pgfinder.validation
===================

.. py:module:: pgfinder.validation

.. autoapi-nested-parse::

   Functions for validation of data.

   ..
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Attributes
----------

.. autoapisummary::

   pgfinder.validation.LOGGER


Functions
---------

.. autoapisummary::

   pgfinder.validation.allowed_modifications
   pgfinder.validation.validate_raw_data_df
   pgfinder.validation.validate_theo_masses_df
   pgfinder.validation.validate_rt_window
   pgfinder.validation.validate_enabled_mod_list
   pgfinder.validation.validate_user_ppm


Module Contents
---------------

.. py:data:: LOGGER

.. py:function:: allowed_modifications(config_file: str | pathlib.Path = 'config/allowed_modifications.txt') -> list

   
   Loads allowable modifications from a csv file as a list.

   :param config_file: Path to a configuration file. Default 'config/allowed_modifications.txt'
   :type config_file: str | Path

   :returns: List of permissible modifications.
   :rtype: list















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.. py:function:: validate_raw_data_df(raw_data_df: pandas.DataFrame, columns: dict = COLUMNS['pgfinder']) -> None | ValueError

   
   Validate that the raw data is a Pandas Dataframe with specific column names and that it has attributes.

   :param raw_data_df: Data frame to be validated.
   :type raw_data_df: pd.DataFrame

   :returns: Error specific to the problem encountered with the data frame if any are encountered.
   :rtype: None | ValueError

   :raises ValueError:















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.. py:function:: validate_theo_masses_df(theo_masses_df: pandas.DataFrame) -> None | ValueError

   
   Validate that the theoretical masses data is a Pandas Dataframe with specific column names and that it has
   attributes.

   :param raw_data_df: Data frame to be validated.
   :type raw_data_df: pd.DataFrame

   :returns: Error specific to the problem encountered with the data frame if any are encountered.
   :rtype: None | ValueError

   :raises ValueError:















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.. py:function:: validate_rt_window(rt_window: float) -> None | ValueError

   
   Validate that rt_window is an float.

   :param rt_window: Value of rt_window to be validated.
   :type rt_window: int

   :returns: If no error nothing is returned, otherwise a ValueError is raised.
   :rtype: None | ValueError

   :raises ValueError:















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.. py:function:: validate_enabled_mod_list(enabled_mod_list: list) -> None | ValueError

   
   Validate that enabled_mod_list is a list and modifications are allowed.

   :param enabled_mod_list: Value of enabled_mod_list to be validated.
   :type enabled_mod_list: int

   :returns: If no error nothing is returned, otherwise a ValueError is raised.
   :rtype: None | ValueError

   :raises ValueError:















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.. py:function:: validate_user_ppm(user_ppm: int) -> None | ValueError

   
   Validate that user_ppm is an integer.

   :param user_ppm: Value of user_ppm to be validated.
   :type user_ppm: int

   :returns: If no error nothing is returned, otherwise a ValueError is raised.
   :rtype: None | ValueError

   :raises ValueError:















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