From 393d4a79542f70fd6975e2a5250b819d5023f590 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@dundee.ac.uk>
Date: Sun, 18 Jan 2015 15:21:00 +0000
Subject: [PATCH] JAL-1628 new method to get a list of insertions in a
 SequenceI

---
 src/jalview/datamodel/Sequence.java      |   36 ++++++++++++++++++++++++++++++
 src/jalview/datamodel/SequenceI.java     |    6 +++++
 test/jalview/datamodel/SequenceTest.java |   15 +++++++++++++
 3 files changed, 57 insertions(+)

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;
diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 46669ae..e8c1d71 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -414,4 +414,10 @@ public interface SequenceI
    */
   public void setRNA(RNA rna);
 
+  /**
+   * 
+   * @return list of insertions (gap characters) in sequence
+   */
+  public List<int[]> getInsertions();
+
 }
diff --git a/test/jalview/datamodel/SequenceTest.java b/test/jalview/datamodel/SequenceTest.java
index d9a4573..40476a0 100644
--- a/test/jalview/datamodel/SequenceTest.java
+++ b/test/jalview/datamodel/SequenceTest.java
@@ -20,6 +20,21 @@ public class SequenceTest
     seq = new Sequence("FER1", "AKPNGVL");
   }
   @Test
+  public void testInsertGapsAndGapmaps()
+  {
+    SequenceI aseq = seq.deriveSequence();
+    aseq.insertCharAt(2, 3, '-');
+    aseq.insertCharAt(6, 3, '-');
+    assertEquals("Gap insertions not correct", "AK---P---NGVL",
+            aseq.getSequenceAsString());
+    List<int[]> gapInt = aseq.getInsertions();
+    assertEquals("Gap interval 1 start wrong", 2, gapInt.get(0)[0]);
+    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]);
+  }
+
+  @Test
   public void testGetAnnotation()
   {
     // initial state returns null not an empty array
-- 
1.7.10.2