Enhancements in MSExperiment and MSSpectrum classes

[jpfeuffer]

User description

Description

Adds faster, simpler and customizable extract and aggregate functions to MSExperiment.

TODOs:

• Decide on final API. Probably templatize in/outputs of aggregation functions, such that you can extract a Chromatogram object instead of just std::vectors or doubles
• More docs
• Add support for grouped extractions with a third aggregation function on how to combine extractions in that group (basically enabling full OpenSwath "feature finding" pipeline). Benefits from extra scheduling of group aggregation threads to start aggregating once a group was fully extracted

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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Type

Enhancement

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Description

• Added new methods for aggregating data in the MSExperiment class. These methods include aggregate functions with various parameters and overloads, getSpectraIdxRangeByRetentionTime, getSpectraIdcsByRetentionTime, getFirstProductSpectrum, and getRangesIdcs_. These methods provide more flexible and efficient ways to aggregate and retrieve data from MSExperiment objects.
• Introduced OpenMP parallelization in some of the new methods in the MSExperiment class to improve performance.
• Added a new test case for the aggregate method in the MSExperiment class.
• Added the maybeGetIMData method in the MSSpectrum class, which returns ion mobility data if available.

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Changes walkthrough

	Relevant files
Enhancement	MSExperiment.cpp                                                                                        src/openms/source/KERNEL/MSExperiment.cpp Added new methods for aggregating data in the MSExperiment class. These methods include aggregate functions with various parameters and overloads, getSpectraIdxRangeByRetentionTime, getSpectraIdcsByRetentionTime, getFirstProductSpectrum, and getRangesIdcs_. Also, OpenMP parallelization was introduced in some of the new methods. +377/-9 MSSpectrum.cpp                                                                                            src/openms/source/KERNEL/MSSpectrum.cpp Added the maybeGetIMData method in the MSSpectrum class, which returns ion mobility data if available. +13/-0
Tests	MSExperiment_test.cpp                                                                              src/tests/class_tests/openms/source/MSExperiment_test.cpp Added a new test case for the aggregate method in the MSExperiment class. +78/-0

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