X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FFeatureColourI.java;h=98a37c4e93698cc7a846aae059506256ae98869d;hb=e086b0c30bee5fe084186c65ef1ded42c58560f9;hp=3b2313d2c468e16f5aa994b6aacfc2eda2b6989e;hpb=50ebdf8f3a7fdce1421a6af7a0afd317c347372c;p=jalview.git

diff --git a/src/jalview/api/FeatureColourI.java b/src/jalview/api/FeatureColourI.java
index 3b2313d..98a37c4 100644
--- a/src/jalview/api/FeatureColourI.java
+++ b/src/jalview/api/FeatureColourI.java
@@ -21,7 +21,6 @@
 package jalview.api;
 
 import jalview.datamodel.SequenceFeature;
-import jalview.util.matcher.KeyedMatcherSetI;
 
 import java.awt.Color;
 
@@ -57,6 +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
    * 
@@ -65,7 +72,8 @@ public interface FeatureColourI
   boolean isSimpleColour();
 
   /**
-   * Answers true if the feature is coloured by label (description)
+   * Answers true if the feature is coloured by label (description) or by text
+   * value of an attribute
    * 
    * @return
    */
@@ -94,18 +102,6 @@ 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
@@ -157,7 +153,10 @@ public interface FeatureColourI
   Color getColor(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
@@ -172,18 +171,45 @@ public interface FeatureColourI
   String toJalviewFormat(String featureType);
 
   /**
-   * Sets the attribute filter conditions, or removes them if the argument is
-   * null
+   * Answers true if colour is by attribute text or numerical value
    * 
-   * @param filter
+   * @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);
+
+  /**
+   * Answers true if colour has a threshold set, and the feature score (or other
+   * attribute selected for colouring) is outwith the threshold.
+   * <p>
+   * Answers false if not a graduated colour, or no threshold is set, or value
+   * is not outwith the threshold, or value is null or non-numeric.
+   * 
+   * @param sf
+   * @return
    */
-  public void setAttributeFilters(KeyedMatcherSetI filter);
+  boolean isOutwithThreshold(SequenceFeature sf);
 
   /**
-   * Answers the attribute value filters for the colour scheme, or null if no
-   * filters are set
+   * Answers a human-readable text description of the colour, suitable for display
+   * as a tooltip, possibly internationalised for the user's locale.
    * 
    * @return
    */
-  public KeyedMatcherSetI getAttributeFilters();
+  String getDescription();
 }