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use utils::*; pub struct LogSaPpfMatrices { pub log_sa_forward_ppf_matrix_4_char_alignment: LogPpfMatrix, pub log_sa_forward_ppf_matrix_4_gap_1: LogPpfMatrix, pub log_sa_forward_ppf_matrix_4_gap_2: LogPpfMatrix, pub log_sa_backward_ppf_matrix_4_char_alignment: LogPpfMatrix, pub log_sa_backward_ppf_matrix_4_gap_1: LogPpfMatrix, pub log_sa_backward_ppf_matrix_4_gap_2: LogPpfMatrix, } impl LogSaPpfMatrices { fn new(slp: &(usize, usize)) -> LogSaPpfMatrices { let ni_matrix = vec![vec![NEG_INFINITY; slp.1]; slp.0]; LogSaPpfMatrices { log_sa_forward_ppf_matrix_4_char_alignment: ni_matrix.clone(), log_sa_forward_ppf_matrix_4_gap_1: ni_matrix.clone(), log_sa_forward_ppf_matrix_4_gap_2: ni_matrix.clone(), log_sa_backward_ppf_matrix_4_char_alignment: ni_matrix.clone(), log_sa_backward_ppf_matrix_4_gap_1: ni_matrix.clone(), log_sa_backward_ppf_matrix_4_gap_2: ni_matrix, } } } impl SaScoringParams { pub fn new(ca_sm: &CaScoreMatrix, base_opening_gap_penalty: SaScore, base_extending_gap_penalty: SaScore) -> SaScoringParams { SaScoringParams { ca_sm: ca_sm.clone(), base_opening_gap_penalty: base_opening_gap_penalty, base_extending_gap_penalty: base_extending_gap_penalty, } } } #[inline] pub fn durbin_algo(seq_pair: &SsPair, sa_sps: &SaScoringParams) -> ProbMatrix { let seq_len_pair = (seq_pair.0.len(), seq_pair.1.len()); let log_sa_ppf_matrices = get_log_sa_ppf_matrices(seq_pair, &seq_len_pair, sa_sps); let log_cap_matrix = get_log_char_alignment_prob_matrix(&log_sa_ppf_matrices, &seq_len_pair); get_cap_matrix(&log_cap_matrix) } #[inline] pub fn get_cap_matrix(log_cap_matrix: &LogProbMatrix) -> ProbMatrix { log_cap_matrix.iter().map(|xs| xs.iter().map(|&x| x.exp()).collect()).collect() } #[inline] pub fn get_log_cap_matrix(seq_pair: &SsPair, sa_sps: &SaScoringParams) -> LogProbMatrix { let seq_len_pair = (seq_pair.0.len(), seq_pair.1.len()); let log_sa_ppf_matrices = get_log_sa_ppf_matrices(seq_pair, &seq_len_pair, sa_sps); get_log_char_alignment_prob_matrix(&log_sa_ppf_matrices, &seq_len_pair) } #[inline] pub fn get_cap_matrix_and_unaligned_char_psp(sp: &SsPair, sa_sps: &SaScoringParams) -> (ProbMatrix, ProbSeqPair) { let slp = (sp.0.len(), sp.1.len()); let log_sa_ppf_matrices = get_log_sa_ppf_matrices(sp, &slp, sa_sps); let log_cap_matrix = get_log_char_alignment_prob_matrix(&log_sa_ppf_matrices, &slp); let mut ucp_seq_pair = (vec![NEG_INFINITY; slp.0], vec![NEG_INFINITY; slp.1]); for i in 0 .. slp.0 { let mut eps_of_terms_4_log_prob = EpsOfTerms4LogProb::new(); let mut max_ep_of_term_4_log_prob = NEG_INFINITY; for j in 0 .. slp.1 { let ep_of_term_4_log_prob = log_cap_matrix[i][j]; if max_ep_of_term_4_log_prob < ep_of_term_4_log_prob {max_ep_of_term_4_log_prob = ep_of_term_4_log_prob;} eps_of_terms_4_log_prob.push(ep_of_term_4_log_prob); } ucp_seq_pair.0[i] = 1. - logsumexp(&eps_of_terms_4_log_prob[..], max_ep_of_term_4_log_prob).exp(); } for i in 0 .. slp.1 { let mut eps_of_terms_4_log_prob = EpsOfTerms4LogProb::new(); let mut max_ep_of_term_4_log_prob = NEG_INFINITY; for j in 0 .. slp.0 { let ep_of_term_4_log_prob = log_cap_matrix[j][i]; if max_ep_of_term_4_log_prob < ep_of_term_4_log_prob {max_ep_of_term_4_log_prob = ep_of_term_4_log_prob;} eps_of_terms_4_log_prob.push(ep_of_term_4_log_prob); } ucp_seq_pair.1[i] = 1. - logsumexp(&eps_of_terms_4_log_prob[..], max_ep_of_term_4_log_prob).exp(); } (get_cap_matrix(&log_cap_matrix), ucp_seq_pair) } #[inline] pub fn get_log_sa_ppf_matrices(sp: &SsPair, slp: &(usize, usize), sa_sps: &SaScoringParams) -> LogSaPpfMatrices { let mut log_sa_ppf_matrices = LogSaPpfMatrices::new(slp); log_sa_ppf_matrices.log_sa_forward_ppf_matrix_4_char_alignment[0][0] = sa_sps.ca_sm[&(sp.0[0], sp.1[0])]; for i in 1 .. slp.0 { log_sa_ppf_matrices.log_sa_forward_ppf_matrix_4_char_alignment[i][0] = sa_sps.base_opening_gap_penalty + get_begp(&(1, i - 1), sa_sps) + sa_sps.ca_sm[&(sp.0[i], sp.1[0])]; } for i in 1 .. slp.1 { log_sa_ppf_matrices.log_sa_forward_ppf_matrix_4_char_alignment[0][i] = sa_sps.base_opening_gap_penalty + get_begp(&(1, i - 1), sa_sps) + sa_sps.ca_sm[&(sp.0[0], sp.1[i])]; } for i in 1 .. slp.0 { for j in 1 .. slp.1 { let mut eps_of_terms_4_log_pf = EpsOfTerms4LogPf::new(); let mut max_ep_of_term_4_log_pf = log_sa_ppf_matrices.log_sa_forward_ppf_matrix_4_char_alignment[i - 1][j - 1]; eps_of_terms_4_log_pf.push(max_ep_of_term_4_log_pf); let ep_of_term_4_log_pf = log_sa_ppf_matrices.log_sa_forward_ppf_matrix_4_gap_1[i - 1][j - 1]; if max_ep_of_term_4_log_pf < ep_of_term_4_log_pf {max_ep_of_term_4_log_pf = ep_of_term_4_log_pf;} eps_of_terms_4_log_pf.push(ep_of_term_4_log_pf); let ep_of_term_4_log_pf = log_sa_ppf_matrices.log_sa_forward_ppf_matrix_4_gap_2[i - 1][j - 1]; if max_ep_of_term_4_log_pf < ep_of_term_4_log_pf {max_ep_of_term_4_log_pf = ep_of_term_4_log_pf;} eps_of_terms_4_log_pf.push(ep_of_term_4_log_pf); log_sa_ppf_matrices.log_sa_forward_ppf_matrix_4_char_alignment[i][j] = logsumexp(&eps_of_terms_4_log_pf[..], max_ep_of_term_4_log_pf) + sa_sps.ca_sm[&(sp.0[i], sp.1[j])]; let mut eps_of_terms_4_log_pf = EpsOfTerms4LogPf::new(); let mut max_ep_of_term_4_log_pf = log_sa_ppf_matrices.log_sa_forward_ppf_matrix_4_char_alignment[i - 1][j] + sa_sps.base_opening_gap_penalty; eps_of_terms_4_log_pf.push(max_ep_of_term_4_log_pf); let ep_of_term_4_log_pf = log_sa_ppf_matrices.log_sa_forward_ppf_matrix_4_gap_1[i - 1][j] + sa_sps.base_extending_gap_penalty; if max_ep_of_term_4_log_pf < ep_of_term_4_log_pf {max_ep_of_term_4_log_pf = ep_of_term_4_log_pf;} eps_of_terms_4_log_pf.push(ep_of_term_4_log_pf); log_sa_ppf_matrices.log_sa_forward_ppf_matrix_4_gap_1[i][j] = logsumexp(&eps_of_terms_4_log_pf[..], max_ep_of_term_4_log_pf); let mut eps_of_terms_4_log_pf = EpsOfTerms4LogPf::new(); let mut max_ep_of_term_4_log_pf = log_sa_ppf_matrices.log_sa_forward_ppf_matrix_4_char_alignment[i][j - 1] + sa_sps.base_opening_gap_penalty; eps_of_terms_4_log_pf.push(max_ep_of_term_4_log_pf); let ep_of_term_4_log_pf = log_sa_ppf_matrices.log_sa_forward_ppf_matrix_4_gap_2[i][j - 1] + sa_sps.base_extending_gap_penalty; if max_ep_of_term_4_log_pf < ep_of_term_4_log_pf {max_ep_of_term_4_log_pf = ep_of_term_4_log_pf;} eps_of_terms_4_log_pf.push(ep_of_term_4_log_pf); log_sa_ppf_matrices.log_sa_forward_ppf_matrix_4_gap_2[i][j] = logsumexp(&eps_of_terms_4_log_pf[..], max_ep_of_term_4_log_pf); } } log_sa_ppf_matrices.log_sa_backward_ppf_matrix_4_char_alignment[slp.0 - 1][slp.1 - 1] = 0.; log_sa_ppf_matrices.log_sa_backward_ppf_matrix_4_gap_1[slp.0 - 1][slp.1 - 1] = 0.; log_sa_ppf_matrices.log_sa_backward_ppf_matrix_4_gap_2[slp.0 - 1][slp.1 - 1] = 0.; for i in 0 .. slp.0 - 1 { log_sa_ppf_matrices.log_sa_backward_ppf_matrix_4_char_alignment[i][slp.1 - 1] = sa_sps.base_opening_gap_penalty + get_begp(&(i + 2, slp.0 - 1), sa_sps); } for i in 0 .. slp.1 - 1 { log_sa_ppf_matrices.log_sa_backward_ppf_matrix_4_char_alignment[slp.0 - 1][i] = sa_sps.base_opening_gap_penalty + get_begp(&(i + 2, slp.1 - 1), sa_sps); } for i in (0 .. slp.0 - 1).rev() { for j in (0 .. slp.1 - 1).rev() { let mut eps_of_terms_4_log_pf = EpsOfTerms4LogPf::new(); let ca_score = sa_sps.ca_sm[&(sp.0[i + 1], sp.1[j + 1])]; let mut max_ep_of_term_4_log_pf = log_sa_ppf_matrices.log_sa_backward_ppf_matrix_4_char_alignment[i + 1][j + 1] + ca_score; eps_of_terms_4_log_pf.push(max_ep_of_term_4_log_pf); let ep_of_term_4_log_pf = log_sa_ppf_matrices.log_sa_backward_ppf_matrix_4_gap_1[i + 1][j] + sa_sps.base_opening_gap_penalty; if max_ep_of_term_4_log_pf < ep_of_term_4_log_pf {max_ep_of_term_4_log_pf = ep_of_term_4_log_pf;} eps_of_terms_4_log_pf.push(ep_of_term_4_log_pf); let ep_of_term_4_log_pf = log_sa_ppf_matrices.log_sa_backward_ppf_matrix_4_gap_2[i][j + 1] + sa_sps.base_opening_gap_penalty; if max_ep_of_term_4_log_pf < ep_of_term_4_log_pf {max_ep_of_term_4_log_pf = ep_of_term_4_log_pf;} eps_of_terms_4_log_pf.push(ep_of_term_4_log_pf); log_sa_ppf_matrices.log_sa_backward_ppf_matrix_4_char_alignment[i][j] = logsumexp(&eps_of_terms_4_log_pf[..], max_ep_of_term_4_log_pf); let mut eps_of_terms_4_log_pf = EpsOfTerms4LogPf::new(); let mut max_ep_of_term_4_log_pf = log_sa_ppf_matrices.log_sa_backward_ppf_matrix_4_char_alignment[i + 1][j + 1] + ca_score; eps_of_terms_4_log_pf.push(max_ep_of_term_4_log_pf); let ep_of_term_4_log_pf = log_sa_ppf_matrices.log_sa_backward_ppf_matrix_4_gap_1[i + 1][j] + sa_sps.base_extending_gap_penalty; if max_ep_of_term_4_log_pf < ep_of_term_4_log_pf {max_ep_of_term_4_log_pf = ep_of_term_4_log_pf;} eps_of_terms_4_log_pf.push(ep_of_term_4_log_pf); log_sa_ppf_matrices.log_sa_backward_ppf_matrix_4_gap_1[i][j] = logsumexp(&eps_of_terms_4_log_pf[..], max_ep_of_term_4_log_pf); let mut eps_of_terms_4_log_pf = EpsOfTerms4LogPf::new(); let mut max_ep_of_term_4_log_pf = log_sa_ppf_matrices.log_sa_backward_ppf_matrix_4_char_alignment[i + 1][j + 1] + ca_score; eps_of_terms_4_log_pf.push(max_ep_of_term_4_log_pf); let ep_of_term_4_log_pf = log_sa_ppf_matrices.log_sa_backward_ppf_matrix_4_gap_2[i][j + 1] + sa_sps.base_extending_gap_penalty; if max_ep_of_term_4_log_pf < ep_of_term_4_log_pf {max_ep_of_term_4_log_pf = ep_of_term_4_log_pf;} eps_of_terms_4_log_pf.push(ep_of_term_4_log_pf); log_sa_ppf_matrices.log_sa_backward_ppf_matrix_4_gap_2[i][j] = logsumexp(&eps_of_terms_4_log_pf[..], max_ep_of_term_4_log_pf); } } log_sa_ppf_matrices } #[inline] fn get_log_char_alignment_prob_matrix(log_sa_ppf_matrices: &LogSaPpfMatrices, slp: &(usize, usize)) -> LogProbMatrix { let mut eps_of_terms_4_log_pf = EpsOfTerms4LogPf::new(); let mut max_ep_of_term_4_log_pf = log_sa_ppf_matrices.log_sa_forward_ppf_matrix_4_char_alignment[slp.0 - 1][slp.1 - 1]; eps_of_terms_4_log_pf.push(max_ep_of_term_4_log_pf); let ep_of_term_4_log_pf = log_sa_ppf_matrices.log_sa_forward_ppf_matrix_4_gap_1[slp.0 - 1][slp.1 - 1]; if max_ep_of_term_4_log_pf < ep_of_term_4_log_pf {max_ep_of_term_4_log_pf = ep_of_term_4_log_pf;} eps_of_terms_4_log_pf.push(ep_of_term_4_log_pf); let ep_of_term_4_log_pf = log_sa_ppf_matrices.log_sa_forward_ppf_matrix_4_gap_2[slp.0 - 1][slp.1 - 1]; if max_ep_of_term_4_log_pf < ep_of_term_4_log_pf {max_ep_of_term_4_log_pf = ep_of_term_4_log_pf;} eps_of_terms_4_log_pf.push(ep_of_term_4_log_pf); let log_sa_ppf = logsumexp(&eps_of_terms_4_log_pf, max_ep_of_term_4_log_pf); let mut log_cap_matrix = vec![vec![NEG_INFINITY; slp.1]; slp.0]; for i in 0 .. slp.0 { for j in 0 .. slp.1 { log_cap_matrix[i][j] = log_sa_ppf_matrices.log_sa_forward_ppf_matrix_4_char_alignment[i][j] + log_sa_ppf_matrices.log_sa_backward_ppf_matrix_4_char_alignment[i][j] - log_sa_ppf; } } log_cap_matrix } #[inline] fn get_begp(pp: &PosPair, sa_sps: &SaScoringParams) -> SaScore { (pp.1 + 1 - pp.0) as SaScore * sa_sps.base_extending_gap_penalty }