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[jalview.git] / src / jalview / datamodel / AlignmentI.java

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index b4075a0..186136f 100755 (executable)
--- 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
@@ -122,7 +122,7 @@ public interface AlignmentI
    * @param s
    *                Sequence to look for.
    * 
-   * @return Index of sequence within the alignment.
+   * @return Index of sequence within the alignment or -1 if not found
    */
   public int findIndex(SequenceI s);
 
@@ -359,4 +359,34 @@ public interface AlignmentI
    */
   public SequenceI findName(SequenceI startAfter, String token, boolean b);
 
+  /**
+   * find first sequence in alignment which is involved in the given search result object
+   * @param results
+   * @return -1 or index of sequence in alignment
+   */
+  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);
 }