alphabet_base expects functions instead of look-up tables. #2427

marehr · 2021-03-03T23:59:52Z

This is part of seqan/product_backlog#295

This changes rank_to_char and char_to_rank to static member functions.

Blocked by #2430.

vercel · 2021-03-03T23:59:56Z

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codecov · 2021-03-05T14:39:05Z

Codecov Report

Merging #2427 (a9ba4d7) into master (a1dd8cd) will increase coverage by 0.01%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##           master    #2427      +/-   ##
==========================================
+ Coverage   98.29%   98.31%   +0.01%     
==========================================
  Files         268      269       +1     
  Lines       11055    11134      +79     
==========================================
+ Hits        10867    10946      +79     
  Misses        188      188

Impacted Files	Coverage Δ
...clude/seqan3/alphabet/aminoacid/aminoacid_base.hpp	`100.00% <ø> (ø)`
...ude/seqan3/alphabet/nucleotide/nucleotide_base.hpp	`100.00% <ø> (ø)`
include/seqan3/alphabet/alphabet_base.hpp	`100.00% <100.00%> (ø)`
include/seqan3/alphabet/aminoacid/aa10li.hpp	`100.00% <100.00%> (ø)`
include/seqan3/alphabet/aminoacid/aa10murphy.hpp	`100.00% <100.00%> (ø)`
include/seqan3/alphabet/aminoacid/aa20.hpp	`100.00% <100.00%> (ø)`
include/seqan3/alphabet/aminoacid/aa27.hpp	`100.00% <100.00%> (ø)`
...alphabet/cigar/exposition_only/cigar_operation.hpp	`100.00% <100.00%> (ø)`
...ude/seqan3/alphabet/composite/alphabet_variant.hpp	`100.00% <100.00%> (ø)`
include/seqan3/alphabet/gap/gap.hpp	`100.00% <100.00%> (ø)`
... and 14 more

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simonsasse

Found just one typo :)

include/seqan3/alphabet/composite/alphabet_variant.hpp

simonsasse

Looks good. Only thing is that when I see chr, I always think of chromosome and not character. Maybe its worth changing the chr to char. Probably just personal preference.

eseiler · 2021-03-15T08:25:01Z

Looks good. Only thing is that when I see chr, I always think of chromosome and not character. Maybe its worth changing the chr to char. Probably just personal preference.

@simonsasse, can you approve and assign core for review?

simonsasse

✅

eseiler

Looks good in general, just some documentation remarks and general questions.

This point does not need / should not be addressed in this PR:

I am missing a bit some documentation on what the advantage of this is. If there is a changelog entry, it should shortly describe why this is good?
I think doc/howto/write_an_alphabet/dna2_derive_from_base.cpp can also shortly mention that there is an alternative to tables (it does show it, but doesn't explicitly mention it).

doc/cookbook/custom_dna4.cpp

include/seqan3/alphabet/alphabet_base.hpp

eseiler · 2021-03-15T10:30:09Z

include/seqan3/alphabet/alphabet_base.hpp

+        using index_t = std::make_unsigned_t<char_type>;
+        index_t const id = static_cast<index_t>(chr);
+        return derived_type::char_to_rank[id];


Why are these lines different?
From what I've read, the bug only refers to deprecation warnings being emitted even when the code is not called.
So this block should also be

using index_t = std::make_unsigned_t<char_type>; return derived_type::char_to_rank[static_cast<index_t>(chr)];

?

include/seqan3/alphabet/aminoacid/aa10li.hpp

include/seqan3/alphabet/composite/alphabet_variant.hpp

include/seqan3/alphabet/gap/gap.hpp

include/seqan3/alphabet/nucleotide/nucleotide_base.hpp

eseiler · 2021-03-15T10:52:16Z

include/seqan3/alphabet/gap/gap.hpp

@@ -43,10 +43,16 @@ class gap : public alphabet_base<gap, 1, char>
    friend base_t;

    //!\brief Value to char conversion table.


Not true anymore :)

include/seqan3/alphabet/quality/quality_base.hpp

include/seqan3/alphabet/alphabet_base.hpp

… function

See https://gcc.gnu.org/bugzilla/show_bug.cgi?id=99318

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marehr force-pushed the alphabet_base_functions branch from afbbc26 to 2537f10 Compare March 5, 2021 14:05

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marehr mentioned this pull request Mar 5, 2021

[FIX] fix internal compiler error on gcc-7 #2430

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marehr force-pushed the alphabet_base_functions branch from 2aafb9d to d270fe0 Compare March 11, 2021 12:01

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marehr commented Mar 15, 2021

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marehr force-pushed the alphabet_base_functions branch from a3e506d to 91f8071 Compare March 17, 2021 16:24

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marehr force-pushed the alphabet_base_functions branch from 91f8071 to 7b001db Compare March 24, 2021 00:37

marehr added 24 commits March 24, 2021 20:08

[MISC] introduce rna4::rank_to_char function

7cd9616

[MISC] introduce [rd]na5::char_to_rank and dna5::rank_to_char function

56f168c

[MISC] introduce rna5::rank_to_char function

f9b373e

[MISC] introduce [rd]na15::char_to_rank and dna15::rank_to_char function

ee8b715

[MISC] introduce rna15::rank_to_char function

9ee7bde

[MISC] introduce sam_dna16::{rank_to_char, char_to_rank} function

9aada46

[MISC] introduce dna3bs::{rank_to_char, char_to_rank} function

8f5f30d

[MISC] introduce aa10li::{rank_to_char, char_to_rank} function

e364cca

[MISC] introduce aa10murphy::{rank_to_char, char_to_rank} function

05589d7

[MISC] introduce aa20::{rank_to_char, char_to_rank} function

9d17309

[MISC] introduce aa27::{rank_to_char, char_to_rank} function

0ed6afb

[MISC] introduce cigar_operation::{rank_to_char, char_to_rank} function

16028f6

[MISC] introduce gap::{rank_to_char, char_to_rank} function

5247a60

[MISC] introduce qualified::rank_to_char function

923751a

[MISC] introduce quality_base::{rank_to_char, char_to_rank} function

fdf35e5

[MISC] introduce dot_bracket3::{rank_to_char, char_to_rank} function

2298752

[MISC] introduce dssp9::{rank_to_char, char_to_rank} function

5e973e2

[MISC] introduce wuss::{rank_to_char, char_to_rank} function

4da973d

[MISC] introduce snippet::my_dna4::{rank_to_char, char_to_rank} function

4e13060

[MISC] introduce snippet::dna2::{rank_to_char, char_to_rank} function

adfa0c8

[MISC] introduce snippet::alphabet_base::{rank_to_char, char_to_rank}…

e4af170

… function

[MISC] introduce alphabet_variant::{rank_to_char, char_to_rank} function

f120257

[FIX] gcc10: throws invalid deprecation warnings

db2b30a

See https://gcc.gnu.org/bugzilla/show_bug.cgi?id=99318

[API] deprecate old alphabet::lookup-tables

a9ba4d7

marehr force-pushed the alphabet_base_functions branch from 7b001db to a9ba4d7 Compare March 24, 2021 19:09

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marehr requested a review from eseiler March 24, 2021 21:27

eseiler approved these changes Mar 24, 2021

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eseiler merged commit f4391dc into seqan:master Mar 24, 2021

marehr deleted the alphabet_base_functions branch March 24, 2021 21:30

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alphabet_base expects functions instead of look-up tables. #2427

alphabet_base expects functions instead of look-up tables. #2427

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eseiler Mar 15, 2021

		@@ -43,10 +43,16 @@ class gap : public alphabet_base<gap, 1, char>
		friend base_t;

		//!\brief Value to char conversion table.

alphabet_base expects functions instead of look-up tables. #2427

alphabet_base expects functions instead of look-up tables. #2427

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