePanel extends GTreePanel
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void bootstrapMenu_actionPerformed(ActionEvent e)
   {
@@ -542,7 +644,7 @@ public class TreePanel extends GTreePanel
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void placeholdersMenu_actionPerformed(ActionEvent e)
   {
@@ -553,7 +655,7 @@ public class TreePanel extends GTreePanel
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void epsTree_actionPerformed(ActionEvent e)
   {
@@ -593,8 +695,8 @@ public class TreePanel extends GTreePanel
               { "eps" }, new String[]
               { "Encapsulated Postscript" }, "Encapsulated Postscript");
       chooser.setFileView(new jalview.io.JalviewFileView());
-      chooser.setDialogTitle("Create EPS file from tree");
-      chooser.setToolTipText("Save");
+      chooser.setDialogTitle(MessageManager.getString("label.create_eps_from_tree"));
+      chooser.setToolTipText(MessageManager.getString("action.save"));
 
       int value = chooser.showSaveDialog(this);
 
@@ -625,7 +727,7 @@ public class TreePanel extends GTreePanel
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void pngTree_actionPerformed(ActionEvent e)
   {
@@ -640,8 +742,8 @@ public class TreePanel extends GTreePanel
               { "Portable network graphics" }, "Portable network graphics");
 
       chooser.setFileView(new jalview.io.JalviewFileView());
-      chooser.setDialogTitle("Create PNG image from tree");
-      chooser.setToolTipText("Save");
+      chooser.setDialogTitle(MessageManager.getString("label.create_png_from_tree"));
+      chooser.setToolTipText(MessageManager.getString("action.save"));
 
       int value = chooser.showSaveDialog(this);
 
@@ -668,4 +770,75 @@ 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);
+          }
+        }
+      }
+    });
+  }
 }