X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFeatureRenderer.java;h=dd2b873926b02676a3171fd522a9cd5dd0838588;hb=497958b4e5217efaa3ddeece38f38c3a6e98cb96;hp=c9cea86acacdad03d30f2ce12c3ea4b5d98d4f61;hpb=e0e8a9222165bd8e64119a5cda570eb6a7a91205;p=jalview.git

diff --git a/src/jalview/appletgui/FeatureRenderer.java b/src/jalview/appletgui/FeatureRenderer.java
old mode 100755
new mode 100644
index c9cea86..dd2b873
--- a/src/jalview/appletgui/FeatureRenderer.java
+++ b/src/jalview/appletgui/FeatureRenderer.java
@@ -1,458 +1,454 @@
 /*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview 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 3
  * 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.
- *
+ *  
+ * Jalview 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
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.appletgui;
 
 import java.util.*;
-
 import java.awt.*;
+import java.awt.event.*;
 
 import jalview.datamodel.*;
+import jalview.schemes.AnnotationColourGradient;
+import jalview.schemes.GraduatedColor;
+import jalview.util.MessageManager;
+import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
 
 /**
  * DOCUMENT ME!
- *
+ * 
  * @author $author$
  * @version $Revision$
  */
-public class FeatureRenderer
+public class FeatureRenderer extends jalview.renderer.seqfeatures.FeatureRenderer
 {
-  AlignViewport av;
-
-  Hashtable featureColours = new Hashtable();
-
-  // A higher level for grouping features of a
-  // particular type
-  Hashtable featureGroups = null;
 
   // Holds web links for feature groups and feature types
   // in the form label|link
   Hashtable featureLinks = null;
 
-  // This is actually an Integer held in the hashtable,
-  // Retrieved using the key feature type
-  Object currentColour;
-
-  String[] renderOrder;
-
-  FontMetrics fm;
-  int charOffset;
-
-  float transparency = 1f;
-
-  TransparencySetter transparencySetter = null;
-
   /**
    * Creates a new FeatureRenderer object.
-   *
-   * @param av DOCUMENT ME!
+   * 
+   * @param av
+   *          DOCUMENT ME!
    */
   public FeatureRenderer(AlignViewport av)
   {
+    super();
     this.av = av;
 
-    if (!System.getProperty("java.version").startsWith("1.1"))
-    {
-      transparencySetter = new TransparencySetter();
-    }
+    setTransparencyAvailable(!System.getProperty("java.version").startsWith("1.1"));
   }
 
-  public void transferSettings(FeatureRenderer fr)
-  {
-    renderOrder = fr.renderOrder;
-    featureGroups = fr.featureGroups;
-    featureColours = fr.featureColours;
-    transparency = fr.transparency;
-  }
-
-  public Color findFeatureColour(Color initialCol, SequenceI seq, int i)
-  {
-    overview = true;
-    if (!av.showSequenceFeatures)
-    {
-      return initialCol;
-    }
+  static String lastFeatureAdded;
 
-    lastSequence = seq;
-    sequenceFeatures = lastSequence.getSequenceFeatures();
-    if (sequenceFeatures == null)
-    {
-      return initialCol;
-    }
+  static String lastFeatureGroupAdded;
 
-    sfSize = sequenceFeatures.length;
+  static String lastDescriptionAdded;
 
-    if (jalview.util.Comparison.isGap(lastSequence.getCharAt(i)))
-    {
-      return Color.white;
-    }
+  int featureIndex = 0;
 
-    currentColour = null;
+  boolean deleteFeature = false;
 
-    drawSequence(null, lastSequence, lastSequence.findPosition(i), -1, -1);
+  FeatureColourPanel colourPanel;
 
-    if (currentColour == null)
-    {
-      return initialCol;
-    }
+  class FeatureColourPanel extends Panel
+  {
+    String label = "";
 
-    return new Color( ( (Integer) currentColour).intValue());
-  }
+    private Color maxCol;
 
-  /**
-   * This is used by the Molecule Viewer to get the accurate colour
-   * of the rendered sequence
-   */
-  boolean overview = false;
+    private boolean isColourByLabel, isGcol;
 
-  int white = Color.white.getRGB();
-  public int findFeatureColour(int initialCol, int seqIndex, int column)
-  {
-    if (!av.showSequenceFeatures)
+    /**
+     * render a feature style in the amend feature dialog box
+     */
+    public void updateColor(Object newcol)
     {
-      return initialCol;
-    }
 
-    if (seqIndex != lastSequenceIndex)
-    {
-      lastSequence = av.alignment.getSequenceAt(seqIndex);
-      lastSequenceIndex = seqIndex;
-      sequenceFeatures = lastSequence.getSequenceFeatures();
-      if (sequenceFeatures == null)
+      Color bg, col = null;
+      GraduatedColor gcol = null;
+      String vlabel = "";
+      if (newcol instanceof Color)
       {
-        return initialCol;
+        isGcol = false;
+        col = (Color) newcol;
+        gcol = null;
       }
-
-      sfSize = sequenceFeatures.length;
+      else if (newcol instanceof GraduatedColor)
+      {
+        isGcol = true;
+        gcol = (GraduatedColor) newcol;
+        col = null;
+      }
+      else
+      {
+        throw new Error(MessageManager.getString("error.invalid_colour_for_mycheckbox"));
+      }
+      if (col != null)
+      {
+        setBackground(bg = col);
+      }
+      else
+      {
+        if (gcol.getThreshType() != AnnotationColourGradient.NO_THRESHOLD)
+        {
+          vlabel += " "
+                  + ((gcol.getThreshType() == AnnotationColourGradient.ABOVE_THRESHOLD) ? "(>)"
+                          : "(<)");
+        }
+        if (isColourByLabel = gcol.isColourByLabel())
+        {
+          setBackground(bg = Color.white);
+          vlabel += " (by Label)";
+        }
+        else
+        {
+          setBackground(bg = gcol.getMinColor());
+          maxCol = gcol.getMaxColor();
+        }
+      }
+      label = vlabel;
+      setBackground(bg);
+      repaint();
     }
 
-    if (jalview.util.Comparison.isGap(lastSequence.getCharAt(column)))
+    FeatureColourPanel()
     {
-      return Color.white.getRGB();
+      super(null);
     }
 
-    currentColour = null;
-
-    drawSequence(null, lastSequence, lastSequence.findPosition(column), -1, -1);
-
-    if (currentColour == null)
+    public void paint(Graphics g)
     {
-      return initialCol;
+      Dimension d = getSize();
+      if (isGcol)
+      {
+        if (isColourByLabel)
+        {
+          g.setColor(Color.white);
+          g.fillRect(d.width / 2, 0, d.width / 2, d.height);
+          g.setColor(Color.black);
+          Font f = new Font("Verdana", Font.PLAIN, 10);
+          g.setFont(f);
+          g.drawString(MessageManager.getString("label.label"), 0, 0);
+        }
+        else
+        {
+          g.setColor(maxCol);
+          g.fillRect(d.width / 2, 0, d.width / 2, d.height);
+
+        }
+      }
     }
 
-    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;
-  int lastSequenceIndex = -1;
-  SequenceI lastSequence;
-  SequenceFeature[] sequenceFeatures;
-  int sfSize, sfindex, spos, epos;
-
-  public void drawSequence(Graphics g, SequenceI seq,
-                           int start, int end, int y1)
+  boolean amendFeatures(final SequenceI[] sequences,
+          final SequenceFeature[] features, boolean newFeatures,
+          final AlignmentPanel ap)
   {
-    if (seq.getSequenceFeatures() == null
-        || seq.getSequenceFeatures().length == 0)
+    Panel bigPanel = new Panel(new BorderLayout());
+    final TextField name = new TextField(16);
+    final TextField source = new TextField(16);
+    final TextArea description = new TextArea(3, 35);
+    final TextField start = new TextField(8);
+    final TextField end = new TextField(8);
+    final Choice overlaps;
+    Button deleteButton = new Button("Delete");
+    deleteFeature = false;
+
+    colourPanel = new FeatureColourPanel();
+    colourPanel.setSize(110, 15);
+    final FeatureRenderer fr = this;
+
+    Panel panel = new Panel(new GridLayout(3, 1));
+
+    featureIndex = 0; // feature to be amended.
+    Panel tmp;
+
+    // /////////////////////////////////////
+    // /MULTIPLE FEATURES AT SELECTED RESIDUE
+    if (!newFeatures && features.length > 1)
     {
-      return;
-    }
+      panel = new Panel(new GridLayout(4, 1));
+      tmp = new Panel();
+      tmp.add(new Label("Select Feature: "));
+      overlaps = new Choice();
+      for (int i = 0; i < features.length; i++)
+      {
+        String item = features[i].getType() + "/" + features[i].getBegin()
+                + "-" + features[i].getEnd();
 
-    if (transparencySetter != null && g != null)
-    {
-      transparencySetter.setTransparency(g, transparency);
-    }
-    
-    if (lastSequence == null || seq != lastSequence || sequenceFeatures!=seq.getSequenceFeatures())
-    {
-      lastSequence = seq;
-      sequenceFeatures = seq.getSequenceFeatures();
-      sfSize = sequenceFeatures.length;
-    }
+        if (features[i].getFeatureGroup() != null)
+          item += " (" + features[i].getFeatureGroup() + ")";
 
-    if (av.featuresDisplayed == null || renderOrder == null)
-    {
-      findAllFeatures();
-      if (av.featuresDisplayed.size() < 1)
-      {
-        return;
+        overlaps.addItem(item);
       }
 
-      sequenceFeatures = seq.getSequenceFeatures();
-      sfSize = sequenceFeatures.length;
-    }
-    if (!overview)
-    {
-      spos = lastSequence.findPosition(start);
-      epos = lastSequence.findPosition(end);
-      if (g != null)
-      {
-        fm = g.getFontMetrics();
-      }
-    }
-    String type;
-    for (int renderIndex = 0; renderIndex < renderOrder.length; renderIndex++)
-    {
-      type = renderOrder[renderIndex];
-      if (!av.featuresDisplayed.containsKey(type))
-      {
-        continue;
-      }
+      tmp.add(overlaps);
 
-      // loop through all features in sequence to find
-      // current feature to render
-      for (sfindex = 0; sfindex < sfSize; sfindex++)
+      overlaps.addItemListener(new java.awt.event.ItemListener()
       {
-        if (!sequenceFeatures[sfindex].type.equals(type))
+        public void itemStateChanged(java.awt.event.ItemEvent e)
         {
-          continue;
-        }
+          int index = overlaps.getSelectedIndex();
+          if (index != -1)
+          {
+            featureIndex = index;
+            name.setText(features[index].getType());
+            description.setText(features[index].getDescription());
+            source.setText(features[index].getFeatureGroup());
+            start.setText(features[index].getBegin() + "");
+            end.setText(features[index].getEnd() + "");
 
-        if (featureGroups != null
-            && sequenceFeatures[sfindex].featureGroup != null
-            &&
-            featureGroups.containsKey(sequenceFeatures[sfindex].featureGroup)
-            &&
-            ! ( (Boolean) featureGroups.get(sequenceFeatures[sfindex].
-                                            featureGroup)).
-            booleanValue())
-        {
-          continue;
-        }
+            SearchResults highlight = new SearchResults();
+            highlight.addResult(sequences[0], features[index].getBegin(),
+                    features[index].getEnd());
 
-        if (!overview && (sequenceFeatures[sfindex].getBegin() > epos
-                          || sequenceFeatures[sfindex].getEnd() < spos))
-        {
-          continue;
-        }
+            ap.seqPanel.seqCanvas.highlightSearchResults(highlight);
 
-        if (overview)
-        {
-          if (sequenceFeatures[sfindex].begin <= start &&
-              sequenceFeatures[sfindex].end >= start)
+          }
+          Object col = getFeatureStyle(name.getText());
+          if (col == null)
           {
-            currentColour = av.featuresDisplayed.get(sequenceFeatures[sfindex].
-                type);
+            col = new jalview.schemes.UserColourScheme()
+                    .createColourFromName(name.getText());
           }
 
+          colourPanel.updateColor(col);
         }
-        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);
+      panel.add(tmp);
+    }
+    // ////////
+    // ////////////////////////////////////
 
-        }
-        else
-        {
-          renderFeature(g, seq,
-                        seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
-                        seq.findIndex(sequenceFeatures[sfindex].end) - 1,
-                        getColour(sequenceFeatures[sfindex].type),
-                        start, end, y1);
-        }
+    tmp = new Panel();
+    panel.add(tmp);
+    tmp.add(new Label("Name: ", Label.RIGHT));
+    tmp.add(name);
 
-      }
-    }
+    tmp = new Panel();
+    panel.add(tmp);
+    tmp.add(new Label("Group: ", Label.RIGHT));
+    tmp.add(source);
+
+    tmp = new Panel();
+    panel.add(tmp);
+    tmp.add(new Label("Colour: ", Label.RIGHT));
+    tmp.add(colourPanel);
+
+    bigPanel.add(panel, BorderLayout.NORTH);
 
-    if (transparencySetter != null && g != null)
+    panel = new Panel();
+    panel.add(new Label("Description: ", Label.RIGHT));
+    panel.add(new ScrollPane().add(description));
+
+    if (!newFeatures)
     {
-      transparencySetter.setTransparency(g, 1.0f);
+      bigPanel.add(panel, BorderLayout.SOUTH);
+
+      panel = new Panel();
+      panel.add(new Label(" Start:", Label.RIGHT));
+      panel.add(start);
+      panel.add(new Label("  End:", Label.RIGHT));
+      panel.add(end);
+      bigPanel.add(panel, BorderLayout.CENTER);
+    }
+    else
+    {
+      bigPanel.add(panel, BorderLayout.CENTER);
     }
-  }
-
-  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 (lastFeatureAdded == null)
     {
-      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 (features[0].type != null)
+      {
+        lastFeatureAdded = features[0].type;
       }
-
-      if (fend >= end)
+      else
       {
-        fend = end;
+        lastFeatureAdded = "feature_1";
       }
+    }
 
-      for (i = fstart; i <= fend; i++)
+    if (lastFeatureGroupAdded == null)
+    {
+      if (features[0].featureGroup != null)
+      {
+        lastFeatureGroupAdded = features[0].featureGroup;
+      }
+      else
       {
-        s = seq.getCharAt(i);
+        lastFeatureAdded = "Jalview";
+      }
+    }
 
-        if (jalview.util.Comparison.isGap(s))
-        {
-          continue;
-        }
+    String title = newFeatures ? MessageManager.getString("label.create_new_sequence_features")
+            : MessageManager.formatMessage("label.amend_delete_features", new String[]{sequences[0].getName()});
 
-        g.setColor(featureColour);
+    final JVDialog dialog = new JVDialog(ap.alignFrame, title, true, 385,
+            240);
 
-        g.fillRect( (i - start) * av.charWidth, y1, av.charWidth, av.charHeight);
+    dialog.setMainPanel(bigPanel);
 
-        if (!av.validCharWidth)
+    if (newFeatures)
+    {
+      name.setText(lastFeatureAdded);
+      source.setText(lastFeatureGroupAdded);
+    }
+    else
+    {
+      dialog.ok.setLabel(MessageManager.getString("label.amend"));
+      dialog.buttonPanel.add(deleteButton, 1);
+      deleteButton.addActionListener(new ActionListener()
+      {
+        public void actionPerformed(ActionEvent evt)
         {
-          continue;
+          deleteFeature = true;
+          dialog.setVisible(false);
         }
-
-        g.setColor(Color.white);
-        charOffset = (av.charWidth - fm.charWidth(s)) / 2;
-        g.drawString(String.valueOf(s),
-                     charOffset + (av.charWidth * (i - start)),
-                     (y1 + av.charHeight) - av.charHeight / 5); //pady = height / 5;
-
-      }
+      });
+      name.setText(features[0].getType());
+      source.setText(features[0].getFeatureGroup());
     }
-  }
 
-  void findAllFeatures()
-  {
-    jalview.schemes.UserColourScheme ucs = new
-        jalview.schemes.UserColourScheme();
-    
-    av.featuresDisplayed = new Hashtable();
-    Vector allfeatures = new Vector();
-    for (int i = 0; i < av.alignment.getHeight(); i++)
+    start.setText(features[0].getBegin() + "");
+    end.setText(features[0].getEnd() + "");
+    description.setText(features[0].getDescription());
+    Color col = getColour(name.getText());
+    if (col == null)
     {
-      SequenceFeature[] features = av.alignment.getSequenceAt(i).
-          getSequenceFeatures();
-
-      if (features == null)
-      {
-        continue;
-      }
-
-      int index = 0;
-      while (index < features.length)
+      col = new jalview.schemes.UserColourScheme()
+              .createColourFromName(name.getText());
+    }
+    Object fcol = getFeatureStyle(name.getText());
+    // simply display the feature color in a box
+    colourPanel.updateColor(fcol);
+    dialog.setResizable(true);
+    // TODO: render the graduated color in the box.
+    colourPanel.addMouseListener(new java.awt.event.MouseAdapter()
+    {
+      public void mousePressed(java.awt.event.MouseEvent evt)
       {
-        if (!av.featuresDisplayed.containsKey(features[index].getType()))
+        if (!colourPanel.isGcol)
         {
-          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());
+          new UserDefinedColours(fr, ap.alignFrame);
+        }
+        else
+        {
+          FeatureColourChooser fcc = new FeatureColourChooser(
+                  ap.alignFrame, name.getText());
+          dialog.transferFocus();
         }
-        index++;
       }
-    }
+    });
+    dialog.setVisible(true);
 
-    renderOrder = new String[allfeatures.size()];
-    Enumeration en = allfeatures.elements();
-    int i = allfeatures.size() - 1;
-    while (en.hasMoreElements())
+    jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();
+
+    if (dialog.accept)
     {
-      renderOrder[i] = en.nextElement().toString();
-      i--;
+      // This ensures that the last sequence
+      // is refreshed and new features are rendered
+      lastSeq = null;
+      lastFeatureAdded = name.getText().trim();
+      lastFeatureGroupAdded = source.getText().trim();
+      lastDescriptionAdded = description.getText().replace('\n', ' ');
     }
-  }
 
-  public Color getColour(String featureType)
-  {
-    return (Color) featureColours.get(featureType);
-  }
+    if (lastFeatureGroupAdded != null && lastFeatureGroupAdded.length() < 1)
+      lastFeatureGroupAdded = null;
 
-  public void addNewFeature(String name, Color col)
-  {
-
-    setColour(name, col);
-    if (av.featuresDisplayed == null)
+    if (!newFeatures)
     {
-      av.featuresDisplayed = new Hashtable();
-    }
 
-    av.featuresDisplayed.put(name, "NOGROUP");
-  }
+      SequenceFeature sf = features[featureIndex];
+      if (dialog.accept)
+      {
+        sf.type = lastFeatureAdded;
+        sf.featureGroup = lastFeatureGroupAdded;
+        sf.description = lastDescriptionAdded;
+        if (!colourPanel.isGcol)
+        {
+          // update colour - otherwise its already done.
+          setColour(sf.type, colourPanel.getBackground());
+        }
+        try
+        {
+          sf.begin = Integer.parseInt(start.getText());
+          sf.end = Integer.parseInt(end.getText());
+        } catch (NumberFormatException ex)
+        {
+        }
 
-  public void setColour(String featureType, Color col)
-  {
-    featureColours.put(featureType, col);
-  }
+        ffile.parseDescriptionHTML(sf, false);
+        setVisible(lastFeatureAdded); // if user edited name then make sure new type is visible
+      }
+      if (deleteFeature)
+      {
+        sequences[0].deleteFeature(sf);
+      }
 
-  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();
     }
-
-    renderOrder = new String[data.length];
-
-    if (data.length > 0)
+    else
     {
-      for (int i = 0; i < data.length; i++)
+      if (dialog.accept && name.getText().length() > 0)
       {
-        String type = data[i][0].toString();
-        setColour(type, (Color) data[i][1]);
-        if ( ( (Boolean) data[i][2]).booleanValue())
+        for (int i = 0; i < sequences.length; i++)
         {
-          av.featuresDisplayed.put(type, new Integer(getColour(type).getRGB()));
+          features[i].type = lastFeatureAdded;
+          features[i].featureGroup = lastFeatureGroupAdded;
+          features[i].description = lastDescriptionAdded;
+          sequences[i].addSequenceFeature(features[i]);
+          ffile.parseDescriptionHTML(features[i], false);
         }
 
-        renderOrder[data.length - i - 1] = type;
+        col = colourPanel.getBackground();
+        // setColour(lastFeatureAdded, fcol);
+
+        if (lastFeatureGroupAdded != null)
+        {
+          setGroupVisibility(lastFeatureGroupAdded, true);
+        }
+        setColour(lastFeatureAdded, fcol);
+        setVisible(lastFeatureAdded);
+        findAllFeatures(false); // different to original applet behaviour ? 
+        // findAllFeatures();
+      }
+      else
+      {
+        // no update to the alignment
+        return false;
       }
     }
-  }
-}
+    // refresh the alignment and the feature settings dialog
+    if (((jalview.appletgui.AlignViewport) av).featureSettings != null)
+    {
+      ((jalview.appletgui.AlignViewport) av).featureSettings.refreshTable();
+    }
+    // findAllFeatures();
 
-class TransparencySetter
-{
-  void setTransparency(Graphics g, float value)
-  {
-     Graphics2D g2 = (Graphics2D) g;
-     g2.setComposite(
-        AlphaComposite.getInstance(
-             AlphaComposite.SRC_OVER, value));
+    ap.paintAlignment(true);
+
+    return true;
   }
 }