X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFastaFile.java;h=8de469d1a38e20aa63e05d200e6ad332eb0ed5f1;hb=17372df0e307273ba8955f08d05ad06d1c7f54e0;hp=c69b8ce6804530264c3cfe5111cd3342ebad9ddf;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git

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!