{"action":"created","issue":{"url":"https://api.github.com/repos/seqan/seqan3/issues/535","repository_url":"https://api.github.com/repos/seqan/seqan3","labels_url":"https://api.github.com/repos/seqan/seqan3/issues/535/labels{/name}","comments_url":"https://api.github.com/repos/seqan/seqan3/issues/535/comments","events_url":"https://api.github.com/repos/seqan/seqan3/issues/535/events","html_url":"https://github.com/seqan/seqan3/pull/535","id":376485112,"node_id":"MDExOlB1bGxSZXF1ZXN0MjI3NjkxOTk1","number":535,"title":"Refactoring of alphabets","user":{"login":"h-2","id":2996863,"node_id":"MDQ6VXNlcjI5OTY4NjM=","avatar_url":"https://avatars2.githubusercontent.com/u/2996863?v=4","gravatar_id":"","url":"https://api.github.com/users/h-2","html_url":"https://github.com/h-2","followers_url":"https://api.github.com/users/h-2/followers","following_url":"https://api.github.com/users/h-2/following{/other_user}","gists_url":"https://api.github.com/users/h-2/gists{/gist_id}","starred_url":"https://api.github.com/users/h-2/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/h-2/subscriptions","organizations_url":"https://api.github.com/users/h-2/orgs","repos_url":"https://api.github.com/users/h-2/repos","events_url":"https://api.github.com/users/h-2/events{/privacy}","received_events_url":"https://api.github.com/users/h-2/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":{"login":"rrahn","id":1529364,"node_id":"MDQ6VXNlcjE1MjkzNjQ=","avatar_url":"https://avatars2.githubusercontent.com/u/1529364?v=4","gravatar_id":"","url":"https://api.github.com/users/rrahn","html_url":"https://github.com/rrahn","followers_url":"https://api.github.com/users/rrahn/followers","following_url":"https://api.github.com/users/rrahn/following{/other_user}","gists_url":"https://api.github.com/users/rrahn/gists{/gist_id}","starred_url":"https://api.github.com/users/rrahn/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rrahn/subscriptions","organizations_url":"https://api.github.com/users/rrahn/orgs","repos_url":"https://api.github.com/users/rrahn/repos","events_url":"https://api.github.com/users/rrahn/events{/privacy}","received_events_url":"https://api.github.com/users/rrahn/received_events","type":"User","site_admin":false},"assignees":[{"login":"rrahn","id":1529364,"node_id":"MDQ6VXNlcjE1MjkzNjQ=","avatar_url":"https://avatars2.githubusercontent.com/u/1529364?v=4","gravatar_id":"","url":"https://api.github.com/users/rrahn","html_url":"https://github.com/rrahn","followers_url":"https://api.github.com/users/rrahn/followers","following_url":"https://api.github.com/users/rrahn/following{/other_user}","gists_url":"https://api.github.com/users/rrahn/gists{/gist_id}","starred_url":"https://api.github.com/users/rrahn/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rrahn/subscriptions","organizations_url":"https://api.github.com/users/rrahn/orgs","repos_url":"https://api.github.com/users/rrahn/repos","events_url":"https://api.github.com/users/rrahn/events{/privacy}","received_events_url":"https://api.github.com/users/rrahn/received_events","type":"User","site_admin":false}],"milestone":null,"comments":12,"created_at":"2018-11-01T17:12:35Z","updated_at":"2018-11-26T17:12:48Z","closed_at":null,"author_association":"MEMBER","pull_request":{"url":"https://api.github.com/repos/seqan/seqan3/pulls/535","html_url":"https://github.com/seqan/seqan3/pull/535","diff_url":"https://github.com/seqan/seqan3/pull/535.diff","patch_url":"https://github.com/seqan/seqan3/pull/535.patch"},"body":"## major refactorisation of all alphabets\r\n\r\n- there are now alphabet base classes that our alphabets inherit from, this reduces code duplication\r\n- alphabets are no longer aggregate types fixing some weird issues\r\n- our alphabets are still PODs although this is not required by the alphabet_concept anymore\r\n- `constexpr` default construction has been fixed everywhere\r\n- cartesian composition no longer inherits pod_tuple, but actually compresses into a single rank value\r\n  - `gapped<dna5>` now consumes one byte, not two\r\n  - all operations are now constant time, not linear in the number of elements\r\n- introduction of alphabet_proxy, a generic proxy base that also models the concepts of it's emulated type\r\n- fixed a heap of bugs I found on the way\r\n\r\n## Reviews:\r\n\r\n- @joshuak94 can you review the changes to the mask alphabet and gap?\r\n- @sarahet can you review the changes regarding the amino acids? It's not much ;)\r\n- @joergi-w can you review the changes to the structure alphabets and the dna alphabets?\r\n- @mariehoffmann can you review the changes to the qualities?\r\n- @smehringer @marehr Can you review rest, in particular the changes to cartesian_composition and the alphabet_proxy?\r\n\r\nFollow-Up TODOs:\r\n  - [ ] investigate the two ICEs\r\n  - [ ] make union_composition require the same char_type on alternatives\r\n  - [ ] rename `composition` module to `composite`\r\n  - [ ] rename `cartesian_composition` to `alphabet_tuple`\r\n  - [ ] rename `union_composition` to `alphabet_variant`\r\n  - [ ] implement `alphabet_any`\r\n  - [ ] switch all alphabets from enum-notation to using a char literal (only done for nucleotides)\r\n"},"comment":{"url":"https://api.github.com/repos/seqan/seqan3/issues/comments/441720068","html_url":"https://github.com/seqan/seqan3/pull/535#issuecomment-441720068","issue_url":"https://api.github.com/repos/seqan/seqan3/issues/535","id":441720068,"node_id":"MDEyOklzc3VlQ29tbWVudDQ0MTcyMDA2OA==","user":{"login":"h-2","id":2996863,"node_id":"MDQ6VXNlcjI5OTY4NjM=","avatar_url":"https://avatars2.githubusercontent.com/u/2996863?v=4","gravatar_id":"","url":"https://api.github.com/users/h-2","html_url":"https://github.com/h-2","followers_url":"https://api.github.com/users/h-2/followers","following_url":"https://api.github.com/users/h-2/following{/other_user}","gists_url":"https://api.github.com/users/h-2/gists{/gist_id}","starred_url":"https://api.github.com/users/h-2/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/h-2/subscriptions","organizations_url":"https://api.github.com/users/h-2/orgs","repos_url":"https://api.github.com/users/h-2/repos","events_url":"https://api.github.com/users/h-2/events{/privacy}","received_events_url":"https://api.github.com/users/h-2/received_events","type":"User","site_admin":false},"created_at":"2018-11-26T17:12:48Z","updated_at":"2018-11-26T17:12:48Z","author_association":"MEMBER","body":"@smehringer @joergi-w @mariehoffmann I think I have addressed all your comments except some minor things in the tests. Can you have a look and mark respective comments as resolved?\r\n\r\n@marehr I can haz review plz? :cat: "}}
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