Merge branch 'develop' into features/JAL-2094_colourInterface

[jalview.git] / src / jalview / api / FeatureColourI.java

diff --git a/src/jalview/api/FeatureColourI.java b/src/jalview/api/FeatureColourI.java
index 1fcbfd0..922a038 100644 (file)
--- a/src/jalview/api/FeatureColourI.java
+++ b/src/jalview/api/FeatureColourI.java
@@ -2,8 +2,6 @@ package jalview.api;
 
 import jalview.datamodel.SequenceFeature;
 
-import java.awt.Color;
-
 public interface FeatureColourI
 {
 
@@ -19,21 +17,21 @@ public interface FeatureColourI
    * 
    * @return
    */
-  Color getColour();
+  ColorI getColour();
 
   /**
    * Returns the minimum colour (when isGraduatedColour answers true)
    * 
    * @return
    */
-  Color getMinColour();
+  ColorI getMinColour();
 
   /**
    * Returns the maximum colour (when isGraduatedColour answers true)
    * 
    * @return
    */
-  Color getMaxColour();
+  ColorI getMaxColour();
 
   /**
    * Answers true if the feature has a single colour, i.e. if isColourByLabel()
@@ -94,6 +92,13 @@ public interface FeatureColourI
   void setThreshold(float f);
 
   /**
+   * Answers true if either isAboveThreshold or isBelowThreshold answers true
+   * 
+   * @return
+   */
+  boolean hasThreshold();
+
+  /**
    * Answers true if the colour varies between the actual minimum and maximum
    * score values of the feature, or false if between absolute minimum and
    * maximum values (or if not a graduated colour).
@@ -105,57 +110,50 @@ public interface FeatureColourI
   void setAutoScaled(boolean b);
 
   /**
-   * Returns the maximum score of the graduated colour range
+   * 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
    */
-  float getMax();
+  boolean isColored(SequenceFeature feature);
 
   /**
-   * Returns the minimum score of the graduated colour range
+   * Update the min-max range for a graduated colour scheme
    * 
-   * @return
+   * @param min
+   * @param max
    */
-  float getMin();
+  void updateBounds(float min, float max);
 
   /**
-   * Answers true if either isAboveThreshold or isBelowThreshold answers true
+   * Returns the colour in Jalview features file format
    * 
    * @return
    */
-  boolean hasThreshold();
+  String toJalviewFormat(String featureType);
 
   /**
-   * Returns the computed colour for the given sequence feature
+   * Returns the maximum score of the graduated colour range
    * 
-   * @param feature
    * @return
    */
-  Color getColor(SequenceFeature feature);
+  float getMax();
 
   /**
-   * 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.
+   * Returns the minimum score of the graduated colour range
    * 
-   * @param feature
    * @return
    */
-  boolean isColored(SequenceFeature feature);
-
-  /**
-   * Update the min-max range for a graduated colour scheme
-   * 
-   * @param min
-   * @param max
-   */
-  void updateBounds(float min, float max);
+  float getMin();
 
   /**
-   * Returns the colour in Jalview features file format
+   * Returns the computed colour for the given sequence feature
    * 
+   * @param feature
    * @return
    */
-  String toJalviewFormat(String featureType);
+  ColorI getColor(SequenceFeature feature);
 }