JAL-845 start cDNA consensus on 'add alignment' (as well as translate or

[jalview.git] / src / jalview / viewmodel / seqfeatures / FeatureRendererModel.java

diff --git a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
index 30d14c2..8c2f0da 100644 (file)
--- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
+++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
@@ -246,6 +246,13 @@ public abstract class FeatureRendererModel implements
   {
     ArrayList<SequenceFeature> tmp = new ArrayList<SequenceFeature>();
     SequenceFeature[] features = sequence.getSequenceFeatures();
+
+    while (features == null && sequence.getDatasetSequence() != null)
+    {
+      sequence = sequence.getDatasetSequence();
+      features = sequence.getSequenceFeatures();
+    }
+
     if (features != null)
     {
       for (int i = 0; i < features.length; i++)
@@ -322,9 +329,7 @@ public abstract class FeatureRendererModel implements
     for (int i = 0; i < alignment.getHeight(); i++)
     {
       SequenceI asq = alignment.getSequenceAt(i);
-      SequenceI dasq = asq.getDatasetSequence();
-      SequenceFeature[] features = dasq != null ? dasq
-              .getSequenceFeatures() : asq.getSequenceFeatures();
+      SequenceFeature[] features = asq.getSequenceFeatures();
 
       if (features == null)
       {
@@ -900,7 +905,7 @@ public abstract class FeatureRendererModel implements
       {
         for (int i = 0; i < typ.length; i++)
         {
-          if (feature_disp.isVisible(typ[i]))
+          if (!feature_disp.isVisible(typ[i]))
           {
             typ[i] = null;
           }