No score colour scheme, group colours saved if conservation applied

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 5d94c3c..a449d7f 100755 (executable)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -297,29 +297,35 @@ public class Jalview2XML
 \r
                 if (sg.cs instanceof ConservationColourScheme)\r
                 {\r
-                    groups[i].setConsThreshold(((ConservationColourScheme) sg.cs).inc);\r
-                }\r
+                  ConservationColourScheme ccs = (ConservationColourScheme) sg.cs;\r
+                  groups[i].setConsThreshold(ccs.inc);\r
+\r
+                  if (ccs.cs instanceof jalview.schemes.UserColourScheme)\r
+                  {\r
+                    groups[i].setColour(SetUserColourScheme(ccs.cs, userColours,\r
+                                                            jms));\r
+                  }\r
 \r
-                if (sg.cs instanceof ResidueColourScheme)\r
-                {\r
-                    groups[i].setPidThreshold(((ResidueColourScheme) sg.cs).getThreshold());\r
-                }\r
-                else if (sg.cs instanceof ScoreColourScheme)\r
-                {\r
-                    groups[i].setPidThreshold(((ScoreColourScheme) sg.cs).getThreshold());\r
                 }\r
 \r
-                if (sg.cs instanceof jalview.schemes.UserColourScheme)\r
+               else if (sg.cs instanceof jalview.schemes.UserColourScheme)\r
                 {\r
                     groups[i].setColour(SetUserColourScheme(sg.cs, userColours,\r
                             jms));\r
                 }\r
                 else\r
                 {\r
-                    groups[i].setColour(ColourSchemeProperty.getColourName(\r
-                            sg.cs));\r
+                  groups[i].setColour(ColourSchemeProperty.getColourName(\r
+                      sg.cs));\r
+                }\r
+\r
+                if (sg.cs instanceof ResidueColourScheme)\r
+                {\r
+                    groups[i].setPidThreshold(((ResidueColourScheme) sg.cs).getThreshold());\r
                 }\r
 \r
+\r
+\r
                 groups[i].setOutlineColour(sg.getOutlineColour().getRGB());\r
                 groups[i].setDisplayBoxes(sg.getDisplayBoxes());\r
                 groups[i].setDisplayText(sg.getDisplayText());\r
@@ -361,17 +367,16 @@ public class Jalview2XML
 \r
         if (cs instanceof ConservationColourScheme)\r
         {\r
-            view.setConsThreshold(((ConservationColourScheme) cs).inc);\r
+            ConservationColourScheme ccs = (ConservationColourScheme)cs;\r
+            view.setConsThreshold(ccs.inc);\r
+            if(ccs.cs instanceof jalview.schemes.UserColourScheme)\r
+              view.setBgColour(SetUserColourScheme(ccs.cs, userColours, jms));\r
         }\r
 \r
         if (cs instanceof ResidueColourScheme)\r
         {\r
             view.setPidThreshold(((ResidueColourScheme) cs).getThreshold());\r
         }\r
-        else if (cs instanceof ScoreColourScheme)\r
-        {\r
-            view.setPidThreshold(((ScoreColourScheme) cs).getThreshold());\r
-        }\r
 \r
         view.setConservationSelected(av.getConservationSelected());\r
         view.setPidSelected(av.getAbovePIDThreshold());\r
@@ -634,10 +639,6 @@ public class Jalview2XML
                     {\r
                         ((ResidueColourScheme) cs).setThreshold(groups[i].getPidThreshold(), true);\r
                     }\r
-                    else if (cs instanceof ScoreColourScheme)\r
-                    {\r
-                        ((ScoreColourScheme) cs).setThreshold(groups[i].getPidThreshold(), true);\r
-                    }\r
                 }\r
 \r
                 Vector seqs = new Vector();\r
@@ -734,10 +735,6 @@ public class Jalview2XML
             {\r
                 ((ResidueColourScheme) cs).setThreshold(view.getPidThreshold(), true);\r
             }\r
-            else if (cs instanceof ScoreColourScheme)\r
-            {\r
-                ((ScoreColourScheme) cs).setThreshold(view.getPidThreshold(), true);\r
-            }\r
 \r
             if(cs!=null)\r
               cs.setConsensus(af.viewport.vconsensus);\r