+\r
+ /**\r
+ * Returns true if alignment is nucleotide sequence\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public boolean isNucleotide();\r
+\r
+ /**\r
+ * Set true if the alignment is a nucleotide sequence\r
+ *\r
+ * @return\r
+ */\r
+ public void setNucleotide(boolean b);\r
+\r
+\r
+ public Alignment getDataset();\r
+\r
+ public void setDataset(Alignment dataset);\r
+ /**\r
+ * pads sequences with gaps (to ensure the set looks like an alignment)\r
+ * @return boolean true if alignment was modified\r
+ */\r
+ public boolean padGaps();\r
+\r
+ public void adjustSequenceAnnotations();\r
+\r
+ public HiddenSequences getHiddenSequences();\r
+ /**\r
+ * Compact representation of alignment\r
+ * @return CigarArray\r
+ */\r
+ public CigarArray getCompactAlignment();\r