+ /**\r
+ * Deletes a specific AlignmentAnnotation from the alignment.\r
+ *\r
+ * @param aa DOCUMENT ME!\r
+ */\r
+ public void deleteAnnotation(AlignmentAnnotation aa);\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public AlignmentAnnotation[] getAlignmentAnnotation();\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param gc DOCUMENT ME!\r
+ */\r
+ public void setGapCharacter(char gc);\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public char getGapCharacter();\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public Vector getAAFrequency();\r
+\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
+}\r