From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Mon, 5 Jun 2017 07:57:27 +0000 (+0100)
Subject: Merge branch 'features/JAL-2446NCList' into
X-Git-Tag: Release_2_10_3b1~215
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=2f219368c3a4a3ff0ed6a34f84d005a3d85c9963

Merge branch 'features/JAL-2446NCList' into
features/JAL-2574findFeaturesByColumn

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

2f219368c3a4a3ff0ed6a34f84d005a3d85c9963
diff --cc src/jalview/datamodel/SequenceI.java
index ec76cb9,cf9d6ad..1615bee
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@@ -486,18 -511,21 +487,25 @@@ 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
 +   * Returns a (possibly empty) list of sequence features that overlap the given
 +   * alignment column range, optionally restricted to one or more specified
 +   * feature types. If the range is all gaps, then features which enclose it are
 +   * included (but not contact features).
     * 
 -   * @param from
 -   * @param to
 +   * @param fromCol
 +   *          start column of range inclusive (1..)
 +   * @param toCol
 +   *          end column of range inclusive (1..)
     * @param types
 +   *          optional feature types to restrict results to
     * @return
     */
 -  List<SequenceFeature> findFeatures(int from, int to, String... types);
 +  List<SequenceFeature> findFeatures(int fromCol, int toCol, String... types);
+   
+   /**
+    * 
+    * @return BitSet corresponding to index [0,length) where Comparison.isGap()
+    *         returns true.
+    */
+   BitSet getInsertionsAsBits();
  }