JAL-2438 FeatureColourFinder refactored from FeatureRenderer, fr not

[jalview.git] / src / jalview / gui / FeatureRenderer.java

diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
index 46bcdab..86b8eba 100644 (file)
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -22,10 +22,11 @@ package jalview.gui;
 
 import jalview.api.FeatureColourI;
 import jalview.datamodel.SearchResults;
+import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.schemes.FeatureColour;
-import jalview.schemes.UserColourScheme;
+import jalview.util.ColorUtils;
 import jalview.util.MessageManager;
 
 import java.awt.BorderLayout;
@@ -39,11 +40,12 @@ import java.awt.event.ItemEvent;
 import java.awt.event.ItemListener;
 import java.awt.event.MouseAdapter;
 import java.awt.event.MouseEvent;
+import java.util.Arrays;
+import java.util.Comparator;
 
 import javax.swing.JColorChooser;
 import javax.swing.JComboBox;
 import javax.swing.JLabel;
-import javax.swing.JOptionPane;
 import javax.swing.JPanel;
 import javax.swing.JScrollPane;
 import javax.swing.JSpinner;
@@ -58,8 +60,7 @@ import javax.swing.SwingConstants;
  * @version $Revision$
  */
 public class FeatureRenderer extends
-        jalview.renderer.seqfeatures.FeatureRenderer implements
-        jalview.api.FeatureRenderer
+        jalview.renderer.seqfeatures.FeatureRenderer
 {
   Color resBoxColour;
 
@@ -73,9 +74,8 @@ public class FeatureRenderer extends
    */
   public FeatureRenderer(AlignmentPanel ap)
   {
-    super();
+    super(ap.av);
     this.ap = ap;
-    this.av = ap.av;
     if (ap != null && ap.getSeqPanel() != null
             && ap.getSeqPanel().seqCanvas != null
             && ap.getSeqPanel().seqCanvas.fr != null)
@@ -172,7 +172,8 @@ public class FeatureRenderer extends
     {
       panel = new JPanel(new GridLayout(4, 1));
       tmp = new JPanel();
-      tmp.add(new JLabel(MessageManager.getString("label.select_feature")));
+      tmp.add(new JLabel(MessageManager.getString("label.select_feature")
+              + ":"));
       overlaps = new JComboBox();
       for (int i = 0; i < features.length; i++)
       {
@@ -198,7 +199,7 @@ public class FeatureRenderer extends
             start.setValue(new Integer(features[index].getBegin()));
             end.setValue(new Integer(features[index].getEnd()));
 
-            SearchResults highlight = new SearchResults();
+            SearchResultsI highlight = new SearchResults();
             highlight.addResult(sequences[0], features[index].getBegin(),
                     features[index].getEnd());
 
@@ -208,7 +209,7 @@ public class FeatureRenderer extends
           FeatureColourI col = getFeatureStyle(name.getText());
           if (col == null)
           {
-            col = new FeatureColour(UserColourScheme
+            col = new FeatureColour(ColorUtils
                     .createColourFromName(name.getText()));
           }
           oldcol = fcol = col;
@@ -223,12 +224,13 @@ public class FeatureRenderer extends
 
     tmp = new JPanel();
     panel.add(tmp);
-    tmp.add(new JLabel(MessageManager.getString("label.name"), JLabel.RIGHT));
+    tmp.add(new JLabel(MessageManager.getString("label.name:"),
+            JLabel.RIGHT));
     tmp.add(name);
 
     tmp = new JPanel();
     panel.add(tmp);
-    tmp.add(new JLabel(MessageManager.getString("label.group") + ":",
+    tmp.add(new JLabel(MessageManager.getString("label.group:"),
             JLabel.RIGHT));
     tmp.add(source);
 
@@ -247,7 +249,7 @@ public class FeatureRenderer extends
     bigPanel.add(panel, BorderLayout.NORTH);
 
     panel = new JPanel();
-    panel.add(new JLabel(MessageManager.getString("label.description"),
+    panel.add(new JLabel(MessageManager.getString("label.description:"),
             JLabel.RIGHT));
     description.setFont(JvSwingUtils.getTextAreaFont());
     description.setLineWrap(true);
@@ -326,14 +328,14 @@ public class FeatureRenderer extends
             : MessageManager.formatMessage("label.amend_delete_features",
                     new String[] { sequences[0].getName() });
 
-    int reply = JOptionPane.showInternalOptionDialog(Desktop.desktop,
-            bigPanel, title, JOptionPane.YES_NO_CANCEL_OPTION,
-            JOptionPane.QUESTION_MESSAGE, null, options,
+    int reply = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
+            bigPanel, title, JvOptionPane.YES_NO_CANCEL_OPTION,
+            JvOptionPane.QUESTION_MESSAGE, null, options,
             MessageManager.getString("action.ok"));
 
     jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();
 
-    if (reply == JOptionPane.OK_OPTION && name.getText().length() > 0)
+    if (reply == JvOptionPane.OK_OPTION && name.getText().length() > 0)
     {
       // This ensures that the last sequence
       // is refreshed and new features are rendered
@@ -352,11 +354,11 @@ public class FeatureRenderer extends
     {
       SequenceFeature sf = features[featureIndex];
 
-      if (reply == JOptionPane.NO_OPTION)
+      if (reply == JvOptionPane.NO_OPTION)
       {
         sequences[0].getDatasetSequence().deleteFeature(sf);
       }
-      else if (reply == JOptionPane.YES_OPTION)
+      else if (reply == JvOptionPane.YES_OPTION)
       {
         sf.type = lastFeatureAdded;
         sf.featureGroup = lastFeatureGroupAdded;
@@ -379,7 +381,7 @@ public class FeatureRenderer extends
     else
     // NEW FEATURES ADDED
     {
-      if (reply == JOptionPane.OK_OPTION && lastFeatureAdded.length() > 0)
+      if (reply == JvOptionPane.OK_OPTION && lastFeatureAdded.length() > 0)
       {
         for (int i = 0; i < sequences.length; i++)
         {
@@ -441,4 +443,15 @@ public class FeatureRenderer extends
       FeatureSettings.renderGraduatedColor(colour, col);
     }
   }
+
+  /**
+   * Orders features in render precedence (last in order is last to render, so
+   * displayed on top of other features)
+   * 
+   * @param order
+   */
+  public void orderFeatures(Comparator<String> order)
+  {
+    Arrays.sort(renderOrder, order);
+  }
 }