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[jalview.git] / src / jalview / gui / Jalview2XML.java

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 70608c4..69ba482 100755 (executable)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -297,29 +297,38 @@ public class Jalview2XML
 \r
                 if (sg.cs instanceof ConservationColourScheme)\r
                 {\r
-                    groups[i].setConsThreshold(((ConservationColourScheme) sg.cs).inc);\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
+                  else\r
+                  {\r
+                    groups[i].setColour(ColourSchemeProperty.getColourName(sg.cs));\r
+                  }\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 +370,16 @@ 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
@@ -523,6 +531,7 @@ public class Jalview2XML
         }\r
         catch (Exception ex)\r
         {\r
+          ex.printStackTrace();\r
             System.err.println("Exception whilst loading jalview XML file : " +\r
                 ex + "\n");\r
              JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
@@ -631,11 +640,7 @@ public class Jalview2XML
 \r
                     if (cs instanceof ResidueColourScheme)\r
                     {\r
-                        ((ResidueColourScheme) cs).setThreshold(groups[i].getPidThreshold());\r
-                    }\r
-                    else if (cs instanceof ScoreColourScheme)\r
-                    {\r
-                        ((ScoreColourScheme) cs).setThreshold(groups[i].getPidThreshold());\r
+                        ((ResidueColourScheme) cs).setThreshold(groups[i].getPidThreshold(), true);\r
                     }\r
                 }\r
 \r
@@ -729,25 +734,24 @@ public class Jalview2XML
                 cs = ColourSchemeProperty.getColour(al, view.getBgColour());\r
             }\r
 \r
-            if (cs instanceof ConservationColourScheme)\r
-            {\r
-                ((ConservationColourScheme) cs).inc = view.getConsThreshold();\r
-            }\r
-\r
             if (cs instanceof ResidueColourScheme)\r
             {\r
-                ((ResidueColourScheme) cs).setThreshold(view.getPidThreshold());\r
-            }\r
-            else if (cs instanceof ScoreColourScheme)\r
-            {\r
-                ((ScoreColourScheme) cs).setThreshold(view.getPidThreshold());\r
+                ((ResidueColourScheme) cs).setThreshold(view.getPidThreshold(), true);\r
             }\r
+\r
+            if(cs!=null)\r
+              cs.setConsensus(af.viewport.vconsensus);\r
         }\r
 \r
+        af.setColourSelected(view.getBgColour());\r
         af.viewport.setGlobalColourScheme(cs);\r
-\r
         af.viewport.setColourAppliesToAllGroups(false);\r
         af.changeColour(af.viewport.getGlobalColourScheme());\r
+        if (view.getConservationSelected())\r
+        {\r
+          ( (ConservationColourScheme) af.viewport.getGlobalColourScheme()).inc = view.getConsThreshold();\r
+        }\r
+\r
         af.viewport.setColourAppliesToAllGroups(true);\r
 \r
         if (view.getShowSequenceFeatures())\r