X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreeCanvas.java;h=79634f6ea97f2c667a7cea1153cf15834480f197;hb=687aca6928c6be41c2693c6c0f5ab651a40e815e;hp=600683fc841a36f8e3329ffc3da6a43fec9bce90;hpb=ac07859006686a2c62bcf57b24742eb610bc46f0;p=jalview.git

diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index 600683f..79634f6 100755
--- a/src/jalview/gui/TreeCanvas.java
+++ b/src/jalview/gui/TreeCanvas.java
@@ -1,481 +1,810 @@
+/*
+ * 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.gui;
 
-
 import jalview.analysis.*;
+
 import jalview.datamodel.*;
-import jalview.util.*;
+
 import jalview.schemes.*;
-import javax.swing.*;
+
+import jalview.util.*;
+
 import java.awt.*;
 import java.awt.event.*;
-import java.util.*;
 import java.awt.print.*;
 
-public class TreeCanvas extends JPanel implements MouseListener, Runnable, Printable
-{
-  NJTree tree;
-  JScrollPane scrollPane;
-  AlignViewport av;
-
-  Font font;
-  int  fontSize = 12;
-
-  boolean fitToWindow = true;
-  boolean showDistances = false;
-  boolean showBootstrap = false;
+import java.util.*;
 
-  int offx = 20;
-  int offy = 20;
+import javax.swing.*;
 
-  float threshold;
 
-  String longestName;
-  int labelLength=-1;
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class TreeCanvas extends JPanel implements MouseListener, Runnable,
+    Printable
+{
+    /** DOCUMENT ME!! */
+    public static final String PLACEHOLDER = " * ";
+    NJTree tree;
+    JScrollPane scrollPane;
+    AlignViewport av;
+    Font font;
+    FontMetrics fm;
+    boolean fitToWindow = true;
+    boolean showDistances = false;
+    boolean showBootstrap = false;
+    boolean markPlaceholders = false;
+    int offx = 20;
+    int offy;
+    float threshold;
+    String longestName;
+    int labelLength = -1;
+
+    //RubberbandRectangle rubberband;
+    Vector listeners;
+    Hashtable nameHash = new Hashtable();
+    Hashtable nodeHash = new Hashtable();
+
+    /**
+     * Creates a new TreeCanvas object.
+     *
+     * @param av DOCUMENT ME!
+     * @param tree DOCUMENT ME!
+     * @param scroller DOCUMENT ME!
+     * @param label DOCUMENT ME!
+     */
+    public TreeCanvas(AlignViewport av, JScrollPane scroller)
+    {
+        this.av = av;
+        font = av.getFont();
+        scrollPane = scroller;
+        addMouseListener(this);
+        PaintRefresher.Register(this, av.alignment);
+    }
 
-  //RubberbandRectangle rubberband;
 
-  Vector    listeners;
+    /**
+     * DOCUMENT ME!
+     *
+     * @param sequence DOCUMENT ME!
+     */
+    public void TreeSelectionChanged(Sequence sequence)
+    {
+        SequenceGroup selected = av.getSelectionGroup();
 
-  Hashtable nameHash = new Hashtable();
-  Hashtable nodeHash = new Hashtable();
+        if (selected == null)
+        {
+            selected = new SequenceGroup();
+            av.setSelectionGroup(selected);
+        }
 
-  public TreeCanvas(AlignViewport av, NJTree tree, JScrollPane scroller, String label)
-  {
-    this.av = av;
-    this.tree     = tree;
-    scrollPane = scroller;
-    addMouseListener(this);
-    tree.findHeight(tree.getTopNode());
-    longestName = label;
+        selected.setEndRes(av.alignment.getWidth()-1);
+        selected.addOrRemove(sequence, true);
 
-    PaintRefresher.Register(this);
-  }
-  public void TreeSelectionChanged(Sequence sequence)
- {
-    SequenceGroup selected = av.getSelectionGroup();
-    if(selected == null)
-    {
-      selected = new SequenceGroup();
-      av.setSelectionGroup(selected);
+        PaintRefresher.Refresh(this, av.alignment);
+        repaint();
     }
 
-    selected.setEndRes(av.alignment.getWidth());
-    selected.addOrRemove(sequence);
-
+    /**
+     * DOCUMENT ME!
+     *
+     * @param tree DOCUMENT ME!
+     */
+    public void setTree(NJTree tree)
+    {
+        this.tree = tree;
+        tree.findHeight(tree.getTopNode());
 
-    PaintRefresher.Refresh(this);
-    repaint();
- }
+        // 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;
+          }
 
-  public void setTree(NJTree tree) {
-    this.tree = tree;
-    tree.findHeight(tree.getTopNode());
-  }
+          if (longestName.length() < ( (Sequence) lf.element()).getName()
+              .length())
+          {
+            longestName = TreeCanvas.PLACEHOLDER +
+                ( (Sequence) lf.element()).getName();
+          }
+        }
 
-    public void drawNode(Graphics g,SequenceNode node, float chunk, float scale, int width,int offx, int offy) {
-    if (node == null) {
-      return;
+        setMarkPlaceholders(has_placeholders);
     }
 
-    if (node.left() == null && node.right() == null) {
-      // Drawing leaf node
+    /**
+     * DOCUMENT ME!
+     *
+     * @param g DOCUMENT ME!
+     * @param node DOCUMENT ME!
+     * @param chunk DOCUMENT ME!
+     * @param scale DOCUMENT ME!
+     * @param width DOCUMENT ME!
+     * @param offx DOCUMENT ME!
+     * @param offy DOCUMENT ME!
+     */
+    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);
+            }
 
-      float height = node.height;
-      float dist   = node.dist;
+            // Draw horizontal line
+            g.drawLine(xstart, ypos, xend, ypos);
 
-      int xstart = (int)((height-dist)*scale) + offx;
-      int xend =   (int)(height*scale)        + offx;
+            String nodeLabel = "";
 
-      int ypos = (int)(node.ycount * chunk) + offy;
+            if (showDistances && (node.dist > 0))
+            {
+                nodeLabel = new Format("%5.2f").form(node.dist);
+            }
 
-      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());
+            if (showBootstrap)
+            {
+                if (showDistances)
+                {
+                    nodeLabel = nodeLabel + " : ";
+                }
 
-      }
-      else
-          g.setColor(Color.black);
+                nodeLabel = nodeLabel + String.valueOf(node.getBootstrap());
+            }
 
+            if (!nodeLabel.equals(""))
+            {
+                g.drawString(nodeLabel, xstart, ypos - 10);
+            }
 
-      // Draw horizontal line
-      g.drawLine(xstart,ypos,xend,ypos);
+            String name = (markPlaceholders && node.isPlaceholder())
+                ? (PLACEHOLDER + node.getName()) : node.getName();
 
-      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);
-      }
+            int charWidth = fm.stringWidth(name) + 3;
+            int charHeight = font.getSize();
 
-      // Colour selected leaves differently
-      String name    = node.getName();
-      FontMetrics fm = g.getFontMetrics(font);
-      int charWidth  = fm.stringWidth(node.getName()) + 3;
-      int charHeight = fm.getHeight();
+            Rectangle rect = new Rectangle(xend+10, ypos-charHeight/2,
+                    charWidth, charHeight);
 
-      Rectangle rect = new Rectangle(xend+20,ypos-charHeight,
-                                     charWidth,charHeight);
+            nameHash.put((SequenceI) node.element(), rect);
 
-      nameHash.put((SequenceI)node.element(),rect);
+            // Colour selected leaves differently
+            SequenceGroup selected = av.getSelectionGroup();
 
-      SequenceGroup selected = av.getSelectionGroup();
-      if (selected!=null && selected.sequences.contains((SequenceI)node.element())) {
-        g.setColor(Color.gray);
+            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(node.getName(),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);
+                g.fillRect(xend + 10, ypos-charHeight/2, charWidth,
+                    charHeight);
+                g.setColor(Color.white);
+            }
 
-      float height = node.height;
-      float dist   = node.dist;
+            g.drawString(name, xend + 10, ypos+fm.getDescent());
+            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);
 
-      int xstart = (int)((height-dist)*scale) + offx;
-      int xend   = (int)(height       *scale) + offx;
-      int ypos   = (int)(node.ycount  *chunk) + offy;
+            float height = node.height;
+            float dist = node.dist;
 
-      g.setColor(((SequenceNode)node).color.darker());
+            int xstart = (int) ((height - dist) * scale) + offx;
+            int xend = (int) (height * scale) + offx;
+            int ypos = (int) (node.ycount * chunk) + offy;
 
-      // Draw horizontal line
-      g.drawLine(xstart,ypos,xend,ypos);
-      g.fillRect(xend-2, ypos-2, 4,4);
+            g.setColor(((SequenceNode) node).color.darker());
 
-      int ystart = (int)(((SequenceNode)node.left()) .ycount * chunk) + offy;
-      int yend   = (int)(((SequenceNode)node.right()).ycount * chunk) + offy;
+            // Draw horizontal line
+            g.drawLine(xstart, ypos, xend, ypos);
+            g.fillRect(xend - 2, ypos - 2, 4, 4);
 
-      Rectangle pos = new Rectangle(xend-2,ypos-2,5,5);
-      nodeHash.put(node,pos);
+            int ystart = (int) (((SequenceNode) node.left()).ycount * chunk) +
+                offy;
+            int yend = (int) (((SequenceNode) node.right()).ycount * chunk) +
+                offy;
 
-      g.drawLine((int)(height*scale) + offx, ystart,
-                 (int)(height*scale) + offx, yend);
+            Rectangle pos = new Rectangle(xend - 2, ypos - 2, 5, 5);
+            nodeHash.put(node, pos);
 
-      if (showDistances && node.dist > 0) {
-        g.drawString(new Format("%5.2f").form(node.dist),xstart,ypos - 5);
-      }
+            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()) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param x DOCUMENT ME!
+     * @param y DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Object findElement(int x, int y)
+    {
+        Enumeration keys = nameHash.keys();
+
+        while (keys.hasMoreElements())
+        {
             Object ob = keys.nextElement();
-            Rectangle rect = (Rectangle)nameHash.get(ob);
+            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;
+            if ((x >= rect.x) && (x <= (rect.x + rect.width)) && (y >= rect.y) &&
+                    (y <= (rect.y + rect.height)))
+            {
+                return ob;
             }
-  }
-  keys = nodeHash.keys();
+        }
+
+        keys = nodeHash.keys();
 
-    while (keys.hasMoreElements()) {
+        while (keys.hasMoreElements())
+        {
             Object ob = keys.nextElement();
-            Rectangle rect = (Rectangle)nodeHash.get(ob);
+            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;
+            if ((x >= rect.x) && (x <= (rect.x + rect.width)) && (y >= rect.y) &&
+                    (y <= (rect.y + rect.height)))
+            {
+                return ob;
             }
+        }
+
+        return null;
     }
-      return null;
 
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param pickBox DOCUMENT ME!
+     */
+    public void pickNodes(Rectangle pickBox)
+    {
+        int width = getWidth();
+        int height = getHeight();
 
-  public void pickNodes(Rectangle pickBox) {
-    int width  = getWidth();
-    int height = getHeight();
+        SequenceNode top = tree.getTopNode();
 
-    SequenceNode top = tree.getTopNode();
+        float wscale = (float) ((width * .8) - (offx * 2)) / tree.getMaxHeight();
 
-    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;
+        if (top.count == 0)
+        {
+            top.count = ((SequenceNode) top.left()).count +
+                ((SequenceNode) top.right()).count;
+        }
 
-    pickNode(pickBox,top,chunk,wscale,width,offx,offy);
-  }
+        float chunk = (float) (height - (offy)) / top.count;
 
-  public void pickNode(Rectangle pickBox, SequenceNode node, float chunk, float scale, int width,int offx, int offy) {
-    if (node == null) {
-      return;
+        pickNode(pickBox, top, chunk, wscale, width, offx, offy);
     }
 
-    if (node.left() == null && node.right() == null) {
-      float height = node.height;
-      float dist   = node.dist;
+    /**
+     * DOCUMENT ME!
+     *
+     * @param pickBox DOCUMENT ME!
+     * @param node DOCUMENT ME!
+     * @param chunk DOCUMENT ME!
+     * @param scale DOCUMENT ME!
+     * @param width DOCUMENT ME!
+     * @param offx DOCUMENT ME!
+     * @param offy DOCUMENT ME!
+     */
+    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 xstart = (int) ((height - dist) * scale) + offx;
+            int xend = (int) (height * scale) + offx;
 
-      int ypos = (int)(node.ycount * chunk) + offy;
+            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);
+            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);
         }
-      }
-    } 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)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param node DOCUMENT ME!
+     * @param c DOCUMENT ME!
+     */
+    public void setColor(SequenceNode node, Color c)
     {
-      node.color = c;
+        if (node == null)
+        {
+            return;
+        }
 
-      if (node.element() instanceof SequenceI)
-          ((SequenceI)node.element()).setColor(c);
-    } else
-    {
-      node.color = c;
-      setColor((SequenceNode)node.left(),c);
-      setColor((SequenceNode)node.right(),c);
+        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);
+        }
     }
-  }
-
-  void startPrinting()
-  {
-    Thread thread = new Thread(this);
-    thread.start();
-  }
-
-  // put printing in a thread to avoid painting problems
-  public void run()
-  {
-    PrinterJob printJob = PrinterJob.getPrinterJob();
-    PageFormat pf = printJob.pageDialog(printJob.defaultPage());
-    printJob.setPrintable(this, pf);
-    if (printJob.printDialog())
+
+    /**
+     * DOCUMENT ME!
+     */
+    void startPrinting()
     {
-      try
-      {
-        printJob.print();
-      }
-      catch (Exception PrintException)
-      {
-        PrintException.printStackTrace();
-      }
+        Thread thread = new Thread(this);
+        thread.start();
     }
-  }
 
+    // put printing in a thread to avoid painting problems
+    public void run()
+    {
+        PrinterJob printJob = PrinterJob.getPrinterJob();
+        PageFormat pf = printJob.pageDialog(printJob.defaultPage());
 
-  public int print(Graphics pg, PageFormat pf, int pi) throws PrinterException
-  {
-    pg.setFont(font);
-    FontMetrics fm = pg.getFontMetrics(font);
-
-    pg.translate((int)pf.getImageableX(), (int)pf.getImageableY());
-
-    int pwidth = (int) pf.getImageableWidth();
-    int pheight = (int) pf.getImageableHeight();
-
-    // adjust pheight to row height
-    pheight -= (pheight%fm.getHeight());
-    pg.setClip(0,0, pwidth, pheight);
+        printJob.setPrintable(this, pf);
 
-    int noPages = (fm.getHeight() * nameHash.size()) / pheight;
+        if (printJob.printDialog())
+        {
+            try
+            {
+                printJob.print();
+            }
+            catch (Exception PrintException)
+            {
+                PrintException.printStackTrace();
+            }
+        }
+    }
 
-    if(pi>noPages)
-      return Printable.NO_SUCH_PAGE;
+    /**
+     * DOCUMENT ME!
+     *
+     * @param pg DOCUMENT ME!
+     * @param pf DOCUMENT ME!
+     * @param pi DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     *
+     * @throws PrinterException DOCUMENT ME!
+     */
+    public int print(Graphics pg, PageFormat pf, int pi)
+        throws PrinterException
+    {
+        pg.setFont(font);
+        pg.translate((int) pf.getImageableX(), (int) pf.getImageableY());
 
-    pg.translate(0, -pheight*pi );
-    draw(pg, pwidth, fm.getHeight() * nameHash.size());
+        int pwidth = (int) pf.getImageableWidth();
+        int pheight = (int) pf.getImageableHeight();
 
-    return Printable.PAGE_EXISTS;
+        int noPages = getHeight() / pheight;
 
-  }
+        if (pi > noPages)
+        {
+            return Printable.NO_SUCH_PAGE;
+        }
 
-  public void paintComponent(Graphics g)
-  {
+        if (pwidth > getWidth())
+        {
+            pwidth = getWidth();
+        }
 
-    font = new Font("Verdana",Font.PLAIN,fontSize);
-    g.setFont(font);
+        if (fitToWindow)
+        {
+            if (pheight > getHeight())
+            {
+                pheight = getHeight();
+            }
 
-    FontMetrics fm = g.getFontMetrics(font);
+            noPages = 0;
+        }
+        else
+        {
+            FontMetrics fm = pg.getFontMetrics(font);
+            int height = fm.getHeight() * nameHash.size();
+            pg.translate(0, -pi * pheight);
+            pg.setClip(0, pi * pheight, pwidth, (pi * pheight) + pheight);
+
+            // translate number of pages,
+            // height is screen size as this is the
+            // non overlapping text size
+            pheight = height;
+        }
 
-    if(nameHash.size()==0)
-      repaint();
+        draw(pg, pwidth, pheight);
 
+        return Printable.PAGE_EXISTS;
+    }
 
-    if( fitToWindow || (!fitToWindow && scrollPane.getHeight() > fm.getHeight() * nameHash.size()+offy ) )
-     {
-         draw(g,scrollPane.getWidth(),scrollPane.getHeight());
-         setPreferredSize(null);
-     }
-    else
-     {
-         setPreferredSize(new Dimension(scrollPane.getWidth(), fm.getHeight() * nameHash.size()));
-         draw( g,scrollPane.getWidth(), fm.getHeight() * nameHash.size());
-     }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param g DOCUMENT ME!
+     */
+    public void paintComponent(Graphics g)
+    {
+        super.paintComponent(g);
+        g.setFont(font);
 
+        if(tree==null)
+        {
+          g.drawString("Calculating tree....", 20, getHeight()/2);
+        }
+        else
+        {
+          fm = g.getFontMetrics(font);
 
-    if (threshold != 0)
-    {
-      if(av.getCurrentTree() == tree)
-        g.setColor(Color.red);
-      else
-        g.setColor(Color.gray);
+          if (nameHash.size() == 0)
+          {
+            repaint();
+          }
 
-        int x = (int)(    threshold * (float)(getWidth()-labelLength - 2*offx) +offx   ) ;
+          if (fitToWindow ||
+              (!fitToWindow &&
+               (scrollPane.getHeight() > ( (fm.getHeight() * nameHash.size()) +
+                                          offy))))
+          {
+            draw(g, scrollPane.getWidth(), scrollPane.getHeight());
+            setPreferredSize(null);
+          }
+          else
+          {
+            setPreferredSize(new Dimension(scrollPane.getWidth(),
+                                           fm.getHeight() * nameHash.size()));
+            draw(g, scrollPane.getWidth(), fm.getHeight() * nameHash.size());
+          }
 
-        g.drawLine(x,0,x,getHeight());
+          scrollPane.revalidate();
+        }
     }
 
-    scrollPane.revalidate();
-  }
-    public int getFontSize() {
-        return fontSize;
-    }
-    public void setFontSize(int fontSize) {
-        this.fontSize = fontSize;
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param fontSize DOCUMENT ME!
+     */
+    public void setFont(Font font)
+    {
+        this.font = font;
         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);
-  }
 
-  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) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param g1 DOCUMENT ME!
+     * @param width DOCUMENT ME!
+     * @param height DOCUMENT ME!
+     */
+    public void draw(Graphics g1, int width, int height)
+    {
+        Graphics2D g2 = (Graphics2D) g1;
+        g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+            RenderingHints.VALUE_ANTIALIAS_ON);
+        g2.setColor(Color.white);
+        g2.fillRect(0, 0, width, height);
 
-      av.setCurrentTree(tree);
+        g2.setFont(font);
 
-      int x = e.getX();
-      int y = e.getY();
+        offy = font.getSize()*2;
 
-      Object ob = findElement(x,y);
+        fm = g2.getFontMetrics(font);
 
-      if (ob instanceof SequenceI)
-      {
-          TreeSelectionChanged((Sequence)ob);
-          repaint();
-          return;
+        labelLength = fm.stringWidth(longestName) + 20; //20 allows for scrollbar
 
-      } else if (ob instanceof SequenceNode) {
-          SequenceNode tmpnode = (SequenceNode)ob;
-          tree.swapNodes(tmpnode);
-          tree.reCount(tree.getTopNode());
-          tree.findHeight(tree.getTopNode());
-      } else {
-          // Find threshold
+        float wscale = (float) (width - labelLength - (offx * 2)) / tree.getMaxHeight();
 
-          if (tree.getMaxHeight() != 0) {
-              threshold = (float)(x - offx)/(float)(getWidth()-labelLength - 2*offx);
+        SequenceNode top = tree.getTopNode();
 
-              tree.getGroups().removeAllElements();
-              tree.groupNodes(tree.getTopNode(),threshold);
-              setColor(tree.getTopNode(),Color.black);
+        if (top.count == 0)
+        {
+            top.count = ((SequenceNode) top.left()).count +
+                ((SequenceNode) top.right()).count;
+        }
 
-              av.setSelectionGroup(null);
-              av.alignment.deleteAllGroups();
+        float chunk = (float) (height - (offy)) / top.count;
 
-              for (int i=0; i < tree.getGroups().size(); i++)
-              {
+        drawNode(g2, tree.getTopNode(), chunk, wscale, width, offx, offy);
 
-                  Color col = new Color((int)(Math.random()*255),
-                                        (int)(Math.random()*255),
-                                        (int)(Math.random()*255));
-                  setColor((SequenceNode)tree.getGroups().elementAt(i),col.brighter());
+        if (threshold != 0)
+        {
+            if (av.getCurrentTree() == tree)
+            {
+                g2.setColor(Color.red);
+            }
+            else
+            {
+                g2.setColor(Color.gray);
+            }
 
-                  Vector l = tree.findLeaves((SequenceNode)tree.getGroups().elementAt(i),new Vector());
-                  SequenceGroup sg = null;
-                  for (int j = 0; j < l.size(); j++)
-                  {
-                    SequenceNode sn = (SequenceNode) l.elementAt(j);
-                    if(sg==null)
-                       sg = new SequenceGroup("TreeGroup", av.getGlobalColourScheme(), true, true,false,0,av.alignment.getWidth());
+            int x = (int) ((threshold * (float) (getWidth() - labelLength -
+                (2 * offx))) + offx);
 
-                    sg.addSequence( (Sequence) sn.element());
-                  }
+            g2.drawLine(x, 0, x, getHeight());
+        }
+    }
 
-                  if (av.getGlobalColourScheme() instanceof ConservationColourScheme)
-                  {
-                    ConservationColourScheme ccs = (ConservationColourScheme) av.getGlobalColourScheme();
-                    Conservation c = new Conservation("Group",
-                                                      ResidueProperties.propHash, 3,
-                                                      sg.sequences, sg.getStartRes(),
-                                                      sg.getEndRes());
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void mouseReleased(MouseEvent e)
+    {
+    }
 
-                    c.calculate();
-                    c.verdict(false, av.ConsPercGaps);
-                    ccs = new ConservationColourScheme(c, ccs.cs);
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void mouseEntered(MouseEvent e)
+    {
+    }
 
-                    sg.cs = ccs;
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void mouseExited(MouseEvent e)
+    {
+    }
 
-                  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void mouseClicked(MouseEvent e)
+    {
+    }
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void mousePressed(MouseEvent e)
+    {
+        av.setCurrentTree(tree);
 
+        int x = e.getX();
+        int y = e.getY();
 
-                  av.alignment.addGroup(sg);
+        Object ob = findElement(x, y);
 
-              }
-          }
-      }
+        if (ob instanceof SequenceI)
+        {
+            TreeSelectionChanged((Sequence) ob);
+            repaint();
 
-      PaintRefresher.Refresh(this);
-      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) (getWidth() -
+                    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());
+
+
+                    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);
+                        sg.cs.setConservation(c);
+                    }
+
+                    av.alignment.addGroup(sg);
+                }
+            }
+        }
 
-  }
+        PaintRefresher.Refresh(this, av.alignment);
+        repaint();
+    }
 
-    public void setShowDistances(boolean state) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param state DOCUMENT ME!
+     */
+    public void setShowDistances(boolean state)
+    {
         this.showDistances = state;
         repaint();
     }
 
-    public void setShowBootstrap(boolean state) {
-      this.showBootstrap = state;
-      repaint();
+    /**
+     * DOCUMENT ME!
+     *
+     * @param state DOCUMENT ME!
+     */
+    public void setShowBootstrap(boolean state)
+    {
+        this.showBootstrap = state;
+        repaint();
     }
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param state DOCUMENT ME!
+     */
+    public void setMarkPlaceholders(boolean state)
+    {
+        this.markPlaceholders = state;
+        repaint();
+    }
 }
-