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BioC++ core-0.7.0
The Modern C++ libraries for Bioinformatics.
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BioC++ core-0.7.0
The Modern C++ libraries for Bioinformatics.
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BioC++ clearly documents which of its interfaces are designed to be used with user-provided types and how this can be realised.
Templates are a core part of generic programming in C++, because they allow instantiating the code with different types or constants. BioC++'s API consists mostly of templates for exactly this reason, although we try to make this less visible by having the template parameters deduced in many scenarios.
We strive to document the exact requirements for every template parameter in the API documentation; often these are also enforced via C++ concepts. Wherever other types meet the given requirements, you can use these types as arguments – independent of whether they are standard library types, your own types or types from another library. See C++ Concepts for more details on this.
Some requirements are more elaborate and depend on a specialisation or "overload" of another entity from the BioC++ library. We call these "customisation points" (also known as "extension points").
An example is the bio::alphabet::alphabet concept. One part of this concept's requirements are from bio::alphabet::semialphabet which requires to_rank() to be available on an object of the type. to_rank() is a "customisation point".
Instead of the bio::alphabet::semialphabet concept looking directly for .to_rank() member functions, it checks for a valid definition of bio::alphabet::to_rank which in turn calls tag_invoke(). This mechanism is widely employed in Modern C++ and may be standardised in the future (P1895). There are (hidden) implementations of tag_invoke() that typically redirect to the respective member functions.
To customise one of our customisation points, follow the instructions in its API documentation. Typically, you just have to add a tag_invoke() function for your type. This can happen as a friend or as a free function in your type's namespace. The lookup happens via argument dependent lookup. The first argument of tag_invoke() is the "tag" used to select the implementation. In BioC++, these are named exactly like the function that you otherwise call, except that they are in a custom subnamespace. E.g. bio::alphabet::to_rank looks for tag_invoke(bio::alphabet::custom::to_rank, YOUR_TYPE).
If you need to specialise the behaviour for a third party type, and you cannot open that type's namespace (or it doesn't have one), you can also add your overload of tag_invoke() to our customisation namespace, e.g. bio::alphabet::custom. Only do this, if there is no other solution.
In some cases, e.g. bio::alphabet::custom::enable_aminoacid, we also provide variable templates that you can specialise directly.
custom) and never explicitly specialise one of our templates (except those in custom namespaces) or overload one of our functions.The HowTo on creating your own alphabet provides many examples of how to satisfy the requirements of customisation point objects.
Since the customisation point objects are functors, you can take their address and use them in higher order functions.
1.9.6