Check for null colour

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index abd76d6..80006c2 100755 (executable)
--- 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)\r
   {\r
     SequenceGroup sg = getGroup();\r
+    if(sg.cs==null)\r
+          return;\r
+\r
     if (abovePIDColour.getState())\r
     {\r
       sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
@@ -435,6 +438,8 @@ public class APopupMenu
   protected void conservationMenuItem_itemStateChanged(ItemEvent ie)\r
   {\r
     SequenceGroup sg = getGroup();\r
+    if(sg.cs==null)\r
+          return;\r
 \r
     if (conservationMenuItem.getState())\r
     {\r

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 6138257..010c73d 100755 (executable)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -879,10 +879,11 @@ public class AlignFrame
           }\r
         }\r
 \r
-        if (viewport.getAbovePIDThreshold())\r
+        if (viewport.getAbovePIDThreshold()\r
+            || cs instanceof PIDColourScheme\r
+            || cs instanceof Blosum62ColourScheme)\r
         {\r
           sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
-\r
           sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
         }\r
 \r

diff --git a/src/jalview/appletgui/TreeCanvas.java b/src/jalview/appletgui/TreeCanvas.java
index a6bc5df..451d663 100755 (executable)
--- 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());\r
 \r
 \r
-          if (av.getGlobalColourScheme().conservationApplied())\r
-          {\r
+          if (  av.getGlobalColourScheme()!=null\r
+             && av.getGlobalColourScheme().conservationApplied())\r
+            {\r
             Conservation c = new Conservation("Group",\r
                                               ResidueProperties.propHash, 3,\r
                                               sg.sequences, sg.getStartRes(),\r

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index fc59062..692f258 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1448,7 +1448,9 @@ public class AlignFrame
           }\r
         }\r
 \r
-        if (viewport.getAbovePIDThreshold())\r
+        if (viewport.getAbovePIDThreshold()\r
+            || cs instanceof PIDColourScheme\r
+            || cs instanceof Blosum62ColourScheme)\r
         {\r
          sg.cs.setThreshold(threshold,\r
                 viewport.getIgnoreGapsConsensus());\r

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 137ca14..153e9fb 100755 (executable)
--- 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)\r
     {\r
         SequenceGroup sg = getGroup();\r
+        if(sg.cs==null)\r
+          return;\r
 \r
         if (abovePIDColour.isSelected())\r
         {\r
@@ -696,6 +698,8 @@ public class PopupMenu extends JPopupMenu
     protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
     {\r
         SequenceGroup sg = getGroup();\r
+        if(sg.cs==null)\r
+          return;\r
 \r
         if (conservationMenuItem.isSelected())\r
         {\r

diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index e923792..f0d63c4 100755 (executable)
--- 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());\r
                     }\r
 \r
-                    if (av.getGlobalColourScheme().conservationApplied())\r
+                    if (  av.getGlobalColourScheme()!=null\r
+                       && av.getGlobalColourScheme().conservationApplied())\r
                     {\r
                         Conservation c = new Conservation("Group",\r
                                 ResidueProperties.propHash, 3, sg.sequences,\r