Extended calibration options

[trishorts]

This pull request adds support for using both Classic and Modern search strategies in the calibration workflow of MetaMorpheus. Users can now select which search engine to use for calibration, and the system will generate and use peptide/fragment indexes as needed for Modern Search. The changes also include new tests to verify the correctness and equivalence of calibration results between the two search types.

Calibration Engine Enhancements:

• Added a SearchType property to CalibrationParameters, allowing selection between Classic and Modern search strategies. The default is set to Classic.
• Updated the calibration workflow (CalibrationTask) to use the selected search type. If Modern Search is selected, the workflow generates peptide and fragment indexes and uses the ModernSearchEngine; otherwise, it uses the ClassicSearchEngine. [1] [2]
• Added private fields to CalibrationTask for storing Modern Search indexes and logic to reset/generate them as needed. [1] [2]

GUI Updates:

• Updated the calibration task window to allow users to select the search type via radio buttons, and to save/load this setting with the task. [1] [2]

Testing Improvements:

• Added comprehensive tests to verify that calibration works with Modern Search and that results are comparable between Classic and Modern search types.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 94.72%. Comparing base (4954590) to head (1f04191).

Additional details and impacted files

@@           Coverage Diff           @@
##           master    #2613   +/-   ##
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  Coverage   94.71%   94.72%           
=======================================
  Files         187      187           
  Lines       19658    19692   +34     
  Branches     3641     3643    +2     
=======================================
+ Hits        18620    18654   +34     
  Misses        566      566           
  Partials      472      472           

Flag	Coverage Δ
unittests	94.72% <100.00%> (+<0.01%)	⬆️

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Files with missing lines	Coverage Δ
...TaskLayer/CalibrationTask/CalibrationParameters.cs	100.00% <100.00%> (ø)
...pheus/TaskLayer/CalibrationTask/CalibrationTask.cs	92.77% <100.00%> (+1.06%)	⬆️

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[pcruzparri]

Should this disabled feature be left out until implemented?