X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAlignFile.java;h=2340283ea2e31f0f538a1b4561f411ca3fb95e6f;hb=0945b9c86976a185f1796430f91756f7d24e7af5;hp=4de510a332ad20c063d28914f5d80cada9732afe;hpb=4815037f13748676b04b91dc761b73cf6f2d6ecd;p=jalview.git

diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index 4de510a..2340283 100755
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -40,7 +40,8 @@ import java.util.Vector;
  * @author $author$
  * @version $Revision$
  */
-public abstract class AlignFile extends FileParse implements AlignmentFileI
+public abstract class AlignFile extends FileParse
+        implements AlignmentFileReaderI, AlignmentFileWriterI
 {
   int noSeqs = 0;
 
@@ -117,8 +118,7 @@ public abstract class AlignFile extends FileParse implements AlignmentFileI
    * @throws IOException
    */
   public AlignFile(boolean parseImmediately, String dataObject,
-          DataSourceType sourceType)
-          throws IOException
+          DataSourceType sourceType) throws IOException
   {
     super(dataObject, sourceType);
     initData();
@@ -174,11 +174,6 @@ public abstract class AlignFile extends FileParse implements AlignmentFileI
     }
     parseCalled = true;
     parse();
-    // sets the index of each sequence in the alignment
-    for (int i = 0, c = seqs.size(); i < c; i++)
-    {
-      seqs.get(i).setIndex(i);
-    }
   }
 
   /**
@@ -281,9 +276,8 @@ public abstract class AlignFile extends FileParse implements AlignmentFileI
   {
     if (key == null)
     {
-      throw new Error(
-              MessageManager
-                      .getString("error.implementation_error_cannot_have_null_alignment"));
+      throw new Error(MessageManager.getString(
+              "error.implementation_error_cannot_have_null_alignment"));
     }
     if (value == null)
     {
@@ -416,4 +410,8 @@ public abstract class AlignFile extends FileParse implements AlignmentFileI
     }
   }
 
+  protected void addSequence(SequenceI seq)
+  {
+    seqs.add(seq);
+  }
 }