orthomam_db.mli 860 Bytes
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type t
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type alignment = private string
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val make : string -> t
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val list_alignments : t -> alignment list
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val tree : t -> string
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val missing_sequences_cdf : t -> string -> unit
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val id_of_alignment : alignment -> string

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type orf_defect = [
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  | `Invalid_codon of int * string
  | `Invalid_character_in_codon of int * string
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  | `Length_not_multiple_of_3
  | `Stop_codon of int
  | `Stop_codon_at_last_position
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]

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val check_orf : string -> (unit, orf_defect) result

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val remove_gaps : string -> string

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type alignment_defect = [
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  | `Sequences_with_different_lengths
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  | `Length_not_multiple_of_3
  | `Invalid_sequences of (string * aligned_sequence_defect) list
]
and aligned_sequence_defect = [
  | `Invalid_codon of int * string
  | `Stop_codon of int
  | `Stop_codon_at_last_position
]
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val check_alignment : Biotk.Fasta.item list -> alignment_defect option