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Merge branch 'pr/178' into 1.4.4
2 parents 71e0340 + 75934f8 commit da4b53b

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‎Writer/MetadataWriter.cs‎

Lines changed: 51 additions & 55 deletions
Original file line numberDiff line numberDiff line change
@@ -176,43 +176,40 @@ private void WriteJsonMetada(IRawDataPlus rawFile, int firstScanNumber, int last
176176
metadata.addInstrumentProperty(new CVTerm("AFR:0001259", "AFO", "firmware version",
177177
rawFile.GetInstrumentData().HardwareVersion));
178178
}
179-
}
180-
181179

182-
// MS Data
183-
foreach (KeyValuePair<string, int> entry in msTypes)
184-
{
185-
if (entry.Key.Equals(MSOrderType.Ms.ToString()))
186-
metadata.addMSData(new CVTerm("PRIDE:0000481", "PRIDE", "Number of MS1 spectra",
187-
entry.Value.ToString()));
188-
if (entry.Key.Equals(MSOrderType.Ms2.ToString()))
189-
metadata.addMSData(new CVTerm("PRIDE:0000482", "PRIDE", "Number of MS2 spectra",
190-
entry.Value.ToString()));
191-
if (entry.Key.Equals(MSOrderType.Ms3.ToString()))
192-
metadata.addMSData(new CVTerm("PRIDE:0000483", "PRIDE", "Number of MS3 spectra",
193-
entry.Value.ToString()));
194-
}
195-
196-
metadata.addMSData(new CVTerm("PRIDE:0000472", "PRIDE", "MS min charge",
197-
minCharge.ToString(CultureInfo.InvariantCulture)));
198-
metadata.addMSData(new CVTerm("PRIDE:0000473", "PRIDE", "MS max charge",
199-
maxCharge.ToString(CultureInfo.InvariantCulture)));
200-
201-
metadata.addMSData(new CVTerm("PRIDE:0000474", "PRIDE", "MS min RT",
202-
minTime.ToString(CultureInfo.InvariantCulture)));
203-
metadata.addMSData(new CVTerm("PRIDE:0000475", "PRIDE", "MS max RT",
204-
maxTime.ToString(CultureInfo.InvariantCulture)));
205-
206-
metadata.addMSData(new CVTerm("PRIDE:0000476", "PRIDE", "MS min MZ",
207-
minMz.ToString(CultureInfo.InvariantCulture)));
208-
metadata.addMSData(new CVTerm("PRIDE:0000477", "PRIDE", "MS max MZ",
209-
maxMz.ToString(CultureInfo.InvariantCulture)));
210-
211-
// Scan Settings
212-
// Get the start and end time from the RAW file
213-
214-
if (rawFile.SelectMsData())
215-
{
180+
181+
182+
// MS Data
183+
foreach (KeyValuePair<string, int> entry in msTypes)
184+
{
185+
if (entry.Key.Equals(MSOrderType.Ms.ToString()))
186+
metadata.addMSData(new CVTerm("PRIDE:0000481", "PRIDE", "Number of MS1 spectra",
187+
entry.Value.ToString()));
188+
if (entry.Key.Equals(MSOrderType.Ms2.ToString()))
189+
metadata.addMSData(new CVTerm("PRIDE:0000482", "PRIDE", "Number of MS2 spectra",
190+
entry.Value.ToString()));
191+
if (entry.Key.Equals(MSOrderType.Ms3.ToString()))
192+
metadata.addMSData(new CVTerm("PRIDE:0000483", "PRIDE", "Number of MS3 spectra",
193+
entry.Value.ToString()));
194+
}
195+
196+
metadata.addMSData(new CVTerm("PRIDE:0000472", "PRIDE", "MS min charge",
197+
minCharge.ToString(CultureInfo.InvariantCulture)));
198+
metadata.addMSData(new CVTerm("PRIDE:0000473", "PRIDE", "MS max charge",
199+
maxCharge.ToString(CultureInfo.InvariantCulture)));
200+
201+
metadata.addMSData(new CVTerm("PRIDE:0000474", "PRIDE", "MS min RT",
202+
minTime.ToString(CultureInfo.InvariantCulture)));
203+
metadata.addMSData(new CVTerm("PRIDE:0000475", "PRIDE", "MS max RT",
204+
maxTime.ToString(CultureInfo.InvariantCulture)));
205+
206+
metadata.addMSData(new CVTerm("PRIDE:0000476", "PRIDE", "MS min MZ",
207+
minMz.ToString(CultureInfo.InvariantCulture)));
208+
metadata.addMSData(new CVTerm("PRIDE:0000477", "PRIDE", "MS max MZ",
209+
maxMz.ToString(CultureInfo.InvariantCulture)));
210+
211+
// Scan Settings
212+
// Get the start and end time from the RAW file
216213
var runHeaderEx = rawFile.RunHeaderEx;
217214
var startTime = runHeaderEx.StartTime;
218215
var endTime = runHeaderEx.EndTime;
@@ -373,21 +370,21 @@ private void WriteTextMetadata(IRawDataPlus rawFile, int firstScanNumber, int la
373370
{
374371
output.Add("Firmware version=" + rawFile.GetInstrumentData().HardwareVersion);
375372
}
376-
}
377-
378-
// MS Data
379-
output.Add("#MsData");
380-
foreach (KeyValuePair<string, int> entry in msTypes)
381-
{
382-
if (entry.Key.Equals(MSOrderType.Ms.ToString()))
383-
output.Add("Number of MS1 spectra=" + entry.Value);
384-
if (entry.Key.Equals(MSOrderType.Ms2.ToString()))
385-
output.Add("Number of MS2 spectra=" + entry.Value);
386-
if (entry.Key.Equals(MSOrderType.Ms3.ToString()))
387-
output.Add("Number of MS3 spectra=" + entry.Value);
388-
}
389373

390-
output.AddRange(new List<string>
374+
375+
// MS Data
376+
output.Add("#MsData");
377+
foreach (KeyValuePair<string, int> entry in msTypes)
378+
{
379+
if (entry.Key.Equals(MSOrderType.Ms.ToString()))
380+
output.Add("Number of MS1 spectra=" + entry.Value);
381+
if (entry.Key.Equals(MSOrderType.Ms2.ToString()))
382+
output.Add("Number of MS2 spectra=" + entry.Value);
383+
if (entry.Key.Equals(MSOrderType.Ms3.ToString()))
384+
output.Add("Number of MS3 spectra=" + entry.Value);
385+
}
386+
387+
output.AddRange(new List<string>
391388
{
392389
$"MS min charge={minCharge.ToString(CultureInfo.InvariantCulture)}",
393390
$"MS max charge={maxCharge.ToString(CultureInfo.InvariantCulture)}",
@@ -396,11 +393,9 @@ private void WriteTextMetadata(IRawDataPlus rawFile, int firstScanNumber, int la
396393
$"MS min MZ={minMz.ToString(CultureInfo.InvariantCulture)}",
397394
$"MS max MZ={maxMz.ToString(CultureInfo.InvariantCulture)}"
398395
}
399-
);
396+
);
400397

401-
// Scan Settings
402-
if (rawFile.SelectMsData())
403-
{
398+
// Scan Settings
404399
// Get the start and end time from the RAW file
405400
var startTime = rawFile.RunHeaderEx.StartTime;
406401
var endTime = rawFile.RunHeaderEx.EndTime;
@@ -410,7 +405,7 @@ private void WriteTextMetadata(IRawDataPlus rawFile, int firstScanNumber, int la
410405
$"Scan start time={startTime.ToString(CultureInfo.InvariantCulture)}",
411406
$"Expected runtime={rawFile.RunHeaderEx.ExpectedRunTime.ToString(CultureInfo.InvariantCulture)}",
412407
$"Mass resolution=[MS, MS:1000011, mass resolution, {rawFile.RunHeaderEx.MassResolution.ToString(CultureInfo.InvariantCulture)}]",
413-
"Units=" + rawFile.GetInstrumentData().Units,
408+
$"Units={rawFile.GetInstrumentData().Units}",
414409
$"Number of scans={rawFile.RunHeaderEx.SpectraCount}",
415410
$"Scan range={firstScanNumber};{lastScanNumber}",
416411
$"Time range={startTime.ToString(CultureInfo.InvariantCulture)};{endTime.ToString(CultureInfo.InvariantCulture)}",
@@ -419,6 +414,7 @@ private void WriteTextMetadata(IRawDataPlus rawFile, int firstScanNumber, int la
419414
}
420415
);
421416
}
417+
422418
// Sample Data
423419
output.Add("#SampleData");
424420

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