added the export function of mztabM in cui application#623
added the export function of mztabM in cui application#623YukiMatsuzawa merged 1 commit intomasterfrom
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Pull Request Overview
This PR adds mzTabM export functionality to the MSDIAL console application across all analytical methods. The change implements mzTabM format export for alignment results in each of the supported analytical workflows (LCMS, LC-IMMS, IMMS, GCMS, and DIMS).
- Adds mzTabM export functionality after alignment processing in all analytical method workflows
- Updates a file path reference to use a relative path instead of an absolute path
- Implements consistent mzTabM export patterns across different analytical platforms
Reviewed Changes
Copilot reviewed 6 out of 6 changed files in this pull request and generated 5 comments.
Show a summary per file
| File | Description |
|---|---|
| Program.cs | Updates file path to use relative path for parameter file |
| LcmsProcess.cs | Adds mzTabM export functionality for LCMS alignment results |
| LcimmsProcess.cs | Adds mzTabM export functionality for LC-IMMS alignment results |
| ImmsProcess.cs | Adds mzTabM export functionality for IMMS alignment results |
| GcmsProcess.cs | Adds mzTabM export functionality for GCMS alignment results |
| DimsProcess.cs | Adds mzTabM export functionality for DIMS alignment results |
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| var spots = result.AlignmentSpotProperties; // TODO: cancellation | ||
| var msdecs = align_decResults; | ||
| var accessor = align_accessor; |
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[nitpick] These variable assignments create unnecessary intermediate variables that don't add clarity. Consider passing the original variables directly to the method call to reduce code complexity.
| var spots = result.AlignmentSpotProperties; // TODO: cancellation | ||
| var msdecs = align_decResults; | ||
| var accessor = align_accessor; |
There was a problem hiding this comment.
[nitpick] These variable assignments create unnecessary intermediate variables that don't add clarity. Consider passing the original variables directly to the method call to reduce code complexity.
| var spots = result.AlignmentSpotProperties; // TODO: cancellation | ||
| var msdecs = align_decResults; | ||
| var accessor = align_accessor; |
There was a problem hiding this comment.
[nitpick] These variable assignments create unnecessary intermediate variables that don't add clarity. Consider passing the original variables directly to the method call to reduce code complexity.
| var msdecs = decResults; | ||
| var mztabM_exporter = new MztabFormatExporter(storage.DataBases); | ||
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| using var tabmstream = File.Open(mztabm_outputfile, FileMode.Create, FileAccess.Write, FileShare.ReadWrite); | ||
| mztabM_exporter.MztabFormatExporterCore( | ||
| tabmstream, | ||
| spots, | ||
| msdecs, |
There was a problem hiding this comment.
[nitpick] These variable assignments create unnecessary intermediate variables that don't add clarity. Consider passing the original variables directly to the method call to reduce code complexity.
| var msdecs = decResults; | |
| var mztabM_exporter = new MztabFormatExporter(storage.DataBases); | |
| using var tabmstream = File.Open(mztabm_outputfile, FileMode.Create, FileAccess.Write, FileShare.ReadWrite); | |
| mztabM_exporter.MztabFormatExporterCore( | |
| tabmstream, | |
| spots, | |
| msdecs, | |
| var mztabM_exporter = new MztabFormatExporter(storage.DataBases); | |
| using var tabmstream = File.Open(mztabm_outputfile, FileMode.Create, FileAccess.Write, FileShare.ReadWrite); | |
| mztabM_exporter.MztabFormatExporterCore( | |
| tabmstream, | |
| spots, | |
| decResults, |
| var spots = result.AlignmentSpotProperties; // TODO: cancellation | ||
| var msdecs = align_decResults; | ||
| var accessor = align_accessor; |
There was a problem hiding this comment.
[nitpick] These variable assignments create unnecessary intermediate variables that don't add clarity. Consider passing the original variables directly to the method call to reduce code complexity.
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