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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?
If so, I propose steps to
Make Profile<S,C> extend LightweightProfile<AlignedSequence<S,C>,C>
Improve documentation clarifying that SimpleProfile is pairwise
Deprecate one of Profile.StringFormat or LightweightProfile.StringFormat
Add constructors to ease conversion between SimpleProfile and MultipleSequenceAlignment instances
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.
The last point regarding formats is relevant to #983. I had difficulties recommending a solution because the pairwise and MSA outputs are different and undocumented.
The text was updated successfully, but these errors were encountered:
I think
Profile
was indended to be general enough to represent multiple sequence alignments. HoweverSimpleProfile
is the only current implementation and it only supports pairwise alignments. There is alsoLightweightProfile
with similarly named methods that is implemented byMultipleSequenceAlignment
and seems intended for ungapped sequences. Is that an accurate summary of the situation?If so, I propose steps to
Profile<S,C>
extendLightweightProfile<AlignedSequence<S,C>,C>
SimpleProfile
is pairwiseProfile.StringFormat
orLightweightProfile.StringFormat
SimpleProfile
andMultipleSequenceAlignment
instancestoString(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.The last point regarding formats is relevant to #983. I had difficulties recommending a solution because the pairwise and MSA outputs are different and undocumented.
The text was updated successfully, but these errors were encountered: