public void MsDataFileUriEncodingTest()
{
var fname = "test.mzML";
var pathSample = SampleHelp.EncodePath(fname, null, -1, null, true, false);
var lockmassParametersA = new LockMassParameters(1.23, 3.45, 4.56);
var lockmassParametersB = new LockMassParameters(1.23, null, 4.56);
Assert.IsTrue(lockmassParametersA.CompareTo(LockMassParameters.EMPTY) > 0);
Assert.IsTrue(lockmassParametersA.CompareTo(null) < 0);
Assert.IsTrue(lockmassParametersB.CompareTo(lockmassParametersA) < 0);
Assert.IsTrue(lockmassParametersA.CompareTo(new LockMassParameters(1.23, 3.45, 4.56)) == 0);
var c = new ChromatogramSet("test", new[] { MsDataFileUri.Parse(pathSample) });
Assert.AreEqual(fname, c.MSDataFilePaths.First().GetFilePath());
Assert.IsTrue(c.MSDataFilePaths.First().GetCentroidMs1());
Assert.IsFalse(c.MSDataFilePaths.First().GetCentroidMs2());
pathSample = SampleHelp.EncodePath(fname, null, -1, lockmassParametersA, false, true);
c = new ChromatogramSet("test", new[] { MsDataFileUri.Parse(pathSample) });
Assert.AreEqual(lockmassParametersA, c.MSDataFilePaths.First().GetLockMassParameters());
Assert.IsTrue(c.MSDataFilePaths.First().GetCentroidMs2());
Assert.IsFalse(c.MSDataFilePaths.First().GetCentroidMs1());
pathSample = SampleHelp.EncodePath(fname, "test_0", 1, lockmassParametersB, false, false);
c = new ChromatogramSet("test", new[] { MsDataFileUri.Parse(pathSample) });
Assert.AreEqual(lockmassParametersB, c.MSDataFilePaths.First().GetLockMassParameters());
Assert.AreEqual("test_0", c.MSDataFilePaths.First().GetSampleName());
Assert.AreEqual(1, c.MSDataFilePaths.First().GetSampleIndex());
Assert.IsFalse(c.MSDataFilePaths.First().GetCentroidMs1());
Assert.IsFalse(c.MSDataFilePaths.First().GetCentroidMs2());
}
private void VerifyFileInfoSerialization(string[] lines, string filePath, bool combinedIms)
{
var encodePath = SampleHelp.EncodePath(filePath, null, -1, null);
var lineFilePath = lines.FirstOrDefault(l => l.Contains(encodePath + '"'));
Assert.IsNotNull(lineFilePath);
// Nothing gets serialized to the XML about whether the MsData had combined spectra - can only be found in the SKYD file
}
public static MsDataFilePath[] GetWiffSubPaths(string filePath, string[] dataIds, Func <string, string[], IEnumerable <int> > sampleChooser)
{
if (dataIds == null)
{
return(null);
}
// WIFF without at least 2 samples just use its file name.
if (dataIds.Length < 2)
{
return new[] { new MsDataFilePath(filePath, null, -1), }
}
;
// Escape all the sample ID names, so that they may be used in file names.
for (int i = 0; i < dataIds.Length; i++)
{
dataIds[i] = SampleHelp.EscapeSampleId(dataIds[i]);
}
IEnumerable <int> sampleIndices;
if (sampleChooser != null)
{
// Allow the user to choose from the list
sampleIndices = sampleChooser(filePath, dataIds);
if (sampleIndices == null)
{
return(null);
}
}
else
{
int[] indexes = new int[dataIds.Length];
for (int i = 0; i < dataIds.Length; i++)
{
indexes[i] = i;
}
sampleIndices = indexes;
}
// Encode sub-paths
var listPaths = new List <MsDataFilePath>();
foreach (int sampleIndex in sampleIndices)
{
listPaths.Add(new MsDataFilePath(filePath, dataIds[sampleIndex], sampleIndex));
}
if (listPaths.Count == 0)
{
return(null);
}
return(listPaths.ToArray());
}
}
private void VerifySerialization(string testPath, bool expect_mz5)
{
var text = File.ReadAllText(testPath);
var filePath = TestFilesDir.GetTestPath(BSA_50fmol_TIMS_InfusionESI_10precd);
var encodePath = SampleHelp.EncodePath(filePath, null, -1, null, false, false, !MsDataFileImpl.ForceUncombinedIonMobility);
Assert.IsTrue(text.Contains(encodePath + '"'));
if (expect_mz5)
{
filePath = TestFilesDir.GetTestPath(bsaFmolTimsInfusionesiPrecMz5Mz5);
encodePath = SampleHelp.EncodePath(filePath, null, -1, null, false, false, false);
Assert.IsTrue(text.Contains(encodePath + '"'));
}
}
private static void WriteRow(TextWriter writer,
PeakTransitionGroupFeatures features,
PeakGroupFeatures peakGroupFeatures,
CultureInfo cultureInfo,
double mProphetScore,
double pValue,
double qValue)
{
char separator = TextUtil.GetCsvSeparator(cultureInfo);
string fileName = SampleHelp.GetFileName(features.Id.FilePath);
var fieldsArray = new List <string>
{
Convert.ToString(features.Id, cultureInfo),
Convert.ToString(features.Id.Run, cultureInfo),
fileName,
Convert.ToString(peakGroupFeatures.RetentionTime, cultureInfo),
Convert.ToString(peakGroupFeatures.StartTime, cultureInfo),
Convert.ToString(peakGroupFeatures.EndTime, cultureInfo),
features.Id.NodePep.RawUnmodifiedTextId, // Unmodified sequence, or custom ion name
features.Id.NodePep.RawTextId, // Modified sequence, or custom ion name
features.Id.NodePepGroup.Name,
Convert.ToString(features.Id.NodePep.IsDecoy ? 1 : 0, cultureInfo),
ToFieldString((float)mProphetScore, cultureInfo),
ToFieldString((float)pValue, cultureInfo),
ToFieldString((float)qValue, cultureInfo)
};
if (IsFilterTestData)
{
fieldsArray.Add(peakGroupFeatures.GetFilterPairsText(cultureInfo));
}
foreach (var name in fieldsArray)
{
writer.WriteDsvField(name, separator);
writer.Write(separator);
}
bool first = true;
foreach (float featureColumn in peakGroupFeatures.Features)
{
if (!first)
{
writer.Write(separator);
}
writer.WriteDsvField(ToFieldString(featureColumn, cultureInfo), separator);
first = false;
}
writer.WriteLine();
}
private static void WriteRow(TextWriter writer,
PeakTransitionGroupFeatures features,
PeakGroupFeatures peakGroupFeatures,
CultureInfo cultureInfo,
double mProphetScore,
double pValue,
double qValue)
{
char separator = TextUtil.GetCsvSeparator(cultureInfo);
string fileName = SampleHelp.GetFileName(features.Id.FilePath);
var fieldsArray = new List <string>
{
Convert.ToString(features.Id, cultureInfo),
Convert.ToString(features.Id.Run, cultureInfo),
fileName,
// CONSIDER: This impacts memory consumption for large-scale DIA, and it is not clear anyone uses these
Convert.ToString(peakGroupFeatures.RetentionTime, cultureInfo),
Convert.ToString(peakGroupFeatures.StartTime, cultureInfo),
Convert.ToString(peakGroupFeatures.EndTime, cultureInfo),
features.Id.RawUnmodifiedTextId, // Unmodified sequence, or custom ion name
features.Id.RawTextId, // Modified sequence, or custom ion name
features.Id.NodePepGroup.Name,
Convert.ToString(features.IsDecoy ? 1 : 0, cultureInfo),
ToFieldString((float)mProphetScore, cultureInfo),
ToFieldString((float)pValue, cultureInfo),
ToFieldString((float)qValue, cultureInfo)
};
foreach (var name in fieldsArray)
{
writer.WriteDsvField(name, separator);
writer.Write(separator);
}
bool first = true;
foreach (float featureColumn in peakGroupFeatures.Features)
{
if (!first)
{
writer.Write(separator);
}
writer.WriteDsvField(ToFieldString(featureColumn, cultureInfo), separator);
first = false;
}
writer.WriteLine();
}
/// <summary>
/// If the predicted retention time is auto calculated, add a "Show {Prediction} score" menu item.
/// If there are retention time alignments available for the specified chromFileInfoId, then adds
/// a "Align Times To {Specified File}" menu item to a context menu.
/// </summary>
private int InsertAlignmentMenuItems(ToolStripItemCollection items, ChromFileInfoId chromFileInfoId, int iInsert)
{
var predictRT = Document.Settings.PeptideSettings.Prediction.RetentionTime;
if (predictRT != null && predictRT.IsAutoCalculated)
{
var menuItem = new ToolStripMenuItem(string.Format(Resources.SkylineWindow_ShowCalculatorScoreFormat, predictRT.Calculator.Name), null,
(sender, eventArgs) => SkylineWindow.AlignToRtPrediction = !SkylineWindow.AlignToRtPrediction)
{
Checked = SkylineWindow.AlignToRtPrediction,
};
items.Insert(iInsert++, menuItem);
}
if (null != chromFileInfoId && DocumentUI.Settings.HasResults &&
!DocumentUI.Settings.DocumentRetentionTimes.FileAlignments.IsEmpty)
{
foreach (var chromatogramSet in DocumentUI.Settings.MeasuredResults.Chromatograms)
{
var chromFileInfo = chromatogramSet.GetFileInfo(chromFileInfoId);
if (null == chromFileInfo)
{
continue;
}
string fileItemName = Path.GetFileNameWithoutExtension(SampleHelp.GetFileName(chromFileInfo.FilePath));
var menuItemText = string.Format(Resources.SkylineWindow_AlignTimesToFileFormat, fileItemName);
var alignToFileItem = new ToolStripMenuItem(menuItemText);
if (ReferenceEquals(chromFileInfoId, SkylineWindow.AlignToFile))
{
alignToFileItem.Click += (sender, eventArgs) => SkylineWindow.AlignToFile = null;
alignToFileItem.Checked = true;
}
else
{
alignToFileItem.Click += (sender, eventArgs) => SkylineWindow.AlignToFile = chromFileInfoId;
alignToFileItem.Checked = false;
}
items.Insert(iInsert++, alignToFileItem);
}
}
return(iInsert);
}
public void WiffResultsTest()
{
TestFilesDir testFilesDir = new TestFilesDir(TestContext, ZIP_FILE);
SrmDocument doc = InitWiffDocument(testFilesDir);
using (var docContainer = new ResultsTestDocumentContainer(doc,
testFilesDir.GetTestPath("SimpleWiffTest.sky")))
{
FileEx.SafeDelete(ChromatogramCache.FinalPathForName(docContainer.DocumentFilePath, null));
var listChromatograms = new List <ChromatogramSet>();
if (ExtensionTestContext.CanImportAbWiff)
{
string pathWiff = testFilesDir.GetTestPath("051309_digestion.wiff");
string[] dataIds = MsDataFileImpl.ReadIds(pathWiff);
for (int i = 0; i < dataIds.Length; i++)
{
string nameSample = dataIds[i];
if (!Equals(nameSample, "test") && listChromatograms.Count == 0)
{
continue;
}
string pathSample = SampleHelp.EncodePath(pathWiff, nameSample, i, LockMassParameters.EMPTY, false, false);
listChromatograms.Add(new ChromatogramSet(nameSample, new[] { MsDataFileUri.Parse(pathSample) }));
}
}
else
{
listChromatograms.Add(new ChromatogramSet("test",
new[] { MsDataFileUri.Parse(testFilesDir.GetTestPath("051309_digestion-test.mzML")) }));
listChromatograms.Add(new ChromatogramSet("rfp9,before,h,1",
new[] { MsDataFileUri.Parse(testFilesDir.GetTestPath("051309_digestion-rfp9,before,h,1.mzML")) }));
}
// Should have added test and one after
Assert.AreEqual(2, listChromatograms.Count);
var docResults = doc.ChangeMeasuredResults(new MeasuredResults(listChromatograms));
Assert.IsTrue(docContainer.SetDocument(docResults, doc, true));
docContainer.AssertComplete();
docResults = docContainer.Document;
AssertEx.IsDocumentState(docResults, 6, 9, 9, 18, 54);
Assert.IsTrue(docResults.Settings.MeasuredResults.IsLoaded);
foreach (var nodeTran in docResults.PeptideTransitions)
{
Assert.IsTrue(nodeTran.HasResults);
Assert.AreEqual(2, nodeTran.Results.Count);
}
// Remove the last chromatogram
listChromatograms.RemoveAt(1);
var docResultsSingle = docResults.ChangeMeasuredResults(new MeasuredResults(listChromatograms));
AssertResult.IsDocumentResultsState(docResultsSingle, "test", 9, 2, 9, 8, 27);
// Add mzXML version of test sample
listChromatograms.Add(new ChromatogramSet("test-mzXML", new[] { MsDataFileUri.Parse(testFilesDir.GetTestPath("051309_digestion-s3.mzXML")) }));
var docMzxml = docResults.ChangeMeasuredResults(new MeasuredResults(listChromatograms));
Assert.IsTrue(docContainer.SetDocument(docMzxml, docResults, true));
docContainer.AssertComplete();
docMzxml = docContainer.Document;
// Verify mzXML and native contained same results
// Unfortunately mzWiff produces chromatograms with now zeros, which
// need to be interpolated into place. This means a .wiff file and
// its mzWiff mzXML file will never be the same.
AssertResult.MatchChromatograms(docMzxml, 0, 1, -1, 0);
}
// TODO: Switch to a using clause when PWiz is fixed, and this assertion fails
// AssertEx.ThrowsException<IOException>(() => testFilesDir.Dispose());
}
