From 4e93b3351cecb6f07f401832fc1658d180c8008d Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 2 May 2007 13:02:47 +0000
Subject: [PATCH] AMSA input set padgaps true

---
 src/jalview/io/FastaFile.java |   18 ++++++++++++++++++
 1 file changed, 18 insertions(+)

diff --git a/src/jalview/io/FastaFile.java b/src/jalview/io/FastaFile.java
index c69b8ce..8de469d 100755
--- a/src/jalview/io/FastaFile.java
+++ b/src/jalview/io/FastaFile.java
@@ -158,6 +158,24 @@ public class FastaFile
   }
 
   /**
+   * called by AppletFormatAdapter to generate
+   * an annotated alignment, rather than bare
+   * sequences.
+   * @param al
+   */
+  public void addAnnotations(Alignment al)
+  {
+    addProperties(al);
+    for (int i = 0; i < annotations.size(); i++)
+    {
+      AlignmentAnnotation aa = (AlignmentAnnotation) annotations.elementAt(i);
+      aa.setPadGaps(true, al.getGapCharacter());
+      al.addAnnotation( aa );
+    }
+  }
+
+
+  /**
    * DOCUMENT ME!
    *
    * @param s DOCUMENT ME!
-- 
1.7.10.2