From ef23c17739a6fba3a8d455b725782bce4607ac9f Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Mon, 22 Aug 2005 17:10:39 +0000
Subject: [PATCH] Check for null colour

---
 src/jalview/appletgui/APopupMenu.java |    5 +++++
 src/jalview/appletgui/AlignFrame.java |    5 +++--
 src/jalview/appletgui/TreeCanvas.java |    5 +++--
 src/jalview/gui/AlignFrame.java       |    4 +++-
 src/jalview/gui/PopupMenu.java        |    4 ++++
 src/jalview/gui/TreeCanvas.java       |    3 ++-
 6 files changed, 20 insertions(+), 6 deletions(-)

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index abd76d6..80006c2 100755
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -379,6 +379,9 @@ public class APopupMenu
   protected void abovePIDColour_itemStateChanged(ItemEvent ie)
   {
     SequenceGroup sg = getGroup();
+    if(sg.cs==null)
+          return;
+
     if (abovePIDColour.getState())
     {
       sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
@@ -435,6 +438,8 @@ public class APopupMenu
   protected void conservationMenuItem_itemStateChanged(ItemEvent ie)
   {
     SequenceGroup sg = getGroup();
+    if(sg.cs==null)
+          return;
 
     if (conservationMenuItem.getState())
     {
diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 6138257..010c73d 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -879,10 +879,11 @@ public class AlignFrame
           }
         }
 
-        if (viewport.getAbovePIDThreshold())
+        if (viewport.getAbovePIDThreshold()
+            || cs instanceof PIDColourScheme
+            || cs instanceof Blosum62ColourScheme)
         {
           sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
-
           sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
         }
 
diff --git a/src/jalview/appletgui/TreeCanvas.java b/src/jalview/appletgui/TreeCanvas.java
index a6bc5df..451d663 100755
--- a/src/jalview/appletgui/TreeCanvas.java
+++ b/src/jalview/appletgui/TreeCanvas.java
@@ -490,8 +490,9 @@ System.out.println("called here");
                                                false, 0, av.alignment.getWidth());
 
 
-          if (av.getGlobalColourScheme().conservationApplied())
-          {
+          if (  av.getGlobalColourScheme()!=null
+             && av.getGlobalColourScheme().conservationApplied())
+            {
             Conservation c = new Conservation("Group",
                                               ResidueProperties.propHash, 3,
                                               sg.sequences, sg.getStartRes(),
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index fc59062..692f258 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1448,7 +1448,9 @@ public class AlignFrame
           }
         }
 
-        if (viewport.getAbovePIDThreshold())
+        if (viewport.getAbovePIDThreshold()
+            || cs instanceof PIDColourScheme
+            || cs instanceof Blosum62ColourScheme)
         {
          sg.cs.setThreshold(threshold,
                 viewport.getIgnoreGapsConsensus());
diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 137ca14..153e9fb 100755
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -606,6 +606,8 @@ public class PopupMenu extends JPopupMenu
     protected void abovePIDColour_actionPerformed(ActionEvent e)
     {
         SequenceGroup sg = getGroup();
+        if(sg.cs==null)
+          return;
 
         if (abovePIDColour.isSelected())
         {
@@ -696,6 +698,8 @@ public class PopupMenu extends JPopupMenu
     protected void conservationMenuItem_actionPerformed(ActionEvent e)
     {
         SequenceGroup sg = getGroup();
+        if(sg.cs==null)
+          return;
 
         if (conservationMenuItem.isSelected())
         {
diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index e923792..f0d63c4 100755
--- a/src/jalview/gui/TreeCanvas.java
+++ b/src/jalview/gui/TreeCanvas.java
@@ -718,7 +718,8 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
                         sg.cs.setThreshold(25, av.getIgnoreGapsConsensus());
                     }
 
-                    if (av.getGlobalColourScheme().conservationApplied())
+                    if (  av.getGlobalColourScheme()!=null
+                       && av.getGlobalColourScheme().conservationApplied())
                     {
                         Conservation c = new Conservation("Group",
                                 ResidueProperties.propHash, 3, sg.sequences,
-- 
1.7.10.2