JAL-2106 rejig test to minimally verify patch that getPDBEntry can be called on local...

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

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 151d8c4..98cd4b2 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -303,8 +303,13 @@ public class Sequence extends ASequence implements SequenceI
     }
     else
     {
-      System.err
+      if (datasetSequence.getSequenceFeatures() != features
+              && datasetSequence.getSequenceFeatures() != null
+              && datasetSequence.getSequenceFeatures().length > 0)
+      {
+        System.err
               .println("Warning: JAL-2046 side effect ? Possible implementation error: overwriting dataset sequence features by setting sequence features on alignment");
+      }
       datasetSequence.setSequenceFeatures(features);
     }
   }
@@ -1086,6 +1091,25 @@ 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)
    * 
@@ -1370,12 +1394,15 @@ public class Sequence extends ASequence implements SequenceI
   @Override
   public PDBEntry getPDBEntry(String pdbIdStr)
   {
-    if (getDatasetSequence() == null
-            || getDatasetSequence().getAllPDBEntries() == null)
+    if (getDatasetSequence() != null)
+    {
+      return getDatasetSequence().getPDBEntry(pdbIdStr);
+    }
+    if (pdbIds == null)
     {
       return null;
     }
-    List<PDBEntry> entries = getDatasetSequence().getAllPDBEntries();
+    List<PDBEntry> entries = getAllPDBEntries();
     for (PDBEntry entry : entries)
     {
       if (entry.getId().equalsIgnoreCase(pdbIdStr))