Functions Supported for Multiple Alignment Data

  • createAlignment (Sequence seq1, Sequence seq2, …) — Returns the alignment created from the sequences.
  • addToAlignment (MAlignment aln, Sequence seq, int row = -1) — Adds the sequence to the specified row of the alignment. If the “row” parameter is not specified, the sequence is added to the end of the alignment.
  • sequenceFromAlignment (MAlignment aln, int row) — Returns the sequence from the specified row of the alignment.
  • findInAlignment (MAlignment aln, Sequence seq) — Searches the alignment for the specified sequence. Returns the number of the row if the sequence has been found or “-1” if it hasn’t been found.
  • findInAlignment (MAlignment aln, QString name) — Searches the alignment for a sequence with the specified name.
  • removeFromAlignment (MAlignment aln, int row) — Removes a sequence from the specified row of the alignment.
  • rowNum (MAlignment aln) — Returns the number of rows in the alignment.
  • columnNum (MAlignment aln) — Returns the length of the alignment.
  • alignmentAlphabetType (MAlignment aln) — Returns the alignment’s alphabet type.
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