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#53 put parameters docs into __init__ in class def
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jalew188 committed Jun 20, 2024
1 parent e355845 commit f1c8679
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Showing 3 changed files with 42 additions and 39 deletions.
15 changes: 8 additions & 7 deletions alpharaw/ms_data_base.py
Original file line number Diff line number Diff line change
Expand Up @@ -7,13 +7,6 @@
class MSData_Base:
"""
The base data structure for MS RAW Data, other MSData loaders inherit this class.
Parameters
----------
centroided : bool, optional
If centroiding the peak data, by default True
save_as_hdf : bool, optional
If automatically save the data into HDF5 format, by default False
"""

column_dtypes = {
Expand Down Expand Up @@ -76,6 +69,14 @@ class MSData_Base:
"""

def __init__(self, centroided: bool = True, save_as_hdf: bool = False, **kwargs):
"""
Parameters
----------
centroided : bool, optional
If centroiding the peak data, by default True
save_as_hdf : bool, optional
If automatically save the data into HDF5 format, by default False
"""
# A spectrum contains peaks
self.spectrum_df: pd.DataFrame = pd.DataFrame()
# A peak contains mz, intensity, and ...
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33 changes: 17 additions & 16 deletions alpharaw/thermo.py
Original file line number Diff line number Diff line change
Expand Up @@ -54,22 +54,6 @@ class ThermoRawData(MSData_Base):
Loading Thermo Raw data as MSData_Base data structure.
This class is registered "thermo" and "thermo_raw" in
:obj:`alpharaw.ms_data_base.ms_reader_provider`.
Parameters
----------
centroided : bool, optional
If peaks will be centroided after loading. By defaults True.
process_count : int, optional
Number of processes to load RAW data, by default 10.
mp_batch_size : int, optional
Number of spectra to load in each batch, by default 5000.
save_as_hdf : bool, optional
Automatically save hdf after load raw data, by default False.
dda : bool, optional
Is DDA data, by default False.
auxiliary_items : list, optional
Additional spectrum items, candidates are in :data:`auxiliary_item_dtypes`.
By default [].
"""

def __init__(
Expand All @@ -82,6 +66,23 @@ def __init__(
auxiliary_items: list = [],
**kwargs,
):
"""
Parameters
----------
centroided : bool, optional
If peaks will be centroided after loading. By defaults True.
process_count : int, optional
Number of processes to load RAW data, by default 10.
mp_batch_size : int, optional
Number of spectra to load in each batch, by default 5000.
save_as_hdf : bool, optional
Automatically save hdf after load raw data, by default False.
dda : bool, optional
Is DDA data, by default False.
auxiliary_items : list, optional
Additional spectrum items, candidates are in :data:`auxiliary_item_dtypes`.
By default [].
"""
super().__init__(centroided, save_as_hdf=save_as_hdf, **kwargs)
self.file_type = "thermo"
self.process_count = process_count
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33 changes: 17 additions & 16 deletions alpharaw/wrappers/alphatims_wrapper.py
Original file line number Diff line number Diff line change
Expand Up @@ -45,25 +45,26 @@ def import_raw(self, burker_d_folder: str):
class AlphaTimsWrapper(TimsTOF):
"""Create a AlphaTims object that contains
all data in-memory (or memory mapping).
Parameters
----------
msdata : MSData_Base
The AlphaRaw data object.
dda : bool
If DDA, precursor indices will be equal to scan numbers.
If not DDA (i.e. DIA), precursor indices will be equal to the
scan number within a DIA cycle.
slice_as_dataframe : bool
If True, slicing returns a pd.DataFrame by default.
If False, slicing provides a np.int64[:] with raw indices.
This value can also be modified after creation.
Default is True.
"""

def __init__(self, msdata: MSData_Base, dda: bool, slice_as_dataframe: bool = True):
"""
Parameters
----------
msdata : MSData_Base
The AlphaRaw data object.
dda : bool
If DDA, precursor indices will be equal to scan numbers.
If not DDA (i.e. DIA), precursor indices will be equal to the
scan number within a DIA cycle.
slice_as_dataframe : bool
If True, slicing returns a pd.DataFrame by default.
If False, slicing provides a np.int64[:] with raw indices.
This value can also be modified after creation.
Default is True.
"""
self._use_calibrated_mz_values_as_default = False
self._import_alpharaw_object(msdata, dda)
self.thermo_raw_file_name = msdata.raw_file_path
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