File Parsing returns Alignments, not Sequence[]

[jalview.git] / src / jalview / io / AlignFile.java

diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index 85f23a4..a800f06 100755 (executable)
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -36,7 +36,7 @@ public abstract class AlignFile extends FileParse
     int noSeqs = 0;\r
     int maxLength = 0;\r
     Vector seqs;\r
-    Vector headers;\r
+    Vector annotations;\r
     long start;\r
     long end;\r
     boolean jvSuffix = true;\r
@@ -86,13 +86,24 @@ public abstract class AlignFile extends FileParse
         return s;\r
     }\r
 \r
+    public void addAnnotations(Alignment al)\r
+    {\r
+      for(int i=0; i<annotations.size(); i++)\r
+      {\r
+        al.addAnnotation(\r
+            (AlignmentAnnotation)annotations.elementAt(i)\r
+            );\r
+      }\r
+\r
+    }\r
+\r
     /**\r
      * Initialise objects to store sequence data in.\r
      */\r
     protected void initData()\r
     {\r
         seqs = new Vector();\r
-        headers = new Vector();\r
+        annotations = new Vector();\r
     }\r
 \r
     /**\r