From b1ec29190c2aceda61a94197040c0d3288cc2702 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Wed, 6 Apr 2005 16:05:43 +0000
Subject: [PATCH] New method for helping to quickly map different aligned
 versions of a sequence.

---
 src/jalview/datamodel/Sequence.java  |   16 ++++++++++++++++
 src/jalview/datamodel/SequenceI.java |    2 +-
 2 files changed, 17 insertions(+), 1 deletion(-)

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 99f2de2..5db051a 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -194,6 +194,22 @@ public class Sequence implements SequenceI
     }
     return pos;
   }
+
+  public int[] gapMap() {
+    // Returns an int array giving the position of each residue in the sequence in the alignment
+    String seq = jalview.analysis.AlignSeq.extractGaps("-. ",sequence);
+    int[] map = new int[seq.length()];
+    int j=0;
+    int p=0;
+    while (j<sequence.length()) {
+      if (!jalview.util.Comparison.isGap(sequence.charAt(j))) {
+        map[p++]=j;
+      }
+      j++;
+    }
+    return map;
+  }
+
   public void deleteCharAt(int i)
   {
     StringBuffer sbuffer = new StringBuffer(sequence);
diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index a056a36..36afd4b 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -29,7 +29,7 @@ public interface SequenceI {
 
   public int         findIndex(int pos);
   public int         findPosition(int i);
-
+  public int[]         gapMap();
   public void       deleteChars(int i, int j);
   public void       deleteCharAt(int i);
   public void       insertCharAt(int i, char c);
-- 
1.7.10.2