+
+ /**
+ * 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);