X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2Fseqfeatures%2FFeatureRenderer.java;fp=src%2Fjalview%2Frenderer%2Fseqfeatures%2FFeatureRenderer.java;h=2d16fcd8222519369d02fd244f2e4717200ef4d6;hb=3459a8a691cb22508d7067f240b7254e588e77d3;hp=aa3328b139f59aeb042c6d460a91ae7564eaed5c;hpb=5b27f1062b2203c4c31702e205f4c78e1992063e;p=jalview.git

diff --git a/src/jalview/renderer/seqfeatures/FeatureRenderer.java b/src/jalview/renderer/seqfeatures/FeatureRenderer.java
index aa3328b..2d16fcd 100644
--- a/src/jalview/renderer/seqfeatures/FeatureRenderer.java
+++ b/src/jalview/renderer/seqfeatures/FeatureRenderer.java
@@ -358,8 +358,8 @@ public class FeatureRenderer extends FeatureRendererModel
         }
 
         int featureStartCol = seq.findIndex(visibleStart);
-        int featureEndCol = sf.begin == sf.end ? featureStartCol : seq
-                .findIndex(visibleEnd);
+        int featureEndCol = sf.begin == sf.end ? featureStartCol
+                : seq.findIndex(visibleEnd);
 
         // Color featureColour = getColour(sequenceFeature);
 
@@ -400,14 +400,13 @@ public class FeatureRenderer extends FeatureRendererModel
           else
           {
           */
-            boolean drawn = renderFeature(g, seq,
-                    featureStartCol - 1,
-                    featureEndCol - 1, featureColour,
-                    start, end, y1, colourOnly);
-            if (drawn)
-            {
-              drawnColour = featureColour;
-            }
+          boolean drawn = renderFeature(g, seq, featureStartCol - 1,
+                  featureEndCol - 1, featureColour, start, end, y1,
+                  colourOnly);
+          if (drawn)
+          {
+            drawnColour = featureColour;
+          }
           /*}*/
         }
       }
@@ -463,8 +462,7 @@ public class FeatureRenderer extends FeatureRendererModel
     for (int pos = visibleStart; pos <= visibleEnd; pos++)
     {
       int column = seq.findIndex(pos);
-      MappedFeatures mf = fr2
-              .findComplementFeaturesAtResidue(seq, pos);
+      MappedFeatures mf = fr2.findComplementFeaturesAtResidue(seq, pos);
       if (mf != null)
       {
         for (SequenceFeature sf : mf.features)
@@ -539,10 +537,15 @@ public class FeatureRenderer extends FeatureRendererModel
         continue;
       }
 
+      /*
+       * find features of this type, and the colour of the _last_ one
+       * (the one that would be drawn on top) that has a colour
+       */
       List<SequenceFeature> overlaps = seq.findFeatures(column, column,
               type);
-      for (SequenceFeature sequenceFeature : overlaps)
+      for (int i = overlaps.size() - 1; i >= 0; i--)
       {
+        SequenceFeature sequenceFeature = overlaps.get(i);
         if (!featureGroupNotShown(sequenceFeature))
         {
           Color col = getColour(sequenceFeature);
@@ -572,8 +575,8 @@ public class FeatureRenderer extends FeatureRendererModel
     AlignViewportI complement = av.getCodingComplement();
     AlignFrame af = Desktop.getAlignFrameFor(complement);
     FeatureRendererModel fr2 = af.getFeatureRenderer();
-    MappedFeatures mf = fr2.findComplementFeaturesAtResidue(
-            seq, seq.findPosition(column - 1));
+    MappedFeatures mf = fr2.findComplementFeaturesAtResidue(seq,
+            seq.findPosition(column - 1));
     if (mf == null)
     {
       return null;