From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Tue, 14 Mar 2017 09:42:40 +0000 (+0000)
Subject: JAL-2438 comment/Javadoc tidies
X-Git-Tag: Release_2_10_2~3^2~164
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=17bea66b37be69a173f6b1ea73c8544bd4c6e2b1;p=jalview.git

JAL-2438 comment/Javadoc tidies
---

diff --git a/src/jalview/renderer/seqfeatures/FeatureRenderer.java b/src/jalview/renderer/seqfeatures/FeatureRenderer.java
index 7915fd0..f826a88 100644
--- a/src/jalview/renderer/seqfeatures/FeatureRenderer.java
+++ b/src/jalview/renderer/seqfeatures/FeatureRenderer.java
@@ -320,10 +320,7 @@ 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 +340,18 @@ 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)
diff --git a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
index 085743f..100b58f 100644
--- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
+++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
@@ -550,11 +550,12 @@ public abstract class FeatureRendererModel implements
   }
 
   /**
-   * calculate the render colour for a specific feature using current feature
-   * settings.
+   * Returns the configured colour for a specific feature using current feature
+   * settings. This does not include any consideration of feature visibility,
+   * colour transparency, graduated colour shading etc.
    * 
    * @param feature
-   * @return render colour for the given feature
+   * @return
    */
   public Color getColour(SequenceFeature feature)
   {
@@ -586,11 +587,13 @@ public abstract class FeatureRendererModel implements
     featureColours.put(featureType, col);
   }
 
+  @Override
   public void setTransparency(float value)
   {
     transparency = value;
   }
 
+  @Override
   public float getTransparency()
   {
     return transparency;