Seqan compat/seqan2 char alphabet #12
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[INFRA] seqan3/std/* header files MUST NOT include any seqan3 header
Selects the correct simd scoring scheme based on the given matrix type. For the moment to test and implement the featurs of protein simd alignment we can use this simple static differentiation. Later this will be replaced by a dynamic dispatching mechanism.
Makes a test template for the alignment benchmark so we can reuse it for different benchmark settings.
When tracking the last cell of the banded column computation the matrix iterator was referring to the wrong alignment cell.
Before, the algorithm always tracked the last cell of the current column irrespective of its position within the global matrix. This means, that the optimum could point to a cell that does not represent the full sequence and hence would not be a valid semi-gobal alignment.
…ble_banded_end_position Optimise alignment/part6 enable banded end position
…microbenchmarks Protein alignment/part1 add microbenchmarks
[DOC] Update cppreference index
[FIX] Timeout in debug nightlies
[FIX] Wrong ranks in search algorithm
pull changes from release-3.0.2 into master - progress of week 05
…eqan_compat/seqan2_char_alphabet
…bility overhead. By applying this type erasure, we are actually generic to allow any user input as long as it fulfils the respective concepts that are modeled explicitly for alphabets and scoring schemes. It also is an initial step to reduce the boiler plate overloads in seqan2 when we start adapting the algorithms step by step.
Codecov Report
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## tcoffee #12 +/- ##
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Coverage 97.87% 97.88%
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Files 269 269
Lines 10119 10146 +27
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+ Hits 9904 9931 +27
Misses 215 215
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So I did look into the PR for multiple alignment. It is quite nice already.
I still got a little scared by the alphabet conversions since that would destroy everything regarding generic code :).
So Marcel and I had to test if it is indeed possible to use type erasure over char to run the multiple sequence alignment. And in fact it does pretty good. And that also means, this would make transferring the parts to seqan3 much easier because a lot of boiler plate that is alphabet dependent in SeqAn already can be removed.
I made a PR for the changes, since I was kind of playing with the code anyway. The only thing I did as well was to make the global interface independent of this default msa config thing, since it is basically not necessary. All defaults are set internally.
The rest is part of the review. I hope this procedure is ok with you. Otherwise, I was afraid that it might have gone wild to explain everything in the github comments :).
I think you should rebase on master before looking into it? It is only the last commit though.