// copied sequences from https://github.com/rust-bio/rust-bio/blob/f04391031526ba48bcf0474a318f8713ac653f9a/benches/distance.rs

#![feature(test)]

extern crate test;
extern crate parasailors;

use parasailors::*;
use test::Bencher;

// 5,000 random nucleotides, GC content = .55
static STR_1: &'static [u8] = b"ATCTAACTATTCCCTGTGCCTTATGGGGGCCTGCGCTATCTGCCTGTCGAACCATAGGACTCGCGCCAGCGCGCAGGCTTGGATCGAGGTGAAATCTCCGGGGCCTAAGACCACGAGCGTCTGGCGTCTTGGCTAACCCCCCTACATGCTGTTATAGACAATCAGTGGAAACCCGGTGCCAGGGGGTGGAGTGACCTTAAGTCAGGGACGATATTAATCGGAAGGAGTATTCAACGCAATGAAGCCGCAGGGTTGGCGTGGGAATGGTGCTTCTGTCCAAGCAGGTAAGGGCATGAGGCCGCAACCGTCCCCCAAGCGTACAGGGTGCACTTTGCAACGATTTCGGAGTCCGGAGACTCGCTGTTTTCGAAATTTGCGCTCAAGGGCGGGTATTGAACCAGGCTTACGCCCAAGAACGTAGCAAGGTGACTCAAACAAGGTACATCTTGCCCGCGTTTCACACGAATCAAGTTGGAGGTTATGGAGCATAGTAACACGTGGGCGGCCAGTGGTCGGTTGCTACACCCCTGCCGCAACGTTGAAGGTCCCGGATTAGACTGGCTGGACCCATGCCGTGACACCCGTCACACTCCATTACCGTCTGCGGGTCACGGCTTGTTGTGGACTGGATTGCCATTCTCTCAGTGTATTACGCAGGCCGGCGCGCGGGTCCCATGTAAACCTGTCATAGCTTACCTGACTCTACTTGGAAGTGTGGCTAGGCCTTTGCCCACGCACCTGGTCGGTCCTCGTTTGCTTTTTAGGACCGGATGAACTACAGAGCGCTGCAAGAATCTCTACCTGCTTTACAAAGCGCTGGGTCCTACTCCAGCGGGATGTTTTATCTAAACACGATGAGAGGAGTATTCGTCAGGCCACATGGCTTTCTTGTCCTGGTCGGATCCATCGTTGGCGCCCGACCCCCCCACTCCGTAGTGAGTTCTTCGTCCGAGCCATTGCATGCCAGATCGGCAGACAGATAGCGGATCCAGTATATCCCTGGAAGCTATAGACGCACAGGTTGGAATCCTAAGCGAAGTCGCGCGTCCGAACCCAGCTCTACTTTAGTGGCCACGGGTTCTGGTCCCCCCGGGCCGCGGAACCGATTAGGGCCATGTACAACAATACTTATTAGTCACCTTTCAGACACGATCTCCCTGCTCAGTGGTATATGGTTCCTGCTATAATTAGCCACCCTCATAAGTTGCACTACTTCTGCGACCCAAGTGCACCCTTACCACGAAGACAGGATTGTCCGATCCCATACTGCGGCCTTGGCAGGGGGTTCGCAAGTCCCACCCCAAACGATGCTGAAGGCTCAGGTTACACAGGCACAAGTGCTATATACGCGAGTTCCCGCTCTTAACCTGGACCGAATGCGGGATCATGCATCGTACCACTGTGTTCGTGTCATCTAGGACGGGCGCAAAGGATACATAGTTCAATCAAGAATACCTTGTATTATTGTACACCTACCGGTCACCAGCCAACAATGTGCGGACGGCGTTGCGACTTGCTGGGCCTGATCTCACCGCCCTAGATACCGCACACTGGGCAATACGAGGTAAAGCCAGTCACCCAGTGTCGATCAACAGCTGACGTAACGGTAAGAGGCTCACAAAATCGCACCGCCGGCGTCCCCTGGGTATTTTACGTCAGCATCGGGTGGACTGGCATGAATCTTTACTCCCAGGCGGAAACGGGTGCGTGGACAAGCGAGCAGCAAACGAAAATTCCTGGCCTGCTTGGTGTCTCGTATCCCTCTTGGAGATCGAGGAAATGTTTCACGACCAAGGGAAAGGTCGCCCTACGAAATAGATTTGCGCTACTGTCCGCATAAGGAGTCCGGTGTAGCGAAGGATGAAGGCGACCCTAGGTAGCAACCGCCGGCTTCGGCGGTAAGGTATCACTCAGGAAGCAGGCACGGAAAGACACGGTCTAGCAGACCGTCTATCGGCTAGGTCAAATAGGGTGCTTTGATATCAGCATGTCCAGCCTTAGAATTCAGTTCAGCGCGCTGGTCTGGGTCGAGATAAAATCACCAGTACCCAAGACCAGGCGGGCTCGCCGCGTTGGCTAATCCTGGTACATCTTGTAATCAATGTTCAGAAGAAAATCTGTGTTAGAGGGACGAGTCACCACGTACCAATAGCGACAACGATCGGTCGGACTATTCATCGTGGTGGTGACGCTCGGATTACGCGGGAAAGGTGCTTGTGTCCCGACAGGCTAGGATATAATGCTGAGGCGCTGCCCCAACCGTTCAGCGTGGGGTTTGCTACAACTTCCGAGTGCTACGTGTGCGAGACCATGTTATGTATGCACAAGGCCGACAATAGGACGTAGCCTTCGAGTTAGTACGTAGCGTGGTCGCACAAGCACAGTAGATCCTCCCCGCGCATCCTATTTATTAAGTTAATTCTATAGCAATACGATCACATGCGGATGGGCAGTGGCCGGTAGTCACACGCCTACCGCGGTGCTCAATGACCGGGACTAGAGAGGCGAAGATTATGGCGTGTGACCCGTTATGCTCGAGTTCGGTCAGAGCGTCATTGCGAGTAGTCGATTGCTTTCCCAATCTCCGAGCGATTTAGCGTGACAGCCCCAGGGAACCCACAAAATGCGATCGCAGTCCACCCGATCGTACACAGAAAGGAGGGTCCCCATACGCCGACGCACCTGTTCGCACGTCGTATGCATAAACGAGCCGCACGAACCAGAGAGCATAAAGAGGACCTCTAGCTCCTTTACAAAGTACAGGTTCGCCTGCCGCCGGGATGCCTTACCTAGACGCAATGACGGACGTATTCCTCTGGCCTCAACGGTTCCTGCTTCCGCTGGGATCCAAGATTGGCGGCCGAAGCCGCCTTTCCAAAGTGAGTCCTTCGTCTGTGACTAACTGTGCCAGATCGTCTTGCAAACTCCCGATCCAGTTTAACTCACCAAACTATAGCCGTACAGACCCAAATCTTAAGTCATATCACGCGACTAGCCTCTGCTCAATTTCTGTGCTCAAGGGTTTTGGTCCGCCCGAGCGGTGCAGCCGATTAGGACCATCTAATGCACTTGTTACAAGACTTCTTTTAAACACTTTCTTCCTGCCCAGTGGCGGATGATAATGGTTGTTGCCAGCCGGCGTGGAAGGTAACAGCACCGGTGCGAGCCTAATGTGCCGTCTCCACCAACACAGGGCTGTCCGGTCGTATAATAGGACTCCGCAATGGGGTTAGCAAGTGGCAGCCTAAACGATGTCGGGGACTCGCGATGTACATGCTCTGGTTCAATACATACGTGACCCGGCAGTTATCCTGCATCGGAACGTCAATCGTGCATCGGGCCAGCGTAATCGTGTCATCTGGGAGGCGGCCGTAGGATAAATAATTCAATAAAGATGTCGTTTTGCTAGTATACGCCTAGGCGTCACCCGCCATCTCTGTGCAGGTGGGCCGACGAGACACTGCCCCTGATTTCTCCGCTACTAATAGCACACACGGGGCAATACCAGCACAAGCCAGTCTCGCGGGAACGCTCGTCAGCATACGAAAGAGCTTGAGGCACGCCAATTCGCACTGTCGGGGTCGCTTGGGTGTTTTGCACTACCGTCAGGTACGCTAGTATGCGTCCTTCCTTCCAGGGGTATGTGGCTGCGTGGTCAAAAGTGCGGCATTCGTATTTGCTCCCCGTGCTTGCTCTCACGAACTTGACCTGGAGATCAAGGAGATGCTTCTTGTGGAACCGGACAGCGCATCAACGCAACGGATCTACGTTACAGCGTGCATAGCGAGAACGGAGTTGCCGACGACGAAAGCGACACTGGGATCTGTCCGTCGTCATTCGCGGAAAGCATCCGCTCACGAGGCGGACACTGATTGACACGGTTTTGCAGAAGGTTAGGGGAATAGGTCAAATTGAGTGGCTTAAAAACGCTATGTCTGGGATTAAAGTGTAGTAAACTGCGGTCAACGGAGACGGTTTTAAGACAGGAGTTCGCAAAACCAGGCGGGGTCGCCACGACGGCTATTCCTGGTGGTTTAGGCGTACAATGTCCTGAAGAATATTTAAGAAAGAAGCACCCCTCGTCGCCTAGAATTACCTACCGCGGTCGACCATACCTTCGATTGTCGCGCCCACCCTCCCATTAGTCGGCAGAGGTGGTTGTGTTGCGATAGCCCAGCATGATATCCTAAGGCGTTACGCCGATGGATATCCCACGGAATTGCCATAGGCGCTGAACGCTACACGGACGATACGAACTTATGTATGGAGCGGGTCATCGAAAGGTCATACCCTTGTAGTTAACATGTAGCCCGGCCCTATTAGTACAGCAGTGCCTTGAGCGGCATTCTCATTATTAAGTTTTCTCTACAGCCAAACGACCAAGTGCACTTCCGCGGAGCGCGGTGGAGACTCGTCCACCCGGCAGCTCTGTAATAGGGACTAAAAGAGTGATGATAATCATGAGTGCCGCGTTATGGTGGTGTCGGAACAGAGCGGTCTTACGGCCAGTCGTATCCCTTCTCGAGTTCCGTCCGGTTAAGCGTGACACTCCCAGTGTACCCGCAAACCGTGATGGCTGTGCTTGGGGTCAATCGCATGTAGGATGGTCTCCAGACACCGGGGCACCAGTTTTCACGCCCAAAGCATAAACGACGAGCAGTCATGAGAGTCTTAGAACTGGACGTGCCGTTTCTCTGCGAACAACACCTCGAGCTGTACCGTTGTTGCGCTGCCTAGATGCAGTGCCGCTCCTATCACATTTGCCTCGACGACTGCCGCCTTCGCTGTTTCCCTAGACACTCAACAGTAAGCGCCTTTTGTAGGCAGGGGCACCCCCTGTCAGTGGCTGCGCCAAAACGTCTTCGGATCCCCTTGTCCAATCAAACTGACCGAATTCTTTCATTTAAGACCCTAATATGACATCATTAGTGACTAAATGCCACTCCCAAAATTCTGCCCAGAAGCGTTTAAGTTCGCCCCACTAAAGTTGTCTAAAACGA";
// 5,000 random nucleotides, GC content = .45
static STR_2: &'static [u8] = b"CTAAAGTGGCGAAATTTATGGTGTGTGACCCGTTATGCTCCATTTCGGTCAGTGGGTCATTGCTAGTAGTCGATTGCATTGTCATTCTCCGAGTGATTTAGCGTGACAGCCGCAGGGAACCCATAAAATGTAATCGTAGTCCATCTGATCGTACTTAGAAATGAAGGTCCCCTTTTACCCACGCACCTGTTTACTCGTCGTTTGCTTTTAAGAACCGCACGAACCACAGAGCATAAAGAGAACCTCTAGTTCCTTTACAAAGTACTGGTTCCCTTTTCAGCAAGATGCCTTATCTAAATGCAATGACAGACGTATTCCTCAGGCCACATCGCTTCCTACTTTCGCTGGGATCCATCATTGGCAGCTGAAACCGCCATTCCATAGTGAGTCCTTCGTCTGTGTCTTTCTGTGCCAAATCGTCTAGCAAATTGCTGATCCAGTTTATCTCACGAAATTATAGTCATACAGACCGAAATTTTAAATCAAATCACGCGACTAGGCTCAGCTTTATTTTAGTGGTCATGGGTTTTGGTCCGCCCGAGCGGTGCAACCGATTAGGACCATGTAAAACATTTGTTACAAGTCTTCTTTTAAATACAATCTTCCTGCTCAGTAGCGCATGATTATCGTTGTTGCTAGCCAGTGTGGTAAGTAACAGCACCACTGCGAGCCTAATGTGCCCTTTCCACGAACACAAGGCTATCCGATCCTATATTAGGATTCCGCAATGGGGTTAGCAAATCGCACCCTAAACGATATTGAAGACTTGCGATGTACATGCTTTGGTACAATACATACGTGTTCCAGTTGTTATCCTGTATCGGAACTTCAATTATGCATCGCACCAGCATATTCATGTCATCTAGGAAGAGCGCGTAGGATAAATAATTCAATTAAGATGTCGTTATGCTAGTATACGTCTACCCGTCACCGGCCATCTGTGTGCAGATGGGGCGACGAGTTATTGACCCTGATTTCTCCACTTCTAATACCACACACTGGGCAATACGAGCTCAAGCTAGTCTCGCAGTAACGCTCATCAGCTAACGAAAGAGTTAAAGGCTCGCTAATTCGCACTGTCAGGGTCTCTTGGGTGTTTTGCACTAGCGTCAGGTAGGCTAGTATGTGTTTTTCCTTCCAGAGGTATGTGGCTGCGTGGTCAAATGTGCAGCATACGTATTTGCTCGACGTGTTTAGTCTCTCATACTTCTCCTGGAGATCAAGGAAATGTTTCTTGTCCAAGTGGACAACGGTTCTACGGAATGGATCTACGTTACTGCCTGCATAAAGAAAACGGAGTTGCTAAGGACGAAAGCGACTTTAGGTTCTAACTGTTGACTTTGGCGGAAAAGTTTCATTCAGGAAGCAGACACTGATTGACACGGTTTAGCAGAACGTTTGAGGATTAGGTTAAATTGAGTGGTTTAATATTGGTATGTCTGGGATTAAAATATAGTATAGTGTGTTAATCGGAGACGAATTAAAGACACGAGTTCCCAAAATCAAGCGGGCTCATTACAACGGTTAATCCTGGTAGTTTACGTGAACAATGTTCTGAAGAAAATTTATGAAAAAAGGACCCGTCATCGCCTACAATTACCTACAACGGTCGACCATACCTTCGATTATCGTGGCCACTCTCGGATTACACGGCAGAGGTGGTTGTGTTCCGATAGGCCAGTATATTATTCTAAGGCGTTACCCTAATCATTTTTCATCGGATTTGCTATAGCCCTTGAACGCTACATGCACGAAACCAAATTATGTATACACTGGGTCATCAATAGGATATAGTCTTGTAGTTAACATGTAGCCCGGCCGTATTAGTACAGTAGAGCCTTCATTGACATTCTGTTTATTAAATTATTTCTACAGCAAAACGATCATATGCAAATCCACAGTGCGCGATAGAGATACATTCACTCGGCTGCTCTGTAATAGGGACTAAAAAAGTGATGATTATCATGAGTGCCCCGTTATGGTCGTGTTCGATCAGAGCGCTCTTACGAGCAGTCGTATACTTTCTCGAATTCCGTGCAGTTAAGCGTGACAGTCCCAGTGAACCCACAAAACGTGATGGCAGTCCATGCAATCATACGCAAGAAGGATGGTCTCCAGACACCGGCGCACCAGTTTTCACGCCGAAAGCATAAACGAGGAGCACAAATGAAAGTGTTTGAACTGGACCTGTAGTTTCTCTACGAAAAATACCTTGAGCTGTTGCGTTGTTGCGCTGCCTAGATGCAGTGTTGCACATATCACTTTTGCTTCAACGACTGCTGCTTTCGCTGTAACCCTAGACAGACAACAATAAGCGCTTTTTGTAGGCAAGAGCTCCGCCTATGACTAACTGCGCCAAAACATCTTCCAATCCCCTTATCCAATTTAATTCATCGAATTCTTACAATTTAGACCCTAATATCACATCATTAGACATTAATTGCCTCTGCCAAAATTCTGTCTACAAATGTTTTAGTTCGCTCCAGTAAAGTTGTTAATAACGACTACTAAATCCGCATGTTACGGGATTTCTTATTAATTCTTTTTTCGTAAGGAACAGCGGATCTTAATGGATGGCGCCAGGTGGTATGGAAGCTAATAGCGCGGGTGAGAGGGTAATTAGCCGTCTTCACCAACACAACGCTATCGGGTCATACTATAAGATTCCACAATGCGACTACTTATAAGATGTCTTAACGGTATCCGCAACTTGTGATGTGCCTACTATGCTTAAATGCATATCTCGCTCAGTAACTTTCCAATATGAGAGCATCAATTGTAGATCGGGCCGAGATAATCATGTCGTCACGGAACTTATTGTAAGAGTAATAATTTAAAAGAGATGTCAGTTTGCTGGTTCACGTAAAGGTTCCTCACACTACCTCTAAATAAGTGAGCGGTCGTGACATTATCCCTGATTTTCTCACTACTATTAGTACTCACGACACAATTCTACCACAGCCTTGTTTCGCCAGAATGCCAGTCAGCATAAAGAAGAGCTCAAGGCAGGTCAACTCGCATTGTGAGAGTTACATGAACGTTCGGCACTACCGACACGAACCTCAGTTAGCGTACATCCTACCAGAGGTCTGTGGCCCCGTGGTCAAAAGTGCGGATTTCGTATTTGCTGCTCGTCAGTACTTTCAGAATCATGACCTGCACGGTAAAAAGACGCTTATTATGGAGTTCGACATGGCAATAACGCGACGAATCTACGTCATGACGAGAATAGTATAAACAAAACTGCTGACGGCAGAAGCGTCAAAGAAGTCTGTAAATTGTTATTCGCGAAAAACATCCGTCTCCGTGGGGGATAATCACCGACGCCATTTTATAGAAGCCTAGGGGAACAGATTGGTTTAATTAGCTTAAGAAAGTAAATTCTGGGATTATACTGTAGTAATCACTAATTTACGGTGAGGGTTTTATGGCGGATTTTTACAAATTCAAACCAGGTGATTTCAACAAATTTTGTTGACGATTTAGGCGCACTATCCCCTAAACTACAAATTAAAAAATAGCGTTCCTTGACGGCTAGAATTACTTACCGGCCTTCACCATACCTTCGATATTCGCGCCCACTCTCCCATTAATCCGTACAAGTGGATGTAATGCGATTGTCCGCTAAGATATTCTAACGTGTAACGTAGATAAGTATTTTACAGAGTTGCCGTACGCGTTGAACACTTCACAGATGATAGGAATTTGCGTATAGAGCGTGTTATTGAGGAGTTATACACCCGTAGACTACAATGGGCCCAACTCAATCAGAACTCGAGTGCCTTGAATAACATACTCATCACTAAACATTCTCAACAATCAATCGAGCAAGTCCATTATCAACGAGTGTGTTGCAGTTTTATTCTCTTGCCAGCATTGTAATAGGCACTAAAAGAATGATGATAGTCATGAGTACTGAGCTAAGACGGCGTCGATGCATAGCGGACTTTCGGTCAATCACAATTCCTCACGAGACTCGTCCTGTTGAGCGTATCACTCTCAATGTACAAGCAACCCAAGAAGGCTGTGCCTGGACTCAACTGGATGCAGGATGAACTCCAGACACGGGGTCACTACTCTTCATACATAAAGCAAGAACGTCGAACAGTCATGAAAGTCTTAGTACCGCACGTACCATCTTACTGTGAATATTGCTTGAAGCTGTACCGTTATTGGGGGGCAAAGATGAAGTTCTCTTCTTTTCATAATTGTACTGACGACAGTCGTGTTCTCGGTTTCTTCAAAGGTTAAAGAATAAAGGCTTATTGTAGGCAGAGGAACGCCCTTTTAGTGGCTGGCGTTAAGTATCTTCGGACCCCCTTGTCTATCCAGATTAATCGAATTCTCTCATTTAGGACCTTAGTAAGTCATCATTGGTATTTGAATGCGACCTTGAAGAAACCGCTTAAAAATGTCAATGGTTGATCCACTAAACTTCATTTAATTAACTCCTAAATCAGCGCGATAGGCTATTAGAGGTTTAATTTTGTATAGCAAGGTACTTCCGATCTTAATGAATGGCCGGAAAAGGTACGGACGCGATATGCGAGGGTGAAAGGGCAAATAGACAGGTTCGTCTTTGTCACGCTAGGAGGCAATTCTATAAGAATGCATATTGCATCGATACATAAAATGTCTCGATCGCATGCGCAATTTGTGAAGTGTCTATTATCCCTAAGCCCATTTCCCGCATAATAACCCCTGATTGTATCCGCATTTGATGCTACCCAGGTTGAGTTAGCGTCGAGCTCGCGGAACTTATTGCATGAGTAGAGTTGAGTAAGAGCTGTTAGATGGCTCGCTGAACTAATAGTTGTCCACAGAACGTCAAGATTAGAAAACGGTTGTAGCATTATCGGAGGTTCTCTAACTACTATCAATACCCGTGTCTTGACTCTGCTGCGGCTACCTATCGCCTGAAAACCAGTTGGTGTTAAGGGATGCTCTGTCCAGGACGCCACATGTAGTGAAACTTACATGTTCGTTGGGTTCACCCGACT";


#[bench]
fn bench_local_reuse_profile(b: &mut Bencher) {
    let identity_matrix = Matrix::new(MatrixType::Identity);
    let profile = Profile::new(STR_1, &identity_matrix);

    b.iter(|| local_alignment_score(&profile, STR_2, 1, 1));
}

#[bench]
fn bench_global_reuse_profile(b: &mut Bencher) {
    let identity_matrix = Matrix::new(MatrixType::Identity);
    let profile = Profile::new(STR_1, &identity_matrix);

    b.iter(|| global_alignment_score(&profile, STR_2, 1, 1));
}

#[bench]
fn bench_semiglobal_reuse_profile(b: &mut Bencher) {
    let identity_matrix = Matrix::new(MatrixType::Identity);
    let profile = Profile::new(STR_1, &identity_matrix);

    b.iter(|| semi_global_alignment_score(&profile, STR_2, 1, 1));
}

#[bench]
fn bench_local_fresh_profile(b: &mut Bencher) {
    let identity_matrix = Matrix::new(MatrixType::Identity);
    b.iter(|| {
        let profile = Profile::new(STR_1, &identity_matrix);
        local_alignment_score(&profile, STR_2, 1, 1)
    });
}

#[bench]
fn bench_global_fresh_profile(b: &mut Bencher) {
    let identity_matrix = Matrix::new(MatrixType::Identity);

    b.iter(|| {
        let profile = Profile::new(STR_1, &identity_matrix);
        global_alignment_score(&profile, STR_2, 1, 1)
    });
}

#[bench]
fn bench_semiglobal_fresh_profile(b: &mut Bencher) {
    let identity_matrix = Matrix::new(MatrixType::Identity);

    b.iter(|| {
        let profile = Profile::new(STR_1, &identity_matrix);
        semi_global_alignment_score(&profile, STR_2, 1, 1)
    });
}