JAL-2046 stack trace for implementation warning

[jalview.git] / src / jalview / datamodel / Sequence.java

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 151d8c4..88f4308 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -303,8 +303,14 @@ public class Sequence extends ASequence implements SequenceI
     }
     else
     {
-      System.err
-              .println("Warning: JAL-2046 side effect ? Possible implementation error: overwriting dataset sequence features by setting sequence features on alignment");
+      if (datasetSequence.getSequenceFeatures() != features
+              && datasetSequence.getSequenceFeatures() != null
+              && datasetSequence.getSequenceFeatures().length > 0)
+      {
+        new Exception(
+                "Warning: JAL-2046 side effect ? Possible implementation error: overwriting dataset sequence features by setting sequence features on alignment")
+                .printStackTrace();
+      }
       datasetSequence.setSequenceFeatures(features);
     }
   }
@@ -1086,6 +1092,25 @@ public class Sequence extends ASequence implements SequenceI
     return new Sequence(this);
   }
 
+  private boolean _isNa;
+
+  private long _seqhash = 0;
+
+  @Override
+  public boolean isProtein()
+  {
+    if (datasetSequence != null)
+    {
+      return datasetSequence.isProtein();
+    }
+    if (_seqhash != sequence.hashCode())
+    {
+      _seqhash = sequence.hashCode();
+      _isNa=jalview.util.Comparison.isNucleotide(new SequenceI[] { this });
+    }
+    return !_isNa;
+  };
+
   /*
    * (non-Javadoc)
    *