public IEnumerable <UMCLight> TestUmcFeatures(string path)
{
var reader = new MsFeatureLightFileReader {
Delimeter = ","
};
var newMsFeatures = reader.ReadFile(path);
var finder = new UmcTreeFeatureFinder
{
MaximumNet = .005,
MaximumScan = 50
};
var tolerances = new FeatureTolerances
{
Mass = 8,
Net = .005
};
var options = new LcmsFeatureFindingOptions(tolerances);
var features = finder.FindFeatures(newMsFeatures.ToList(), options, null);
// Work on total feature count here.
Assert.Greater(features.Count, 0);
return(features);
}
public IEnumerable <UMCLight> TestUmcFeatures(string relativePath, int expectedFeatureCount)
{
// Get the absolute path
var path = GetPath(relativePath);
var reader = new MsFeatureLightFileReader {
Delimiter = ','
};
var newMsFeatures = reader.ReadFile(path);
var finder = new UmcTreeFeatureFinder
{
MaximumNet = .005,
MaximumScan = 50
};
var tolerances = new FeatureTolerances
{
Mass = 8,
Net = .005
};
var options = new LcmsFeatureFindingOptions(tolerances);
IScanSummaryProvider provider = null;
var rawFilePath = path.Replace("_isos.csv", ".raw");
UpdateStatus("Using raw data to create better features.");
var providerCache = new ScanSummaryProviderCache();
provider = providerCache.GetScanSummaryProvider(rawFilePath, 1);
var features = finder.FindFeatures(newMsFeatures.ToList(), options, provider);
// Work on total feature count here.
Assert.Greater(features.Count, 0);
Assert.AreEqual(expectedFeatureCount, features.Count);
return(features);
}
public void TestUmcFeatures(string relativePath, string relativeRawPath)
{
// Get absolute paths
var path = GetPath(relativePath);
var rawPath = GetPath(relativeRawPath);
var reader = new MsFeatureLightFileReader {
Delimiter = ','
};
var newMsFeatures = reader.ReadFile(path);
var finder = new UmcTreeFeatureFinder();
var featureTolerances = new FeatureTolerances
{
Mass = 12,
Net = .04
};
var options = new LcmsFeatureFindingOptions(featureTolerances)
{
MaximumNetRange = .003,
MaximumScanRange = 50
};
var provider = RawLoaderFactory.CreateFileReader(rawPath, 0);
var start = DateTime.Now;
IEnumerable <UMCLight> features = finder.FindFeatures(newMsFeatures.ToList(), options, provider);
var end = DateTime.Now;
Console.WriteLine(@"Test Took: " + end.Subtract(start).TotalSeconds);
if (features == null)
{
throw new NullReferenceException("The feature list came back empty. This is a problem.");
}
var dirPath = Path.GetDirectoryName(path);
if (dirPath != null)
{
using (
var writer =
File.CreateText(Path.Combine(dirPath, Path.GetFileName(path).Replace("_isos.csv", "_xics.csv")))
)
{
foreach (var feature in features)
{
writer.WriteLine();
writer.WriteLine("Feature {0}", feature.Id);
var chargeMap = feature.CreateChargeMap();
foreach (var charge in chargeMap.Keys)
{
writer.WriteLine();
foreach (var msFeature in chargeMap[charge])
{
var count = msFeature.MSnSpectra.Count;
writer.WriteLine("{0},{1},{2},{3},{4}", charge, msFeature.Mz, msFeature.Scan,
msFeature.Abundance, count);
}
}
}
}
}
// Work on total feature count here.
Assert.Greater(features.Count(), 0);
}
public void TestUmcFeaturesMultipleCharges(string path, string rawPath, int maxScanDiff)
{
var reader = new MsFeatureLightFileReader {
Delimeter = ","
};
var newMsFeatures = reader.ReadFile(path);
var finder = new UmcTreeFeatureFinder();
var featureTolerances = new FeatureTolerances
{
Mass = 12,
Net = .05
};
var options = new LcmsFeatureFindingOptions(featureTolerances)
{
MaximumNetRange = .002,
MaximumScanRange = 50
};
var provider = RawLoaderFactory.CreateFileReader(rawPath);
provider.AddDataFile(rawPath, 0);
var start = DateTime.Now;
IEnumerable <UMCLight> features = finder.FindFeatures(newMsFeatures.ToList(), options, provider);
var end = DateTime.Now;
Console.WriteLine(@"Test Took: " + end.Subtract(start).TotalSeconds);
if (features == null)
{
throw new NullReferenceException("The feature list came back empty. This is a problem.");
}
var dirPath = Path.GetDirectoryName(path);
if (dirPath != null)
{
using (
var writer =
File.CreateText(Path.Combine(dirPath, Path.GetFileName(path).Replace("_isos.csv", "_xics.csv")))
)
{
foreach (var feature in features)
{
writer.WriteLine();
writer.WriteLine("Feature {0}", feature.Id);
var chargeMap = feature.CreateChargeMap();
if (chargeMap.Keys.Count < 2)
{
continue;
}
foreach (var charge in chargeMap.Keys)
{
writer.WriteLine();
foreach (var msFeature in chargeMap[charge])
{
var count = msFeature.MSnSpectra.Count;
writer.WriteLine("{0},{1},{2},{3},{4}", charge, msFeature.Mz, msFeature.Scan,
msFeature.Abundance, count);
}
}
var charges = chargeMap.Keys.ToList();
for (var i = 0; i < charges.Count; i++)
{
for (var j = i; j < charges.Count; j++)
{
var x = chargeMap[charges[i]];
var y = chargeMap[charges[j]];
var diff = x.MinScan() - y.MinScan();
if (diff > maxScanDiff)
{
throw new Exception(
"There is a problem with the feature finder across charge states");
}
}
}
}
}
}
// Work on total feature count here.
Assert.Greater(features.Count(), 0);
}
