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Fix null RT correction selection path #771

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Merged
YukiMatsuzawa merged 1 commit into from
Aug 17, 2026
Merged

Fix null RT correction selection path #771

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4 changes: 1 addition & 3 deletions src/MSDIAL5/MsdialCore/Parameter/ParameterBase.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -107,8 +107,6 @@ public ParameterBase(bool isLabUseOnly) {
[IgnoreMember]
public string CompoundListForRtCorrectionPath { get => ReferenceFileParam.CompoundListForRtCorrectionPath; set => ReferenceFileParam.CompoundListForRtCorrectionPath = value; }
[IgnoreMember]
public string RtCorrectionPeakSelectionFilePath { get => ReferenceFileParam.RtCorrectionPeakSelectionFilePath; set => ReferenceFileParam.RtCorrectionPeakSelectionFilePath = value; }
[IgnoreMember]
public List<AdductIon> SearchedAdductIons { get => ReferenceFileParam.SearchedAdductIons; set => ReferenceFileParam.SearchedAdductIons = value; }

// Export
Expand Down Expand Up @@ -538,7 +536,7 @@ public virtual List<string> ParametersAsText() {
pStrings.Add(String.Join(": ", new string[] { "Isotope text DB file path", IsotopeTextDBFilePath.ToString() }));
pStrings.Add(String.Join(": ", new string[] { "Compounds library file path for target detection", CompoundListInTargetModePath.ToString() }));
pStrings.Add(String.Join(": ", new string[] { "Compounds library file path for RT correction", CompoundListForRtCorrectionPath.ToString() }));
pStrings.Add(String.Join(": ", new string[] { "RT correction peak selection file path", RtCorrectionPeakSelectionFilePath.ToString() }));
pStrings.Add(String.Join(": ", new string[] { "RT correction peak selection file path", ReferenceFileParam.RtCorrectionPeakSelectionFilePath?.ToString() ?? string.Empty }));
pStrings.Add(String.Join(": ", new string[] { "Searched adduct ions", String.Join(",", SearchedAdductIons.Select(n => n.AdductIonName).ToArray()) }));

pStrings.Add("\r\n");
Expand Down
2 changes: 1 addition & 1 deletion tests/MSDIAL5/MsdialCoreTestApp/Parser/ConfigParser.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -617,7 +617,7 @@ public static bool ReadCommonParameter(ParameterBase param, string method, strin
}
}
return true;
case "rt correction peak selection file path": param.RtCorrectionPeakSelectionFilePath = value; return true;
case "rt correction peak selection file path": param.ReferenceFileParam.RtCorrectionPeakSelectionFilePath = value; return true;

// Private version
case "is private version of tada":
Expand Down
2 changes: 1 addition & 1 deletion tests/MSDIAL5/MsdialCoreTestApp/Process/EicProcess.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -131,7 +131,7 @@ public int RunRtCorrection(
parameter.IonMode = ionMode;
parameter.CompoundListForRtCorrectionPath = libraryFile.FullName;
parameter.RetentionTimeCorrectionCommon.RetentionTimeCorrectionParam.ExcuteRtCorrection = true;
parameter.RtCorrectionPeakSelectionFilePath = selectionFile?.FullName ?? string.Empty;
parameter.ReferenceFileParam.RtCorrectionPeakSelectionFilePath = selectionFile?.FullName ?? string.Empty;
var analysisFiles = CreateRtCorrectionAnalysisFiles(rawFiles, acquisitionType, outputFile.FullName);
RetentionTimeCorrectionProcess.Prepare(
analysisFiles,
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4 changes: 2 additions & 2 deletions tests/MSDIAL5/MsdialCoreTestApp/Process/RetentionTimeCorrectionProcess.cs
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Expand Up @@ -53,9 +53,9 @@ public static void Prepare(IReadOnlyList<AnalysisFileBean> analysisFiles, Parame
}

Directory.CreateDirectory(outputFolder);
var selectionInput = parameter.RtCorrectionPeakSelectionFilePath;
var selectionInput = parameter.ReferenceFileParam.RtCorrectionPeakSelectionFilePath;
var detectedRts = SnapshotDetectedRetentionTimes(analysisFiles);
if (!selectionInput.IsEmptyOrNull()) {
if (!string.IsNullOrEmpty(selectionInput)) {
ApplySelectionFile(selectionInput, analysisFiles, parameter.RetentionTimeCorrectionCommon);
}
else {
Expand Down
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