X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureRenderer.java;h=634dbedae985fed6de65e73ef909d673811aad68;hb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;hp=b5b53fd86722bdbd336bf05a809fdebfeda3cefd;hpb=219069b19ed66908ea5ec0819802f772df3493f3;p=jalview.git

diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
index b5b53fd..634dbed 100755
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -18,17 +18,14 @@
  */
 package jalview.gui;
 
-import jalview.datamodel.*;
-
-import java.awt.*;
-
 import java.util.*;
 
+import java.awt.*;
+import java.awt.event.*;
 import java.awt.image.*;
 import javax.swing.*;
-import javax.swing.JOptionPane;
-import java.awt.event.*;
 
+import jalview.datamodel.*;
 
 /**
  * DOCUMENT ME!
@@ -38,668 +35,754 @@ import java.awt.event.*;
  */
 public class FeatureRenderer
 {
-    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 = 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)
+  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 = 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;
+  }
+
+  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)
     {
-        this.av = av;
+      return initialCol;
     }
 
-    public void transferSettings(FeatureRenderer fr)
+    if (seq != lastSeq)
     {
-      renderOrder = fr.renderOrder;
-      featureGroups = fr.featureGroups;
-      featureColours = fr.featureColours;
-      transparency =  fr.transparency;
+      lastSeq = seq;
+      sequenceFeatures = lastSeq.getDatasetSequence().getSequenceFeatures();
+      if (sequenceFeatures == null)
+      {
+        return initialCol;
+      }
+
+      sfSize = sequenceFeatures.length;
     }
 
-    BufferedImage offscreenImage;
-    boolean offscreenRender = false;
-    public Color findFeatureColour(Color initialCol, SequenceI seq, int res)
+    if (jalview.util.Comparison.isGap(lastSeq.getCharAt(column)))
     {
-      return new Color( findFeatureColour (initialCol.getRGB(),
-                        seq, res ));
+      return Color.white.getRGB();
     }
 
-    /**
-     * 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)
+    //Only bother making an offscreen image if transparency is applied
+    if (transparency != 1.0f && offscreenImage == null)
     {
-      if(!av.showSequenceFeatures)
-        return initialCol;
-
-      if(seq!=lastSeq)
-      {
-        lastSeq = seq;
-        sequenceFeatures = lastSeq.getDatasetSequence().getSequenceFeatures();
-        if(sequenceFeatures==null)
-          return initialCol;
-
-        sfSize = sequenceFeatures.length;
-      }
-
-      if(jalview.util.Comparison.isGap(lastSeq.getCharAt(column)))
-        return Color.white.getRGB();
+      offscreenImage = new BufferedImage(1, 1, BufferedImage.TYPE_INT_ARGB);
+    }
 
+    currentColour = null;
 
-      //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);
-      }
+    offscreenRender = true;
 
-      currentColour = null;
+    if (offscreenImage != null)
+    {
+      offscreenImage.setRGB(0, 0, initialCol);
+      drawSequence(offscreenImage.getGraphics(),
+                   lastSeq,
+                   column, column, 0);
 
-      offscreenRender = true;
+      return offscreenImage.getRGB(0, 0);
+    }
+    else
+    {
+      drawSequence(null,
+                   lastSeq,
+                   lastSeq.findPosition(column),
+                   -1, -1);
 
-      if(offscreenImage!=null)
+      if (currentColour == null)
       {
-        offscreenImage.setRGB(0,0,initialCol);
-        drawSequence(offscreenImage.getGraphics(),
-                     lastSeq,
-                     column,column,0);
-
-        return offscreenImage.getRGB(0,0);
+        return initialCol;
       }
       else
       {
-        drawSequence(null,
-                    lastSeq,
-                    lastSeq.findPosition(column),
-                    -1, -1);
-
-        if (currentColour == null)
-          return initialCol;
-        else
-          return  ((Integer)currentColour).intValue();
+        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;
+    }
 
-    /**
-     * 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;
+    if (g != null)
+    {
+      fm = g.getFontMetrics();
+    }
 
-    public void drawSequence(Graphics g, SequenceI seq,
-                             int start, int end, int y1)
+    if (av.featuresDisplayed == null
+        || renderOrder == null
+        || newFeatureAdded)
     {
-      if ( seq.getDatasetSequence().getSequenceFeatures() == null
-          || seq.getDatasetSequence().getSequenceFeatures().length==0)
+      findAllFeatures();
+      if (av.featuresDisplayed.size() < 1)
+      {
         return;
+      }
 
-      if(g!=null)
-        fm = g.getFontMetrics();
-
+      sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();
+      sfSize = sequenceFeatures.length;
+    }
 
-      if (av.featuresDisplayed == null
-          || renderOrder==null
-          || newFeatureAdded)
-       {
-         findAllFeatures();
-         if(av.featuresDisplayed.size()<1)
-           return;
+    if (lastSeq == null || seq != lastSeq)
+    {
+      lastSeq = seq;
+      sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();
+      sfSize = sequenceFeatures.length;
+    }
 
-         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(lastSeq==null || seq!=lastSeq)
-      {
-        lastSeq = seq;
-        sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();
-        sfSize = sequenceFeatures.length;
-      }
+    if (!offscreenRender)
+    {
+      spos = lastSeq.findPosition(start);
+      epos = lastSeq.findPosition(end);
+    }
 
+    String type;
+    for (int renderIndex = 0; renderIndex < renderOrder.length; renderIndex++)
+    {
+      type = renderOrder[renderIndex];
 
-      if (transparency != 1 && g!=null)
+      if (type == null || !av.featuresDisplayed.containsKey(type))
       {
-        Graphics2D g2 = (Graphics2D) g;
-        g2.setComposite(
-            AlphaComposite.getInstance(
-                AlphaComposite.SRC_OVER, transparency));
+        continue;
       }
 
-      if(!offscreenRender)
+      // loop through all features in sequence to find
+      // current feature to render
+      for (sfindex = 0; sfindex < sfSize; sfindex++)
       {
-        spos = lastSeq.findPosition(start);
-        epos = lastSeq.findPosition(end);
-      }
-
-
-      String type;
-      for(int renderIndex=0; renderIndex<renderOrder.length; renderIndex++)
-       {
-        type =  renderOrder[renderIndex];
-
-        if(!av.featuresDisplayed.containsKey(type))
+        if (sequenceFeatures.length <= sfindex)
+        {
           continue;
+        }
+        if (!sequenceFeatures[sfindex].type.equals(type))
+        {
+          continue;
+        }
 
-        // loop through all features in sequence to find
-        // current feature to render
-        for (sfindex = 0; sfindex < sfSize; sfindex++)
+        if (featureGroups != null
+            && sequenceFeatures[sfindex].featureGroup != null
+            &&
+            featureGroups.containsKey(sequenceFeatures[sfindex].featureGroup)
+            &&
+            ! ( (Boolean) featureGroups.get(sequenceFeatures[sfindex].
+                                            featureGroup)).
+            booleanValue())
         {
-          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;
-          }
+          continue;
+        }
 
-          if (!offscreenRender && (sequenceFeatures[sfindex].getBegin() > epos
-                            || sequenceFeatures[sfindex].getEnd() < spos))
-            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"))
+        if (offscreenRender && offscreenImage == null)
+        {
+          if (sequenceFeatures[sfindex].begin <= start &&
+              sequenceFeatures[sfindex].end >= start)
           {
-
-            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);
-
+            currentColour = av.featuresDisplayed.get(sequenceFeatures[sfindex].
+                type);
           }
-          else
-            renderFeature(g, seq,
-                          seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
-                          seq.findIndex(sequenceFeatures[sfindex].end) - 1,
-                          getColour(sequenceFeatures[sfindex].type),
-                          start, end, y1);
+        }
+        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));
-        }
     }
 
+    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)
+  {
 
-    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 (((fstart <= end) && (fend >= start)))
+      if (fend >= end)
       {
-        if (fstart < start)
-        { // fix for if the feature we have starts before the sequence start,
-          fstart = start; // but the feature end is still valid!!
-        }
+        fend = end;
+      }
+      int pady = (y1 + av.charHeight) - av.charHeight / 5;
+      for (i = fstart; i <= fend; i++)
+      {
+        s = seq.getCharAt(i);
 
-        if (fend >= end)
+        if (jalview.util.Comparison.isGap(s))
         {
-          fend = end;
+          continue;
         }
-          int pady = (y1 + av.charHeight) - av.charHeight / 5;
-          for (i = fstart; i <= fend; i++)
-          {
-            s = seq.getSequence().charAt(i);
 
-            if (jalview.util.Comparison.isGap(s))
-            {
-              continue;
-            }
+        g.setColor(featureColour);
 
-            g.setColor(featureColour);
+        g.fillRect( (i - start) * av.charWidth, y1, av.charWidth, av.charHeight);
 
-            g.fillRect( (i - start) * av.charWidth, y1, av.charWidth,av.charHeight);
-
-            if(offscreenRender || !av.validCharWidth)
-              continue;
+        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);
+        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 newFeatureAdded = false;
+  boolean findingFeatures = false;
+  synchronized void findAllFeatures()
+  {
+    newFeatureAdded = false;
 
-    public void featuresAdded()
+    if (findingFeatures)
     {
-      findAllFeatures();
+      newFeatureAdded = true;
+      return;
     }
 
-   boolean findingFeatures = false;
-   synchronized void findAllFeatures()
-   {
-      newFeatureAdded = false;
+    findingFeatures = true;
+    jalview.schemes.UserColourScheme ucs = new
+        jalview.schemes.UserColourScheme();
 
-      if(findingFeatures)
-      {
-        newFeatureAdded = true;
-        return;
-      }
-
-      findingFeatures = true;
-      jalview.schemes.UserColourScheme ucs = new
-          jalview.schemes.UserColourScheme();
+    if (av.featuresDisplayed == null)
+    {
+      av.featuresDisplayed = new Hashtable();
+    }
 
-      if(av.featuresDisplayed==null)
-        av.featuresDisplayed = new Hashtable();
+    av.featuresDisplayed.clear();
 
-      av.featuresDisplayed.clear();
+    Vector allfeatures = new Vector();
+    for (int i = 0; i < av.alignment.getHeight(); i++)
+    {
+      SequenceFeature[] features
+          = av.alignment.getSequenceAt(i).getDatasetSequence().
+          getSequenceFeatures();
 
-      Vector allfeatures = new Vector();
-      for (int i = 0; i < av.alignment.getHeight(); i++)
+      if (features == null)
       {
-        SequenceFeature [] features
-            = av.alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();
-
-        if (features == null)
-          continue;
+        continue;
+      }
 
-        int index = 0;
-        while (index < features.length)
+      int index = 0;
+      while (index < features.length)
+      {
+        if (!av.featuresDisplayed.containsKey(features[index].getType()))
         {
-          if (!av.featuresDisplayed.containsKey(features[index].getType()))
+          if (! (features[index].begin == 0 && features[index].end == 0))
           {
-            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 (getColour(features[index].getType()) == null)
             {
-              // 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());
+              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++;
         }
+        index++;
       }
+    }
+
+    renderOrder = new String[allfeatures.size()];
+    Enumeration en = allfeatures.elements();
+    int i = allfeatures.size() - 1;
+    while (en.hasMoreElements())
+    {
+      renderOrder[i] = en.nextElement().toString();
+      i--;
+    }
 
-      renderOrder = new String[allfeatures.size()];
-      Enumeration en = allfeatures.elements();
-      int i = allfeatures.size()-1;
-      while(en.hasMoreElements())
+    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)
       {
-        renderOrder[i] = en.nextElement().toString();
-        i--;
+        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);
 
-      findingFeatures = false;
+      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);
     }
-
-    public Color getColour(String featureType)
+    else
     {
-      Color colour = (Color)featureColours.get(featureType);
-      return colour;
+      bigPanel.add(panel, BorderLayout.CENTER);
     }
 
-
-    static String lastFeatureAdded;
-    static String lastFeatureGroupAdded;
-    static String lastDescriptionAdded;
-
-    public boolean createNewFeatures(SequenceI[] sequences,
-                                  SequenceFeature [] features)
+    if (lastFeatureAdded == null)
     {
-      return amendFeatures(sequences, features, true);
+      if (features[0].type != null)
+      {
+        lastFeatureAdded = features[0].type;
+      }
+      else
+      {
+        lastFeatureAdded = "feature_1";
+      }
     }
 
-    int featureIndex = 0;
-    boolean amendFeatures(SequenceI[] sequences,
-                           final SequenceFeature [] features,
-                           boolean newFeatures)
+    if (lastFeatureGroupAdded == null)
     {
-      JPanel bigPanel = new JPanel(new BorderLayout());
-      final JComboBox name = new JComboBox();
-      final JComboBox source = new JComboBox();
-      final JTextArea description = new JTextArea(3,25);
-      final JTextField start = new JTextField(6);
-      final JTextField end = new JTextField(6);
-      final JButton colour = new JButton("     ");
-      colour.setMaximumSize(new Dimension(40,10));
-      colour.addActionListener(new ActionListener()
-          {
-            public void actionPerformed(ActionEvent 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)
+      if (features[0].featureGroup != null)
       {
-        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);
+        lastFeatureGroupAdded = features[0].featureGroup;
       }
       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";
+      {
+        lastFeatureAdded = "Jalview";
+      }
+    }
 
+    Enumeration en;
+    if (featureGroups != null)
+    {
+      en = featureGroups.keys();
+      while (en.hasMoreElements())
+      {
+        source.addItem(en.nextElement().toString());
+      }
+    }
 
-      Enumeration en;
-      if (featureGroups != null)
+    if (newFeatures)
+    {
+      if (av.featuresDisplayed != null)
       {
-        en = featureGroups.keys();
+        en = av.featuresDisplayed.keys();
         while (en.hasMoreElements())
         {
-          source.addItem(en.nextElement().toString());
+          name.addItem(en.nextElement().toString());
         }
       }
 
-      if (newFeatures)
+      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()
       {
-        if(av.featuresDisplayed != null)
+        public void itemStateChanged(ItemEvent e)
         {
-          en = av.featuresDisplayed.keys();
-          while (en.hasMoreElements())
+          int index = name.getSelectedIndex();
+          if (index != -1)
           {
-            name.addItem(en.nextElement().toString());
-          }
-        }
+            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()));
 
-        name.setSelectedItem(lastFeatureAdded);
-        source.setSelectedItem(lastFeatureGroupAdded);
-        description.setText(
-            lastDescriptionAdded == null ?
-            features[0].description : lastDescriptionAdded);
+            SearchResults highlight = new SearchResults();
+            highlight.addResult(sequences[0],
+                                features[index].getBegin(),
+                                features[index].getEnd());
 
-        if (getColour(lastFeatureAdded) != null)
-          colour.setBackground(getColour(lastFeatureAdded));
-        else
-          colour.setBackground(new Color(60, 160, 115));
+            ap.seqPanel.seqCanvas.highlightSearchResults(highlight);
 
-      }
-      else if (!newFeatures)
-      {
-        featureIndex = 0;
-        for(int f=0; f<features.length; f++)
-        {
-          name.addItem(features[f].getType().toString());
+          }
+          Color col = getColour(name.getSelectedItem().toString());
+          if (col == null)
+          {
+            col = new
+                jalview.schemes.UserColourScheme()
+                .createColourFromName(name.getSelectedItem().toString());
+          }
+
+          colour.setBackground(col);
         }
+      });
 
-        description.setText(features[0].getDescription());
-        source.setSelectedItem(features[0].getFeatureGroup());
-        start.setText(features[0].getBegin()+"");
-        end.setText(features[0].getEnd()+"");
-        colour.setBackground(
-                getColour(name.getSelectedItem().toString()));
-        name.addItemListener(new ItemListener()
-        {
-          public void itemStateChanged(ItemEvent e)
+    }
+
+    Object[] options;
+    if (!newFeatures)
+    {
+      options = new Object[]
           {
-            int index = name.getSelectedIndex();
-            if(index!=-1)
-            {
-              featureIndex = index;
-              description.setText(features[index].getDescription());
-              source.setSelectedItem(features[index].getFeatureGroup());
-              start.setText(features[index].getBegin() + "");
-              end.setText(features[index].getEnd() + "");
-              colour.setBackground(
-                  getColour(name.getSelectedItem().toString()));
-            }
-          }
-        });
+          "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");
 
-      Object [] options;
-      if(!newFeatures)
-        options = new Object[]{"Amend", "Delete", "Cancel"};
-      else
-        options = new Object[]{"OK", "Cancel"};
+    jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();
 
-      int reply = JOptionPane.showInternalOptionDialog(Desktop.desktop,
-                                                   bigPanel,
-                                                   newFeatures ?
-                                                   "Create New Sequence Feature(s)" :
-                                                   "Amend/Delete Features",
-                                                   JOptionPane.YES_NO_CANCEL_OPTION,
-                                                   JOptionPane.QUESTION_MESSAGE,
-                                                   null,
-                                                   options, "OK");
+    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", " ");
+    }
 
-      jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();
+    if (!newFeatures)
+    {
+      SequenceFeature sf = features[featureIndex];
 
-      if (reply == JOptionPane.OK_OPTION
-          && name.getSelectedItem() != null
-          && source.getSelectedItem() != null)
+      if (reply == JOptionPane.NO_OPTION)
       {
-        lastFeatureAdded = name.getSelectedItem().toString();
-        lastFeatureGroupAdded = source.getSelectedItem().toString();
-        lastDescriptionAdded = description.getText().replaceAll("\n", " ");
+        sequences[0].getDatasetSequence().deleteFeature(sf);
       }
-
-      if(!newFeatures)
+      else if (reply == JOptionPane.YES_OPTION)
       {
-        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.type = lastFeatureAdded;
-          sf.featureGroup = lastFeatureGroupAdded;
-          sf.description = lastDescriptionAdded;
-          setColour(sf.type, colour.getBackground());
-          try{
-            sf.begin = Integer.parseInt( start.getText() );
-            sf.end = Integer.parseInt( end.getText() );
-          }catch(NumberFormatException ex)
-          {}
-
-          ffile.parseDescriptionHTML(sf, false);
+          sf.begin = ( (Integer) start.getValue()).intValue();
+          sf.end = ( (Integer) end.getValue()).intValue();
         }
+        catch (NumberFormatException ex)
+        {}
+
+        ffile.parseDescriptionHTML(sf, false);
       }
-      else
+    }
+    else
+    {
+      if (reply == JOptionPane.OK_OPTION
+          && name.getSelectedItem() != null
+          && source.getSelectedItem() != null)
       {
-        if (reply == JOptionPane.OK_OPTION
-            && name.getSelectedItem() != null
-            && source.getSelectedItem() != null)
+        for (int i = 0; i < sequences.length; i++)
         {
-          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();
+          features[i].type = lastFeatureAdded;
+          features[i].featureGroup = lastFeatureGroupAdded;
+          features[i].description = lastDescriptionAdded;
+          sequences[i].addSequenceFeature(features[i]);
+          ffile.parseDescriptionHTML(features[i], false);
+        }
 
-          if (featureGroups == null)
-            featureGroups = new Hashtable();
+        if (av.featuresDisplayed == null)
+        {
+          av.featuresDisplayed = new Hashtable();
+        }
 
-          featureGroups.put(lastFeatureGroupAdded, new Boolean(true));
+        if (featureGroups == null)
+        {
+          featureGroups = new Hashtable();
+        }
 
-          Color col = colour.getBackground();
-          setColour(lastFeatureAdded, colour.getBackground());
+        featureGroups.put(lastFeatureGroupAdded, new Boolean(true));
 
-          av.featuresDisplayed.put(lastFeatureGroupAdded,
-                                   new Integer(col.getRGB()));
+        Color col = colour.getBackground();
+        setColour(lastFeatureAdded, colour.getBackground());
 
-          findAllFeatures();
+        av.featuresDisplayed.put(lastFeatureGroupAdded,
+                                 new Integer(col.getRGB()));
 
-          return true;
-        }
-        else
-          return false;
-      }
-
-      if(name.getSelectedIndex()==-1)
         findAllFeatures();
 
-
-      return true;
+        return true;
+      }
+      else
+      {
+        return false;
+      }
     }
 
-    public void setColour(String featureType, Color col)
+    if (name.getSelectedIndex() == -1)
     {
-      featureColours.put(featureType, col);
+      findAllFeatures();
     }
 
-    public void setTransparency(float value)
+    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)
     {
-      transparency = value;
+      av.featuresDisplayed.clear();
     }
-
-    public float getTransparency()
+    else
     {
-      return transparency;
+      av.featuresDisplayed = new Hashtable();
     }
 
-    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];
+    renderOrder = new String[data.length];
 
-      if (data.length > 0)
-        for (int i = 0; i < data.length; i++)
+    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())
         {
-          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;
+          av.featuresDisplayed.put(type, new Integer(getColour(type).getRGB()));
         }
 
+        renderOrder[data.length - i - 1] = type;
+      }
     }
 
-
-
+  }
 
 }