X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=a8fb28dfe4c1e567eb5a946dbddfedb16a328e9b;hb=95a46891288f4fc63d690cab4f56879678f54fb6;hp=a449d7f0e15136e9ba17199bdce34f6a5b073d8e;hpb=f7bcceb4efd723c25d5169fd2fa139b3610eb84e;p=jalview.git

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index a449d7f..a8fb28d 100755
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -295,17 +295,19 @@ public class Jalview2XML
                 groups[i].setEnd(sg.getEndRes());
                 groups[i].setName(sg.getName());
 
-                if (sg.cs instanceof ConservationColourScheme)
+                if (sg.cs.conservationApplied())
                 {
-                  ConservationColourScheme ccs = (ConservationColourScheme) sg.cs;
-                  groups[i].setConsThreshold(ccs.inc);
+                  groups[i].setConsThreshold(sg.cs.getConservationInc());
 
-                  if (ccs.cs instanceof jalview.schemes.UserColourScheme)
+                  if (sg.cs instanceof jalview.schemes.UserColourScheme)
                   {
-                    groups[i].setColour(SetUserColourScheme(ccs.cs, userColours,
+                    groups[i].setColour(SetUserColourScheme(sg.cs, userColours,
                                                             jms));
                   }
-
+                  else
+                  {
+                    groups[i].setColour(ColourSchemeProperty.getColourName(sg.cs));
+                  }
                 }
 
                else if (sg.cs instanceof jalview.schemes.UserColourScheme)
@@ -319,12 +321,8 @@ public class Jalview2XML
                       sg.cs));
                 }
 
-                if (sg.cs instanceof ResidueColourScheme)
-                {
-                    groups[i].setPidThreshold(((ResidueColourScheme) sg.cs).getThreshold());
-                }
-
 
+                groups[i].setPidThreshold( sg.cs.getThreshold() );
 
                 groups[i].setOutlineColour(sg.getOutlineColour().getRGB());
                 groups[i].setDisplayBoxes(sg.getDisplayBoxes());
@@ -365,17 +363,16 @@ public class Jalview2XML
 
         ColourSchemeI cs = av.getGlobalColourScheme();
 
-        if (cs instanceof ConservationColourScheme)
+        if (cs.conservationApplied())
         {
-            ConservationColourScheme ccs = (ConservationColourScheme)cs;
-            view.setConsThreshold(ccs.inc);
-            if(ccs.cs instanceof jalview.schemes.UserColourScheme)
-              view.setBgColour(SetUserColourScheme(ccs.cs, userColours, jms));
+            view.setConsThreshold(cs.getConservationInc());
+            if(cs instanceof jalview.schemes.UserColourScheme)
+              view.setBgColour(SetUserColourScheme(cs, userColours, jms));
         }
 
         if (cs instanceof ResidueColourScheme)
         {
-            view.setPidThreshold(((ResidueColourScheme) cs).getThreshold());
+            view.setPidThreshold( cs.getThreshold() );
         }
 
         view.setConservationSelected(av.getConservationSelected());
@@ -635,10 +632,7 @@ public class Jalview2XML
                                 groups[i].getColour());
                     }
 
-                    if (cs instanceof ResidueColourScheme)
-                    {
-                        ((ResidueColourScheme) cs).setThreshold(groups[i].getPidThreshold(), true);
-                    }
+                    cs.setThreshold(groups[i].getPidThreshold(), true);
                 }
 
                 Vector seqs = new Vector();
@@ -665,8 +659,7 @@ public class Jalview2XML
                             sg.getWidth() - 1);
                     c.calculate();
                     c.verdict(false, 25);
-                    cs = new ConservationColourScheme(c, cs);
-                    sg.cs = cs;
+                    sg.cs.setConservation(c);
                 }
 
                 al.addGroup(sg);
@@ -731,10 +724,7 @@ public class Jalview2XML
                 cs = ColourSchemeProperty.getColour(al, view.getBgColour());
             }
 
-            if (cs instanceof ResidueColourScheme)
-            {
-                ((ResidueColourScheme) cs).setThreshold(view.getPidThreshold(), true);
-            }
+           cs.setThreshold(view.getPidThreshold(), true);
 
             if(cs!=null)
               cs.setConsensus(af.viewport.vconsensus);
@@ -746,7 +736,7 @@ public class Jalview2XML
         af.changeColour(af.viewport.getGlobalColourScheme());
         if (view.getConservationSelected())
         {
-          ( (ConservationColourScheme) af.viewport.getGlobalColourScheme()).inc = view.getConsThreshold();
+          af.viewport.getGlobalColourScheme().setConservationInc(view.getConsThreshold());
         }
 
         af.viewport.setColourAppliesToAllGroups(true);