X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureRenderer.java;h=beef70c25c67a68e50f9df5b5a550ea84b355f4e;hb=bc77e2f0f477053147a4e56b681131c710eb3ec8;hp=e73679582db90930fa10098d1eb943d84694bd23;hpb=197359781e7142ec6bcb53740831fc626c4675cd;p=jalview.git

diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
index e736795..beef70c 100755
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -212,7 +212,7 @@ public class FeatureRenderer
        {
         type =  renderOrder[renderIndex];
 
-        if(!av.featuresDisplayed.containsKey(type))
+        if(type==null || !av.featuresDisplayed.containsKey(type))
           continue;
 
         // loop through all features in sequence to find
@@ -423,13 +423,14 @@ public class FeatureRenderer
     public boolean createNewFeatures(SequenceI[] sequences,
                                   SequenceFeature [] features)
     {
-      return amendFeatures(sequences, features, true);
+      return amendFeatures(sequences, features, true, null);
     }
 
     int featureIndex = 0;
-    boolean amendFeatures(SequenceI[] sequences,
-                           final SequenceFeature [] features,
-                           boolean newFeatures)
+    boolean amendFeatures(final SequenceI[] sequences,
+                          final SequenceFeature[] features,
+                          boolean newFeatures,
+                          final AlignmentPanel ap)
     {
       JPanel bigPanel = new JPanel(new BorderLayout());
       final JComboBox name = new JComboBox();
@@ -437,7 +438,8 @@ public class FeatureRenderer
       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));
@@ -477,9 +479,9 @@ public class FeatureRenderer
         bigPanel.add(panel, BorderLayout.SOUTH);
 
         panel = new JPanel();
-        panel.add(new JLabel(" Start: ", JLabel.RIGHT));
+        panel.add(new JLabel(" Start:", JLabel.RIGHT));
         panel.add(start);
-        panel.add(new JLabel("  End: ", JLabel.RIGHT));
+        panel.add(new JLabel("  End:", JLabel.RIGHT));
         panel.add(end);
         bigPanel.add(panel, BorderLayout.CENTER);
       }
@@ -529,12 +531,10 @@ public class FeatureRenderer
         if (getColour(lastFeatureAdded) != null)
         {
           colour.setBackground(getColour(lastFeatureAdded));
-          colour.setForeground(getColour(lastFeatureAdded));
         }
         else
         {
           colour.setBackground(new Color(60, 160, 115));
-          colour.setForeground(new Color(60, 160, 115));
         }
 
       }
@@ -566,9 +566,22 @@ public class FeatureRenderer
               end.setValue(new Integer(features[index].getEnd()));
               colour.setBackground(
                   getColour(name.getSelectedItem().toString()));
-              colour.setForeground(
-                  getColour(name.getSelectedItem().toString()));
+
+              SearchResults highlight = new SearchResults();
+              highlight.addResult(sequences[0],
+                                  features[index].getBegin(),
+                                  features[index].getEnd());
+
+              ap.seqPanel.seqCanvas.highlightSearchResults(highlight);
+
             }
+            Color col = getColour(name.getSelectedItem().toString());
+            if (col == null)
+              col = new
+                  jalview.schemes.UserColourScheme()
+                  .createColourFromName(name.getSelectedItem().toString());
+
+            colour.setBackground(col);
           }
         });
 
@@ -582,7 +595,8 @@ public class FeatureRenderer
         options = new Object[]{"OK", "Cancel"};
 
       String title = newFeatures ?  "Create New Sequence Feature(s)" :
-                                    "Amend/Delete Features";
+                                    "Amend/Delete Features for "
+                                    +sequences[0].getName();
 
       int reply = JOptionPane.showInternalOptionDialog(Desktop.desktop,
                                                    bigPanel,