AMSA input set padgaps true

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