X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FFeatureColour.java;h=54d1c6cf76a45bff99cc020c18dc90e12ffe6c18;hb=6c118f968f6e8f726fdbb6ce6c24d870b22419bb;hp=23087a8a0e6954e61e18ad6f2b88d54fa094d36d;hpb=604cbee405a837565ba1a74aa9bddd62aed685ab;p=jalview.git

diff --git a/src/jalview/schemes/FeatureColour.java b/src/jalview/schemes/FeatureColour.java
index 23087a8..54d1c6c 100644
--- 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;
@@ -121,11 +122,11 @@ 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: "
-                + descriptor);
+        throw new IllegalArgumentException(
+                "Invalid colour descriptor: " + descriptor);
       }
       return new FeatureColour(colour);
     }
@@ -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
@@ -235,8 +236,8 @@ public class FeatureColour implements FeatureColourI
         {
           if (!ttype.toLowerCase().startsWith("no"))
           {
-            System.err.println("Ignoring unrecognised threshold type : "
-                    + ttype);
+            System.err.println(
+                    "Ignoring unrecognised threshold type : " + ttype);
           }
         }
       }
@@ -255,8 +256,8 @@ public class FeatureColour implements FeatureColourI
       }
       if (gcol.hasMoreTokens())
       {
-        System.err
-                .println("Ignoring additional tokens in parameters in graduated colour specification\n");
+        System.err.println(
+                "Ignoring additional tokens in parameters in graduated colour specification\n");
         while (gcol.hasMoreTokens())
         {
           System.err.println("|" + gcol.nextToken());
@@ -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;
@@ -533,8 +542,7 @@ public class FeatureColour implements FeatureColourI
   {
     if (isColourByLabel())
     {
-      return UserColourScheme
-              .createColourFromName(feature.getDescription());
+      return ColorUtils.createColourFromName(feature.getDescription());
     }
 
     if (!isGraduatedColour())
@@ -542,16 +550,27 @@ public class FeatureColour implements FeatureColourI
       return getColour();
     }
 
-    // todo should we check for above/below threshold here?
-    if (range == 0.0)
-    {
-      return getMaxColour();
-    }
+    /*
+     * graduated colour case, optionally with threshold
+     * Float.NaN is assigned minimum visible score colour
+     */
     float scr = feature.getScore();
     if (Float.isNaN(scr))
     {
       return getMinColour();
     }
+    if (isAboveThreshold() && scr <= threshold)
+    {
+      return null;
+    }
+    if (isBelowThreshold() && scr >= threshold)
+    {
+      return null;
+    }
+    if (range == 0.0)
+    {
+      return getMaxColour();
+    }
     float scl = (scr - base) / range;
     if (isHighToLow)
     {
@@ -593,44 +612,6 @@ public class FeatureColour implements FeatureColourI
     return (isHighToLow) ? (base + range) : base;
   }
 
-  /**
-   * Answers true if the feature has a simple colour, or is coloured by label,
-   * or has a graduated colour and the score of this feature instance is within
-   * the range to render (if any), i.e. does not lie below or above any
-   * threshold set.
-   * 
-   * @param feature
-   * @return
-   */
-  @Override
-  public boolean isColored(SequenceFeature feature)
-  {
-    if (isColourByLabel() || !isGraduatedColour())
-    {
-      return true;
-    }
-
-    float val = feature.getScore();
-    if (Float.isNaN(val))
-    {
-      return true;
-    }
-    if (Float.isNaN(this.threshold))
-    {
-      return true;
-    }
-
-    if (isAboveThreshold() && val <= threshold)
-    {
-      return false;
-    }
-    if (isBelowThreshold() && val >= threshold)
-    {
-      return false;
-    }
-    return true;
-  }
-
   @Override
   public boolean isSimpleColour()
   {