cs 0.0.4

Find common substrings among multiple input strings
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
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137

//! # Example
//!
//! ```
//! use cs::longest_common_substring;
//! let lcs = longest_common_substring(&[
//!     "ZYABCAGB",
//!     "BCAGDTZYY",
//!     "DACAGZZYSC",
//!     "CAGYZYSAU",
//!     "CAZYUCAGF",
//! ]);
//! assert_eq!(lcs, "CAG");
//! ```

use suffix::SuffixTable;
/// Compute the longest common substring among a slice of strings
///
/// # Example
///
/// ```
/// use cs::longest_common_substring;
/// let lcs = longest_common_substring(&[
///     "ZYABCAGB",
///     "BCAGDTZYY",
///     "DACAGZZYSC",
///     "CAGYZYSAU",
///     "CAZYUCAGF",
/// ]);
/// assert_eq!(lcs, "CAG");
/// ```
pub fn longest_common_substring<T: AsRef<str>>(strs: &[T]) -> String {
    let number_of_strings = strs.len();
    let mut boundaries = Vec::new();
    let mut concatenated = String::new();
    for s in strs.iter() {
        concatenated.push_str(s.as_ref());
        boundaries.push(concatenated.len());
    }
    let sa = SuffixTable::new(&concatenated);
    let pos = sa.table();
    let lcp = sa.lcp_lens();
    let mut lcs_len = 0u32;
    let mut lcs_pos: u32 = 0;

    'outer: for (win_p, win_l) in pos
        .windows(number_of_strings)
        .zip(lcp.windows(number_of_strings))
    {
        // examine if each window contains substrings coming from different original strings
        // use a vector of booleans to track whether a substring has been included.
        // upon duplication, abort and continue scanning the next frame
        let mut included = vec![false; number_of_strings];
        for &p in win_p {
            let n = string_number(p, &boundaries);
            if included[n] {
                continue 'outer;
            } else {
                included[n] = true;
            }
        }
        // this window contains one and only one suffixes from each original strings
        // calculate the LCS within this window
        let m = win_l.iter().skip(1).min().unwrap(); // win_l always has length 3
        let this_cs_len = *m;
        let this_cs_pos = win_p[0];
        // let this_cs = concatenated
        //     .chars()
        //     .skip(this_cs_pos as usize)
        //     .take(this_cs_len as usize)
        //     .collect::<String>();

        if *m > lcs_len {
            lcs_len = this_cs_len;
            lcs_pos = this_cs_pos;
        }
    }

    let lcs_len = lcs_len as usize;
    let lcs_pos = lcs_pos as usize;

    std::str::from_utf8(&concatenated.as_bytes()[lcs_pos..lcs_pos + lcs_len])
        .unwrap()
        .to_owned()
}

/// compute a vector of common substring among a slice of input substrings. The output is sorted lexicographically.
pub fn common_substrings<T: AsRef<str>>(strs: &[T]) -> Vec<String> {
    let number_of_strings = strs.len();
    let mut boundaries = Vec::new();
    let mut concatenated = String::new();
    for s in strs.iter() {
        concatenated.push_str(s.as_ref());
        boundaries.push(concatenated.len());
    }
    let sa = SuffixTable::new(&concatenated);
    let pos = sa.table();
    let lcp = sa.lcp_lens();

    let mut css = Vec::new();

    'outer: for (win_p, win_l) in pos
        .windows(number_of_strings)
        .zip(lcp.windows(number_of_strings))
    {
        // examine if each window contains substrings coming from different original strings
        // use a vector of booleans to track whether a substring has been included.
        // upon duplication, abort and continue scanning the next frame
        let mut included = vec![false; number_of_strings];
        for &p in win_p {
            let n = string_number(p, &boundaries);
            if included[n] {
                continue 'outer;
            } else {
                included[n] = true;
            }
        }
        // this window contains one and only one suffixes from each original strings
        // calculate the LCS within this window
        let m = win_l.iter().skip(1).min().unwrap(); // win_l always has length 3
        let this_cs_len = *m as usize;
        let this_cs_pos = win_p[0] as usize;
        let this_cs =
            std::str::from_utf8(&concatenated.as_bytes()[this_cs_pos..this_cs_pos + this_cs_len])
                .unwrap()
                .to_owned();
        css.push(this_cs);
    }

    css
}

fn string_number(position: u32, boundaries: &[usize]) -> usize {
    match boundaries.binary_search(&(position as usize)) {
        Ok(idx) => idx + 1,
        Err(idx) => idx,
    }
}