X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureRenderer.java;h=46f574e03ec4d9f4c3b9f8183582c6aa80079767;hb=e16e9699b56f3db4e42dc694aaafad76dae66c4b;hp=4c4be5c9d8326bd8475b8d6a467db4706a493623;hpb=eafcdaa3f6786f1f00a0c5d551f5ec7401b118fb;p=jalview.git

diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
old mode 100755
new mode 100644
index 4c4be5c..46f574e
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -1,871 +1,491 @@
 /*
- * 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 ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.gui;
 
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-import java.awt.image.*;
-import java.beans.PropertyChangeListener;
-import java.beans.PropertyChangeSupport;
-
-import javax.swing.*;
-
-import jalview.datamodel.*;
+import jalview.api.FeatureColourI;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SearchResultsI;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.io.FeaturesFile;
+import jalview.schemes.FeatureColour;
+import jalview.util.ColorUtils;
+import jalview.util.MessageManager;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.GridLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Comparator;
+import java.util.List;
+
+import javax.swing.JColorChooser;
+import javax.swing.JComboBox;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JSpinner;
+import javax.swing.JTextArea;
+import javax.swing.JTextField;
+import javax.swing.SwingConstants;
+import javax.swing.event.DocumentEvent;
+import javax.swing.event.DocumentListener;
 
 /**
  * DOCUMENT ME!
- *
+ * 
  * @author $author$
  * @version $Revision$
  */
 public class FeatureRenderer
+        extends jalview.renderer.seqfeatures.FeatureRenderer
 {
-  AlignmentPanel ap;
-  AlignViewport av;
-  Color resBoxColour;
-  float transparency = 1.0f;
-  FontMetrics fm;
-  int charOffset;
-
-  Hashtable featureColours = new Hashtable();
-
-  // A higher level for grouping features of a
-  // particular type
-  Hashtable featureGroups = new Hashtable();
+  /*
+   * defaults for creating a new feature are the last created
+   * feature type and group
+   */
+  static String lastFeatureAdded = "feature_1";
 
-  // This is actually an Integer held in the hashtable,
-  // Retrieved using the key feature type
-  Object currentColour;
+  static String lastFeatureGroupAdded = "Jalview";
 
-  String[] renderOrder;
-  PropertyChangeSupport changeSupport=new PropertyChangeSupport(this);
+  Color resBoxColour;
 
-  Vector allfeatures;
+  AlignmentPanel ap;
 
   /**
-   * Creates a new FeatureRenderer object.
-   *
-   * @param av
-   *          DOCUMENT ME!
+   * Creates a new FeatureRenderer object
+   * 
+   * @param alignPanel
    */
-  public FeatureRenderer(AlignmentPanel ap)
+  public FeatureRenderer(AlignmentPanel alignPanel)
   {
-    this.ap = ap;
-    this.av = ap.av;
+    super(alignPanel.av);
+    this.ap = alignPanel;
+    if (alignPanel.getSeqPanel() != null
+            && alignPanel.getSeqPanel().seqCanvas != null
+            && alignPanel.getSeqPanel().seqCanvas.fr != null)
+    {
+      transferSettings(alignPanel.getSeqPanel().seqCanvas.fr);
+    }
   }
 
+  FeatureColourI oldcol, fcol;
 
-  public void transferSettings(FeatureRenderer fr)
-  {
-    this.renderOrder = fr.renderOrder;
-    this.featureGroups = fr.featureGroups;
-    this.featureColours = fr.featureColours;
-    this.transparency = fr.transparency;
-    this.featureOrder = fr.featureOrder;
-  }
-
-  BufferedImage offscreenImage;
-  boolean offscreenRender = false;
-  public Color findFeatureColour(Color initialCol, SequenceI seq, int res)
-  {
-    return new Color(findFeatureColour(initialCol.getRGB(),
-                                       seq, res));
-  }
+  int featureIndex = 0;
 
   /**
-   * This is used by the Molecule Viewer and Overview to get the accurate
-   * colourof the rendered sequence
+   * Presents a dialog allowing the user to add new features, or amend or delete
+   * existing features. Currently this can be on
+   * <ul>
+   * <li>double-click on a sequence - Amend/Delete features at position</li>
+   * <li>Create sequence feature from pop-up menu on selected region</li>
+   * <li>Create features for pattern matches from Find</li>
+   * </ul>
+   * If the supplied feature type is null, show (and update on confirm) the type
+   * and group of the last new feature created (with initial defaults of
+   * "feature_1" and "Jalview").
+   * 
+   * @param sequences
+   *          the sequences features are to be created on (if creating
+   *          features), or a single sequence (if amending features)
+   * @param features
+   *          the current features at the position (if amending), or template
+   *          new feature(s) with start/end position set (if creating)
+   * @param create
+   *          true to create features, false to amend or delete
+   * @param alignPanel
+   * @return
    */
-  public int findFeatureColour(int initialCol, SequenceI seq, int column)
+  protected boolean amendFeatures(final List<SequenceI> sequences,
+          final List<SequenceFeature> features, boolean create,
+          final AlignmentPanel alignPanel)
   {
-    if (!av.showSequenceFeatures)
-    {
-      return initialCol;
-    }
+    featureIndex = 0;
+
+    final JPanel mainPanel = new JPanel(new BorderLayout());
 
-    if (seq != lastSeq)
+    final JTextField name = new JTextField(25);
+    name.getDocument().addDocumentListener(new DocumentListener()
     {
-      lastSeq = seq;
-      sequenceFeatures = lastSeq.getDatasetSequence().getSequenceFeatures();
-      if (sequenceFeatures!=null)
+      @Override
+      public void insertUpdate(DocumentEvent e)
       {
-        sfSize = sequenceFeatures.length;
+        warnIfTypeHidden(mainPanel, name.getText());
       }
-    }
 
-    if (sequenceFeatures!=lastSeq.getDatasetSequence().getSequenceFeatures()) {
-      sequenceFeatures = lastSeq.getDatasetSequence().getSequenceFeatures();
-      if (sequenceFeatures != null)
+      @Override
+      public void removeUpdate(DocumentEvent e)
       {
-        sfSize = sequenceFeatures.length;
+        warnIfTypeHidden(mainPanel, name.getText());
       }
-    }
-
-    if (sequenceFeatures == null || sfSize==0)
-    {
-      return initialCol;
-    }
-
-
-    if (jalview.util.Comparison.isGap(lastSeq.getCharAt(column)))
-    {
-      return Color.white.getRGB();
-    }
-
-    // Only bother making an offscreen image if transparency is applied
-    if (transparency != 1.0f && offscreenImage == null)
-    {
-      offscreenImage = new BufferedImage(1, 1, BufferedImage.TYPE_INT_ARGB);
-    }
-
-    currentColour = null;
-
-    offscreenRender = true;
-
-    if (offscreenImage != null)
-    {
-      offscreenImage.setRGB(0, 0, initialCol);
-      drawSequence(offscreenImage.getGraphics(),
-                   lastSeq,
-                   column, column, 0);
-
-      return offscreenImage.getRGB(0, 0);
-    }
-    else
-    {
-      drawSequence(null,
-                   lastSeq,
-                   lastSeq.findPosition(column),
-                   -1, -1);
 
-      if (currentColour == null)
+      @Override
+      public void changedUpdate(DocumentEvent e)
       {
-        return initialCol;
+        warnIfTypeHidden(mainPanel, name.getText());
       }
-      else
-      {
-        return ( (Integer) currentColour).intValue();
-      }
-    }
-
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param g
-   *          DOCUMENT ME!
-   * @param seq
-   *          DOCUMENT ME!
-   * @param sg
-   *          DOCUMENT ME!
-   * @param start
-   *          DOCUMENT ME!
-   * @param end
-   *          DOCUMENT ME!
-   * @param x1
-   *          DOCUMENT ME!
-   * @param y1
-   *          DOCUMENT ME!
-   * @param width
-   *          DOCUMENT ME!
-   * @param height
-   *          DOCUMENT ME!
-   */
-  // String type;
-  // SequenceFeature sf;
-  SequenceI lastSeq;
-  SequenceFeature[] sequenceFeatures;
-  int sfSize, sfindex, spos, epos;
-
-  synchronized public void drawSequence(Graphics g, SequenceI seq,
-                           int start, int end, int y1)
-  {
-
-    if (seq.getDatasetSequence().getSequenceFeatures() == null
-        || seq.getDatasetSequence().getSequenceFeatures().length == 0)
-    {
-      return;
-    }
-
-    if (g != null)
-    {
-      fm = g.getFontMetrics();
-    }
+    });
 
-    if (av.featuresDisplayed == null
-        || renderOrder == null
-        || newFeatureAdded)
+    final JTextField group = new JTextField(25);
+    group.getDocument().addDocumentListener(new DocumentListener()
     {
-      findAllFeatures();
-      if (av.featuresDisplayed.size() < 1)
+      @Override
+      public void insertUpdate(DocumentEvent e)
       {
-        return;
+        warnIfGroupHidden(mainPanel, group.getText());
       }
 
-      sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();
-    }
-
-    if (lastSeq == null || seq != lastSeq
-        || seq.getDatasetSequence().getSequenceFeatures()!=sequenceFeatures)
-    {
-      lastSeq = seq;
-      sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();
-    }
-
-    if (transparency != 1 && g != null)
-    {
-      Graphics2D g2 = (Graphics2D) g;
-      g2.setComposite(
-          AlphaComposite.getInstance(
-              AlphaComposite.SRC_OVER, transparency));
-    }
-
-    if (!offscreenRender)
-    {
-      spos = lastSeq.findPosition(start);
-      epos = lastSeq.findPosition(end);
-    }
-
-    sfSize = sequenceFeatures.length;
-    String type;
-    for (int renderIndex = 0; renderIndex < renderOrder.length; renderIndex++)
-    {
-      type = renderOrder[renderIndex];
-
-      if (type == null || !av.featuresDisplayed.containsKey(type))
+      @Override
+      public void removeUpdate(DocumentEvent e)
       {
-        continue;
+        warnIfGroupHidden(mainPanel, group.getText());
       }
 
-      // loop through all features in sequence to find
-      // current feature to render
-      for (sfindex = 0; sfindex < sfSize; sfindex++)
+      @Override
+      public void changedUpdate(DocumentEvent e)
       {
-        if (!sequenceFeatures[sfindex].type.equals(type))
-        {
-          continue;
-        }
-
-        if (featureGroups != null
-            && sequenceFeatures[sfindex].featureGroup != null
-            &&
-            sequenceFeatures[sfindex].featureGroup.length()!=0
-            && featureGroups.containsKey(sequenceFeatures[sfindex].featureGroup)
-            &&
-            ! ( (Boolean) featureGroups.get(sequenceFeatures[sfindex].
-                                            featureGroup)).
-            booleanValue())
-        {
-          continue;
-        }
-
-        if (!offscreenRender && (sequenceFeatures[sfindex].getBegin() > epos
-                                 || sequenceFeatures[sfindex].getEnd() < spos))
-        {
-          continue;
-        }
+        warnIfGroupHidden(mainPanel, group.getText());
+      }
+    });
 
-        if (offscreenRender && offscreenImage == null)
+    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 JLabel colour = new JLabel();
+    colour.setOpaque(true);
+    // colour.setBorder(BorderFactory.createEtchedBorder());
+    colour.setMaximumSize(new Dimension(30, 16));
+    colour.addMouseListener(new MouseAdapter()
+    {
+      /*
+       * open colour chooser on click in colour panel
+       */
+      @Override
+      public void mousePressed(MouseEvent evt)
+      {
+        if (fcol.isSimpleColour())
         {
-          if (sequenceFeatures[sfindex].begin <= start &&
-              sequenceFeatures[sfindex].end >= start)
+          Color col = JColorChooser.showDialog(Desktop.desktop,
+                  MessageManager.getString("label.select_feature_colour"),
+                  fcol.getColour());
+          if (col != null)
           {
-            currentColour = av.featuresDisplayed.get(sequenceFeatures[sfindex].
-                type);
+            fcol = new FeatureColour(col);
+            updateColourButton(mainPanel, colour, fcol);
           }
         }
-        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);
+          /*
+           * variable colour dialog - on OK, refetch the updated
+           * feature colour and update this display
+           */
+          final String ft = features.get(featureIndex).getType();
+          final String type = ft == null ? lastFeatureAdded : ft;
+          FeatureTypeSettings fcc = new FeatureTypeSettings(
+                  FeatureRenderer.this, type);
+          fcc.setRequestFocusEnabled(true);
+          fcc.requestFocus();
+          fcc.addActionListener(new ActionListener()
+          {
+            @Override
+            public void actionPerformed(ActionEvent e)
+            {
+              fcol = FeatureRenderer.this.getFeatureStyle(ft);
+              setColour(type, fcol);
+              updateColourButton(mainPanel, colour, fcol);
+            }
+          });
         }
-
-      }
-
-    }
-
-    if (transparency != 1.0f && g != null)
-    {
-      Graphics2D g2 = (Graphics2D) g;
-      g2.setComposite(
-          AlphaComposite.getInstance(
-              AlphaComposite.SRC_OVER, 1.0f));
-    }
-  }
-
-  char s;
-  int i;
-  void renderFeature(Graphics g, SequenceI seq,
-                     int fstart, int fend, Color featureColour, int start,
-                     int end, int y1)
-  {
-
-    if ( ( (fstart <= end) && (fend >= start)))
-    {
-      if (fstart < start)
-      { // fix for if the feature we have starts before the sequence start,
-        fstart = start; // but the feature end is still valid!!
-      }
-
-      if (fend >= end)
-      {
-        fend = end;
       }
-      int pady = (y1 + av.charHeight) - av.charHeight / 5;
-      for (i = fstart; i <= fend; i++)
+    });
+    JPanel gridPanel = new JPanel(new GridLayout(3, 1));
+
+    if (!create && features.size() > 1)
+    {
+      /*
+       * more than one feature at selected position - 
+       * add a drop-down to choose the feature to amend
+       * space pad text if necessary to make entries distinct
+       */
+      gridPanel = new JPanel(new GridLayout(4, 1));
+      JPanel choosePanel = new JPanel();
+      choosePanel.add(new JLabel(
+              MessageManager.getString("label.select_feature") + ":"));
+      final JComboBox<String> overlaps = new JComboBox<>();
+      List<String> added = new ArrayList<>();
+      for (SequenceFeature sf : features)
       {
-        s = seq.getCharAt(i);
-
-        if (jalview.util.Comparison.isGap(s))
-        {
-          continue;
-        }
-
-        g.setColor(featureColour);
-
-        g.fillRect( (i - start) * av.charWidth, y1, av.charWidth, av.charHeight);
-
-        if (offscreenRender || !av.validCharWidth)
-        {
-          continue;
-        }
-
-        g.setColor(Color.white);
-        charOffset = (av.charWidth - fm.charWidth(s)) / 2;
-        g.drawString(String.valueOf(s),
-                     charOffset + (av.charWidth * (i - start)),
-                     pady);
-
-      }
-    }
-  }
-
-  boolean newFeatureAdded = false;
-  /**
-   * Called when alignment in associated view has new/modified features
-   * to discover and display.
-   *
-   */
-  public void featuresAdded()
-  {
-    lastSeq=null;
-    findAllFeatures();
-  }
-
-  boolean findingFeatures = false;
-  /**
-   * search the alignment for all new features, give them a colour and display
-   * them. Then fires a PropertyChangeEvent on the changeSupport object.
-   *
-   */
-  synchronized void findAllFeatures()
-  {
-    findAllFeatures(true); // add all new features as visible
-    if (!firing) {
-      firing=true;
-      changeSupport.firePropertyChange("changeSupport",null,null);
-      firing=false;
-    }
-  }
-  /**
-   * Searches alignment for all features and updates colours
-   *
-   * @param newMadeVisible
-   *          if true newly added feature types will be rendered immediatly
-   */
-  synchronized void findAllFeatures(boolean newMadeVisible) {
-    newFeatureAdded = false;
-
-    if (findingFeatures)
-    {
-      newFeatureAdded = true;
-      return;
-    }
-
-    findingFeatures = true;
-
-    if (av.featuresDisplayed == null)
-    {
-      av.featuresDisplayed = new Hashtable();
-    }
-
-    allfeatures = new Vector();
-    Vector oldfeatures = new Vector();
-    if (renderOrder!=null)
-    {
-      for (int i=0; i<renderOrder.length; i++) {
-        if (renderOrder[i]!=null)
+        String text = String.format("%s/%d-%d (%s)", sf.getType(),
+                sf.getBegin(), sf.getEnd(), sf.getFeatureGroup());
+        while (added.contains(text))
         {
-          oldfeatures.addElement(renderOrder[i]);
+          text += " ";
         }
+        overlaps.addItem(text);
+        added.add(text);
       }
-    }
-    for (int i = 0; i < av.alignment.getHeight(); i++)
-    {
-      SequenceFeature[] features
-          = av.alignment.getSequenceAt(i).getDatasetSequence().
-          getSequenceFeatures();
+      choosePanel.add(overlaps);
 
-      if (features == null)
+      overlaps.addItemListener(new ItemListener()
       {
-        continue;
-      }
-
-      int index = 0;
-      while (index < features.length)
-      {
-        if (!av.featuresDisplayed.containsKey(features[index].getType()))
+        @Override
+        public void itemStateChanged(ItemEvent e)
         {
-
-          if(featureGroups.containsKey(features[index].getType()))
+          int index = overlaps.getSelectedIndex();
+          if (index != -1)
           {
-            boolean visible = ( (Boolean) featureGroups.get(
-                features[index].featureGroup)).booleanValue();
-
-            if(!visible)
-            {
-              System.out.println(features[index].featureGroup
-                                 +" not visible");
-              index++;
-              continue;
-            }
+            featureIndex = index;
+            SequenceFeature sf = features.get(index);
+            name.setText(sf.getType());
+            description.setText(sf.getDescription());
+            group.setText(sf.getFeatureGroup());
+            start.setValue(new Integer(sf.getBegin()));
+            end.setValue(new Integer(sf.getEnd()));
+
+            SearchResultsI highlight = new SearchResults();
+            highlight.addResult(sequences.get(0), sf.getBegin(),
+                    sf.getEnd());
+
+            alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(
+                    highlight, false);
           }
-
-
-          if (! (features[index].begin == 0 && features[index].end == 0))
-          {
-            // If beginning and end are 0, the feature is for the whole sequence
-            // and we don't want to render the feature in the normal way
-
-            if (newMadeVisible && !oldfeatures.contains(features[index].getType())) {
-              // this is a new feature type on the alignment. Mark it for
-              // display.
-              av.featuresDisplayed.put(features[index].getType(),
-                                     new Integer(getColour(features[index].
-                getType()).getRGB()));
-              setOrder(features[index].getType(),0);
-            }
-           }
-        }
-        if (!allfeatures.contains(features[index].getType()))
-        {
-          allfeatures.addElement(features[index].getType());
-        }
-        index++;
-      }
-    }
-    updateRenderOrder(allfeatures);
-    findingFeatures = false;
-  }
-  protected boolean firing=false;
-  /**
-   * replaces the current renderOrder with the unordered features in allfeatures.
-   * The ordering of any types in both renderOrder and allfeatures is preserved,
-   * and all new feature types are rendered on top of the existing types, in
-   * the order given by getOrder or the order given in allFeatures.
-   * Note. this operates directly on the featureOrder hash for efficiency. TODO:
-   * eliminate the float storage for computing/recalling the persistent ordering
-   *
-   * @param allFeatures
-   */
-  private void updateRenderOrder(Vector allFeatures) {
-    Vector allfeatures = new Vector(allFeatures);
-    String[] oldRender = renderOrder;
-    renderOrder = new String[allfeatures.size()];
-    boolean initOrders=(featureOrder==null);
-    int opos=0;
-    if (oldRender!=null && oldRender.length>0)
-    {
-      for (int j=0; j<oldRender.length; j++)
-      {
-        if (oldRender[j]!=null)
+          FeatureColourI col = getFeatureStyle(name.getText());
+          if (col == null)
           {
-            if (initOrders)
-            {
-              setOrder(oldRender[j], (1-(1+(float)j)/(float) oldRender.length));
-            }
-            if (allfeatures.contains(oldRender[j])) {
-              renderOrder[opos++]  = oldRender[j]; // existing features always
-                                                    // appear below new features
-              allfeatures.removeElement(oldRender[j]);
-            }
+            col = new FeatureColour(
+                    ColorUtils.createColourFromName(name.getText()));
           }
+          oldcol = fcol = col;
+          updateColourButton(mainPanel, colour, col);
         }
-    }
-    if (allfeatures.size()==0) {
-      // no new features - leave order unchanged.
-      return;
-    }
-    int i=allfeatures.size()-1;
-    int iSize=i;
-    boolean sort=false;
-    String[] newf = new String[allfeatures.size()];
-    float[] sortOrder = new float[allfeatures.size()];
-    Enumeration en = allfeatures.elements();
-    // sort remaining elements
-    while (en.hasMoreElements())
-    {
-      newf[i] = en.nextElement().toString();
-      if (initOrders || !featureOrder.containsKey(newf[i]))
-      {
-        int denom = initOrders ? allfeatures.size() : featureOrder.size();
-          // new unordered feature - compute persistent ordering at head of
-          // existing features.
-        setOrder(newf[i], i/(float) denom);
-      }
-      // set order from newly found feature from persisted ordering.
-      sortOrder[i] = 2-((Float) featureOrder.get(newf[i])).floatValue();
-      if (i<iSize)
-      {
-        // only sort if we need to
-        sort = sort || sortOrder[i]>sortOrder[i+1];
-      }
-      i--;
-    }
-    if (iSize>1 && sort)
-      jalview.util.QuickSort.sort(sortOrder, newf);
-    sortOrder=null;
-    System.arraycopy(newf, 0, renderOrder, opos, newf.length);
-  }
-  public Color getColour(String featureType)
-  {
-    if (!featureColours.containsKey(featureType))
-    {
-      jalview.schemes.UserColourScheme ucs = new
-          jalview.schemes.UserColourScheme();
-      Color col = ucs.createColourFromName(featureType);
-      featureColours.put(featureType, col);
-      return col;
-    }
-    else
-      return (Color) featureColours.get(featureType);
-  }
+      });
 
-  static String lastFeatureAdded;
-  static String lastFeatureGroupAdded;
-  static String lastDescriptionAdded;
-
-  int featureIndex = 0;
-  boolean amendFeatures(final SequenceI[] sequences,
-                        final SequenceFeature[] features,
-                        boolean newFeatures,
-                        final AlignmentPanel ap)
-  {
-
-    featureIndex = 0;
-
-    JPanel bigPanel = new JPanel(new BorderLayout());
-    final JComboBox overlaps;
-    final JTextField name = new JTextField(25);
-    final JTextField source = new JTextField(25);
-    final JTextArea description = new JTextArea(3, 25);
-    final JSpinner start = new JSpinner();
-    final JSpinner end = new JSpinner();
-    start.setPreferredSize(new Dimension(80, 20));
-    end.setPreferredSize(new Dimension(80, 20));
-
-    final JPanel colour = new JPanel();
-    colour.setBorder(BorderFactory.createEtchedBorder());
-    colour.setMaximumSize(new Dimension(40, 10));
-    colour.addMouseListener(new MouseAdapter()
-    {
-      public void mousePressed(MouseEvent evt)
-      {
-        Color col = JColorChooser.showDialog(Desktop.desktop,
-                                             "Select Feature Colour",
-                                             colour.getBackground());
-        if (col != null)
-          colour.setBackground(col);
+      gridPanel.add(choosePanel);
+    }
 
-      }
-    });
+    JPanel namePanel = new JPanel();
+    gridPanel.add(namePanel);
+    namePanel.add(new JLabel(MessageManager.getString("label.name:"),
+            JLabel.RIGHT));
+    namePanel.add(name);
 
-    JPanel tmp = new JPanel();
-    JPanel panel = new JPanel(new GridLayout(3, 1));
+    JPanel groupPanel = new JPanel();
+    gridPanel.add(groupPanel);
+    groupPanel.add(new JLabel(MessageManager.getString("label.group:"),
+            JLabel.RIGHT));
+    groupPanel.add(group);
 
-    ///////////////////////////////////////
-    ///MULTIPLE FEATURES AT SELECTED RESIDUE
-    if(!newFeatures && features.length>1)
-    {
-     panel = new JPanel(new GridLayout(4, 1));
-     tmp = new JPanel();
-     tmp.add(new JLabel("Select Feature: "));
-     overlaps = new JComboBox();
-     for(int i=0; i<features.length; i++)
-     {
-       overlaps.addItem(features[i].getType()
-        +"/"+features[i].getBegin()+"-"+features[i].getEnd()
-        +" ("+features[i].getFeatureGroup()+")");
-     }
-
-     tmp.add(overlaps);
-
-     overlaps.addItemListener(new ItemListener()
-     {
-       public void itemStateChanged(ItemEvent e)
-       {
-         int index = overlaps.getSelectedIndex();
-         if (index != -1)
-         {
-           featureIndex = index;
-           name.setText(features[index].getType());
-           description.setText(features[index].getDescription());
-           source.setText(features[index].getFeatureGroup());
-           start.setValue(new Integer(features[index].getBegin()));
-           end.setValue(new Integer(features[index].getEnd()));
-
-           SearchResults highlight = new SearchResults();
-           highlight.addResult(sequences[0],
-                               features[index].getBegin(),
-                               features[index].getEnd());
-
-           ap.seqPanel.seqCanvas.highlightSearchResults(highlight);
-
-         }
-         Color col = getColour(name.getText());
-         if (col == null)
-         {
-           col = new
-               jalview.schemes.UserColourScheme()
-               .createColourFromName(name.getText());
-         }
-
-         colour.setBackground(col);
-       }
-     });
-
-
-     panel.add(tmp);
-    }
-    //////////
-    //////////////////////////////////////
-
-    tmp = new JPanel();
-    panel.add(tmp);
-    tmp.add(new JLabel("Name: ", JLabel.RIGHT));
-    tmp.add(name);
-
-    tmp = new JPanel();
-    panel.add(tmp);
-    tmp.add(new JLabel("Group: ", JLabel.RIGHT));
-    tmp.add(source);
-
-    tmp = new JPanel();
-    panel.add(tmp);
-    tmp.add(new JLabel("Colour: ", JLabel.RIGHT));
-    tmp.add(colour);
+    JPanel colourPanel = new JPanel();
+    gridPanel.add(colourPanel);
+    colourPanel.add(new JLabel(MessageManager.getString("label.colour"),
+            JLabel.RIGHT));
+    colourPanel.add(colour);
     colour.setPreferredSize(new Dimension(150, 15));
-
-    bigPanel.add(panel, BorderLayout.NORTH);
-
-    panel = new JPanel();
-    panel.add(new JLabel("Description: ", JLabel.RIGHT));
-    description.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    colour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 9));
+    colour.setForeground(Color.black);
+    colour.setHorizontalAlignment(SwingConstants.CENTER);
+    colour.setVerticalAlignment(SwingConstants.CENTER);
+    colour.setHorizontalTextPosition(SwingConstants.CENTER);
+    colour.setVerticalTextPosition(SwingConstants.CENTER);
+    mainPanel.add(gridPanel, BorderLayout.NORTH);
+
+    JPanel descriptionPanel = new JPanel();
+    descriptionPanel.add(new JLabel(
+            MessageManager.getString("label.description:"), JLabel.RIGHT));
+    description.setFont(JvSwingUtils.getTextAreaFont());
     description.setLineWrap(true);
-    panel.add(new JScrollPane(description));
+    descriptionPanel.add(new JScrollPane(description));
 
-    if (!newFeatures)
+    if (!create)
     {
-      bigPanel.add(panel, BorderLayout.SOUTH);
-
-      panel = new JPanel();
-      panel.add(new JLabel(" Start:", JLabel.RIGHT));
-      panel.add(start);
-      panel.add(new JLabel("  End:", JLabel.RIGHT));
-      panel.add(end);
-      bigPanel.add(panel, BorderLayout.CENTER);
-    }
-    else
-    {
-      bigPanel.add(panel, BorderLayout.CENTER);
-    }
+      mainPanel.add(descriptionPanel, BorderLayout.SOUTH);
 
-    if (lastFeatureAdded == null)
-    {
-      if (features[0].type != null)
-      {
-        lastFeatureAdded = features[0].type;
-      }
-      else
-      {
-        lastFeatureAdded = "feature_1";
-      }
-    }
-
-    if (lastFeatureGroupAdded == null)
-    {
-      if (features[0].featureGroup != null)
-      {
-        lastFeatureGroupAdded = features[0].featureGroup;
-      }
-      else
-      {
-        lastFeatureGroupAdded = "Jalview";
-      }
-    }
-
-    if(newFeatures)
-    {
-      name.setText(lastFeatureAdded);
-      source.setText(lastFeatureGroupAdded);
+      JPanel startEndPanel = new JPanel();
+      startEndPanel.add(new JLabel(MessageManager.getString("label.start"),
+              JLabel.RIGHT));
+      startEndPanel.add(start);
+      startEndPanel.add(new JLabel(MessageManager.getString("label.end"),
+              JLabel.RIGHT));
+      startEndPanel.add(end);
+      mainPanel.add(startEndPanel, BorderLayout.CENTER);
     }
     else
     {
-      name.setText(features[0].getType());
-      source.setText(features[0].getFeatureGroup());
-    }
-
-    start.setValue(new Integer(features[0].getBegin()));
-    end.setValue(new Integer(features[0].getEnd()));
-    description.setText(features[0].getDescription());
-    colour.setBackground(getColour(name.getText()));
-
-
+      mainPanel.add(descriptionPanel, BorderLayout.CENTER);
+    }
+
+    /*
+     * default feature type and group to that of the first feature supplied,
+     * or to the last feature created if not supplied (null value) 
+     */
+    SequenceFeature firstFeature = features.get(0);
+    boolean useLastDefaults = firstFeature.getType() == null;
+    final String featureType = useLastDefaults ? lastFeatureAdded
+            : firstFeature.getType();
+    final String featureGroup = useLastDefaults ? lastFeatureGroupAdded
+            : firstFeature.getFeatureGroup();
+    name.setText(featureType);
+    group.setText(featureGroup);
+
+    start.setValue(new Integer(firstFeature.getBegin()));
+    end.setValue(new Integer(firstFeature.getEnd()));
+    description.setText(firstFeature.getDescription());
+    updateColourButton(mainPanel, colour,
+            (oldcol = fcol = getFeatureStyle(featureType)));
     Object[] options;
-    if (!newFeatures)
+    if (!create)
     {
-      options = new Object[]
-          {
-          "Amend", "Delete", "Cancel"};
+      options = new Object[] { MessageManager.getString("label.amend"),
+          MessageManager.getString("action.delete"),
+          MessageManager.getString("action.cancel") };
     }
     else
     {
-      options = new Object[]
-          {
-          "OK", "Cancel"};
+      options = new Object[] { MessageManager.getString("action.ok"),
+          MessageManager.getString("action.cancel") };
     }
 
-    String title = newFeatures ? "Create New Sequence Feature(s)" :
-        "Amend/Delete Features for "
-        + sequences[0].getName();
+    String title = create
+            ? MessageManager.getString("label.create_new_sequence_features")
+            : MessageManager.formatMessage("label.amend_delete_features",
+                    new String[]
+                    { sequences.get(0).getName() });
 
-    int reply = JOptionPane.showInternalOptionDialog(Desktop.desktop,
-        bigPanel,
-        title,
-        JOptionPane.YES_NO_CANCEL_OPTION,
-        JOptionPane.QUESTION_MESSAGE,
-        null,
-        options, "OK");
+    /*
+     * show the dialog
+     */
+    int reply = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
+            mainPanel, title, JvOptionPane.YES_NO_CANCEL_OPTION,
+            JvOptionPane.QUESTION_MESSAGE, null, options,
+            MessageManager.getString("action.ok"));
 
-    jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();
+    FeaturesFile ffile = new FeaturesFile();
 
-    if (reply == JOptionPane.OK_OPTION && name.getText().length()>0)
+    final String enteredType = name.getText().trim();
+    final String enteredGroup = group.getText().trim();
+    final String enteredDescription = description.getText().replaceAll("\n", " ");
+
+    if (reply == JvOptionPane.OK_OPTION && enteredType.length() > 0)
     {
-      // This ensures that the last sequence
-      // is refreshed and new features are rendered
-      lastSeq = null;
-      lastFeatureAdded = name.getText().trim();
-      lastFeatureGroupAdded = source.getText().trim();
-      lastDescriptionAdded = description.getText().replaceAll("\n", " ");
-
-      if(lastFeatureGroupAdded.length()<1)
-        lastFeatureGroupAdded = null;
+      /*
+       * update default values only if creating using default values
+       */
+      if (useLastDefaults)
+      {
+        lastFeatureAdded = enteredType;
+        lastFeatureGroupAdded = enteredGroup;
+        // TODO: determine if the null feature group is valid
+        if (lastFeatureGroupAdded.length() < 1)
+        {
+          lastFeatureGroupAdded = null;
+        }
+      }
     }
 
-    if (!newFeatures)
+    if (!create)
     {
-      SequenceFeature sf = features[featureIndex];
+      SequenceFeature sf = features.get(featureIndex);
 
-      if (reply == JOptionPane.NO_OPTION)
+      if (reply == JvOptionPane.NO_OPTION)
       {
-        sequences[0].getDatasetSequence().deleteFeature(sf);
+        /*
+         * NO_OPTION corresponds to the Delete button
+         */
+        sequences.get(0).getDatasetSequence().deleteFeature(sf);
+        // update Feature Settings for removal of feature / group
+        featuresAdded();
       }
-      else if (reply == JOptionPane.YES_OPTION)
+      else if (reply == JvOptionPane.YES_OPTION)
       {
-        sf.type = lastFeatureAdded;
-        sf.featureGroup = lastFeatureGroupAdded;
-        sf.description = lastDescriptionAdded;
-
-        setColour(sf.type, colour.getBackground());
-        av.featuresDisplayed.put(sf.type,
-                                 new Integer(colour.getBackground().getRGB()));
-
+        /*
+         * YES_OPTION corresponds to the Amend button
+         * need to refresh Feature Settings if type, group or colour changed;
+         * note we don't force the feature to be visible - the user has been
+         * warned if a hidden feature type or group was entered
+         */
+        boolean refreshSettings = (!featureType.equals(enteredType) || !featureGroup
+                .equals(enteredGroup));
+        refreshSettings |= (fcol != oldcol);
+        setColour(enteredType, fcol);
+        int newBegin = sf.begin;
+        int newEnd = sf.end;
         try
         {
-          sf.begin = ( (Integer) start.getValue()).intValue();
-          sf.end = ( (Integer) end.getValue()).intValue();
+          newBegin = ((Integer) start.getValue()).intValue();
+          newEnd = ((Integer) end.getValue()).intValue();
+        } catch (NumberFormatException ex)
+        {
+          // JSpinner doesn't accept invalid format data :-)
         }
-        catch (NumberFormatException ex)
-        {}
 
-        ffile.parseDescriptionHTML(sf, false);
+        /*
+         * replace the feature by deleting it and adding a new one
+         * (to ensure integrity of SequenceFeatures data store)
+         */
+        sequences.get(0).deleteFeature(sf);
+        SequenceFeature newSf = new SequenceFeature(sf, enteredType,
+                newBegin, newEnd, enteredGroup, sf.getScore());
+        newSf.setDescription(enteredDescription);
+        ffile.parseDescriptionHTML(newSf, false);
+        // amend features dialog only updates one sequence at a time
+        sequences.get(0).addSequenceFeature(newSf);
+
+        if (refreshSettings)
+        {
+          featuresAdded();
+        }
       }
     }
-    else //NEW FEATURES ADDED
+    else
+    // NEW FEATURES ADDED
     {
-      if (reply == JOptionPane.OK_OPTION
-          && lastFeatureAdded.length()>0)
+      if (reply == JvOptionPane.OK_OPTION && enteredType.length() > 0)
       {
-        for (int i = 0; i < sequences.length; i++)
+        for (int i = 0; i < sequences.size(); i++)
         {
-          features[i].type = lastFeatureAdded;
-          if (lastFeatureGroupAdded!=null)
-            features[i].featureGroup = lastFeatureGroupAdded;
-          features[i].description = lastDescriptionAdded;
-          sequences[i].addSequenceFeature(features[i]);
-          ffile.parseDescriptionHTML(features[i], false);
+          SequenceFeature sf = features.get(i);
+          SequenceFeature sf2 = new SequenceFeature(enteredType,
+                  enteredDescription, sf.getBegin(), sf.getEnd(),
+                  enteredGroup);
+          ffile.parseDescriptionHTML(sf2, false);
+          sequences.get(i).addSequenceFeature(sf2);
         }
 
-        if (av.featuresDisplayed == null)
-        {
-          av.featuresDisplayed = new Hashtable();
-        }
-
-        if (lastFeatureGroupAdded != null)
-        {
-          if (featureGroups == null)
-            featureGroups = new Hashtable();
-          featureGroups.put(lastFeatureGroupAdded, new Boolean(true));
-        }
+        setColour(enteredType, fcol);
 
-        Color col = colour.getBackground();
-        setColour(lastFeatureAdded, colour.getBackground());
-        av.featuresDisplayed.put(lastFeatureAdded,
-                                   new Integer(col.getRGB()));
-
-        findAllFeatures(false);
-
-        ap.paintAlignment(true);
+        featuresAdded();
 
+        alignPanel.paintAlignment(true, true);
 
         return true;
       }
@@ -875,129 +495,83 @@ public class FeatureRenderer
       }
     }
 
-    ap.paintAlignment(true);
+    alignPanel.paintAlignment(true, true);
 
     return true;
   }
 
-  public void setColour(String featureType, Color col)
-  {
-    featureColours.put(featureType, col);
-  }
-
-  public void setTransparency(float value)
-  {
-    transparency = value;
-  }
-
-  public float getTransparency()
-  {
-    return transparency;
-  }
-  /**
-   * Replace current ordering with new ordering
-   * @param data { String(Type), Colour(Type), Boolean(Displayed) }
-   */
-  public void setFeaturePriority(Object[][] data)
-  {
-    setFeaturePriority(data, true);
-  }
   /**
-   *
-   * @param data { String(Type), Colour(Type), Boolean(Displayed) }
-   * @param visibleNew when true current featureDisplay list will be cleared
+   * Show a warning message if the entered type is one that is currently hidden
+   * 
+   * @param panel
+   * @param type
    */
-  public void setFeaturePriority(Object[][] data, boolean visibleNew)
+  protected void warnIfTypeHidden(JPanel panel, String type)
   {
-    if (visibleNew)
-      {
-      if (av.featuresDisplayed != null)
-      {
-        av.featuresDisplayed.clear();
-      }
-      else
-      {
-        av.featuresDisplayed = new Hashtable();
-      }
-    }
-    if (data==null)
+    if (getRenderOrder().contains(type))
     {
-      return;
-    }
-
-    // The feature table will display high priority
-    // features at the top, but theses are the ones
-    // we need to render last, so invert the data
-    renderOrder = new String[data.length];
-
-    if (data.length > 0)
-    {
-      for (int i = 0; i < data.length; i++)
+      if (!showFeatureOfType(type))
       {
-        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;
+        String msg = MessageManager.formatMessage("label.warning_hidden",
+                MessageManager.getString("label.feature_type"), type);
+        JvOptionPane.showMessageDialog(panel, msg, "",
+                JvOptionPane.OK_OPTION);
       }
     }
-
   }
-  Hashtable featureOrder=null;
+
   /**
-   * analogous to colour - store a normalized ordering for all feature types in
-   * this rendering context.
-   *
-   * @param type
-   *          Feature type string
-   * @param position
-   *          normalized priority - 0 means always appears on top, 1 means
-   *          always last.
+   * Show a warning message if the entered group is one that is currently hidden
+   * 
+   * @param panel
+   * @param group
    */
-  public float setOrder(String type, float position)
+  protected void warnIfGroupHidden(JPanel panel, String group)
   {
-    if (featureOrder==null)
-    {
-      featureOrder = new Hashtable();
-    }
-    featureOrder.put(type, new Float(position));
-    return position;
-  }
-  /**
-   * get the global priority (0 (top) to 1 (bottom))
-   *
-   * @param type
-   * @return [0,1] or -1 for a type without a priority
-   */
-  public float getOrder(String type) {
-    if (featureOrder!=null)
+    if (featureGroups.containsKey(group) && !featureGroups.get(group))
     {
-      if (featureOrder.containsKey(type))
-      {
-        return ((Float)featureOrder.get(type)).floatValue();
-      }
+      String msg = MessageManager.formatMessage("label.warning_hidden",
+              MessageManager.getString("label.group"), group);
+      JvOptionPane.showMessageDialog(panel, msg, "",
+              JvOptionPane.OK_OPTION);
     }
-    return -1;
   }
 
   /**
-   * @param listener
-   * @see java.beans.PropertyChangeSupport#addPropertyChangeListener(java.beans.PropertyChangeListener)
+   * update the amend feature button dependent on the given style
+   * 
+   * @param bigPanel
+   * @param col
+   * @param col
    */
-  public void addPropertyChangeListener(PropertyChangeListener listener)
+  protected void updateColourButton(JPanel bigPanel, JLabel colour,
+          FeatureColourI col)
   {
-    changeSupport.addPropertyChangeListener(listener);
+    colour.removeAll();
+    colour.setIcon(null);
+    colour.setToolTipText(null);
+    colour.setText("");
+
+    if (col.isSimpleColour())
+    {
+      colour.setBackground(col.getColour());
+    }
+    else
+    {
+      colour.setBackground(bigPanel.getBackground());
+      colour.setForeground(Color.black);
+      FeatureSettings.renderGraduatedColor(colour, col);
+    }
   }
 
   /**
-   * @param listener
-   * @see java.beans.PropertyChangeSupport#removePropertyChangeListener(java.beans.PropertyChangeListener)
+   * Orders features in render precedence (last in order is last to render, so
+   * displayed on top of other features)
+   * 
+   * @param order
    */
-  public void removePropertyChangeListener(PropertyChangeListener listener)
+  public void orderFeatures(Comparator<String> order)
   {
-    changeSupport.removePropertyChangeListener(listener);
+    Arrays.sort(renderOrder, order);
   }
 }