/* 

  Rosalind problem Transcribing DNA into RNA in Picat.

  https://rosalind.info/problems/rna/
  """
  Problem
  An RNA string is a string formed from the alphabet containing 'A', 'C', 'G', and 'U'.

  Given a DNA string t corresponding to a coding strand, its transcribed RNA string 
  u is formed by replacing all occurrences of 'T' in t with 'U' in u.

  Given: A DNA string t having length at most 1000 nt.

  Return: The transcribed RNA string of t.

  Sample Dataset
  GATGGAACTTGACTACGTAAATT

  Sample Output
  GAUGGAACUUGACUACGUAAAUU
  """

  This model was created by Hakan Kjellerstrand, hakank@gmail.com
  See also my Picat page: http://www.hakank.org/picat/

*/

import util.
import v3_utils.
import rosalind_utils.

main => go.

go ?=>
  DNA = "GATGGAACTTGACTACGTAAATT",
  rna1(RNA,DNA,[]),
  println(rna1=RNA),

  println(rna2=rna2(DNA)),

  rna3(DNA,RNA3),
  println(rna3=RNA3),

  RNA4 = rna4(DNA),
  println(rna4=RNA4),


  nl.
go => true.

/*
  - rna1: 0.915s (as first run: about 10s)
  - rna2: 0.052s (as first run: 0.609s)
  - rna3: 0.011s (as first run: 0.609s)
  - rna4: 0.089s (as first run: 0.283s)
*/
go2 ?=>
  garbage_collect(300_000),
  _ = random2(),
  
  println(gen_dna),
  Len = 1_000_000,
  DNA = new_list(Len),
  time(dna_gen1(DNA,"",[])),
  % println(DNA),

  garbage_collect(300_000),
  println(rna1),
  time(rna1(_RNA1,DNA,[])),
  % println(rna1=RNA1),

  garbage_collect(300_000),
  println(rna2),
  time(_RNA2=rna2(DNA)),
  % println(rna2=RNA2),

  garbage_collect(300_000),
  println(rna3),
  time(rna3(DNA,_RNA3)),
  % println(rna3=RNA3),

  garbage_collect(300_000),
  println(rna4),
  time(_RNA4 = rna4(DNA)),
  % println(rna4=RNA4),

  % go2,

  nl.
go2 => true.

% The Challenge.
go3 =>
  DNA = "GGTTGGACGCTGGTTGTGGAATAGCCCAAGCAACGTTTGGTGGCTGCCTATCACCTATTCCTCATGTGCGAACAAAATACGCGTAAGAAGTTATGCCGACGAGATTCTTCTCTAGGCGCAATTATCCGATGGGCGTGAGGAATGAAAAGACATTAGTCGGGACTCACCTTCCTCTATTCCGTTTTAATTTCACCGGACGTCGTAAGTCGGGCTTAGAATGTTTCGCCTGGTACTCGTAAGGCGACGGTTCGTGGTTTACCCATCCCGGCGCTTGAGCAGCAAGGATTAACTCATCTGATGGAGTATTCAACATGTAGAGCTTATACACGCACAACGACTAAATGGCCGCTCATGTACAGGCCATCCAGCCATCGACATCCACATATCCCGCCACCCTGTTTGGCGCTCCGGGCCCCTGGCGAGCAGACTCTGGTTTCGCGGGTGCATCCGACGCGTGTTTTCCGGAGTCTCTACCTACTCGGTATTGCGCTAGCCTGTGGCCGCATGCCAGCATTCTGCGTTCGTCTTTCTTGTCGCTCAGAAGATCCATCTCATCTTCACCCATTAAGCTGCCCTCTCTTTAACCAACCCGAGTAAATTTGGGTATGCGTTATAGGCACGTTTATACGTGCGGCTTCGGTAAGTAAACTTTCTGTGATAGGAGCCTAAAGTCAGTAGAGCCTGAAGATCGGCAAGGCCGGAGGGCCCCTCTGGTTTAGCCAAGCAGAGAGCTTGATCTTGCCACATGGGGTAACCGATGCCGTAGCTGACAGCATAGGAGCTCGGTACTCTACGCATGCTCAGAACGTAGTGGTTATCCTTTGGAGAACAGGGTAATGCACCTACAGCGGCGAATCATACCAAGACTATCTGCCAGTCGCCGCTTGTTGGCTTAACATGCAATCCCCAAGCGAACTGCGTTTTCCAGACACATAATTCCACTAACTACATAA",
  % rna3(DNA,RNA),
  rna1(RNA,DNA,[]),
  println(RNA),
  nl.
go3 => true.  

rna1([R|Rs]) --> [C], {(C == 'T' -> R = 'U' ; R = C)}, rna1(Rs).
rna1([]) --> [].


rna2(DNA) = replace(DNA,'T','U').

rna3(DNA,RNA) :-
  rna3(DNA,[],RNA).
rna3([],RNA,RNA).
rna3([C|Cs],RNA0,[R|RNA]) :-
  (C == 'T' ->
    R = 'U'
  ;
    R = C
  ),
  rna3(Cs,RNA0,RNA).

rna4(DNA) = [R : C in DNA, R = cond(C == 'T', 'U',C)].