public Vector getSequences();\r
\r
/**\r
+ * Gets sequences as a SequenceI[]\r
+ *\r
+ * @return All sequences in alignment.\r
+ */\r
+ public SequenceI [] getSequencesArray();\r
+\r
+ /**\r
* Find a specific sequence in this alignment.\r
*\r
* @param i Index of required sequence.\r
* @param start Start index of columns to delete.\r
* @param end End index to columns to delete.\r
*/\r
- public void deleteColumns(int start, int end);\r
+ public void deleteColumns(SequenceI seqs [], int start, int end);\r
\r
- /**\r
- * Deletes all residues in every sequence of alignment within given columns.\r
- *\r
- * @param seq1 Index of first sequence to delete columns from.\r
- * @param seq2 Index of last sequence to delete columns from.\r
- * @param start Start index of columns to delete.\r
- * @param end End index of columns to delete.\r
- */\r
- public void deleteColumns(int seq1, int seq2, int start, int end);\r
\r
/**\r
* Finds sequence in alignment using sequence name as query.\r
*/\r
public void removeGaps();\r
\r
- /**\r
- * Removes redundant sequences from alignment.\r
- *\r
- * @param threshold Remove all sequences above the given threshold.\r
- * @param sel Set of sequences which will have redundant sequences removed from.\r
- *\r
- * @return All sequences below redundancy threshold.\r
- */\r
- public Vector removeRedundancy(float threshold, Vector sel);\r
\r
- /**\r
- * Finds group that sequence at index i in alignment is part of.\r
- *\r
- * @param i Index in alignment.\r
- *\r
- * @return First group found for sequence at position i. WARNING :\r
- * Sequences may be members of several groups. This method is incomplete.\r
- */\r
- public SequenceGroup findGroup(int i);\r
\r
/**\r
* Finds group that given sequence is part of.\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
- */\r
- public void removeSuperGroup(SuperGroup sg);\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
- */\r
- public SuperGroup getSuperGroup(SequenceGroup sg);\r
\r
/**\r
* Adds a new AlignmentAnnotation to this alignment\r
*/\r
public void addAnnotation(AlignmentAnnotation aa);\r
\r
+\r
+ public void setAnnotationIndex(AlignmentAnnotation aa, int index);\r
+\r
/**\r
* Deletes a specific AlignmentAnnotation from the alignment.\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