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nielshulstaertnielshulstaert
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small fixes
1 parent 35709fe commit 1d0e34a

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3 files changed

+47
-31
lines changed

3 files changed

+47
-31
lines changed

‎Query/ProxiSpectrumReader.cs‎

Lines changed: 30 additions & 20 deletions
Original file line numberDiff line numberDiff line change
@@ -159,16 +159,16 @@ public List<ProxiSpectrum> Retrieve()
159159
proxiSpectrum.AddAttribute(accession: "MS:10000512", name: "filter string",
160160
value: scanEvent.ToString());
161161

162-
if (!queryParameters.noPeakPicking) //centroiding requested
162+
if (!queryParameters.noPeakPicking) // centroiding requested
163163
{
164-
proxiSpectrum.AddAttribute(accession: "MS:1000525", name: "spectrum representation",
165-
value: "centroid spectrum", valueAccession: "MS:1000127");
166-
167-
// Check if the scan has a centroid stream
164+
// check if the scan has a centroid stream
168165
if (scan.HasCentroidStream)
169166
{
170167
if (scan.CentroidScan.Length > 0)
171168
{
169+
proxiSpectrum.AddAttribute(accession: "MS:1000525", name: "spectrum representation",
170+
value: "centroid spectrum", valueAccession: "MS:1000127");
171+
172172
proxiSpectrum.AddMz(scan.CentroidScan.Masses);
173173
proxiSpectrum.AddIntensities(scan.CentroidScan.Intensities);
174174
}
@@ -180,28 +180,38 @@ public List<ProxiSpectrum> Retrieve()
180180
? Scan.ToCentroid(scan).SegmentedScan
181181
: scan.SegmentedScan;
182182

183-
proxiSpectrum.AddMz(segmentedScan.Positions);
184-
proxiSpectrum.AddIntensities(segmentedScan.Intensities);
183+
if (segmentedScan.PositionCount > 0)
184+
{
185+
proxiSpectrum.AddAttribute(accession: "MS:1000525", name: "spectrum representation",
186+
value: "centroid spectrum", valueAccession: "MS:1000127");
187+
188+
proxiSpectrum.AddMz(segmentedScan.Positions);
189+
proxiSpectrum.AddIntensities(segmentedScan.Intensities);
190+
}
185191
}
186192
}
187193
else // use the segmented data as is
188194
{
189-
switch (scanEvent.ScanData) //check if the data is centroided already
195+
if (scan.SegmentedScan.Positions.Length > 0)
190196
{
191-
case ScanDataType.Centroid:
192-
proxiSpectrum.AddAttribute(accession: "MS:1000525", name: "spectrum representation",
193-
value: "centroid spectrum", valueAccession: "MS:1000127");
194-
break;
197+
switch (scanEvent.ScanData) //check if the data is centroided already
198+
{
199+
case ScanDataType.Centroid:
200+
proxiSpectrum.AddAttribute(accession: "MS:1000525",
201+
name: "spectrum representation",
202+
value: "centroid spectrum", valueAccession: "MS:1000127");
203+
break;
204+
205+
case ScanDataType.Profile:
206+
proxiSpectrum.AddAttribute(accession: "MS:1000525",
207+
name: "spectrum representation",
208+
value: "profile spectrum", valueAccession: "MS:1000128");
209+
break;
210+
}
195211

196-
case ScanDataType.Profile:
197-
proxiSpectrum.AddAttribute(accession: "MS:1000525", name: "spectrum representation",
198-
value: "profile spectrum", valueAccession: "MS:1000128");
199-
break;
212+
proxiSpectrum.AddMz(scan.SegmentedScan.Positions);
213+
proxiSpectrum.AddIntensities(scan.SegmentedScan.Intensities);
200214
}
201-
202-
// Get the segmented (low res and profile) scan data
203-
proxiSpectrum.AddMz(scan.SegmentedScan.Positions);
204-
proxiSpectrum.AddIntensities(scan.SegmentedScan.Intensities);
205215
}
206216

207217
resultList.Add(proxiSpectrum);

‎Writer/MgfSpectrumWriter.cs‎

Lines changed: 1 addition & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -125,7 +125,7 @@ public override void Write(IRawDataPlus rawFile, int firstScanNumber, int lastSc
125125

126126
if (!ParseInput.NoPeakPicking)
127127
{
128-
// Check if the scan has a centroid stream
128+
// check if the scan has a centroid stream
129129
if (scan.HasCentroidStream)
130130
{
131131
if (scan.CentroidScan.Length > 0)
@@ -161,7 +161,6 @@ public override void Write(IRawDataPlus rawFile, int firstScanNumber, int lastSc
161161
}
162162
else // use the segmented data as is
163163
{
164-
// Get the segmented (low res and profile) scan data
165164
for (var i = 0; i < scan.SegmentedScan.Positions.Length; i++)
166165
{
167166
Writer.WriteLine(

‎Writer/MzMlSpectrumWriter.cs‎

Lines changed: 16 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -972,19 +972,19 @@ private SpectrumType ConstructSpectrum(int scanNumber)
972972

973973
if (!ParseInput.NoPeakPicking)
974974
{
975-
spectrumCvParams.Add(new CVParamType
976-
{
977-
accession = "MS:1000127",
978-
cvRef = "MS",
979-
name = "centroid spectrum",
980-
value = ""
981-
});
982-
983975
// Check if the scan has a centroid stream
984976
if (scan.HasCentroidStream)
985977
{
986978
if (scan.CentroidScan.Length > 0)
987979
{
980+
spectrumCvParams.Add(new CVParamType
981+
{
982+
accession = "MS:1000127",
983+
cvRef = "MS",
984+
name = "centroid spectrum",
985+
value = ""
986+
});
987+
988988
basePeakMass = scan.CentroidScan.BasePeakMass;
989989
basePeakIntensity = scan.CentroidScan.BasePeakIntensity;
990990
lowestObservedMz = scan.CentroidScan.Masses[0];
@@ -1005,6 +1005,14 @@ private SpectrumType ConstructSpectrum(int scanNumber)
10051005

10061006
if (segmentedScan.PositionCount > 0)
10071007
{
1008+
spectrumCvParams.Add(new CVParamType
1009+
{
1010+
accession = "MS:1000127",
1011+
cvRef = "MS",
1012+
name = "centroid spectrum",
1013+
value = ""
1014+
});
1015+
10081016
lowestObservedMz = segmentedScan.Positions[0];
10091017
highestObservedMz = segmentedScan.Positions[segmentedScan.PositionCount - 1];
10101018
masses = segmentedScan.Positions;
@@ -1017,7 +1025,6 @@ private SpectrumType ConstructSpectrum(int scanNumber)
10171025
basePeakMass = scan.ScanStatistics.BasePeakMass;
10181026
basePeakIntensity = scan.ScanStatistics.BasePeakIntensity;
10191027

1020-
// Get the segmented scan data
10211028
if (scan.SegmentedScan.Positions.Length > 0)
10221029
{
10231030
switch (scanEvent.ScanData) //check if the data centroided already

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