*/
AlignedCodonFrame getMapping(SequenceI mapFrom, SequenceI mapTo);
+ public void setHiddenColumns(HiddenColumns cols);
+
/**
- * Calculate the visible start and end index of an alignment. The result is
- * returned an int array where: int[0] = startIndex, and int[1] = endIndex.
+ * Insert a sequence at a position in an alignment
*
- * @param hiddenCols
- * @return
+ * @param i
+ * The idnex of the position.
+ * @param snew
+ * The new sequence.
*/
- public int[] getVisibleStartAndEndIndex(List<int[]> hiddenCols);
-
- public void setHiddenColumns(HiddenColumns cols);
-
- public Map<Integer, SequenceI> getHMMConsensusSequences(boolean remove);
-
- public List<SequenceI> getHMMConsensusSequences();
-
+ void insertSequenceAt(int i, SequenceI snew);