From: Jim Procter <jprocter@issues.jalview.org>
Date: Tue, 9 Oct 2018 12:23:25 +0000 (+0100)
Subject: JAL-3127 TODO - resolve reference to Viewport for group colour schemes instantiated... 
X-Git-Tag: Release_2_11_0~17^2~46^2~18
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=1071f76c49d1e3278948651638b18e11298e6766;p=jalview.git

JAL-3127 TODO - resolve reference to Viewport for group colour schemes instantiated before the viewport has been created.
---

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 0c31a2a..133c186 100644
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -52,7 +52,6 @@ import jalview.schemabinding.version2.Annotation;
 import jalview.schemabinding.version2.AnnotationColours;
 import jalview.schemabinding.version2.AnnotationElement;
 import jalview.schemabinding.version2.CalcIdParam;
-import jalview.schemabinding.version2.Colour;
 import jalview.schemabinding.version2.CompoundMatcher;
 import jalview.schemabinding.version2.DBRef;
 import jalview.schemabinding.version2.Features;
@@ -3424,7 +3423,8 @@ public class Jalview2XML
           }
           else
           {
-            cs = ColourSchemeProperty.getColourScheme(al,
+            // TODO: notify of view reference when available
+            cs = ColourSchemeProperty.getColourScheme(null, al,
                     jGroup.getColour());
           }
         }
diff --git a/src/jalview/gui/Jalview2XML_V1.java b/src/jalview/gui/Jalview2XML_V1.java
index eb494e3..aef69e7 100755
--- a/src/jalview/gui/Jalview2XML_V1.java
+++ b/src/jalview/gui/Jalview2XML_V1.java
@@ -335,7 +335,8 @@ public class Jalview2XML_V1
           }
           else
           {
-            cs = ColourSchemeProperty.getColourScheme(al,
+            // TODO: update colourscheme with view reference
+            cs = ColourSchemeProperty.getColourScheme(null, al,
                     groups[i].getColour());
           }
         }
diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index e578a45..dd385d2 100755
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -1617,8 +1617,10 @@ public class AnnotationFile
         }
         else if (key.equalsIgnoreCase("colour"))
         {
+          // TODO need to notify colourscheme of view reference once it is
+          // available
           sg.cs.setColourScheme(
-                  ColourSchemeProperty.getColourScheme(al, value));
+                  ColourSchemeProperty.getColourScheme(null, al, value));
         }
         else if (key.equalsIgnoreCase("pidThreshold"))
         {