X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FFeatureColour.java;h=c73e32bdfea0551c4c267a5e6fe6978e64f2f47b;hb=3c8a25936a2d805e7e3d7ab82f83b13135406d18;hp=55fdf243c9984a963d7ca4bc347a5a8185579dec;hpb=e42eed3a0089a8a064560df4cf17a5021fd1e16a;p=jalview.git

diff --git a/src/jalview/schemes/FeatureColour.java b/src/jalview/schemes/FeatureColour.java
index 55fdf24..c73e32b 100644
--- a/src/jalview/schemes/FeatureColour.java
+++ b/src/jalview/schemes/FeatureColour.java
@@ -321,8 +321,8 @@ public class FeatureColour implements FeatureColourI
       } catch (Exception e)
       {
         throw new IllegalArgumentException(
-                "Couldn't parse the minimum value for graduated colour ("
-                        + descriptor + ")");
+                "Couldn't parse the minimum value for graduated colour ('"
+                        + minval + "')");
       }
       try
       {
@@ -672,9 +672,12 @@ public class FeatureColour implements FeatureColourI
 
   /**
    * Returns the colour for the given instance of the feature. This may be a
-   * simple colour, a colour generated from the feature description (if
-   * isColourByLabel()), or a colour derived from the feature score (if
-   * isGraduatedColour()).
+   * simple colour, a colour generated from the feature description or other
+   * attribute (if isColourByLabel()), or a colour derived from the feature
+   * score or other attribute (if isGraduatedColour()).
+   * <p>
+   * Answers null if feature score (or attribute) value lies outside a
+   * configured threshold.
    * 
    * @param feature
    * @return
@@ -884,4 +887,32 @@ public class FeatureColour implements FeatureColourI
     attributeName = name;
   }
 
+  @Override
+  public boolean isOutwithThreshold(SequenceFeature feature)
+  {
+    if (!isGraduatedColour())
+    {
+      return false;
+    }
+    float scr = feature.getScore();
+    if (attributeName != null)
+    {
+      try
+      {
+        String attVal = feature.getValueAsString(attributeName);
+        scr = Float.valueOf(attVal);
+      } catch (Throwable e)
+      {
+        scr = Float.NaN;
+      }
+    }
+    if (Float.isNaN(scr))
+    {
+      return false;
+    }
+
+    return ((isAboveThreshold() && scr <= threshold)
+            || (isBelowThreshold() && scr >= threshold));
+  }
+
 }