*/\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
*/\r
public void deleteAllGroups();\r
\r
- /**\r
- * Adds a super group. A SuperGroup is a group of groups.\r
- *\r
- * @param sg Adds a new SuperGroup to alignment\r
- */\r
- public void addSuperGroup(SuperGroup sg);\r
\r
/**\r
- * Removes SuperGroup from alignment.\r
- *\r
- * @param sg This SuperGroup will be deleted from alignment.\r
+ * Adds a new AlignmentAnnotation to this alignment\r
*/\r
- public void removeSuperGroup(SuperGroup sg);\r
+ public void addAnnotation(AlignmentAnnotation aa);\r
\r
/**\r
- * Finds any SuperGroup that a given SequenceGroup may be part of.\r
- *\r
- * @param sg SequenceGroup to search for.\r
- *\r
- * @return SuperGroup that contains the given SequenceGroup.\r
+ * Adds a new AlignmentAnnotation to this alignment,\r
+ * associated to Sequence starting at sequence index\r
*/\r
- public SuperGroup getSuperGroup(SequenceGroup sg);\r
+ public AlignmentAnnotation addAnnotation(AlignmentAnnotation aa, SequenceI seqRef);\r
\r
- /**\r
- * Adds a new AlignmentAnnotation to this alignment\r
- */\r
- public void addAnnotation(AlignmentAnnotation aa);\r
+ public void setAnnotationIndex(AlignmentAnnotation aa, int index);\r
\r
/**\r
* Deletes a specific AlignmentAnnotation from the alignment.\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