JAL-2189 apply license

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

diff --git a/src/jalview/api/FeatureColourI.java b/src/jalview/api/FeatureColourI.java
index d8363f4..01eb7fa 100644 (file)
--- 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 +56,22 @@ public interface FeatureColourI
   Color getMaxColour();
 
   /**
-   * Answers true if the feature is coloured by label (description); only
-   * applicable when isGraduatedColour answers true
+   * Answers true if the feature has a single colour, i.e. if isColourByLabel()
+   * and isGraduatedColour() both answer false
+   * 
+   * @return
+   */
+  boolean isSimpleColour();
+
+  /**
+   * Answers true if the feature is coloured by label (description)
    * 
    * @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 +80,8 @@ 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
@@ -58,14 +90,20 @@ 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
+   * 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
    * 
@@ -73,10 +111,71 @@ public interface FeatureColourI
    */
   float getThreshold();
 
+  void setThreshold(float f);
+
+  /**
+   * 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
+   */
+  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
+   * 
+   * @param feature
+   * @return
+   */
+  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
+   * 
+   * @param min
+   * @param max
+   */
+  void updateBounds(float min, float max);
+
   /**
-   * Answers true if ?
+   * Returns the colour in Jalview features file format
    * 
    * @return
    */
-  boolean isLowToHigh();
+  String toJalviewFormat(String featureType);
 }