X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2Fseqfeatures%2FFeatureRenderer.java;h=13885b45370b005378ac348fdbf7edca256bc3a2;hb=8d0d4cb4f21a2f15d61b90b0eb764041c664c81d;hp=e81e519718f721684305dee9d2351d9c5bee152a;hpb=be762d8d9c71a7aa3121e845c45911c7192b7827;p=jalview.git

diff --git a/src/jalview/renderer/seqfeatures/FeatureRenderer.java b/src/jalview/renderer/seqfeatures/FeatureRenderer.java
index e81e519..13885b4 100644
--- a/src/jalview/renderer/seqfeatures/FeatureRenderer.java
+++ b/src/jalview/renderer/seqfeatures/FeatureRenderer.java
@@ -22,7 +22,7 @@ package jalview.renderer.seqfeatures;
 
 import jalview.api.AlignViewportI;
 import jalview.api.FeatureColourI;
-import jalview.datamodel.Range;
+import jalview.datamodel.ContiguousI;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.util.Comparison;
@@ -216,7 +216,8 @@ public class FeatureRenderer extends FeatureRendererModel
       return null;
     }
 
-    if (Comparison.isGap(seq.getCharAt(column)))
+    // column is 'base 1' but getCharAt is an array index (ie from 0)
+    if (Comparison.isGap(seq.getCharAt(column - 1)))
     {
       /*
        * returning null allows the colour scheme to provide gap colour
@@ -271,7 +272,7 @@ public class FeatureRenderer extends FeatureRendererModel
     /*
      * if columns are all gapped, or sequence has no features, nothing to do
      */
-    Range visiblePositions = seq.findPositions(start+1, end+1);
+    ContiguousI visiblePositions = seq.findPositions(start + 1, end + 1);
     if (visiblePositions == null || !seq.getFeatures().hasFeatures())
     {
       return null;
@@ -303,14 +304,19 @@ public class FeatureRenderer extends FeatureRendererModel
       List<SequenceFeature> overlaps = seq.getFeatures().findFeatures(
               visiblePositions.getBegin(), visiblePositions.getEnd(), type);
 
-      filterFeaturesForDisplay(overlaps, fc);
+      if (fc.isSimpleColour())
+      {
+        filterFeaturesForDisplay(overlaps);
+      }
 
       for (SequenceFeature sf : overlaps)
       {
-        Color featureColour = fc.getColor(sf);
+        Color featureColour = getColor(sf, fc);
         if (featureColour == null)
         {
-          // score feature outwith threshold for colouring
+          /*
+           * feature excluded by visibility settings, filters, or colour threshold
+           */
           continue;
         }
 
@@ -401,27 +407,6 @@ public class FeatureRenderer extends FeatureRendererModel
   }
 
   /**
-<<<<<<< HEAD
-=======
-   * Answers true if the feature belongs to a feature group which is not
-   * currently displayed, else false
-   * 
-   * @param sequenceFeature
-   * @return
-   */
-  @Override
-  protected boolean featureGroupNotShown(
-          final SequenceFeature sequenceFeature)
-  {
-    return featureGroups != null && sequenceFeature.featureGroup != null
-            && sequenceFeature.featureGroup.length() != 0
-            && featureGroups.containsKey(sequenceFeature.featureGroup)
-            && !featureGroups.get(sequenceFeature.featureGroup)
-                    .booleanValue();
-  }
-
-  /**
->>>>>>> refs/heads/develop
    * Called when alignment in associated view has new/modified features to
    * discover and display.
    *