timsrust 0.5.3

A crate to read Bruker timsTOF data
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

use std::path::PathBuf;

use timsrust_core::io::Uri;
use timsrust_minitdf::MiniTDFPath;
use timsrust_parquet_spectra::parquet_path::ParquetSpectrumPath;
use timsrust_tdf::{FrameReaderError, TDFPath, TdfFrameReader};

use crate::{
    ImConverter, MzConverter, RtConverter,
    precursor_reader::{
        PrecursorReader, PrecursorReaderBuilder, PrecursorReaderError,
    },
    spectrum_reader::{
        SpectrumReader, SpectrumReaderBuilder, SpectrumReaderError,
    },
};

#[derive(Debug, Clone, PartialEq, Eq, Hash)]
pub(crate) enum TimsTofFileType {
    MiniTdf(MiniTDFPath),
    Tdf(TDFPath),

    Parquet(ParquetSpectrumPath),
}

#[derive(Debug, Clone, PartialEq, Eq, Hash)]
pub struct TimsTofPath {
    uri: Uri,
    file_type: TimsTofFileType,
}

impl TimsTofPath {
    pub fn new(path: impl AsRef<str>) -> Result<Self, TimsTofPathError> {
        if let Ok(tdf) = TDFPath::new(&path) {
            return Ok(Self {
                uri: tdf.uri().clone(),
                file_type: TimsTofFileType::Tdf(tdf),
            });
        }
        if let Ok(minitdf) = MiniTDFPath::new(&path) {
            return Ok(Self {
                uri: minitdf.uri().clone(),
                file_type: TimsTofFileType::MiniTdf(minitdf),
            });
        }

        if let Ok(parquet) = ParquetSpectrumPath::new(&path) {
            return Ok(Self {
                uri: parquet.uri().clone(),
                file_type: TimsTofFileType::Parquet(parquet),
            });
        }
        Err(TimsTofPathError::UnknownType(PathBuf::from(path.as_ref())))
    }

    pub(crate) fn file_type(&self) -> &TimsTofFileType {
        &self.file_type
    }

    /// Create a [`SpectrumReader`] for this path.
    pub fn spectrum_reader(
        &self,
    ) -> Result<SpectrumReader, SpectrumReaderError> {
        SpectrumReaderBuilder::default().with_path(self).finalize()
    }

    /// Create a [`PrecursorReader`] for this path.
    pub fn precursor_reader(
        &self,
    ) -> Result<PrecursorReader, PrecursorReaderError> {
        PrecursorReaderBuilder::default().with_path(self).finalize()
    }

    /// Create a [`TdfFrameReader`] for this path.
    ///
    /// Only supported for `.d` (TDF) files; returns
    /// [`TimsTofFrameReaderError::NotSupported`] for all other file types.
    pub fn frame_reader(
        &self,
    ) -> Result<TdfFrameReader, TimsTofFrameReaderError> {
        match &self.file_type {
            TimsTofFileType::Tdf(tdf_path) => {
                Ok(TdfFrameReader::new(tdf_path)?)
            },
            _ => Err(TimsTofFrameReaderError::NotSupported),
        }
    }

    /// Create an [`MzConverter`] (TOF index → m/z) for this path.
    pub fn mz_converter(&self) -> Option<MzConverter> {
        MzConverter::new(self)
    }

    /// Create an [`ImConverter`] (scan index → ion mobility) for this path.
    pub fn im_converter(&self) -> Option<ImConverter> {
        ImConverter::new(self)
    }

    /// Create an [`RtConverter`] (frame index → retention time) for this path.
    pub fn rt_converter(&self) -> Option<RtConverter> {
        RtConverter::new(self)
    }
}

impl AsRef<str> for TimsTofPath {
    fn as_ref(&self) -> &str {
        self.uri.as_ref()
    }
}

pub trait TimsTofPathLike: AsRef<str> {
    fn to_timstof_path(&self) -> Result<TimsTofPath, TimsTofPathError>;
}

impl<T: AsRef<str>> TimsTofPathLike for T {
    fn to_timstof_path(&self) -> Result<TimsTofPath, TimsTofPathError> {
        TimsTofPath::new(self)
    }
}

#[derive(Debug, thiserror::Error)]
pub enum TimsTofPathError {
    #[error("{0}")]
    IO(#[from] std::io::Error),
    #[error("No valid type found for {0}")]
    UnknownType(PathBuf),
}

/// Error returned by [`TimsTofPath::frame_reader`].
#[derive(Debug, thiserror::Error)]
pub enum TimsTofFrameReaderError {
    #[error("{0}")]
    FrameReaderError(#[from] FrameReaderError),
    #[error("Frame reading is not supported for this file type")]
    NotSupported,
}