remove debug messages. fix order/reverse order issue for sortByFeature

diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index 5598af2..def0a09 100755 (executable)
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -1040,18 +1040,29 @@ public class FeatureSettings extends JPanel
     gps = getDisplayedFeatureGroups();
     if (typ != null)
     {
+      ArrayList types = new ArrayList();
       for (int i = 0; i < typ.length; i++)
       {
-        System.err.println("Sorting on Types:" + typ[i]);
+        if (typ[i]!=null)
+        {
+          types.add(typ[i]);
+        }
+        typ = new String[types.size()];
+        types.toArray(typ);
       }
     }
     if (gps != null)
     {
+      ArrayList grps = new ArrayList();
 
       for (int i = 0; i < gps.length; i++)
       {
-        System.err.println("Sorting on groups:" + gps[i]);
+        if (gps[i]!=null) {
+          grps.add(gps[i]);
+        }
       }
+      gps = new String[grps.size()];
+      grps.toArray(gps);
     }
     AlignmentPanel alignPanel = af.alignPanel;
     AlignmentI al = alignPanel.av.getAlignment();
@@ -1474,7 +1485,7 @@ public class FeatureSettings extends JPanel
     {
       Color newColor = gcol.getMaxColor();
       comp.setBackground(newColor);
-      System.err.println("Width is " + w / 2);
+      // System.err.println("Width is " + w / 2);
       Icon ficon = new FeatureIcon(gcol, comp.getBackground(), w / 2, h);
       comp.setIcon(ficon);
       // tt+="RGB value: Max (" + newColor.getRed() + ", "