Make "Searched adduct ions" in a console method file take effect - #815
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The console reader stored AdductIon.GetAdductIon's shared cached instances, whose IsIncluded is false. PeakCharacterEstimator keeps only included adducts and otherwise falls back to [M+H]+ / [M-H]-, so every console run searched the proton adduct alone whatever the method file listed, while the method-file key report said the key had been applied. The reader now stores included copies (never mutating the shared cache), trims each entry, still drops entries that fail FormatCheck, and reports the value as unusable when none of the listed adducts can be read. This changes results for method files that list adducts other than the proton adduct. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
…ched-adducts-included # Conflicts: # tests/MSDIAL5/MsdialCoreTestAppTests/Parser/ConfigParserTests.cs
…ched-adducts-included
…ched-adducts-included # Conflicts: # tests/MSDIAL5/MsdialCoreTestAppTests/Parser/ConfigParserTests.cs
The console reader no longer builds AdductIon instances of its own. It stores GetAdductIon's shared instances and sets IsIncluded on them, as the GUI's AdductIonSettingModel already does. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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Method files that listed adducts beyond the proton adduct were silently searched with
[M+H]+(Positive) or[M-H]-(Negative) only. After this change, the listed adducts are searched. Console reanalyses of such method files will get different adduct assignments and peak-character links than before.Bug
ConfigParser.ReadCommonParameter'ssearched adduct ionsarm filledparam.SearchedAdductIonswithAdductIon.GetAdductIon(...). That returns a shared instance from the static cache, and itsIsIncludedisfalse.PeakCharacterEstimator.SearchedAdductInitialize(both the MsdialCore and the DIMS copy) keeps onlyIsIncludedadducts and falls back to the proton adduct when none are left. Only the GUI'sAdductIonSettingModelever set the flag. SoSearched adduct ions: [M+H]+,[M+Na]+,[M+NH4]+ran with[M+H]+alone, and the method-file key report still recorded the key as applied.Fix
SearchedAdductIonshelper. It setsIsIncluded = truedirectly on the adductsGetAdductIonreturns. These are the shared cached instances, so the flag stays set for later callers in the same process. The GUI'sAdductIonSettingModelalready sets the flag this way, and a console run reads one method file per process.FormatCheckare still dropped. Entries are now trimmed, so[M+H]+, [M+Na]+keeps both.MethodKeyOutcome.UnusableValueand the built-in list is kept, following the file's documented convention.Other readers
ReadForGcms,ReadForDimsParameter,ReadForImmsParameterandReadForLcImMsParameterall send this key throughReadCommonParameter, so this one change fixes them all. No other place in the console buildsSearchedAdductIons.Tests (
ConfigParserTests)IsIncluded, and the key report stays silent.GetAdductIoninstances, now markedIsIncluded.UnusableValue.PeakCharacterEstimator.Processsearches exactly the listed adducts.Verification
dotnet test tests/MSDIAL5/MsdialCoreTestAppTests/MsdialCoreTestAppTests.csproj: 68/68 passed (after merging the latest master)dotnet build tests/MSDIAL5/MsdialCoreTestApp/MsdialCoreTestApp.csproj: net472, net48 and net8 build with 0 errors🤖 Generated with Claude Code