X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=796937d73e22045e6e2cce84a7f3da025d6682e3;hb=d3dd5dd279c8253afa522f11b3e944ba422d12d3;hp=a01d185c24267ea6368818907139a0ce9d5a6c86;hpb=d8d9dadb23ea69882877e511b5fb62352bc9ed63;p=jalview.git

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index a01d185..796937d 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -89,7 +89,7 @@ public class Sequence extends ASequence implements SequenceI
    */
   int index = -1;
 
-  private SequenceFeatures sequenceFeatureStore;
+  private SequenceFeaturesI sequenceFeatureStore;
 
   /*
    * A cursor holding the approximate current view position to the sequence,
@@ -155,8 +155,8 @@ public class Sequence extends ASequence implements SequenceI
   {
     if (name == null)
     {
-      System.err
-              .println("POSSIBLE IMPLEMENTATION ERROR: null sequence name passed to constructor.");
+      System.err.println(
+              "POSSIBLE IMPLEMENTATION ERROR: null sequence name passed to constructor.");
       name = "";
     }
     // Does sequence have the /start-end signature?
@@ -1364,8 +1364,9 @@ public class Sequence extends ASequence implements SequenceI
   @Override
   public AlignmentAnnotation[] getAnnotation()
   {
-    return annotation == null ? null : annotation
-            .toArray(new AlignmentAnnotation[annotation.size()]);
+    return annotation == null ? null
+            : annotation
+                    .toArray(new AlignmentAnnotation[annotation.size()]);
   }
 
   @Override
@@ -1477,8 +1478,9 @@ public class Sequence extends ASequence implements SequenceI
   {
     if (datasetSequence == null)
     {
-      Sequence dsseq = new Sequence(getName(), AlignSeq.extractGaps(
-              jalview.util.Comparison.GapChars, getSequenceAsString()),
+      Sequence dsseq = new Sequence(getName(),
+              AlignSeq.extractGaps(jalview.util.Comparison.GapChars,
+                      getSequenceAsString()),
               getStart(), getEnd());
 
       datasetSequence = dsseq;
@@ -1620,7 +1622,7 @@ public class Sequence extends ASequence implements SequenceI
       List<SequenceFeature> sfs = entry.getSequenceFeatures();
       for (SequenceFeature feature : sfs)
       {
-        SequenceFeature sf[] = (mp != null) ? mp.locateFeature(feature)
+       SequenceFeature sf[] = (mp != null) ? mp.locateFeature(feature)
                 : new SequenceFeature[] { new SequenceFeature(feature) };
         if (sf != null)
         {
@@ -1777,8 +1779,8 @@ public class Sequence extends ASequence implements SequenceI
           }
         }
         // whilst it looks like it is a primary ref, we also sanity check type
-        if (DBRefUtils.getCanonicalName(DBRefSource.PDB).equals(
-                DBRefUtils.getCanonicalName(ref.getSource())))
+        if (DBRefUtils.getCanonicalName(DBRefSource.PDB)
+                .equals(DBRefUtils.getCanonicalName(ref.getSource())))
         {
           // PDB dbrefs imply there should be a PDBEntry associated
           // TODO: tighten PDB dbrefs