X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FFeatureColourI.java;h=078027139a1d900157d0ce6452094121fe223ceb;hb=9e926ac4305fd9dff38b6e079e55b4f50664d544;hp=01eb7faa20f9d7ebf964fe353686b25698cac9a3;hpb=604cbee405a837565ba1a74aa9bddd62aed685ab;p=jalview.git

diff --git a/src/jalview/api/FeatureColourI.java b/src/jalview/api/FeatureColourI.java
index 01eb7fa..0780271 100644
--- a/src/jalview/api/FeatureColourI.java
+++ b/src/jalview/api/FeatureColourI.java
@@ -56,6 +56,14 @@ public interface FeatureColourI
   Color getMaxColour();
 
   /**
+   * Returns the 'no value' colour (used when a feature lacks score, or the
+   * attribute, being used for colouring)
+   * 
+   * @return
+   */
+  Color getNoColour();
+
+  /**
    * Answers true if the feature has a single colour, i.e. if isColourByLabel()
    * and isGraduatedColour() both answer false
    * 
@@ -93,18 +101,6 @@ public interface FeatureColourI
   void setAboveThreshold(boolean b);
 
   /**
-   * Answers true if the threshold is the minimum value (when
-   * isAboveThreshold()) or maximum value (when isBelowThreshold()) of the
-   * colour range; only applicable when isGraduatedColour and either
-   * isAboveThreshold() or isBelowThreshold() answers true
-   * 
-   * @return
-   */
-  boolean isThresholdMinMax();
-
-  void setThresholdMinMax(boolean b);
-
-  /**
    * Returns the threshold value (if any), else zero
    * 
    * @return
@@ -146,7 +142,9 @@ public interface FeatureColourI
   boolean hasThreshold();
 
   /**
-   * Returns the computed colour for the given sequence feature
+   * Returns the computed colour for the given sequence feature. Answers null if
+   * the score of this feature instance is outside the range to render (if any),
+   * i.e. lies below or above a configured threshold.
    * 
    * @param feature
    * @return
@@ -154,18 +152,10 @@ public interface FeatureColourI
   Color getColor(SequenceFeature feature);
 
   /**
-   * 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
-   */
-  boolean isColored(SequenceFeature feature);
-
-  /**
-   * Update the min-max range for a graduated colour scheme
+   * Update the min-max range for a graduated colour scheme. Note that the
+   * colour scheme may be configured to colour by feature score, or a
+   * (numeric-valued) attribute - the caller should ensure that the correct
+   * range is being set.
    * 
    * @param min
    * @param max
@@ -178,4 +168,27 @@ public interface FeatureColourI
    * @return
    */
   String toJalviewFormat(String featureType);
+
+  /**
+   * Answers true if colour is by attribute text or numerical value
+   * 
+   * @return
+   */
+  boolean isColourByAttribute();
+
+  /**
+   * Answers the name of the attribute (and optional sub-attribute...) used for
+   * colouring if any, or null
+   * 
+   * @return
+   */
+  String[] getAttributeName();
+
+  /**
+   * Sets the name of the attribute (and optional sub-attribute...) used for
+   * colouring if any, or null to remove this property
+   * 
+   * @return
+   */
+  void setAttributeName(String... name);
 }