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{"@context":"https://schema.org","@type":"DiscussionForumPosting","headline":"Harmonize Profile and LightweightProfile","articleBody":"I think `Profile` was indended to be general enough to represent multiple sequence alignments. However `SimpleProfile` is the only current implementation and it only supports pairwise alignments. There is also `LightweightProfile` with similarly named methods that is implemented by `MultipleSequenceAlignment` and seems intended for ungapped sequences. Is that an accurate summary of the situation?\r\n\r\nIf so, I propose steps to \r\n\r\n- Make `Profile\u003cS,C\u003e` extend `LightweightProfile\u003cAlignedSequence\u003cS,C\u003e,C\u003e`\r\n- Improve documentation clarifying that `SimpleProfile` is pairwise\r\n- Deprecate one of `Profile.StringFormat` or `LightweightProfile.StringFormat`\r\n- Add constructors to ease conversion between `SimpleProfile` and `MultipleSequenceAlignment` instances\r\n- Document what `toString(StringFormat)` is expected to produce for each format. Ideally it should be the same for two or more sequences. If a format is only applicable to pairwise alignments this needs to be clearly documented.\r\n\r\nThe last point regarding formats is relevant to #983. I had difficulties recommending a solution because the pairwise and MSA outputs are different and undocumented.","author":{"url":"https://github.com/sbliven","@type":"Person","name":"sbliven"},"datePublished":"2022-01-27T15:18:34.000Z","interactionStatistic":{"@type":"InteractionCounter","interactionType":"https://schema.org/CommentAction","userInteractionCount":0},"url":"https://github.com/1018/biojava/issues/1018"}