X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureRenderer.java;h=634dbedae985fed6de65e73ef909d673811aad68;hb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;hp=6a0daa8cd940ee49420eee283bcb5e6570ea2550;hpb=170c4f875570a1f17224b6cfea21ac696bfe3c6f;p=jalview.git

diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
index 6a0daa8..634dbed 100755
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -1,73 +1,788 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 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.datamodel.*;
-import jalview.schemes.*;
-import java.awt.*;
 import java.util.*;
 
-public class FeatureRenderer implements RendererI
+import java.awt.*;
+import java.awt.event.*;
+import java.awt.image.*;
+import javax.swing.*;
+
+import jalview.datamodel.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class FeatureRenderer
 {
   AlignViewport av;
-
-  SequenceGroup currentSequenceGroup = null;
-  SequenceGroup [] allGroups = null;
   Color resBoxColour;
-  Graphics graphics;
+  float transparency = 1.0f;
+  FontMetrics fm;
+  int charOffset;
+
+  Hashtable featureColours = new Hashtable();
+
+  // A higher level for grouping features of a
+  // particular type
+  Hashtable featureGroups = null;
+
+  // This is actually an Integer held in the hashtable,
+  // Retrieved using the key feature type
+  Object currentColour;
 
+  String[] renderOrder;
+
+  /**
+   * Creates a new FeatureRenderer object.
+   *
+   * @param av DOCUMENT ME!
+   */
   public FeatureRenderer(AlignViewport av)
   {
     this.av = av;
   }
 
+  public void transferSettings(FeatureRenderer fr)
+  {
+    renderOrder = fr.renderOrder;
+    featureGroups = fr.featureGroups;
+    featureColours = fr.featureColours;
+    transparency = fr.transparency;
+  }
 
-  public void drawSequence(Graphics g,SequenceI seq,SequenceGroup [] sg, int start, int end, int x1, int y1, int width, int height, Vector pid, int seqnum)
+  BufferedImage offscreenImage;
+  boolean offscreenRender = false;
+  public Color findFeatureColour(Color initialCol, SequenceI seq, int res)
   {
-    Vector features = seq.getSequenceFeatures();
-    Enumeration e = features.elements();
-    while( e.hasMoreElements() )
+    return new Color(findFeatureColour(initialCol.getRGB(),
+                                       seq, res));
+  }
+
+  /**
+   * This is used by the Molecule Viewer and Overview to
+   * get the accurate colourof the rendered sequence
+   */
+  public int findFeatureColour(int initialCol, SequenceI seq, int column)
+  {
+    if (!av.showSequenceFeatures)
     {
-      SequenceFeature sf = (SequenceFeature)e.nextElement();
-      int fstart = seq.findIndex(sf.getStart())-1;
-      int fend = seq.findIndex(sf.getEnd())-1;
+      return initialCol;
+    }
 
-      if(   (fstart<=end && fend>=start)  )
+    if (seq != lastSeq)
+    {
+      lastSeq = seq;
+      sequenceFeatures = lastSeq.getDatasetSequence().getSequenceFeatures();
+      if (sequenceFeatures == null)
       {
-        if(fstart<0) // fix for if the feature we have starts before the sequence start,
-          fstart = 0;// but the feature end is still valid!!
+        return initialCol;
+      }
 
-        if(fstart==fend)
+      sfSize = sequenceFeatures.length;
+    }
+
+    if (jalview.util.Comparison.isGap(lastSeq.getCharAt(column)))
+    {
+      return Color.white.getRGB();
+    }
+
+    //Only bother making an offscreen image if transparency is applied
+    if (transparency != 1.0f && offscreenImage == null)
+    {
+      offscreenImage = new BufferedImage(1, 1, BufferedImage.TYPE_INT_ARGB);
+    }
+
+    currentColour = null;
+
+    offscreenRender = true;
+
+    if (offscreenImage != null)
+    {
+      offscreenImage.setRGB(0, 0, initialCol);
+      drawSequence(offscreenImage.getGraphics(),
+                   lastSeq,
+                   column, column, 0);
+
+      return offscreenImage.getRGB(0, 0);
+    }
+    else
+    {
+      drawSequence(null,
+                   lastSeq,
+                   lastSeq.findPosition(column),
+                   -1, -1);
+
+      if (currentColour == null)
+      {
+        return initialCol;
+      }
+      else
+      {
+        return ( (Integer) currentColour).intValue();
+      }
+    }
+
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param g DOCUMENT ME!
+   * @param seq DOCUMENT ME!
+   * @param sg DOCUMENT ME!
+   * @param start DOCUMENT ME!
+   * @param end DOCUMENT ME!
+   * @param x1 DOCUMENT ME!
+   * @param y1 DOCUMENT ME!
+   * @param width DOCUMENT ME!
+   * @param height DOCUMENT ME!
+   */
+  // String type;
+  // SequenceFeature sf;
+  SequenceI lastSeq;
+  SequenceFeature[] sequenceFeatures;
+  int sfSize, sfindex, spos, epos;
+
+  public void drawSequence(Graphics g, SequenceI seq,
+                           int start, int end, int y1)
+  {
+    if (seq.getDatasetSequence().getSequenceFeatures() == null
+        || seq.getDatasetSequence().getSequenceFeatures().length == 0)
+    {
+      return;
+    }
+
+    if (g != null)
+    {
+      fm = g.getFontMetrics();
+    }
+
+    if (av.featuresDisplayed == null
+        || renderOrder == null
+        || newFeatureAdded)
+    {
+      findAllFeatures();
+      if (av.featuresDisplayed.size() < 1)
+      {
+        return;
+      }
+
+      sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();
+      sfSize = sequenceFeatures.length;
+    }
+
+    if (lastSeq == null || seq != lastSeq)
+    {
+      lastSeq = seq;
+      sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();
+      sfSize = sequenceFeatures.length;
+    }
+
+    if (transparency != 1 && g != null)
+    {
+      Graphics2D g2 = (Graphics2D) g;
+      g2.setComposite(
+          AlphaComposite.getInstance(
+              AlphaComposite.SRC_OVER, transparency));
+    }
+
+    if (!offscreenRender)
+    {
+      spos = lastSeq.findPosition(start);
+      epos = lastSeq.findPosition(end);
+    }
+
+    String type;
+    for (int renderIndex = 0; renderIndex < renderOrder.length; renderIndex++)
+    {
+      type = renderOrder[renderIndex];
+
+      if (type == null || !av.featuresDisplayed.containsKey(type))
+      {
+        continue;
+      }
+
+      // loop through all features in sequence to find
+      // current feature to render
+      for (sfindex = 0; sfindex < sfSize; sfindex++)
+      {
+        if (sequenceFeatures.length <= sfindex)
+        {
+          continue;
+        }
+        if (!sequenceFeatures[sfindex].type.equals(type))
+        {
+          continue;
+        }
+
+        if (featureGroups != null
+            && sequenceFeatures[sfindex].featureGroup != null
+            &&
+            featureGroups.containsKey(sequenceFeatures[sfindex].featureGroup)
+            &&
+            ! ( (Boolean) featureGroups.get(sequenceFeatures[sfindex].
+                                            featureGroup)).
+            booleanValue())
+        {
+          continue;
+        }
+
+        if (!offscreenRender && (sequenceFeatures[sfindex].getBegin() > epos
+                                 || sequenceFeatures[sfindex].getEnd() < spos))
+        {
+          continue;
+        }
+
+        if (offscreenRender && offscreenImage == null)
+        {
+          if (sequenceFeatures[sfindex].begin <= start &&
+              sequenceFeatures[sfindex].end >= start)
+          {
+            currentColour = av.featuresDisplayed.get(sequenceFeatures[sfindex].
+                type);
+          }
+        }
+        else if (sequenceFeatures[sfindex].type.equals("disulfide bond"))
         {
-          g.setColor(Color.red);
-          g.fillRoundRect( (fstart - start) * width, y1, width, height, 4,4);
-          g.setColor(Color.white);
 
-          char s = seq.getSequence().charAt(fstart);
-          FontMetrics fm = g.getFontMetrics();
-          int charOffset =  (width - fm.charWidth(s))/2;
-          int pady = height/5;
-          g.drawString(String.valueOf(s), charOffset + x1 + width * (fstart - start), y1 + height - pady);
+          renderFeature(g, seq,
+                        seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
+                        seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
+                        new Color( ( (Integer) av.featuresDisplayed.get(
+                            sequenceFeatures[sfindex].type)).intValue()),
+                        start, end, y1);
+          renderFeature(g, seq,
+                        seq.findIndex(sequenceFeatures[sfindex].end) - 1,
+                        seq.findIndex(sequenceFeatures[sfindex].end) - 1,
+                        new Color( ( (Integer) av.featuresDisplayed.get(
+                            sequenceFeatures[sfindex].type)).intValue()),
+                        start, end, y1);
 
         }
         else
         {
-          for (int i = fstart; i <= fend; i++)
+          renderFeature(g, seq,
+                        seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
+                        seq.findIndex(sequenceFeatures[sfindex].end) - 1,
+                        getColour(sequenceFeatures[sfindex].type),
+                        start, end, y1);
+        }
+
+      }
+
+    }
+
+    if (transparency != 1.0f && g != null)
+    {
+      Graphics2D g2 = (Graphics2D) g;
+      g2.setComposite(
+          AlphaComposite.getInstance(
+              AlphaComposite.SRC_OVER, 1.0f));
+    }
+  }
+
+  char s;
+  int i;
+  void renderFeature(Graphics g, SequenceI seq,
+                     int fstart, int fend, Color featureColour, int start,
+                     int end, int y1)
+  {
+
+    if ( ( (fstart <= end) && (fend >= start)))
+    {
+      if (fstart < start)
+      { // fix for if the feature we have starts before the sequence start,
+        fstart = start; // but the feature end is still valid!!
+      }
+
+      if (fend >= end)
+      {
+        fend = end;
+      }
+      int pady = (y1 + av.charHeight) - av.charHeight / 5;
+      for (i = fstart; i <= fend; i++)
+      {
+        s = seq.getCharAt(i);
+
+        if (jalview.util.Comparison.isGap(s))
+        {
+          continue;
+        }
+
+        g.setColor(featureColour);
+
+        g.fillRect( (i - start) * av.charWidth, y1, av.charWidth, av.charHeight);
+
+        if (offscreenRender || !av.validCharWidth)
+        {
+          continue;
+        }
+
+        g.setColor(Color.white);
+        charOffset = (av.charWidth - fm.charWidth(s)) / 2;
+        g.drawString(String.valueOf(s),
+                     charOffset + (av.charWidth * (i - start)),
+                     pady);
+
+      }
+    }
+  }
+
+  boolean newFeatureAdded = false;
+
+  public void featuresAdded()
+  {
+    findAllFeatures();
+  }
+
+  boolean findingFeatures = false;
+  synchronized void findAllFeatures()
+  {
+    newFeatureAdded = false;
+
+    if (findingFeatures)
+    {
+      newFeatureAdded = true;
+      return;
+    }
+
+    findingFeatures = true;
+    jalview.schemes.UserColourScheme ucs = new
+        jalview.schemes.UserColourScheme();
+
+    if (av.featuresDisplayed == null)
+    {
+      av.featuresDisplayed = new Hashtable();
+    }
+
+    av.featuresDisplayed.clear();
+
+    Vector allfeatures = new Vector();
+    for (int i = 0; i < av.alignment.getHeight(); i++)
+    {
+      SequenceFeature[] features
+          = av.alignment.getSequenceAt(i).getDatasetSequence().
+          getSequenceFeatures();
+
+      if (features == null)
+      {
+        continue;
+      }
+
+      int index = 0;
+      while (index < features.length)
+      {
+        if (!av.featuresDisplayed.containsKey(features[index].getType()))
+        {
+          if (! (features[index].begin == 0 && features[index].end == 0))
           {
-            g.setColor(Color.blue);
-            g.fillRect( (i-start) * width, y1, width, height);
-
-            g.setColor(Color.white);
-            char s = seq.getSequence().charAt(i);
-            FontMetrics fm = g.getFontMetrics();
-            int charOffset = (width - fm.charWidth(s)) / 2;
-            int pady = height / 5;
-            g.drawString(String.valueOf(s),
-                         charOffset + x1 + width * (i-start),
-                         y1 + height - pady);
+            // If beginning and end are 0, the feature is for the whole sequence
+            // and we don't want to render the feature in the normal way
+
+            if (getColour(features[index].getType()) == null)
+            {
+              featureColours.put(features[index].getType(),
+                                 ucs.createColourFromName(features[index].
+                  getType()));
+            }
+
+            av.featuresDisplayed.put(features[index].getType(),
+                                     new Integer(getColour(features[index].
+                getType()).getRGB()));
+            allfeatures.addElement(features[index].getType());
           }
         }
+        index++;
       }
+    }
 
+    renderOrder = new String[allfeatures.size()];
+    Enumeration en = allfeatures.elements();
+    int i = allfeatures.size() - 1;
+    while (en.hasMoreElements())
+    {
+      renderOrder[i] = en.nextElement().toString();
+      i--;
     }
-   }
+
+    findingFeatures = false;
+  }
+
+  public Color getColour(String featureType)
+  {
+    Color colour = (Color) featureColours.get(featureType);
+    return colour;
+  }
+
+  static String lastFeatureAdded;
+  static String lastFeatureGroupAdded;
+  static String lastDescriptionAdded;
+
+  public boolean createNewFeatures(SequenceI[] sequences,
+                                   SequenceFeature[] features)
+  {
+    return amendFeatures(sequences, features, true, null);
+  }
+
+  int featureIndex = 0;
+  boolean amendFeatures(final SequenceI[] sequences,
+                        final SequenceFeature[] features,
+                        boolean newFeatures,
+                        final AlignmentPanel ap)
+  {
+    JPanel bigPanel = new JPanel(new BorderLayout());
+    final JComboBox name = new JComboBox();
+    final JComboBox source = new JComboBox();
+    final JTextArea description = new JTextArea(3, 25);
+    final JSpinner start = new JSpinner();
+    final JSpinner end = new JSpinner();
+    start.setPreferredSize(new Dimension(80, 20));
+    end.setPreferredSize(new Dimension(80, 20));
+    final JPanel colour = new JPanel();
+    colour.setBorder(BorderFactory.createEtchedBorder());
+    colour.setMaximumSize(new Dimension(40, 10));
+    colour.addMouseListener(new MouseAdapter()
+    {
+      public void mousePressed(MouseEvent evt)
+      {
+        colour.setBackground(
+            JColorChooser.showDialog(Desktop.desktop,
+                                     "Select Feature Colour",
+                                     colour.getBackground()));
+      }
+    });
+
+    JPanel panel = new JPanel(new GridLayout(3, 2));
+    panel.add(new JLabel("Sequence Feature Name: ", JLabel.RIGHT));
+    panel.add(name);
+    panel.add(new JLabel("Feature Group: ", JLabel.RIGHT));
+    panel.add(source);
+    panel.add(new JLabel("Feature Colour: ", JLabel.RIGHT));
+    JPanel tmp = new JPanel();
+    tmp.add(colour);
+    colour.setPreferredSize(new Dimension(150, 15));
+    panel.add(tmp);
+    name.setEditable(true);
+    source.setEditable(true);
+
+    bigPanel.add(panel, BorderLayout.NORTH);
+    panel = new JPanel();
+    panel.add(new JLabel("Description: ", JLabel.RIGHT));
+    description.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    description.setLineWrap(true);
+    panel.add(new JScrollPane(description));
+
+    if (!newFeatures)
+    {
+      bigPanel.add(panel, BorderLayout.SOUTH);
+
+      panel = new JPanel();
+      panel.add(new JLabel(" Start:", JLabel.RIGHT));
+      panel.add(start);
+      panel.add(new JLabel("  End:", JLabel.RIGHT));
+      panel.add(end);
+      bigPanel.add(panel, BorderLayout.CENTER);
+    }
+    else
+    {
+      bigPanel.add(panel, BorderLayout.CENTER);
+    }
+
+    if (lastFeatureAdded == null)
+    {
+      if (features[0].type != null)
+      {
+        lastFeatureAdded = features[0].type;
+      }
+      else
+      {
+        lastFeatureAdded = "feature_1";
+      }
+    }
+
+    if (lastFeatureGroupAdded == null)
+    {
+      if (features[0].featureGroup != null)
+      {
+        lastFeatureGroupAdded = features[0].featureGroup;
+      }
+      else
+      {
+        lastFeatureAdded = "Jalview";
+      }
+    }
+
+    Enumeration en;
+    if (featureGroups != null)
+    {
+      en = featureGroups.keys();
+      while (en.hasMoreElements())
+      {
+        source.addItem(en.nextElement().toString());
+      }
+    }
+
+    if (newFeatures)
+    {
+      if (av.featuresDisplayed != null)
+      {
+        en = av.featuresDisplayed.keys();
+        while (en.hasMoreElements())
+        {
+          name.addItem(en.nextElement().toString());
+        }
+      }
+
+      name.setSelectedItem(lastFeatureAdded);
+      source.setSelectedItem(lastFeatureGroupAdded);
+      description.setText(
+          lastDescriptionAdded == null ?
+          features[0].description : lastDescriptionAdded);
+
+      if (getColour(lastFeatureAdded) != null)
+      {
+        colour.setBackground(getColour(lastFeatureAdded));
+      }
+      else
+      {
+        colour.setBackground(new Color(60, 160, 115));
+      }
+
+    }
+    else if (!newFeatures)
+    {
+      featureIndex = 0;
+      for (int f = 0; f < features.length; f++)
+      {
+        name.addItem(features[f].getType().toString());
+      }
+
+      description.setText(features[0].getDescription());
+      source.setSelectedItem(features[0].getFeatureGroup());
+      start.setValue(new Integer(features[0].getBegin()));
+      end.setValue(new Integer(features[0].getEnd()));
+      colour.setBackground(
+          getColour(name.getSelectedItem().toString()));
+      name.addItemListener(new ItemListener()
+      {
+        public void itemStateChanged(ItemEvent e)
+        {
+          int index = name.getSelectedIndex();
+          if (index != -1)
+          {
+            featureIndex = index;
+            description.setText(features[index].getDescription());
+            source.setSelectedItem(features[index].getFeatureGroup());
+            start.setValue(new Integer(features[index].getBegin()));
+            end.setValue(new Integer(features[index].getEnd()));
+            colour.setBackground(
+                getColour(name.getSelectedItem().toString()));
+
+            SearchResults highlight = new SearchResults();
+            highlight.addResult(sequences[0],
+                                features[index].getBegin(),
+                                features[index].getEnd());
+
+            ap.seqPanel.seqCanvas.highlightSearchResults(highlight);
+
+          }
+          Color col = getColour(name.getSelectedItem().toString());
+          if (col == null)
+          {
+            col = new
+                jalview.schemes.UserColourScheme()
+                .createColourFromName(name.getSelectedItem().toString());
+          }
+
+          colour.setBackground(col);
+        }
+      });
+
+    }
+
+    Object[] options;
+    if (!newFeatures)
+    {
+      options = new Object[]
+          {
+          "Amend", "Delete", "Cancel"};
+    }
+    else
+    {
+      options = new Object[]
+          {
+          "OK", "Cancel"};
+    }
+
+    String title = newFeatures ? "Create New Sequence Feature(s)" :
+        "Amend/Delete Features for "
+        + sequences[0].getName();
+
+    int reply = JOptionPane.showInternalOptionDialog(Desktop.desktop,
+        bigPanel,
+        title,
+        JOptionPane.YES_NO_CANCEL_OPTION,
+        JOptionPane.QUESTION_MESSAGE,
+        null,
+        options, "OK");
+
+    jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();
+
+    if (reply == JOptionPane.OK_OPTION
+        && name.getSelectedItem() != null
+        && source.getSelectedItem() != null)
+    {
+      //This ensures that the last sequence
+      //is refreshed and new features are rendered
+      lastSeq = null;
+      lastFeatureAdded = name.getSelectedItem().toString();
+      lastFeatureGroupAdded = source.getSelectedItem().toString();
+      lastDescriptionAdded = description.getText().replaceAll("\n", " ");
+    }
+
+    if (!newFeatures)
+    {
+      SequenceFeature sf = features[featureIndex];
+
+      if (reply == JOptionPane.NO_OPTION)
+      {
+        sequences[0].getDatasetSequence().deleteFeature(sf);
+      }
+      else if (reply == JOptionPane.YES_OPTION)
+      {
+        sf.type = lastFeatureAdded;
+        sf.featureGroup = lastFeatureGroupAdded;
+        sf.description = lastDescriptionAdded;
+        setColour(sf.type, colour.getBackground());
+        try
+        {
+          sf.begin = ( (Integer) start.getValue()).intValue();
+          sf.end = ( (Integer) end.getValue()).intValue();
+        }
+        catch (NumberFormatException ex)
+        {}
+
+        ffile.parseDescriptionHTML(sf, false);
+      }
+    }
+    else
+    {
+      if (reply == JOptionPane.OK_OPTION
+          && name.getSelectedItem() != null
+          && source.getSelectedItem() != null)
+      {
+        for (int i = 0; i < sequences.length; i++)
+        {
+          features[i].type = lastFeatureAdded;
+          features[i].featureGroup = lastFeatureGroupAdded;
+          features[i].description = lastDescriptionAdded;
+          sequences[i].addSequenceFeature(features[i]);
+          ffile.parseDescriptionHTML(features[i], false);
+        }
+
+        if (av.featuresDisplayed == null)
+        {
+          av.featuresDisplayed = new Hashtable();
+        }
+
+        if (featureGroups == null)
+        {
+          featureGroups = new Hashtable();
+        }
+
+        featureGroups.put(lastFeatureGroupAdded, new Boolean(true));
+
+        Color col = colour.getBackground();
+        setColour(lastFeatureAdded, colour.getBackground());
+
+        av.featuresDisplayed.put(lastFeatureGroupAdded,
+                                 new Integer(col.getRGB()));
+
+        findAllFeatures();
+
+        return true;
+      }
+      else
+      {
+        return false;
+      }
+    }
+
+    if (name.getSelectedIndex() == -1)
+    {
+      findAllFeatures();
+    }
+
+    return true;
+  }
+
+  public void setColour(String featureType, Color col)
+  {
+    featureColours.put(featureType, col);
+  }
+
+  public void setTransparency(float value)
+  {
+    transparency = value;
+  }
+
+  public float getTransparency()
+  {
+    return transparency;
+  }
+
+  public void setFeaturePriority(Object[][] data)
+  {
+    // The feature table will display high priority
+    // features at the top, but theses are the ones
+    // we need to render last, so invert the data
+    if (av.featuresDisplayed != null)
+    {
+      av.featuresDisplayed.clear();
+    }
+    else
+    {
+      av.featuresDisplayed = new Hashtable();
+    }
+
+    renderOrder = new String[data.length];
+
+    if (data.length > 0)
+    {
+      for (int i = 0; i < data.length; i++)
+      {
+        String type = data[i][0].toString();
+        setColour(type, (Color) data[i][1]);
+        if ( ( (Boolean) data[i][2]).booleanValue())
+        {
+          av.featuresDisplayed.put(type, new Integer(getColour(type).getRGB()));
+        }
+
+        renderOrder[data.length - i - 1] = type;
+      }
+    }
+
+  }
 
 }