mzident 0.1.0

Handle all kinds of identified peptidoform 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
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157

use std::{borrow::Cow, marker::PhantomData, ops::Range};

use serde::{Deserialize, Serialize};

use crate::{
    BoxedIdentifiedPeptideIter, FastaIdentifier, IdentifiedPeptidoform, IdentifiedPeptidoformData,
    IdentifiedPeptidoformSource, IdentifiedPeptidoformVersion, KnownFileFormat, MetaData,
    PeptidoformPresent, SpectrumId, SpectrumIds, common_parser::Location,
};
use mzcore::{
    csv::{CsvLine, parse_csv},
    ontology::Ontologies,
    sequence::{
        CompoundPeptidoformIon, FlankingSequence, Peptidoform, SemiAmbiguous,
        SloppyParsingParameters,
    },
    system::{Mass, MassOverCharge, Ratio, Time, isize::Charge},
};

static NUMBER_ERROR: (&str, &str) = (
    "Invalid π-HelixNovo line",
    "This column is not a number but it is required to be a number in this format",
);

format_family!(
    PiHelixNovo,
    SemiAmbiguous, PeptidoformPresent, [&PIHELIXNOVO_V1_1], b'\t', Some(vec!["title".to_string(),"peptide".to_string(),"score".to_string()]);
    required {
        title: String, |location: Location, _| Ok(location.get_string());
        peptide: Peptidoform<SemiAmbiguous>, |location: Location, ontologies: &Ontologies| Peptidoform::sloppy_pro_forma(
            location.full_line(),
            location.location.clone(),
            ontologies,
            &SloppyParsingParameters {
                allow_unwrapped_modifications: true,
                ..Default::default()
            },
        ).map_err(BoxedError::to_owned);
        score: f64, |location: Location, _| location.parse::<f64>(NUMBER_ERROR);
    }
    optional { }
);

/// The only known version of π-HelixNovo
pub const PIHELIXNOVO_V1_1: PiHelixNovoFormat = PiHelixNovoFormat {
    version: PiHelixNovoVersion::V1_1,
    title: "title",
    peptide: "peptide",
    score: "score",
};

/// All possible π-HelixNovo versions
#[derive(
    Copy, Clone, Eq, PartialEq, Ord, PartialOrd, Hash, Debug, Default, Serialize, Deserialize,
)]
pub enum PiHelixNovoVersion {
    #[default]
    /// π-HelixNovo version 1.1
    V1_1,
}

impl std::fmt::Display for PiHelixNovoVersion {
    fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> Result<(), std::fmt::Error> {
        write!(f, "{}", self.name())
    }
}

impl IdentifiedPeptidoformVersion<PiHelixNovoFormat> for PiHelixNovoVersion {
    fn format(self) -> PiHelixNovoFormat {
        match self {
            Self::V1_1 => PIHELIXNOVO_V1_1,
        }
    }
    fn name(self) -> &'static str {
        match self {
            Self::V1_1 => "v1.1",
        }
    }
}

impl MetaData for PiHelixNovoData {
    fn compound_peptidoform_ion(&self) -> Option<Cow<'_, CompoundPeptidoformIon>> {
        Some(Cow::Owned(self.peptide.clone().into()))
    }

    fn format(&self) -> KnownFileFormat {
        KnownFileFormat::PiHelixNovo(self.version)
    }

    fn id(&self) -> String {
        "-".to_string() // TODO: best would be to use the scan index in some way shape or form
    }

    fn confidence(&self) -> Option<f64> {
        Some(self.score)
    }

    fn local_confidence(&self) -> Option<Cow<'_, [f64]>> {
        None
    }

    fn original_confidence(&self) -> Option<f64> {
        Some(self.score)
    }

    fn original_local_confidence(&self) -> Option<&[f64]> {
        None
    }

    fn charge(&self) -> Option<Charge> {
        None
    }

    fn mode(&self) -> Option<Cow<'_, str>> {
        None
    }

    fn retention_time(&self) -> Option<Time> {
        None
    }

    fn scans(&self) -> SpectrumIds {
        SpectrumIds::FileNotKnown(vec![SpectrumId::Native(self.title.clone())])
    }

    fn experimental_mz(&self) -> Option<MassOverCharge> {
        None
    }

    fn experimental_mass(&self) -> Option<Mass> {
        None
    }

    fn ppm_error(&self) -> Option<Ratio> {
        None
    }

    fn protein_names(&self) -> Option<Cow<'_, [FastaIdentifier<String>]>> {
        None
    }

    fn protein_id(&self) -> Option<usize> {
        None
    }

    fn protein_location(&self) -> Option<Range<u16>> {
        None
    }

    fn flanking_sequences(&self) -> (&FlankingSequence, &FlankingSequence) {
        (&FlankingSequence::Unknown, &FlankingSequence::Unknown)
    }

    fn database(&self) -> Option<(&str, Option<&str>)> {
        None
    }
}