rosalind 0.10.0

extern crate rosalind;
extern crate num;

use rosalind::RosalindError::*;
use rosalind::dna::*;
use rosalind::rna::*;
use rosalind::revc::*;
use rosalind::fib::*;
use rosalind::prot::*;
use rosalind::hamm::*;
use rosalind::subs::*;
use rosalind::gc::*;
use rosalind::iprb::*;
use rosalind::cons::*;
use rosalind::utils::*;

use num::{BigUint};
use num::bigint::{ToBigUint};

// DNA ============================================================================================
#[test]
fn dna_should_return_error_when_unknown_nucleotide_found() {
    assert_eq!(count_dna_nucleotides("Z").unwrap_err(), UnknownNucleotide('Z'));
}

#[test]
fn dna_should_count_dna_nucleotides() {
    let dna = "AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC";
    let dna_nucleotides = DNANucleotides {A: 20, C: 12, G: 17, T: 21};
    assert_eq!(count_dna_nucleotides(dna).unwrap(), dna_nucleotides);
}

#[test]
fn dna_should_format_dna_nucleotides() {
    let dna_nucleotides = DNANucleotides {A: 1, C: 2, G: 3, T: 4};
    assert_eq!(dna_nucleotides.to_string(), "1 2 3 4");
}

#[test]
fn dna_should_skip_new_line_symbol() {
    assert_eq!(count_dna_nucleotides("\n").unwrap(), DNANucleotides {A: 0, C: 0, G: 0, T: 0});
}

// RNA ============================================================================================
#[test]
fn rna_should_return_error_when_unknown_nucleotide_found() {
    assert_eq!(transcribe_dna_into_rna("Z").unwrap_err(), UnknownNucleotide('Z'));
}

#[test]
fn rna_should_transcribe_dna_into_rna() {
    let dna = "GATGGAACTTGACTACGTAAATT";
    assert_eq!(transcribe_dna_into_rna(dna).unwrap(), "GAUGGAACUUGACUACGUAAAUU");
}

#[test]
fn rna_should_skip_new_line_symbol() {
    assert_eq!(transcribe_dna_into_rna("\n").unwrap(), "");
}

// REVC ===========================================================================================
#[test]
fn revc_should_return_error_when_unknown_nucleotide_found() {
    assert_eq!(reverse_complement_dna("Z").unwrap_err(), UnknownNucleotide('Z'));
}

#[test]
fn revc_should_reverse_complement_dna() {
    let dna = "AAAACCCGGT";
    assert_eq!(reverse_complement_dna(dna).unwrap(), "ACCGGGTTTT");
}

#[test]
fn revc_should_skip_new_line_symbol() {
    assert_eq!(reverse_complement_dna("\n").unwrap(), "");
}

// FIB ============================================================================================
#[test]
fn fib_should_return_recurrence_relation() {
    let expected_relation: BigUint = 19.to_biguint().unwrap();
    assert_eq!(recurrence_relation(5, 3).unwrap(), expected_relation);
}

#[test]
fn fib_should_return_recurrence_relation_with_stop() {
    let expected_relation: BigUint = 4.to_biguint().unwrap();
    assert_eq!(recurrence_relation_with_stop(6, 3).unwrap(), expected_relation);
}

// PROT ===========================================================================================
#[test]
fn prot_should_translate_rna_into_protein() {
    let rna = "AUGGCCAUGGCGCCCAGAACUGAGAUCAAUAGUACCCGUAUUAACGGGUGA";
    assert_eq!(translate_rna_into_protein(rna).unwrap(), "MAMAPRTEINSTRING");
}

#[test]
fn prot_should_ignore_new_line_symbol() {
    let rna = "AUGUGA\n";
    assert_eq!(translate_rna_into_protein(rna).unwrap(), "M");
}

#[test]
fn prot_should_return_error_when_cannot_parse_codons() {
    assert_eq!(translate_rna_into_protein("Z").unwrap_err(), CodonParseError);
}

#[test]
fn prot_should_return_error_when_unknown_codon_found() {
    assert_eq!(translate_rna_into_protein("ZZZ").unwrap_err(), UnknownCodon("ZZZ".to_string()));
}

#[test]
fn prot_should_return_number_of_rna_from_protein() {
    assert_eq!(get_number_of_rna_from_protein("MA").unwrap(), 12);
}

#[test]
fn prot_should_return_zero_for_empty_string() {
    assert_eq!(get_number_of_rna_from_protein("").unwrap(), 0);
}

#[test]
fn prot_should_return_amount_of_stop_codons_string() {
    assert_eq!(get_number_of_rna_from_protein("\n").unwrap(), 3);
}

#[test]
fn prot_should_return_error_when_unknown_aminoacid_found() {
    assert_eq!(get_number_of_rna_from_protein("B").unwrap_err(), UnknownAminoAcid('B'));
}

#[test]
fn prot_should_calculate_protein_mass() {
    assert_eq!(get_protein_mass("SKADYEK\n").unwrap(), 821.392f64);
}

#[test]
fn prot_should_not_calculate_protein_mass() {
    assert_eq!(get_protein_mass("AB").unwrap_err(), UnknownAminoAcid('B'));
}

// HAMM ===========================================================================================
#[test]
fn hamm_should_return_hamming_distance() {
    let s = "GAGCCTACTAACGGGAT";
    let t = "CATCGTAATGACGGCCT";
    assert_eq!(hamming_distance(s, t).unwrap(), 7);
}

#[test]
fn hamm_should_return_error_when_strings_have_different_length() {
    assert_eq!(hamming_distance("G", "").unwrap_err(), HammingStringsLengthError);
}

// SUBS ===========================================================================================
#[test]
fn subs_should_return_all_locations_of_substring_t_in_s() {
    let s = "GATATATGCATATACTT";
    let t = "ATAT";
    assert_eq!(motif_lookup(s, t).unwrap(), vec![2, 4, 10]);
}

#[test]
fn subs_should_return_error_when_substring_t_is_longer_than_s() {
    let s = "ATAT";
    let t = "GATATATGCATATACTT";
    assert_eq!(motif_lookup(s, t).unwrap_err(), MotifStringsLengthError);
}

// GC =============================================================================================
#[test]
fn gc_should_return_0_for_empty_dna_string() {
    assert_eq!(gc_content("").unwrap(), 0f32);
}

#[test]
fn gc_should_calculate_gc_content_of_dna() {
    assert_eq!(gc_content("AGCTATAG").unwrap(), 37.5f32);
}

#[test]
fn gc_should_calculate_best_gc_content() {
    let dataset = ">Rosalind_6404
        CCTGCGGAAGATCGGCACTAGAATAGCCAGAACCGTTTCTCTGAGGCTTCCGGCCTTCCC
        TCCCACTAATAATTCTGAGG
        >Rosalind_5959
        CCATCGGTAGCGCATCCTTAGTCCAATTAAGTCCCTATCCAGGCGCTCCGCCGAAGGTCT
        ATATCCATTTGTCAGCAGACACGC
        >Rosalind_0808
        CCACCCTCGTGGTATGGCTAGGCATTCAGGAACCGGAGAACGCTTCAGACCAGCCCGGAC
        TGGGAACCTGCGGGCAGTAGGTGGAAT";

    assert_eq!(best_gc_content_in_dataset(dataset).unwrap(),
    GCcontent {string_id: "Rosalind_0808".to_string(), gc_content: 60.919540f32});
}

// IPRB ===========================================================================================
#[test]
fn iprb_should_retutn_error_when_invalid_input_parameters_provided() {
    assert_eq!(dominant_allele_probability(0, 1, 1).unwrap_err(), InvalidInputParameters);
    assert_eq!(dominant_allele_probability(1, 0, 1).unwrap_err(), InvalidInputParameters);
    assert_eq!(dominant_allele_probability(1, 1, 0).unwrap_err(), InvalidInputParameters);
}

#[test]
fn iprb_should_retutn_dominant_allele_probability() {
    assert_eq!(dominant_allele_probability(2, 2, 2).unwrap(), 0.7833333);
}

// CONS ===========================================================================================
#[test]
fn cons_should_return_error_when_unknown_nucleotide_found() {
  assert_eq!(profile(vec!["Z"]).unwrap_err(), UnknownNucleotide('Z'));
}

#[test]
fn cons_should_calculate_profile() {
    let dna_list = vec![
        "ATCCAGCT",
        "GGGCAACT",
        "ATGGATCT",
        "AAGCAACC",
        "TTGGAACT",
        "ATGCCATT",
        "ATGGCACT",
    ];

    let expected_profile = Profile {
        A: vec![5, 1, 0, 0, 5, 5, 0, 0],
        C: vec![0, 0, 1, 4, 2, 0, 6, 1],
        G: vec![1, 1, 6, 3, 0, 1, 0, 0],
        T: vec![1, 5, 0, 0, 0, 1, 1, 6],
    };

    let prof = profile(dna_list).unwrap();
    assert_eq!(prof, expected_profile);
}

#[test]
fn cons_should_calculate_consensus() {
    let prof = Profile {
        A: vec![5, 1, 0, 0, 5, 5, 0, 0],
        C: vec![0, 0, 1, 4, 2, 0, 6, 1],
        G: vec![1, 1, 6, 3, 0, 1, 0, 0],
        T: vec![1, 5, 0, 0, 0, 1, 1, 6],
    };

    let expected_consensus = "ATGCAACT";

    let cens = consensus(prof).unwrap();
    assert_eq!(cens, expected_consensus);
}

// UTILS ==========================================================================================
#[test]
fn utils_should_parse_fasta_dataset() {
    let fasta_dataset = ">Rosalind_1
        CCTGCGGAAG
        TCCCACTAAT
        >Rosalind_2
        CCATCGGTAG
        ATATCCATTT
        >Rosalind_3
        CCACCCTCGT
        TGGGAACCTG";

    let expected_dataset = vec![
        "CCTGCGGAAGTCCCACTAAT",
        "CCATCGGTAGATATCCATTT",
        "CCACCCTCGTTGGGAACCTG",
    ];

    let dataset = parse_fasta_dataset(fasta_dataset).unwrap();

    assert_eq!(dataset, expected_dataset)
}