X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=96e469a53da247e036ef07a80d0129894f5e1ca8;hb=393d4a79542f70fd6975e2a5250b819d5023f590;hp=cf1c9839309fa4b4a502302c81185dd440187fb7;hpb=a8b52dee30e7bfde2b11aaf3c5091e285f1e27e6;p=jalview.git

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index cf1c983..96e469a 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -682,6 +682,42 @@ public class Sequence implements SequenceI
   }
 
   @Override
+  public List<int[]> getInsertions()
+  {
+    ArrayList<int[]> map = new ArrayList<int[]>();
+    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.add(new int[]
+          { lastj, j - 1 });
+          lastj = -1;
+        }
+      }
+      j++;
+    }
+    if (lastj != -1)
+    {
+      map.add(new int[]
+      { lastj, j - 1 });
+      lastj = -1;
+    }
+    return map;
+  }
+
+  @Override
   public void deleteChars(int i, int j)
   {
     int newstart = start, newend = end;