Merge branch 'develop' into bug/JAL-2255_seq-fetcher-broken-on-linux

[jalview.git] / src / jalview / schemes / FeatureColour.java

diff --git a/src/jalview/schemes/FeatureColour.java b/src/jalview/schemes/FeatureColour.java
index 23087a8..dbe4901 100644 (file)
--- a/src/jalview/schemes/FeatureColour.java
+++ b/src/jalview/schemes/FeatureColour.java
@@ -22,6 +22,7 @@ package jalview.schemes;
 
 import jalview.api.FeatureColourI;
 import jalview.datamodel.SequenceFeature;
+import jalview.util.ColorUtils;
 import jalview.util.Format;
 
 import java.awt.Color;
@@ -121,7 +122,7 @@ public class FeatureColour implements FeatureColourI
       /*
        * only a simple colour specification - parse it
        */
-      Color colour = UserColourScheme.getColourFromString(descriptor);
+      Color colour = ColorUtils.parseColourString(descriptor);
       if (colour == null)
       {
         throw new IllegalArgumentException("Invalid colour descriptor: "
@@ -212,9 +213,9 @@ public class FeatureColour implements FeatureColourI
     FeatureColour featureColour;
     try
     {
-      featureColour = new FeatureColour(
-              new UserColourScheme(mincol).findColour('A'),
-              new UserColourScheme(maxcol).findColour('A'), min, max);
+      Color minColour = ColorUtils.parseColourString(mincol);
+      Color maxColour = ColorUtils.parseColourString(maxcol);
+      featureColour = new FeatureColour(minColour, maxColour, min, max);
       featureColour.setColourByLabel(labelColour);
       featureColour.setAutoScaled(autoScaled);
       // add in any additional parameters
@@ -306,6 +307,14 @@ public class FeatureColour implements FeatureColourI
    */
   public FeatureColour(Color low, Color high, float min, float max)
   {
+    if (low == null)
+    {
+      low = Color.white;
+    }
+    if (high == null)
+    {
+      high = Color.black;
+    }
     graduatedColour = true;
     colour = null;
     minColour = low;
@@ -533,7 +542,7 @@ public class FeatureColour implements FeatureColourI
   {
     if (isColourByLabel())
     {
-      return UserColourScheme
+      return ColorUtils
               .createColourFromName(feature.getDescription());
     }