corems.mass_spectra.input.parserbase 

 1from abc import ABC, abstractmethod
 2
 3
 4class SpectraParserInterface(ABC):
 5    """
 6    Interface for parsing mass spectra data into MassSpectraBase objects.
 7
 8    Methods
 9    -------
10    * load().
11        Load mass spectra data.
12    * run().
13        Parse mass spectra data.
14    * get_mass_spectra_obj().
15        Return MassSpectraBase object with several attributes populated
16    * get_mass_spectrum_from_scan(scan_number).
17        Return MassSpecBase data object from scan number.
18
19    Notes
20    -----
21    This is an abstract class and should not be instantiated directly.
22    """
23
24    @abstractmethod
25    def load(self):
26        """
27        Load mass spectra data.
28        """
29        pass
30
31    @abstractmethod
32    def run(self):
33        """
34        Parse mass spectra data.
35        """
36        pass
37
38    @abstractmethod
39    def get_scan_df(self):
40        """
41        Return scan data as a pandas DataFrame.
42        """
43        pass
44
45    @abstractmethod
46    def get_ms_raw(self, spectra, scan_df):
47        """
48        Return a dictionary of mass spectra data as a pandas DataFrame.
49        """
50        pass
51
52    @abstractmethod
53    def get_mass_spectra_obj(self):
54        """
55        Return mass spectra data object.
56        """
57        pass
58
59    @abstractmethod
60    def get_mass_spectrum_from_scan(
61        self, scan_number, spectrum_mode, auto_process=True
62    ):
63        """
64        Return mass spectrum data object from scan number.
65        """
66        pass
class SpectraParserInterface(abc.ABC): 
 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

Interface for parsing mass spectra data into MassSpectraBase objects.

Methods
  • load(). Load mass spectra data.
  • run(). Parse mass spectra data.
  • get_mass_spectra_obj(). Return MassSpectraBase object with several attributes populated
  • get_mass_spectrum_from_scan(scan_number). Return MassSpecBase data object from scan number.
Notes

This is an abstract class and should not be instantiated directly.

@abstractmethod
def load(self): 
25    @abstractmethod
26    def load(self):
27        """
28        Load mass spectra data.
29        """
30        pass

Load mass spectra data.

@abstractmethod
def run(self): 
32    @abstractmethod
33    def run(self):
34        """
35        Parse mass spectra data.
36        """
37        pass

Parse mass spectra data.

@abstractmethod
def get_scan_df(self): 
39    @abstractmethod
40    def get_scan_df(self):
41        """
42        Return scan data as a pandas DataFrame.
43        """
44        pass

Return scan data as a pandas DataFrame.

@abstractmethod
def get_ms_raw(self, spectra, scan_df): 
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

Return a dictionary of mass spectra data as a pandas DataFrame.

@abstractmethod
def get_mass_spectra_obj(self): 
53    @abstractmethod
54    def get_mass_spectra_obj(self):
55        """
56        Return mass spectra data object.
57        """
58        pass

Return mass spectra data object.

@abstractmethod
def get_mass_spectrum_from_scan(self, scan_number, spectrum_mode, auto_process=True): 
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

Return mass spectrum data object from scan number.