X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureRenderer.java;h=9eacb6c3fcb311b5e65f3158fd13a77d4760e2b3;hb=12e7f97678ce85b0238f987d5f4eaf18512a0b94;hp=cd188d297eab86a8d327880f5a636b3127d73044;hpb=4a419b95bd696cc544a5bbad184be61b85ec4789;p=jalview.git

diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
index cd188d2..9eacb6c 100755
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
@@ -32,59 +32,116 @@ 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 = null;
+  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);
+
+  PropertyChangeSupport changeSupport = new PropertyChangeSupport(this);
 
   Vector allfeatures;
 
   /**
    * Creates a new FeatureRenderer object.
-   *
+   * 
    * @param av
-   *          DOCUMENT ME!
+   *                DOCUMENT ME!
    */
-  public FeatureRenderer(AlignViewport av)
+  public FeatureRenderer(AlignmentPanel ap)
+  {
+    this.ap = ap;
+    this.av = ap.av;
+  }
+
+  public class FeatureRendererSettings implements Cloneable
+  {
+    String[] renderOrder;
+
+    Hashtable featureGroups;
+
+    Hashtable featureColours;
+
+    float transparency;
+
+    Hashtable featureOrder;
+
+    public FeatureRendererSettings(String[] renderOrder,
+            Hashtable featureGroups, Hashtable featureColours,
+            float transparency, Hashtable featureOrder)
+    {
+      super();
+      this.renderOrder = renderOrder;
+      this.featureGroups = featureGroups;
+      this.featureColours = featureColours;
+      this.transparency = transparency;
+      this.featureOrder = featureOrder;
+    }
+
+    public FeatureRendererSettings(FeatureRenderer fr)
+    {
+      this.renderOrder = fr.renderOrder;
+      this.featureGroups = fr.featureGroups;
+      this.featureColours = fr.featureColours;
+      this.transparency = fr.transparency;
+      this.featureOrder = fr.featureOrder;
+    }
+  }
+
+  public FeatureRendererSettings getSettings()
+  {
+    return new FeatureRendererSettings(this);
+  }
+
+  public void transferSettings(FeatureRendererSettings fr)
   {
-    this.av = av;
+    this.renderOrder = fr.renderOrder;
+    this.featureGroups = fr.featureGroups;
+    this.featureColours = fr.featureColours;
+    this.transparency = fr.transparency;
+    this.featureOrder = fr.featureOrder;
   }
 
   public void transferSettings(FeatureRenderer fr)
   {
-    renderOrder = fr.renderOrder;
-    featureGroups = fr.featureGroups;
-    featureColours = fr.featureColours;
-    transparency = fr.transparency;
-    featureOrder = fr.featureOrder;
+    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));
+    return new Color(findFeatureColour(initialCol.getRGB(), seq, res));
   }
 
   /**
@@ -102,13 +159,15 @@ public class FeatureRenderer
     {
       lastSeq = seq;
       sequenceFeatures = lastSeq.getDatasetSequence().getSequenceFeatures();
-      if (sequenceFeatures!=null)
+      if (sequenceFeatures != null)
       {
         sfSize = sequenceFeatures.length;
       }
     }
 
-    if (sequenceFeatures!=lastSeq.getDatasetSequence().getSequenceFeatures()) {
+    if (sequenceFeatures != lastSeq.getDatasetSequence()
+            .getSequenceFeatures())
+    {
       sequenceFeatures = lastSeq.getDatasetSequence().getSequenceFeatures();
       if (sequenceFeatures != null)
       {
@@ -116,12 +175,11 @@ public class FeatureRenderer
       }
     }
 
-    if (sequenceFeatures == null)
+    if (sequenceFeatures == null || sfSize == 0)
     {
       return initialCol;
     }
 
-
     if (jalview.util.Comparison.isGap(lastSeq.getCharAt(column)))
     {
       return Color.white.getRGB();
@@ -140,18 +198,13 @@ public class FeatureRenderer
     if (offscreenImage != null)
     {
       offscreenImage.setRGB(0, 0, initialCol);
-      drawSequence(offscreenImage.getGraphics(),
-                   lastSeq,
-                   column, column, 0);
+      drawSequence(offscreenImage.getGraphics(), lastSeq, column, column, 0);
 
       return offscreenImage.getRGB(0, 0);
     }
     else
     {
-      drawSequence(null,
-                   lastSeq,
-                   lastSeq.findPosition(column),
-                   -1, -1);
+      drawSequence(null, lastSeq, lastSeq.findPosition(column), -1, -1);
 
       if (currentColour == null)
       {
@@ -159,7 +212,7 @@ public class FeatureRenderer
       }
       else
       {
-        return ( (Integer) currentColour).intValue();
+        return ((Integer) currentColour).intValue();
       }
     }
 
@@ -167,37 +220,40 @@ public class FeatureRenderer
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param g
-   *          DOCUMENT ME!
+   *                DOCUMENT ME!
    * @param seq
-   *          DOCUMENT ME!
+   *                DOCUMENT ME!
    * @param sg
-   *          DOCUMENT ME!
+   *                DOCUMENT ME!
    * @param start
-   *          DOCUMENT ME!
+   *                DOCUMENT ME!
    * @param end
-   *          DOCUMENT ME!
+   *                DOCUMENT ME!
    * @param x1
-   *          DOCUMENT ME!
+   *                DOCUMENT ME!
    * @param y1
-   *          DOCUMENT ME!
+   *                DOCUMENT ME!
    * @param width
-   *          DOCUMENT ME!
+   *                DOCUMENT ME!
    * @param height
-   *          DOCUMENT ME!
+   *                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)
+  synchronized public void drawSequence(Graphics g, SequenceI seq,
+          int start, int end, int y1)
   {
+
     if (seq.getDatasetSequence().getSequenceFeatures() == null
-        || seq.getDatasetSequence().getSequenceFeatures().length == 0)
+            || seq.getDatasetSequence().getSequenceFeatures().length == 0)
     {
       return;
     }
@@ -207,9 +263,8 @@ public class FeatureRenderer
       fm = g.getFontMetrics();
     }
 
-    if (av.featuresDisplayed == null
-        || renderOrder == null
-        || newFeatureAdded)
+    if (av.featuresDisplayed == null || renderOrder == null
+            || newFeatureAdded)
     {
       findAllFeatures();
       if (av.featuresDisplayed.size() < 1)
@@ -218,23 +273,21 @@ public class FeatureRenderer
       }
 
       sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();
-      sfSize = sequenceFeatures.length;
     }
 
-    if (lastSeq == null || seq != lastSeq
-        || seq.getDatasetSequence().getSequenceFeatures()!=sequenceFeatures)
+    if (lastSeq == null
+            || seq != lastSeq
+            || seq.getDatasetSequence().getSequenceFeatures() != sequenceFeatures)
     {
       lastSeq = seq;
       sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();
-      sfSize = sequenceFeatures.length;
     }
 
     if (transparency != 1 && g != null)
     {
       Graphics2D g2 = (Graphics2D) g;
-      g2.setComposite(
-          AlphaComposite.getInstance(
-              AlphaComposite.SRC_OVER, transparency));
+      g2.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER,
+              transparency));
     }
 
     if (!offscreenRender)
@@ -243,6 +296,7 @@ public class FeatureRenderer
       epos = lastSeq.findPosition(end);
     }
 
+    sfSize = sequenceFeatures.length;
     String type;
     for (int renderIndex = 0; renderIndex < renderOrder.length; renderIndex++)
     {
@@ -257,66 +311,66 @@ public class FeatureRenderer
       // current feature to render
       for (sfindex = 0; sfindex < sfSize; sfindex++)
       {
-        if (sequenceFeatures.length <= sfindex)
-        {
-          continue;
-        }
         if (!sequenceFeatures[sfindex].type.equals(type))
         {
           continue;
         }
 
         if (featureGroups != null
-            && sequenceFeatures[sfindex].featureGroup != null
-            &&
-            featureGroups.containsKey(sequenceFeatures[sfindex].featureGroup)
-            &&
-            ! ( (Boolean) featureGroups.get(sequenceFeatures[sfindex].
-                                            featureGroup)).
-            booleanValue())
+                && 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))
+        if (!offscreenRender
+                && (sequenceFeatures[sfindex].getBegin() > epos || sequenceFeatures[sfindex]
+                        .getEnd() < spos))
         {
           continue;
         }
 
         if (offscreenRender && offscreenImage == null)
         {
-          if (sequenceFeatures[sfindex].begin <= start &&
-              sequenceFeatures[sfindex].end >= start)
+          if (sequenceFeatures[sfindex].begin <= start
+                  && sequenceFeatures[sfindex].end >= start)
           {
-            currentColour = av.featuresDisplayed.get(sequenceFeatures[sfindex].
-                type);
+            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);
+          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);
+          renderFeature(g, seq, seq
+                  .findIndex(sequenceFeatures[sfindex].begin) - 1, seq
+                  .findIndex(sequenceFeatures[sfindex].end) - 1,
+                  getColour(sequenceFeatures[sfindex].type), start, end, y1);
         }
 
       }
@@ -326,20 +380,20 @@ public class FeatureRenderer
     if (transparency != 1.0f && g != null)
     {
       Graphics2D g2 = (Graphics2D) g;
-      g2.setComposite(
-          AlphaComposite.getInstance(
-              AlphaComposite.SRC_OVER, 1.0f));
+      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)
+
+  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 <= end) && (fend >= start)))
     {
       if (fstart < start)
       { // fix for if the feature we have starts before the sequence start,
@@ -362,7 +416,8 @@ public class FeatureRenderer
 
         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)
         {
@@ -371,48 +426,56 @@ public class FeatureRenderer
 
         g.setColor(Color.white);
         charOffset = (av.charWidth - fm.charWidth(s)) / 2;
-        g.drawString(String.valueOf(s),
-                     charOffset + (av.charWidth * (i - start)),
-                     pady);
+        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.
-   *
+   * Called when alignment in associated view has new/modified features to
+   * discover and display.
+   * 
    */
   public void featuresAdded()
   {
-    lastSeq=null;
+    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.
-   *
+   * 
    */
-  synchronized void findAllFeatures()
+  void findAllFeatures()
   {
-    findAllFeatures(true); // add all new features as visible
-    if (!firing) {
-      firing=true;
-      changeSupport.firePropertyChange("changeSupport",null,null);
-      firing=false;
+    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
+   *                if true newly added feature types will be rendered
+   *                immediatly
    */
-  synchronized void findAllFeatures(boolean newMadeVisible) {
+  synchronized void findAllFeatures(boolean newMadeVisible)
+  {
     newFeatureAdded = false;
 
     if (findingFeatures)
@@ -430,10 +493,11 @@ public class FeatureRenderer
 
     allfeatures = new Vector();
     Vector oldfeatures = new Vector();
-    if (renderOrder!=null)
+    if (renderOrder != null)
     {
-      for (int i=0; i<renderOrder.length; i++) {
-        if (renderOrder[i]!=null)
+      for (int i = 0; i < renderOrder.length; i++)
+      {
+        if (renderOrder[i] != null)
         {
           oldfeatures.addElement(renderOrder[i]);
         }
@@ -441,9 +505,8 @@ public class FeatureRenderer
     }
     for (int i = 0; i < av.alignment.getHeight(); i++)
     {
-      SequenceFeature[] features
-          = av.alignment.getSequenceAt(i).getDatasetSequence().
-          getSequenceFeatures();
+      SequenceFeature[] features = av.alignment.getSequenceAt(i)
+              .getDatasetSequence().getSequenceFeatures();
 
       if (features == null)
       {
@@ -455,20 +518,35 @@ public class FeatureRenderer
       {
         if (!av.featuresDisplayed.containsKey(features[index].getType()))
         {
-          if (! (features[index].begin == 0 && features[index].end == 0))
+
+          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())) {
+            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);
+                      new Integer(getColour(features[index].getType())
+                              .getRGB()));
+              setOrder(features[index].getType(), 0);
             }
-           }
+          }
         }
         if (!allfeatures.contains(features[index].getType()))
         {
@@ -480,48 +558,54 @@ public class FeatureRenderer
     updateRenderOrder(allfeatures);
     findingFeatures = false;
   }
-  protected boolean firing=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.
+   * 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) {
+  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)
+    boolean initOrders = (featureOrder == null);
+    int opos = 0;
+    if (oldRender != null && oldRender.length > 0)
     {
-      for (int j=0; j<oldRender.length; j++)
+      for (int j = 0; j < oldRender.length; j++)
       {
-        if (oldRender[j]!=null)
+        if (oldRender[j] != null)
+        {
+          if (initOrders)
           {
-            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]);
-            }
+            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) {
+    if (allfeatures.size() == 0)
+    {
       // no new features - leave order unchanged.
       return;
     }
-    int i=allfeatures.size()-1;
-    int iSize=i;
-    boolean sort=false;
+    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();
@@ -532,30 +616,30 @@ public class FeatureRenderer
       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);
+        // 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)
+      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];
+        sort = sort || sortOrder[i] > sortOrder[i + 1];
       }
       i--;
     }
-    if (iSize>1 && sort)
+    if (iSize > 1 && sort)
       jalview.util.QuickSort.sort(sortOrder, newf);
-    sortOrder=null;
+    sortOrder = null;
     System.arraycopy(newf, 0, renderOrder, opos, newf.length);
   }
+
   public Color getColour(String featureType)
   {
-    if (featureColours.get(featureType) == null)
+    if (!featureColours.containsKey(featureType))
     {
-      jalview.schemes.UserColourScheme ucs = new
-          jalview.schemes.UserColourScheme();
+      jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme();
       Color col = ucs.createColourFromName(featureType);
       featureColours.put(featureType, col);
       return col;
@@ -565,22 +649,17 @@ public class FeatureRenderer
   }
 
   static String lastFeatureAdded;
+
   static String lastFeatureGroupAdded;
-  static String lastDescriptionAdded;
 
-  public boolean createNewFeatures(SequenceI[] sequences,
-                                   SequenceFeature[] features)
-  {
-    return amendFeatures(sequences, features, true, null);
-  }
+  static String lastDescriptionAdded;
 
   int featureIndex = 0;
+
   boolean amendFeatures(final SequenceI[] sequences,
-                        final SequenceFeature[] features,
-                        boolean newFeatures,
-                        final AlignmentPanel ap)
+          final SequenceFeature[] features, boolean newFeatures,
+          final AlignmentPanel ap)
   {
-    findAllFeatures();
 
     featureIndex = 0;
 
@@ -601,72 +680,70 @@ public class FeatureRenderer
     {
       public void mousePressed(MouseEvent evt)
       {
-        colour.setBackground(
-            JColorChooser.showDialog(Desktop.desktop,
-                                     "Select Feature Colour",
-                                     colour.getBackground()));
+        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);
-    }
-    //////////
-    //////////////////////////////////////
+    // /////////////////////////////////////
+    // /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);
@@ -732,7 +809,7 @@ public class FeatureRenderer
       }
     }
 
-    if(newFeatures)
+    if (newFeatures)
     {
       name.setText(lastFeatureAdded);
       source.setText(lastFeatureGroupAdded);
@@ -748,45 +825,38 @@ public class FeatureRenderer
     description.setText(features[0].getDescription());
     colour.setBackground(getColour(name.getText()));
 
-
     Object[] options;
     if (!newFeatures)
     {
       options = new Object[]
-          {
-          "Amend", "Delete", "Cancel"};
+      { "Amend", "Delete", "Cancel" };
     }
     else
     {
       options = new Object[]
-          {
-          "OK", "Cancel"};
+      { "OK", "Cancel" };
     }
 
-    String title = newFeatures ? "Create New Sequence Feature(s)" :
-        "Amend/Delete Features for "
-        + sequences[0].getName();
+    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");
+            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() != null
-        && source.getText() != null)
+    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();
-      lastFeatureGroupAdded = source.getText();
+      lastFeatureAdded = name.getText().trim();
+      lastFeatureGroupAdded = source.getText().trim();
       lastDescriptionAdded = description.getText().replaceAll("\n", " ");
+
+      if (lastFeatureGroupAdded.length() < 1)
+        lastFeatureGroupAdded = null;
     }
 
     if (!newFeatures)
@@ -802,28 +872,32 @@ public class FeatureRenderer
         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();
+          sf.begin = ((Integer) start.getValue()).intValue();
+          sf.end = ((Integer) end.getValue()).intValue();
+        } catch (NumberFormatException ex)
+        {
         }
-        catch (NumberFormatException ex)
-        {}
 
         ffile.parseDescriptionHTML(sf, false);
       }
     }
     else
+    // NEW FEATURES ADDED
     {
-      if (reply == JOptionPane.OK_OPTION
-          && name.getText() != null
-          && source.getText() != null)
+      if (reply == JOptionPane.OK_OPTION && lastFeatureAdded.length() > 0)
       {
         for (int i = 0; i < sequences.length; i++)
         {
           features[i].type = lastFeatureAdded;
-          features[i].featureGroup = lastFeatureGroupAdded;
+          if (lastFeatureGroupAdded != null)
+            features[i].featureGroup = lastFeatureGroupAdded;
           features[i].description = lastDescriptionAdded;
           sequences[i].addSequenceFeature(features[i]);
           ffile.parseDescriptionHTML(features[i], false);
@@ -834,20 +908,21 @@ public class FeatureRenderer
           av.featuresDisplayed = new Hashtable();
         }
 
-        if (featureGroups == null)
+        if (lastFeatureGroupAdded != null)
         {
-          featureGroups = new Hashtable();
+          if (featureGroups == null)
+            featureGroups = new Hashtable();
+          featureGroups.put(lastFeatureGroupAdded, new Boolean(true));
         }
 
-        featureGroups.put(lastFeatureGroupAdded, new Boolean(true));
-
         Color col = colour.getBackground();
         setColour(lastFeatureAdded, colour.getBackground());
+        av.featuresDisplayed.put(lastFeatureAdded,
+                new Integer(col.getRGB()));
 
-        av.featuresDisplayed.put(lastFeatureGroupAdded,
-                                 new Integer(col.getRGB()));
+        findAllFeatures(false);
 
-        findAllFeatures();
+        ap.paintAlignment(true);
 
         return true;
       }
@@ -857,7 +932,7 @@ public class FeatureRenderer
       }
     }
 
-    findAllFeatures();
+    ap.paintAlignment(true);
 
     return true;
   }
@@ -876,23 +951,29 @@ public class FeatureRenderer
   {
     return transparency;
   }
+
   /**
    * Replace current ordering with new ordering
-   * @param data { String(Type), Colour(Type), Boolean(Displayed) }
+   * 
+   * @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
+   * 
+   * @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();
@@ -902,7 +983,7 @@ public class FeatureRenderer
         av.featuresDisplayed = new Hashtable();
       }
     }
-    if (data==null)
+    if (data == null)
     {
       return;
     }
@@ -918,9 +999,10 @@ public class FeatureRenderer
       {
         String type = data[i][0].toString();
         setColour(type, (Color) data[i][1]);
-        if ( ( (Boolean) data[i][2]).booleanValue())
+        if (((Boolean) data[i][2]).booleanValue())
         {
-          av.featuresDisplayed.put(type, new Integer(getColour(type).getRGB()));
+          av.featuresDisplayed.put(type, new Integer(getColour(type)
+                  .getRGB()));
         }
 
         renderOrder[data.length - i - 1] = type;
@@ -928,38 +1010,42 @@ public class FeatureRenderer
     }
 
   }
-  Hashtable featureOrder=null;
+
+  Hashtable featureOrder = null;
+
   /**
    * analogous to colour - store a normalized ordering for all feature types in
    * this rendering context.
-   *
+   * 
    * @param type
-   *          Feature type string
+   *                Feature type string
    * @param position
-   *          normalized priority - 0 means always appears on top, 1 means
-   *          always last.
+   *                normalized priority - 0 means always appears on top, 1 means
+   *                always last.
    */
   public float setOrder(String type, float position)
   {
-    if (featureOrder==null)
+    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)
+  public float getOrder(String type)
+  {
+    if (featureOrder != null)
     {
       if (featureOrder.containsKey(type))
       {
-        return ((Float)featureOrder.get(type)).floatValue();
+        return ((Float) featureOrder.get(type)).floatValue();
       }
     }
     return -1;