X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAMSAFile.java;h=34eace418f27ed7921c20679d6e73fbe995a35e7;hb=5022579ec6cc4eecfabd9df69e0fb039e3186a0a;hp=db1b7cb0042de1c75f04abb3e62a9ae7d8cc8fff;hpb=ab43013b7e357b84b4abade0dba949668dfb2a0e;p=jalview.git

diff --git a/src/jalview/io/AMSAFile.java b/src/jalview/io/AMSAFile.java
index db1b7cb..34eace4 100644
--- a/src/jalview/io/AMSAFile.java
+++ b/src/jalview/io/AMSAFile.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,7 +20,11 @@
  */
 package jalview.io;
 
-import jalview.datamodel.*;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+
+import java.io.IOException;
 
 public class AMSAFile extends jalview.io.FastaFile
 {
@@ -35,14 +39,26 @@ public class AMSAFile extends jalview.io.FastaFile
     this.al = al;
   }
 
+  public AMSAFile(String inFile, DataSourceType sourceType)
+          throws IOException
+  {
+    super(inFile, sourceType);
+  }
+
+  public AMSAFile(FileParse source) throws IOException
+  {
+    super(source);
+  }
+
   /**
    * DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
-  public String print()
+  @Override
+  public String print(SequenceI[] sqs, boolean jvsuffix)
   {
-    super.print(getSeqsAsArray());
+    super.print(sqs, jvsuffix);
 
     AlignmentAnnotation aa;
     if (al.getAlignmentAnnotation() != null)