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_mass_spectra_from_scan_list(
 71        self, scan_list, spectrum_mode, auto_process=True
 72    ):
 73        """
 74        Return a list of mass spectrum data objects from a list of scan numbers.
 75        """
 76        pass
 77
 78    @abstractmethod
 79    def get_instrument_info(self):
 80        """
 81        Return instrument information.
 82
 83        Returns
 84        -------
 85        dict
 86            A dictionary with the keys 'model', and 'serial_number'.
 87        """
 88        pass
 89
 90    @abstractmethod
 91    def get_creation_time(self) -> datetime.datetime:
 92        """
 93        Return the creation time of the mass spectra data.
 94
 95        Returns
 96        -------
 97        datetime.datetime
 98            The creation time of the mass spectra data.
 99        """
100        pass