1
  2
  3
  4
  5
  6
  7
  8
  9
 10
 11
 12
 13
 14
 15
 16
 17
 18
 19
 20
 21
 22
 23
 24
 25
 26
 27
 28
 29
 30
 31
 32
 33
 34
 35
 36
 37
 38
 39
 40
 41
 42
 43
 44
 45
 46
 47
 48
 49
 50
 51
 52
 53
 54
 55
 56
 57
 58
 59
 60
 61
 62
 63
 64
 65
 66
 67
 68
 69
 70
 71
 72
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177

use utils::*;
use std::f64::NEG_INFINITY;

struct LogSaPpfMatrices {
  log_sa_forward_ppf_matrix_4_char_alignment: LogPpfMatrix,
  log_sa_forward_ppf_matrix_4_gap_1: LogPpfMatrix,
  log_sa_forward_ppf_matrix_4_gap_2: LogPpfMatrix,
  log_sa_backward_ppf_matrix_4_char_alignment: LogPpfMatrix,
  log_sa_backward_ppf_matrix_4_gap_1: LogPpfMatrix,
  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]
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_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]
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 + (i - 1) as SaScore * sa_sps.base_extending_gap_penalty + 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 + (i - 1) as SaScore * sa_sps.base_extending_gap_penalty + 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 ca_score = sa_sps.ca_sm[&(sp.0[i], sp.1[j])];
      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] + 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_forward_ppf_matrix_4_gap_1[i - 1][j - 1] + ca_score;
      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] + ca_score;
      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);
      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 1 .. 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 + (slp.0 - 2 - i) as SaScore * sa_sps.base_extending_gap_penalty;
  }
  for i in 1 .. 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 + (slp.1 - 2 - i) as SaScore * sa_sps.base_extending_gap_penalty;
  }
  for i in (1 .. slp.0 - 1).rev() {
    for j in (1 .. slp.1 - 1).rev() {
      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] + sa_sps.ca_sm[&(sp.0[i + 1], sp.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_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] + sa_sps.ca_sm[&(sp.0[i + 1], sp.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_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] + sa_sps.ca_sm[&(sp.0[i + 1], sp.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_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
}