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Usage
=======

You will need to supply your own copy of the NIST Mass Spectral library to use this software.

The main class in this library is the :class:`~pyms_nist_search.win_engine.Engine` class. This class performs the actual searching.
Start by initialising the search engine as follows:

.. code-block:: python

	search = pyms_nist_search.Engine(
			FULL_PATH_TO_MAIN_LIBRARY,
			pyms_nist_search.NISTMS_MAIN_LIB,
			FULL_PATH_TO_WORK_DIR,
			)

Where ``FULL_PATH_TO_MAIN_LIBRARY`` is the path to the location of your mass spectral library,
and ``FULL_PATH_TO_WORK_DIR`` is the path to the working directory to be used by the search engine.

A :class:`pyms.Spectrum.MassSpectrum` object can then be searched as follows:

.. code-block:: python

	search.full_search_with_ref_data(mass_spec)

This will return a list of tuples consisting of :class:`~.SearchResult` and :class:`~.ReferenceData`
objects for the possible identities of the mass spectrum.

A list of just the :class:`~.SearchResult` objects can be obtained with this method:

.. code-block:: python

	hit_list = search.full_search(mass_spec)

For each of these hits, the reference data can be obtained as follows:

.. code-block:: python

	for hit in hit_list:
		ref_data = search.get_reference_data(hit.spec_loc)