*/\r
public SequenceI findName(String name);\r
\r
- /**\r
- * Finds sequence in alignment using full displayId as query.\r
- *\r
- * @param name displayId, ie <em>NAME/25-100</em>\r
- *\r
- * @return Sequence matching query, if found. If not found returns null.\r
- */\r
- public SequenceI findbyDisplayId(String name);\r
\r
/**\r
* Finds index of a given sequence in the alignment.\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
+\r
}\r