Merge branch 'develop' into features/JAL-2360colourSchemeApplicability

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

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index d8537bb..7057c2a 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -1186,7 +1186,7 @@ public class Jalview2XML
             }
             else
             {
-              jGroup.setColour(ColourSchemeProperty.getColourName(sg.cs));
+              jGroup.setColour(sg.cs.getSchemeName());
             }
           }
           else if (sg.cs instanceof jalview.schemes.AnnotationColourGradient)
@@ -1202,7 +1202,7 @@ public class Jalview2XML
           }
           else
           {
-            jGroup.setColour(ColourSchemeProperty.getColourName(sg.cs));
+            jGroup.setColour(sg.cs.getSchemeName());
           }
 
           jGroup.setPidThreshold(sg.cs.getThreshold());
@@ -1723,8 +1723,7 @@ public class Jalview2XML
     }
     else
     {
-      ac.setColourScheme(ColourSchemeProperty.getColourName(acg
-              .getBaseColour()));
+      ac.setColourScheme(ColourSchemeProperty.getColourName(acg.getBaseColour()));
     }
 
     ac.setMaxColour(acg.getMaxColour().getRGB());
@@ -3345,7 +3344,7 @@ public class Jalview2XML
           }
           else
           {
-            cs = ColourSchemeProperty.getColour(al, jGroup.getColour());
+            cs = ColourSchemeProperty.getColourScheme(al, jGroup.getColour());
           }
 
           if (cs != null)
@@ -4471,7 +4470,7 @@ public class Jalview2XML
       }
       else
       {
-        cs = ColourSchemeProperty.getColour(al, view.getBgColour());
+        cs = ColourSchemeProperty.getColourScheme(al, view.getBgColour());
       }
 
       if (cs != null)
@@ -4730,7 +4729,8 @@ public class Jalview2XML
                     );
           }
 
-          if (viewAnnColour.getColourScheme().equals("None"))
+          if (viewAnnColour.getColourScheme().equals(
+                  ResidueColourScheme.NONE))
           {
             cs = new AnnotationColourGradient(
                     annAlignment.getAlignmentAnnotation()[i],
@@ -4750,7 +4750,7 @@ public class Jalview2XML
           {
             cs = new AnnotationColourGradient(
                     annAlignment.getAlignmentAnnotation()[i],
-                    ColourSchemeProperty.getColour(al,
+                    ColourSchemeProperty.getColourScheme(al,
                             viewAnnColour.getColourScheme()),
                     viewAnnColour.getAboveThreshold());
           }
@@ -4778,7 +4778,7 @@ public class Jalview2XML
               }
 
               /*
-               * if (viewAnnColour.getColourScheme().equals("None" )) { sg.cs =
+               * if (viewAnnColour.getColourScheme().equals(ResidueColourScheme.NONE)) { sg.cs =
                * new AnnotationColourGradient(
                * annAlignment.getAlignmentAnnotation()[i], new
                * java.awt.Color(viewAnnColour. getMinColour()), new