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.. sidebar:: ToC
.. contents::
.. _how-to-recipes-work-with-custom-score-matrices:
Working With Custom Score Matrices
==================================
This How To describes how to create new scoring matrices for Amino Acids and DNA alphabets and how to load score matrices from files.
Creating A New Built-In Score Matrix
------------------------------------
The following program demonstrates how to implement a new built-in score matrix.
.. includefrags:: demos/howto/scores/init_score.cpp
:fragment: includes
We need to perform the necessary definitions for the matrix.
This consists of two steps:
#. Defining a tag struct.
#. Specializing the class ``ScoringMatrixData_`` with your tag.
Note how we use enum values to compute the matrix size which itself is retrieved from the :dox:`FiniteOrderedAlphabetConcept#ValueSize` metafunction.
.. includefrags:: demos/howto/scores/init_score.cpp
:fragment: user-defined-matrix
Now we define a function ``showScoringMatrix`` for displaying a matrix.
.. includefrags:: demos/howto/scores/init_score.cpp
:fragment: show-scoring-matrix
Finally, the ``main`` function demostrates some of the things you can do with scores:
* Construct an empty score matrix object (2.)
* Fill the score matrix in a loop (3.1)
* Fill the matrix with the user-defined matrix values (3.2)
* Directly create a score matrix with the user-defined matrix values (4)
.. includefrags:: demos/howto/scores/init_score.cpp
:fragment: main
Here is the output of the program:
.. includefrags:: demos/howto/scores/init_score.cpp.stdout
Loading Score Matrices From File
------------------------------------
This small demo program shows how to load a score matrix from a file.
Examples for a score file are ``demos/howto/scores/dna_example.txt`` for DNA alphabets and ``tests/sPAM250`` for amino acids.
Include the necessary headers.
.. includefrags:: demos/howto/scores/load_score.cpp
:fragment: includes
We define a function that can show a scoring matrix.
.. includefrags:: demos/howto/scores/load_score.cpp
:fragment: show-scoring-matrix
Finally, the main program loads the scoring matrix and then shows it.
.. includefrags:: demos/howto/scores/load_score.cpp
:fragment: main
Here's the program output.
.. includefrags:: demos/howto/scores/load_score.cpp.stdout
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