JAL-2438 unit test, fixes, Javadoc updates

[jalview.git] / src / jalview / renderer / seqfeatures / FeatureRenderer.java

diff --git a/src/jalview/renderer/seqfeatures/FeatureRenderer.java b/src/jalview/renderer/seqfeatures/FeatureRenderer.java
index 7915fd0..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
@@ -320,10 +317,7 @@ public class FeatureRenderer extends FeatureRendererModel
     Color drawnColour = null;
 
     /*
-     * iterate over features in ordering of their rendering;
-     * if drawing a range of columns, use render order to ensure last is on top
-     * if drawing a single column (as in findFeatureColour), with no 
-     * transparency, work backwards to find the topmost rendered feature colour
+     * iterate over features in ordering of their rendering (last is on top)
      */
     for (int renderIndex = 0; renderIndex < renderOrder.length; renderIndex++)
     {
@@ -343,15 +337,18 @@ public class FeatureRenderer extends FeatureRendererModel
           continue;
         }
 
+        /*
+         * a feature type may be flagged as shown but the group 
+         * an instance of it belongs to may be hidden
+         */
         if (featureGroupNotShown(sequenceFeature))
         {
           continue;
         }
 
         /*
-         * check feature overlaps the visible part of the alignment, 
-         * unless doing offscreenRender (to the Overview window or a 
-         * structure viewer) which is not limited 
+         * check feature overlaps the target range
+         * TODO: efficient retrieval of features overlapping a range
          */
         if (sequenceFeature.getBegin() > endPos
                 || sequenceFeature.getEnd() < startPos)