X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureRenderer.java;h=a1de62e32e04b55c9a784222d380eaad92610fe4;hb=5c57814f95e73a63e012479651b919fdc4099f53;hp=22789a1d99f063a2e1c84fa2d4ca7e9e38e65962;hpb=22b9e04a8351aef1cb23a66d898502601499b673;p=jalview.git

diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
index 22789a1..a1de62e 100755
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -1,336 +1,1004 @@
-/*
- * 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.datamodel.*;
-
-import java.awt.*;
-
-import java.util.*;
-
-import java.awt.image.*;
-
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class FeatureRenderer
-{
-    AlignViewport av;
-    Color resBoxColour;
-    float transparency = 1.0f;
-    FontMetrics fm;
-    int charOffset;
-    boolean drawText = true;
-
-    // The following vector holds the features which are
-    // to be added, in the correct order or rendering
-    Vector featuresDisplayed = null;
-
-    // A higher level for grouping features of a
-   // particular type
-    Hashtable featureGroups = null;
-
-
-    /**
-     * Creates a new FeatureRenderer object.
-     *
-     * @param av DOCUMENT ME!
-     */
-    public FeatureRenderer(AlignViewport av)
-    {
-        this.av = av;
-        initColours();
-    }
-
-    /**
-     * This is used by the Molecule Viewer to get the accurate colour
-     * of the rendered sequence
-     */
-    BufferedImage bi;
-    public Color findFeatureColour(Color initialCol, SequenceI seq, int i)
-    {
-      if(!av.showSequenceFeatures)
-        return initialCol;
-
-      if (bi == null)
-        bi = new BufferedImage(1, 1, BufferedImage.TYPE_INT_RGB);
-
-      bi.setRGB(0,0, initialCol.getRGB());
-
-      drawText = false;
-
-      drawSequence(bi.getGraphics(), seq, i, i, 0, 0, 1, 1);
-      drawText = true;
-
-      return new Color(bi.getRGB(0, 0));
-    }
-
-
-    /**
-     * 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,
-                             int start, int end, int x1, int y1, int width, int height)
-    {
-
-        //System.out.println(start+" "+end+" "+x1+" "+y1);
-      if (seq.getDatasetSequence().getSequenceFeatures() == null
-          || seq.getDatasetSequence().getSequenceFeatures().size()==0)
-        return;
-
-      fm = g.getFontMetrics();
-
-      if (transparency != 1)
-      {
-        Graphics2D g2 = (Graphics2D) g;
-        g2.setComposite(
-            AlphaComposite.getInstance(
-                AlphaComposite.SRC_OVER, transparency));
-      }
-
-      String type;
-      SequenceFeature sf;
-      if (featuresDisplayed == null)
-        findAllFeatures();
-
-      Enumeration e = featuresDisplayed.elements(), e2;
-
-      // Loop through each visible feature
-      while (e.hasMoreElements())
-      {
-
-        type = e.nextElement().toString();
-        e2 = seq.getDatasetSequence().getSequenceFeatures().elements();
-        // loop through all features in sequence to find
-        // current feature to render
-          while (e2.hasMoreElements())
-        {
-
-          sf = (SequenceFeature) e2.nextElement();
-          if (!type.equals(sf.getType()))
-            continue;
-
-          if(featureGroups!=null
-             && sf.getFeatureGroup()!=null
-             && featureGroups.containsKey(sf.getFeatureGroup())
-             && !((Boolean)featureGroups.get(sf.getFeatureGroup())).booleanValue())
-          {
-            continue;
-          }
-
-          if (sf.getBegin() > seq.getEnd())
-            continue;
-
-          if (type.equals("disulfide bond"))
-          {
-
-            renderFeature(g, seq,
-                          seq.findIndex(sf.getBegin()) - 1,
-                          seq.findIndex(sf.getBegin()) - 1,
-                          type, start, end, x1, y1, width, height);
-            renderFeature(g, seq,
-                          seq.findIndex(sf.getEnd()) - 1,
-                          seq.findIndex(sf.getEnd()) - 1,
-                          type, start, end, x1, y1, width, height);
-
-          }
-          else
-            renderFeature(g, seq,
-                          seq.findIndex(sf.getBegin()) - 1,
-                          seq.findIndex(sf.getEnd()) - 1,
-                          type, start, end, x1, y1, width, height);
-        }
-      }
-
-        if(transparency!=1.0f)
-        {
-          Graphics2D g2 = (Graphics2D) g;
-          g2.setComposite(
-              AlphaComposite.getInstance(
-                  AlphaComposite.SRC_OVER, 1.0f));
-        }
-    }
-
-
-    void renderFeature(Graphics g, SequenceI seq,
-                       int fstart, int fend, String type, int start, int end, int x1, int y1, int width, int height)
-    {
-
-      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 (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);
-
-            if(drawText)
-           {
-             g.setColor(Color.white);
-             charOffset = (width - fm.charWidth(s)) / 2;
-             g.drawString(String.valueOf(s),
-                          charOffset + x1 + (width * (i - start)),
-                          (y1 + height) - height / 5); //pady = height / 5;
-           }
-          }
-        }
-    }
-
-    void findAllFeatures()
-    {
-      Vector features = new Vector();
-      SequenceFeature sf;
-      featuresDisplayed = new Vector();
-      Enumeration e;
-      for (int i = 0; i < av.alignment.getHeight(); i++)
-      {
-        features = av.alignment.getSequenceAt(i).getDatasetSequence().
-            getSequenceFeatures();
-        if (features == null)
-          continue;
-
-        e = features.elements();
-        while (e.hasMoreElements())
-        {
-          sf = (SequenceFeature) e.nextElement();
-          if (!featuresDisplayed.contains(sf.getType()))
-          {
-            featuresDisplayed.addElement(sf.getType());
-          }
-        }
-      }
-    }
-
-    public Color getColour(String featureType)
-    {
-      return (Color)featureColours.get(featureType);
-    }
-
-    public void addNewFeature(String name, Color col)
-    {
-      setColour(name, col);
-      if(featuresDisplayed==null)
-        featuresDisplayed = new Vector();
-      featuresDisplayed.insertElementAt(name, 0);
-    }
-
-    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.clear();
-      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(230,230,0));
-      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.gui;
+
+import java.util.*;
+
+import java.awt.*;
+import java.awt.event.*;
+import java.awt.image.*;
+import java.beans.PropertyChangeListener;
+import java.beans.PropertyChangeSupport;
+
+import javax.swing.*;
+
+import jalview.datamodel.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class FeatureRenderer
+{
+  AlignmentPanel ap;
+  AlignViewport av;
+  Color resBoxColour;
+  float transparency = 1.0f;
+  FontMetrics fm;
+  int charOffset;
+
+  Hashtable featureColours = new Hashtable();
+
+  // A higher level for grouping features of a
+  // particular type
+  Hashtable featureGroups = new Hashtable();
+
+  // This is actually an Integer held in the hashtable,
+  // Retrieved using the key feature type
+  Object currentColour;
+
+  String[] renderOrder;
+  PropertyChangeSupport changeSupport=new PropertyChangeSupport(this);
+
+  Vector allfeatures;
+
+  /**
+   * Creates a new FeatureRenderer object.
+   *
+   * @param av
+   *          DOCUMENT ME!
+   */
+  public FeatureRenderer(AlignmentPanel ap)
+  {
+    this.ap = ap;
+    this.av = ap.av;
+  }
+
+
+  public void transferSettings(FeatureRenderer fr)
+  {
+    this.renderOrder = fr.renderOrder;
+    this.featureGroups = fr.featureGroups;
+    this.featureColours = fr.featureColours;
+    this.transparency = fr.transparency;
+    this.featureOrder = fr.featureOrder;
+  }
+
+  BufferedImage offscreenImage;
+  boolean offscreenRender = false;
+  public Color findFeatureColour(Color initialCol, SequenceI seq, int res)
+  {
+    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)
+    {
+      return initialCol;
+    }
+
+    if (seq != lastSeq)
+    {
+      lastSeq = seq;
+      sequenceFeatures = lastSeq.getDatasetSequence().getSequenceFeatures();
+      if (sequenceFeatures!=null)
+      {
+        sfSize = sequenceFeatures.length;
+      }
+    }
+
+    if (sequenceFeatures!=lastSeq.getDatasetSequence().getSequenceFeatures()) {
+      sequenceFeatures = lastSeq.getDatasetSequence().getSequenceFeatures();
+      if (sequenceFeatures != null)
+      {
+        sfSize = sequenceFeatures.length;
+      }
+    }
+
+    if (sequenceFeatures == null || sfSize==0)
+    {
+      return initialCol;
+    }
+
+
+    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;
+
+  synchronized 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();
+    }
+
+    if (lastSeq == null || seq != lastSeq
+        || seq.getDatasetSequence().getSequenceFeatures()!=sequenceFeatures)
+    {
+      lastSeq = seq;
+      sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();
+    }
+
+    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);
+    }
+
+    sfSize = sequenceFeatures.length;
+    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[sfindex].type.equals(type))
+        {
+          continue;
+        }
+
+        if (featureGroups != null
+            && sequenceFeatures[sfindex].featureGroup != null
+            &&
+            sequenceFeatures[sfindex].featureGroup.length()!=0
+            && 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"))
+        {
+
+          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 (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;
+  /**
+   * Called when alignment in associated view has new/modified features
+   * to discover and display.
+   *
+   */
+  public void featuresAdded()
+  {
+    lastSeq=null;
+    findAllFeatures();
+  }
+
+  boolean findingFeatures = false;
+  /**
+   * search the alignment for all new features, give them a colour and display
+   * them. Then fires a PropertyChangeEvent on the changeSupport object.
+   *
+   */
+  void findAllFeatures()
+  {
+    synchronized (firing)
+    {
+        if (firing.equals(Boolean.FALSE)) {
+          firing=Boolean.TRUE;
+          findAllFeatures(true); // add all new features as visible
+          changeSupport.firePropertyChange("changeSupport",null,null);
+          firing=Boolean.FALSE;
+      }
+    }
+  }
+  /**
+   * Searches alignment for all features and updates colours
+   *
+   * @param newMadeVisible
+   *          if true newly added feature types will be rendered immediatly
+   */
+  synchronized void findAllFeatures(boolean newMadeVisible) {
+    newFeatureAdded = false;
+
+    if (findingFeatures)
+    {
+      newFeatureAdded = true;
+      return;
+    }
+
+    findingFeatures = true;
+
+    if (av.featuresDisplayed == null)
+    {
+      av.featuresDisplayed = new Hashtable();
+    }
+
+    allfeatures = new Vector();
+    Vector oldfeatures = new Vector();
+    if (renderOrder!=null)
+    {
+      for (int i=0; i<renderOrder.length; i++) {
+        if (renderOrder[i]!=null)
+        {
+          oldfeatures.addElement(renderOrder[i]);
+        }
+      }
+    }
+    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(featureGroups.containsKey(features[index].getType()))
+          {
+            boolean visible = ( (Boolean) featureGroups.get(
+                features[index].featureGroup)).booleanValue();
+
+            if(!visible)
+            {
+              index++;
+              continue;
+            }
+          }
+
+
+          if (! (features[index].begin == 0 && features[index].end == 0))
+          {
+            // 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 (newMadeVisible && !oldfeatures.contains(features[index].getType())) {
+              // this is a new feature type on the alignment. Mark it for
+              // display.
+              av.featuresDisplayed.put(features[index].getType(),
+                                     new Integer(getColour(features[index].
+                getType()).getRGB()));
+              setOrder(features[index].getType(),0);
+            }
+           }
+        }
+        if (!allfeatures.contains(features[index].getType()))
+        {
+          allfeatures.addElement(features[index].getType());
+        }
+        index++;
+      }
+    }
+    updateRenderOrder(allfeatures);
+    findingFeatures = false;
+  }
+  protected Boolean firing=Boolean.FALSE;
+  /**
+   * replaces the current renderOrder with the unordered features in allfeatures.
+   * The ordering of any types in both renderOrder and allfeatures is preserved,
+   * and all new feature types are rendered on top of the existing types, in
+   * the order given by getOrder or the order given in allFeatures.
+   * Note. this operates directly on the featureOrder hash for efficiency. TODO:
+   * eliminate the float storage for computing/recalling the persistent ordering
+   *
+   * @param allFeatures
+   */
+  private void updateRenderOrder(Vector allFeatures) {
+    Vector allfeatures = new Vector(allFeatures);
+    String[] oldRender = renderOrder;
+    renderOrder = new String[allfeatures.size()];
+    boolean initOrders=(featureOrder==null);
+    int opos=0;
+    if (oldRender!=null && oldRender.length>0)
+    {
+      for (int j=0; j<oldRender.length; j++)
+      {
+        if (oldRender[j]!=null)
+          {
+            if (initOrders)
+            {
+              setOrder(oldRender[j], (1-(1+(float)j)/(float) oldRender.length));
+            }
+            if (allfeatures.contains(oldRender[j])) {
+              renderOrder[opos++]  = oldRender[j]; // existing features always
+                                                    // appear below new features
+              allfeatures.removeElement(oldRender[j]);
+            }
+          }
+        }
+    }
+    if (allfeatures.size()==0) {
+      // no new features - leave order unchanged.
+      return;
+    }
+    int i=allfeatures.size()-1;
+    int iSize=i;
+    boolean sort=false;
+    String[] newf = new String[allfeatures.size()];
+    float[] sortOrder = new float[allfeatures.size()];
+    Enumeration en = allfeatures.elements();
+    // sort remaining elements
+    while (en.hasMoreElements())
+    {
+      newf[i] = en.nextElement().toString();
+      if (initOrders || !featureOrder.containsKey(newf[i]))
+      {
+        int denom = initOrders ? allfeatures.size() : featureOrder.size();
+          // new unordered feature - compute persistent ordering at head of
+          // existing features.
+        setOrder(newf[i], i/(float) denom);
+      }
+      // set order from newly found feature from persisted ordering.
+      sortOrder[i] = 2-((Float) featureOrder.get(newf[i])).floatValue();
+      if (i<iSize)
+      {
+        // only sort if we need to
+        sort = sort || sortOrder[i]>sortOrder[i+1];
+      }
+      i--;
+    }
+    if (iSize>1 && sort)
+      jalview.util.QuickSort.sort(sortOrder, newf);
+    sortOrder=null;
+    System.arraycopy(newf, 0, renderOrder, opos, newf.length);
+  }
+  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);
+  }
+
+  static String lastFeatureAdded;
+  static String lastFeatureGroupAdded;
+  static String lastDescriptionAdded;
+
+  int featureIndex = 0;
+  boolean amendFeatures(final SequenceI[] sequences,
+                        final SequenceFeature[] features,
+                        boolean newFeatures,
+                        final AlignmentPanel ap)
+  {
+
+    featureIndex = 0;
+
+    JPanel bigPanel = new JPanel(new BorderLayout());
+    final JComboBox overlaps;
+    final JTextField name = new JTextField(25);
+    final JTextField source = new JTextField(25);
+    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)
+      {
+        Color col = JColorChooser.showDialog(Desktop.desktop,
+                                             "Select Feature Colour",
+                                             colour.getBackground());
+        if (col != null)
+          colour.setBackground(col);
+
+      }
+    });
+
+    JPanel tmp = new JPanel();
+    JPanel panel = new JPanel(new GridLayout(3, 1));
+
+    ///////////////////////////////////////
+    ///MULTIPLE FEATURES AT SELECTED RESIDUE
+    if(!newFeatures && features.length>1)
+    {
+     panel = new JPanel(new GridLayout(4, 1));
+     tmp = new JPanel();
+     tmp.add(new JLabel("Select Feature: "));
+     overlaps = new JComboBox();
+     for(int i=0; i<features.length; i++)
+     {
+       overlaps.addItem(features[i].getType()
+        +"/"+features[i].getBegin()+"-"+features[i].getEnd()
+        +" ("+features[i].getFeatureGroup()+")");
+     }
+
+     tmp.add(overlaps);
+
+     overlaps.addItemListener(new ItemListener()
+     {
+       public void itemStateChanged(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.setValue(new Integer(features[index].getBegin()));
+           end.setValue(new Integer(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());
+         }
+
+         colour.setBackground(col);
+       }
+     });
+
+
+     panel.add(tmp);
+    }
+    //////////
+    //////////////////////////////////////
+
+    tmp = new JPanel();
+    panel.add(tmp);
+    tmp.add(new JLabel("Name: ", JLabel.RIGHT));
+    tmp.add(name);
+
+    tmp = new JPanel();
+    panel.add(tmp);
+    tmp.add(new JLabel("Group: ", JLabel.RIGHT));
+    tmp.add(source);
+
+    tmp = new JPanel();
+    panel.add(tmp);
+    tmp.add(new JLabel("Colour: ", JLabel.RIGHT));
+    tmp.add(colour);
+    colour.setPreferredSize(new Dimension(150, 15));
+
+    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
+      {
+        lastFeatureGroupAdded = "Jalview";
+      }
+    }
+
+    if(newFeatures)
+    {
+      name.setText(lastFeatureAdded);
+      source.setText(lastFeatureGroupAdded);
+    }
+    else
+    {
+      name.setText(features[0].getType());
+      source.setText(features[0].getFeatureGroup());
+    }
+
+    start.setValue(new Integer(features[0].getBegin()));
+    end.setValue(new Integer(features[0].getEnd()));
+    description.setText(features[0].getDescription());
+    colour.setBackground(getColour(name.getText()));
+
+
+    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.getText().length()>0)
+    {
+      // 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().replaceAll("\n", " ");
+
+      if(lastFeatureGroupAdded.length()<1)
+        lastFeatureGroupAdded = null;
+    }
+
+    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());
+        av.featuresDisplayed.put(sf.type,
+                                 new Integer(colour.getBackground().getRGB()));
+
+        try
+        {
+          sf.begin = ( (Integer) start.getValue()).intValue();
+          sf.end = ( (Integer) end.getValue()).intValue();
+        }
+        catch (NumberFormatException ex)
+        {}
+
+        ffile.parseDescriptionHTML(sf, false);
+      }
+    }
+    else //NEW FEATURES ADDED
+    {
+      if (reply == JOptionPane.OK_OPTION
+          && lastFeatureAdded.length()>0)
+      {
+        for (int i = 0; i < sequences.length; i++)
+        {
+          features[i].type = lastFeatureAdded;
+          if (lastFeatureGroupAdded!=null)
+            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 (lastFeatureGroupAdded != null)
+        {
+          if (featureGroups == null)
+            featureGroups = new Hashtable();
+          featureGroups.put(lastFeatureGroupAdded, new Boolean(true));
+        }
+
+        Color col = colour.getBackground();
+        setColour(lastFeatureAdded, colour.getBackground());
+        av.featuresDisplayed.put(lastFeatureAdded,
+                                   new Integer(col.getRGB()));
+
+        findAllFeatures(false);
+
+        ap.paintAlignment(true);
+
+
+        return true;
+      }
+      else
+      {
+        return false;
+      }
+    }
+
+    ap.paintAlignment(true);
+
+    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;
+  }
+  /**
+   * Replace current ordering with new ordering
+   * @param data { String(Type), Colour(Type), Boolean(Displayed) }
+   */
+  public void setFeaturePriority(Object[][] data)
+  {
+    setFeaturePriority(data, true);
+  }
+  /**
+   *
+   * @param data { String(Type), Colour(Type), Boolean(Displayed) }
+   * @param visibleNew when true current featureDisplay list will be cleared
+   */
+  public void setFeaturePriority(Object[][] data, boolean visibleNew)
+  {
+    if (visibleNew)
+      {
+      if (av.featuresDisplayed != null)
+      {
+        av.featuresDisplayed.clear();
+      }
+      else
+      {
+        av.featuresDisplayed = new Hashtable();
+      }
+    }
+    if (data==null)
+    {
+      return;
+    }
+
+    // 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
+    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;
+      }
+    }
+
+  }
+  Hashtable featureOrder=null;
+  /**
+   * analogous to colour - store a normalized ordering for all feature types in
+   * this rendering context.
+   *
+   * @param type
+   *          Feature type string
+   * @param position
+   *          normalized priority - 0 means always appears on top, 1 means
+   *          always last.
+   */
+  public float setOrder(String type, float position)
+  {
+    if (featureOrder==null)
+    {
+      featureOrder = new Hashtable();
+    }
+    featureOrder.put(type, new Float(position));
+    return position;
+  }
+  /**
+   * get the global priority (0 (top) to 1 (bottom))
+   *
+   * @param type
+   * @return [0,1] or -1 for a type without a priority
+   */
+  public float getOrder(String type) {
+    if (featureOrder!=null)
+    {
+      if (featureOrder.containsKey(type))
+      {
+        return ((Float)featureOrder.get(type)).floatValue();
+      }
+    }
+    return -1;
+  }
+
+  /**
+   * @param listener
+   * @see java.beans.PropertyChangeSupport#addPropertyChangeListener(java.beans.PropertyChangeListener)
+   */
+  public void addPropertyChangeListener(PropertyChangeListener listener)
+  {
+    changeSupport.addPropertyChangeListener(listener);
+  }
+
+  /**
+   * @param listener
+   * @see java.beans.PropertyChangeSupport#removePropertyChangeListener(java.beans.PropertyChangeListener)
+   */
+  public void removePropertyChangeListener(PropertyChangeListener listener)
+  {
+    changeSupport.removePropertyChangeListener(listener);
+  }
+}