Merge branch 'develop' into bug/JAL-2255_seq-fetcher-broken-on-linux

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

diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
index 426ea32..f519f99 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;
@@ -45,7 +46,6 @@ 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;
@@ -60,8 +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;
 
@@ -200,7 +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());
 
@@ -210,7 +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;
@@ -329,18 +328,15 @@ 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
-      lastSeq = null;
       lastFeatureAdded = name.getText().trim();
       lastFeatureGroupAdded = source.getText().trim();
       lastDescriptionAdded = description.getText().replaceAll("\n", " ");
@@ -355,11 +351,11 @@ 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;
@@ -382,7 +378,7 @@ 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++)
         {