X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FTreeCanvas.java;h=a50abfa4a7f0f04941e5823702631672c26011fd;hb=a8f483d04205bb8273ee311c12968b7e86d205fa;hp=94834363056bfa073c0acff835e1bf330022c8aa;hpb=beaa65409fc4cf865392c4e6e57116b64af37dfc;p=jalview.git

diff --git a/src/jalview/appletgui/TreeCanvas.java b/src/jalview/appletgui/TreeCanvas.java
index 9483436..a50abfa 100755
--- a/src/jalview/appletgui/TreeCanvas.java
+++ b/src/jalview/appletgui/TreeCanvas.java
@@ -1,553 +1,690 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 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
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * 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.
- *
- * 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
- */
-
-package jalview.appletgui;
-
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.analysis.*;
-import jalview.datamodel.*;
-import jalview.schemes.*;
-import jalview.util.*;
-
-public class TreeCanvas
-    extends Panel implements MouseListener
-{
-  NJTree tree;
-  ScrollPane scrollPane;
-  AlignViewport av;
-  public static final String PLACEHOLDER = " * ";
-  Font font;
-  int fontSize = 12;
-
-  boolean fitToWindow = true;
-  boolean showDistances = false;
-  boolean showBootstrap = false;
-  boolean markPlaceholders = false;
-
-  int offx = 20;
-  int offy = 20;
-
-  float threshold;
-
-  String longestName;
-  int labelLength = -1;
-
-  //RubberbandRectangle rubberband;
-
-  Vector listeners;
-
-  Hashtable nameHash = new Hashtable();
-  Hashtable nodeHash = new Hashtable();
-
-  public TreeCanvas(AlignViewport av, NJTree tree, ScrollPane scroller,
-                    String label)
-  {
-    this.av = av;
-    this.tree = tree;
-    scrollPane = scroller;
-    addMouseListener(this);
-    tree.findHeight(tree.getTopNode());
-    longestName = label;
-    setLayout(null);
-
-    PaintRefresher.Register(this, av.alignment);
-  }
-
-  public void TreeSelectionChanged(Sequence sequence)
-  {
-    SequenceGroup selected = av.getSelectionGroup();
-    if (selected == null)
-    {
-      selected = new SequenceGroup();
-      av.setSelectionGroup(selected);
-    }
-
-    selected.setEndRes(av.alignment.getWidth()-1);
-    selected.addOrRemove(sequence, true);
-
-    PaintRefresher.Refresh(this, av.alignment);
-    repaint();
-  }
-
-  public void setTree(NJTree tree)
-  {
-    this.tree = tree;
-    tree.findHeight(tree.getTopNode());
-  }
-
-  public void drawNode(Graphics g, SequenceNode node, float chunk, float scale,
-                       int width, int offx, int offy)
-  {
-    if (node == null)
-    {
-      return;
-    }
-
-    if (node.left() == null && node.right() == null)
-    {
-      // Drawing leaf node
-
-      float height = node.height;
-      float dist = node.dist;
-
-      int xstart = (int) ( (height - dist) * scale) + offx;
-      int xend = (int) (height * scale) + offx;
-
-      int ypos = (int) (node.ycount * chunk) + offy;
-
-      if (node.element() instanceof SequenceI)
-      {
-        if ( ( (SequenceI) ( (SequenceNode) node).element()).getColor() ==
-            Color.white)
-        {
-          g.setColor(Color.black);
-        }
-        else
-        {
-          g.setColor( ( (SequenceI) ( (SequenceNode) node).element()).getColor().
-                     darker());
-        }
-
-      }
-      else
-      {
-        g.setColor(Color.black);
-      }
-
-      // Draw horizontal line
-      g.drawLine(xstart, ypos, xend, ypos);
-
-      String nodeLabel = "";
-      if (showDistances && node.dist > 0)
-      {
-        nodeLabel = new Format("%5.2f").form(node.dist);
-      }
-      if (showBootstrap)
-      {
-        if (showDistances)
-        {
-          nodeLabel = nodeLabel + " : ";
-        }
-        nodeLabel = nodeLabel + String.valueOf(node.getBootstrap());
-      }
-      if (!nodeLabel.equals(""))
-      {
-        g.drawString(nodeLabel, xstart, ypos - 10);
-      }
-
-      String name = (markPlaceholders && node.isPlaceholder()) ?
-          (PLACEHOLDER + node.getName()) : node.getName();
-      FontMetrics fm = g.getFontMetrics(font);
-      int charWidth = fm.stringWidth(name) + 3;
-      int charHeight = fm.getHeight();
-
-      Rectangle rect = new Rectangle(xend + 20, ypos - charHeight,
-                                     charWidth, charHeight);
-
-      nameHash.put( (SequenceI) node.element(), rect);
-
-      // Colour selected leaves differently
-      SequenceGroup selected = av.getSelectionGroup();
-      if (selected != null &&
-          selected.sequences.contains( (SequenceI) node.element()))
-      {
-        g.setColor(Color.gray);
-
-        g.fillRect(xend + 10, ypos - charHeight + 3, charWidth, charHeight);
-        g.setColor(Color.white);
-      }
-      g.drawString(name, xend + 10, ypos);
-      g.setColor(Color.black);
-    }
-    else
-    {
-      drawNode(g, (SequenceNode) node.left(), chunk, scale, width, offx, offy);
-      drawNode(g, (SequenceNode) node.right(), chunk, scale, width, offx, offy);
-
-      float height = node.height;
-      float dist = node.dist;
-
-      int xstart = (int) ( (height - dist) * scale) + offx;
-      int xend = (int) (height * scale) + offx;
-      int ypos = (int) (node.ycount * chunk) + offy;
-
-      g.setColor( ( (SequenceNode) node).color.darker());
-
-      // Draw horizontal line
-      g.drawLine(xstart, ypos, xend, ypos);
-      g.fillRect(xend - 2, ypos - 2, 4, 4);
-
-      int ystart = (int) ( ( (SequenceNode) node.left()).ycount * chunk) + offy;
-      int yend = (int) ( ( (SequenceNode) node.right()).ycount * chunk) + offy;
-
-      Rectangle pos = new Rectangle(xend - 2, ypos - 2, 5, 5);
-      nodeHash.put(node, pos);
-
-      g.drawLine( (int) (height * scale) + offx, ystart,
-                 (int) (height * scale) + offx, yend);
-
-      if (showDistances && node.dist > 0)
-      {
-        g.drawString(new Format("%5.2f").form(node.dist), xstart, ypos - 5);
-      }
-
-    }
-  }
-
-  public Object findElement(int x, int y)
-  {
-    Enumeration keys = nameHash.keys();
-
-    while (keys.hasMoreElements())
-    {
-      Object ob = keys.nextElement();
-      Rectangle rect = (Rectangle) nameHash.get(ob);
-
-      if (x >= rect.x && x <= (rect.x + rect.width) &&
-          y >= rect.y && y <= (rect.y + rect.height))
-      {
-        return ob;
-      }
-    }
-    keys = nodeHash.keys();
-
-    while (keys.hasMoreElements())
-    {
-      Object ob = keys.nextElement();
-      Rectangle rect = (Rectangle) nodeHash.get(ob);
-
-      if (x >= rect.x && x <= (rect.x + rect.width) &&
-          y >= rect.y && y <= (rect.y + rect.height))
-      {
-        return ob;
-      }
-    }
-    return null;
-
-  }
-
-  public void pickNodes(Rectangle pickBox)
-  {
-    int width = getSize().width;
-    int height = getSize().height;
-
-    SequenceNode top = tree.getTopNode();
-
-    float wscale = (float) (width * .8 - offx * 2) / tree.getMaxHeight()
-        ;
-    if (top.count == 0)
-    {
-      top.count = ( (SequenceNode) top.left()).count +
-          ( (SequenceNode) top.right()).count;
-    }
-    float chunk = (float) (height - offy * 2) / top.count;
-
-    pickNode(pickBox, top, chunk, wscale, width, offx, offy);
-  }
-
-  public void pickNode(Rectangle pickBox, SequenceNode node, float chunk,
-                       float scale, int width, int offx, int offy)
-  {
-    if (node == null)
-    {
-      return;
-    }
-
-    if (node.left() == null && node.right() == null)
-    {
-      float height = node.height;
-      float dist = node.dist;
-
-      int xstart = (int) ( (height - dist) * scale) + offx;
-      int xend = (int) (height * scale) + offx;
-
-      int ypos = (int) (node.ycount * chunk) + offy;
-
-      if (pickBox.contains(new Point(xend, ypos)))
-      {
-        if (node.element() instanceof SequenceI)
-        {
-          SequenceI seq = (SequenceI) node.element();
-          SequenceGroup sg = av.getSelectionGroup();
-          if (sg != null)
-          {
-            sg.addOrRemove(seq, true);
-          }
-        }
-      }
-    }
-    else
-    {
-      pickNode(pickBox, (SequenceNode) node.left(), chunk, scale, width, offx,
-               offy);
-      pickNode(pickBox, (SequenceNode) node.right(), chunk, scale, width, offx,
-               offy);
-    }
-  }
-
-  public void setColor(SequenceNode node, Color c)
-  {
-    if (node == null)
-    {
-      return;
-    }
-
-    if (node.left() == null && node.right() == null)
-    {
-      node.color = c;
-
-      if (node.element() instanceof SequenceI)
-      {
-        ( (SequenceI) node.element()).setColor(c);
-      }
-    }
-    else
-    {
-      node.color = c;
-      setColor( (SequenceNode) node.left(), c);
-      setColor( (SequenceNode) node.right(), c);
-    }
-  }
-
-  public void paint(Graphics g)
-  {
-
-    font = new Font("Verdana", Font.PLAIN, fontSize);
-    g.setFont(font);
-
-    FontMetrics fm = g.getFontMetrics(font);
-
-    if (nameHash.size() == 0)
-    {
-      repaint();
-    }
-
-    if (fitToWindow ||
-        (!fitToWindow &&
-         scrollPane.getSize().height > fm.getHeight() * nameHash.size() + offy))
-    {
-      draw(g, scrollPane.getSize().width, scrollPane.getSize().height);
-    }
-    else
-    {
-      setSize(new Dimension(scrollPane.getSize().width,
-                            fm.getHeight() * nameHash.size()));
-      draw(g, scrollPane.getSize().width, fm.getHeight() * nameHash.size());
-    }
-
-    scrollPane.validate();
-  }
-
-  public int getFontSize()
-  {
-    return fontSize;
-  }
-
-  public void setFontSize(int fontSize)
-  {
-    this.fontSize = fontSize;
-    repaint();
-  }
-
-  public void draw(Graphics g, int width, int height)
-  {
-
-    g.setColor(Color.white);
-    g.fillRect(0, 0, width, height);
-
-    labelLength = g.getFontMetrics(font).stringWidth(longestName) + 20; //20 allows for scrollbar
-
-    float wscale = (float) (width - labelLength - offx * 2) / tree.getMaxHeight();
-
-    SequenceNode top = tree.getTopNode();
-
-    if (top.count == 0)
-    {
-      top.count = ( (SequenceNode) top.left()).count +
-          ( (SequenceNode) top.right()).count;
-    }
-    float chunk = (float) (height - offy * 2) / top.count;
-
-    drawNode(g, tree.getTopNode(), chunk, wscale, width, offx, offy);
-
-    if (threshold != 0)
-    {
-      if (av.getCurrentTree() == tree)
-      {
-        g.setColor(Color.red);
-      }
-      else
-      {
-        g.setColor(Color.gray);
-      }
-
-      int x = (int) (threshold *
-                     (float) (getSize().width - labelLength - 2 * offx) + offx);
-
-      g.drawLine(x, 0, x, getSize().height);
-    }
-
-  }
-
-  public void mouseReleased(MouseEvent e)
-  {}
-
-  public void mouseEntered(MouseEvent e)
-  {}
-
-  public void mouseExited(MouseEvent e)
-  {}
-
-  public void mouseClicked(MouseEvent e)
-  {
-  }
-
-  public void mousePressed(MouseEvent e)
-  {
-    av.setCurrentTree(tree);
-
-    int x = e.getX();
-    int y = e.getY();
-
-    Object ob = findElement(x, y);
-
-    if (ob instanceof SequenceI)
-    {
-      TreeSelectionChanged( (Sequence) ob);
-      repaint();
-      return;
-
-    }
-    else if (ob instanceof SequenceNode)
-    {
-      SequenceNode tmpnode = (SequenceNode) ob;
-      tree.swapNodes(tmpnode);
-      tree.reCount(tree.getTopNode());
-      tree.findHeight(tree.getTopNode());
-    }
-    else
-    {
-      // Find threshold
-
-      if (tree.getMaxHeight() != 0)
-      {
-        threshold = (float) (x - offx) /
-            (float) (getSize().width - labelLength - 2 * offx);
-
-        tree.getGroups().removeAllElements();
-        tree.groupNodes(tree.getTopNode(), threshold);
-        setColor(tree.getTopNode(), Color.black);
-
-        av.setSelectionGroup(null);
-        av.alignment.deleteAllGroups();
-
-        for (int i = 0; i < tree.getGroups().size(); i++)
-        {
-
-          Color col = new Color( (int) (Math.random() * 255),
-                                (int) (Math.random() * 255),
-                                (int) (Math.random() * 255));
-          setColor( (SequenceNode) tree.getGroups().elementAt(i), col.brighter());
-
-          Vector l = tree.findLeaves( (SequenceNode) tree.getGroups().elementAt(
-              i), new Vector());
-
-          Vector sequences = new Vector();
-          for (int j = 0; j < l.size(); j++)
-          {
-            SequenceI s1 = (SequenceI) ( (SequenceNode) l.elementAt(j)).element();
-            if(!sequences.contains(s1))
-              sequences.addElement(s1);
-          }
-
-          ColourSchemeI cs = null;
-
-          if (av.getGlobalColourScheme() != null)
-          {
-            if (av.getGlobalColourScheme() instanceof UserColourScheme)
-            {
-              cs = new UserColourScheme(
-                  ( (UserColourScheme) av.getGlobalColourScheme()).getColours());
-
-            }
-            else
-              cs = ColourSchemeProperty.getColour(sequences,
-                                                  av.alignment.getWidth(),
-                                                  ColourSchemeProperty.getColourName(
-                                                      av.getGlobalColourScheme()));
-
-              cs.setThreshold(av.getGlobalColourScheme().getThreshold(),
-                                                   av.getIgnoreGapsConsensus());
-          }
-
-          SequenceGroup sg = new SequenceGroup(sequences, "TreeGroup",
-                                               cs, true, true,
-                                               false, 0, av.alignment.getWidth()-1);
-
-
-          if (  av.getGlobalColourScheme()!=null
-             && av.getGlobalColourScheme().conservationApplied())
-            {
-            Conservation c = new Conservation("Group",
-                                              ResidueProperties.propHash, 3,
-                                              sg.sequences, sg.getStartRes(),
-                                              sg.getEndRes());
-
-            c.calculate();
-            c.verdict(false, av.ConsPercGaps);
-            cs.setConservation(c);
-
-            sg.cs = cs;
-
-          }
-
-          av.alignment.addGroup(sg);
-
-        }
-      }
-    }
-
-    PaintRefresher.Refresh(this, av.alignment);
-    repaint();
-
-  }
-
-  public void setShowDistances(boolean state)
-  {
-    this.showDistances = state;
-    repaint();
-  }
-
-  public void setShowBootstrap(boolean state)
-  {
-    this.showBootstrap = state;
-    repaint();
-  }
-
-  public void setMarkPlaceholders(boolean state)
-  {
-    this.markPlaceholders = state;
-    repaint();
-  }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.appletgui;
+
+import java.util.*;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import jalview.analysis.*;
+import jalview.datamodel.*;
+import jalview.schemes.*;
+import jalview.util.*;
+
+public class TreeCanvas extends Panel implements MouseListener,
+        MouseMotionListener
+{
+  NJTree tree;
+
+  ScrollPane scrollPane;
+
+  AlignViewport av;
+
+  public static final String PLACEHOLDER = " * ";
+
+  Font font;
+
+  boolean fitToWindow = true;
+
+  boolean showDistances = false;
+
+  boolean showBootstrap = false;
+
+  boolean markPlaceholders = false;
+
+  int offx = 20;
+
+  int offy;
+
+  float threshold;
+
+  String longestName;
+
+  int labelLength = -1;
+
+  Hashtable nameHash = new Hashtable();
+
+  Hashtable nodeHash = new Hashtable();
+
+  SequenceNode highlightNode;
+
+  AlignmentPanel ap;
+
+  public TreeCanvas(AlignmentPanel ap, ScrollPane scroller)
+  {
+    this.ap = ap;
+    this.av = ap.av;
+    font = av.getFont();
+    scrollPane = scroller;
+    addMouseListener(this);
+    addMouseMotionListener(this);
+    setLayout(null);
+
+    PaintRefresher.Register(this, av.getSequenceSetId());
+  }
+
+  public void treeSelectionChanged(SequenceI sequence)
+  {
+    SequenceGroup selected = av.getSelectionGroup();
+    if (selected == null)
+    {
+      selected = new SequenceGroup();
+      av.setSelectionGroup(selected);
+    }
+
+    selected.setEndRes(av.getAlignment().getWidth() - 1);
+    selected.addOrRemove(sequence, true);
+  }
+
+  public void setTree(NJTree tree)
+  {
+    this.tree = tree;
+    tree.findHeight(tree.getTopNode());
+
+    // Now have to calculate longest name based on the leaves
+    Vector leaves = tree.findLeaves(tree.getTopNode(), new Vector());
+    boolean has_placeholders = false;
+    longestName = "";
+
+    for (int i = 0; i < leaves.size(); i++)
+    {
+      SequenceNode lf = (SequenceNode) leaves.elementAt(i);
+
+      if (lf.isPlaceholder())
+      {
+        has_placeholders = true;
+      }
+
+      if (longestName.length() < ((Sequence) lf.element()).getName()
+              .length())
+      {
+        longestName = TreeCanvas.PLACEHOLDER
+                + ((Sequence) lf.element()).getName();
+      }
+    }
+
+    setMarkPlaceholders(has_placeholders);
+  }
+
+  public void drawNode(Graphics g, SequenceNode node, float chunk,
+          float scale, int width, int offx, int offy)
+  {
+    if (node == null)
+    {
+      return;
+    }
+
+    if (node.left() == null && node.right() == null)
+    {
+      // Drawing leaf node
+
+      float height = node.height;
+      float dist = node.dist;
+
+      int xstart = (int) ((height - dist) * scale) + offx;
+      int xend = (int) (height * scale) + offx;
+
+      int ypos = (int) (node.ycount * chunk) + offy;
+
+      if (node.element() instanceof SequenceI)
+      {
+        SequenceI seq = (SequenceI) node.element();
+
+        if (av.getSequenceColour(seq) == Color.white)
+        {
+          g.setColor(Color.black);
+        }
+        else
+        {
+          g.setColor(av.getSequenceColour(seq).darker());
+        }
+
+      }
+      else
+      {
+        g.setColor(Color.black);
+      }
+
+      // Draw horizontal line
+      g.drawLine(xstart, ypos, xend, ypos);
+
+      String nodeLabel = "";
+      if (showDistances && node.dist > 0)
+      {
+        nodeLabel = new Format("%-.2f").form(node.dist);
+      }
+      if (showBootstrap)
+      {
+        int btstrap = node.getBootstrap();
+        if (btstrap > -1)
+        {
+          if (showDistances)
+          {
+            nodeLabel = nodeLabel + " : ";
+          }
+          nodeLabel = nodeLabel + String.valueOf(node.getBootstrap());
+        }
+      }
+      if (!nodeLabel.equals(""))
+      {
+        g.drawString(nodeLabel, xstart + 2, ypos - 2);
+      }
+
+      String name = (markPlaceholders && node.isPlaceholder()) ? (PLACEHOLDER + node
+              .getName()) : node.getName();
+      FontMetrics fm = g.getFontMetrics(font);
+      int charWidth = fm.stringWidth(name) + 3;
+      int charHeight = fm.getHeight();
+
+      Rectangle rect = new Rectangle(xend + 10, ypos - charHeight,
+              charWidth, charHeight);
+
+      nameHash.put(node.element(), rect);
+
+      // Colour selected leaves differently
+      SequenceGroup selected = av.getSelectionGroup();
+      if (selected != null
+              && selected.getSequences(null).contains(node.element()))
+      {
+        g.setColor(Color.gray);
+
+        g.fillRect(xend + 10, ypos - charHeight + 3, charWidth, charHeight);
+        g.setColor(Color.white);
+      }
+      g.drawString(name, xend + 10, ypos);
+      g.setColor(Color.black);
+    }
+    else
+    {
+      drawNode(g, (SequenceNode) node.left(), chunk, scale, width, offx,
+              offy);
+      drawNode(g, (SequenceNode) node.right(), chunk, scale, width, offx,
+              offy);
+
+      float height = node.height;
+      float dist = node.dist;
+
+      int xstart = (int) ((height - dist) * scale) + offx;
+      int xend = (int) (height * scale) + offx;
+      int ypos = (int) (node.ycount * chunk) + offy;
+
+      g.setColor(node.color.darker());
+
+      // Draw horizontal line
+      g.drawLine(xstart, ypos, xend, ypos);
+      if (node == highlightNode)
+      {
+        g.fillRect(xend - 3, ypos - 3, 6, 6);
+      }
+      else
+      {
+        g.fillRect(xend - 2, ypos - 2, 4, 4);
+      }
+
+      int ystart = (int) (((SequenceNode) node.left()).ycount * chunk)
+              + offy;
+      int yend = (int) (((SequenceNode) node.right()).ycount * chunk)
+              + offy;
+
+      Rectangle pos = new Rectangle(xend - 2, ypos - 2, 5, 5);
+      nodeHash.put(node, pos);
+
+      g.drawLine((int) (height * scale) + offx, ystart,
+              (int) (height * scale) + offx, yend);
+
+      String nodeLabel = "";
+
+      if (showDistances && (node.dist > 0))
+      {
+        nodeLabel = new Format("%-.2f").form(node.dist);
+      }
+
+      if (showBootstrap)
+      {
+        int btstrap = node.getBootstrap();
+        if (btstrap > -1)
+        {
+          if (showDistances)
+          {
+            nodeLabel = nodeLabel + " : ";
+          }
+          nodeLabel = nodeLabel + String.valueOf(node.getBootstrap());
+        }
+      }
+
+      if (!nodeLabel.equals(""))
+      {
+        g.drawString(nodeLabel, xstart + 2, ypos - 2);
+      }
+
+    }
+  }
+
+  public Object findElement(int x, int y)
+  {
+    Enumeration keys = nameHash.keys();
+
+    while (keys.hasMoreElements())
+    {
+      Object ob = keys.nextElement();
+      Rectangle rect = (Rectangle) nameHash.get(ob);
+
+      if (x >= rect.x && x <= (rect.x + rect.width) && y >= rect.y
+              && y <= (rect.y + rect.height))
+      {
+        return ob;
+      }
+    }
+    keys = nodeHash.keys();
+
+    while (keys.hasMoreElements())
+    {
+      Object ob = keys.nextElement();
+      Rectangle rect = (Rectangle) nodeHash.get(ob);
+
+      if (x >= rect.x && x <= (rect.x + rect.width) && y >= rect.y
+              && y <= (rect.y + rect.height))
+      {
+        return ob;
+      }
+    }
+    return null;
+
+  }
+
+  public void pickNodes(Rectangle pickBox)
+  {
+    int width = getSize().width;
+    int height = getSize().height;
+
+    SequenceNode top = tree.getTopNode();
+
+    float wscale = (float) (width * .8 - offx * 2) / tree.getMaxHeight();
+    if (top.count == 0)
+    {
+      top.count = ((SequenceNode) top.left()).count
+              + ((SequenceNode) top.right()).count;
+    }
+    float chunk = (float) (height - offy) / top.count;
+
+    pickNode(pickBox, top, chunk, wscale, width, offx, offy);
+  }
+
+  public void pickNode(Rectangle pickBox, SequenceNode node, float chunk,
+          float scale, int width, int offx, int offy)
+  {
+    if (node == null)
+    {
+      return;
+    }
+
+    if (node.left() == null && node.right() == null)
+    {
+      float height = node.height;
+      // float dist = node.dist;
+
+      // int xstart = (int) ( (height - dist) * scale) + offx;
+      int xend = (int) (height * scale) + offx;
+
+      int ypos = (int) (node.ycount * chunk) + offy;
+
+      if (pickBox.contains(new Point(xend, ypos)))
+      {
+        if (node.element() instanceof SequenceI)
+        {
+          SequenceI seq = (SequenceI) node.element();
+          SequenceGroup sg = av.getSelectionGroup();
+          if (sg != null)
+          {
+            sg.addOrRemove(seq, true);
+          }
+        }
+      }
+    }
+    else
+    {
+      pickNode(pickBox, (SequenceNode) node.left(), chunk, scale, width,
+              offx, offy);
+      pickNode(pickBox, (SequenceNode) node.right(), chunk, scale, width,
+              offx, offy);
+    }
+  }
+
+  public void setColor(SequenceNode node, Color c)
+  {
+    if (node == null)
+    {
+      return;
+    }
+
+    if (node.left() == null && node.right() == null)
+    {
+      node.color = c;
+
+      if (node.element() instanceof SequenceI)
+      {
+        av.setSequenceColour((SequenceI) node.element(), c);
+      }
+    }
+    else
+    {
+      node.color = c;
+      setColor((SequenceNode) node.left(), c);
+      setColor((SequenceNode) node.right(), c);
+    }
+  }
+
+  @Override
+  public void update(Graphics g)
+  {
+    paint(g);
+  }
+
+  @Override
+  public void paint(Graphics g)
+  {
+    if (tree == null)
+    {
+      return;
+    }
+
+    if (nameHash.size() == 0)
+    {
+      repaint();
+    }
+
+    int width = scrollPane.getSize().width;
+    int height = scrollPane.getSize().height;
+    if (!fitToWindow)
+    {
+      height = g.getFontMetrics(font).getHeight() * nameHash.size();
+    }
+
+    if (getSize().width > width)
+    {
+      setSize(new Dimension(width, height));
+      scrollPane.validate();
+      return;
+    }
+
+    setSize(new Dimension(width, height));
+
+    g.setFont(font);
+    draw(g, width, height);
+    validate();
+  }
+
+  public void draw(Graphics g, int width, int height)
+  {
+    offy = font.getSize() + 10;
+
+    g.setColor(Color.white);
+    g.fillRect(0, 0, width, height);
+
+    labelLength = g.getFontMetrics(font).stringWidth(longestName) + 20; // 20
+    // allows
+    // for
+    // scrollbar
+
+    float wscale = (width - labelLength - offx * 2) / tree.getMaxHeight();
+
+    SequenceNode top = tree.getTopNode();
+
+    if (top.count == 0)
+    {
+      top.count = ((SequenceNode) top.left()).count
+              + ((SequenceNode) top.right()).count;
+    }
+    float chunk = (float) (height - offy) / top.count;
+
+    drawNode(g, tree.getTopNode(), chunk, wscale, width, offx, offy);
+
+    if (threshold != 0)
+    {
+      if (av.getCurrentTree() == tree)
+      {
+        g.setColor(Color.red);
+      }
+      else
+      {
+        g.setColor(Color.gray);
+      }
+
+      int x = (int) (threshold * (getSize().width - labelLength - 2 * offx) + offx);
+
+      g.drawLine(x, 0, x, getSize().height);
+    }
+
+  }
+
+  @Override
+  public void mouseReleased(MouseEvent e)
+  {
+  }
+
+  @Override
+  public void mouseEntered(MouseEvent e)
+  {
+  }
+
+  @Override
+  public void mouseExited(MouseEvent e)
+  {
+  }
+
+  @Override
+  public void mouseClicked(MouseEvent evt)
+  {
+    if (highlightNode != null)
+    {
+      if (evt.getClickCount() > 1)
+      {
+        tree.swapNodes(highlightNode);
+        tree.reCount(tree.getTopNode());
+        tree.findHeight(tree.getTopNode());
+      }
+      else
+      {
+        Vector leaves = new Vector();
+        tree.findLeaves(highlightNode, leaves);
+
+        for (int i = 0; i < leaves.size(); i++)
+        {
+          SequenceI seq = (SequenceI) ((SequenceNode) leaves.elementAt(i))
+                  .element();
+          treeSelectionChanged(seq);
+        }
+      }
+
+      PaintRefresher.Refresh(this, av.getSequenceSetId());
+      repaint();
+      av.sendSelection();
+    }
+  }
+
+  @Override
+  public void mouseDragged(MouseEvent ect)
+  {
+  }
+
+  @Override
+  public void mouseMoved(MouseEvent evt)
+  {
+    av.setCurrentTree(tree);
+
+    Object ob = findElement(evt.getX(), evt.getY());
+
+    if (ob instanceof SequenceNode)
+    {
+      highlightNode = (SequenceNode) ob;
+      repaint();
+    }
+    else
+    {
+      if (highlightNode != null)
+      {
+        highlightNode = null;
+        repaint();
+      }
+    }
+  }
+
+  @Override
+  public void mousePressed(MouseEvent e)
+  {
+    av.setCurrentTree(tree);
+
+    int x = e.getX();
+    int y = e.getY();
+
+    Object ob = findElement(x, y);
+
+    if (ob instanceof SequenceI)
+    {
+      treeSelectionChanged((Sequence) ob);
+      PaintRefresher.Refresh(this, av.getSequenceSetId());
+      repaint();
+      av.sendSelection();
+      return;
+    }
+    else if (!(ob instanceof SequenceNode))
+    {
+      // Find threshold
+
+      if (tree.getMaxHeight() != 0)
+      {
+        threshold = (float) (x - offx)
+                / (float) (getSize().width - labelLength - 2 * offx);
+
+        tree.getGroups().removeAllElements();
+        tree.groupNodes(tree.getTopNode(), threshold);
+        setColor(tree.getTopNode(), Color.black);
+
+        av.setSelectionGroup(null);
+        av.getAlignment().deleteAllGroups();
+        av.clearSequenceColours();
+
+        colourGroups();
+
+      }
+    }
+
+    PaintRefresher.Refresh(this, av.getSequenceSetId());
+    repaint();
+
+  }
+
+  void colourGroups()
+  {
+    for (int i = 0; i < tree.getGroups().size(); i++)
+    {
+
+      Color col = new Color((int) (Math.random() * 255),
+              (int) (Math.random() * 255), (int) (Math.random() * 255));
+      setColor((SequenceNode) tree.getGroups().elementAt(i), col.brighter());
+
+      Vector l = tree.findLeaves(
+              (SequenceNode) tree.getGroups().elementAt(i), new Vector());
+
+      Vector sequences = new Vector();
+      for (int j = 0; j < l.size(); j++)
+      {
+        SequenceI s1 = (SequenceI) ((SequenceNode) l.elementAt(j))
+                .element();
+        if (!sequences.contains(s1))
+        {
+          sequences.addElement(s1);
+        }
+      }
+
+      ColourSchemeI cs = null;
+
+      SequenceGroup sg = new SequenceGroup(sequences, "", cs, true, true,
+              false, 0, av.getAlignment().getWidth() - 1);
+
+      if (av.getGlobalColourScheme() != null)
+      {
+        if (av.getGlobalColourScheme() instanceof UserColourScheme)
+        {
+          cs = new UserColourScheme(
+                  ((UserColourScheme) av.getGlobalColourScheme())
+                          .getColours());
+
+        }
+        else
+        {
+          cs = ColourSchemeProperty.getColour(sg, ColourSchemeProperty
+                  .getColourName(av.getGlobalColourScheme()));
+        }
+        // cs is null if shading is an annotationColourGradient
+        if (cs != null)
+        {
+          cs.setThreshold(av.getGlobalColourScheme().getThreshold(),
+                  av.getIgnoreGapsConsensus());
+        }
+      }
+      // TODO: cs used to be initialized with a sequence collection and
+      // recalcConservation called automatically
+      // instead we set it manually - recalc called after updateAnnotation
+      sg.cs = cs;
+
+      sg.setName("JTreeGroup:" + sg.hashCode());
+      sg.setIdColour(col);
+      if (av.getGlobalColourScheme() != null
+              && av.getGlobalColourScheme().conservationApplied())
+      {
+        Conservation c = new Conservation("Group",
+                ResidueProperties.propHash, 3, sg.getSequences(null),
+                sg.getStartRes(), sg.getEndRes());
+
+        c.calculate();
+        c.verdict(false, av.getConsPercGaps());
+        cs.setConservation(c);
+
+        sg.cs = cs;
+
+      }
+
+      av.getAlignment().addGroup(sg);
+
+    }
+    ap.updateAnnotation();
+
+  }
+
+  public void setShowDistances(boolean state)
+  {
+    this.showDistances = state;
+    repaint();
+  }
+
+  public void setShowBootstrap(boolean state)
+  {
+    this.showBootstrap = state;
+    repaint();
+  }
+
+  public void setMarkPlaceholders(boolean state)
+  {
+    this.markPlaceholders = state;
+    repaint();
+  }
+
+}