mzdata 0.63.4

A library to read mass spectrometry data formats and a data model for mass spectra
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

use std::{io, path};

use flate2::bufread::MultiGzDecoder;
use std::io::prelude::*;

pub fn is_gzipped(header: &[u8]) -> bool {
    header.starts_with(b"\x1f\x8b")
}

pub fn is_gzipped_extension(path: path::PathBuf) -> (bool, path::PathBuf) {
    if let Some(ext) = path.extension() {
        if ext.eq_ignore_ascii_case("gz") {
            (true, path.with_extension(""))
        } else {
            (false, path)
        }
    } else {
        (false, path)
    }
}

/// A [`flate2::bufread::MultiGzDecoder`] that implements [`std::io::Seek`] by
/// by incrementally reading ahead, or rewinding to the beginning of the file and
/// doing the same.
///
/// Not intended to be efficient, but provides a workable interface.
pub struct RestartableGzDecoder<R: BufRead + Seek> {
    handle: Option<MultiGzDecoder<R>>,
    offset: u64,
}

impl<R: BufRead + Seek> RestartableGzDecoder<R> {
    pub fn new(handle: R) -> Self {
        Self {
            handle: Some(MultiGzDecoder::new(handle)),
            offset: 0,
        }
    }

    fn reset(&mut self) -> io::Result<u64> {
        let handle = self.handle.take().unwrap();
        let mut inner = handle.into_inner();
        let res = inner.seek(io::SeekFrom::Start(0));
        self.handle = Some(MultiGzDecoder::new(inner));
        self.offset = 0;
        res
    }
}

impl<R: BufRead + Seek> Read for RestartableGzDecoder<R> {
    fn read(&mut self, buf: &mut [u8]) -> io::Result<usize> {
        let handle = self.handle.as_mut().unwrap();
        match handle.read(buf) {
            Ok(b) => {
                self.offset += b as u64;
                Ok(b)
            }
            Err(e) => Err(e),
        }
    }
}

impl<R: BufRead + Seek> Seek for RestartableGzDecoder<R> {
    fn seek(&mut self, pos: io::SeekFrom) -> io::Result<u64> {
        match pos {
            io::SeekFrom::Start(o) => {
                self.reset()?;
                let mut buf = vec![0u8; o as usize];
                self.read_exact(&mut buf)?;
                Ok(o)
            }
            io::SeekFrom::End(_) => Err(io::Error::new(
                io::ErrorKind::Unsupported,
                "Cannot seek relative to end of a gzip stream",
            )),
            io::SeekFrom::Current(o) => match o {
                0 => Ok(self.offset),
                _ if o < 0 => {
                    if o.unsigned_abs() > self.offset {
                        Err(io::Error::new(
                            io::ErrorKind::Unsupported,
                            "Cannot earlier than the start of the stream",
                        ))
                    } else {
                        self.seek(io::SeekFrom::Start((self.offset as i64 + o) as u64))
                    }
                }
                _ => {
                    let mut buf = vec![0; o as usize];
                    self.read_exact(&mut buf)?;
                    Ok(self.offset)
                }
            },
        }
    }
}

#[cfg(test)]
mod test {
    use std::fs;

    use super::*;

    #[test]
    fn exercise_restartable() -> io::Result<()> {
        let handle = io::BufReader::new(fs::File::open("test/data/small.mzML.gz")?);
        let mut reader = RestartableGzDecoder::new(handle);
        reader.seek(io::SeekFrom::Current(5113415))?;
        let mut buf = String::new();
        reader.read_to_string(&mut buf)?;
        assert!(buf.starts_with("<indexList count=\"2\">"));
        reader.seek(io::SeekFrom::Start(5145))?;
        buf.clear();
        io::BufReader::new(&mut reader).read_line(&mut buf)?;
        assert!(buf.contains("controllerType=0 controllerNumber=1 scan=1"));
        Ok(())
    }
}