From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 17 Aug 2005 09:08:50 +0000 (+0000)
Subject: No score colour scheme, group colours saved if conservation applied
X-Git-Tag: Release_2_03~34
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=f7bcceb4efd723c25d5169fd2fa139b3610eb84e;hp=d65fda1b7cee986dadd46083e25bdd274f3055df;p=jalview.git

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