+ /**\r
+ * All sequences will be cut from given index.\r
+ *\r
+ * @param i Remove all residues in sequences beyond this column.\r
+ */\r
+ public void trimRight(int i);\r
+\r
+ /**\r
+ * Removes all columns containing entirely gap characters.\r
+ */\r
+ public void removeGaps();\r
+\r
+ /**\r
+ * Removes redundant sequences from alignment.\r
+ *\r
+ * @param threshold Remove all sequences above the given threshold.\r
+ * @param sel Set of sequences which will have redundant sequences removed from.\r
+ *\r
+ * @return All sequences below redundancy threshold.\r
+ */\r
+ public Vector removeRedundancy(float threshold, Vector sel);\r
+\r
+ /**\r
+ * Finds group that sequence at index i in alignment is part of.\r
+ *\r
+ * @param i Index in alignment.\r
+ *\r
+ * @return First group found for sequence at position i. WARNING :\r
+ * Sequences may be members of several groups. This method is incomplete.\r
+ */\r
+ public SequenceGroup findGroup(int i);\r
+\r
+ /**\r
+ * Finds group that given sequence is part of.\r
+ *\r
+ * @param s Sequence in alignment.\r
+ *\r
+ * @return First group found for sequence. WARNING :\r
+ * Sequences may be members of several groups. This method is incomplete.\r
+ */\r
+ public SequenceGroup findGroup(SequenceI s);\r
+\r
+ /**\r
+ * Finds all groups that a given sequence is part of.\r
+ *\r
+ * @param s Sequence in alignment.\r
+ *\r
+ * @return All groups containing given sequence.\r
+ */\r
+ public SequenceGroup[] findAllGroups(SequenceI s);\r
+\r
+ /**\r
+ * Adds a new SequenceGroup to this alignment.\r
+ *\r
+ * @param sg New group to be added.\r
+ */\r
+ public void addGroup(SequenceGroup sg);\r
+\r
+ /**\r
+ * Deletes a specific SequenceGroup\r
+ *\r
+ * @param g Group will be deleted from alignment.\r
+ */\r
+ public void deleteGroup(SequenceGroup g);\r
+\r
+ /**\r
+ * Get all the groups associated with this alignment.\r
+ *\r
+ * @return All groups as a Vector.\r
+ */\r
+ public Vector getGroups();\r
+\r
+ /**\r
+ * Deletes all groups from this alignment.\r
+ */\r
+ public void deleteAllGroups();\r
+\r
+\r
+ /**\r
+ * Adds a new AlignmentAnnotation to this alignment\r
+ */\r
+ public void addAnnotation(AlignmentAnnotation aa);\r