Optional Digestion Count Output #2460
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Added a generic Increment method to DictionaryExtensions.cs that increments the value of a specified key or initializes it to one if the key does not exist. Included XML documentation for the method. Updated DictionaryExtensionsTests.cs with unit tests covering various scenarios for the Increment method.
Added IsNullOrEmpty method to DictionaryExtensions.cs to check if a dictionary is null or empty. Included XML documentation for the method. Added unit tests in DictionaryExtensionsTests.cs to verify the method's behavior for null, empty, and non-empty dictionaries.
Introduced functionality to track and write digestion product counts for proteins during a search task. Key changes include: - Made `DigestionCountDictionary` a public readonly field in `ClassicSearchEngine.cs` and adjusted the constructor accordingly. - Added an internal property `DigestionCountDictionary` in `PostSearchAnalysisTask.cs` and implemented methods to write counts to .tsv files. - Modified `SearchTask.cs` to initialize and pass `digestionCountDictionary` to `PostSearchAnalysisTask`. - Added tests in `PostSearchAnalysisTaskTests.cs` to verify the correct writing of digestion counts and histograms.
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Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## master #2460 +/- ##
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Coverage 93.89% 93.90%
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Files 146 147 +1
Lines 22206 22320 +114
Branches 3059 3076 +17
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+ Hits 20851 20960 +109
- Misses 906 909 +3
- Partials 449 451 +2
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I don't understand the figures shown. If the max is 1024, how does the x-axis go out to 2000 or 3000? |
Alexander-Sol
requested changes
Jan 29, 2025
| { | ||
| if (dictionary.TryGetValue(key, out TValue value)) | ||
| { | ||
| dictionary[key] = value + TValue.One; |
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Directly accessing a dictionary element through dictionary[key] can cause race conditions with concurrent dictionaries. Adding/updating a concurrent dict should use the AddOrUpdate method.
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Added handling of concurrent dictionary to ensure these methods could be used in a thread safe or normal environment.
Alexander-Sol
requested changes
Jan 30, 2025
| concurrentDictionary.AddOrUpdate(key, new List<TValues> { value }, (k, v) => | ||
| { | ||
| lock (AddOrCreateLock) | ||
| { |
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I don't think you should call the lock inside the addOrUpdate method. That should be handled internally by the AddOrUpdate method
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This is to ensure the internal lists are thread safe. This is needed otherwise unit test AddOrCreate_ThreadSafeWithDictionary fails.
Updated `DigestionCountDictionary` to track by protein accession and base sequence. Modified `PostSearchAnalysisTask` and `SearchTask` to use the new type. Updated file output logic to include primary sequence and added checks for `WriteDecoys` parameter. Enhanced unit tests to reflect these changes and added new tests for decoy handling.
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PR Summary
New feature to track and output the number of digestion products from each protein during a classic search.
The number of digestion products that are generated per protein accession is a function of MaxModifiedIsoforms, MaxModsPerPeptide, Initiator Methionine behavior, and splice variants.
Detailed Changes
Introduced functionality to track and write digestion product counts, including GUI updates and new methods for output files.
ClassicSearchEngine: Added tracking of digestion counts and methods to retrieve and increment counts.SearchTaskWindow.xaml: Added checkbox for enabling digestion count tracking.PostSearchAnalysisTask: Added methods to write digestion counts and histograms to.tsvfiles.DictionaryExtensions: Created extension methods for dictionary operations.PostSearchAnalysisTaskTests.csandSearchEngineTests.csfor new features.Figures
These output files will only be generated when the option is checked deep in the advanced parameters of the search task window.