X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFeatureRenderer.java;h=5e654093f98d42efcc0681479cb7928307be7566;hb=952ae154954fe87b94cccb765d32718689b9e9a0;hp=4a97e43b4e00355f59b4bcde416b159a98d7d377;hpb=55e2e9b22b133db8b9ff0979b0338a33081fc8fd;p=jalview.git

diff --git a/src/jalview/appletgui/FeatureRenderer.java b/src/jalview/appletgui/FeatureRenderer.java
index 4a97e43..5e65409 100755
--- a/src/jalview/appletgui/FeatureRenderer.java
+++ b/src/jalview/appletgui/FeatureRenderer.java
@@ -1,272 +1,975 @@
-/*
- * 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 jalview.datamodel.*;
-
-import java.awt.*;
-
-import java.util.*;
-
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class FeatureRenderer
-{
-    AlignViewport av;
-    SequenceGroup currentSequenceGroup = null;
-    SequenceGroup[] allGroups = null;
-    Color resBoxColour;
-    Graphics graphics;
-    float transparency = .4f;
-
-    // The following vector holds the features which are
-    // to be added, in the correct order or rendering
-    Vector featuresDisplayed;
-
-    /**
-     * Creates a new FeatureRenderer object.
-     *
-     * @param av DOCUMENT ME!
-     */
-    public FeatureRenderer(AlignViewport av)
-    {
-        this.av = av;
-        initColours();
-        String version = System.getProperty("java.version");
-        if (version.indexOf("1.1") == 0)
-          highlightTransparent = false;
-
-    }
-
-boolean highlightTransparent = true;
-    /**
-     * 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!
-     */
-    public void drawSequence(Graphics g, SequenceI seq, SequenceGroup[] sg,
-        int start, int end, int x1, int y1, int width, int height)
-    {
-
-        if(seq.getSequenceFeatures()==null)
-          return;
-
-        Enumeration e = null, e2;
-        String type;
-        if(featuresDisplayed!=null)
-          e = featuresDisplayed.elements();
-        else
-         e = seq.getSequenceFeatures().elements();
-
-       if(highlightTransparent)
-        {
-        //  MyGraphics.SetTransparency(g, transparency);
-        }
-
-
-        while (e.hasMoreElements())
-        {
-            SequenceFeature sf=null;
-            if(featuresDisplayed!=null)
-            {
-              e2 = seq.getSequenceFeatures().elements();
-              type = e.nextElement().toString();
-              while(e2.hasMoreElements())
-              {
-                sf = (SequenceFeature) e2.nextElement();
-                if(sf.getType().equals(type))
-                  break;
-                else
-                  sf = null;
-              }
-            }
-            else
-            {
-              sf = (SequenceFeature) e.nextElement();
-              type = sf.getType();
-            }
-
-            if(sf==null)
-              continue;
-
-
-            if (sf.getBegin() > seq.getEnd())
-            {
-                continue;
-            }
-
-            int fstart = seq.findIndex(sf.getBegin()) - 1;
-            int fend = seq.findIndex(sf.getEnd()) - 1;
-
-            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;
-                }
-
-                if (fstart == fend)
-                {
-                    g.setColor(getColour(type));
-                    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);
-                }
-                else
-                {
-                    for (int i = fstart; i <= fend; i++)
-                    {
-                        char s = seq.getSequence().charAt(i);
-
-                        if (jalview.util.Comparison.isGap(s))
-                        {
-                            continue;
-                        }
-
-                        g.setColor(getColour(type));
-                        g.fillRect((i - start) * width, y1, width, height);
-
-                        g.setColor(Color.white);
-
-                        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 (highlightTransparent)
-          {
-        //    MyGraphics.SetTransparency(g, 1.0f);
-          }
-    }
-
-    public Color getColour(String featureType)
-    {
-      return (Color)featureColours.get(featureType);
-    }
-
-    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
-      featuresDisplayed = new Vector();
-      for(int i=data.length-1; i>-1; i--)
-      {
-       String type = data[i][0].toString();
-       setColour(type, (Color)data[i][1]);
-       if( ((Boolean)data[i][2]).booleanValue() )
-         featuresDisplayed.addElement(type);
-      }
-    }
-
-    Hashtable featureColours = new Hashtable();
-    void initColours()
-    {
-      featureColours.put("active site", new Color(255, 75, 0));
-      featureColours.put("binding site", new Color(245, 85, 0));
-      featureColours.put("calcium-binding region", new Color(235, 95, 0));
-      featureColours.put("chain", new Color(225, 105, 0));
-      featureColours.put("coiled-coil region", new Color(215, 115, 0));
-      featureColours.put("compositionally biased region", new Color(205, 125, 0));
-      featureColours.put("cross-link", new Color(195, 135, 0));
-      featureColours.put("disulfide bond", new Color(185, 145, 0));
-      featureColours.put("DNA-binding region", new Color(175, 155, 0));
-      featureColours.put("domain", new Color(165, 165, 0));
-      featureColours.put("glycosylation site", new Color(155, 175, 0));
-      featureColours.put("helix", new Color(145, 185, 0));
-      featureColours.put("initiator methionine", new Color(135, 195, 5));
-      featureColours.put("lipid moiety-binding region", new Color(125, 205, 15));
-      featureColours.put("metal ion-binding site", new Color(115, 215, 25));
-      featureColours.put("modified residue", new Color(105, 225, 35));
-      featureColours.put("mutagenesis site", new Color(95, 235, 45));
-      featureColours.put("non-consecutive residues", new Color(85, 245, 55));
-      featureColours.put("non-terminal residue", new Color(75, 255, 65));
-      featureColours.put("nucleotide phosphate-binding region",
-                         new Color(65, 245, 75));
-      featureColours.put("peptide", new Color(55, 235, 85));
-      featureColours.put("propeptide", new Color(45, 225, 95));
-      featureColours.put("region of interest", new Color(35, 215, 105));
-      featureColours.put("repeat", new Color(25, 205, 115));
-      featureColours.put("selenocysteine", new Color(15, 195, 125));
-      featureColours.put("sequence conflict", new Color(5, 185, 135));
-      featureColours.put("sequence variant", new Color(0, 175, 145));
-      featureColours.put("short sequence motif", new Color(0, 165, 155));
-      featureColours.put("signal peptide", new Color(0, 155, 165));
-      featureColours.put("site", new Color(0, 145, 175));
-      featureColours.put("splice variant", new Color(0, 135, 185));
-      featureColours.put("strand", new Color(0, 125, 195));
-      featureColours.put("topological domain", new Color(0, 115, 205));
-      featureColours.put("transit peptide", new Color(0, 105, 215));
-      featureColours.put("transmembrane region", new Color(0, 95, 225));
-      featureColours.put("turn", new Color(0, 85, 235));
-      featureColours.put("unsure residue", new Color(0, 75, 245));
-      featureColours.put("zinc finger region", new Color(0, 65, 255));
-    }
-
-}
-
-
-
+/*
+ * 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.appletgui;
+
+import java.util.*;
+
+import java.awt.*;
+
+import java.awt.event.*;
+
+
+import jalview.appletgui.FeatureSettings.MyCheckbox;
+import jalview.datamodel.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class FeatureRenderer
+{
+  AlignViewport av;
+
+  Hashtable featureColours = new Hashtable();
+
+  // A higher level for grouping features of a
+  // particular type
+  Hashtable featureGroups = null;
+
+  // Holds web links for feature groups and feature types
+  // in the form label|link
+  Hashtable featureLinks = null;
+
+  // This is actually an Integer held in the hashtable,
+  // Retrieved using the key feature type
+  Object currentColour;
+
+  String[] renderOrder;
+
+  FontMetrics fm;
+  int charOffset;
+
+  float transparency = 1f;
+
+  TransparencySetter transparencySetter = null;
+
+  /**
+   * Creates a new FeatureRenderer object.
+   *
+   * @param av DOCUMENT ME!
+   */
+  public FeatureRenderer(AlignViewport av)
+  {
+    this.av = av;
+
+    if (!System.getProperty("java.version").startsWith("1.1"))
+    {
+      transparencySetter = new TransparencySetter();
+    }
+  }
+
+  public void transferSettings(FeatureRenderer fr)
+  {
+    renderOrder = fr.renderOrder;
+    featureGroups = fr.featureGroups;
+    featureColours = fr.featureColours;
+    transparency = fr.transparency;
+  }
+
+
+  static String lastFeatureAdded;
+  static String lastFeatureGroupAdded;
+  static String lastDescriptionAdded;
+
+  int featureIndex = 0;
+  boolean deleteFeature = false;
+  Panel colourPanel;
+  boolean amendFeatures(final SequenceI[] sequences,
+                        final SequenceFeature[] features,
+                        boolean newFeatures,
+                        final AlignmentPanel ap)
+  {
+    Panel bigPanel = new Panel(new BorderLayout());
+    final TextField name = new TextField(16);
+    final TextField source = new TextField(16);
+    final TextArea description = new TextArea(3, 35);
+    final TextField start = new TextField(8);
+    final TextField end = new TextField(8);
+    final Choice overlaps;
+    Button deleteButton = new Button("Delete");
+    deleteFeature = false;
+
+    colourPanel = new Panel(null);
+    colourPanel.setSize(110,15);
+    final FeatureRenderer fr = this;
+
+    Panel panel = new Panel(new GridLayout(3, 1));
+
+    Panel tmp;
+
+    ///////////////////////////////////////
+    ///MULTIPLE FEATURES AT SELECTED RESIDUE
+    if(!newFeatures && features.length>1)
+    {
+     panel = new Panel(new GridLayout(4, 1));
+     tmp = new Panel();
+     tmp.add(new Label("Select Feature: "));
+     overlaps = new Choice();
+     for(int i=0; i<features.length; i++)
+     {
+       String item = features[i].getType()
+        +"/"+features[i].getBegin()+"-"+features[i].getEnd();
+
+       if(features[i].getFeatureGroup()!=null)
+         item += " ("+features[i].getFeatureGroup()+")";
+
+       overlaps.addItem(item);
+     }
+
+     tmp.add(overlaps);
+
+     overlaps.addItemListener(new java.awt.event.ItemListener()
+     {
+       public void itemStateChanged(java.awt.event.ItemEvent e)
+       {
+         int index = overlaps.getSelectedIndex();
+         if (index != -1)
+         {
+           featureIndex = index;
+           name.setText(features[index].getType());
+           description.setText(features[index].getDescription());
+           source.setText(features[index].getFeatureGroup());
+           start.setText(features[index].getBegin()+"");
+           end.setText(features[index].getEnd()+"");
+
+           SearchResults highlight = new SearchResults();
+           highlight.addResult(sequences[0],
+                               features[index].getBegin(),
+                               features[index].getEnd());
+
+           ap.seqPanel.seqCanvas.highlightSearchResults(highlight);
+
+         }
+         Color col = getColour(name.getText());
+         if (col == null)
+         {
+           col = new
+               jalview.schemes.UserColourScheme()
+               .createColourFromName(name.getText());
+         }
+
+         colourPanel.setBackground(col);
+       }
+     });
+
+
+     panel.add(tmp);
+    }
+    //////////
+    //////////////////////////////////////
+
+
+    tmp = new Panel();
+    panel.add(tmp);
+    tmp.add(new Label("Name: ", Label.RIGHT));
+    tmp.add(name);
+
+    tmp = new Panel();
+    panel.add(tmp);
+    tmp.add(new Label("Group: ",Label.RIGHT));
+    tmp.add(source);
+
+    tmp = new Panel();
+    panel.add(tmp);
+    tmp.add(new Label("Colour: ", Label.RIGHT));
+    tmp.add(colourPanel);
+
+    bigPanel.add(panel, BorderLayout.NORTH);
+
+    panel = new Panel();
+    panel.add(new Label("Description: ", Label.RIGHT));
+    panel.add(new ScrollPane().add(description));
+
+    if (!newFeatures)
+    {
+      bigPanel.add(panel, BorderLayout.SOUTH);
+
+      panel = new Panel();
+      panel.add(new Label(" Start:", Label.RIGHT));
+      panel.add(start);
+      panel.add(new Label("  End:", Label.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";
+      }
+    }
+
+
+    String title = newFeatures ? "Create New Sequence Feature(s)" :
+        "Amend/Delete Features for "
+        + sequences[0].getName();
+
+    final JVDialog dialog = new JVDialog(ap.alignFrame,
+                               title,
+                               true,
+                               385,240);
+
+    dialog.setMainPanel(bigPanel);
+
+    if(newFeatures)
+    {
+      name.setText(lastFeatureAdded);
+      source.setText(lastFeatureGroupAdded);
+    }
+    else
+    {
+      dialog.ok.setLabel("Amend");
+      dialog.buttonPanel.add(deleteButton, 1);
+      deleteButton.addActionListener(new ActionListener()
+          {
+            public void actionPerformed(ActionEvent evt)
+            {
+              deleteFeature = true;
+              dialog.setVisible(false);
+            }
+          });
+      name.setText(features[0].getType());
+      source.setText(features[0].getFeatureGroup());
+    }
+
+    start.setText(features[0].getBegin()+"");
+    end.setText(features[0].getEnd()+"");
+    description.setText(features[0].getDescription());
+
+    Color col = getColour(name.getText());
+    if (col == null)
+    {
+      col = new
+          jalview.schemes.UserColourScheme()
+          .createColourFromName(name.getText());
+    }
+
+    colourPanel.setBackground(col);
+
+    dialog.setResizable(true);
+
+
+    colourPanel.addMouseListener(new java.awt.event.MouseAdapter()
+    {
+      public void mousePressed(java.awt.event.MouseEvent evt)
+      {
+        new UserDefinedColours(fr, ap.alignFrame);
+      }
+    });
+
+    dialog.setVisible(true);
+
+    jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();
+
+    if (dialog.accept)
+    {
+      //This ensures that the last sequence
+      //is refreshed and new features are rendered
+      lastSeq = null;
+      lastFeatureAdded = name.getText().trim();
+      lastFeatureGroupAdded = source.getText().trim();
+      lastDescriptionAdded = description.getText().replace('\n', ' ');
+    }
+
+    if(lastFeatureGroupAdded !=null && lastFeatureGroupAdded.length()<1)
+      lastFeatureGroupAdded = null;
+
+
+    if (!newFeatures)
+    {
+      SequenceFeature sf = features[featureIndex];
+
+      if (dialog.accept)
+      {
+        sf.type = lastFeatureAdded;
+        sf.featureGroup = lastFeatureGroupAdded;
+        sf.description = lastDescriptionAdded;
+        setColour(sf.type, colourPanel.getBackground());
+        try
+        {
+          sf.begin = Integer.parseInt(start.getText());
+          sf.end =  Integer.parseInt(end.getText());
+        }
+        catch (NumberFormatException ex)
+        {}
+
+        ffile.parseDescriptionHTML(sf, false);
+      }
+      if (deleteFeature)
+      {
+        sequences[0].deleteFeature(sf);
+      }
+
+    }
+    else
+    {
+      if (dialog.accept && name.getText().length()>0)
+      {
+        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();
+        }
+
+        col = colourPanel.getBackground();
+        setColour(lastFeatureAdded, col);
+
+        if(lastFeatureGroupAdded!=null)
+        {
+          featureGroups.put(lastFeatureGroupAdded, new Boolean(true));
+          av.featuresDisplayed.put(lastFeatureGroupAdded,
+                                   new Integer(col.getRGB()));
+        }
+        findAllFeatures();
+
+        String [] tro = new String[renderOrder.length];
+        tro[0] = renderOrder[renderOrder.length-1];
+        System.arraycopy(renderOrder,0,tro,1,renderOrder.length-1);
+        renderOrder = tro;
+
+        ap.paintAlignment(true);
+
+        return true;
+      }
+      else
+      {
+        return false;
+      }
+    }
+
+    findAllFeatures();
+
+    ap.paintAlignment(true);
+
+    return true;
+  }
+
+
+  public Color findFeatureColour(Color initialCol, SequenceI seq, int i)
+  {
+    overview = true;
+    if (!av.showSequenceFeatures)
+    {
+      return initialCol;
+    }
+
+    lastSeq = seq;
+    sequenceFeatures = lastSeq.getSequenceFeatures();
+    if (sequenceFeatures == null)
+    {
+      return initialCol;
+    }
+
+    sfSize = sequenceFeatures.length;
+
+    if (jalview.util.Comparison.isGap(lastSeq.getCharAt(i)))
+    {
+      return Color.white;
+    }
+
+    currentColour = null;
+
+    drawSequence(null, lastSeq, lastSeq.findPosition(i), -1, -1);
+
+    if (currentColour == null)
+    {
+      return initialCol;
+    }
+
+    return new Color( ( (Integer) currentColour).intValue());
+  }
+
+  /**
+   * This is used by the Molecule Viewer to get the accurate colour
+   * of the rendered sequence
+   */
+  boolean overview = false;
+
+
+  /**
+   * 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;
+
+  synchronized public void drawSequence(Graphics g, SequenceI seq,
+                           int start, int end, int y1)
+  {
+    if (seq.getSequenceFeatures() == null
+        || seq.getSequenceFeatures().length == 0)
+    {
+      return;
+    }
+
+    if (transparencySetter != null && g != null)
+    {
+      transparencySetter.setTransparency(g, transparency);
+    }
+
+    if (lastSeq == null || seq != lastSeq || sequenceFeatures!=seq.getSequenceFeatures())
+    {
+      lastSeq = seq;
+      sequenceFeatures = seq.getSequenceFeatures();
+      sfSize = sequenceFeatures.length;
+    }
+
+    if (av.featuresDisplayed == null || renderOrder == null)
+    {
+      findAllFeatures();
+      if (av.featuresDisplayed.size() < 1)
+      {
+        return;
+      }
+
+      sequenceFeatures = seq.getSequenceFeatures();
+      sfSize = sequenceFeatures.length;
+    }
+    if (!overview)
+    {
+      spos = lastSeq.findPosition(start);
+      epos = lastSeq.findPosition(end);
+      if (g != null)
+      {
+        fm = g.getFontMetrics();
+      }
+    }
+    String type;
+    for (int renderIndex = 0; renderIndex < renderOrder.length; renderIndex++)
+    {
+      type = renderOrder[renderIndex];
+      if (!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[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 (!overview && (sequenceFeatures[sfindex].getBegin() > epos
+                          || sequenceFeatures[sfindex].getEnd() < spos))
+        {
+          continue;
+        }
+
+        if (overview)
+        {
+          if (sequenceFeatures[sfindex].begin <= start &&
+              sequenceFeatures[sfindex].end >= start)
+          {
+            currentColour = av.featuresDisplayed.get(sequenceFeatures[sfindex].
+                type);
+          }
+
+        }
+        else if (sequenceFeatures[sfindex].type.equals("disulfide bond"))
+        {
+
+          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
+        {
+          renderFeature(g, seq,
+                        seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
+                        seq.findIndex(sequenceFeatures[sfindex].end) - 1,
+                        getColour(sequenceFeatures[sfindex].type),
+                        start, end, y1);
+        }
+
+      }
+    }
+
+    if (transparencySetter != null && g != null)
+    {
+      transparencySetter.setTransparency(g, 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;
+      }
+
+      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 (!av.validCharWidth)
+        {
+          continue;
+        }
+
+        g.setColor(Color.white);
+        charOffset = (av.charWidth - fm.charWidth(s)) / 2;
+        g.drawString(String.valueOf(s),
+                     charOffset + (av.charWidth * (i - start)),
+                     (y1 + av.charHeight) - av.charHeight / 5); //pady = height / 5;
+
+      }
+    }
+  }
+
+  void findAllFeatures()
+  {
+    jalview.schemes.UserColourScheme ucs = new
+        jalview.schemes.UserColourScheme();
+
+    av.featuresDisplayed = new Hashtable();
+    Vector allfeatures = new Vector();
+    for (int i = 0; i < av.alignment.getHeight(); i++)
+    {
+      SequenceFeature[] features = av.alignment.getSequenceAt(i).
+          getSequenceFeatures();
+
+      if (features == null)
+      {
+        continue;
+      }
+
+      int index = 0;
+      while (index < features.length)
+      {
+        if (!av.featuresDisplayed.containsKey(features[index].getType()))
+        {
+          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--;
+    }
+  }
+
+  public Color getColour(String featureType)
+  {
+    if (!featureColours.containsKey(featureType))
+    {
+      jalview.schemes.UserColourScheme ucs = new
+          jalview.schemes.UserColourScheme();
+      Color col = ucs.createColourFromName(featureType);
+      featureColours.put(featureType, col);
+      return col;
+    }
+    else
+      return (Color) featureColours.get(featureType);
+  }
+
+
+  public void setColour(String featureType, Color col)
+  {
+    featureColours.put(featureType, col);
+  }
+
+  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();
+    }
+
+   /* if (visibleNew)
+    {
+      if (av.featuresDisplayed != null)
+      {
+        av.featuresDisplayed.clear();
+      }
+      else
+      {
+        av.featuresDisplayed = new Hashtable();
+      }
+    }
+    if (data == null)
+    {
+      return;
+    }*/
+
+
+    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;
+      }
+    }
+  }
+  /**
+   * @return a simple list of feature group names or null 
+   */
+  public String[] getGroups()
+  {
+    buildGroupHash();
+    if (featureGroups!=null)
+    {
+      String[] gps = new String[featureGroups.size()];
+      Enumeration gn = featureGroups.keys();
+      int i=0;
+      while (gn.hasMoreElements())
+      {
+        gps[i++]  = (String) gn.nextElement();
+      }
+      return gps;
+    }
+    return null;
+  }
+  /**
+   * get visible or invisible groups
+   * @param visible true to return visible groups, false to return hidden ones.
+   * @return list of groups
+   */
+  public String[] getGroups(boolean visible) 
+  {
+    buildGroupHash();
+    if (featureGroups!=null)
+    {
+      Vector gp = new Vector();
+      
+      Enumeration gn = featureGroups.keys();
+      while (gn.hasMoreElements())
+      {
+        String nm = (String) gn.nextElement();
+        Boolean state = (Boolean) featureGroups.get(nm);
+        if (state.booleanValue()==visible)
+        {
+          gp.addElement(nm);
+        }
+      }
+      String[] gps = new String[gp.size()];
+      gp.copyInto(gps);
+      
+      int i=0;
+      while (gn.hasMoreElements())
+      {
+        gps[i++]  = (String) gn.nextElement();
+      }
+      return gps;
+    }
+    return null;
+  }
+  /**
+   * set all feature groups in toset to be visible or invisible
+   * @param toset group names
+   * @param visible the state of the named groups to set
+   */
+  public void setGroupState(String[] toset, boolean visible)
+  {
+    buildGroupHash();
+    if (toset!=null && toset.length>0 && featureGroups!=null)
+    {
+      boolean rdrw = false;
+      for (int i=0;i<toset.length; i++)
+      {
+        Object st = featureGroups.get(toset[i]);
+        if (st!=null)
+        {
+          featureGroups.put(toset[i], new Boolean(visible));
+          rdrw = rdrw || (visible!=((Boolean) st).booleanValue());
+        }
+      }
+      if (rdrw)
+      {
+        if (this.av!=null)
+          if (this.av.featureSettings!=null)
+          {
+            av.featureSettings.rebuildGroups();
+            this.av.featureSettings.resetTable(true);
+          } else {
+            buildFeatureHash();
+          }
+          if (av!=null)
+          {
+            av.alignmentChanged(null);
+          }
+      }
+    }
+  }
+  /**
+   * analyse alignment for groups and hash tables
+   * (used to be embedded in FeatureSettings.setTableData)
+   * @return true if features are on the alignment
+   */
+  public boolean buildGroupHash()
+  {
+    boolean alignmentHasFeatures=false;
+    if (featureGroups == null)
+    {
+      featureGroups = new Hashtable();
+    }
+    Vector allFeatures = new Vector();
+    Vector allGroups = new Vector();
+    SequenceFeature[] tmpfeatures;
+    String group;
+    for (int i = 0; i < av.alignment.getHeight(); i++)
+    {
+      if (av.alignment.getSequenceAt(i).getSequenceFeatures() == null)
+      {
+        continue;
+      }
+
+      alignmentHasFeatures = true;
+
+      tmpfeatures = av.alignment.getSequenceAt(i).getSequenceFeatures();
+      int index = 0;
+      while (index < tmpfeatures.length)
+      {
+        if (tmpfeatures[index].getFeatureGroup() != null)
+        {
+          group = tmpfeatures[index].featureGroup;
+          if (!allGroups.contains(group))
+          {
+            allGroups.addElement(group);
+
+            boolean visible = true;
+            if (featureGroups.containsKey(group))
+            {
+              visible = ( (Boolean) featureGroups.get(group)).booleanValue();
+            } else {
+              featureGroups.put(group, new Boolean(visible));
+            }
+          }
+        }
+
+        if (!allFeatures.contains(tmpfeatures[index].getType()))
+        {
+          allFeatures.addElement(tmpfeatures[index].getType());
+        }
+        index++;
+      }
+    }
+    
+    return alignmentHasFeatures;
+  }
+  /**
+   * rebuild the featuresDisplayed and renderorder list based on the featureGroups hash and any existing display state
+   * and force a repaint if necessary
+   * @return true if alignment has visible features
+   */
+  public boolean buildFeatureHash() {
+    boolean alignmentHasFeatures=false;
+    if (featureGroups==null)
+    {
+      alignmentHasFeatures = buildGroupHash();
+    }
+    if (!alignmentHasFeatures)
+      return false;
+    Hashtable fdisp = av.featuresDisplayed;
+    Vector allFeatures = new Vector();
+    SequenceFeature[] tmpfeatures;
+    String group;
+    for (int i = 0; i < av.alignment.getHeight(); i++)
+    {
+      if (av.alignment.getSequenceAt(i).getSequenceFeatures() == null)
+      {
+        continue;
+      }
+
+      alignmentHasFeatures = true;
+
+      tmpfeatures = av.alignment.getSequenceAt(i).getSequenceFeatures();
+      int index = 0;
+      while (index < tmpfeatures.length)
+      {
+        boolean visible = true;
+        if (tmpfeatures[index].getFeatureGroup() != null)
+        {
+          group = tmpfeatures[index].featureGroup;
+          if (featureGroups.containsKey(group))
+          {
+            visible = ( (Boolean) featureGroups.get(group)).booleanValue();
+          }
+        }
+        
+        if (visible && !allFeatures.contains(tmpfeatures[index].getType()))
+        {
+          allFeatures.addElement(tmpfeatures[index].getType());
+        }
+        index++;
+      }
+    }
+    if (allFeatures.size()>0)
+    {
+      String[] neworder = new String[allFeatures.size()];
+      int p=neworder.length-1;
+      for (int i=renderOrder.length-1; i>=0; i--)
+      {
+        if (allFeatures.contains(renderOrder[i]))
+        {
+          neworder[p--] = renderOrder[i];
+          allFeatures.removeElement(renderOrder[i]);
+        } else {
+          av.featuresDisplayed.remove(renderOrder[i]);
+        }
+      }
+      for (int i=allFeatures.size()-1; i>0; i++)
+      {
+        Object e = allFeatures.elementAt(i);
+        if (e!=null)
+        {
+          neworder[p--] = (String) e;
+          av.featuresDisplayed.put(e, getColour((String)e));
+        }
+      }
+      renderOrder = neworder;
+      return true;
+    }
+    
+    return alignmentHasFeatures;
+  }
+}
+
+class TransparencySetter
+{
+  void setTransparency(Graphics g, float value)
+  {
+     Graphics2D g2 = (Graphics2D) g;
+     g2.setComposite(
+        AlphaComposite.getInstance(
+             AlphaComposite.SRC_OVER, value));
+  }
+}