*/\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
public void addAnnotation(AlignmentAnnotation aa);\r
\r
/**\r
+ * Adds a new AlignmentAnnotation to this alignment,\r
+ * associated to Sequence starting at sequence index\r
+ */\r
+ public AlignmentAnnotation addAnnotation(AlignmentAnnotation aa, SequenceI seqRef);\r
+\r
+ public void setAnnotationIndex(AlignmentAnnotation aa, int index);\r
+\r
+ /**\r
* Deletes a specific AlignmentAnnotation from the alignment.\r
*\r
* @param aa DOCUMENT ME!\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
+\r
}\r