corems.mass_spectra.input.parserbase

 1from abc import ABC, abstractmethod
 2import datetime
 3
 4
 5class SpectraParserInterface(ABC):
 6    """
 7    Interface for parsing mass spectra data into MassSpectraBase objects.
 8
 9    Methods
10    -------
11    * load().
12        Load mass spectra data.
13    * run().
14        Parse mass spectra data.
15    * get_mass_spectra_obj().
16        Return MassSpectraBase object with several attributes populated
17    * get_mass_spectrum_from_scan(scan_number).
18        Return MassSpecBase data object from scan number.
19
20    Notes
21    -----
22    This is an abstract class and should not be instantiated directly.
23    """
24
25    @abstractmethod
26    def load(self):
27        """
28        Load mass spectra data.
29        """
30        pass
31
32    @abstractmethod
33    def run(self):
34        """
35        Parse mass spectra data.
36        """
37        pass
38
39    @abstractmethod
40    def get_scan_df(self):
41        """
42        Return scan data as a pandas DataFrame.
43        """
44        pass
45
46    @abstractmethod
47    def get_ms_raw(self, spectra, scan_df):
48        """
49        Return a dictionary of mass spectra data as a pandas DataFrame.
50        """
51        pass
52
53    @abstractmethod
54    def get_mass_spectra_obj(self):
55        """
56        Return mass spectra data object.
57        """
58        pass
59
60    @abstractmethod
61    def get_mass_spectrum_from_scan(
62        self, scan_number, spectrum_mode, auto_process=True
63    ):
64        """
65        Return mass spectrum data object from scan number.
66        """
67        pass
68
69    @abstractmethod
70    def get_instrument_info(self):
71        """
72        Return instrument information.
73
74        Returns
75        -------
76        dict
77            A dictionary with the keys 'model', and 'serial_number'.
78        """
79        pass
80
81    @abstractmethod
82    def get_creation_time(self) -> datetime.datetime:
83        """
84        Return the creation time of the mass spectra data.
85
86        Returns
87        -------
88        datetime.datetime
89            The creation time of the mass spectra data.
90        """
91        pass