From 6568287d7ca9ab336a83e27b9bfbd548a10cf748 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Sun, 4 Jun 2017 10:41:56 +0100
Subject: [PATCH] JAL-2291 SequenceI.getInsertionsAsBits for convenient
 logical operations

---
 src/jalview/datamodel/Sequence.java      |   35 ++++++++++++++++++++++++++++++
 src/jalview/datamodel/SequenceI.java     |    8 +++++++
 test/jalview/datamodel/SequenceTest.java |    8 +++++++
 3 files changed, 51 insertions(+)

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index b0faf21..a8cff26 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -29,6 +29,7 @@ import jalview.util.StringUtils;
 
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.BitSet;
 import java.util.Collections;
 import java.util.Enumeration;
 import java.util.List;
@@ -819,6 +820,40 @@ public class Sequence extends ASequence implements SequenceI
   }
 
   @Override
+  public BitSet getInsertionsAsBits()
+  {
+    BitSet map = new BitSet();
+    int lastj = -1, j = 0;
+    int pos = start;
+    int seqlen = sequence.length;
+    while ((j < seqlen))
+    {
+      if (jalview.util.Comparison.isGap(sequence[j]))
+      {
+        if (lastj == -1)
+        {
+          lastj = j;
+        }
+      }
+      else
+      {
+        if (lastj != -1)
+        {
+          map.set(lastj, j - 1);
+          lastj = -1;
+        }
+      }
+      j++;
+    }
+    if (lastj != -1)
+    {
+      map.set(lastj, j - 1);
+      lastj = -1;
+    }
+    return map;
+  }
+
+  @Override
   public void deleteChars(int i, int j)
   {
     int newstart = start, newend = end;
diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index e81553b..12ddf60 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -20,6 +20,7 @@
  */
 package jalview.datamodel;
 
+import java.util.BitSet;
 import java.util.List;
 import java.util.Vector;
 
@@ -476,4 +477,11 @@ public interface SequenceI extends ASequenceI
    *         list
    */
   public List<DBRefEntry> getPrimaryDBRefs();
+
+  /**
+   * 
+   * @return BitSet corresponding to index [0,length) where Comparison.isGap()
+   *         returns true.
+   */
+  BitSet getInsertionsAsBits();
 }
diff --git a/test/jalview/datamodel/SequenceTest.java b/test/jalview/datamodel/SequenceTest.java
index 08e6f7d..ae82d13 100644
--- a/test/jalview/datamodel/SequenceTest.java
+++ b/test/jalview/datamodel/SequenceTest.java
@@ -35,6 +35,7 @@ import jalview.util.MapList;
 import java.io.File;
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.BitSet;
 import java.util.List;
 import java.util.Vector;
 
@@ -74,6 +75,13 @@ public class SequenceTest
     assertEquals("Gap interval 1 end wrong", 4, gapInt.get(0)[1]);
     assertEquals("Gap interval 2 start wrong", 6, gapInt.get(1)[0]);
     assertEquals("Gap interval 2 end wrong", 8, gapInt.get(1)[1]);
+
+    BitSet gapfield = aseq.getInsertionsAsBits();
+    BitSet expectedgaps = new BitSet();
+    expectedgaps.set(2, 4);
+    expectedgaps.set(6, 8);
+
+    assertEquals("getInsertionsAsBits not correct.", expectedgaps, gapfield);
   }
 
   @Test(groups = ("Functional"))
-- 
1.7.10.2