X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentI.java;h=186136f990e7536cb5ee923c3f2919c2d07761c3;hb=1dabf099b7c77fb0a80039f72cef34669df9b2e1;hp=af5b7c45d4c0b814f397380f38fd11d1777e04d9;hpb=961b10e4c895aadb7fc9df82a641c6c53c0d5c70;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index af5b7c4..186136f 100755
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
+ * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -366,4 +366,27 @@ public interface AlignmentI
    */
   public int findIndex(SearchResults results);
 
+  /**
+   * append sequences and annotation from another alignment object to this one.
+   * Note: this is a straight transfer of object references, and may result in 
+   * toappend's dependent data being transformed to fit the alignment (changing gap characters, etc...).
+   * If you are uncertain, use the copy Alignment copy constructor to create a new version
+   * which can be appended without side effect.
+   * @param toappend - the alignment to be appended. 
+   */
+  public void append(AlignmentI toappend);
+  /**
+   * Justify the sequences to the left or right by deleting and inserting gaps before the initial residue or after the terminal residue
+   * @param right true if alignment padded to right, false to justify to left
+   * @return true if alignment was changed
+   * TODO: return undo object
+   */
+  public boolean justify(boolean right);
+
+  /**
+   * add given annotation row at given position (0 is start, -1 is end)
+   * @param consensus
+   * @param i
+   */
+  public void addAnnotation(AlignmentAnnotation consensus, int i);
 }