nafcodec 0.3.1

Rust coder/decoder for Nucleotide Archive Format (NAF) files.
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
138

use std::io::Error as IoError;
use std::io::Read;
use std::io::Seek;
use std::io::SeekFrom;
use std::sync::RwLock;

use super::Rc;

pub struct IoSlice<R: Read + Seek> {
    reader: Rc<RwLock<R>>,
    pos: u64,
    start: u64,
    end: u64,
}

impl<R: Read + Seek> IoSlice<R> {
    pub fn new(reader: Rc<RwLock<R>>, start: u64, end: u64) -> Self {
        Self {
            reader,
            start,
            end,
            pos: start,
        }
    }
}

impl<R: Read + Seek> Read for IoSlice<R> {
    fn read(&mut self, mut buffer: &mut [u8]) -> Result<usize, IoError> {
        let mut reader = self.reader.write().unwrap();
        reader.seek(SeekFrom::Start(self.pos))?;

        let remaining = (self.end - self.pos) as usize;
        if buffer.len() > remaining {
            buffer = &mut buffer[..remaining];
        }

        let n = reader.read(buffer)?;
        self.pos += n as u64;

        Ok(n)
    }
}

impl<R: Read + Seek> Seek for IoSlice<R> {
    fn seek(&mut self, pos: SeekFrom) -> Result<u64, IoError> {
        match pos {
            SeekFrom::Start(n) => {
                if self.start + n > self.end {
                    self.pos = self.end;
                } else {
                    self.pos = self.start + n;
                }
            }
            SeekFrom::End(n) => {
                if n > 0 {
                    self.pos = self.end;
                } else if n + (self.end as i64) < (self.start as i64) {
                    return Err(IoError::new(
                        std::io::ErrorKind::InvalidInput,
                        "invalid seek to a negative or overflowing position",
                    ));
                } else {
                    self.pos = (self.end as i64 + n) as u64;
                }
            }
            SeekFrom::Current(n) => {
                if n + (self.pos as i64) > (self.end as i64) {
                    self.pos = self.end;
                } else {
                    self.pos = (self.pos as i64 + n) as u64;
                }
            }
        }
        Ok(self.pos)
    }

    fn rewind(&mut self) -> Result<(), IoError> {
        self.pos = self.start;
        Ok(())
    }

    #[cfg(feature = "nightly")]
    fn stream_len(&mut self) -> Result<u64, IoError> {
        Ok(self.end - self.start)
    }

    fn stream_position(&mut self) -> Result<u64, IoError> {
        Ok(self.pos - self.start)
    }
}

#[cfg(test)]
mod tests {
    use super::*;

    use std::io::Cursor;

    #[test]
    fn read() {
        let data = b"ABCDEF";
        let cursor = Cursor::new(&data);
        let f = Rc::new(RwLock::new(cursor));

        let mut s1 = IoSlice::new(f.clone(), 0, 2);
        let mut s2 = IoSlice::new(f.clone(), 2, 4);
        let mut s3 = IoSlice::new(f.clone(), 4, 6);

        assert_eq!(std::io::read_to_string(&mut s2).unwrap(), "CD");
        assert_eq!(std::io::read_to_string(&mut s1).unwrap(), "AB");
        assert_eq!(std::io::read_to_string(&mut s3).unwrap(), "EF");
        assert_eq!(std::io::read_to_string(&mut s2).unwrap(), "");
    }

    #[test]
    fn seek() {
        let data = b"ABCDEF";
        let cursor = Cursor::new(&data);
        let f = Rc::new(RwLock::new(cursor));

        let mut s1 = IoSlice::new(f.clone(), 0, 2);
        let mut s2 = IoSlice::new(f.clone(), 2, 4);
        let mut s3 = IoSlice::new(f.clone(), 4, 6);

        s2.seek(SeekFrom::Start(1)).unwrap();
        assert_eq!(std::io::read_to_string(&mut s1).unwrap(), "AB");
        assert_eq!(std::io::read_to_string(&mut s2).unwrap(), "D");

        s3.seek(SeekFrom::End(-1)).unwrap();
        assert_eq!(std::io::read_to_string(&mut s3).unwrap(), "F");

        s1.seek(SeekFrom::End(-2)).unwrap();
        assert_eq!(std::io::read_to_string(&mut s3).unwrap(), "");
        assert_eq!(std::io::read_to_string(&mut s1).unwrap(), "AB");

        s1.seek(SeekFrom::Current(-1)).unwrap();
        assert_eq!(std::io::read_to_string(&mut s1).unwrap(), "B");
    }
}