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 static bool HasUnmatchedLibraryRuns(SrmDocument doc)
{
var libraries = doc.Settings.PeptideSettings.Libraries;
if (!libraries.HasLibraries || !libraries.HasDocumentLibrary)
{
return(false);
}
for (int i = 0; i < libraries.LibrarySpecs.Count; i++)
{
if (libraries.LibrarySpecs[i].IsDocumentLibrary)
{
var documentLibrary = libraries.Libraries[i];
// CONSIDER: Load the library?
if (documentLibrary == null)
{
return(false);
}
foreach (var dataFile in documentLibrary.LibraryFiles.FilePaths)
{
if (!doc.Settings.HasResults ||
doc.Settings.MeasuredResults.FindMatchingMSDataFile(MsDataFileUri.Parse(dataFile)) == null)
{
return(true);
}
}
}
}
return(false);
}
public override IEnumerable <double> GetRetentionTimesWithSequences(string filePath, IEnumerable <Target> peptideSequences, ref int?iFile)
{
if (!iFile.HasValue)
{
iFile = FindFileInList(MsDataFileUri.Parse(filePath), _sourceFiles);
}
if (iFile.Value < 0)
{
return(new double[0]);
}
var times = new List <double>();
foreach (var entry in LibraryEntriesWithSequences(peptideSequences))
{
FileData fileData;
if (entry.FileDatas.TryGetValue(iFile.Value, out fileData))
{
if (fileData.ApexTime.HasValue)
{
times.Add(fileData.ApexTime.Value);
}
}
}
return(times);
}
protected override void DoTest()
{
TestFilesZip = GetPerfTestDataURL(@"PerfNegativeIonDIA.zip");
TestFilesPersistent = new[] { "neg.mzML", "pos.mzML" }; // list of files that we'd like to unzip alongside parent zipFile, and (re)use in place
var testFilesDir = new TestFilesDir(TestContext, TestFilesZip, null, TestFilesPersistent);
RunUI(() => SkylineWindow.OpenFile(testFilesDir.GetTestPath("Test positive-negative.sky")));
WaitForDocumentLoaded();
ImportResultsFiles(TestFilesPersistent.Select(file => MsDataFileUri.Parse(testFilesDir.GetTestPath(file))));
// Verify that pos ion has a chromatogram for pos replicate, and neg ion has one for neg replicate
var doc = WaitForDocumentLoaded(400000);
var results = doc.Settings.MeasuredResults;
var negIndex = results.Chromatograms[0].Name.Equals("neg") ? 0 : 1;
var posIndex = (negIndex == 1) ? 0 : 1;
var tolerance = .005f;
foreach (var pair in doc.MoleculePrecursorPairs)
{
var index = pair.NodeGroup.PrecursorCharge < 0 ? negIndex : posIndex;
var message = "expected a chromatogram for precursor and for product in replicate \"" + results.Chromatograms[index].Name + "\"";
ChromatogramGroupInfo[] chromGroupInfo;
Assert.IsTrue(results.TryLoadChromatogram(index, pair.NodePep, pair.NodeGroup, tolerance, true, out chromGroupInfo), message);
foreach (var chromGroup in chromGroupInfo)
{
Assert.AreEqual(2, chromGroup.TransitionPointSets.Count(), message);
}
}
}
public void DoAgilentMseChromatogramTest(RefinementSettings.ConvertToSmallMoleculesMode asSmallMolecules)
{
if (asSmallMolecules != RefinementSettings.ConvertToSmallMoleculesMode.none && !RunSmallMoleculeTestVersions)
{
System.Console.Write(MSG_SKIPPING_SMALLMOLECULE_TEST_VERSION);
return;
}
var testFilesDir = new TestFilesDir(TestContext, ZIP_FILE);
TestSmallMolecules = false; // We have an explicit test for that here
string docPath;
SrmDocument document = InitAgilentMseDocument(testFilesDir, out docPath);
if (asSmallMolecules != RefinementSettings.ConvertToSmallMoleculesMode.none)
{
var refine = new RefinementSettings();
document = refine.ConvertToSmallMolecules(document, asSmallMolecules);
}
using (var docContainer = new ResultsTestDocumentContainer(document, docPath))
{
var doc = docContainer.Document;
var listChromatograms = new List <ChromatogramSet>();
var path = MsDataFileUri.Parse(@"AgilentMse\BSA-AI-0-10-25-41_first_100_scans.mzML");
listChromatograms.Add(AssertResult.FindChromatogramSet(doc, path) ??
new ChromatogramSet(path.GetFileName().Replace('.', '_'), new[] { path }));
var docResults = doc.ChangeMeasuredResults(new MeasuredResults(listChromatograms));
Assert.IsTrue(docContainer.SetDocument(docResults, doc, true));
docContainer.AssertComplete();
document = docContainer.Document;
float tolerance = (float)document.Settings.TransitionSettings.Instrument.MzMatchTolerance;
var results = document.Settings.MeasuredResults;
foreach (var pair in document.MoleculePrecursorPairs)
{
ChromatogramGroupInfo[] chromGroupInfo;
Assert.IsTrue(results.TryLoadChromatogram(0, pair.NodePep, pair.NodeGroup,
tolerance, true, out chromGroupInfo));
Assert.AreEqual(1, chromGroupInfo.Length);
}
// now drill down for specific values
int nPeptides = 0;
foreach (var nodePep in document.Molecules.Where(nodePep => nodePep.Results[0] != null))
{
// expecting just one peptide result in this small data set
if (nodePep.Results[0].Sum(chromInfo => chromInfo.PeakCountRatio > 0 ? 1 : 0) > 0)
{
Assert.AreEqual(0.2462, (double)nodePep.GetMeasuredRetentionTime(0), .0001, "averaged retention time differs in node " + nodePep.RawTextId);
Assert.AreEqual(0.3333, (double)nodePep.GetPeakCountRatio(0), 0.0001);
nPeptides++;
}
}
Assert.AreEqual(1, nPeptides);
}
testFilesDir.Dispose();
}
private void RunMultiplePeptidesSameMz(RefinementSettings.ConvertToSmallMoleculesMode asSmallMolecules)
{
if (asSmallMolecules != RefinementSettings.ConvertToSmallMoleculesMode.none)
{
TestDirectoryName = asSmallMolecules.ToString();
}
TestSmallMolecules = false; // Don't need the magic test node, we have an explicit test
var testFilesDir = new TestFilesDir(TestContext, ZIP_FILE);
string docPath;
SrmDocument document = InitMultiplePeptidesSameMzDocument(testFilesDir, out docPath);
document = (new RefinementSettings()).ConvertToSmallMolecules(document, asSmallMolecules);
var docContainer = new ResultsTestDocumentContainer(document, docPath);
var doc = docContainer.Document;
var listChromatograms = new List <ChromatogramSet>();
var path = MsDataFileUri.Parse(@"AMultiplePeptidesSameMz\ljz_20131201k_Newvariant_standards_braf.mzML");
listChromatograms.Add(AssertResult.FindChromatogramSet(doc, path) ??
new ChromatogramSet(path.GetFileName().Replace('.', '_'), new[] { path }));
var docResults = doc.ChangeMeasuredResults(new MeasuredResults(listChromatograms));
Assert.IsTrue(docContainer.SetDocument(docResults, doc, true));
docContainer.AssertComplete();
document = docContainer.Document;
float tolerance = (float)document.Settings.TransitionSettings.Instrument.MzMatchTolerance;
var results = document.Settings.MeasuredResults;
foreach (var pair in document.MoleculePrecursorPairs)
{
ChromatogramGroupInfo[] chromGroupInfo;
Assert.IsTrue(results.TryLoadChromatogram(0, pair.NodePep, pair.NodeGroup,
tolerance, true, out chromGroupInfo));
Assert.AreEqual(1, chromGroupInfo.Length); // without the fix, only the first pair will have a chromatogram
}
// now drill down for specific values
int nPeptides = 0;
foreach (var nodePep in document.Molecules.Where(nodePep => nodePep.Results[0] != null))
{
// expecting three peptide result in this small data set
if (nodePep.Results[0].Sum(chromInfo => chromInfo.PeakCountRatio > 0 ? 1 : 0) > 0)
{
Assert.AreEqual(34.2441024780273, (double)nodePep.GetMeasuredRetentionTime(0), .0001);
nPeptides++;
}
}
Assert.AreEqual(3, nPeptides); // without the fix this will give just one result
// Release file handles
docContainer.Release();
testFilesDir.Dispose();
}
private static IDictionary <Target, double> GetFirstRetentionTimes(
SrmSettings settings, RetentionTimeSource retentionTimeSource)
{
var libraryRetentionTimes = settings.GetRetentionTimes(MsDataFileUri.Parse(retentionTimeSource.Name));
if (null == libraryRetentionTimes)
{
return(new Dictionary <Target, double>());
}
return(libraryRetentionTimes.GetFirstRetentionTimes());
}
private static void doTest(TestFilesDir testFilesDir, string skyFile, double expectedRT, string[] filenames, double?expectedRatio)
{
string docPath;
var document = InitExplicitRTDocument(testFilesDir, skyFile, out docPath);
var docContainer = new ResultsTestDocumentContainer(document, docPath);
var doc = docContainer.Document;
var listChromatograms = new List <ChromatogramSet>();
foreach (var filename in filenames)
{
var path = MsDataFileUri.Parse(filename + ExtensionTestContext.ExtWatersRaw);
listChromatograms.Add(AssertResult.FindChromatogramSet(doc, path) ??
new ChromatogramSet(path.GetFileName().Replace('.', '_'), new[] { path }));
}
var docResults = doc.ChangeMeasuredResults(new MeasuredResults(listChromatograms));
Assert.IsTrue(docContainer.SetDocument(docResults, doc, true));
docContainer.AssertComplete();
document = docContainer.Document;
float tolerance = (float)document.Settings.TransitionSettings.Instrument.MzMatchTolerance;
foreach (var pair in document.MoleculePrecursorPairs)
{
ChromatogramGroupInfo[] chromGroupInfo;
Assert.IsTrue(document.Settings.MeasuredResults.TryLoadChromatogram(0, pair.NodePep, pair.NodeGroup, tolerance,
true, out chromGroupInfo));
Assert.IsTrue(document.Settings.MeasuredResults.TryLoadChromatogram(1, pair.NodePep, pair.NodeGroup, tolerance,
true, out chromGroupInfo));
}
var nResults = 0;
foreach (var nodePep in document.Molecules)
{
foreach (var results in nodePep.Results)
{
foreach (var result in results)
{
Assert.AreEqual(expectedRT, result.RetentionTime ?? 0, .1); // We should pick peaks based on explicit RT
if (expectedRatio.HasValue) // If we didn't, ratios won't be right
{
Assert.IsNotNull(result.LabelRatios[0].Ratio);
Assert.AreEqual(expectedRatio.Value, result.LabelRatios[0].Ratio.Ratio, .1);
}
nResults++;
}
}
}
Assert.AreEqual(filenames.Length * document.MoleculeGroupCount, nResults);
// Release file handles
docContainer.Release();
}
protected override void DoTest()
{
string chorusRequestOutputDirectory;
if (null != TestContext.TestResultsDirectory)
{
chorusRequestOutputDirectory = Path.Combine(TestContext.TestResultsDirectory, "chorusrequests");
Directory.CreateDirectory(chorusRequestOutputDirectory);
}
else
{
// When running unit tests under resharper, we have no TestResultsDirectory, so we only send
// the output to Console.Out.
chorusRequestOutputDirectory = null;
}
var xmlSerializer = new XmlSerializer(typeof(pwiz.Skyline.Model.Results.RemoteApi.GeneratedCode.ChromatogramRequestDocument));
foreach (var chorusDataSet in ChorusDataSets)
{
TestFilesDir testFilesDir = TestFilesDirForUrl(chorusDataSet.SkyZipUrl);
string skyFileName = Path.GetFileName(testFilesDir.FullPath);
Assert.IsNotNull(skyFileName, "skyFileName != null");
StringAssert.EndsWith(skyFileName, ".sky");
skyFileName = Uri.UnescapeDataString(skyFileName);
string skyFilePath = Path.Combine(testFilesDir.FullPath, skyFileName);
RunUI(() => SkylineWindow.OpenFile(skyFilePath));
WaitForDocumentLoaded();
SrmDocument document = null;
RunUI(() => { document = SkylineWindow.DocumentUI; });
Assert.IsNotNull(document);
SpectrumFilter spectrumFilterData = new SpectrumFilter(document, MsDataFileUri.Parse(""), null);
var chorusRequestDocument = spectrumFilterData.ToChromatogramRequestDocument();
Console.Out.WriteLine("***BEGIN {0}.chorusrequest.xml***", chorusDataSet.Name);
using (var xmlWriter = XmlWriter.Create(Console.Out, new XmlWriterSettings {
Encoding = Encoding.UTF8
}))
{
xmlSerializer.Serialize(xmlWriter, chorusRequestDocument);
}
Console.Out.WriteLine("***END {0}.chorusrequest.xml***", chorusDataSet.Name);
if (null != chorusRequestOutputDirectory)
{
string outputFile = Path.Combine(chorusRequestOutputDirectory,
chorusDataSet.Name + ".chorusrequest.xml");
using (var stream = new FileStream(outputFile, FileMode.Create))
{
xmlSerializer.Serialize(stream, chorusRequestDocument);
}
}
}
}
protected void ImportFile(string fileName)
{
var importResultsDlg = ShowDialog <ImportResultsDlg>(SkylineWindow.ImportResults);
RunUI(() =>
{
importResultsDlg.RadioAddNewChecked = true;
var path = new KeyValuePair <string, MsDataFileUri[]> [1];
path[0] = new KeyValuePair <string, MsDataFileUri[]>(Path.GetFileNameWithoutExtension(fileName),
new[] { MsDataFileUri.Parse(fileName) });
importResultsDlg.NamedPathSets = path;
});
OkDialog(importResultsDlg, importResultsDlg.OkDialog);
WaitForCondition(2 * 60 * 1000, () => SkylineWindow.Document.Settings.MeasuredResults.IsLoaded); // 2 minutes
}
public bool VerifyRetentionTimes(IEnumerable <string> resultsFiles)
{
foreach (var resultsFile in resultsFiles)
{
LibraryRetentionTimes retentionTimes;
if (DocLib.TryGetRetentionTimes(MsDataFileUri.Parse(resultsFile), out retentionTimes))
{
if (retentionTimes.PeptideRetentionTimes.Any(t => t.RetentionTime <= 0))
{
return(false);
}
}
}
return(true);
}
public void ThermoMixedPeptidesTest()
{
var testFilesDir = new TestFilesDir(TestContext, ZIP_FILE);
string docPath;
SrmDocument docMixed = InitMixedDocument(testFilesDir, out docPath);
FileEx.SafeDelete(Path.ChangeExtension(docPath, ChromatogramCache.EXT));
SrmDocument docUnmixed = InitUnmixedDocument(testFilesDir, out docPath);
FileEx.SafeDelete(Path.ChangeExtension(docPath, ChromatogramCache.EXT));
string extRaw = ExtensionTestContext.ExtThermoRaw;
var listChromatograms = new List <ChromatogramSet>
{
new ChromatogramSet("rep03", new[]
{
MsDataFileUri.Parse(testFilesDir.GetTestPath(
"Site20_STUDY9P_PHASEII_QC_03" + extRaw))
}),
new ChromatogramSet("rep05", new[]
{
MsDataFileUri.Parse(testFilesDir.GetTestPath(
"Site20_STUDY9P_PHASEII_QC_05" + extRaw))
})
};
var docResults = docMixed.ChangeMeasuredResults(new MeasuredResults(listChromatograms));
var docContainerMixed = new ResultsTestDocumentContainer(docMixed, docPath);
Assert.IsTrue(docContainerMixed.SetDocument(docResults, docMixed, true));
docContainerMixed.AssertComplete();
docMixed = docContainerMixed.Document;
SrmDocument docMixedUnmixed = (SrmDocument)docMixed.ChangeChildren(new DocNode[0]);
IdentityPath tempPath;
docMixedUnmixed = docMixedUnmixed.AddPeptideGroups(docUnmixed.PeptideGroups, true, IdentityPath.ROOT,
out tempPath, out tempPath);
docResults = docUnmixed.ChangeMeasuredResults(new MeasuredResults(listChromatograms));
var docContainerUnmixed = new ResultsTestDocumentContainer(docUnmixed, docPath);
Assert.IsTrue(docContainerUnmixed.SetDocument(docResults, docUnmixed, true));
docContainerUnmixed.AssertComplete();
docUnmixed = docContainerUnmixed.Document;
AssertEx.DocumentCloned(docMixedUnmixed, docUnmixed);
docContainerMixed.Release();
docContainerUnmixed.Release();
}
public void ThermoNonMatchingRTTest()
{
var testFilesDir = new TestFilesDir(TestContext, ZIP_FILE);
string docPath;
SrmDocument doc = InitThermoDocument(testFilesDir, out docPath);
string extRaw = ExtensionTestContext.ExtThermoRaw;
var listChromatograms = new List <ChromatogramSet>
{
new ChromatogramSet("rep03", new[]
{
MsDataFileUri.Parse(testFilesDir.GetTestPath(
"Site20_STUDY9P_PHASEII_QC_03" + extRaw))
}),
};
ValidateRelativeRT(RelativeRT.Preceding, doc, docPath, listChromatograms);
ValidateRelativeRT(RelativeRT.Overlapping, doc, docPath, listChromatograms);
ValidateRelativeRT(RelativeRT.Unknown, doc, docPath, listChromatograms);
}
public static ResultNameMap <IDictionary <Target, double> > ReadAllRetentionTimes(SrmDocument document, ResultNameMap <RetentionTimeSource> sources)
{
var allRetentionTimes = new Dictionary <string, IDictionary <Target, double> >();
foreach (var source in sources)
{
var library = document.Settings.PeptideSettings.Libraries.GetLibrary(source.Value.Library);
if (null == library)
{
continue;
}
LibraryRetentionTimes libraryRetentionTimes;
if (!library.TryGetRetentionTimes(MsDataFileUri.Parse(source.Value.Name), out libraryRetentionTimes))
{
continue;
}
allRetentionTimes.Add(source.Key, libraryRetentionTimes.GetFirstRetentionTimes());
}
return(ResultNameMap.FromDictionary(allRetentionTimes));
}
protected override void DoTest()
{
var resultsPath = TestFilesDir.GetTestPath("PeakSortingIssue.raw");
var docPath = TestFilesDir.GetTestPath("PeakSortingIssue.sky");
var doc = ResultsUtil.DeserializeDocument(docPath);
AssertEx.IsDocumentState(doc, 0, 1, 3, 6, 90);
using (var docContainer = new ResultsTestDocumentContainer(doc, docPath))
{
var replicateName = Path.GetFileNameWithoutExtension(resultsPath);
var listChromatograms =
new List <ChromatogramSet> {
new ChromatogramSet(replicateName, new[] { MsDataFileUri.Parse(resultsPath) })
};
var docResults = doc.ChangeMeasuredResults(new MeasuredResults(listChromatograms));
Assert.IsTrue(docContainer.SetDocument(docResults, doc, true));
docContainer.AssertComplete();
docResults = docContainer.Document;
AssertResult.IsDocumentResultsState(docResults, replicateName, 0, 0, 0, 0, 3);
}
}
private void btnExport_Click(object sender, EventArgs e)
{
string strReferenceFile = (string)comboBoxReferenceFile.SelectedItem;
string strSaveFileName = string.Empty;
if (!string.IsNullOrEmpty(_documentFilePath))
{
strSaveFileName = Path.GetFileNameWithoutExtension(_documentFilePath);
}
if (!string.IsNullOrEmpty(strReferenceFile))
{
strSaveFileName += Path.GetFileNameWithoutExtension(strReferenceFile);
}
strSaveFileName += ".ChorusRequest.xml"; // Not L10N
strSaveFileName = strSaveFileName.Replace(' ', '_');
using (var saveFileDialog = new SaveFileDialog {
FileName = strSaveFileName
})
{
if (saveFileDialog.ShowDialog(this) != DialogResult.OK || string.IsNullOrEmpty(saveFileDialog.FileName))
{
return;
}
SpectrumFilter spectrumFilterData = new SpectrumFilter(Document, MsDataFileUri.Parse(strReferenceFile), null);
using (var saver = new FileSaver(saveFileDialog.FileName))
{
if (!saver.CanSave(this))
{
return;
}
using (var stream = new StreamWriter(saver.SafeName))
{
var xmlSerializer = new XmlSerializer(typeof(Model.Results.RemoteApi.GeneratedCode.ChromatogramRequestDocument));
xmlSerializer.Serialize(stream, spectrumFilterData.ToChromatogramRequestDocument());
}
saver.Commit();
}
}
Close();
}
public static void MatchChromatograms(ResultsTestDocumentContainer docContainer,
string path1, string path2, int delta, int missing, LockMassParameters lockMassParameters = null)
{
MatchChromatograms(docContainer, MsDataFileUri.Parse(path1), MsDataFileUri.Parse(path2), delta, missing, lockMassParameters);
}
public void Open()
{
List <MsDataFileUri> dataSourceList = new List <MsDataFileUri>();
foreach (ListViewItem item in listView.SelectedItems)
{
if (!DataSourceUtil.IsFolderType(item.SubItems[1].Text))
{
dataSourceList.Add(((SourceInfo)item.Tag).MsDataFileUri);
}
}
if (dataSourceList.Count > 0)
{
DataSources = dataSourceList.ToArray();
_abortPopulateList = true;
DialogResult = DialogResult.OK;
return;
}
// No files selected: see if there is a folder selected that we
// should navigate to
foreach (ListViewItem item in listView.SelectedItems)
{
if (DataSourceUtil.IsFolderType(item.SubItems[1].Text))
{
OpenFolderItem(item);
return;
}
}
try
{
// perhaps the user has typed an entire filename into the text box - or just garbage
var fileOrDirName = sourcePathTextBox.Text;
bool exists;
bool triedAddingDirectory = false;
while (!(exists = ((File.Exists(fileOrDirName) || Directory.Exists(fileOrDirName)))))
{
if (triedAddingDirectory)
{
break;
}
MsDataFilePath currentDirectoryPath = CurrentDirectory as MsDataFilePath;
if (null == currentDirectoryPath)
{
break;
}
fileOrDirName = Path.Combine(currentDirectoryPath.FilePath, fileOrDirName);
triedAddingDirectory = true;
}
if (exists)
{
if (DataSourceUtil.IsDataSource(fileOrDirName))
{
DataSources = new[] { MsDataFileUri.Parse(fileOrDirName) };
DialogResult = DialogResult.OK;
return;
}
else if (Directory.Exists(fileOrDirName))
{
OpenFolder(new MsDataFilePath(fileOrDirName));
return;
}
}
}
// ReSharper disable once EmptyGeneralCatchClause
catch {} // guard against user typed-in-garbage
// No files or folders selected: Show an error message.
MessageDlg.Show(this, Resources.OpenDataSourceDialog_Open_Please_select_one_or_more_data_sources);
}
private IList <SpectrumDisplayInfo> GetSpectra(TransitionGroupDocNode nodeGroup, Target lookupSequence, ExplicitMods lookupMods)
{
var settings = DocumentUI.Settings;
var charge = nodeGroup.PrecursorAdduct;
var spectra = settings.GetBestSpectra(lookupSequence, charge, lookupMods).Select(s => new SpectrumDisplayInfo(s)).ToList();
// Showing redundant spectra is only supported for full-scan filtering when
// the document has results files imported.
if ((!settings.TransitionSettings.FullScan.IsEnabled && !settings.PeptideSettings.Libraries.HasMidasLibrary) || !settings.HasResults)
{
return(spectra);
}
try
{
var spectraRedundant = new List <SpectrumDisplayInfo>();
var dictReplicateNameFiles = new Dictionary <string, HashSet <string> >();
foreach (var spectrumInfo in settings.GetRedundantSpectra(nodeGroup.Peptide, lookupSequence, charge, nodeGroup.TransitionGroup.LabelType, lookupMods))
{
var matchingFile = settings.MeasuredResults.FindMatchingMSDataFile(MsDataFileUri.Parse(spectrumInfo.FilePath));
if (matchingFile == null)
{
continue;
}
string replicateName = matchingFile.Chromatograms.Name;
spectraRedundant.Add(new SpectrumDisplayInfo(spectrumInfo,
replicateName,
matchingFile.FilePath,
matchingFile.FileOrder,
spectrumInfo.RetentionTime,
false));
// Include the best spectrum twice, once displayed in the normal
// way and once displayed with its replicate and retetion time.
if (spectrumInfo.IsBest)
{
string libName = spectrumInfo.LibName;
var labelType = spectrumInfo.LabelType;
int iBest = spectra.IndexOf(s => Equals(s.LibName, libName) &&
Equals(s.LabelType, labelType));
if (iBest != -1)
{
spectra[iBest] = new SpectrumDisplayInfo(spectra[iBest].SpectrumInfo,
replicateName,
matchingFile.FilePath,
0,
spectrumInfo.RetentionTime,
true);
}
}
HashSet <string> setFiles;
if (!dictReplicateNameFiles.TryGetValue(replicateName, out setFiles))
{
setFiles = new HashSet <string>();
dictReplicateNameFiles.Add(replicateName, setFiles);
}
setFiles.Add(spectrumInfo.FilePath);
}
// Determine if replicate name is sufficient to uniquely identify the file
foreach (var spectrumInfo in spectraRedundant)
{
string replicateName = spectrumInfo.ReplicateName;
if (replicateName != null && dictReplicateNameFiles[replicateName].Count < 2)
{
spectrumInfo.IsReplicateUnique = true;
}
}
spectraRedundant.Sort();
spectra.AddRange(spectraRedundant);
return(spectra);
}
catch (Exception)
{
return(spectra);
}
}
public SpectrumIdentifier(string sourceFile, double retentionTime)
: this(MsDataFileUri.Parse(sourceFile), retentionTime)
{
}
public SrmDocument Import(TextReader reader, IProgressMonitor progressMonitor, long lineCount, bool isMinutes, bool removeMissing = false, bool changePeaks = true)
{
IProgressStatus status = new ProgressStatus(Resources.PeakBoundaryImporter_Import_Importing_Peak_Boundaries);
double timeConversionFactor = isMinutes ? 1.0 : 60.0;
int linesRead = 0;
int progressPercent = 0;
var docNew = (SrmDocument)Document.ChangeIgnoreChangingChildren(true);
var docReference = docNew;
var sequenceToNode = MakeSequenceDictionary(Document);
var fileNameToFileMatch = new Dictionary <string, ChromSetFileMatch>();
var trackAdjustedResults = new HashSet <ResultsKey>();
var modMatcher = new ModificationMatcher();
var canonicalSequenceDict = new Dictionary <string, string>();
// Add annotations as possible columns
var allFieldNames = new List <string[]>(FIELD_NAMES);
allFieldNames.AddRange(from def in Document.Settings.DataSettings.AnnotationDefs
where def.AnnotationTargets.Contains(AnnotationDef.AnnotationTarget.precursor_result)
select new[] { def.Name });
string line = reader.ReadLine();
linesRead++;
int[] fieldIndices;
int fieldsTotal;
// If we aren't changing peaks, allow start and end time to be missing
var requiredFields = changePeaks ? REQUIRED_FIELDS : REQUIRED_NO_CHROM;
char correctSeparator = ReadFirstLine(line, allFieldNames, requiredFields, out fieldIndices, out fieldsTotal);
while ((line = reader.ReadLine()) != null)
{
linesRead++;
if (progressMonitor != null)
{
if (progressMonitor.IsCanceled)
{
return(Document);
}
int progressNew = (int)(linesRead * 100 / lineCount);
if (progressPercent != progressNew)
{
progressMonitor.UpdateProgress(status = status.ChangePercentComplete(progressNew));
progressPercent = progressNew;
}
}
var dataFields = new DataFields(fieldIndices, line.ParseDsvFields(correctSeparator), allFieldNames);
if (dataFields.Length != fieldsTotal)
{
throw new IOException(string.Format(Resources.PeakBoundaryImporter_Import_Line__0__field_count__1__differs_from_the_first_line__which_has__2_,
linesRead, dataFields.Length, fieldsTotal));
}
string modifiedPeptideString = dataFields.GetField(Field.modified_peptide);
string fileName = dataFields.GetField(Field.filename);
bool isDecoy = dataFields.IsDecoy(linesRead);
IList <IdentityPath> pepPaths;
if (!sequenceToNode.TryGetValue(Tuple.Create(modifiedPeptideString, isDecoy), out pepPaths))
{
string canonicalSequence;
if (!canonicalSequenceDict.TryGetValue(modifiedPeptideString, out canonicalSequence))
{
if (modifiedPeptideString.Any(c => c < 'A' || c > 'Z'))
{
modMatcher.CreateMatches(Document.Settings,
new List <string> {
modifiedPeptideString
},
Settings.Default.StaticModList,
Settings.Default.HeavyModList);
var nodeForModPep = modMatcher.GetModifiedNode(modifiedPeptideString);
if (nodeForModPep == null)
{
throw new IOException(string.Format(Resources.PeakBoundaryImporter_Import_Peptide_has_unrecognized_modifications__0__at_line__1_, modifiedPeptideString, linesRead));
}
nodeForModPep = nodeForModPep.ChangeSettings(Document.Settings, SrmSettingsDiff.ALL);
// Convert the modified peptide string into a standardized form that
// converts unimod, names, etc, into masses, eg [+57.0]
canonicalSequence = nodeForModPep.ModifiedTarget.Sequence;
canonicalSequenceDict.Add(modifiedPeptideString, canonicalSequence);
}
}
if (null != canonicalSequence)
{
sequenceToNode.TryGetValue(Tuple.Create(canonicalSequence, isDecoy), out pepPaths);
}
}
if (null == pepPaths)
{
UnrecognizedPeptides.Add(modifiedPeptideString);
continue;
}
Adduct charge;
bool chargeSpecified = dataFields.TryGetCharge(linesRead, out charge);
string sampleName = dataFields.GetField(Field.sample_name);
double?apexTime = dataFields.GetTime(Field.apex_time, timeConversionFactor,
Resources.PeakBoundaryImporter_Import_The_value___0___on_line__1__is_not_a_valid_time_, linesRead);
double?startTime = dataFields.GetTime(Field.start_time, timeConversionFactor,
Resources.PeakBoundaryImporter_Import_The_value___0___on_line__1__is_not_a_valid_start_time_, linesRead);
double?endTime = dataFields.GetTime(Field.end_time, timeConversionFactor,
Resources.PeakBoundaryImporter_Import_The_value___0___on_line__1__is_not_a_valid_end_time_, linesRead);
// Error if only one of startTime and endTime is null
if (startTime == null && endTime != null)
{
if (changePeaks)
{
throw new IOException(string.Format(Resources.PeakBoundaryImporter_Import_Missing_start_time_on_line__0_, linesRead));
}
endTime = null;
}
if (startTime != null && endTime == null)
{
if (changePeaks)
{
throw new IOException(string.Format(Resources.PeakBoundaryImporter_Import_Missing_end_time_on_line__0_, linesRead));
}
startTime = null;
}
// Add filename to second dictionary if not yet encountered
ChromSetFileMatch fileMatch;
if (!fileNameToFileMatch.TryGetValue(fileName, out fileMatch))
{
fileMatch = Document.Settings.MeasuredResults.FindMatchingMSDataFile(MsDataFileUri.Parse(fileName));
fileNameToFileMatch.Add(fileName, fileMatch);
}
if (fileMatch == null)
{
UnrecognizedFiles.Add(fileName);
continue;
}
var chromSet = fileMatch.Chromatograms;
string nameSet = chromSet.Name;
ChromFileInfoId[] fileIds;
if (sampleName == null)
{
fileIds = chromSet.MSDataFileInfos.Select(x => x.FileId).ToArray();
}
else
{
var sampleFile = chromSet.MSDataFileInfos.FirstOrDefault(info => Equals(sampleName, info.FilePath.GetSampleName()));
if (sampleFile == null)
{
throw new IOException(string.Format(Resources.PeakBoundaryImporter_Import_Sample__0__on_line__1__does_not_match_the_file__2__, sampleName, linesRead, fileName));
}
fileIds = new[] { sampleFile.FileId };
}
// Define the annotations to be added
var annotations = dataFields.GetAnnotations();
if (!changePeaks)
{
if (apexTime.HasValue)
{
annotations.Add(ComparePeakBoundaries.APEX_ANNOTATION, dataFields.GetField(Field.apex_time));
}
if (startTime.HasValue && endTime.HasValue)
{
annotations.Add(ComparePeakBoundaries.START_TIME_ANNOTATION, dataFields.GetField(Field.start_time));
annotations.Add(ComparePeakBoundaries.END_TIME_ANNOTATION, dataFields.GetField(Field.end_time));
}
}
AnnotationsAdded = annotations.Keys.ToList();
// Loop over all the transition groups in that peptide to find matching charge,
// or use all transition groups if charge not specified
bool foundSample = false;
foreach (var pepPath in pepPaths)
{
var nodePep = (PeptideDocNode)docNew.FindNode(pepPath);
foreach (TransitionGroupDocNode groupNode in nodePep.Children)
{
if (chargeSpecified && charge != groupNode.TransitionGroup.PrecursorAdduct)
{
continue;
}
// Loop over the files in this groupNode to find the correct sample
// Change peak boundaries for the transition group
foreach (var fileId in GetApplicableFiles(fileIds, groupNode))
{
var groupPath = new IdentityPath(pepPath, groupNode.Id);
// Attach annotations
if (annotations.Any())
{
docNew = docNew.AddPrecursorResultsAnnotations(groupPath, fileId, annotations);
}
// Change peak
var filePath = chromSet.GetFileInfo(fileId).FilePath;
if (changePeaks)
{
docNew = docNew.ChangePeak(groupPath, nameSet, filePath,
null, startTime, endTime, UserSet.IMPORTED, null, false);
}
// For removing peaks that are not in the file, if removeMissing = true
trackAdjustedResults.Add(new ResultsKey(fileId.GlobalIndex, groupNode.Id));
foundSample = true;
}
}
}
if (!foundSample)
{
UnrecognizedChargeStates.Add(new UnrecognizedChargeState(charge, fileName, modifiedPeptideString));
}
}
// Remove peaks from the document that weren't in the file.
if (removeMissing)
{
docNew = RemoveMissing(docNew, trackAdjustedResults, changePeaks);
}
// If nothing has changed, return the old Document before ChangeIgnoreChangingChildren was turned off
if (!ReferenceEquals(docNew, docReference))
{
Document = (SrmDocument)Document.ChangeIgnoreChangingChildren(false).ChangeChildrenChecked(docNew.Children);
}
return(Document);
}
public void InitializeSpectrumSourceFiles(SrmDocument document)
{
if (!IsDDASearch)
{
if (DocLib == null)
{
return;
}
var measuredResults = document.Settings.MeasuredResults;
foreach (var dataFile in DocLib.LibraryFiles.FilePaths)
{
var msDataFilePath = new MsDataFilePath(dataFile);
SpectrumSourceFiles[dataFile] = new FoundResultsFilePossibilities(msDataFilePath.GetFileNameWithoutExtension());
// If a matching file is already in the document, then don't include
// this library spectrum source in the set of files to find.
if (measuredResults != null && measuredResults.FindMatchingMSDataFile(MsDataFileUri.Parse(dataFile)) != null)
{
continue;
}
if (File.Exists(dataFile) && DataSourceUtil.IsDataSource(dataFile))
{
// We've found the dataFile in the exact location
// specified in the document library, so just add it
// to the "FOUND" list.
SpectrumSourceFiles[dataFile].ExactMatch = msDataFilePath.ToString();
}
}
DocLib.ReadStream.CloseStream();
}
}
public void ThermoCancelImportTest()
{
var testFilesDir = new TestFilesDir(TestContext, ZIP_FILE);
string docPath;
SrmDocument doc = InitThermoDocument(testFilesDir, out docPath);
var docContainer = new ResultsTestDocumentContainer(doc, docPath);
string resultsPath = testFilesDir.GetTestPath("Site20_STUDY9P_PHASEII_QC_03" +
ExtensionTestContext.ExtThermoRaw);
string dirPath = Path.GetDirectoryName(resultsPath) ?? "";
// Remove any existing temp and cache files
foreach (var path in Directory.GetFiles(dirPath))
{
if (IsCacheOrTempFile(path))
{
FileEx.SafeDelete(path);
}
}
string name = Path.GetFileNameWithoutExtension(resultsPath);
var listChromatograms = new List <ChromatogramSet> {
new ChromatogramSet(name, new[] { MsDataFileUri.Parse(resultsPath) })
};
var docResults = doc.ChangeMeasuredResults(new MeasuredResults(listChromatograms));
// Start cache load, but don't wait for completion
Assert.IsTrue(docContainer.SetDocument(docResults, doc));
// Wait up to 1 second for the cache to start being written
for (int i = 0; i < 100; i++)
{
if (Directory.GetFiles(dirPath).IndexOf(IsCacheOrTempFile) != -1)
{
break;
}
Thread.Sleep(10);
}
Assert.IsTrue(Directory.GetFiles(dirPath).IndexOf(IsCacheOrTempFile) != -1, "Failed to create cache file");
// Cancel by reverting to the original document
Assert.IsTrue(docContainer.SetDocument(doc, docResults));
// Wait up to 5 seconds for cancel to occur
for (int i = 0; i < 50; i++)
{
if (docContainer.LastProgress.IsCanceled)
{
break;
}
Thread.Sleep(100);
}
if (!docContainer.LastProgress.IsCanceled)
{
Assert.Fail("Attempt to cancel results load failed. {0}", docContainer.LastProgress.ErrorException != null
? docContainer.LastProgress.ErrorException.Message : string.Empty);
}
// Wait up to 20 seconds for the cache to be removed
for (int i = 0; i < 200; i++)
{
if (Directory.GetFiles(dirPath).IndexOf(IsCacheOrTempFile) == -1)
{
break;
}
Thread.Sleep(100);
}
// Cache file has been removed
Assert.IsTrue(Directory.GetFiles(dirPath).IndexOf(IsCacheOrTempFile) == -1, "Failed to remove cache file");
testFilesDir.Dispose();
}
protected override void DoTest()
{
// Lest we get "To export a scheduled method, you must first choose a retention time predictor in Peptide Settings / Prediction, or import results for all peptides in the document."
TestSmallMolecules = false;
// Skyline Collision Energy Optimization
RunUI(() => SkylineWindow.OpenFile(GetTestPath("CE_Vantage_15mTorr.sky"))); // Not L10N
if (AsSmallMolecules)
{
var doc = WaitForDocumentLoaded();
var refine = new RefinementSettings();
SkylineWindow.SetDocument(refine.ConvertToSmallMolecules(doc), doc);
}
// Deriving a New Linear Equation, p. 2
var transitionSettingsUI = ShowDialog <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
var editList =
ShowDialog <EditListDlg <SettingsListBase <CollisionEnergyRegression>, CollisionEnergyRegression> >
(transitionSettingsUI.EditCEList);
RunUI(() => editList.SelectItem("Thermo")); // Not L10N
EditCEDlg editItem = ShowDialog <EditCEDlg>(editList.EditItem);
PauseForScreenShot <EditCEDlg>("Edit Collision Energy Equation form", 3);
ChargeRegressionLine regressionLine2 = new ChargeRegressionLine(2, 0.034, 3.314);
ChargeRegressionLine regressionLine3 = new ChargeRegressionLine(3, 0.044, 3.314);
CheckRegressionLines(new[] { regressionLine2, regressionLine3 }, editItem.Regression.Conversions);
RunUI(() =>
{
editItem.DialogResult = DialogResult.OK;
editList.DialogResult = DialogResult.Cancel;
transitionSettingsUI.DialogResult = DialogResult.Cancel;
});
WaitForClosedForm(transitionSettingsUI);
// Measuring Retention Times for Method Scheduling, p. 3
{
var exportMethodDlg = ShowDialog <ExportMethodDlg>(() => SkylineWindow.ShowExportMethodDialog(ExportFileType.List));
RunUI(() =>
{
exportMethodDlg.InstrumentType = ExportInstrumentType.THERMO;
exportMethodDlg.ExportStrategy = ExportStrategy.Single;
exportMethodDlg.OptimizeType = ExportOptimize.NONE;
exportMethodDlg.MethodType = ExportMethodType.Standard;
});
PauseForScreenShot <ExportMethodDlg.TransitionListView>("Export Transition List form", 4);
RunUI(() => exportMethodDlg.OkDialog(GetTestPath("CE_Vantage_15mTorr_unscheduled.csv"))); // Not L10N
WaitForClosedForm(exportMethodDlg);
}
string filePathTemplate = GetTestPath("CE_Vantage_15mTorr_unscheduled.csv"); // Not L10N
CheckTransitionList(filePathTemplate, 1, 6);
const string unscheduledName = "Unscheduled"; // Not L10N
RunDlg <ImportResultsDlg>(SkylineWindow.ImportResults, importResultsDlg =>
{
importResultsDlg.RadioAddNewChecked = true;
var path =
new[] { new KeyValuePair <string, MsDataFileUri[]>(unscheduledName,
// This is not actually a valid file path (missing OptimizeCE)
// but Skyline should correctly find the file in the same folder
// as the document.
new[] { MsDataFileUri.Parse(GetTestPath("CE_Vantage_15mTorr_unscheduled" + ExtThermoRaw)) }) }; // Not L10N
importResultsDlg.NamedPathSets = path;
importResultsDlg.OkDialog();
});
WaitForCondition(5 * 60 * 1000, () => SkylineWindow.Document.Settings.MeasuredResults.IsLoaded); // 5 minutes
AssertEx.IsDocumentState(SkylineWindow.Document, null, 7, 27, 30, 120);
var docUnsched = SkylineWindow.Document;
AssertResult.IsDocumentResultsState(SkylineWindow.Document,
unscheduledName,
docUnsched.MoleculeCount,
docUnsched.MoleculeTransitionGroupCount, 0,
docUnsched.MoleculeTransitionCount - 1, 0);
RunUI(() =>
{
SkylineWindow.ExpandProteins();
SkylineWindow.ExpandPeptides();
});
PauseForScreenShot("Main Skyline window", 5);
// Creating Optimization Methods, p. 5
{
var exportMethodDlg = ShowDialog <ExportMethodDlg>(() => SkylineWindow.ShowExportMethodDialog(ExportFileType.List));
RunUI(() =>
{
exportMethodDlg.InstrumentType = ExportInstrumentType.THERMO;
exportMethodDlg.ExportStrategy = ExportStrategy.Buckets;
exportMethodDlg.MaxTransitions = 110;
exportMethodDlg.IgnoreProteins = true;
exportMethodDlg.OptimizeType = ExportOptimize.CE;
exportMethodDlg.MethodType = ExportMethodType.Scheduled;
});
PauseForScreenShot <ExportMethodDlg.TransitionListView>("Export Transition List form", 6);
RunUI(() => exportMethodDlg.OkDialog(GetTestPath("CE_Vantage_15mTorr.csv"))); // Not L10N
WaitForClosedForm(exportMethodDlg);
}
string filePathTemplate1 = GetTestPath("CE_Vantage_15mTorr_000{0}.csv"); // Not L10N
CheckTransitionList(filePathTemplate1, 5, 9);
var filePath = GetTestPath("CE_Vantage_15mTorr_0001.csv"); // Not L10N
CheckCEValues(filePath, 11);
// Analyze Optimization Data, p. 7
RunDlg <ImportResultsDlg>(SkylineWindow.ImportResults, importResultsDlg =>
{
importResultsDlg.RadioAddNewChecked = true;
importResultsDlg.OptimizationName = ExportOptimize.CE;
importResultsDlg.NamedPathSets = DataSourceUtil.GetDataSourcesInSubdirs(TestFilesDirs[0].FullPath).ToArray();
importResultsDlg.NamedPathSets[0] =
new KeyValuePair <string, MsDataFileUri[]>("Optimize CE", importResultsDlg.NamedPathSets[0].Value.Take(5).ToArray()); // Not L10N
importResultsDlg.OkDialog();
});
RunUI(() =>
{
SkylineWindow.ShowSingleTransition();
SkylineWindow.AutoZoomBestPeak();
SkylineWindow.ShowPeakAreaReplicateComparison();
});
WaitForDocumentLoaded(15 * 60 * 1000); // 10 minutes
if (AsSmallMolecules)
{
return; // Too peptide-centric from here to end of test
}
FindNode("IHGFDLAAINLQR");
RestoreViewOnScreen(8);
PauseForScreenShot("Main Skyline window", 8);
// p. 8
// Not L10N
RemovePeptide("EGIHAQQK");
FindNode("IDALNENK");
RunUI(() => SkylineWindow.NormalizeAreaGraphTo(AreaNormalizeToView.area_percent_view));
PauseForScreenShot("Main Skyline window", 9);
RunUI(SkylineWindow.EditDelete);
RemovePeptide("LICDNTHITK");
// Creating a New Equation for CE, p. 9
var transitionSettingsUI1 = ShowDialog <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
var editCEDlg1 = ShowDialog <EditListDlg <SettingsListBase <CollisionEnergyRegression>, CollisionEnergyRegression> >(transitionSettingsUI1.EditCEList);
var addItem = ShowDialog <EditCEDlg>(editCEDlg1.AddItem);
RunUI(() =>
{
addItem.RegressionName = "Thermo Vantage Tutorial"; // Not L10N
addItem.UseCurrentData();
});
var graphRegression = ShowDialog <GraphRegression>(addItem.ShowGraph);
PauseForScreenShot <GraphRegression>("Collision Energy Regression graphs", 10);
var graphDatas = graphRegression.RegressionGraphDatas.ToArray();
Assert.AreEqual(2, graphDatas.Length);
ChargeRegressionLine regressionLine21 = new ChargeRegressionLine(2, 0.0305, 2.5061);
ChargeRegressionLine regressionLine31 = new ChargeRegressionLine(3, 0.0397, 1.4217);
var expectedRegressions = new[] { regressionLine21, regressionLine31 };
CheckRegressionLines(expectedRegressions, new[]
{
new ChargeRegressionLine(2,
Math.Round(graphDatas[0].RegressionLine.Slope, 4),
Math.Round(graphDatas[0].RegressionLine.Intercept, 4)),
new ChargeRegressionLine(3,
Math.Round(graphDatas[1].RegressionLine.Slope, 4),
Math.Round(graphDatas[1].RegressionLine.Intercept, 4)),
});
RunUI(graphRegression.CloseDialog);
WaitForClosedForm(graphRegression);
RunUI(addItem.OkDialog);
WaitForClosedForm(addItem);
RunUI(editCEDlg1.OkDialog);
WaitForClosedForm(editCEDlg1);
RunUI(transitionSettingsUI1.OkDialog);
WaitForClosedForm(transitionSettingsUI1);
// Optimizing Each Transition, p. 10
RunDlg <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI, transitionSettingsUI2 =>
{
transitionSettingsUI2.UseOptimized = true;
transitionSettingsUI2.OptimizeType = OptimizedMethodType.Transition.GetLocalizedString();
transitionSettingsUI2.OkDialog();
});
RunDlg <ExportMethodDlg>(() => SkylineWindow.ShowExportMethodDialog(ExportFileType.List), exportMethodDlg =>
{
exportMethodDlg.ExportStrategy = ExportStrategy.Single;
exportMethodDlg.OkDialog(GetTestPath("CE_Vantage_15mTorr_optimized.csv")); // Not L10N
});
var filePathTemplate2 = GetTestPath("CE_Vantage_15mTorr_optimized.csv"); // Not L10N
CheckTransitionList(filePathTemplate2, 1, 9);
RunUI(() => SkylineWindow.SaveDocument());
WaitForConditionUI(() => !SkylineWindow.Dirty);
}
public void DoThermoRatioTest(RefinementSettings.ConvertToSmallMoleculesMode smallMoleculesTestMode)
{
TestSmallMolecules = false; // We do this explicitly
var testFilesDir = new TestFilesDir(TestContext, ZIP_FILE);
string docPath;
SrmDocument doc = InitThermoDocument(testFilesDir, out docPath);
SrmSettings settings = doc.Settings.ChangePeptideModifications(mods =>
mods.ChangeInternalStandardTypes(new[] { IsotopeLabelType.light }));
doc = doc.ChangeSettings(settings);
if (smallMoleculesTestMode != RefinementSettings.ConvertToSmallMoleculesMode.none)
{
var docOrig = doc;
var refine = new RefinementSettings();
doc = refine.ConvertToSmallMolecules(doc, smallMoleculesTestMode);
// This is our first example of a converted label doc - check roundtripping
AssertEx.ConvertedSmallMoleculeDocumentIsSimilar(docOrig, doc);
AssertEx.Serializable(doc);
}
var docContainer = new ResultsTestDocumentContainer(doc, docPath);
string extRaw = ExtensionTestContext.ExtThermoRaw;
var listChromatograms = new List <ChromatogramSet>
{
new ChromatogramSet("rep03", new[]
{
MsDataFileUri.Parse(testFilesDir.GetTestPath(
"Site20_STUDY9P_PHASEII_QC_03" + extRaw))
}),
new ChromatogramSet("rep05", new[]
{
MsDataFileUri.Parse(testFilesDir.GetTestPath(
"Site20_STUDY9P_PHASEII_QC_05" + extRaw))
})
};
var docResults = doc.ChangeMeasuredResults(new MeasuredResults(listChromatograms));
Assert.IsTrue(docContainer.SetDocument(docResults, doc, true));
docContainer.AssertComplete();
docResults = docContainer.Document;
// Make sure all groups have at least 5 transitions (of 6) with ratios
int ratioGroupMissingCount = 0;
foreach (var nodeGroup in docResults.MoleculeTransitionGroups)
{
if (nodeGroup.TransitionGroup.LabelType.IsLight)
{
foreach (var result in nodeGroup.Results)
{
Assert.IsFalse(result[0].Ratio.HasValue, "Light group found with a ratio");
}
foreach (TransitionDocNode nodeTran in nodeGroup.Children)
{
foreach (var resultTran in nodeTran.Results)
{
Assert.IsFalse(resultTran[0].Ratio.HasValue, "Light transition found with a ratio");
}
}
}
else
{
bool missingRatio = false;
foreach (ChromInfoList <TransitionGroupChromInfo> chromInfoList in nodeGroup.Results)
{
var ratioHeavy = chromInfoList[0].Ratio;
if (!ratioHeavy.HasValue)
{
missingRatio = true;
}
}
int ratioCount1 = 0;
int ratioCount2 = 0;
foreach (TransitionDocNode nodeTranHeavy in nodeGroup.Children)
{
float?ratioHeavy = nodeTranHeavy.Results[0][0].Ratio;
if (ratioHeavy.HasValue)
{
Assert.IsFalse(float.IsNaN(ratioHeavy.Value) || float.IsInfinity(ratioHeavy.Value));
ratioCount1++;
}
ratioHeavy = nodeTranHeavy.Results[1][0].Ratio;
if (ratioHeavy.HasValue)
{
Assert.IsFalse(float.IsNaN(ratioHeavy.Value) || float.IsInfinity(ratioHeavy.Value));
ratioCount2++;
}
}
Assert.AreEqual(3, ratioCount1);
if (ratioCount2 < 2)
{
ratioGroupMissingCount++;
}
else
{
Assert.IsFalse(missingRatio, "Precursor missing ratio when transitions have ratios");
}
}
}
// 3 groups with less than 2 transition ratios
Assert.AreEqual(3, ratioGroupMissingCount);
// Remove the first light transition, checking that this removes the ratio
// from the corresponding heavy transition, but not the entire group, until
// after all light transitions have been removed.
IdentityPath pathFirstPep = docResults.GetPathTo((int)SrmDocument.Level.Molecules, 0);
var nodePep = (PeptideDocNode)docResults.FindNode(pathFirstPep);
Assert.AreEqual(2, nodePep.Children.Count);
var nodeGroupLight = (TransitionGroupDocNode)nodePep.Children[0];
IdentityPath pathGroupLight = new IdentityPath(pathFirstPep, nodeGroupLight.TransitionGroup);
Assert.IsNull(nodeGroupLight.Results[0][0].Ratio, "Light group has ratio");
var nodeGroupHeavy = (TransitionGroupDocNode)nodePep.Children[1];
IdentityPath pathGroupHeavy = new IdentityPath(pathFirstPep, nodeGroupHeavy.TransitionGroup);
float? ratioStart = nodeGroupHeavy.Results[0][0].Ratio;
Assert.IsTrue(ratioStart.HasValue, "No starting heavy group ratio");
var expectedValues = new[] { 1.403414, 1.38697791, 1.34598482 };
for (int i = 0; i < 3; i++)
{
var pathLight = docResults.GetPathTo((int)SrmDocument.Level.Transitions, 0);
var pathHeavy = docResults.GetPathTo((int)SrmDocument.Level.Transitions, 3);
TransitionDocNode nodeTran = (TransitionDocNode)docResults.FindNode(pathHeavy);
float? ratioTran = nodeTran.Results[0][0].Ratio;
Assert.IsTrue(ratioTran.HasValue, "Expected transition ratio not found");
Assert.AreEqual(ratioTran.Value, expectedValues[i], 1.0e-5);
docResults = (SrmDocument)docResults.RemoveChild(pathLight.Parent, docResults.FindNode(pathLight));
nodeTran = (TransitionDocNode)docResults.FindNode(pathHeavy);
Assert.IsFalse(nodeTran.Results[0][0].Ratio.HasValue, "Unexpected transiton ratio found");
Assert.AreEqual(pathGroupHeavy, pathHeavy.Parent, "Transition found outside expected group");
// nodePep = (PeptideDocNode) docResults.FindNode(pathFirstPep);
nodeGroupHeavy = (TransitionGroupDocNode)docResults.FindNode(pathGroupHeavy);
// Assert.AreEqual(nodePep.Results[0][0].RatioToStandard, nodeGroupHeavy.Results[0][0].Ratio,
// "Peptide and group ratios not equal");
if (i < 2)
{
float?ratioGroup = nodeGroupHeavy.Results[0][0].Ratio;
Assert.IsTrue(ratioGroup.HasValue, "Group ratio removed with transition ratios");
Assert.AreEqual(ratioStart.Value, ratioGroup.Value, 0.1,
"Unexpected group ratio change by more than 0.1");
}
else
{
Assert.IsFalse(nodeGroupHeavy.Results[0][0].Ratio.HasValue,
"Group ratio still present with no transition ratios");
}
}
bool asSmallMolecules = (smallMoleculesTestMode != RefinementSettings.ConvertToSmallMoleculesMode.none);
if (!asSmallMolecules) // GetTransitions() doesn't work the same way for small molecules - it only lists existing ones
{
bool firstAdd = true;
var nodeGroupLightOrig = (TransitionGroupDocNode)doc.FindNode(pathGroupLight);
DocNode[] lightChildrenOrig = nodeGroupLightOrig.Children.ToArray();
foreach (var nodeTran in nodeGroupLightOrig.GetTransitions(docResults.Settings,
null, nodeGroupLightOrig.PrecursorMz, null, null, null, false))
{
var transition = nodeTran.Transition;
if (!firstAdd && lightChildrenOrig.IndexOf(node => Equals(node.Id, transition)) == -1)
{
continue;
}
// Add the first transition, and then the original transitions
docResults = (SrmDocument)docResults.Add(pathGroupLight, nodeTran);
nodeGroupHeavy = (TransitionGroupDocNode)docResults.FindNode(pathGroupHeavy);
if (firstAdd)
{
Assert.IsNull(nodeGroupHeavy.Results[0][0].Ratio, "Unexpected heavy ratio found");
}
else
{
Assert.IsNotNull(nodeGroupHeavy.Results[0][0].Ratio,
"Heavy ratio null after adding light children");
}
firstAdd = false;
}
Assert.AreEqual(ratioStart, nodeGroupHeavy.Results[0][0].Ratio);
}
// Release file handles
docContainer.Release();
testFilesDir.Dispose();
}
public void ThermoCancelImportTest()
{
var testFilesDir = new TestFilesDir(TestContext, ZIP_FILE);
string resultsPath = testFilesDir.GetTestPath("Site20_STUDY9P_PHASEII_QC_03" +
ExtensionTestContext.ExtThermoRaw);
string dirPath = Path.GetDirectoryName(resultsPath) ?? "";
string docPath;
SrmDocument doc = InitThermoDocument(testFilesDir, out docPath);
// Give this two chances to succeed. It can succeed tens of thousands of times
// in a row, but it still occasionally fails on nightly tests. Hopefully two
// tries will make this extremely unlikely.
for (int tries = 0; tries < 2; tries++)
{
using (var docContainer = new ResultsTestDocumentContainer(doc, docPath))
{
// Remove any existing temp and cache files
foreach (var path in Directory.GetFiles(dirPath))
{
if (IsCacheOrTempFile(path))
{
FileEx.SafeDelete(path);
}
}
string name = Path.GetFileNameWithoutExtension(resultsPath);
var listChromatograms = new List <ChromatogramSet> {
new ChromatogramSet(name, new[] { MsDataFileUri.Parse(resultsPath) })
};
var docResults = doc.ChangeMeasuredResults(new MeasuredResults(listChromatograms));
// Start cache load, but don't wait for completion
Assert.IsTrue(docContainer.SetDocument(docResults, doc));
// Wait up to 10 second for the cache to start being written
bool cacheFound = false;
for (int i = 0; i < 1000; i++)
{
if (Directory.GetFiles(dirPath).IndexOf(IsCacheOrTempFile) != -1)
{
cacheFound = true;
break;
}
Thread.Sleep(10);
}
if (!cacheFound)
{
Assert.Fail(TextUtil.LineSeparate("Failed to create cache file. Found files:", TextUtil.LineSeparate(Directory.GetFiles(dirPath))));
}
// Cancel by reverting to the original document
Assert.IsTrue(docContainer.SetDocument(doc, docResults));
// Wait up to 10 seconds for cancel to occur
bool cancelOccurred = false;
for (int i = 0; i < 1000; i++)
{
if (docContainer.LastProgress != null && docContainer.LastProgress.IsCanceled)
{
cancelOccurred = true;
break;
}
Thread.Sleep(10);
}
// Wait up to 20 seconds for the cache to be removed
bool cacheRemoved = false;
for (int i = 0; i < 200; i++)
{
if (Directory.GetFiles(dirPath).IndexOf(IsCacheOrTempFile) == -1)
{
cacheRemoved = true;
break;
}
Thread.Sleep(100);
}
if (!cacheRemoved)
{
if (tries == 0 && File.Exists(Path.ChangeExtension(docPath, ChromatogramCache.EXT)))
{
// Allow a single failure where we end up with the final cache instead of a cancelation
FileEx.SafeDelete(docPath);
continue; // Try again
}
if (!cancelOccurred)
{
Assert.Fail("Attempt to cancel results load failed on try {0}. {1}", tries + 1,
docContainer.LastProgress != null && docContainer.LastProgress.ErrorException != null
? docContainer.LastProgress.ErrorException.Message : string.Empty);
}
Assert.Fail(TextUtil.LineSeparate("Failed to remove cache file. Found files:", TextUtil.LineSeparate(Directory.GetFiles(dirPath))));
}
break; // If we make it here then, successful
}
}
// Cache file has been removed
testFilesDir.Dispose();
}
private void RemoveCorrespondingReplicatesForLibraryRuns()
{
if (listResults.Items.Count != 0)
{
var newChromRemList = new List <ChromatogramSet>(ChromatogramsRemovedList);
foreach (var dataFile in LibraryRunsRemovedList)
{
var matchingFile =
DocumentUIContainer.Document.Settings.MeasuredResults.FindMatchingMSDataFile(MsDataFileUri.Parse(dataFile));
if (null != matchingFile)
{
int foundIndex = listResults.FindString(matchingFile.Chromatograms.Name);
if (ListBox.NoMatches != foundIndex)
{
newChromRemList.Add(matchingFile.Chromatograms);
listResults.Items.RemoveAt(foundIndex);
if (listResults.Items.Count == 0)
{
break;
}
}
}
}
ChromatogramsRemovedList = newChromRemList;
}
}
public void TestCollectStatistics()
{
var testFilesDir = new TestFilesDir(TestContext, ZIP_FILE);
string docPath = testFilesDir.GetTestPath("BSA_Protea_label_free_20100323_meth3_multi.sky");
SrmDocument doc = ResultsUtil.DeserializeDocument(docPath);
using (var docContainer = new ResultsTestDocumentContainer(doc, docPath))
{
// Import the first RAW file (or mzML for international)
string rawPath = testFilesDir.GetTestPath("ah_20101011y_BSA_MS-MS_only_5-2" +
ExtensionTestContext.ExtThermoRaw);
var measuredResults = new MeasuredResults(new[] { new ChromatogramSet("Single", new[] { MsDataFileUri.Parse(rawPath) }) });
SrmDocument docResults = docContainer.ChangeMeasuredResults(measuredResults, 3, 3, 21);
ChromCacheMinimizer chromCacheMinimizer =
docResults.Settings.MeasuredResults.GetChromCacheMinimizer(docResults);
ChromCacheMinimizer.Settings settings =
new ChromCacheMinimizer.Settings().ChangeDiscardUnmatchedChromatograms(true);
ChromCacheMinimizer.MinStatistics minStatistics = null;
chromCacheMinimizer.Minimize(settings, s => minStatistics = s, null);
Assert.AreEqual(100, minStatistics.PercentComplete);
Assert.AreEqual(1.0, minStatistics.MinimizedRatio);
var docMissingFirstPeptide =
(SrmDocument)
docResults.ReplaceChild(
docResults.PeptideGroups.First().RemoveChild(docResults.PeptideGroups.First().Children[0]));
var docWithOnlyFirstPeptide =
(SrmDocument)
docResults.ReplaceChild(
docResults.PeptideGroups.First().ChangeChildren(new[] { docResults.PeptideGroups.First().Children[0] }));
ChromCacheMinimizer.MinStatistics statsMissingFirstProtein = null;
ChromCacheMinimizer.MinStatistics statsWithOnlyFirstProtein = null;
settings = settings.ChangeDiscardUnmatchedChromatograms(true);
ChromCacheMinimizer minimizerMissingFirstProtein =
docMissingFirstPeptide.Settings.MeasuredResults.GetChromCacheMinimizer(docMissingFirstPeptide);
ChromCacheMinimizer minimizerWithOnlyFirstProtein =
docWithOnlyFirstPeptide.Settings.MeasuredResults.GetChromCacheMinimizer(docWithOnlyFirstPeptide);
minimizerMissingFirstProtein.Minimize(settings, s => statsMissingFirstProtein = s, null);
minimizerWithOnlyFirstProtein.Minimize(settings, s => statsWithOnlyFirstProtein = s, null);
Assert.AreEqual(100, statsMissingFirstProtein.PercentComplete);
Assert.AreEqual(100, statsWithOnlyFirstProtein.PercentComplete);
Assert.AreEqual(1.0, statsMissingFirstProtein.MinimizedRatio + statsWithOnlyFirstProtein.MinimizedRatio,
.00001);
settings = settings.ChangeDiscardUnmatchedChromatograms(false);
ChromCacheMinimizer.MinStatistics statsMissingFirstProteinKeepAll = null;
ChromCacheMinimizer.MinStatistics statsWithOnlyFirstProteinKeepAll = null;
minimizerMissingFirstProtein.Minimize(settings, s => statsMissingFirstProteinKeepAll = s, null);
minimizerWithOnlyFirstProtein.Minimize(settings, s => statsWithOnlyFirstProteinKeepAll = s, null);
Assert.AreEqual(100, statsMissingFirstProteinKeepAll.PercentComplete);
Assert.AreEqual(1.0, statsMissingFirstProteinKeepAll.MinimizedRatio);
Assert.AreEqual(100, statsWithOnlyFirstProteinKeepAll.PercentComplete);
Assert.AreEqual(1.0, statsWithOnlyFirstProteinKeepAll.MinimizedRatio);
}
}
private void DoSubTest(TestFilesDir testFilesDir, string skyFile, double[] expectedRTs, string[] filenames, double?expectedRatio)
{
string docPath;
var doc = InitExplicitRTDocument(testFilesDir, skyFile, out docPath);
var listChromatograms = new List <ChromatogramSet>();
foreach (var filename in filenames)
{
var path = MsDataFileUri.Parse(filename + ExtensionTestContext.ExtWatersRaw);
listChromatograms.Add(AssertResult.FindChromatogramSet(doc, path) ??
new ChromatogramSet(path.GetFileName().Replace('.', '_'), new[] { path }));
}
var docResults = doc.ChangeMeasuredResults(new MeasuredResults(listChromatograms));
Assert.IsTrue(SkylineWindow.SetDocument(docResults, doc));
var document = WaitForDocumentLoaded();
float tolerance = (float)document.Settings.TransitionSettings.Instrument.MzMatchTolerance;
var infos = new List <ChromatogramGroupInfo[]>();
foreach (var pair in document.MoleculePrecursorPairs)
{
for (var f = 0; f < filenames.Length; f++)
{
ChromatogramGroupInfo[] chromGroupInfo;
Assert.IsTrue(document.Settings.MeasuredResults.TryLoadChromatogram(f, pair.NodePep, pair.NodeGroup, tolerance,
true, out chromGroupInfo));
infos.Add(chromGroupInfo);
}
}
for (int i = 0; i < infos.Count; i++)
{
if (infos[i].Length == 0)
{
Assert.AreEqual(0, expectedRTs[i], "expected to find a peak at " + expectedRTs[i]);
continue;
}
var chromatogramInfo = infos[i][0].GetTransitionInfo(0);
var chromPeaks = chromatogramInfo.Peaks.ToList();
if (expectedRTs[i] == 0) // Not expecting to find a good peak
{
var errmsg = chromatogramInfo.BestPeakIndex >= 0 ? string.Format("Did not expect to find a peak at RT {0} in {1} ", chromPeaks[chromatogramInfo.BestPeakIndex].RetentionTime, skyFile) : string.Empty;
Assert.AreEqual(-1, chromatogramInfo.BestPeakIndex, errmsg);
}
else if (chromatogramInfo.BestPeakIndex == -1)
{
Assert.Fail("expected to find a peak at {0} in {1}", expectedRTs[i], skyFile);
}
else
{
var peakRT = chromPeaks[chromatogramInfo.BestPeakIndex].RetentionTime;
Assert.AreEqual(expectedRTs[i], peakRT, 0.1, string.Format("Expected to find a peak at RT {0} in {1}", expectedRTs[i], skyFile));
}
}
if (expectedRatio.HasValue)
{
var nResults = 0;
foreach (var nodePep in document.Molecules)
{
foreach (var results in nodePep.Results)
{
foreach (var result in results)
{
Assert.IsNotNull(result.LabelRatios[0].Ratio);
Assert.AreEqual(expectedRatio.Value, result.LabelRatios[0].Ratio.Ratio, .1);
nResults++;
}
}
}
Assert.AreEqual(filenames.Length * document.MoleculeCount, nResults);
}
WaitForClosedAllChromatogramsGraph();
}
protected override void DoTest()
{
Settings.Default.PeakScoringModelList.Clear();
// Open the file
RunUI(() => SkylineWindow.OpenFile(GetTestPath("SRMCourse_DosR-hDP__20130501-tutorial-empty.sky"))); // Not L10N
WaitForDocumentLoaded();
// Add decoys
var generateDecoysDlg = ShowDialog <GenerateDecoysDlg>(() => SkylineWindow.ShowGenerateDecoysDlg());
RunUI(() =>
{
generateDecoysDlg.DecoysMethod = DecoyGeneration.REVERSE_SEQUENCE;
generateDecoysDlg.NumDecoys = 29;
});
PauseForScreenShot <GenerateDecoysDlg>("Add Decoy Peptides form", 2);
RunUI(generateDecoysDlg.OkDialog);
WaitForClosedForm(generateDecoysDlg);
RestoreViewOnScreen(3);
RunUI(() => SkylineWindow.SequenceTree.TopNode = SkylineWindow.SequenceTree.Nodes[11]);
PauseForScreenShot("Targets view clipped from main window", 3);
// Open the file with decoys
RunUI(() => SkylineWindow.OpenFile(GetTestPath("SRMCourse_DosR-hDP__20130501-tutorial-empty-decoys.sky"))); // Not L10N
WaitForDocumentLoaded();
// Import the raw data
var importResultsDlg = ShowDialog <ImportResultsDlg>(SkylineWindow.ImportResults);
RunUI(() =>
{
importResultsDlg.RadioAddNewChecked = true;
var path = new KeyValuePair <string, MsDataFileUri[]> [5];
for (int i = 0; i < 5; ++i)
{
path[i] = new KeyValuePair <string, MsDataFileUri[]>(_importFiles[i],
new[] { MsDataFileUri.Parse(GetTestPath(_importFiles[i] + ExtAbWiff)) });
}
importResultsDlg.NamedPathSets = path;
});
var importResultsNameDlg = ShowDialog <ImportResultsNameDlg>(importResultsDlg.OkDialog);
PauseForScreenShot <ImportResultsNameDlg>("Import Results common prefix form", 4);
RunUI(() =>
{
string prefix = importResultsNameDlg.Prefix;
importResultsNameDlg.Prefix = prefix.Substring(0, prefix.Length - 1);
importResultsNameDlg.YesDialog();
});
WaitForClosedForm(importResultsNameDlg);
WaitForClosedForm(importResultsDlg);
WaitForConditionUI(5 * 60 * 1000, () =>
SkylineWindow.DocumentUI.Settings.HasResults &&
SkylineWindow.DocumentUI.Settings.MeasuredResults.IsLoaded); // 5 minutes
RestoreViewOnScreen(5);
const string peptideSeqHighlight = "LPDGNGIELCR";
RunUI(() =>
{
var nodeGroup = SkylineWindow.DocumentUI.PeptideTransitionGroups.ToArray()[71];
Assert.AreEqual(nodeGroup.TransitionGroup.Peptide.Sequence, peptideSeqHighlight);
var chromGroupInfo = nodeGroup.ChromInfos.ToList()[0];
Assert.IsNotNull(chromGroupInfo.RetentionTime);
// TODO: Fix the tutorial. This was supposed to be an incorrectly picked peak, but our default scoring is now good enough to pick it correctly
Assert.AreEqual(chromGroupInfo.RetentionTime.Value, 18.0, 0.1);
SkylineWindow.ChangeTextSize(TreeViewMS.LRG_TEXT_FACTOR);
});
RunDlg <ChromChartPropertyDlg>(SkylineWindow.ShowChromatogramProperties, dlg =>
{
dlg.FontSize = GraphFontSize.LARGE;
dlg.OkDialog();
});
PauseForScreenShot("Main window", 5);
// Test different point types on RTLinearRegressionGraph
RunUI(() =>
{
SkylineWindow.ShowRTRegressionGraphScoreToRun();
SkylineWindow.ShowPlotType(PlotTypeRT.correlation);
SkylineWindow.ChooseCalculator("iRT_SRMAtlas_20121202_noLGG");
});
const int numDecoys = 30;
CheckPointsTypeRT(PointsTypeRT.targets, SkylineWindow.Document.PeptideCount - numDecoys);
CheckPointsTypeRT(PointsTypeRT.standards, SkylineWindow.Document.GetRetentionTimeStandards().Count);
CheckPointsTypeRT(PointsTypeRT.decoys, numDecoys);
RunUI(() => SkylineWindow.ShowGraphRetentionTime(false));
WaitForDocumentLoaded();
// Train the peak scoring model
var reintegrateDlg = ShowDialog <ReintegrateDlg>(SkylineWindow.ShowReintegrateDialog);
PauseForScreenShot <ReintegrateDlg>("Reintegrate form", 6);
var editDlg = ShowDialog <EditPeakScoringModelDlg>(reintegrateDlg.AddPeakScoringModel);
RunUI(() => editDlg.TrainModel());
PauseForScreenShot <EditPeakScoringModelDlg.ModelTab>("Edit Peak Scoring Model form trained model", 6);
RunUI(() => Assert.AreEqual(0.5926, editDlg.PeakCalculatorsGrid.Items[3].PercentContribution ?? 0, 0.005));
RunUI(() => editDlg.SelectedGraphTab = 2);
PauseForScreenShot <EditPeakScoringModelDlg.PvalueTab>("Edit Peak Scoring Model form p value graph metafile", 7);
RunUI(() => editDlg.SelectedGraphTab = 3);
PauseForScreenShot <EditPeakScoringModelDlg.QvalueTab>("Edit Peak Scoring Model form q value graph metafile", 8);
RunUI(() => editDlg.SelectedGraphTab = 1);
RunUI(() => editDlg.PeakCalculatorsGrid.SelectRow(3));
PauseForScreenShot <EditPeakScoringModelDlg.FeaturesTab>("Edit Peak Scoring Model form feature score", 10);
RunUI(() =>
{
Assert.AreEqual(18, editDlg.PeakCalculatorsGrid.RowCount);
// The rows which the tutorial says are missing scores are in fact missing scores
foreach (int i in new[] { 2, 7, 8, 9, 10, 11, 13, 15 }) // MS1 scores are now missing, 19, 20, 21, 22
{
Assert.IsFalse(editDlg.IsActiveCell(i, 0));
}
editDlg.IsFindButtonVisible = true;
editDlg.FindMissingValues(2); // Retention time
editDlg.PeakScoringModelName = "test1";
});
PauseForScreenShot <EditPeakScoringModelDlg.FeaturesTab>("Edit Peak Scoring Model form find missing scores", 11);
OkDialog(editDlg, editDlg.OkDialog);
OkDialog(reintegrateDlg, reintegrateDlg.CancelDialog);
PauseForScreenShot <FindResultsForm>("Find Results view clipped from main window", 12);
// Remove the peptide with no library dot product, and train again
FindResultsForm findResultsForm = null;
var missingPeptides = new List <string> {
"LGGNEQVTR", "IPVDSIYSPVLK", "YFNDGDIVEGTIVK",
"DFDSLGTLR", "GGYAGMLVGSVGETVAQLAR", "GGYAGMLVGSVGETVAQLAR"
};
var isDecoys = new List <bool> {
false, false, false, false, false, true
};
RunUI(() =>
{
findResultsForm = FormUtil.OpenForms.OfType <FindResultsForm>().FirstOrDefault();
Assert.IsNotNull(findResultsForm);
// ReSharper disable once PossibleNullReferenceException
Assert.AreEqual(findResultsForm.ItemCount, 6);
for (int i = 0; i < 6; ++i)
{
findResultsForm.ActivateItem(i);
Assert.AreEqual(SkylineWindow.SelectedPeptideSequence, missingPeptides[i]);
if (0 < i && i < 5)
{
SkylineWindow.SetStandardType(PeptideDocNode.STANDARD_TYPE_QC);
}
}
});
RunUI(() => findResultsForm.Close());
for (int i = 0; i < 6; ++i)
{
if (!(0 < i && i < 5))
{
RemovePeptide(missingPeptides[i], isDecoys[i]);
}
}
if (IsCoverShotMode)
{
RestoreCoverViewOnScreen();
var reintegrateDlgCover = ShowDialog <ReintegrateDlg>(SkylineWindow.ShowReintegrateDialog);
var editModelCover = ShowDialog <EditPeakScoringModelDlg>(reintegrateDlgCover.AddPeakScoringModel);
RunUI(() =>
{
editModelCover.Top = SkylineWindow.Top + 8;
editModelCover.Left = SkylineWindow.Right - editModelCover.Width - 8;
editModelCover.PeakScoringModelName = "SRMCourse";
editModelCover.TrainModelClick();
});
TakeCoverShot();
OkDialog(editModelCover, editModelCover.CancelDialog);
OkDialog(reintegrateDlgCover, reintegrateDlgCover.CancelDialog);
return;
}
var reintegrateDlgNew = ShowDialog <ReintegrateDlg>(SkylineWindow.ShowReintegrateDialog);
var editListLibrary = ShowDialog <EditListDlg <SettingsListBase <PeakScoringModelSpec>, PeakScoringModelSpec> >(
reintegrateDlgNew.EditPeakScoringModel);
RunUI(() => editListLibrary.SelectItem("test1"));
var editDlgLibrary = ShowDialog <EditPeakScoringModelDlg>(editListLibrary.EditItem);
RunUI(() =>
{
foreach (int i in new[] { 2, 8, 9, 10, 11 })
{
Assert.IsTrue(editDlgLibrary.IsActiveCell(i, 0));
Assert.IsFalse(editDlgLibrary.PeakCalculatorsGrid.Items[i].IsEnabled);
editDlgLibrary.PeakCalculatorsGrid.Items[i].IsEnabled = true;
}
editDlgLibrary.TrainModel(true);
});
PauseForScreenShot <EditPeakScoringModelDlg.ModelTab>("Edit Peak Scoring Model form with library score", 13);
RunUI(() => editDlgLibrary.SelectedGraphTab = 3);
PauseForScreenShot <EditPeakScoringModelDlg.QvalueTab>("Edit Peak Scoring Model form q value graph with library score metafile", 14);
OkDialog(editDlgLibrary, editDlgLibrary.OkDialog);
// Open up the model again for editing, re-train with second best peaks and removing some scores
RunUI(() => editListLibrary.SelectItem("test1")); // Not L10N
var editDlgNew = ShowDialog <EditPeakScoringModelDlg>(editListLibrary.EditItem);
RunUI(() =>
{
Assert.IsFalse(editDlgNew.UsesSecondBest);
Assert.IsTrue(editDlgNew.UsesDecoys);
Assert.IsTrue(editDlgNew.PeakCalculatorsGrid.Items[4].IsEnabled);
Assert.IsTrue(editDlgNew.PeakCalculatorsGrid.Items[4].PercentContribution < 0);
Assert.IsTrue(editDlgNew.PeakCalculatorsGrid.Items[2].IsEnabled);
Assert.IsTrue(editDlgNew.PeakCalculatorsGrid.Items[2].PercentContribution > 0);
editDlgNew.UsesSecondBest = true;
editDlgNew.PeakCalculatorsGrid.Items[4].IsEnabled = false;
editDlgNew.PeakCalculatorsGrid.Items[2].IsEnabled = false;
editDlgNew.TrainModel(true);
// Check that these cells are still active even though they've been unchecked
Assert.IsTrue(editDlgNew.IsActiveCell(6, 0));
});
PauseForScreenShot <EditPeakScoringModelDlg.ModelTab>("Edit Peak Scoring Model form with second best", 15);
OkDialog(editDlgNew, editDlgNew.CancelDialog);
OkDialog(editListLibrary, editListLibrary.OkDialog);
// Apply the model to reintegrate peaks
RunUI(() =>
{
reintegrateDlgNew.ComboPeakScoringModelSelected = "test1";
reintegrateDlgNew.ReintegrateAll = true;
reintegrateDlgNew.OverwriteManual = true;
});
PauseForScreenShot <ReintegrateDlg>("Reintegrate form", 16);
OkDialog(reintegrateDlgNew, reintegrateDlgNew.OkDialog);
RunUI(() =>
{
var nodeGroup = SkylineWindow.DocumentUI.PeptideTransitionGroups.ToArray()[70];
Assert.AreEqual(nodeGroup.TransitionGroup.Peptide.Sequence, peptideSeqHighlight);
var chromGroupInfo = nodeGroup.ChromInfos.ToList()[0];
Assert.IsNotNull(chromGroupInfo.RetentionTime);
Assert.AreEqual(18.0, chromGroupInfo.RetentionTime.Value, 0.1);
});
FindNode(peptideSeqHighlight);
PauseForScreenShot <GraphChromatogram>("Chromatogram graph metafile corrected peak at 18.0", 17);
// Reintegrate slightly differently, with a q value cutoff
var reintegrateDlgQ = ShowDialog <ReintegrateDlg>(SkylineWindow.ShowReintegrateDialog);
RunUI(() =>
{
reintegrateDlgQ.ReintegrateAll = false;
reintegrateDlgQ.Cutoff = 0.001;
reintegrateDlgQ.OverwriteManual = true;
});
OkDialog(reintegrateDlgQ, reintegrateDlgQ.OkDialog);
PauseForScreenShot("Targets view with some null peaks clipped from main window", 17);
PauseForScreenShot <GraphChromatogram>("Chromatogram graph metafile with no picked peak", 18);
RestoreViewOnScreen(14);
FindNode((622.3086).ToString(CultureInfo.CurrentCulture) + "++");
PauseForScreenShot("Main window with interference on transition", 19);
// Export the mProphet features
var mProphetExportDlg = ShowDialog <MProphetFeaturesDlg>(SkylineWindow.ShowMProphetFeaturesDialog);
RunUI(() => mProphetExportDlg.BestScoresOnly = true);
PauseForScreenShot <MProphetFeaturesDlg>("Export mProphet Features form", 20);
// TODO: actually write the features here using WriteFeatures
OkDialog(mProphetExportDlg, mProphetExportDlg.CancelDialog);
// Export a report
string pathReport = GetTestPath("qValues_Exported_report.csv");
const string qvalueHeader = "annotation_QValue";
string reportName = Resources.ReportSpecList_GetDefaults_Peptide_RT_Results;
var reportExportDlg = ShowDialog <ExportLiveReportDlg>(SkylineWindow.ShowExportReportDialog);
var manageViewsForm = ShowDialog <ManageViewsForm>(reportExportDlg.EditList);
RunUI(() => manageViewsForm.SelectView(reportName));
PauseForScreenShot <ManageViewsForm>("Edit Reports form", 21);
var customizeViewDlg = ShowDialog <ViewEditor>(manageViewsForm.EditView);
PauseForScreenShot <ViewEditor.ChooseColumnsView>("Edit Report form", 22);
RunUI(() => customizeViewDlg.ChooseColumnsTab.AddColumn(PropertyPath.Parse("Proteins!*.Peptides!*.Precursors!*.Results!*.Value")
.Property(AnnotationDef.ANNOTATION_PREFIX + qvalueHeader)));
PauseForScreenShot <ViewEditor.ChooseColumnsView>("Edit Report form with selected columns", 23);
OkDialog(customizeViewDlg, customizeViewDlg.OkDialog);
OkDialog(manageViewsForm, manageViewsForm.Close);
RunUI(() => reportExportDlg.ReportName = reportName);
OkDialog(reportExportDlg, () => reportExportDlg.OkDialog(pathReport, TextUtil.CsvSeparator));
Assert.IsTrue(File.Exists(pathReport));
using (var reader = new StreamReader(pathReport))
{
string line = reader.ReadLine();
Assert.IsNotNull(line);
var fieldHeaders = line.Split(TextUtil.CsvSeparator);
const int qvalueColumnIndex = 6;
Assert.AreEqual(qvalueColumnIndex + 1, fieldHeaders.Length);
Assert.AreEqual(qvalueHeader, fieldHeaders[qvalueColumnIndex]);
int qvalueCount = 0;
while ((line = reader.ReadLine()) != null)
{
var fields = line.Split(TextUtil.CsvSeparator);
double qvalue;
if (double.TryParse(fields[qvalueColumnIndex], out qvalue))
{
qvalueCount++;
}
}
Assert.AreEqual(290, qvalueCount); // PrecursorResults field means 29 peptides * 5 replicates * 2 label types
}
// Open OpenSWATH gold standard dataset
RunUI(() => SkylineWindow.OpenFile(GetTestPath("AQUA4_Human_picked_napedro2-mod2.sky"))); // Not L10N
WaitForDocumentLoaded();
// Perform re-score of DIA data
var manageResults = ShowDialog <ManageResultsDlg>(SkylineWindow.ManageResults);
PauseForScreenShot <ManageResultsDlg>("Manage Results form", 25);
var rescoreResultsDlg = ShowDialog <RescoreResultsDlg>(manageResults.Rescore);
PauseForScreenShot <RescoreResultsDlg>("Re-score Results form", 25);
RunUI(() => rescoreResultsDlg.Rescore(false));
WaitForCondition(10 * 60 * 1000, () => SkylineWindow.Document.Settings.MeasuredResults.IsLoaded); // 10 minutes (usually needs less, but code coverage analysis can be slow)
WaitForClosedForm(rescoreResultsDlg);
WaitForClosedForm(manageResults);
WaitForConditionUI(() => FindOpenForm <AllChromatogramsGraph>() == null);
WaitForDocumentLoaded();
// Train the peak scoring model for the DIA dataset
var reintegrateDlgDia = ShowDialog <ReintegrateDlg>(SkylineWindow.ShowReintegrateDialog);
// Open the previous scoring model for use with the DIA dataset
var editListDia = ShowDialog <EditListDlg <SettingsListBase <PeakScoringModelSpec>, PeakScoringModelSpec> >(
reintegrateDlgDia.EditPeakScoringModel);
RunUI(() => editListDia.SelectItem("test1"));
var editDlgFromSrm = ShowDialog <EditPeakScoringModelDlg>(editListDia.EditItem);
PauseForScreenShot <EditPeakScoringModelDlg.ModelTab>("Edit Peak Scoring Model form SRM model applied to DIA data", 26);
RunUI(() =>
{
ValidateCoefficients(editDlgFromSrm, 0);
for (int j = 0; j < editDlgFromSrm.PeakCalculatorsGrid.Items.Count; ++j)
{
Assert.AreEqual(editDlgFromSrm.PeakCalculatorsGrid.Items[j].PercentContribution, null);
}
int i = 0;
Assert.IsTrue(editDlgFromSrm.IsActiveCell(i++, 0));
Assert.IsFalse(editDlgFromSrm.IsActiveCell(i++, 0));
// Assert.IsFalse(editDlgFromSrm.IsActiveCell(i++, 0));
Assert.IsFalse(editDlgFromSrm.IsActiveCell(i++, 0));
Assert.IsTrue(editDlgFromSrm.IsActiveCell(i++, 0));
Assert.IsTrue(editDlgFromSrm.IsActiveCell(i++, 0));
Assert.IsTrue(editDlgFromSrm.IsActiveCell(i++, 0));
Assert.IsTrue(editDlgFromSrm.IsActiveCell(i++, 0));
Assert.IsFalse(editDlgFromSrm.IsActiveCell(i++, 0));
Assert.IsFalse(editDlgFromSrm.IsActiveCell(i++, 0));
Assert.IsFalse(editDlgFromSrm.IsActiveCell(i++, 0));
Assert.IsFalse(editDlgFromSrm.IsActiveCell(i, 0));
});
OkDialog(editDlgFromSrm, editDlgFromSrm.CancelDialog);
OkDialog(editListDia, editListDia.CancelDialog);
// Train a new model for the DIA dataset
var editDlgDia = ShowDialog <EditPeakScoringModelDlg>(reintegrateDlgDia.AddPeakScoringModel);
RunUI(() =>
{
editDlgDia.UsesDecoys = false;
editDlgDia.UsesSecondBest = true;
editDlgDia.TrainModel();
});
RunUI(() => ValidateCoefficients(editDlgDia, 1));
PauseForScreenShot <EditPeakScoringModelDlg.ModelTab>("Edit Peak Scoring Model form DIA peak scoring dialog with second best", 27);
RunUI(() =>
{
editDlgDia.SelectedGraphTab = 1;
editDlgDia.PeakCalculatorsGrid.SelectRow(2);
editDlgDia.IsFindButtonVisible = true;
editDlgDia.FindMissingValues(2); // Retention times
editDlgDia.PeakScoringModelName = "testDIA";
});
OkDialog(editDlgDia, editDlgDia.OkDialog);
RunUI(() =>
{
reintegrateDlgDia.ReintegrateAll = true;
reintegrateDlgDia.OverwriteManual = true;
});
OkDialog(reintegrateDlgDia, reintegrateDlgDia.OkDialog);
findResultsForm = FormUtil.OpenForms.OfType <FindResultsForm>().FirstOrDefault();
Assert.IsNotNull(findResultsForm);
Assert.AreEqual(34, findResultsForm.ItemCount);
}
