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Merged
YukiMatsuzawa merged 2 commits into from
Aug 17, 2026
Merged

Improve LCMS alignment initialization performance #770

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98ebdaf
Improve LCMS alignment initialization
YukiMatsuzawa Aug 7, 2026
71135f4
Lazy-load MS-FINDER databases
YukiMatsuzawa Aug 7, 2026
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16 changes: 8 additions & 8 deletions src/MSDIAL5/MsdialGuiApp/Model/Dims/DimsMethodModel.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -184,17 +184,17 @@ public override async Task RunAsync(ProcessOption processOption, CancellationTok


_matchResultEvaluator = FacadeMatchResultEvaluator.FromDataBases(Storage.DataBases);
IAnnotationProcess annotationProcess;
if (Storage.Parameter.TargetOmics == TargetOmics.Lipidomics &&
(Storage.Parameter.CollistionType == CollisionType.EIEIO || Storage.Parameter.CollistionType == CollisionType.OAD || Storage.Parameter.CollistionType == CollisionType.EID)) {
annotationProcess = BuildEadLipidomicsAnnotationProcess();
}
else {
annotationProcess = BuildAnnotationProcess();
}

// Run Identification
if (processOption.HasFlag(ProcessOption.Identification)) {
IAnnotationProcess annotationProcess;
if (Storage.Parameter.TargetOmics == TargetOmics.Lipidomics &&
(Storage.Parameter.CollistionType == CollisionType.EIEIO || Storage.Parameter.CollistionType == CollisionType.OAD || Storage.Parameter.CollistionType == CollisionType.EID)) {
annotationProcess = BuildEadLipidomicsAnnotationProcess();
}
else {
annotationProcess = BuildAnnotationProcess();
}
var usable = Math.Max(Storage.Parameter.ProcessBaseParam.UsableNumThreads / 2, 1);
var processor = new ProcessFile(ProviderFactory, Storage, annotationProcess, _matchResultEvaluator);
var runner = new ProcessRunner(processor, usable);
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6 changes: 3 additions & 3 deletions src/MSDIAL5/MsdialGuiApp/Model/Lcimms/LcimmsMethodModel.cs
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Expand Up @@ -220,11 +220,11 @@ public override async Task RunAsync(ProcessOption processOption, CancellationTok
var starttimestamp = DateTime.Now.ToString("yyyyMMddHHmm");
var stopwatch = Stopwatch.StartNew();

// Set analysis param
var annotationProcess = BuildAnnotationProcess();

// Run Identification
if (processOption.HasFlag(ProcessOption.Identification)) {
// Set analysis param
var annotationProcess = BuildAnnotationProcess();

int usable = Math.Max(Storage.Parameter.ProcessBaseParam.UsableNumThreads / 2, 1);
FileProcess processor = new FileProcess(providerFactory, accProviderFactory, annotationProcess, matchResultEvaluator, Storage, isGuiProcess: true);
var runner = new ProcessRunner(processor, usable);
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23 changes: 11 additions & 12 deletions src/MSDIAL5/MsdialGuiApp/Model/Lcms/LcmsMethodModel.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,6 @@
using Reactive.Bindings.Notifiers;
using System;
using System.Collections.Generic;
using System.ComponentModel;
using System.Diagnostics;
using System.Linq;
using System.Reactive.Linq;
Expand Down Expand Up @@ -252,20 +251,20 @@ public override async Task RunAsync(ProcessOption processOption, CancellationTok
var parameter = _storage.Parameter;
var starttimestamp = DateTime.Now.ToString("yyyyMMddHHmm");
var stopwatch = Stopwatch.StartNew();
IAnnotationProcess annotationProcess;
if (parameter.TargetOmics == TargetOmics.Proteomics) {
annotationProcess = BuildProteoMetabolomicsAnnotationProcess();
}
else if(parameter.TargetOmics == TargetOmics.Lipidomics &&
(parameter.CollistionType == CollisionType.EIEIO || parameter.CollistionType == CollisionType.OAD || parameter.CollistionType == CollisionType.EID)) {
annotationProcess = BuildEadLipidomicsAnnotationProcess();
}
else {
annotationProcess = BuildAnnotationProcess();
}

// Run Identification
if (processOption.HasFlag(ProcessOption.Identification)) {
IAnnotationProcess annotationProcess;
if (parameter.TargetOmics == TargetOmics.Proteomics) {
annotationProcess = BuildProteoMetabolomicsAnnotationProcess();
}
else if(parameter.TargetOmics == TargetOmics.Lipidomics &&
(parameter.CollistionType == CollisionType.EIEIO || parameter.CollistionType == CollisionType.OAD || parameter.CollistionType == CollisionType.EID)) {
annotationProcess = BuildEadLipidomicsAnnotationProcess();
}
else {
annotationProcess = BuildAnnotationProcess();
}
var processor = new MsdialLcMsApi.Process.FileProcess(_providerFactory, _storage, annotationProcess, _matchResultEvaluator);
var runner = new ProcessRunner(processor, Math.Max(1, _storage.Parameter.ProcessBaseParam.UsableNumThreads / 2));
if (!ProcessFiles(_storage.AnalysisFiles, runner, processOption)) {
Expand Down
78 changes: 42 additions & 36 deletions src/MSDIAL5/MsdialGuiApp/Model/Setting/InternalMsfinderSettingModel.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -25,56 +25,62 @@ namespace CompMs.App.Msdial.Model.Setting
{
internal class InternalMsfinderSettingModel : BindableBase
{
internal readonly MsfinderParameterSetting parameter;
internal readonly AnalysisParamOfMsfinder analysisParam;
internal readonly AlignmentSpectraExportGroupModel exporter;
internal readonly ReadOnlyReactivePropertySlim<IAlignmentModel?> CurrentAlignmentModel;
private readonly MsfinderParameterSetting _parameter;
private readonly AnalysisParamOfMsfinder _analysisParam;
private readonly AlignmentSpectraExportGroupModel _exporter;
private readonly ReadOnlyReactivePropertySlim<IAlignmentModel?> _currentAlignmentModel;

public InternalMsfinderSettingModel(MsfinderParameterSetting projectParameter, AlignmentSpectraExportGroupModel alignmentExporter, ReadOnlyReactivePropertySlim<IAlignmentModel?> currentAlignmentModel) {
parameter = projectParameter;
exporter = alignmentExporter;
CurrentAlignmentModel = currentAlignmentModel;
analysisParam = projectParameter.AnalysisParameter;
_parameter = projectParameter;
_exporter = alignmentExporter;
_currentAlignmentModel = currentAlignmentModel;
_analysisParam = projectParameter.AnalysisParameter;
}

private readonly List<ProductIon> productIonDB = CompMs.Common.FormulaGenerator.Parser.FragmentDbParser.GetProductIonDB(
private List<ProductIon> ProductIonDB => _productIonDB ??= CompMs.Common.FormulaGenerator.Parser.FragmentDbParser.GetProductIonDB(
@"Resources\msfinderLibrary\ProductIonLib_vs1.pid", out string _);
private readonly List<NeutralLoss> neutralLossDB = CompMs.Common.FormulaGenerator.Parser.FragmentDbParser.GetNeutralLossDB(
private List<ProductIon>? _productIonDB;
private List<NeutralLoss> NeutralLossDB => _neutralLossDB ??= CompMs.Common.FormulaGenerator.Parser.FragmentDbParser.GetNeutralLossDB(
@"Resources\msfinderLibrary\NeutralLossDB_vs2.ndb", out string _);
private readonly List<ExistFormulaQuery> existFormulaDB = ExistFormulaDbParcer.ReadExistFormulaDB(
private List<NeutralLoss>? _neutralLossDB;
private List<ExistFormulaQuery> ExistFormulaDB => _existFormulaDB ??= ExistFormulaDbParcer.ReadExistFormulaDB(
@"Resources\msfinderLibrary\MsfinderFormulaDB-VS13.efd", out string _);
private readonly List<ExistStructureQuery> existStructureDB = FileStorageUtility.GetExistStructureDB();
private List<ExistFormulaQuery>? _existFormulaDB;
private List<ExistStructureQuery> ExistStructureDB => _existStructureDB ??= FileStorageUtility.GetExistStructureDB();
private List<ExistStructureQuery>? _existStructureDB;
private List<ExistStructureQuery> MineStructureDB => _mineStructureDB ??= FileStorageUtility.GetMinesStructureDB();
private List<ExistStructureQuery>? _mineStructureDB;
private List<FragmentOntology> FragmentOntologyDB => _fragmentOntologyDB ??= FileStorageUtility.GetUniqueFragmentDB();
private List<FragmentOntology>? _fragmentOntologyDB;
private List<FragmentLibrary> EiFragmentDB => _eiFragmentDB ??= FileStorageUtility.GetEiFragmentDB();
private List<FragmentLibrary>? _eiFragmentDB;

private readonly List<ExistStructureQuery> mineStructureDB = FileStorageUtility.GetMinesStructureDB();
private readonly List<FragmentOntology> fragmentOntologyDB = FileStorageUtility.GetUniqueFragmentDB();
private readonly List<MoleculeMsReference> mspDB = [];
private List<ExistStructureQuery> userDefinedStructureDB = [];
private readonly List<FragmentLibrary> eiFragmentDB = FileStorageUtility.GetEiFragmentDB();


public InternalMsFinder? Process() {
if (CurrentAlignmentModel.Value is null) {
if (_currentAlignmentModel.Value is null) {
return null;
}
SetUserDefinedStructureDB();

string fullpath;
var dt = DateTime.Now;
if (parameter.IsCreateNewProject) {
var directory = Path.GetDirectoryName(CurrentAlignmentModel.Value.AlignmentFile.FilePath); // project folder
if (_parameter.IsCreateNewProject) {
var directory = Path.GetDirectoryName(_currentAlignmentModel.Value.AlignmentFile.FilePath); // project folder
string foldername;
if (parameter.IsUseAutoDefinedFolderName) {
foldername = $"{CurrentAlignmentModel.Value.AlignmentFile.FileName}_{dt:yyyyMMddHHmmss}";
if (_parameter.IsUseAutoDefinedFolderName) {
foldername = $"{_currentAlignmentModel.Value.AlignmentFile.FileName}_{dt:yyyyMMddHHmmss}";
}else{
foldername = parameter.UserDefinedProjectFolderName;
foldername = _parameter.UserDefinedProjectFolderName;
}
fullpath = Path.Combine(directory, foldername); // export folder
if (!Directory.Exists(fullpath)) {
Directory.CreateDirectory(fullpath);
}
exporter.Export(CurrentAlignmentModel.Value.AlignmentFile, fullpath, null);
_exporter.Export(_currentAlignmentModel.Value.AlignmentFile, fullpath, null);
}else{
fullpath = parameter.ExistProjectPath;
fullpath = _parameter.ExistProjectPath;
}

var matFilePaths = Directory.GetFiles(fullpath, "*.mat");
Expand All @@ -89,30 +95,30 @@ public InternalMsfinderSettingModel(MsfinderParameterSetting projectParameter, A
msfinderQueryFiles.Add(msfinderQueryFile);
}

if (parameter.IsFormulaFinder) {
if (_parameter.IsFormulaFinder) {
var paramfile = Path.Combine(fullpath, $"batchparam-{dt:yyyy_MM_dd_HH_mm_ss}.txt");
MsFinderIniParser.Write(analysisParam, paramfile);
MsFinderIniParser.Write(_analysisParam, paramfile);

foreach (var msfinderQueryFile in msfinderQueryFiles) {
var rawData = RawDataParcer.RawDataFileReader(msfinderQueryFile.RawDataFilePath, analysisParam);
var formulaResults = MolecularFormulaFinder.GetMolecularFormulaList(productIonDB, neutralLossDB, existFormulaDB, rawData, analysisParam);
var rawData = RawDataParcer.RawDataFileReader(msfinderQueryFile.RawDataFilePath, _analysisParam);
var formulaResults = MolecularFormulaFinder.GetMolecularFormulaList(ProductIonDB, NeutralLossDB, ExistFormulaDB, rawData, _analysisParam);
FormulaResultParcer.FormulaResultsWriter(msfinderQueryFile.FormulaFilePath, formulaResults);
}
}
if (parameter.IsStructureFinder) {
if (_parameter.IsStructureFinder) {
var finder = new StructureFinderBatchProcess();
finder.Process(msfinderQueryFiles, analysisParam, existStructureDB, userDefinedStructureDB, mineStructureDB, fragmentOntologyDB, mspDB, eiFragmentDB);
finder.Process(msfinderQueryFiles, _analysisParam, ExistStructureDB, userDefinedStructureDB, MineStructureDB, FragmentOntologyDB, mspDB, EiFragmentDB);
}

if (CurrentAlignmentModel.Value.AlignmentSpotSource.Spots is null) {
if (_currentAlignmentModel.Value.AlignmentSpotSource.Spots is null) {
return null;
}
return new InternalMsFinder(msfinderQueryFiles, analysisParam, userDefinedStructureDB);
return new InternalMsFinder(msfinderQueryFiles, _analysisParam, userDefinedStructureDB);
}

private void SetUserDefinedStructureDB() {
if (parameter.IsUserDefinedDB) {
var userDefinedDbFilePath = parameter.UserDefinedDbFilePath;
if (_parameter.IsUserDefinedDB) {
var userDefinedDbFilePath = _parameter.UserDefinedDbFilePath;
if (userDefinedDbFilePath == null || userDefinedDbFilePath == string.Empty) {
MessageBox.Show("Select your own structure database, or uncheck the user-defined database option.", "Error", MessageBoxButton.OK, MessageBoxImage.Error);
return;
Comment on lines +121 to 124
Expand All @@ -122,13 +128,13 @@ private void SetUserDefinedStructureDB() {
return;
}

var userDefinedDb = ExistStructureDbParser.ReadExistStructureDB(parameter.UserDefinedDbFilePath);
var userDefinedDb = ExistStructureDbParser.ReadExistStructureDB(_parameter.UserDefinedDbFilePath);
if (userDefinedDb == null || userDefinedDb.Count == 0) {
MessageBox.Show("Your own structure DB does not have the queries or the data format is not correct.", "Error", MessageBoxButton.OK, MessageBoxImage.Error);
return;
}

ExistStructureDbParser.SetExistStructureDbInfoToUserDefinedDB(existStructureDB, userDefinedDb);
ExistStructureDbParser.SetExistStructureDbInfoToUserDefinedDB(ExistStructureDB, userDefinedDb);
userDefinedStructureDB = userDefinedDb;
}
else
Expand Down
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