*/
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.
+ * Returns all HMM consensus sequences.
*
- * @param hiddenCols
+ * @param remove
+ * If true, remove all HMM consensus sequences from the alignment.
* @return
*/
- public int[] getVisibleStartAndEndIndex(List<int[]> hiddenCols);
-
- public void setHiddenColumns(HiddenColumns cols);
-
public List<SequenceI> getHMMConsensusSequences(boolean remove);
-
+
+ /**
+ * Insert a sequence at a position in an alignment
+ *
+ * @param i
+ * The idnex of the position.
+ * @param snew
+ * The new sequence.
+ */
+ void insertSequenceAt(int i, SequenceI snew);