JAL-2438 unit test, fixes, Javadoc updates

diff --git a/src/jalview/api/FeatureRenderer.java b/src/jalview/api/FeatureRenderer.java
index 3565488..839119d 100644 (file)
--- a/src/jalview/api/FeatureRenderer.java
+++ b/src/jalview/api/FeatureRenderer.java
@@ -38,17 +38,24 @@ public interface FeatureRenderer
 {
 
   /**
-   * compute the perceived colour for a given column position in sequenceI,
-   * taking transparency and feature visibility into account.
+   * Returns the combined feature colour for a given sequence and column
+   * position, taking into account feature colour schemes, ordering, feature and
+   * feature group visibility, and transparency. Returns null if there is no
+   * visible feature at the position.
+   * <p>
+   * The Graphics argument is optional and may be null if no transparency is
+   * applied. With feature transparency, visible features are written to the
+   * graphics context and the composite colour can be read off.
+   * <p>
+   * This is provided for use by Structure Viewers and the Overview Window to
+   * get the feature colour of the rendered sequence.
    * 
-   * @param sequenceI
-   *          - sequence providing features
-   * @param r
-   *          - column position
+   * @param sequence
+   * @param column
    * @param g
    * @return
    */
-  Color findFeatureColour(SequenceI sequenceI, int r, Graphics g);
+  Color findFeatureColour(SequenceI sequence, int column, Graphics g);
 
   /**
    * trigger the feature discovery process for a newly created feature renderer.

diff --git a/src/jalview/renderer/seqfeatures/FeatureColourFinder.java b/src/jalview/renderer/seqfeatures/FeatureColourFinder.java
index 761f418..9a1ecf9 100644 (file)
--- a/src/jalview/renderer/seqfeatures/FeatureColourFinder.java
+++ b/src/jalview/renderer/seqfeatures/FeatureColourFinder.java
@@ -67,10 +67,20 @@ public class FeatureColourFinder
       return defaultColour; // nothing to see here folks
     }
 
-    Graphics g = featureRenderer.getTransparency() == 1f ? null
-            : offscreenImage.getGraphics();
+    Graphics g = null;
+
+    /*
+     * if transparency applies, get colours drawn to a 1x1 pixel
+     * graphics context that has been primed with the default colour
+     */
+    if (featureRenderer.getTransparency() != 1f)
+    {
+      g = offscreenImage.getGraphics();
+      offscreenImage.setRGB(0, 0, defaultColour.getRGB());
+    }
 
     Color c = featureRenderer.findFeatureColour(seq, column, g);
+
     if (c != null && g != null)
     {
       c = new Color(offscreenImage.getRGB(0, 0));

diff --git a/src/jalview/renderer/seqfeatures/FeatureRenderer.java b/src/jalview/renderer/seqfeatures/FeatureRenderer.java
index f826a88..49b98a5 100644 (file)
--- a/src/jalview/renderer/seqfeatures/FeatureRenderer.java
+++ b/src/jalview/renderer/seqfeatures/FeatureRenderer.java
@@ -210,12 +210,7 @@ public class FeatureRenderer extends FeatureRendererModel
   }
 
   /**
-   * This is used by Structure Viewers and the Overview Window to get the
-   * feature colour of the rendered sequence
-   * 
-   * @param seq
-   * @param column
-   * @return
+   * {@inheritDoc}
    */
   @Override
   public Color findFeatureColour(SequenceI seq, int column, Graphics g)
@@ -271,15 +266,17 @@ public class FeatureRenderer extends FeatureRendererModel
 
   /**
    * Draws the sequence features on the graphics context, or just determines the
-   * colour that would be drawn (if flag offscreenrender is true).
+   * colour that would be drawn (if flag colourOnly is true). Returns the last
+   * colour drawn (which may not be the effective colour if transparency
+   * applies), or null if no feature is drawn in the range given.
    * 
    * @param g
    *          the graphics context to draw on (may be null if colourOnly==true)
    * @param seq
    * @param start
-   *          start column (or sequence position in offscreenrender mode)
+   *          start column
    * @param end
-   *          end column (not used in offscreenrender mode)
+   *          end column
    * @param y1
    *          vertical offset at which to draw on the graphics
    * @param colourOnly

diff --git a/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java b/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java
index 6074e85..127b6c2 100644 (file)
--- a/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java
+++ b/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java
@@ -327,10 +327,12 @@ public class FeatureColourFinderTest
     /*
      * the FeatureSettings transparency slider has range 0-70 which
      * corresponds to a transparency value of 1 - 0.3
+     * A value of 0.4 gives a combination of
+     * 0.4 * red(255, 0, 0) + 0.6 * cyan(0, 255, 255) = (102, 153, 153)
      */
-    fr.setTransparency(0.5f);
-    Color c = finder.findFeatureColour(Color.blue, seq, 10);
-    assertEquals(c, new Color(85, 170, 0));
+    fr.setTransparency(0.4f);
+    Color c = finder.findFeatureColour(Color.cyan, seq, 10);
+    assertEquals(c, new Color(102, 153, 153));
   }
 
   @Test(groups = "Functional")
@@ -349,30 +351,37 @@ public class FeatureColourFinderTest
     av.setShowSequenceFeatures(true);
   
     /*
-     * Domain (green(0, 255, 0)) rendered above Metal (red(255, 0, 0))
+     * Domain (green) rendered above Metal (red) above background (cyan)
+     * 1) 0.6 * red(255, 0, 0) + 0.4 * cyan(0, 255, 255) = (153, 102, 102)
+     * 2) 0.6* green(0, 255, 0) + 0.4 * (153, 102, 102) = (61, 194, 41) rounded
      */
-    fr.setTransparency(0.5f);
-    Color c = finder.findFeatureColour(Color.blue, seq, 10);
-    assertEquals(c, new Color(85, 170, 0));
+    fr.setTransparency(0.6f);
+    Color c = finder.findFeatureColour(Color.cyan, seq, 10);
+    assertEquals(c, new Color(61, 194, 41));
   
     /*
      * now promote Metal above Domain
      * - currently no way other than mimicking reordering of
      * table in Feature Settings
+     * Metal (red) rendered above Domain (green) above background (cyan)
+     * 1) 0.6 * green(0, 255, 0) + 0.4 * cyan(0, 255, 255) = (0, 255, 102)
+     * 2) 0.6* red(255, 0, 0) + 0.4 * (0, 255, 102) = (153, 102, 41) rounded
      */
     Object[][] data = new Object[2][];
     data[0] = new Object[] { "Metal", red, true };
     data[1] = new Object[] { "Domain", green, true };
     fr.setFeaturePriority(data);
-    c = finder.findFeatureColour(Color.blue, seq, 10);
-    assertEquals(c, new Color(153, 102, 0));
+    c = finder.findFeatureColour(Color.cyan, seq, 10);
+    assertEquals(c, new Color(153, 102, 41));
   
     /*
      * ..and turn off display of Metal
+     * Domain (green) above background (pink)
+     * 0.6 * green(0, 255, 0) + 0.4 * pink(255, 175, 175) = (102, 223, 70)
      */
     data[0][2] = false;
     fr.setFeaturePriority(data);
-    c = finder.findFeatureColour(Color.blue, seq, 10);
-    assertEquals(c, Color.green);
+    c = finder.findFeatureColour(Color.pink, seq, 10);
+    assertEquals(c, new Color(102, 223, 70));
   }
 }