WIP Make LongSequence and LongSubSeq use Memory [DO NOT MERGE] #317
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This makes these two data types more lightweight, requiring only two memory allocations (one for the sequence and one for its memory) as opposed to two. It also improves data locality since loading from the sequences won't require a double load through the indirection of `Vector`. The disadvanges are twofold: First, we lose support for Julia 1.10 since Memory was introduced in Julia 1.11 Second, Vector's code to grow its underlying memory is much more optimised and tested than the manual implementation here in BioSequences. This would matter if users did a lot of resizing operations on biosequences, like `push!` or so. However, I think they don't - they are instead much more likely to create a lot of sequences. If necessary, we can always implement better resizing / growth behaviour for these types.
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## master #317 +/- ##
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- Coverage 90.87% 87.66% -3.22%
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Files 31 31
Lines 2400 2342 -58
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- Hits 2181 2053 -128
- Misses 219 289 +70
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This makes these two data types more lightweight, requiring only two memory allocations (one for the sequence and one for its memory) as opposed to two. It also improves data locality since loading from the sequences won't require a double load through the indirection of
Vector.The disadvanges are twofold:
First, we lose support for Julia 1.10 since Memory was introduced in Julia 1.11
Second, Vector's code to grow its underlying memory is much more optimised and tested than the manual implementation here in BioSequences. This would matter if users did a lot of resizing operations on biosequences, like
push!or so. However, I think they don't - they are instead much more likely to create a lot of sequences.If necessary, we can always implement better resizing / growth behaviour for these types.
TODO
pushfirst!is O(N)