X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=2f1da7f9ad9c125d334178b5e34a4bbc40422b24;hb=f1e2d882404c5cdc821a772f0bd6103a226822ac;hp=96a2fa17b5b6c3253130b8df9552b83cfc0a2ad8;hpb=bba9e58f08fc55c0f789f8354d1444e5c5e1b0e6;p=jalview.git

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 96a2fa1..2f1da7f 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -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
@@ -1821,12 +1823,11 @@ public class Sequence extends ASequence implements SequenceI
             endPos, types);
 
     /*
-     * if the start or end column is gapped, startPos or endPos may be to the 
-     * left or right, and we may have included adjacent or enclosing features;
-     * remove any that are not enclosing features
+     * if end column is gapped, endPos may be to the right, 
+     * and we may have included adjacent or enclosing features;
+     * remove any that are not enclosing, non-contact features
      */
-    if (endPos > this.end || Comparison.isGap(sequence[fromColumn - 1])
-            || Comparison.isGap(sequence[toColumn - 1]))
+    if (endPos > this.end || Comparison.isGap(sequence[toColumn - 1]))
     {
       ListIterator<SequenceFeature> it = result.listIterator();
       while (it.hasNext())
@@ -1847,6 +1848,13 @@ public class Sequence extends ASequence implements SequenceI
           {
             it.remove();
           }
+          else if (featureEndColumn > toColumn && sf.isContactFeature())
+          {
+            /*
+             * remove an enclosing feature if it is a contact feature
+             */
+            it.remove();
+          }
         }
       }
     }