/*
- * 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
*/
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);
}