Add getter methods (and forwarded getter methods) for alignment types #83
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alignment(::AlignedSequence) and alignment(::PairwiseAlignmentResult) both return an Alignment, but alignment(::PairwiseAlignmentResult) has always returned a PairwiseAlignment. I don't want to break the current implementation for alignment(::PairwiseAlignmentResult), but the the implementation of the two others makes sense in the context of their types. Ideally, I would separate the alignment(::PairwiseAlignmentResult) function into separate getter functions like alignment(::PairwiseAlignmentResult)::Alignment and pairwise_alignment(::PairwiseAlignmentResult)::PairwiseAlignment, but again, that would be breaking. So instead, settle for a really dirty-feeling compromise of documenting the difference and explaining the reasoning behind it with the hope that BioAlignments v4 is able to reconcile this bandaged solution.
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Codecov ReportBase: 88.50% // Head: 87.60% // Decreases project coverage by
Additional details and impacted files@@ Coverage Diff @@
## master #83 +/- ##
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- Coverage 88.50% 87.60% -0.91%
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Files 16 16
Lines 1114 1138 +24
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+ Hits 986 997 +11
- Misses 128 141 +13
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Types of changes
This PR implements the following changes:
📋 Additional detail
The idea for these getter functions first came up in the discussion at #80 (comment). These functions are intended to be user-friendly band-aids over the disjointed API between
Alignment,AlignedSequence,PairwiseAlignment, andPairwiseAlignmentResult. There are five new methods, with one new exported function.alignment(::AlignedSequence) -> Alignmentalignment(::PairwiseAlignment) -> Alignmentsequence(::AlignedSequence) -> LongSequencesequence(::PairwiseAlignment) -> LongSequencesequence(::PairwiseAlignmentResult) -> LongSequenceNote that
alignment(::PairwiseAlignmentResult)already returns aPairwiseAlignment. I opted for liberal documentation over breaking the API.I added extra documentation and tests in the form of doctests. I didn't add any additional tests to the regular test suite, as getter function tests are pretty redundant.
My hope is that this closes out the feature list of BioAlignments v2, and we can get #44 merged and move on to BioAlignments v3 after this.
☑️ Checklist
docs/src/.[UNRELEASED]section of the manually curatedCHANGELOG.mdfile for this repository.