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
use quick_xml;
use quick_xml::events::Event;
use std::io::BufRead;
use std::io::Cursor;
use crate::io::mzml_parser::types;
pub struct MzMLReader<R: BufRead> {
reader: quick_xml::Reader<R>,
}
impl<R> MzMLReader<R>
where
R: BufRead,
{
pub fn new(reader: quick_xml::Reader<R>) -> Self {
Self { reader }
}
pub fn from_reader(buf_reader: R) -> Self {
let mut xml_reader = quick_xml::Reader::from_reader(buf_reader);
xml_reader.trim_text(false);
Self::new(xml_reader)
}
pub fn read_spectrum(&mut self) -> std::io::Result<types::Spectrum> {
let mut buf = Vec::new();
loop {
match self.reader.read_event(&mut buf) {
Ok(Event::Start(e)) if e.name() != b"spectrum" => {
continue;
}
Ok(Event::Start(e)) => {
let end = b"spectrum";
let mut buf3 = Vec::new();
let mut writer = quick_xml::Writer::new(Cursor::new(&mut buf3));
writer.write_event(Event::Start(e)).unwrap();
loop {
match self.reader.read_event(&mut buf) {
Ok(Event::Start(e)) => {
writer.write_event(Event::Start(e)).unwrap();
}
Ok(Event::Empty(e)) => {
writer.write_event(Event::Empty(e)).unwrap();
}
Ok(Event::Text(e)) => {
writer.write_event(Event::Text(e)).unwrap();
}
Ok(Event::End(e)) => {
if e.name() == end {
writer.write_event(Event::End(e)).unwrap();
break;
} else {
writer.write_event(Event::End(e)).unwrap();
}
}
Ok(Event::Eof) => {
return Err(std::io::Error::new(
std::io::ErrorKind::Other,
"Unexpected Eof Event",
))
}
Err(_) => panic!("fuck"),
Ok(e) => panic!("event: {:?}", e),
}
}
let c = Cursor::new(buf3);
let spectrum: types::Spectrum = quick_xml::de::from_reader(c).unwrap();
return Ok(spectrum);
}
Ok(Event::Eof) => {
return Err(std::io::Error::new(
std::io::ErrorKind::Other,
"Unexpected Eof Event",
))
}
Err(e) => println!("{:?}", e),
_ => {
buf.clear();
}
}
}
}
}
#[cfg(test)]
mod tests {
use super::*;
use std::fs::File;
use std::io::BufReader;
use std::path::PathBuf;
#[test]
fn reader_test() -> Result<(), String> {
let mut d = PathBuf::from(env!("CARGO_MANIFEST_DIR"));
d.push("resources/test/test.mzml.xml");
let file = File::open(d).expect("Couldn't open test file.");
let buf_reader = BufReader::new(file);
let mut xml_reader = quick_xml::Reader::from_reader(buf_reader);
xml_reader.trim_text(false);
let mut mzml_reader = MzMLReader::new(xml_reader);
let spectrum = mzml_reader.read_spectrum();
assert!(spectrum.is_ok());
let spectrum = spectrum.unwrap();
let data = spectrum.binary_data_array_list.binary_data_array[0]
.binary_array_to_vector()
.unwrap();
let expected = vec![
0.0, 1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0, 9.0, 10.0, 11.0, 12.0, 13.0, 14.0,
];
assert_eq!(expected, data);
Ok(())
}
}