* @param start Start index of columns to delete.\r
* @param end End index to columns to delete.\r
*/\r
- public void deleteColumns(int start, int end);\r
+ public void deleteColumns(SequenceI seqs [], int start, int end);\r
\r
- /**\r
- * Deletes all residues in every sequence of alignment within given columns.\r
- *\r
- * @param seq1 Index of first sequence to delete columns from.\r
- * @param seq2 Index of last sequence to delete columns from.\r
- * @param start Start index of columns to delete.\r
- * @param end End index of columns to delete.\r
- */\r
- public void deleteColumns(int seq1, int seq2, int start, int end);\r
\r
/**\r
* Finds sequence in alignment using sequence name as query.\r
public void adjustSequenceAnnotations();\r
\r
public HiddenSequences getHiddenSequences();\r
-\r
+ /**\r
+ * Compact representation of alignment\r
+ * @return CigarArray\r
+ */\r
+ public CigarArray getCompactAlignment();\r
}\r