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Fixes to get the code running on my system #83

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95d64e0
Fixes to get the code running on my system.
romanzenka Jun 20, 2023
01a1138
Speeding up finding closest mass
romanzenka Jun 23, 2023
9cff38f
Percentile calculation does not crash when no values passed in
romanzenka Jun 23, 2023
3cd0226
Support "fixedScans" option for repeatable, predictable analysis
romanzenka Jun 23, 2023
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8 changes: 4 additions & 4 deletions RawTools.sln
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@

Microsoft Visual Studio Solution File, Format Version 12.00
# Visual Studio Version 16
VisualStudioVersion = 16.0.30621.155
# Visual Studio Version 17
VisualStudioVersion = 17.5.33424.131
MinimumVisualStudioVersion = 10.0.40219.1
Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "RawTools", "RawTools\RawTools.csproj", "{A9BF3DB6-A6E6-4324-AA7A-625639C17E64}"
EndProject
Expand Down Expand Up @@ -31,8 +31,8 @@ Global
{A9BF3DB6-A6E6-4324-AA7A-625639C17E64}.Debug|Any CPU.Build.0 = Debug|x64
{A9BF3DB6-A6E6-4324-AA7A-625639C17E64}.Debug|x64.ActiveCfg = Debug|x64
{A9BF3DB6-A6E6-4324-AA7A-625639C17E64}.Debug|x64.Build.0 = Debug|x64
{A9BF3DB6-A6E6-4324-AA7A-625639C17E64}.Release|Any CPU.ActiveCfg = Release|Any CPU
{A9BF3DB6-A6E6-4324-AA7A-625639C17E64}.Release|Any CPU.Build.0 = Release|Any CPU
{A9BF3DB6-A6E6-4324-AA7A-625639C17E64}.Release|Any CPU.ActiveCfg = Release|x64
{A9BF3DB6-A6E6-4324-AA7A-625639C17E64}.Release|Any CPU.Build.0 = Release|x64
{A9BF3DB6-A6E6-4324-AA7A-625639C17E64}.Release|x64.ActiveCfg = Release|x64
{A9BF3DB6-A6E6-4324-AA7A-625639C17E64}.Release|x64.Build.0 = Release|x64
{BFF243DD-CEB4-489C-9726-9E5A6E9EB9AC}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
Expand Down
40 changes: 25 additions & 15 deletions RawTools/Algorithms/PrecursorPeaks.cs
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Expand Up @@ -60,7 +60,7 @@ private static PrecursorPeakData OnePeak(CentroidStreamCollection centroids, Ret
List<double> profileTimes = new List<double>();
List<double> profileIntensities = new List<double>();

double[] masses, intensities, massDiff;
double[] masses, intensities;

Dictionary<int, double> indexedIntensities = new Dictionary<int, double>();

Expand All @@ -78,15 +78,17 @@ private static PrecursorPeakData OnePeak(CentroidStreamCollection centroids, Ret
return peak;
}

massDiff = new double[masses.Length];
minMassDiff = Double.PositiveInfinity;

for (int i = 0; i < masses.Length; i++)
{
massDiff[i] = Math.Abs(masses[i] - targetMass);
var massDiff = Math.Min(minMassDiff, Math.Abs(masses[i] - targetMass));
if(massDiff < minMassDiff)
{
minMassDiff = massDiff;
}
}

minMassDiff = massDiff.Min();

if (minMassDiff / targetMass * 1e6 < 10)
{
peak.PeakFound = true;
Expand All @@ -106,20 +108,24 @@ private static PrecursorPeakData OnePeak(CentroidStreamCollection centroids, Ret
masses = centroids[currentScan].Masses;
intensities = centroids[currentScan].Intensities;

massDiff = new double[masses.Length];
minMassDiff = Double.PositiveInfinity;
int minMassDiffIndex = -1;

for (int i = 0; i < masses.Length; i++)
{
massDiff[i] = Math.Abs(masses[i] - targetMass);
var massDiff = Math.Abs(masses[i] - targetMass);
if(massDiff < minMassDiff)
{
minMassDiff = massDiff;
minMassDiffIndex = i;
}
}

minMassDiff = massDiff.Min();

if (minMassDiff / targetMass * 1e6 < 10)
{
scans.Add(currentScan);
scanIndex -= 1;
indexedIntensities.Add(currentScan, intensities[Array.IndexOf(massDiff, minMassDiff)]);
indexedIntensities.Add(currentScan, intensities[minMassDiffIndex]);
if (scanIndex < 0)
{
previousMS1scan = currentScan;
Expand Down Expand Up @@ -157,20 +163,24 @@ private static PrecursorPeakData OnePeak(CentroidStreamCollection centroids, Ret
masses = centroids[currentScan].Masses;
intensities = centroids[currentScan].Intensities;

massDiff = new double[masses.Length];
minMassDiff = Double.PositiveInfinity;
int minMassDiffIndex = -1;

for (int i = 0; i < masses.Length; i++)
{
massDiff[i] = Math.Abs(masses[i] - targetMass);
double massDiff = Math.Abs(masses[i] - targetMass);
if (massDiff < minMassDiff)
{
minMassDiff = massDiff;
minMassDiffIndex = i;
}
}

minMassDiff = massDiff.Min();

if (minMassDiff / targetMass * 1e6 < 10)
{
scans.Add(currentScan);
scanIndex += 1;
indexedIntensities.Add(currentScan, intensities[Array.IndexOf(massDiff, minMassDiff)]);
indexedIntensities.Add(currentScan, intensities[minMassDiffIndex]);
if (scanIndex >= MS1Scans.Length)
{
nextMS1scan = currentScan;
Expand Down
2 changes: 1 addition & 1 deletion RawTools/App.config
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
<?xml version="1.0" encoding="utf-8"?>
<configuration>
<startup>
<supportedRuntime version="v4.0" sku=".NETFramework,Version=v4.6.2" />
<supportedRuntime version="v4.0" sku=".NETFramework,Version=v4.8" />
</startup>
<runtime>
<assemblyBinding xmlns="urn:schemas-microsoft-com:asm.v1">
Expand Down
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