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Add support for files containing only MSAnalog traces (no MS) #157

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wolfgangcolsman wants to merge 14 commits into from
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Add support for files containing only MSAnalog traces (no MS) #157

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467506b
ZSPACE-12467 Check if the file is MS type
zhaoheting-zontal Mar 3, 2023
65f14e5
ZSPACE-12467 Solve code review issues.
zhaoheting-zontal Mar 9, 2023
bceb3dd
ZSPACE-12467 Fix code review issues.
zhaoheting-zontal Mar 10, 2023
cfa25a2
ZSPACE-12467 Remove ms data for not MS type.
zhaoheting-zontal Mar 14, 2023
a29ac4c
ZSPACE-12467 Solve code review issues.
zhaoheting-zontal Mar 14, 2023
adc3417
ZSPACE-12467 Replace whitespace with underscore.
zhaoheting-zontal Mar 14, 2023
1a4c9a1
cleanup code
wolfgangcolsman Mar 14, 2023
93a5974
handle empty channel name
wolfgangcolsman Mar 20, 2023
878596b
add unitAccession for Volts
wolfgangcolsman Mar 20, 2023
6153039
unique channel name
wolfgangcolsman Apr 10, 2023
abc6be5
fix
wolfgangcolsman Apr 10, 2023
07b69d5
Treat as if it is never set when the last spectrum is 0.
zhaoheting-zontal Aug 15, 2023
fa3c8ec
Merge branch 'feature/support_non_ms_instruments' into bugfix/treat-l…
wolfgangcolsman Aug 15, 2023
50842a2
Merge pull request #15 from zontal/bugfix/treat-last-spectrum-0-opens…
wolfgangcolsman Aug 15, 2023
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21 changes: 10 additions & 11 deletions RawFileParser.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -136,20 +136,19 @@ private static void ProcessFile(ParseInput parseInput)

// Get the number of instruments (controllers) present in the RAW file and set the
// selected instrument to the MS instrument, first instance of it
rawFile.SelectInstrument(Device.MS, 1);

rawFile.IncludeReferenceAndExceptionData = !parseInput.ExData;
var firstScanNumber = -1;
var lastScanNumber = -1;
if (rawFile.GetInstrumentCountOfType(Device.MS) != 0)
{
rawFile.SelectInstrument(Device.MS, 1);

// Get the first and last scan from the RAW file
var firstScanNumber = rawFile.RunHeaderEx.FirstSpectrum;
var lastScanNumber = rawFile.RunHeaderEx.LastSpectrum;
rawFile.IncludeReferenceAndExceptionData = !parseInput.ExData;

// Check for empty file
if (lastScanNumber < 1)
{
throw new RawFileParserException("Empty RAW file, no output will be produced");
// Get the first and last scan from the RAW file
firstScanNumber = rawFile.RunHeaderEx.FirstSpectrum;
lastScanNumber = rawFile.RunHeaderEx.LastSpectrum;
}

if (parseInput.MetadataFormat != MetadataFormat.NONE)
{
MetadataWriter metadataWriter = new MetadataWriter(parseInput);
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