public Vector getSequences();\r
\r
/**\r
+ * Gets sequences as a SequenceI[]\r
+ *\r
+ * @return All sequences in alignment.\r
+ */\r
+ public SequenceI [] getSequencesArray();\r
+\r
+ /**\r
* Find a specific sequence in this alignment.\r
*\r
* @param i Index of required sequence.\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