Conservation colour scheme is no more

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

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 5d94c3c..a8fb28d 100755 (executable)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -295,31 +295,35 @@ public class Jalview2XML
                 groups[i].setEnd(sg.getEndRes());\r
                 groups[i].setName(sg.getName());\r
 \r
-                if (sg.cs instanceof ConservationColourScheme)\r
+                if (sg.cs.conservationApplied())\r
                 {\r
-                    groups[i].setConsThreshold(((ConservationColourScheme) sg.cs).inc);\r
-                }\r
+                  groups[i].setConsThreshold(sg.cs.getConservationInc());\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
+                  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(sg.cs));\r
+                  }\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
+\r
+                groups[i].setPidThreshold( sg.cs.getThreshold() );\r
+\r
                 groups[i].setOutlineColour(sg.getOutlineColour().getRGB());\r
                 groups[i].setDisplayBoxes(sg.getDisplayBoxes());\r
                 groups[i].setDisplayText(sg.getDisplayText());\r
@@ -359,18 +363,16 @@ public class Jalview2XML
 \r
         ColourSchemeI cs = av.getGlobalColourScheme();\r
 \r
-        if (cs instanceof ConservationColourScheme)\r
+        if (cs.conservationApplied())\r
         {\r
-            view.setConsThreshold(((ConservationColourScheme) cs).inc);\r
+            view.setConsThreshold(cs.getConservationInc());\r
+            if(cs instanceof jalview.schemes.UserColourScheme)\r
+              view.setBgColour(SetUserColourScheme(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
+            view.setPidThreshold( cs.getThreshold() );\r
         }\r
 \r
         view.setConservationSelected(av.getConservationSelected());\r
@@ -630,14 +632,7 @@ public class Jalview2XML
                                 groups[i].getColour());\r
                     }\r
 \r
-                    if (cs instanceof ResidueColourScheme)\r
-                    {\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
+                    cs.setThreshold(groups[i].getPidThreshold(), true);\r
                 }\r
 \r
                 Vector seqs = new Vector();\r
@@ -664,8 +659,7 @@ public class Jalview2XML
                             sg.getWidth() - 1);\r
                     c.calculate();\r
                     c.verdict(false, 25);\r
-                    cs = new ConservationColourScheme(c, cs);\r
-                    sg.cs = cs;\r
+                    sg.cs.setConservation(c);\r
                 }\r
 \r
                 al.addGroup(sg);\r
@@ -730,14 +724,7 @@ public class Jalview2XML
                 cs = ColourSchemeProperty.getColour(al, view.getBgColour());\r
             }\r
 \r
-            if (cs instanceof ResidueColourScheme)\r
-            {\r
-                ((ResidueColourScheme) cs).setThreshold(view.getPidThreshold(), true);\r
-            }\r
-            else if (cs instanceof ScoreColourScheme)\r
-            {\r
-                ((ScoreColourScheme) cs).setThreshold(view.getPidThreshold(), true);\r
-            }\r
+           cs.setThreshold(view.getPidThreshold(), true);\r
 \r
             if(cs!=null)\r
               cs.setConsensus(af.viewport.vconsensus);\r
@@ -749,7 +736,7 @@ public class Jalview2XML
         af.changeColour(af.viewport.getGlobalColourScheme());\r
         if (view.getConservationSelected())\r
         {\r
-          ( (ConservationColourScheme) af.viewport.getGlobalColourScheme()).inc = view.getConsThreshold();\r
+          af.viewport.getGlobalColourScheme().setConservationInc(view.getConsThreshold());\r
         }\r
 \r
         af.viewport.setColourAppliesToAllGroups(true);\r