X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FFeatureColourI.java;h=44bc321c8a213b138ac9012a7b9584c151356f29;hb=74d5ca6390288f6cd6cb445cccc728802806a29a;hp=d8363f4aeafa6d661191dffed71b4ddc8955cddc;hpb=8b9c85b131fbaa1b9b29c489b661089c0ea404bd;p=jalview.git

diff --git a/src/jalview/api/FeatureColourI.java b/src/jalview/api/FeatureColourI.java
index d8363f4..44bc321 100644
--- a/src/jalview/api/FeatureColourI.java
+++ b/src/jalview/api/FeatureColourI.java
@@ -1,13 +1,34 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.api;
 
+import jalview.datamodel.SequenceFeature;
+
 import java.awt.Color;
 
 public interface FeatureColourI
 {
 
   /**
-   * Answers true when either isColourByLabel, isAboveThreshold or
-   * isBelowThreshold answers true
+   * Answers true when the feature colour varies across the score range
    * 
    * @return
    */
@@ -35,13 +56,31 @@ public interface FeatureColourI
   Color getMaxColour();
 
   /**
-   * Answers true if the feature is coloured by label (description); only
-   * applicable when isGraduatedColour answers true
+   * 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; else answers false
+   * 
+   * @return
+   */
+  boolean isSimpleColour();
+
+  /**
+   * Answers true if the feature is coloured by label (description) or by text
+   * value of an attribute
    * 
    * @return
    */
   boolean isColourByLabel();
 
+  void setColourByLabel(boolean b);
+
   /**
    * Answers true if the feature is coloured below a threshold value; only
    * applicable when isGraduatedColour answers true
@@ -50,6 +89,8 @@ public interface FeatureColourI
    */
   boolean isBelowThreshold();
 
+  void setBelowThreshold(boolean b);
+
   /**
    * Answers true if the feature is coloured above a threshold value; only
    * applicable when isGraduatedColour answers true
@@ -58,25 +99,117 @@ public interface FeatureColourI
    */
   boolean isAboveThreshold();
 
+  void setAboveThreshold(boolean b);
+
   /**
-   * Answers true if the threshold is the min (or max) of the colour range; only
-   * applicable when isGraduatedColour answers true
+   * Returns the threshold value (if any), else zero
    * 
    * @return
    */
-  boolean isThresholdMinMax();
+  float getThreshold();
+
+  void setThreshold(float f);
 
   /**
-   * Returns the threshold value (if any), else zero
+   * 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).
    * 
    * @return
    */
-  float getThreshold();
+  boolean isAutoScaled();
+
+  void setAutoScaled(boolean b);
+
+  /**
+   * Returns the maximum score of the graduated colour range
+   * 
+   * @return
+   */
+  float getMax();
+
+  /**
+   * Returns the minimum score of the graduated colour range
+   * 
+   * @return
+   */
+  float getMin();
+
+  /**
+   * Answers true if either isAboveThreshold or isBelowThreshold answers true
+   * 
+   * @return
+   */
+  boolean hasThreshold();
+
+  /**
+   * 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
+   */
+  Color getColor(SequenceFeature feature);
+
+  /**
+   * 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
+   */
+  void updateBounds(float min, float max);
 
   /**
-   * Answers true if ?
+   * Returns the colour in Jalview features file format
+   * 
+   * @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);
+
+  /**
+   * 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
+   */
+  boolean isOutwithThreshold(SequenceFeature sf);
+
+  /*
+   * Answers a human-readable text description of the colour, suitable for
+   * display as a tooltip, possibly internationalised for the user's locale.
    * 
    * @return
    */
-  boolean isLowToHigh();
+  String getDescription();
 }