RIAssigner.data.MatchMSData
===========================

.. py:module:: RIAssigner.data.MatchMSData


Classes
-------

.. autoapisummary::

   RIAssigner.data.MatchMSData.MatchMSData


Functions
---------

.. autoapisummary::

   RIAssigner.data.MatchMSData.safe_read_key
   RIAssigner.data.MatchMSData._assign_ri_value


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

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

   Bases: :py:obj:`RIAssigner.data.Data.Data`


   Class to handle data from filetypes which can be imported
   using 'matchms'.


   .. py:method:: _read()

      Load data into object and initialize properties.



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

      Write data to back to the spectra file

      :param filename: Path to filename under which to store the data.
      :type filename: str



   .. py:method:: _write_RIs_to_spectra() -> None

      Write the RI values stored in the object to the spectra metadata.



   .. py:method:: _read_retention_times() -> None

      Read retention times from spectrum metadata.



   .. py:method:: _read_retention_indices() -> None

      Read retention indices from spectrum metadata.



   .. py:method:: _sort_spectra_by_rt() -> None

      Sort objects (peaks) in spectra list by their retention times.



   .. py:method:: __eq__(o: object) -> bool

      Comparison operator `==`.

      :param o: Object to compare with.
      :type o: object

      :returns: State of equality.
      :rtype: bool



   .. py:property:: retention_times
      :type: Iterable[RIAssigner.data.Data.Data.RetentionTimeType]


      Get retention times in seconds.


   .. py:property:: retention_indices
      :type: Iterable[RIAssigner.data.Data.Data.RetentionIndexType]


      Get retention indices.


   .. py:property:: comment
      :type: Iterable[RIAssigner.data.Data.Data.CommentFieldType]


      Get comments.


   .. py:property:: spectra_metadata
      :type: Tuple[numpy.array, List[str]]



.. py:function:: safe_read_key(spectrum: matchms.Spectrum, key: str) -> float

   Read key from spectrum and convert to float or return 0.0.
   Tries to read the given key from the spectrum metadata and convert it to a float.
   In case an exception is thrown or the key is not present, returns 0.0.

   :param spectrum: Spectrum from which to read the key.
   :param key: Key to be read from the spectrum metadata.

   :rtype: Either the key's value converted to float or 0.0.


.. py:function:: _assign_ri_value(spectrum: matchms.Spectrum, key: str, value: RIAssigner.data.Data.Data.RetentionIndexType) -> None

   Assign RI value to Spectrum object

   :param spectrum: Spectrum to add RI to
   :type spectrum: Spectrum
   :param value: RI to be added to Spectrum
   :type value: Data.RetentionIndexType