API Stability of Alphabet Module #269

marehr · 2020-12-06T00:31:56Z

Open: How to do conversion between two compatible types of the same group (aminoacid, nucleotide)
- MOVED TO Release 3.2: API Stability of Alphabet Module in Release 3.2 #389
./alphabet/adaptation
- ./alphabet/adaptation/all.hpp API_STABLE
- ./alphabet/adaptation/char.hpp API_STABLE
- ./alphabet/adaptation/uint.hpp API_STABLE
./alphabet/all.hpp API_STABLE
./alphabet/alphabet_base.hpp
- alphabet_base API_STABLE
- alphabet_base.char_type protected API_STABLE
- alphabet_base.rank_type protected API_STABLE
- alphabet_base.to_char API_STABLE
- alphabet_base.to_rank API_STABLE
- alphabet_base.assign_char API_STABLE
- alphabet_base.assign_rank API_STABLE
- alphabet_base.alphabet_size API_STABLE
- alphabet_base.<=> API_STABLE
./alphabet/aminoacid
- ./alphabet/aminoacid/aa10li.hpp
  - aa10li API_STABLE
  - aa10li_vector API_STABLE
  - ""_aa10li API_STABLE
- ./alphabet/aminoacid/aa10murphy.hpp
  - aa10murphy API_STABLE
  - aa10murphy_vector API_STABLE
  - ""_aa10murphy API_STABLE
- ./alphabet/aminoacid/aa20.hpp
  - aa20 API_STABLE
  - aa20_vector API_STABLE
  - ""_aa20 API_STABLE
- ./alphabet/aminoacid/aa27.hpp
  - aa27 API_STABLE
  - aa27_vector API_STABLE
  - ""_aa27 API_STABLE
- ./alphabet/aminoacid/all.hpp API_STABLE
- ./alphabet/aminoacid/aminoacid_base.hpp
  - aminoacid_base API_STABLE
  - aminoacid_base.char_is_valid API_EXPERIMENTAL (API Stability of Alphabet Module #269 (comment))
- ./alphabet/aminoacid/concept.hpp
  - aminoacid_empty_base API_STABLE
  - enable_aminoacid API_STABLE (except for ADL CPO, this is marked API_EXPERIMENTAL)
  - aminoacid_alphabet API_STABLE
- ~~./alphabet/aminoacid/translation_details.hpp~~
- lower case seqan3::detail::translation_table::value #318
- ./alphabet/aminoacid/translation_genetic_code.hpp
  - genetic_code API_EXPERIMENTAL
- ./alphabet/aminoacid/translation.hpp
  - translate_triplet API_EXPERIMENTAL
./alphabet/cigar
- ./alphabet/cigar/all.hpp
- ./alphabet/cigar/cigar.hpp
  - cigar API_STABLE
  - cigar.to_string API_EXPERIMENTAL
  - cigar.assign_string API_EXPERIMENTAL
- ./alphabet/cigar/cigar_op.hpp API_EXPOSITION_ONLY (we put this into the seqan3::cigar class)
./alphabet/composite
- ./alphabet/composite/all.hpp
- ./alphabet/composite/alphabet_tuple_base.hpp
  - alphabet_tuple_base API_STABLE
  - alphabet_tuple_base.get API_STABLE
- ./alphabet/composite/alphabet_variant.hpp
  - alphabet_variant
  - alphabet_variant.holds_alternative; rename to is_alternative API_STABLE
  - alphabet_variant.is_alternative; rename to holds_alternative API_STABLE (holds_alternative is API_EXPERIMENTAL)
  - switch meaning of seqan3::alphabet_variant::{is_alternative, holds_alternative} #314
  - alphabet_variant.convert_to API_EXPERIMENTAL
  - alphabet_variant.convert_unsafely_to API_EXPERIMENTAL
- ~~./alphabet/composite/detail.hpp~~
- ./alphabet/composite/semialphabet_any.hpp API_STABLE
./alphabet/concept.hpp
- alphabet_rank_t API_STABLE
- alphabet_char_t API_STABLE
- to_rank API_STABLE (except for ADL CPO, this is marked API_EXPERIMENTAL)
- assign_rank_to API_STABLE (except for ADL CPO, this is marked API_EXPERIMENTAL)
- to_char API_STABLE (except for ADL CPO, this is marked API_EXPERIMENTAL)
- assign_char_to API_STABLE (except for ADL CPO, this is marked API_EXPERIMENTAL)
- char_is_valid_for (API Stability of Alphabet Module #269 (comment)) API_EXPERIMENTAL
- assign_char_strictly_to (API Stability of Alphabet Module #269 (comment)) API_EXPERIMENTAL
- alphabet_size API_STABLE (except for ADL CPO, this is marked API_EXPERIMENTAL)
- semialphabet API_STABLE
- writable_semialphabet API_STABLE
- alphabet API_STABLE
- writable_alphabet (API Stability of Alphabet Module #269 (comment)) API_STABLE
./alphabet/detail
- ./alphabet/detail/alphabet_proxy.hpp
- ./alphabet/detail/convert.hpp
./alphabet/exception.hpp
- invalid_char_assignment API_EXPERIMENTAL
./alphabet/gap
- ./alphabet/gap/all.hpp
- ./alphabet/gap/gap.hpp
- ./alphabet/gap/gapped.hpp
./alphabet/hash.hpp std::hash overload
./alphabet/mask
- ./alphabet/mask/all.hpp
- ./alphabet/mask/masked.hpp TODO: add article which explains lower and upper ans use cases
  - add article that explains lower/upper case for (un-)masked #313
  - masked API_STABLE
  - masked.sequence_alphabet_type API_STABLE
- ./alphabet/mask/mask.hpp
  - mask API_STABLE
  - mask.UNMASKED lower case API_STABLE
  - mask.MASKED lower case API_STABLE
  - lower case seqan3::mask::{un,}masked #311
  - add article that explains lower/upper case for (un-)masked #313
./alphabet/nucleotide
- ./alphabet/nucleotide/all.hpp
- ./alphabet/nucleotide/concept.hpp
  - complement API_STABLE (except for ADL CPO, this is marked API_EXPERIMENTAL)
  - nucleotide_alphabet API_STABLE
- ./alphabet/nucleotide/dna15.hpp API_STABLE
- ./alphabet/nucleotide/dna3bs.hpp
- ./alphabet/nucleotide/dna4.hpp API_STABLE
- implicit conversion of dna4 from rna4. #320
- ./alphabet/nucleotide/dna5.hpp API_STABLE
- ./alphabet/nucleotide/nucleotide_base.hpp
  - nucleotide_base
  - nucleotide_base.complement API_STABLE
  - nucleotide_base.char_is_valid API_EXPERIMENTAL (API Stability of Alphabet Module #269 (comment))
- ./alphabet/nucleotide/rna15.hpp API_STABLE
- ./alphabet/nucleotide/rna4.hpp API_STABLE
- ./alphabet/nucleotide/rna5.hpp API_STABLE
- ./alphabet/nucleotide/sam_dna16.hpp API_STABLE TODO rename to dna16sam.hpp
- rename seqan3::sam_dna16 to seqan3::dna16sam #312
./alphabet/quality
- ./alphabet/quality/aliases.hpp
- ./alphabet/quality/all.hpp
- ./alphabet/quality/concept.hpp
  - to_phred API_STABLE (except for ADL CPO, this is marked API_EXPERIMENTAL)
  - alphabet_phred_t API_STABLE
  - assign_phred_to API_STABLE (except for ADL CPO, this is marked API_EXPERIMENTAL)
  - quality_alphabet API_STABLE
  - writable_quality_alphabet API_STABLE
- ./alphabet/quality/phred42.hpp
  - phred42 API_STABLE
  - phred42.offset_phred API_STABLE
  - phred42.offset_char API_STABLE
- ./alphabet/quality/phred63.hpp API_STABLE
- ./alphabet/quality/phred68legacy.hpp API_STABLE
- rename phred68{legacy,solexa} #315
- ./alphabet/quality/phred94.hpp API_STABLE
- ./alphabet/quality/qualified.hpp
  - qualified API_STABLE
  - qualified.sequence_alphabet_type API_STABLE
  - qualified.quality_alphabet_type API_STABLE
  - qualified.char_type API_STABLE
  - qualified.phred_type API_STABLE
  - qualified.assign_char API_STABLE
  - qualified.assign_phred API_STABLE
  - qualified.to_phred API_STABLE
  - qualified.to_char API_STABLE
  - qualified.complement API_STABLE
  - qualified.char_is_valid API_EXPERIMENTAL (API Stability of Alphabet Module #269 (comment))
- ./alphabet/quality/quality_base.hpp rename to phred_base (see API Stability of Alphabet Module #269 (comment))
  - rename seqan3::quality_base to seqan3::phred_base #358
  - quality_base API_STABLE (except for implicit constructor for phred_type, e.g. seqan3::phred42 a = 9;)
  - deprecate phred_type constructor #316
  - quality_base.to_phred API_STABLE
  - quality_base.assign_phred API_STABLE
./alphabet/structure
- ./alphabet/structure/all.hpp
- ./alphabet/structure/concept.hpp
  - is_pair_open API_EXPERIMENTAL
  - is_pair_close API_EXPERIMENTAL
  - is_unpaired API_EXPERIMENTAL
  - max_pseudoknot_depth API_EXPERIMENTAL
  - pseudoknot_id API_EXPERIMENTAL
  - rna_structure_alphabet API_EXPERIMENTAL
- ./alphabet/structure/dot_bracket3.hpp
  - dot_bracket3 : alphabet_base API_EXPERIMENTAL
  - dot_bracket3.is_pair_open API_EXPERIMENTAL
  - dot_bracket3.is_pair_close API_EXPERIMENTAL
  - dot_bracket3.is_unpaired API_EXPERIMENTAL
  - dot_bracket3.max_pseudoknot_depth API_EXPERIMENTAL
  - dot_bracket3.pseudoknot_id API_EXPERIMENTAL
- ./alphabet/structure/dssp9.hpp
  - dssp9 : alphabet_base API_EXPERIMENTAL
- ./alphabet/structure/structured_aa.hpp
  - structured_aa : alphabet_tuple_base API_EXPERIMENTAL
  - structured_aa.sequence_alphabet_type API_EXPERIMENTAL
  - structured_aa.structure_alphabet_type API_EXPERIMENTAL
  - structured_aa.char_type API_EXPERIMENTAL
  - structured_aa.assign_char API_EXPERIMENTAL
  - structured_aa.to_char API_EXPERIMENTAL
  - structured_aa.char_is_valid API_EXPERIMENTAL (API Stability of Alphabet Module #269 (comment))
- ./alphabet/structure/structured_rna.hpp
  - structured_rna : alphabet_tuple_base API_EXPERIMENTAL
  - sequence_alphabet_type API_EXPERIMENTAL
  - structure_alphabet_type API_EXPERIMENTAL
  - char_type API_EXPERIMENTAL
  - assign_char API_EXPERIMENTAL
  - to_char API_EXPERIMENTAL
  - complement API_EXPERIMENTAL
  - char_is_valid API_EXPERIMENTAL (API Stability of Alphabet Module #269 (comment))
  - is_pair_open API_EXPERIMENTAL
  - is_pair_close API_EXPERIMENTAL
  - is_unpaired API_EXPERIMENTAL
  - max_pseudoknot_depth API_EXPERIMENTAL
  - pseudoknot_id API_EXPERIMENTAL
- ./alphabet/structure/wuss.hpp
  - wuss : alphabet_base API_EXPERIMENTAL
  - wuss.is_pair_open API_EXPERIMENTAL
  - wuss.is_pair_close API_EXPERIMENTAL
  - wuss.is_unpaired API_EXPERIMENTAL
  - wuss.max_pseudoknot_depth API_EXPERIMENTAL
  - wuss.pseudoknot_id API_EXPERIMENTAL
***********************

The text was updated successfully, but these errors were encountered:

marehr · 2021-01-11T10:24:06Z

Core Meeting 2021-01-11:

char_is_valid in all alphabets (mark experimental)
seqan3::char_is_valid_for (mark experimental)
seqan3::assign_char_strictly_to (mark experimental, is currently a dead CPO, no one uses it)
seqan3::writable_alphabet and seqan3::writable_constexpr_alphabet remove seqan3::char_is_valid_for. (Update writable_alphabet concept #278)
- Let's see if we need this feature (uses cases by user) and a possible concept could be added later which has as base writable_alphabet

smehringer · 2021-01-18T11:44:00Z

Core Meeting 2021-01-18:

Todos:

High Priority

alphabet conversion currently works by converting to char and back. Is this the way we want it to be? Might have implications on the behaviour of alphabets and is thus API relevant (@rrahn will work out the details/problems)
- MOVED TO Release 3.2: API Stability of Alphabet Module in Release 3.2 #389
alphabet conversion is weird; dna4 = 'Y' results in Y being converted to dna15, and then to dna4 (results in 'C' instead of 'A'). dna5 and aminoacid alphabets just define one letter that is used for unknown symbols
- MOVED TO Release 3.2: API Stability of Alphabet Module in Release 3.2 #389
What about alphabet_base? Is this marked as stable API?

Low Priority

Why is cigar not stable?
Check documentation of alphabets that use non-stable alphabet_variant and alphabet_tuple, to make sure the documentation is stand alone and does not refer to unstable entities. Does it have implications on seqan3::sam_dna16.
- We marked alphabet_variant and alphabet_tuple mostly stable.
Why are the quality alphabets not stable?
- MOVED TO Release 3.2: API Stability of Alphabet Module in Release 3.2 #389

marehr · 2021-02-15T12:12:04Z

Core Meeting 2021-02-15:

We talked about making the look-up tables static functions, so that we can make use cases like [Alphabet] dna4 complement and SIMD seqan3#1970 possible. We can still use look-up tables within the functions itself if we want to. See alphabet_base should expect that char_to_rank, rank_to_char, ... are static member functions. #295.

Open Questions:

Should we make ADL-lookups in CPOs API-stable? (We marked those as experimental)
enable_aminoacid:
- should we allow partial specialisation of seqan3::enable_aminoacid? (Undecided)
  - MOVED TO Release 3.2: API Stability of Alphabet Module in Release 3.2 #389
- should we allow ADL? (We marked this as experimental)
- seqan3::custom::alphabet seems to be the most flexible way to define custom / third-party alphabets.

marehr · 2021-02-17T10:55:28Z

Core-Meeting 2021-02-17:

Resolution:

Rename seqan3::cigar_op to seqan3::cigar_operation and if possible make this part of seqan3::cigar::operation. See Make seqan3::cigar_op part of seqan3::cigar::operation #294

marehr · 2021-02-22T11:16:51Z

Core-Meeting 2021-02-22:

Documentation: How to deal with assignment operator which are inherited, e.g. cigar defines an assignment operator for documentation, but the documentations also displays the assignment operator for the tuple_base.
alphabet_tuple_base uses hidden get friend, so seqan3::get<0>(tuple) is not possible. How about std::get<0>(tuple)?
- https://stackoverflow.com/questions/16173902/enable-stdget-support-on-class: This means hidden friends are okay.
- seqan3::get not usable; add documentation to explain this.
alphabet_tuple_base is ==, !=, <= commutative with indirect alphabets?
- MOVED TO Release 3.2: API Stability of Alphabet Module in Release 3.2 #389
Doxygen strikes again:

marehr · 2021-03-22T12:05:50Z

2021-03-22 Core-Meeting:

rename seqan3::sam_dna16 to seqan3::dna16sam (to reflect the general naming scheme of alphabets, e.g. aa10li "alphabet_category""alphabet_size""alphabet_unique_identifier").
rename seqan3::phred68legacy to seqan3::phred68solexa
conversion between seqan3::phred68solexa and seqan3::phred42 should be over the failure probability and not the phred scores.
- MOVED TO Release 3.2: API Stability of Alphabet Module in Release 3.2 #389
rename seqan3::quality_base to seqan3::phred_base

TODO:

alphabet/concept.hpp: CPOs mark ADL cpo_overloads experimental
alphabet/nucleotide/concept.hpp: CPOs mark ADL cpo_overloads experimental
alphabet/quality/concept.hpp: CPOs mark ADL cpo_overloads experimental

marehr · 2021-04-13T12:40:50Z

We talked about "uint64_t is not an alphabet?" #200

What to do?
- MOVED TO Release 3.2: API Stability of Alphabet Module in Release 3.2 #389

marehr · 2021-05-18T15:59:43Z

Open todos were collected in epic #389.

marehr mentioned this issue Dec 6, 2020

API Stability seqan3.1 #274

Closed

19 tasks

marehr added the Epic label Feb 16, 2021

marehr mentioned this issue Feb 16, 2021

alphabet 02: things that are marked stable / experimental. seqan/seqan3#2385

Merged

marehr mentioned this issue Feb 24, 2021

[API] remove seqan3::alphabet_base specialisation for alphabet_size == 1 seqan/seqan3#2399

Merged

This was referenced Mar 3, 2021

Move seqan3::cigar_op into seqan3::cigar class. seqan/seqan3#2426

Merged

Make seqan3::cigar_op part of seqan3::cigar::operation #294

Closed

alphabet_base should expect that char_to_rank, rank_to_char, ... are static member functions. #295

Closed

marehr added this to the 3.0.3 Release Sprint milestone Apr 12, 2021

marehr modified the milestones: 3.0.3 Release Sprint, 3.0.3 2nd Release Sprint Apr 28, 2021

marehr assigned eseiler, marehr and SGSSGene May 6, 2021

marehr mentioned this issue May 18, 2021

API Stability of Alphabet Module in Release 3.2 #389

Closed

10 tasks

marehr closed this as completed May 18, 2021

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API Stability of Alphabet Module #269

API Stability of Alphabet Module #269

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API Stability of Alphabet Module #269

API Stability of Alphabet Module #269

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marehr commented Dec 6, 2020 • edited Loading

marehr commented Jan 11, 2021 • edited Loading

smehringer commented Jan 18, 2021 • edited by marehr Loading

Core Meeting 2021-01-18:

Todos:

High Priority

Low Priority

marehr commented Feb 15, 2021 • edited Loading

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