X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2Fseqfeatures%2FFeatureRenderer.java;h=e66b7d5189753053692555297a9c9bb1d11b2451;hb=7e3a6674abdd31bf48e7e249a74eff50fd2ce589;hp=7a92a8890c4b654007e43d9f8d00573e960443f7;hpb=0eca06f81d58886f044eb37f8a1a702f497434cf;p=jalview.git

diff --git a/src/jalview/renderer/seqfeatures/FeatureRenderer.java b/src/jalview/renderer/seqfeatures/FeatureRenderer.java
index 7a92a88..e66b7d5 100644
--- a/src/jalview/renderer/seqfeatures/FeatureRenderer.java
+++ b/src/jalview/renderer/seqfeatures/FeatureRenderer.java
@@ -112,13 +112,14 @@ public class FeatureRenderer extends FeatureRendererModel
         continue;
       }
 
-      if (av.getShowText())
-      {
-        g.setColor(Color.white);
-        int charOffset = (charWidth - fm.charWidth(s)) / 2;
-        g.drawString(String.valueOf(s),
-                charOffset + (charWidth * (i - start)), pady);
-      }
+      /*
+       * JAL-3045 text is always drawn over features, even if
+       * 'Show Text' is unchecked in the format menu
+       */
+      g.setColor(Color.white);
+      int charOffset = (charWidth - fm.charWidth(s)) / 2;
+      g.drawString(String.valueOf(s),
+              charOffset + (charWidth * (i - start)), pady);
     }
     return true;
   }
@@ -322,7 +323,7 @@ public class FeatureRenderer extends FeatureRendererModel
       List<SequenceFeature> overlaps = seq.getFeatures().findFeatures(
               visiblePositions.getBegin(), visiblePositions.getEnd(), type);
 
-      if (fc.isSimpleColour())
+      if (overlaps.size() > 1 && fc.isSimpleColour())
       {
         filterFeaturesForDisplay(overlaps);
       }
@@ -357,8 +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);
 
@@ -399,14 +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;
+          }
           /*}*/
         }
       }
@@ -462,8 +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)
@@ -538,10 +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);
@@ -571,8 +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;