[INTERNAL] OpenSwath diaPASEF Speedup

[jcharkow]

Description

3-4 fold speedup of OpenSwathWorkflow.

Background: Filtering spectra by their ion mobility is very computationally expensive. Currently DIA scores are "blind" to the ion mobility dimension and thus require spectra to be filtered by ion mobility. Since the spectra are not sorted by ion mobility (rather by m/z) this is very computationally expensive.

Solution: Instead of filtering spectra examine only the regions of interest and compute scores from these. This takes advantage of the fact that the spectra are sorted by their m/z.

This PR involves creating new functions and deprecating old ones however it should not affect the output.

Some of the functions augmented include:

• integrateWindow + integrateWindows = Now support integration of an ion mobility enhanced window. Accomplishes this adding drift_start and drift_end arguments. This family of function all rely on a new function _integrateWindowHelper(). This function can now integrate across a vector of spectra. This means that the spectra do not need to be added up by the expensive _addUpSpectra() function.
• add DIA Scoring functions can now handle ion mobility
• computeIonMobilogram() (from IonMobilityScoring) = Computes ion mobilogram in more efficient manner than previous filterByDriftSpectrum
• fetchSpectrumSwath now does not automatically call _addUpSpectra() (which can be quite computationally expensive with ion mobility as it calls filterByDrift())

Some Functions Removed include:

• DIAHelpers::integrateDriftSpectrum = not needed because the base function now supports integrating spectra.

Tests:

• integrateWindow tests were added.
• OpenSwathTest 23_b was added to test the -add_up_spectra flag

Issues

• With the new implementation this removes support for resampling spectra addition with ion mobility
  • Possibly deprecate resampling spectra?
• Currently SONAR still uses the old implementation of adding up spectra

Checklist

• Make sure that you are listed in the AUTHORS file
• Add relevant changes and new features to the CHANGELOG file
• I have commented my code, particularly in hard-to-understand areas
• New and existing unit tests pass locally with my changes
• Updated or added python bindings for changed or new classes (Tick if no updates were necessary.)

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