From 854fa199e6dd89266237dc803ddc88bf7ba5bdcc Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@dundee.ac.uk>
Date: Thu, 1 May 2014 15:03:33 +0100
Subject: [PATCH] fix for JAL-1494 tweaked logic to fix NPEs and modify
 settings for both background and all defined groups

---
 src/jalview/appletgui/SliderPanel.java |   26 +++++++++----------
 src/jalview/gui/SliderPanel.java       |   43 +++++++++++---------------------
 2 files changed, 28 insertions(+), 41 deletions(-)

diff --git a/src/jalview/appletgui/SliderPanel.java b/src/jalview/appletgui/SliderPanel.java
index bda4489..1bd5fd8 100644
--- a/src/jalview/appletgui/SliderPanel.java
+++ b/src/jalview/appletgui/SliderPanel.java
@@ -196,25 +196,16 @@ public class SliderPanel extends Panel implements ActionListener,
       return;
     }
 
-    ColourSchemeI toChange = null;
+    ColourSchemeI toChange = cs;
     Iterator<SequenceGroup> allGroups = null;
 
     if (allGroupsCheck.getState())
     {
       allGroups = ap.av.getAlignment().getGroups().listIterator();
     }
-    else
-    {
-      toChange = cs;
-    }
 
-    do
+    while (toChange != null)
     {
-      if (allGroups != null)
-      {
-        toChange = allGroups.next().cs;
-      }
-
       if (forConservation)
       {
         toChange.setConservationInc(i);
@@ -223,8 +214,17 @@ public class SliderPanel extends Panel implements ActionListener,
       {
         toChange.setThreshold(i, ap.av.getIgnoreGapsConsensus());
       }
-
-    } while (allGroups != null && allGroups.hasNext());
+      if (allGroups != null && allGroups.hasNext())
+      {
+        while ((toChange = allGroups.next().cs) == null
+                && allGroups.hasNext())
+          ;
+      }
+      else
+      {
+        toChange = null;
+      }
+    }
 
     ap.seqPanel.seqCanvas.repaint();
 
diff --git a/src/jalview/gui/SliderPanel.java b/src/jalview/gui/SliderPanel.java
index 3eff177..f53204e 100755
--- a/src/jalview/gui/SliderPanel.java
+++ b/src/jalview/gui/SliderPanel.java
@@ -267,47 +267,34 @@ public class SliderPanel extends GSliderPanel
       return;
     }
 
-    ColourSchemeI toChange = null;
-    List<SequenceGroup> allGroups = null;
-    int groupIndex = 0;
+    ColourSchemeI toChange = cs;
+    Iterator<SequenceGroup> allGroups = null;
 
     if (allGroupsCheck.isSelected())
     {
-      allGroups = ap.av.getAlignment().getGroups();
-      groupIndex = allGroups.size() - 1;
-    }
-    else
-    {
-      toChange = cs;
+      allGroups = ap.av.getAlignment().getGroups().listIterator();
     }
 
-    while (groupIndex > -1)
+    while (toChange != null)
     {
-      if (allGroups != null)
-      {
-        toChange = ((SequenceGroup) allGroups.get(groupIndex)).cs;
-
-        if (toChange == null)
-        {
-          groupIndex--;
-
-          continue;
-        }
-      }
-
       if (forConservation)
       {
-        if (toChange.conservationApplied())
-        {
-          toChange.setConservationInc(i);
-        }
+        toChange.setConservationInc(i);
       }
       else
       {
         toChange.setThreshold(i, ap.av.getIgnoreGapsConsensus());
       }
-
-      groupIndex--;
+      if (allGroups != null && allGroups.hasNext())
+      {
+        while ((toChange = allGroups.next().cs) == null
+                && allGroups.hasNext())
+          ;
+      }
+      else
+      {
+        toChange = null;
+      }
     }
 
     ap.seqPanel.seqCanvas.repaint();
-- 
1.7.10.2