conshomfold 0.1.1

ConsHomfold, which Predicts Global Single RNA Secondary Structures to Consider Sparse Global Pairwise RNA Structural Alignments
Documentation 
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

extern crate consprob;

pub use consprob::*;

pub type Mea = Prob;
#[derive(Clone)]
pub struct MeaSs<T> {
  pub bp_pos_pairs: PosPairs<T>,
  pub ea: Mea,
}
pub type Meas = Vec<Mea>;
// pub type MeaMat = HashMap<PosPair, Mea>;
pub type MeaMat<T> = HashMap<PosPair<T>, Mea>;
// pub type Poss = Vec<Pos>;
// pub type PosSeqsWithPoss = HashMap<Pos, Poss>;
pub type PosSeqsWithPoss<T> = HashMap<T, Poss<T>>;
// pub type PosPairs = Vec<PosPair>;
pub type PosPairs<T> = Vec<PosPair<T>>;
// pub type PosPairSeqsWithPosPairs = HashMap<PosPair, PosPairs>;
pub type PosPairSeqsWithPosPairs<T> = HashMap<PosPair<T>, PosPairs<T>>;
pub type MeaSsChar = u8;
pub type MeaSsStr = Vec<MeaSsChar>;

impl<T> MeaSs<T> {
  pub fn new() -> MeaSs<T> {
    MeaSs {
      bp_pos_pairs: PosPairs::<T>::new(),
      ea: 0.,
    }
  }
}

pub const UNPAIRING_BASE: MeaSsChar = '.' as MeaSsChar;
pub const BASE_PAIRING_LEFT_BASE: MeaSsChar = '(' as MeaSsChar;
pub const BASE_PAIRING_RIGHT_BASE: MeaSsChar = ')' as MeaSsChar;

pub fn conshomfold<T: Hash>(bpp_mat: &SparseProbMat<T>, upp_mat: &Probs, seq_len: usize, gamma: Prob) -> MeaSs<T>
where
  T: Unsigned + PrimInt + Hash + FromPrimitive + Integer,
{
  let mut mea_mat = vec![vec![0.; seq_len]; seq_len];
  // let seq_len = seq_len as Pos;
  let seq_len = T::from_usize(seq_len).unwrap();
  // for sub_seq_len in 1 .. seq_len - 1 {
  for sub_seq_len in range(T::one(), seq_len - T::one()) {
    // for i in 1 .. seq_len - sub_seq_len {
    for i in range(T::one(), seq_len - sub_seq_len) {
      // let j = i + sub_seq_len - 1;
      let j = i + sub_seq_len - T::one();
      // let (long_i, long_j) = (i as usize, j as usize);
      let (long_i, long_j) = (i.to_usize().unwrap(), j.to_usize().unwrap());
      if i == j {
        mea_mat[long_i][long_j] = upp_mat[long_i];
        continue;
      }
      let mut mea = mea_mat[long_i + 1][long_j] + upp_mat[long_i];
      let ea = mea_mat[long_i][long_j - 1] + upp_mat[long_j];
      if ea > mea {
        mea = ea;
      }
      let pos_pair = (i, j);
      match bpp_mat.get(&pos_pair) {
        Some(&bpp) => {
          let ea = mea_mat[long_i + 1][long_j - 1] + gamma * bpp;
          if ea > mea {
            mea = ea;
          }
        }, None => {},
      }
      for k in long_i + 1 .. long_j {
        let ea = mea_mat[long_i][k] + mea_mat[k + 1][long_j];
        if ea > mea {
          mea = ea;
        }
      }
      mea_mat[long_i][long_j] = mea;
    }
  }
  // let mut mea_ss = MeaSs::new();
  let mut mea_ss = MeaSs::<T>::new();
  // let mut pos_pair_stack = vec![(1, seq_len - 2)];
  let mut pos_pair_stack = vec![(T::one(), seq_len - T::from_usize(2).unwrap())];
  while pos_pair_stack.len() > 0 {
    let pos_pair = pos_pair_stack.pop().unwrap();
    let (i, j) = pos_pair;
    if j <= i {continue;}
    // let (long_i, long_j) = (i as usize, j as usize);
    let (long_i, long_j) = (i.to_usize().unwrap(), j.to_usize().unwrap());
    let mea = mea_mat[long_i][long_j];
    if mea == mea_mat[long_i + 1][long_j] + upp_mat[long_i] {
      // pos_pair_stack.push((i + 1, j));
      pos_pair_stack.push((i + T::one(), j));
    } else if mea == mea_mat[long_i][long_j - 1] + upp_mat[long_j] {
      // pos_pair_stack.push((i, j - 1));
      pos_pair_stack.push((i, j - T::one()));
    } else if bpp_mat.contains_key(&pos_pair) && mea == mea_mat[long_i + 1][long_j - 1] + gamma * bpp_mat[&pos_pair] {
      // pos_pair_stack.push((i + 1, j - 1));
      pos_pair_stack.push((i + T::one(), j - T::one()));
      mea_ss.bp_pos_pairs.push(pos_pair);
    } else {
      // for k in i + 1 .. j {
      for k in range(i + T::one(), j) {
        // let long_k = k as usize;
        let long_k = k.to_usize().unwrap();
        if mea == mea_mat[long_i][long_k] + mea_mat[long_k + 1][long_j] {
          pos_pair_stack.push((i, k));
          // pos_pair_stack.push((k + 1, j));
          pos_pair_stack.push((k + T::one(), j));
          break;
        }
      }
    }
  }
  // mea_ss.ea = mea_mat[1][seq_len as usize - 2];
  mea_ss.ea = mea_mat[1][seq_len.to_usize().unwrap() - 2];
  mea_ss
}