From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Mon, 5 Jun 2017 07:52:40 +0000 (+0100)
Subject: Merge branch 'develop' into features/JAL-2446NCList
X-Git-Tag: Release_2_10_3b1~215^2
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=f41d78dbf890fbb7597f75019d05841312fa4f52;p=jalview.git

Merge branch 'develop' into features/JAL-2446NCList

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

f41d78dbf890fbb7597f75019d05841312fa4f52
diff --cc src/jalview/datamodel/SequenceI.java
index dbf3ed3,12ddf60..cf9d6ad
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@@ -20,8 -20,7 +20,9 @@@
   */
  package jalview.datamodel;
  
 +import jalview.datamodel.features.SequenceFeaturesI;
 +
+ import java.util.BitSet;
  import java.util.List;
  import java.util.Vector;
  
@@@ -510,14 -479,9 +511,21 @@@ public interface SequenceI extends ASeq
    public List<DBRefEntry> getPrimaryDBRefs();
  
    /**
 +   * Returns a (possibly empty) list of sequence features that overlap the range
 +   * from-to (inclusive), optionally restricted to one or more specified feature
 +   * types
 +   * 
 +   * @param from
 +   * @param to
 +   * @param types
 +   * @return
 +   */
 +  List<SequenceFeature> findFeatures(int from, int to, String... types);
++  
++  /**
+    * 
+    * @return BitSet corresponding to index [0,length) where Comparison.isGap()
+    *         returns true.
+    */
+   BitSet getInsertionsAsBits();
  }