RIAssigner.data.Data
====================

.. py:module:: RIAssigner.data.Data


Classes
-------

.. autoapisummary::

   RIAssigner.data.Data.Data


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

.. py:class:: Data(filename: str, filetype: str, rt_unit: str)

   Bases: :py:obj:`abc.ABC`


   Base class for data managers.


   .. py:attribute:: RetentionTimeType


   .. py:attribute:: RetentionIndexType


   .. py:attribute:: CommentFieldType


   .. py:attribute:: URegistry


   .. py:attribute:: _keys_conversions


   .. py:attribute:: _rt_possible_keys


   .. py:attribute:: _ri_possible_keys


   .. py:method:: is_valid(value: Union[RetentionTimeType, RetentionIndexType]) -> bool
      :staticmethod:


      Determine whether a retention time value is valid

      :param rt: Value to check for validity.
      :type rt: RetentionTimeType

      :returns: State of validity (True/False).
      :rtype: bool



   .. py:method:: can_be_float(rt: Union[pint.Quantity, float, int]) -> bool
      :staticmethod:


      Determine whether a value can be converted to a float.

      This function checks if the provided input is an instance of either
      Quantity, float, or int.

      :param rt: Value to check for float conversion.
      :type rt: Union[Quantity, float, int]

      :returns: True if the input is an instance of Quantity, float, or int, False otherwise.
      :rtype: bool



   .. py:method:: add_possible_rt_keys(keys: List[str]) -> None
      :classmethod:


      A method that adds new identifiers to get retention time information.

      :param keys: A list of new identifiers (keys) to be added to the `_rt_possible_keys`.
      :type keys: List[str]

      :returns: None



   .. py:method:: add_possible_ri_keys(keys: List[str]) -> None
      :classmethod:


      A method that adds new identifiers to get retention index information.

      :param keys: A list of new identifiers (keys) to be added to the `_ri_possible_keys`.
      :type keys: List[str]

      :returns: None



   .. py:method:: get_possible_rt_keys() -> List[str]
      :classmethod:


      A method that returns the possible keys to get retention times.

      :returns: A list of possible keys to get retention times.
      :rtype: List[str]



   .. py:method:: get_possible_ri_keys() -> List[str]
      :classmethod:


      A method that returns the possible keys to get retention indices.

      :returns: A list of possible keys to get retention indices.
      :rtype: List[str]



   .. py:attribute:: _filename


   .. py:attribute:: _filetype


   .. py:attribute:: _rt_unit


   .. py:attribute:: _unit


   .. py:method:: write(filename: str) -> None
      :abstractmethod:


      Store current content to disk.

      :param filename: Path to output filename.
      :type filename: str



   .. py:property:: filename
      :type: str


      Getter for filename property.

      :returns: Filename of originally loaded data.
      :rtype: str


   .. py:property:: retention_times
      :type: Iterable[RetentionTimeType]

      :abstractmethod:


      Getter for `retention_times` property.

      :returns: RT values contained in data.
      :rtype: Iterable[RetentionTimeType]


   .. py:property:: retention_indices
      :type: Iterable[RetentionIndexType]

      :abstractmethod:


      Getter for `retention_indices` property.

      :returns: RI values stored in data.
      :rtype: Iterable[RetentionIndexType]


   .. py:method:: has_retention_indices() -> bool

      Check if all retention indices in the spectra exist.

      This method iterates over the retention indices in the spectra. If it encounters a value that is None,
      it immediately returns False. If it iterates over all retention indices without finding a None value,
      it returns True.

      :returns: True if all retention indices exist, False otherwise.
      :rtype: bool



   .. py:method:: has_retention_times() -> bool

      Check if all retention times in the spectra exist.

      This method iterates over the retention times in the spectra. If it encounters a value that is None,
      it immediately returns False. If it iterates over all retention times without finding a None value,
      it returns True.

      :returns: True if all retention times exist, False otherwise.
      :rtype: bool



   .. py:property:: comment
      :type: Iterable[CommentFieldType]

      :abstractmethod:


      Getter for `comment` property.

      :returns: Comment field values stored in data.
      :rtype: Iterable[CommentFieldType]


   .. py:method:: init_ri_from_comment(ri_source: str) -> None

      Extract RI from comment field.
      Extracts the RI from the comment field of the data file. The RI is expected to be
      in the format 'ri_source=RI_value'. The function extracts the RI value and
      sets it on the retention_index property.

      :param content_comment: Comment field of the data file.
      :param ri_source: String that is expected to be in the comment field before the RI value.