X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=c53319e4851e7a555e647b65f25f120885c5a8f3;hb=2f219368c3a4a3ff0ed6a34f84d005a3d85c9963;hp=0055d0e605b71e889530ed3fee929e1e8b867cf5;hpb=8eaa775e59bf928f8899f9ada5c9811200c2853a;p=jalview.git

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 0055d0e..c53319e 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -31,6 +31,7 @@ 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;
@@ -784,6 +785,40 @@ 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);
+          lastj = -1;
+        }
+      }
+      j++;
+    }
+    if (lastj != -1)
+    {
+      map.set(lastj, j);
+      lastj = -1;
+    }
+    return map;
+  }
+
+  @Override
   public void deleteChars(int i, int j)
   {
     int newstart = start, newend = end;