From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Mon, 5 Jun 2017 07:54:11 +0000 (+0100)
Subject: Merge branch 'features/JAL-2446NCList' into
X-Git-Tag: Release_2_10_3b1~214^2
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=refs%2Fheads%2Ffeatures%2FJAL-2526sequenceCursor;p=jalview.git

Merge branch 'features/JAL-2446NCList' into
features/JAL-2526sequenceCursor

Conflicts:
	src/jalview/datamodel/SequenceI.java
---

88694463a2aea303694231603b61970f72a5a259
diff --cc src/jalview/datamodel/SequenceI.java
index 18f0948,cf9d6ad..38be37f
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@@ -520,11 -521,11 +521,18 @@@ public interface SequenceI extends ASeq
     * @return
     */
    List<SequenceFeature> findFeatures(int from, int to, String... types);
 +
 +  /**
 +   * Method to call to indicate that the sequence (characters or alignment/gaps)
 +   * has been modified. Provided to allow any cursors on residue/column
 +   * positions to be invalidated.
 +   */
 +  void sequenceChanged();
+   
+   /**
+    * 
+    * @return BitSet corresponding to index [0,length) where Comparison.isGap()
+    *         returns true.
+    */
+   BitSet getInsertionsAsBits();
  }