Merge branch 'develop' into features/JAL-2094_colourInterface

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

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 7093a9a..e490c4e 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -70,6 +70,7 @@ import jalview.schemabinding.version2.Tree;
 import jalview.schemabinding.version2.UserColours;
 import jalview.schemabinding.version2.Viewport;
 import jalview.schemes.AnnotationColourGradient;
+import jalview.schemes.Colour;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
 import jalview.schemes.FeatureColour;
@@ -3365,8 +3366,8 @@ public class Jalview2XML
 
         sg.setOutlineColour(new java.awt.Color(jGroup.getOutlineColour()));
 
-        sg.textColour = new java.awt.Color(jGroup.getTextCol1());
-        sg.textColour2 = new java.awt.Color(jGroup.getTextCol2());
+        sg.textColour = new Colour(jGroup.getTextCol1());
+        sg.textColour2 = new Colour(jGroup.getTextCol2());
         sg.setShowNonconserved(jGroup.hasShowUnconserved() ? jGroup
                 .isShowUnconserved() : false);
         sg.thresholdTextColour = jGroup.getTextColThreshold();
@@ -4341,7 +4342,7 @@ public class Jalview2XML
     for (int i = 0; i < JSEQ.length; i++)
     {
       af.viewport.setSequenceColour(af.viewport.getAlignment()
-              .getSequenceAt(i), new java.awt.Color(JSEQ[i].getColour()));
+              .getSequenceAt(i), new Colour(JSEQ[i].getColour()));
     }
 
     if (al.hasSeqrep())
@@ -4433,8 +4434,8 @@ public class Jalview2XML
 
     af.viewport.setShowText(view.getShowText());
 
-    af.viewport.setTextColour(new java.awt.Color(view.getTextCol1()));
-    af.viewport.setTextColour2(new java.awt.Color(view.getTextCol2()));
+    af.viewport.setTextColour(new Colour(view.getTextCol1()));
+    af.viewport.setTextColour2(new Colour(view.getTextCol2()));
     af.viewport.setThresholdTextColour(view.getTextColThreshold());
     af.viewport.setShowUnconserved(view.hasShowUnconserved() ? view
             .isShowUnconserved() : false);
@@ -4562,10 +4563,11 @@ public class Jalview2XML
         if (setting.hasMincolour())
         {
           FeatureColourI gc = setting.hasMin() ? new FeatureColour(
-                  new Color(setting.getMincolour()), new Color(
-                          setting.getColour()), setting.getMin(),
-                  setting.getMax()) : new FeatureColour(new Color(
-                  setting.getMincolour()), new Color(setting.getColour()),
+                  new Colour(new Color(setting.getMincolour())),
+                  new Colour(new Color(setting.getColour())),
+                  setting.getMin(), setting.getMax()) : new FeatureColour(
+                  new Colour(new Color(setting.getMincolour())),
+                  new Colour(new Color(setting.getColour())),
                   0, 1);
           if (setting.hasThreshold())
           {
@@ -4596,7 +4598,7 @@ public class Jalview2XML
         else
         {
           featureColours.put(setting.getType(), new FeatureColour(
-                  new Color(setting.getColour())));
+                  new Colour(new Color(setting.getColour()))));
         }
         renderOrder[fs] = setting.getType();
         if (setting.hasOrder())