X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureRenderer.java;h=12876edb05e464d704cf1a736cad7ae595332d27;hb=cfbeda226e2ac27f6d02572b1c9589a3e2f1c747;hp=72f4bef38790e90c3b65579c637ddfdb6138e08a;hpb=a50dc1e9537d68da7263cb5b4ca9ba6a0b4b8b5a;p=jalview.git

diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
index 72f4bef..12876ed 100755
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -309,7 +309,7 @@ public class FeatureRenderer
           int pady = (y1 + av.charHeight) - av.charHeight / 5;
           for (i = fstart; i <= fend; i++)
           {
-            s = seq.getSequence().charAt(i);
+            s = seq.getCharAt(i);
 
             if (jalview.util.Comparison.isGap(s))
             {
@@ -438,6 +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));
         }
 
       }
@@ -566,8 +566,6 @@ 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],
@@ -577,6 +575,13 @@ public class FeatureRenderer
               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);
           }
         });
 
@@ -607,6 +612,9 @@ public class FeatureRenderer
           && name.getSelectedItem() != null
           && source.getSelectedItem() != null)
       {
+        //This ensures that the last sequence
+        //is refreshed and new features are rendered
+        lastSeq=null;
         lastFeatureAdded = name.getSelectedItem().toString();
         lastFeatureGroupAdded = source.getSelectedItem().toString();
         lastDescriptionAdded = description.getText().replaceAll("\n", " ");