From 87b5fe5acb60c8474e6a3c5dc5eaf48f23f8c2ec Mon Sep 17 00:00:00 2001
From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Sat, 17 Nov 2012 18:34:37 +0000
Subject: [PATCH] convenience method for performing pairwise alignment

---
 src/jalview/analysis/AlignSeq.java |   19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index 8b20554..3ede7a8 100755
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -922,6 +922,25 @@ public class AlignSeq
   }
 
   /**
+   * Compute a globally optimal needleman and wunsch alignment between two
+   * sequences
+   * 
+   * @param s1
+   * @param s2
+   * @param type
+   *          AlignSeq.DNA or AlignSeq.PEP
+   */
+  public static AlignSeq doGlobalNWAlignment(SequenceI s1, SequenceI s2,
+          String type)
+  {
+    AlignSeq as = new AlignSeq(s1, s2, type);
+
+    as.calcScoreMatrix();
+    as.traceAlignment();
+    return as;
+  }
+
+
    * compute the PID vector used by the redundancy filter.
    * 
    * @param originalSequences
-- 
1.7.10.2