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

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

diff --git a/src/jalview/schemes/FeatureColour.java b/src/jalview/schemes/FeatureColour.java
index bdc70c9..dbe4901 100644 (file)
--- a/src/jalview/schemes/FeatureColour.java
+++ b/src/jalview/schemes/FeatureColour.java
@@ -1,7 +1,28 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.schemes;
 
 import jalview.api.FeatureColourI;
 import jalview.datamodel.SequenceFeature;
+import jalview.util.ColorUtils;
 import jalview.util.Format;
 
 import java.awt.Color;
@@ -101,7 +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: "
@@ -192,9 +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
@@ -286,6 +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;
@@ -336,9 +365,10 @@ public class FeatureColour implements FeatureColourI
     setAutoScaled(fc.isAutoScaled());
     setColourByLabel(fc.isColourByLabel());
   }
-  
+
   /**
    * Copy constructor with new min/max ranges
+   * 
    * @param fc
    * @param min
    * @param max
@@ -406,6 +436,7 @@ public class FeatureColour implements FeatureColourI
       setGraduatedColour(false);
     }
   }
+
   @Override
   public boolean isBelowThreshold()
   {
@@ -511,7 +542,7 @@ public class FeatureColour implements FeatureColourI
   {
     if (isColourByLabel())
     {
-      return UserColourScheme
+      return ColorUtils
               .createColourFromName(feature.getDescription());
     }
 
@@ -543,7 +574,8 @@ public class FeatureColour implements FeatureColourI
     {
       scl = 1f;
     }
-    return new Color(minRed + scl * deltaRed, minGreen + scl * deltaGreen, minBlue + scl * deltaBlue);
+    return new Color(minRed + scl * deltaRed, minGreen + scl * deltaGreen,
+            minBlue + scl * deltaBlue);
   }
 
   /**