Additional OpenSwath Speedups (IsotopeCacher + LinearResampler)#3
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jcharkow wants to merge 15 commits intofeature/oswSpeedUpfrom
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Additional OpenSwath Speedups (IsotopeCacher + LinearResampler)#3jcharkow wants to merge 15 commits intofeature/oswSpeedUpfrom
jcharkow wants to merge 15 commits intofeature/oswSpeedUpfrom
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Add additional class which will cache generated isotope patterns. This should speed up the execution of OpenSwathWorkflow This commit is very preliminary with nothing implmented yet
Revamped code when creating the test. Might not be the most efficient way right now however it is quite readable
now reads out the number of isotopes from command line dia_nr_isotopes when using this full size cache, the performance suffers. Takes significantly longer with the cache
Cache was actually taking longer because it was getting copied with function called unintentionally. Pass by address in all cases in order to prevent copying.
This gets without mutating the cache (such that it is compatible with multthreading)
clean up code, and ensure that all tests are passing
Fix unit tests so that they pass including DIAPrescoring_test, DIAScoring_test, MRMFeatureFinderScoring_test and MRMFeatureScoring_test
update function signatures of other tools to allow building
score behaviour was undefined because taking X isotopes for theoretical spectrum and X+1 isotopes for actual spectrum leading to non reproducible scoring. Edit cache to produce an extra isotope. Also revert getImmutable back to using upper bound because the rounding was a bit buggy.
don't create new linear resampler each time in order to speed up workflow
Also fix test in DIAScoring because isotopeCacher was empty by modifying getImmutable()
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Description
Speedups for OpenSwathWorkflow
Checklist
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