JAL-3187 return a colour for linked features with transparency

[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 ac8f6d9..4e81e69 100644 (file)
--- a/src/jalview/renderer/seqfeatures/FeatureRenderer.java
+++ b/src/jalview/renderer/seqfeatures/FeatureRenderer.java
@@ -28,6 +28,7 @@ import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
 import jalview.gui.Desktop;
 import jalview.util.Comparison;
+import jalview.util.ReverseListIterator;
 import jalview.viewmodel.seqfeatures.FeatureRendererModel;
 
 import java.awt.AlphaComposite;
@@ -408,7 +409,6 @@ public class FeatureRenderer extends FeatureRendererModel
       for (int pos = visiblePositions.start; pos <= visiblePositions.end; pos++)
       {
         int column = seq.findIndex(pos);
-        // TODO ensure these are in complement's render order (last on top)
         List<SequenceFeature> features = fr2
                 .findComplementFeaturesAtResidue(seq, pos);
         for (SequenceFeature sf : features)
@@ -417,6 +417,7 @@ public class FeatureRenderer extends FeatureRendererModel
           Color featureColour = fr2.getColor(sf, fc);
           renderFeature(g, seq, column - 1, column - 1, featureColour,
                   start, end, y1, colourOnly);
+          drawnColour = featureColour;
         }
       }
     }
@@ -476,10 +477,13 @@ public class FeatureRenderer extends FeatureRendererModel
       AlignFrame af = Desktop.getAlignFrameFor(complement);
       FeatureRendererModel fr2 = af.getFeatureRenderer();
       List<SequenceFeature> features = fr2.findComplementFeaturesAtResidue(
-              seq, seq.findPosition(column));
-      // todo: ensure ordered by feature render order
-      for (SequenceFeature sf : features)
+              seq, seq.findPosition(column - 1));
+
+      ReverseListIterator<SequenceFeature> it = new ReverseListIterator<>(
+              features);
+      while (it.hasNext())
       {
+        SequenceFeature sf = it.next();
         if (!fr2.featureGroupNotShown(sf))
         {
           Color col = fr2.getColour(sf);