public void DoTestDemux(bool asSmallMolecules)
{
var testFilesDir = new TestFilesDir(TestContext, ZIP_FILE);
string docPathMsx = testFilesDir.GetTestPath("MsxTest.sky");
string dataPathMsx = testFilesDir.GetTestPath("MsxTest.mzML");
string cachePathMsx = ChromatogramCache.FinalPathForName(docPathMsx, null);
FileEx.SafeDelete(cachePathMsx);
SrmDocument docMsx = ResultsUtil.DeserializeDocument(docPathMsx);
if (asSmallMolecules)
{
var refine = new RefinementSettings();
docMsx = refine.ConvertToSmallMolecules(docMsx);
}
var fullScanInitialMsx = docMsx.Settings.TransitionSettings.FullScan;
Assert.IsTrue(fullScanInitialMsx.IsEnabledMsMs);
TestMsx(docMsx, dataPathMsx);
string docPathOverlap = testFilesDir.GetTestPath("OverlapTest.sky");
string dataPathOverlap = testFilesDir.GetTestPath("OverlapTest.mzML");
string cachePathOverlap = ChromatogramCache.FinalPathForName(docPathOverlap, null);
FileEx.SafeDelete(cachePathOverlap);
SrmDocument docOverlap = ResultsUtil.DeserializeDocument(docPathOverlap);
if (asSmallMolecules)
{
var refine = new RefinementSettings();
docOverlap = refine.ConvertToSmallMolecules(docOverlap);
}
var fullScanInitialOverlap = docMsx.Settings.TransitionSettings.FullScan;
Assert.IsTrue(fullScanInitialOverlap.IsEnabledMsMs);
TestOverlap(docOverlap,dataPathOverlap);
}
public void DoTestTargetedMSMSTutorial(RefinementSettings.ConvertToSmallMoleculesMode smallMoleculesTestMode)
{
// Set true to look at tutorial screenshots.
//IsPauseForScreenShots = true;
TestSmallMolecules = false; // Don't need that magic extra node, we have an explict test
ForceMzml = true; // 2-3x faster than raw files for this test.
AsSmallMoleculesTestMode = smallMoleculesTestMode;
if (smallMoleculesTestMode != RefinementSettings.ConvertToSmallMoleculesMode.none)
TestDirectoryName = "AsSmMol_" + smallMoleculesTestMode;
LinkPdf = "https://skyline.gs.washington.edu/labkey/_webdav/home/software/Skyline/%40files/tutorials/TargetedMSMS-2_5.pdf";
TestFilesZipPaths = new[]
{
UseRawFiles
? @"http://skyline.gs.washington.edu/tutorials/TargetedMSMS_2.zip"
: @"http://skyline.gs.washington.edu/tutorials/TargetedMSMSMzml_2.zip",
@"TestTutorial\TargetedMSMSViews.zip"
};
RunFunctionalTest();
}
public void RefineConvertToSmallMoleculeMassesTest()
{
TestFilesDir testFilesDir = new TestFilesDir(TestContext, @"TestA\Refine.zip");
var document = InitRefineDocument(testFilesDir);
var refineSettings = new RefinementSettings();
var converted = refineSettings.ConvertToSmallMolecules(document, RefinementSettings.ConvertToSmallMoleculesMode.masses_only);
AssertEx.ConvertedSmallMoleculeDocumentIsSimilar(document, converted);
}
public void DoAgilentMseChromatogramTest(RefinementSettings.ConvertToSmallMoleculesMode asSmallMolecules)
{
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);
}
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);
// Release file handles
docContainer.Release();
testFilesDir.Dispose();
}
public void RefineConvertToSmallMoleculesTest()
{
// Exercise the code that helps match heavy labeled ion formulas with unlabled
Assert.AreEqual("C5H12NO2S", BioMassCalc.MONOISOTOPIC.StripLabelsFromFormula("C5H9H'3NO2S"));
Assert.IsNull(BioMassCalc.MONOISOTOPIC.StripLabelsFromFormula(""));
Assert.IsNull(BioMassCalc.MONOISOTOPIC.StripLabelsFromFormula(null));
TestFilesDir testFilesDir = new TestFilesDir(TestContext, @"TestA\Refine.zip");
var document = InitRefineDocument(testFilesDir);
var refineSettings = new RefinementSettings();
var converted = refineSettings.ConvertToSmallMolecules(document);
AssertEx.ConvertedSmallMoleculeDocumentIsSimilar(document, converted);
}
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();
}
public void GenerateDecoysTest()
{
TestFilesDir testFilesDir = new TestFilesDir(TestContext, @"TestA\SimpleDecoys.zip");
string docPath = testFilesDir.GetTestPath("SimpleDecoys.sky");
SrmDocument simpleDecoysDoc = ResultsUtil.DeserializeDocument(docPath);
AssertEx.IsDocumentState(simpleDecoysDoc, 0, 1, 18, 18, 56);
// First check right number of decoy peptide groups and transtions are generated
var refineSettings = new RefinementSettings();
int numDecoys = simpleDecoysDoc.PeptideCount;
var decoysDoc = refineSettings.GenerateDecoys(simpleDecoysDoc, numDecoys, DecoyGeneration.ADD_RANDOM);
ValidateDecoys(simpleDecoysDoc, decoysDoc, false);
// Second call to generate decoys to make sure that it removes the original Decoys group and generates a completely new one.
var newDecoysDoc = refineSettings.GenerateDecoys(decoysDoc, numDecoys, DecoyGeneration.ADD_RANDOM);
Assert.AreNotEqual(decoysDoc.PeptideGroups.First(nodePeptideGroup => nodePeptideGroup.IsDecoy),
newDecoysDoc.PeptideGroups.First(nodePeptideGroup => nodePeptideGroup.IsDecoy));
// MS1 document with precursors and variable modifications, shuffled
docPath = testFilesDir.GetTestPath("Ms1FilterTutorial.sky");
SrmDocument variableDecoysDoc = ResultsUtil.DeserializeDocument(docPath);
AssertEx.IsDocumentState(variableDecoysDoc, 0, 11, 50, 51, 153);
numDecoys = variableDecoysDoc.PeptideCount;
var decoysVariableShuffle = refineSettings.GenerateDecoys(variableDecoysDoc, numDecoys, DecoyGeneration.SHUFFLE_SEQUENCE);
ValidateDecoys(variableDecoysDoc, decoysVariableShuffle, true);
// Document with explicit modifications, reversed
SrmDocument docStudy7 = ResultsUtil.DeserializeDocument("Study7.sky", GetType());
AssertEx.IsDocumentState(docStudy7, 0, 7, 11, 22, 66);
numDecoys = docStudy7.PeptideCount;
var decoysExplicitReverse = refineSettings.GenerateDecoys(docStudy7, numDecoys, DecoyGeneration.REVERSE_SEQUENCE);
ValidateDecoys(docStudy7, decoysExplicitReverse, true);
// Random mass shifts with precursors (used to throw an exception due to bad range check that assumed product ions only)
while (true)
{
// As this is random we may need to make a few attempts before we get the values we need
SrmDocument doc = ResultsUtil.DeserializeDocument(testFilesDir.GetTestPath("precursor_decoy_test.sky"));
AssertEx.IsDocumentState(doc, null, 1, 1, 2, 6);
numDecoys = 2;
var decoysRandom = refineSettings.GenerateDecoys(doc, numDecoys, DecoyGeneration.ADD_RANDOM);
// Verify that we successfully set a precursor transition decoy mass outside the allowed range of product transitions
if (decoysRandom.PeptideTransitions.Any(x => x.IsDecoy &&
(x.Transition.DecoyMassShift > Transition.MAX_PRODUCT_DECOY_MASS_SHIFT ||
x.Transition.DecoyMassShift < Transition.MIN_PRODUCT_DECOY_MASS_SHIFT)))
break;
}
}
public void DoTestExportIsolationList(RefinementSettings.ConvertToSmallMoleculesMode asSmallMolecules,
bool asExplicitRetentionTimes = false, bool negativeCharges = false, bool withSLens = false)
{
SmallMoleculeTestMode = asSmallMolecules;
AsSmallMoleculesNegative = (SmallMoleculeTestMode != RefinementSettings.ConvertToSmallMoleculesMode.none) && negativeCharges;
AsExplicitRetentionTimes = asExplicitRetentionTimes;
WithSLens = withSLens;
TestFilesZip = @"TestFunctional\ExportIsolationListTest.zip";
// Avoid trying to reuse the .skyd file while another test is still extant
if (AsExplicitRetentionTimes)
TestDirectoryName = "AsExplicitRetentionTimes";
else if (AsSmallMoleculesNegative)
TestDirectoryName = "AsSmallMoleculesNegative_" + SmallMoleculeTestMode;
else if (SmallMoleculeTestMode != RefinementSettings.ConvertToSmallMoleculesMode.none)
TestDirectoryName = "AsSmallMolecules_" + SmallMoleculeTestMode;
if (WithSLens)
TestDirectoryName += "WithSLens";
RunFunctionalTest();
}
private void DoTestImportSim(bool asSmallMolecules)
{
TestSmallMolecules = false; // Don't need that magic extra node
var testFilesDir = new TestFilesDir(TestContext, ZIP_FILE);
string docPath = testFilesDir.GetTestPath(DOCUMENT_NAME);
string cachePath = ChromatogramCache.FinalPathForName(docPath, null);
FileEx.SafeDelete(cachePath);
SrmDocument doc = ResultsUtil.DeserializeDocument(docPath);
var pepdoc = doc;
if (asSmallMolecules)
{
var refine = new RefinementSettings();
doc = refine.ConvertToSmallMolecules(pepdoc);
}
var docContainer = new ResultsTestDocumentContainer(doc, docPath);
// Import the mzML file and verify Mz range
Import(docContainer, testFilesDir.GetTestPath(RESULTS_NAME), 510, 512);
Import(docContainer, testFilesDir.GetTestPath(RESULTS_NAME2), 555, 557);
}
public void RefineDocumentTest()
{
TestFilesDir testFilesDir = new TestFilesDir(TestContext, @"TestA\Refine.zip");
var document = InitRefineDocument(testFilesDir);
AssertEx.Serializable(document); // This checks a longstanding schema error
// First check a few refinements which should not change the document
var refineSettings = new RefinementSettings();
Assert.AreSame(document, refineSettings.Refine(document));
refineSettings.MinPeptidesPerProtein = (TestSmallMolecules ? 1 : 3); // That magic small molecule node has just one child
Assert.AreSame(document, refineSettings.Refine(document));
refineSettings.MinTransitionsPepPrecursor = (TestSmallMolecules ? 1 : 2);
Assert.AreSame(document, refineSettings.Refine(document));
// Remove the protein with only 3 peptides
refineSettings.MinPeptidesPerProtein = 4;
Assert.AreEqual(document.PeptideGroupCount - 1, refineSettings.Refine(document).PeptideGroupCount);
refineSettings.MinPeptidesPerProtein = 1;
// Remove the precursor with only 2 transitions
refineSettings.MinTransitionsPepPrecursor = 3;
Assert.AreEqual(document.PeptideTransitionGroupCount - 1, refineSettings.Refine(document).PeptideTransitionGroupCount);
refineSettings.MinTransitionsPepPrecursor = null;
// Remove the heavy precursor
refineSettings.RefineLabelType = IsotopeLabelType.heavy;
Assert.AreEqual(document.PeptideTransitionGroupCount - 1, refineSettings.Refine(document).PeptideTransitionGroupCount);
// Remove everything but the heavy precursor
refineSettings.RefineLabelType = IsotopeLabelType.light;
var docRefined = refineSettings.Refine(document);
AssertEx.IsDocumentState(docRefined, 1, 1, 1, 1, 4);
// Perform the operation again without protein removal
refineSettings.MinPeptidesPerProtein = null;
docRefined = refineSettings.Refine(document);
AssertEx.IsDocumentState(docRefined, 1, 4, 1, 1, 4);
refineSettings.RefineLabelType = null;
// Remove repeated peptides
refineSettings.RemoveRepeatedPeptides = true;
Assert.AreEqual(document.PeptideCount - 2, refineSettings.Refine(document).PeptideCount);
// Remove duplicate peptides
refineSettings.RemoveDuplicatePeptides = true;
Assert.AreEqual(document.PeptideCount - 3, refineSettings.Refine(document).PeptideCount);
// Try settings that remove everything from the document
refineSettings = new RefinementSettings { MinPeptidesPerProtein = 20 };
Assert.AreEqual(0, refineSettings.Refine(document).PeptideGroupCount);
refineSettings.MinPeptidesPerProtein = 1;
refineSettings.MinTransitionsPepPrecursor = 20;
Assert.AreEqual(0, refineSettings.Refine(document).PeptideGroupCount);
testFilesDir.Dispose();
}
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 OkDialog()
{
var helper = new MessageBoxHelper(this);
int? minPeptidesPerProtein = null;
if (!string.IsNullOrEmpty(textMinPeptides.Text))
{
int minVal;
if (!helper.ValidateNumberTextBox(tabControl1, 0, textMinPeptides, 0, 10, out minVal))
return;
minPeptidesPerProtein = minVal;
}
int? minTransitionsPerPrecursor = null;
if (!string.IsNullOrEmpty(textMinTransitions.Text))
{
int minVal;
if (!helper.ValidateNumberTextBox(tabControl1, 0, textMinTransitions, 0, 100, out minVal))
return;
minTransitionsPerPrecursor = minVal;
}
bool removeDuplicatePeptides = cbRemoveDuplicatePeptides.Checked;
bool removeRepeatedPeptides = cbRemoveRepeatedPeptides.Checked;
IsotopeLabelType refineLabelType = RefineLabelType;
bool addLabelType = cbAdd.Checked;
// If adding, make sure there is something to add
if (addLabelType && refineLabelType != null && !CanAddLabelType(refineLabelType))
{
MessageDlg.Show(this, string.Format(Resources.RefineDlg_OkDialog_The_label_type__0__cannot_be_added_There_are_no_modifications_for_this_type,
refineLabelType.Name));
tabControl1.SelectedIndex = 0;
comboRefineLabelType.Focus();
return;
}
double? minPeakFoundRatio = null, maxPeakFoundRatio = null;
if (!string.IsNullOrEmpty(textMinPeakFoundRatio.Text))
{
double minVal;
if (!helper.ValidateDecimalTextBox(tabControl1, 1, textMinPeakFoundRatio, 0, 1, out minVal))
return;
minPeakFoundRatio = minVal;
}
if (!string.IsNullOrEmpty(textMaxPeakFoundRatio.Text))
{
double maxVal;
if (!helper.ValidateDecimalTextBox(tabControl1, 1, textMaxPeakFoundRatio, 0, 1, out maxVal))
return;
maxPeakFoundRatio = maxVal;
}
if (minPeakFoundRatio.HasValue && maxPeakFoundRatio.HasValue &&
minPeakFoundRatio.Value > maxPeakFoundRatio.Value)
{
helper.ShowTextBoxError(textMaxPeakFoundRatio,
Resources.RefineDlg_OkDialog__0__must_be_less_than_min_peak_found_ratio);
return;
}
int? maxPepPeakRank = null;
if (!string.IsNullOrEmpty(textMaxPepPeakRank.Text))
{
int maxVal;
if (!helper.ValidateNumberTextBox(tabControl1, 1, textMaxPepPeakRank, 1, 10, out maxVal))
return;
maxPepPeakRank = maxVal;
}
int? maxPeakRank = null;
if (!string.IsNullOrEmpty(textMaxPeakRank.Text))
{
int maxVal;
if (!helper.ValidateNumberTextBox(tabControl1, 1, textMaxPeakRank, 1, 10, out maxVal))
return;
maxPeakRank = maxVal;
}
bool removeMissingResults = radioRemoveMissing.Checked;
double? rtRegressionThreshold = null;
if (!string.IsNullOrEmpty(textRTRegressionThreshold.Text))
{
double minVal;
if (!helper.ValidateDecimalTextBox(tabControl1, 1, textRTRegressionThreshold, 0, 1, out minVal))
return;
rtRegressionThreshold = minVal;
}
double? dotProductThreshold = null;
if (!string.IsNullOrEmpty(textMinDotProduct.Text))
{
double minVal;
if (!helper.ValidateDecimalTextBox(tabControl1, 1, textMinDotProduct, 0, 1, out minVal))
return;
dotProductThreshold = minVal;
}
double? idotProductThreshold = null;
if (!string.IsNullOrEmpty(textMinIdotProduct.Text))
{
double minVal;
if (!helper.ValidateDecimalTextBox(tabControl1, 1, textMinIdotProduct, 0, 1, out minVal))
return;
idotProductThreshold = minVal;
}
bool useBestResult = comboReplicateUse.SelectedIndex > 0;
RefinementSettings = new RefinementSettings
{
MinPeptidesPerProtein = minPeptidesPerProtein,
RemoveDuplicatePeptides = removeDuplicatePeptides,
RemoveRepeatedPeptides = removeRepeatedPeptides,
MinTransitionsPepPrecursor = minTransitionsPerPrecursor,
RefineLabelType = refineLabelType,
AddLabelType = addLabelType,
MinPeakFoundRatio = minPeakFoundRatio,
MaxPeakFoundRatio = maxPeakFoundRatio,
MaxPepPeakRank = maxPepPeakRank,
MaxPeakRank = maxPeakRank,
PreferLargeIons = cbPreferLarger.Checked,
RemoveMissingResults = removeMissingResults,
RTRegressionThreshold = rtRegressionThreshold,
DotProductThreshold = dotProductThreshold,
IdotProductThreshold = idotProductThreshold,
UseBestResult = useBestResult,
AutoPickChildrenAll = (cbAutoPeptides.Checked ? PickLevel.peptides : 0) |
(cbAutoPrecursors.Checked ? PickLevel.precursors : 0) |
(cbAutoTransitions.Checked ? PickLevel.transitions : 0)
};
DialogResult = DialogResult.OK;
Close();
}
public void RefineResultsTest()
{
TestFilesDir testFilesDir = new TestFilesDir(TestContext, @"TestA\Refine.zip");
Settings.Default.RTCalculatorName = Settings.Default.RTScoreCalculatorList.GetDefaults().First().Name;
var document = InitRefineDocument(testFilesDir);
// First check a few refinements which should not change the document
var refineSettings = new RefinementSettings {RTRegressionThreshold = 0.3};
Assert.AreSame(document, refineSettings.Refine(document));
refineSettings.RTRegressionThreshold = null;
refineSettings.DotProductThreshold = Statistics.AngleToNormalizedContrastAngle(0.1); // Convert form original cos(angle) dot-product
Assert.AreSame(document, refineSettings.Refine(document));
refineSettings.DotProductThreshold = null;
refineSettings.MinPeakFoundRatio = 0;
refineSettings.MaxPeakFoundRatio = 1.0;
Assert.AreSame(document, refineSettings.Refine(document));
refineSettings.MinPeakFoundRatio = refineSettings.MaxPeakFoundRatio = null;
// refineSettings.MaxPeakRank = 15; This will remove unmeasured transitions
Assert.AreSame(document, refineSettings.Refine(document));
// Remove nodes without results
refineSettings.MinPeptidesPerProtein = 1;
refineSettings.RemoveMissingResults = true;
var docRefined = refineSettings.Refine(document);
Assert.AreEqual(document.PeptideGroupCount, docRefined.PeptideGroupCount);
// First three children should be unchanged
for (int i = 0; i < 3; i++)
Assert.AreSame(document.Children[i], docRefined.Children[i]);
var nodePepGroupRefined = (PeptideGroupDocNode) docRefined.Children[3];
Assert.AreEqual(1, nodePepGroupRefined.MoleculeCount);
Assert.AreEqual(1, nodePepGroupRefined.TransitionGroupCount);
Assert.AreEqual(5, nodePepGroupRefined.TransitionCount);
// Filter for dot product, ignoring nodes without results
refineSettings.RemoveMissingResults = false;
double dotProductThreshold = Statistics.AngleToNormalizedContrastAngle(0.9); // Convert form original cos(angle) dot-product
refineSettings.DotProductThreshold = dotProductThreshold;
docRefined = refineSettings.Refine(document);
int missingResults = 0;
foreach (var nodeGroup in docRefined.PeptideTransitionGroups)
{
if (!nodeGroup.HasResults || nodeGroup.Results[0] == null)
missingResults++;
else
Assert.IsTrue(nodeGroup.Results[0][0].LibraryDotProduct >= dotProductThreshold);
}
Assert.AreNotEqual(0, missingResults);
Assert.IsTrue(missingResults < docRefined.PeptideTransitionGroupCount);
// Further refine with retention time refinement
refineSettings.RTRegressionThreshold = 0.95;
refineSettings.RTRegressionPrecision = 2; // Backward compatibility
var docRefinedRT = refineSettings.Refine(document);
Assert.AreNotEqual(docRefined.PeptideCount, docRefinedRT.PeptideCount);
// And peak count ratio
refineSettings.MinPeakFoundRatio = 1.0;
var docRefinedRatio = refineSettings.Refine(document);
Assert.AreNotEqual(docRefinedRT.PeptideCount, docRefinedRatio.PeptideCount);
Assert.IsTrue(ArrayUtil.EqualsDeep(docRefinedRatio.Children,
refineSettings.Refine(docRefinedRT).Children));
foreach (var nodeGroup in docRefinedRatio.PeptideTransitionGroups)
{
Assert.IsTrue(nodeGroup.HasResults);
Assert.IsTrue(nodeGroup.HasLibInfo);
Assert.AreEqual(1.0, nodeGroup.Results[0][0].PeakCountRatio);
}
Assert.AreEqual(2, docRefinedRatio.PeptideGroupCount);
Assert.AreEqual(7, docRefinedRatio.PeptideTransitionGroupCount);
// Pick only most intense transtions
refineSettings.MaxPeakRank = 4;
var docRefineMaxPeaks = refineSettings.Refine(document);
Assert.AreEqual(28, docRefineMaxPeaks.PeptideTransitionCount);
// Make sure the remaining peaks really started as the right rank,
// and did not change.
var dictIdTran = new Dictionary<int, TransitionDocNode>();
foreach (var nodeTran in document.PeptideTransitions)
dictIdTran.Add(nodeTran.Id.GlobalIndex, nodeTran);
foreach (var nodeGroup in docRefineMaxPeaks.PeptideTransitionGroups)
{
Assert.AreEqual(refineSettings.MaxPeakRank, nodeGroup.TransitionCount);
foreach (TransitionDocNode nodeTran in nodeGroup.Children)
{
int rank = nodeTran.Results[0][0].Rank;
Assert.IsTrue(rank <= refineSettings.MaxPeakRank);
var nodeTranOld = dictIdTran[nodeTran.Id.GlobalIndex];
Assert.AreEqual(nodeTranOld.Results[0][0].Rank, nodeTran.Results[0][0].Rank);
}
}
// Pick only most intenst peptides
refineSettings = new RefinementSettings { MaxPepPeakRank = 5 };
var docRefinePepMaxPeaks = refineSettings.Refine(document);
// 4 groups, one unmeasured and one with only 3 peptides
Assert.AreEqual(13, docRefinePepMaxPeaks.PeptideCount);
Assert.AreEqual(docRefinePepMaxPeaks.PeptideCount, docRefinePepMaxPeaks.PeptideTransitionGroupCount);
// Add heavy labeled precursors for everything
var settingsNew = docRefineMaxPeaks.Settings.ChangeTransitionFilter(f => f.ChangeAutoSelect(false));
settingsNew = settingsNew.ChangePeptideModifications(m => m.ChangeHeavyModifications(new[]
{
new StaticMod("13C K", "K", ModTerminus.C, null, LabelAtoms.C13, null, null),
new StaticMod("13C R", "R", ModTerminus.C, null, LabelAtoms.C13, null, null),
}));
var docPrepareAdd = docRefineMaxPeaks.ChangeSettings(settingsNew);
refineSettings = new RefinementSettings {RefineLabelType = IsotopeLabelType.heavy, AddLabelType = true};
var docHeavy = refineSettings.Refine(docPrepareAdd);
Assert.AreEqual(docRefineMaxPeaks.PeptideTransitionCount*2, docHeavy.PeptideTransitionCount);
// Verify that the precursors were added with the right transitions
foreach (var nodePep in docHeavy.Peptides)
{
Assert.AreEqual(2, nodePep.Children.Count);
var lightGroup = (TransitionGroupDocNode) nodePep.Children[0];
Assert.AreEqual(IsotopeLabelType.light, lightGroup.TransitionGroup.LabelType);
var heavyGroup = (TransitionGroupDocNode)nodePep.Children[1];
Assert.AreEqual(IsotopeLabelType.heavy, heavyGroup.TransitionGroup.LabelType);
Assert.AreEqual(lightGroup.TransitionGroup.PrecursorCharge,
heavyGroup.TransitionGroup.PrecursorCharge);
Assert.AreEqual(lightGroup.Children.Count, heavyGroup.Children.Count);
for (int i = 0; i < lightGroup.Children.Count; i++)
{
var lightTran = (TransitionDocNode) lightGroup.Children[i];
var heavyTran = (TransitionDocNode) heavyGroup.Children[i];
Assert.AreEqual(lightTran.Transition.FragmentIonName, heavyTran.Transition.FragmentIonName);
}
}
testFilesDir.Dispose();
}
public void RunTestFindNode(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
SrmDocument doc = CreateStudy7Doc();
doc = (new RefinementSettings()).ConvertToSmallMolecules(doc, asSmallMolecules);
var displaySettings = new DisplaySettings(null, false, 0, 0); //, ProteinDisplayMode.ByName);
// Find every other transition, searching down.
List<TransitionDocNode> listTransitions = doc.MoleculeTransitions.ToList();
var pathFound = doc.GetPathTo(0, 0);
int i;
for (i = 0; i < doc.MoleculeTransitionCount; i += 2)
{
pathFound = doc.SearchDocumentForString(pathFound, String.Format("{0:F04}", listTransitions[i].Mz), displaySettings, false, false);
Assert.AreEqual(doc.GetPathTo((int)SrmDocument.Level.Transitions, i), pathFound);
}
// Test wrapping in search down.
pathFound = doc.SearchDocumentForString(pathFound, String.Format("{0:F04}", listTransitions[0].Mz), displaySettings, false, false);
Assert.AreEqual(doc.GetPathTo((int)SrmDocument.Level.Transitions, 0), pathFound);
// Find every other peptide searching up while for each finding one of its children searching down.
pathFound = doc.LastNodePath;
List<PeptideDocNode> listPeptides = new List<PeptideDocNode>();
listPeptides.AddRange(doc.Molecules);
List<TransitionGroupDocNode> listTransitionGroups = new List<TransitionGroupDocNode>();
listTransitionGroups.AddRange(doc.MoleculeTransitionGroups);
for (int x = doc.MoleculeCount; x > 0; x -= 2)
{
// Test case insensitivity.
pathFound = doc.SearchDocumentForString(pathFound, listPeptides[x-1].ToString().ToLower(), displaySettings, true, false);
Assert.AreEqual(doc.GetPathTo((int)SrmDocument.Level.Molecules, x-1), pathFound);
// Test parents can find children.
pathFound = doc.SearchDocumentForString(pathFound, String.Format("{0:F04}", listTransitionGroups[x * 2 - 1].PrecursorMz), displaySettings,
false, true);
Assert.AreEqual(doc.GetPathTo((int)SrmDocument.Level.TransitionGroups, x * 2 - 1), pathFound);
// Test Children can find parents.
pathFound = doc.SearchDocumentForString(pathFound, listPeptides[x - 1].ToString().ToLower(), displaySettings, true, false);
Assert.AreEqual(doc.GetPathTo((int)SrmDocument.Level.Molecules, x - 1), pathFound);
}
// Test wrapping in search up.
pathFound = doc.SearchDocumentForString(pathFound, String.Format("{0:F04}", listTransitionGroups[listTransitionGroups.Count - 1].PrecursorMz),
displaySettings, false, true);
Assert.AreEqual(doc.GetPathTo((int)SrmDocument.Level.TransitionGroups, listTransitionGroups.Count - 1), pathFound);
// Test children can find other parents.
pathFound = doc.SearchDocumentForString(pathFound, listPeptides[0].ToString().ToLowerInvariant(), displaySettings, true, false);
Assert.AreEqual(doc.GetPathTo((int)SrmDocument.Level.Molecules, 0), pathFound);
// Test forward and backward searching in succession
const string heavyText = "heavy";
int countHeavyForward = CountOccurrances(doc, heavyText, displaySettings, false, true);
Assert.IsTrue(countHeavyForward > 0);
Assert.AreEqual(countHeavyForward, CountOccurrances(doc, heavyText, displaySettings, true, true));
// More tests of case insensitive searching
Assert.AreEqual(0, CountOccurrances(doc, heavyText.ToUpperInvariant(), displaySettings, false, true));
Assert.AreEqual(countHeavyForward, CountOccurrances(doc, heavyText.ToUpperInvariant(), displaySettings, false, false));
if (asSmallMolecules != RefinementSettings.ConvertToSmallMoleculesMode.masses_only)
Assert.AreEqual(1, CountOccurrances(doc, "hgflpr", displaySettings, true, false));
// Test mismatched transitions finder
var missmatchFinder = new FindOptions().ChangeCustomFinders(new[] {new MismatchedIsotopeTransitionsFinder()});
Assert.AreEqual(4, CountOccurrances(doc, missmatchFinder, displaySettings));
var docRemoved = (SrmDocument) doc.RemoveChild(doc.Children[1]).RemoveChild(doc.Children[2]);
Assert.AreEqual(0, CountOccurrances(docRemoved, missmatchFinder, displaySettings));
var refineRemoveHeavy = new RefinementSettings {RefineLabelType = IsotopeLabelType.heavy};
var docLight = refineRemoveHeavy.Refine(doc);
Assert.AreEqual(0, CountOccurrances(docLight, missmatchFinder, displaySettings));
var refineRemoveLight = new RefinementSettings {RefineLabelType = IsotopeLabelType.light};
var docHeavy = refineRemoveLight.Refine(doc);
Assert.AreEqual(0, CountOccurrances(docHeavy, missmatchFinder, displaySettings));
var docMulti = ResultsUtil.DeserializeDocument("MultiLabel.sky", typeof(MultiLabelRatioTest));
docMulti = (new RefinementSettings()).ConvertToSmallMolecules(docMulti, asSmallMolecules);
Assert.AreEqual(0, CountOccurrances(docMulti, missmatchFinder, displaySettings));
var pathTranMultiRemove = docMulti.GetPathTo((int) SrmDocument.Level.Transitions, 7);
var tranMultiRemove = docMulti.FindNode(pathTranMultiRemove);
var docMultiRemoved = (SrmDocument) docMulti.RemoveChild(pathTranMultiRemove.Parent, tranMultiRemove);
Assert.AreEqual(2, CountOccurrances(docMultiRemoved, missmatchFinder, displaySettings));
var tranGroupMultiRemove = docMulti.FindNode(pathTranMultiRemove.Parent);
var docMultiGroupRemoved = (SrmDocument)
docMulti.RemoveChild(pathTranMultiRemove.Parent.Parent, tranGroupMultiRemove);
Assert.AreEqual(0, CountOccurrances(docMultiGroupRemoved, missmatchFinder, displaySettings));
}
private static SrmDocument InitFullScanDocument(string docPath, int prot, ref int pep, ref int prec, ref int tran, RefinementSettings.ConvertToSmallMoleculesMode smallMoleculeTestMode)
{
SrmDocument doc = ResultsUtil.DeserializeDocument(docPath);
int? expectedRevisionNumber = 0;
if (smallMoleculeTestMode != RefinementSettings.ConvertToSmallMoleculesMode.none)
{
var refine = new RefinementSettings();
var oldDoc = doc;
AssertEx.Serializable(oldDoc);
doc = refine.ConvertToSmallMolecules(doc, smallMoleculeTestMode);
AssertEx.ConvertedSmallMoleculeDocumentIsSimilar(oldDoc, doc);
AssertEx.Serializable(doc);
expectedRevisionNumber = null;
}
AssertEx.IsDocumentState(doc, expectedRevisionNumber, prot, pep, prec, tran);
return doc;
}
public void DoAsymmetricIsolationTest(RefinementSettings.ConvertToSmallMoleculesMode asSmallMolecules)
{
TestSmallMolecules = false; // We test small molecules explicitly in this test
LocalizationHelper.InitThread(); // TODO: All unit tests should be correctly initialized
var testFilesDir = new TestFilesDir(TestContext, ZIP_FILE);
string docPath = testFilesDir.GetTestPath("Asym_DIA.sky");
string cachePath = ChromatogramCache.FinalPathForName(docPath, null);
FileEx.SafeDelete(cachePath);
SrmDocument doc = ResultsUtil.DeserializeDocument(docPath);
var refine = new RefinementSettings();
doc = refine.ConvertToSmallMolecules(doc, asSmallMolecules);
const int expectedMoleculeCount = 1; // At first small molecules did not support multiple charge states, and this was 2 for that test mode
AssertEx.IsDocumentState(doc, null, 1, expectedMoleculeCount, 2, 4);
var fullScanInitial = doc.Settings.TransitionSettings.FullScan;
Assert.IsTrue(fullScanInitial.IsEnabledMsMs);
Assert.AreEqual(FullScanAcquisitionMethod.DIA, fullScanInitial.AcquisitionMethod);
Assert.AreEqual(25, fullScanInitial.PrecursorFilter);
AssertEx.Serializable(doc);
var docContainer = new ResultsTestDocumentContainer(doc, docPath);
// Import the first RAW file (or mzML for international)
string rawPath = testFilesDir.GetTestPath("Asym_DIA_data.mzML");
var measuredResults = new MeasuredResults(new[] { new ChromatogramSet("Single", new[] { rawPath }) });
TransitionGroupDocNode nodeGroup;
double ratio;
{
// Import with symmetric isolation window
SrmDocument docResults = docContainer.ChangeMeasuredResults(measuredResults, expectedMoleculeCount, 1, 1, 2, 2);
nodeGroup = docResults.MoleculeTransitionGroups.First();
ratio = nodeGroup.Results[0][0].Ratio ?? 0;
// The expected ratio is 1.0, but the symmetric isolation window should produce poor results
if (asSmallMolecules != RefinementSettings.ConvertToSmallMoleculesMode.masses_only) // Can't use labels without a formula
Assert.AreEqual(0.25, ratio, 0.05);
// Revert to original document, and get rid of results cache
Assert.IsTrue(docContainer.SetDocument(doc, docResults, false));
FileEx.SafeDelete(testFilesDir.GetTestPath("Asym_DIA.skyd"));
}
{
// Import with asymmetric isolation window
SrmDocument docAsym = doc.ChangeSettings(doc.Settings.ChangeTransitionFullScan(fullScan =>
fullScan.ChangeAcquisitionMethod(fullScan.AcquisitionMethod, new IsolationScheme("Test asym", 5, 20))));
AssertEx.Serializable(docAsym);
Assert.IsTrue(docContainer.SetDocument(docAsym, doc, false));
SrmDocument docResults = docContainer.ChangeMeasuredResults(measuredResults, expectedMoleculeCount, 1, 1, 2, 2);
nodeGroup = docResults.MoleculeTransitionGroups.First();
ratio = nodeGroup.Results[0][0].Ratio ?? 0;
// Asymmetric should be a lot closer to 1.0
if (asSmallMolecules != RefinementSettings.ConvertToSmallMoleculesMode.masses_only) // Can't use labels without a formula
Assert.AreEqual(1.05, ratio, 0.05);
// Revert to original document, and get rid of results cache
Assert.IsTrue(docContainer.SetDocument(doc, docResults, false));
FileEx.SafeDelete(testFilesDir.GetTestPath("Asym_DIA.skyd"));
}
{
// Import with prespecified isolation windows
var windowList = new List<IsolationWindow>
{
new IsolationWindow(999.2702214, 1024.270221),
new IsolationWindow(1024.27267, 1049.27267)
};
SrmDocument docPrespecified = doc.ChangeSettings(doc.Settings.ChangeTransitionFullScan(fullScan =>
fullScan.ChangeAcquisitionMethod(fullScan.AcquisitionMethod, new IsolationScheme("Test prespecified", windowList))));
AssertEx.Serializable(docPrespecified);
Assert.IsTrue(docContainer.SetDocument(docPrespecified, doc, false));
SrmDocument docResults = docContainer.ChangeMeasuredResults(measuredResults, expectedMoleculeCount, 1, 1, 2, 2);
nodeGroup = docResults.MoleculeTransitionGroups.First();
ratio = nodeGroup.Results[0][0].Ratio ?? 0;
// Asymmetric should be a lot closer to 1.0
if (asSmallMolecules != RefinementSettings.ConvertToSmallMoleculesMode.masses_only) // Can't use labels without a formula
Assert.AreEqual(1.05, ratio, 0.05);
// Revert to original document, and get rid of results cache
Assert.IsTrue(docContainer.SetDocument(doc, docResults, false));
FileEx.SafeDelete(testFilesDir.GetTestPath("Asym_DIA.skyd"));
}
{
// Import with prespecified targets
var windowList = new List<IsolationWindow>
{
new IsolationWindow(999.2702214, 1024.270221, 1004.27),
new IsolationWindow(1024.27267, 1049.27267, 1029.27)
};
SrmDocument docPrespecified = doc.ChangeSettings(doc.Settings.ChangeTransitionFullScan(fullScan =>
fullScan.ChangeAcquisitionMethod(fullScan.AcquisitionMethod, new IsolationScheme("Test target", windowList))));
AssertEx.Serializable(docPrespecified);
Assert.IsTrue(docContainer.SetDocument(docPrespecified, doc, false));
SrmDocument docResults = docContainer.ChangeMeasuredResults(measuredResults, expectedMoleculeCount, 1, 1, 2, 2);
nodeGroup = docResults.MoleculeTransitionGroups.First();
ratio = nodeGroup.Results[0][0].Ratio ?? 0;
// Asymmetric should be a lot closer to 1.0
if (asSmallMolecules != RefinementSettings.ConvertToSmallMoleculesMode.masses_only) // Can't use labels without a formula
Assert.AreEqual(1.05, ratio, 0.05);
// Revert to original document, and get rid of results cache
Assert.IsTrue(docContainer.SetDocument(doc, docResults, false));
FileEx.SafeDelete(testFilesDir.GetTestPath("Asym_DIA.skyd"));
}
{
// Import with ambiguous prespecified targets
var windowList = new List<IsolationWindow>
{
new IsolationWindow(999.2702214, 1024.270221, 1004.27),
new IsolationWindow(1000.0, 1049.27267, 1004.28)
};
SrmDocument docAmbiguous = doc.ChangeSettings(doc.Settings.ChangeTransitionFullScan(fullScan =>
fullScan.ChangeAcquisitionMethod(fullScan.AcquisitionMethod, new IsolationScheme("Test ambiguous", windowList))));
AssertEx.Serializable(docAmbiguous);
Assert.IsTrue(docContainer.SetDocument(docAmbiguous, doc, false));
try
{
docContainer.ChangeMeasuredResults(measuredResults, expectedMoleculeCount, 1, 1, 2, 2);
Assert.Fail("Expected ambiguous isolation targets.");
}
catch (Exception x)
{
AssertEx.AreComparableStrings(Resources.SpectrumFilter_FindFilterPairs_Two_isolation_windows_contain_targets_which_match_the_isolation_target__0__, x.Message, 1);
}
// Revert to original document, and get rid of results cache
Assert.IsTrue(docContainer.SetDocument(doc, docContainer.Document, false));
FileEx.SafeDelete(testFilesDir.GetTestPath("Asym_DIA.skyd"));
}
{
// Import with one isolation window, so one result is discarded.
var windowList = new List<IsolationWindow>
{
new IsolationWindow(999.2702214, 1024.270221),
};
SrmDocument docOneWindow = doc.ChangeSettings(doc.Settings.ChangeTransitionFullScan(fullScan =>
fullScan.ChangeAcquisitionMethod(fullScan.AcquisitionMethod, new IsolationScheme("Test one window", windowList))));
AssertEx.Serializable(docOneWindow);
Assert.IsTrue(docContainer.SetDocument(docOneWindow, doc, false));
SrmDocument docResults = docContainer.ChangeMeasuredResults(measuredResults, 1, 1, 0, 2, 0);
nodeGroup = docResults.MoleculeTransitionGroups.First();
Assert.IsNull(nodeGroup.Results[0][0].Ratio);
// Revert to original document, and get rid of results cache
Assert.IsTrue(docContainer.SetDocument(doc, docResults, false));
FileEx.SafeDelete(testFilesDir.GetTestPath("Asym_DIA.skyd"));
}
testFilesDir.Dispose();
}
private static SrmDocument InitWatersImsMseDocument(TestFilesDir testFilesDir, string skyFile,
RefinementSettings.ConvertToSmallMoleculesMode asSmallMolecules,
out string docPath)
{
docPath = testFilesDir.GetTestPath(skyFile);
var consoleBuffer = new StringBuilder();
var consoleOutput = new CommandStatusWriter(new StringWriter(consoleBuffer));
var cmdline = new CommandLine(consoleOutput);
Assert.IsTrue(cmdline.OpenSkyFile(docPath)); // Handles any path shifts in database files, like our .imdb file
SrmDocument doc = cmdline.Document;
var refine = new RefinementSettings();
doc = refine.ConvertToSmallMolecules(doc, asSmallMolecules);
return doc;
}
private void CheckRoundTrip()
{
// Verify that document roundtrips properly as small molecule
var refine = new RefinementSettings();
var doc = refine.ConvertToSmallMolecules(SkylineWindow.Document, ignoreDecoys: true);
AssertEx.RoundTrip(doc);
// Verify that document roundtrips properly
AssertEx.RoundTrip(SkylineWindow.Document);
}
public void RemoveDuplicatePeptidesTest()
{
// First try removals with no impact
SrmDocument document = new SrmDocument(SrmSettingsList.GetDefault0_6());
IdentityPath path;
SrmDocument docFasta = document.ImportFasta(new StringReader(string.Format(TEXT_FASTA_YEAST_FRAGMENT, 1)),
false, IdentityPath.ROOT, out path);
AssertEx.IsDocumentState(docFasta, 1, 1, 11, 36);
var refinementSettings = new RefinementSettings {RemoveDuplicatePeptides = true};
SrmDocument docFasta2 = refinementSettings.Refine(docFasta);
Assert.AreSame(docFasta, docFasta2);
docFasta2 = docFasta.ImportFasta(new StringReader(string.Format(TEXT_FASTA_YEAST_FRAGMENT, 2)),
false, IdentityPath.ROOT, out path);
// Adding same sequence twice, even with different custom names is ignored
Assert.AreSame(docFasta, docFasta2);
// Try a successful removal of duplicates that leaves no peptides
SrmDocument docPeptides = document.ImportFasta(new StringReader(TEXT_BOVINE_PEPTIDES1),
true, IdentityPath.ROOT, out path);
SrmDocument docPeptides2 = docPeptides.ImportFasta(new StringReader(TEXT_BOVINE_PEPTIDES1),
true, IdentityPath.ROOT, out path);
AssertEx.IsDocumentState(docPeptides2, 2, 2, 26, 82);
SrmDocument docPeptides3 = refinementSettings.Refine(docPeptides2);
Assert.AreNotSame(docPeptides2, docPeptides3);
AssertEx.IsDocumentState(docPeptides3, 3, 2, 0, 0);
// Try again leaving a single peptide
docPeptides2 = docPeptides.ImportFasta(new StringReader(TEXT_BOVINE_PEPTIDES1 + "\n" + TEXT_BOVINE_SINGLE_PEPTIDE),
true, IdentityPath.ROOT, out path);
docPeptides3 = refinementSettings.Refine(docPeptides2);
Assert.AreNotSame(docPeptides2, docPeptides3);
AssertEx.IsDocumentState(docPeptides3, 3, 2, 1, 3);
}
protected override void DoTest()
{
// Creating a MS/MS Spectral Library, p. 1
PeptideSettingsUI peptideSettingsUI = ShowDialog<PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
RunDlg<BuildLibraryDlg>(peptideSettingsUI.ShowBuildLibraryDlg, buildLibraryDlg =>
{
buildLibraryDlg.LibraryPath = TestFilesDirs[0].GetTestPath(@"MethodEdit\Library\"); // Not L10N
buildLibraryDlg.LibraryName = YEAST_ATLAS;
buildLibraryDlg.LibraryCutoff = 0.95;
buildLibraryDlg.LibraryAuthority = "peptideatlas.org"; // Not L10N
buildLibraryDlg.OkWizardPage();
IList<string> inputPaths = new List<string>
{
TestFilesDirs[0].GetTestPath(@"MethodEdit\Yeast_atlas\interact-prob.pep.xml") // Not L10N
};
buildLibraryDlg.AddInputFiles(inputPaths);
buildLibraryDlg.OkWizardPage();
});
PeptideSettingsUI peptideSettingsUI1 = peptideSettingsUI;
RunUI(() =>
{
peptideSettingsUI1.SelectedTab = PeptideSettingsUI.TABS.Library;
peptideSettingsUI1.PickedLibraries = new[] { YEAST_ATLAS };
});
WaitForOpenForm<PeptideSettingsUI>(); // To show Library tab for Forms testing
PauseForScreenShot<PeptideSettingsUI.LibraryTab>("Peptide Settings - Library tab", 4); // Not L10N
RunUI(() => peptideSettingsUI1.SelectedTab = PeptideSettingsUI.TABS.Digest);
WaitForOpenForm<PeptideSettingsUI>(); // To show Digestion tab for Forms testing
// Creating a Background Proteome File, p. 3
FileEx.SafeDelete(TestFilesDirs[0].GetTestPath(@"MethodEdit\FASTA\Yeast" + ProteomeDb.EXT_PROTDB)); // Not L10N
var buildBackgroundProteomeDlg =
ShowDialog<BuildBackgroundProteomeDlg>(peptideSettingsUI.ShowBuildBackgroundProteomeDlg);
RunUI(() =>
{
buildBackgroundProteomeDlg.BackgroundProteomePath =
TestFilesDirs[0].GetTestPath(@"MethodEdit\FASTA\Yeast"); // Not L10N
buildBackgroundProteomeDlg.BackgroundProteomeName = "Yeast"; // Not L10N
buildBackgroundProteomeDlg.AddFastaFile(
TestFilesDirs[0].GetTestPath(@"MethodEdit\FASTA\sgd_yeast.fasta")); // Not L10N
});
PauseForScreenShot<BuildBackgroundProteomeDlg>("Edit Background Proteome form", 5); // Not L10N
OkDialog(buildBackgroundProteomeDlg, buildBackgroundProteomeDlg.OkDialog);
PauseForScreenShot<PeptideSettingsUI.DigestionTab>("Peptide Settings - Digestion tab", 6); // Not L10N
OkDialog(peptideSettingsUI, peptideSettingsUI.OkDialog);
if (!TryWaitForCondition(() =>
SkylineWindow.Document.Settings.PeptideSettings.Libraries.IsLoaded &&
SkylineWindow.Document.Settings.PeptideSettings.Libraries.Libraries.Count > 0))
{
Assert.Fail("Timed out loading libraries: libCount={0}, NotLoadedExplained={1}",
SkylineWindow.Document.Settings.PeptideSettings.Libraries.Libraries.Count,
SkylineWindow.Document.Settings.PeptideSettings.Libraries.IsNotLoadedExplained ?? "<null>");
}
WaitForCondition(() =>
{
var peptideSettings = SkylineWindow.Document.Settings.PeptideSettings;
var backgroundProteome = peptideSettings.BackgroundProteome;
return (backgroundProteome.HasDigestion(peptideSettings));
}, "backgroundProteome.HasDigestion");
// Wait a bit in case web access is turned on and backgroundProteome is actually resolving protein metadata
int millis = (AllowInternetAccess ? 300 : 60) * 1000;
WaitForCondition(millis, () => !SkylineWindow.Document.Settings.PeptideSettings.BackgroundProteome.NeedsProteinMetadataSearch, "backgroundProteome.NeedsProteinMetadataSearch");
// Pasting FASTA Sequences, p. 5
RunUI(() => SetClipboardFileText(@"MethodEdit\FASTA\fasta.txt")); // Not L10N
// New in v0.7 : Skyline asks about removing empty proteins.
using (new CheckDocumentState(35, 25, 25, 75))
{
var emptyProteinsDlg = ShowDialog<EmptyProteinsDlg>(SkylineWindow.Paste);
RunUI(() => emptyProteinsDlg.IsKeepEmptyProteins = true);
OkDialog(emptyProteinsDlg, emptyProteinsDlg.OkDialog);
WaitForCondition(millis, () => SkylineWindow.SequenceTree.Nodes.Count > 4);
}
RunUI(() =>
{
SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SequenceTree.Nodes[3].Nodes[0];
});
RestoreViewOnScreen(07);
PauseForScreenShot("Main window", 7); // Not L10N
RunUI(() =>
{
Settings.Default.ShowBIons = true;
SkylineWindow.SequenceTree.SelectedNode.Expand();
SkylineWindow.SequenceTree.SelectedNode =
SkylineWindow.SequenceTree.SelectedNode.Nodes[0].Nodes[1];
});
PauseForScreenShot("Main window showing effect of selection on Library Match graph", 8); // Not L10N
CheckTransitionCount("VDIIANDQGNR", 3); // Not L10N
using (new CheckDocumentState(35, 28, 31, 155))
{
var transitionSettingsUI = ShowDialog<TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
RunUI(() =>
{
transitionSettingsUI.SelectedTab = TransitionSettingsUI.TABS.Filter;
transitionSettingsUI.PrecursorCharges = "2, 3"; // Not L10N
transitionSettingsUI.ProductCharges = "1"; // Not L10N
transitionSettingsUI.FragmentTypes = "y, b"; // Not L10N
});
WaitForOpenForm<TransitionSettingsUI>(); // To show Filter tab for Forms testing
PauseForScreenShot<TransitionSettingsUI.FilterTab>("Transition Settings - Filter tab", 9); // Not L10N
RunUI(() =>
{
transitionSettingsUI.SelectedTab = TransitionSettingsUI.TABS.Library;
transitionSettingsUI.IonCount = 5;
});
PauseForScreenShot<TransitionSettingsUI.LibraryTab>("Transition Settings - Library tab", 10); // Not L10N
OkDialog(transitionSettingsUI, transitionSettingsUI.OkDialog);
}
PauseForScreenShot("Targets tree clipped from main window", 11); // Not L10N
CheckTransitionCount("VDIIANDQGNR", 5); // Not L10N
// Using a Public Spectral Library, p. 9
peptideSettingsUI = ShowDialog<PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
var editListUI =
ShowDialog<EditListDlg<SettingsListBase<LibrarySpec>, LibrarySpec>>(peptideSettingsUI.EditLibraryList);
var addLibUI = ShowDialog<EditLibraryDlg>(editListUI.AddItem);
RunUI(() => addLibUI.LibrarySpec =
new BiblioSpecLibSpec(YEAST_GPM, TestFilesDirs[0].GetTestPath(@"MethodEdit\Library\yeast_cmp_20.hlf"))); // Not L10N
OkDialog(addLibUI, addLibUI.OkDialog);
WaitForClosedForm(addLibUI);
OkDialog(editListUI, editListUI.OkDialog);
// Limiting Peptides per Protein, p. 11
using (new CheckDocumentState(35, 182, 219, 1058))
{
RunUI(() =>
{
peptideSettingsUI.SelectedTab = PeptideSettingsUI.TABS.Library;
peptideSettingsUI.PickedLibraries = new[] {YEAST_ATLAS, YEAST_GPM};
});
PauseForScreenShot<PeptideSettingsUI.LibraryTab>("Peptide Settings - Library tab", 12); // Not L10N
OkDialog(peptideSettingsUI, peptideSettingsUI.OkDialog);
Assert.IsTrue(WaitForCondition(
() =>
SkylineWindow.Document.Settings.PeptideSettings.Libraries.IsLoaded &&
SkylineWindow.Document.Settings.PeptideSettings.Libraries.Libraries.Count > 0));
}
using (new CheckDocumentState(35, 47, 47, 223, 2, true)) // Wait for change loaded, and expect 2 document revisions.
{
RunDlg<PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI, peptideSettingsUI2 =>
{
peptideSettingsUI2.PickedLibraries = new[] {YEAST_GPM};
peptideSettingsUI2.LimitPeptides = true;
peptideSettingsUI2.RankID = XHunterLibSpec.PEP_RANK_EXPECT;
peptideSettingsUI2.PeptidesPerProtein = 3;
peptideSettingsUI2.OkDialog();
});
}
using (new CheckDocumentState(19, 47, 47, 223))
{
RunUI(() =>
{
var refinementSettings = new RefinementSettings {MinPeptidesPerProtein = 1};
SkylineWindow.ModifyDocument("Remove empty proteins", refinementSettings.Refine); // Not L10N
});
}
// Inserting a Protein List, p. 11
using (new CheckDocumentState(36, 58, 58, 278))
{
PasteDlg pasteProteinsDlg = ShowDialog<PasteDlg>(SkylineWindow.ShowPasteProteinsDlg);
RunUI(() =>
{
var node = SkylineWindow.SequenceTree.Nodes[SkylineWindow.SequenceTree.Nodes.Count - 1];
SkylineWindow.SequenceTree.SelectedNode = node;
SetClipboardFileText(@"MethodEdit\FASTA\Protein list.txt"); // Not L10N
pasteProteinsDlg.SelectedPath = SkylineWindow.SequenceTree.SelectedPath;
pasteProteinsDlg.PasteProteins();
});
PauseForScreenShot<PasteDlg.ProteinListTab>("Insert Protein List - For Screenshot, select last (empty) item in list", 14); // Not L10N
OkDialog(pasteProteinsDlg, pasteProteinsDlg.OkDialog);
}
using (new CheckDocumentState(24, 58, 58, 278))
{
RunUI(() =>
{
var refinementSettings = new RefinementSettings {MinPeptidesPerProtein = 1};
SkylineWindow.ModifyDocument("Remove empty proteins", refinementSettings.Refine); // Not L10N
});
}
// Inserting a Peptide List, p. 13
using (new CheckDocumentState(25, 70, 70, 338))
{
RunUI(() =>
{
SetClipboardFileText(@"MethodEdit\FASTA\Peptide list.txt"); // Not L10N
SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SequenceTree.Nodes[0];
SkylineWindow.Paste();
// ReSharper disable LocalizableElement
SkylineWindow.SequenceTree.Nodes[0].Text = "Primary Peptides"; // Not L10N
// ReSharper restore LocalizableElement
});
FindNode("TLTAQSMQNSTQSAPNK"); // Not L10N
PauseForScreenShot("Main window", 16); // Not L10N
}
using (new CheckDocumentState(35, 70, 70, 338))
{
RunUI(() => SkylineWindow.Undo());
PasteDlg pastePeptidesDlg = ShowDialog<PasteDlg>(SkylineWindow.ShowPastePeptidesDlg);
RunUI(pastePeptidesDlg.PastePeptides);
PauseForScreenShot<PasteDlg.PeptideListTab>("Insert Peptide List - For screenshot, select last (empty) line in list", 17); // Not L10N
OkDialog(pastePeptidesDlg, pastePeptidesDlg.OkDialog);
}
// Simple Refinement, p. 16
var findPeptideDlg = ShowDialog<FindNodeDlg>(SkylineWindow.ShowFindNodeDlg);
RunUI(() => findPeptideDlg.SearchString = "IPEE"); // Not L10N
OkDialog(findPeptideDlg, () =>
{
findPeptideDlg.FindNext();
findPeptideDlg.Close();
});
PauseForScreenShot<GraphSpectrum>("Library Match graph metafile", 18); // Not L10N
using (new CheckDocumentState(35, 64, 64, 320))
{
RefineDlg refineDlg = ShowDialog<RefineDlg>(SkylineWindow.ShowRefineDlg);
RunUI(() => refineDlg.MinTransitions = 5);
OkDialog(refineDlg, refineDlg.OkDialog);
PauseForScreenShot("29/35 prot 50/64 pep 50/64 prec 246/320 tran", 18); // Not L10N
}
// Checking Peptide Uniqueness, p. 18
RunUI(() =>
{
var node = SkylineWindow.SequenceTree.Nodes[SkylineWindow.SequenceTree.Nodes.Count - (TestSmallMolecules ? 3 : 2)];
SkylineWindow.SequenceTree.SelectedNode = node;
});
using (new CheckDocumentState(34, 63, 63, 315))
{
var uniquePeptidesDlg = ShowDialog<UniquePeptidesDlg>(SkylineWindow.ShowUniquePeptidesDlg);
WaitForConditionUI(() => uniquePeptidesDlg.GetDataGridView().RowCount == 1);
RunUI(() =>
{
Assert.AreEqual(1, uniquePeptidesDlg.GetDataGridView().RowCount);
Assert.AreEqual(7, uniquePeptidesDlg.GetDataGridView().ColumnCount);
});
PauseForScreenShot<UniquePeptidesDlg>("Unique Peptides form", 19); // Not L10N
OkDialog(uniquePeptidesDlg, uniquePeptidesDlg.OkDialog);
RunUI(() => SkylineWindow.EditDelete());
}
// Protein Name Auto-Completion
PauseForScreenShot("(fig. 1): For screenshot, click at bottom of document tree, type 'ybl087' and see the autocomplete text. Make sure to undo this new entry before proceeding.", 20); // Not L10N
TestAutoComplete("ybl087", 0); // Not L10N
var peptideGroups = new List<PeptideGroupDocNode>(Program.ActiveDocument.PeptideGroups);
Assert.AreEqual("YBL087C", peptideGroups[peptideGroups.Count - 1].Name); // Not L10N
// Protein Description Auto-Completion
PauseForScreenShot("(fig. 2): For screenshot, click at bottom of document tree, type 'eft2' and see the autocomplete text, then down-arrow twice. Make sure to undo this new entry before proceeding.", 20); // Not L10N
TestAutoComplete("eft2", 0); // Sorting logic puts this at the 0th entry in the list - Not L10N
peptideGroups = new List<PeptideGroupDocNode>(Program.ActiveDocument.PeptideGroups);
Assert.AreEqual("YDR385W", peptideGroups[peptideGroups.Count - 1].Name); // Not L10N
// Peptide Sequence Auto-Completion, p. 21
TestAutoComplete("IQGP", 0); // Not L10N
var peptides = new List<PeptideDocNode>(Program.ActiveDocument.Peptides);
Assert.AreEqual("K.AYLPVNESFGFTGELR.Q [769, 784]", peptides[peptides.Count - 1].Peptide.ToString()); // Not L10N
PauseForScreenShot("(fig. 1) - For screenshot, click at the bottom of the document tree", 21); // Not L10N
// Pop-up Pick-Lists, p. 21
using (new CheckDocumentState(36, 71, 71, 355))
{
RunUI(() =>
{
var node = SkylineWindow.SequenceTree.Nodes[SkylineWindow.SequenceTree.Nodes.Count - (TestSmallMolecules ? 4 : 3)];
SkylineWindow.SequenceTree.SelectedNode = node;
});
var pickList = ShowDialog<PopupPickList>(SkylineWindow.ShowPickChildrenInTest);
RunUI(() =>
{
pickList.ApplyFilter(false);
pickList.SetItemChecked(8, true);
pickList.AutoManageChildren = false; // TODO: Because calling SetItemChecked does not do this
});
PauseForScreenShot<PopupPickList>("(fig. 2) - YBL087C Peptides picklist", 21); // Not L10N
RunUI(pickList.OnOk);
}
using (new CheckDocumentState(36, 71, 71, 355))
{
RunUI(() =>
{
SkylineWindow.SequenceTree.Nodes[34].ExpandAll();
var node =
SkylineWindow.SequenceTree.Nodes[34].Nodes[0].Nodes[0];
SkylineWindow.SequenceTree.SelectedNode = node;
});
var pickList1 = ShowDialog<PopupPickList>(SkylineWindow.ShowPickChildrenInTest);
RunUI(() =>
{
pickList1.SearchString = "y"; // Not L10N
pickList1.SetItemChecked(0, false);
pickList1.SetItemChecked(1, false);
pickList1.ApplyFilter(false);
pickList1.ToggleFind();
pickList1.SearchString = "b ++"; // Not L10N
pickList1.SetItemChecked(4, true);
pickList1.SetItemChecked(6, true);
});
PauseForScreenShot<PopupPickList>("b ++ filtered picklist", 22); // Not L10N
RunUI(pickList1.OnOk);
}
// Bigger Picture, p. 22. Drag and Drop, p. 23
RunUI(() =>
{
ITipProvider nodeTip = SkylineWindow.SequenceTree.SelectedNode as ITipProvider;
Assert.IsTrue(nodeTip != null && nodeTip.HasTip);
var nodeName = SkylineWindow.SequenceTree.Nodes[1].Name;
IdentityPath selectPath;
SkylineWindow.ModifyDocument("Drag and drop", // Not L10N
doc => doc.MoveNode(SkylineWindow.Document.GetPathTo(0, 1), SkylineWindow.Document.GetPathTo(0, 0), out selectPath));
Assert.IsTrue(SkylineWindow.SequenceTree.Nodes[0].Name == nodeName);
});
FindNode(string.Format("L [b5] - {0:F04}+", 484.3130)); // Not L10N - may be localized " (rank 3)"
PauseForScreenShot("For Screenshots, First hover over YBL087C, then over 672.671+++", 23); // Not L10N
// Preparing to Measure, p. 25
RunDlg<TransitionSettingsUI>(() => SkylineWindow.ShowTransitionSettingsUI(TransitionSettingsUI.TABS.Prediction), transitionSettingsUI =>
{
transitionSettingsUI.RegressionCE = Settings.Default.GetCollisionEnergyByName("ABI 4000 QTrap"); // Not L10N
transitionSettingsUI.RegressionDP = Settings.Default.GetDeclusterPotentialByName("ABI"); // Not L10N
transitionSettingsUI.InstrumentMaxMz = 1800;
transitionSettingsUI.OkDialog();
});
RunUI(() => SkylineWindow.SaveDocument(TestFilesDirs[0].GetTestPath("MethodEdit Tutorial.sky"))); // Not L10N
var exportDialog = ShowDialog<ExportMethodDlg>(() =>
SkylineWindow.ShowExportMethodDialog(ExportFileType.List));
RunUI(() =>
{
exportDialog.ExportStrategy = ExportStrategy.Buckets;
exportDialog.MethodType = ExportMethodType.Standard;
exportDialog.OptimizeType = ExportOptimize.NONE;
exportDialog.IgnoreProteins = true;
exportDialog.MaxTransitions = 75;
});
PauseForScreenShot<ExportMethodDlg.TransitionListView>("Export Transition List form", 25); // Not L10N
const string basename = "Yeast_list"; // Not L10N
OkDialog(exportDialog, () => exportDialog.OkDialog(TestFilesDirs[0].GetTestPath(basename))); // write Yeast_list_000n.csv
// check the output files
for (int n = 0; n++ < 5;)
{
var csvname = String.Format("{0}_{1}.csv", basename, n.ToString("D4")); // Not L10N
// AssertEx.FieldsEqual is hard-coded with CultureInfo.InvariantCulture, but so is transition list CSV export, so OK
using (TextReader actual = new StreamReader(TestFilesDirs[0].GetTestPath(csvname)))
using (TextReader target = new StreamReader(TestFilesDirs[1].GetTestPath(csvname)))
{
AssertEx.FieldsEqual(target, actual, 6, null, true, TestSmallMolecules ? 3 : 0);
}
}
}
public void DoFullScanSettingsTest(RefinementSettings.ConvertToSmallMoleculesMode asSmallMolecules,
out List<SrmDocument> docCheckPoints)
{
TestSmallMolecules = false; // Don't need that magic extra node, we have an explicit test
docCheckPoints = new List<SrmDocument>();
var doc = ResultsUtil.DeserializeDocument("MultiLabel.sky", GetType());
var refine = new RefinementSettings();
doc = refine.ConvertToSmallMolecules(doc, asSmallMolecules);
Assert.IsFalse(doc.MoleculeTransitionGroups.Any(nodeGroup => nodeGroup.IsotopeDist != null));
AssertEx.Serializable(doc, AssertEx.Cloned);
double c13Delta = BioMassCalc.MONOISOTOPIC.GetMass(BioMassCalc.C13) -
BioMassCalc.MONOISOTOPIC.GetMass(BioMassCalc.C);
double n15Delta = BioMassCalc.MONOISOTOPIC.GetMass(BioMassCalc.N15) -
BioMassCalc.MONOISOTOPIC.GetMass(BioMassCalc.N);
// Verify isotope distributions calculated when MS1 filtering enabled
var enrichments = IsotopeEnrichments.DEFAULT;
var docIsotopes = doc.ChangeSettings(doc.Settings.ChangeTransitionFullScan(fs =>
fs.ChangePrecursorIsotopes(FullScanPrecursorIsotopes.Count, 3, enrichments)));
docCheckPoints.Add(docIsotopes);
Assert.AreEqual(FullScanMassAnalyzerType.tof,
docIsotopes.Settings.TransitionSettings.FullScan.PrecursorMassAnalyzer);
Assert.IsFalse(docIsotopes.MoleculeTransitionGroups.Any(nodeGroup => nodeGroup.IsotopeDist == null));
foreach (var nodeGroup in docIsotopes.MoleculeTransitionGroups)
{
Assert.AreEqual(3, nodeGroup.Children.Count);
var isotopePeaks = nodeGroup.IsotopeDist;
Assert.IsNotNull(isotopePeaks);
Assert.IsTrue(nodeGroup.HasIsotopeDist);
// The peaks should always includ at least M-1
Assert.IsTrue(isotopePeaks.MassIndexToPeakIndex(0) > 0);
// Within 2.5% of 100% of the entire isotope distribution
Assert.AreEqual(1.0, isotopePeaks.ExpectedProportions.Sum(), 0.025);
// Precursor mass and m/z values are expected to match exactly (well, within XML roundtrip accuracy anyway)
Assert.AreEqual(nodeGroup.PrecursorMz, nodeGroup.IsotopeDist.GetMZI(0), SequenceMassCalc.MassTolerance);
Assert.AreEqual(nodeGroup.PrecursorMz, nodeGroup.TransitionGroup.IsCustomIon ?
BioMassCalc.CalculateIonMz(nodeGroup.IsotopeDist.GetMassI(0),
nodeGroup.TransitionGroup.PrecursorCharge) :
SequenceMassCalc.GetMZ(nodeGroup.IsotopeDist.GetMassI(0),
nodeGroup.TransitionGroup.PrecursorCharge), SequenceMassCalc.MassTolerance);
// Check isotope distribution masses
for (int i = 1; i < isotopePeaks.CountPeaks; i++)
{
int massIndex = isotopePeaks.PeakIndexToMassIndex(i);
Assert.IsTrue(isotopePeaks.GetMZI(massIndex - 1) < isotopePeaks.GetMZI(massIndex));
double massDelta = GetMassDelta(isotopePeaks, massIndex);
if (nodeGroup.TransitionGroup.LabelType.IsLight)
{
// All positive should be close to 13C - C, and 0 should be the same as the next delta
double expectedDelta = (massIndex > 0 ? c13Delta : GetMassDelta(isotopePeaks, massIndex + 1));
Assert.AreEqual(expectedDelta, massDelta, 0.001);
}
else if (nodeGroup.TransitionGroup.LabelType.Name.Contains("15N"))
{
// All positive should be close to 13C, and all negative 15N
double expectedDelta = (massIndex > 0 ? c13Delta : n15Delta);
Assert.AreEqual(expectedDelta, massDelta, 0.0015);
}
else if (massIndex == 0)
{
double expectedDelta = (isotopePeaks.GetProportionI(massIndex - 1) == 0
? GetMassDelta(isotopePeaks, massIndex + 1)
: 1.0017);
Assert.AreEqual(expectedDelta, massDelta, 0.001);
}
else
{
Assert.AreEqual(c13Delta, massDelta, 0.001);
}
}
}
AssertEx.Serializable(docIsotopes, AssertEx.Cloned);
// Narrow the resolution, and verify that predicted proportion of the isotope
// distribution captured is reduced for all precursors
var docIsotopesFt = docIsotopes.ChangeSettings(docIsotopes.Settings.ChangeTransitionFullScan(fs =>
fs.ChangePrecursorResolution(FullScanMassAnalyzerType.ft_icr, 500 * 1000, 400)));
docCheckPoints.Add(docIsotopesFt);
var tranGroupsOld = docIsotopes.MoleculeTransitionGroups.ToArray();
var tranGroupsNew = docIsotopesFt.MoleculeTransitionGroups.ToArray();
Assert.AreEqual(tranGroupsOld.Length, tranGroupsNew.Length);
for (int i = 0; i < tranGroupsOld.Length; i++)
{
Assert.AreNotSame(tranGroupsOld[i], tranGroupsNew[i]);
Assert.AreNotSame(tranGroupsOld[i].IsotopeDist, tranGroupsNew[i].IsotopeDist);
Assert.IsTrue(tranGroupsOld[i].IsotopeDist.ExpectedProportions.Sum() >
tranGroupsNew[i].IsotopeDist.ExpectedProportions.Sum());
}
// Use Min % of base peak and verify variation in transitions used
const float minPercent1 = 10;
var docIsotopesP1 = docIsotopes.ChangeSettings(docIsotopes.Settings.ChangeTransitionFullScan(fs =>
fs.ChangePrecursorIsotopes(FullScanPrecursorIsotopes.Percent, minPercent1, enrichments)));
docCheckPoints.Add(docIsotopesP1);
tranGroupsNew = docIsotopesP1.MoleculeTransitionGroups.ToArray();
int maxTran = 0;
for (int i = 0; i < tranGroupsOld.Length; i++)
{
// Isotope distributions should not have changed
var isotopePeaks = tranGroupsNew[i].IsotopeDist;
Assert.AreSame(tranGroupsOld[i].IsotopeDist, isotopePeaks);
// Expected transitions should be present
maxTran = Math.Max(maxTran, tranGroupsNew[i].Children.Count);
foreach (TransitionDocNode nodeTran in tranGroupsNew[i].Children)
{
int massIndex = nodeTran.Transition.MassIndex;
Assert.IsTrue(minPercent1 <= isotopePeaks.GetProportionI(massIndex)*100.0/isotopePeaks.BaseMassPercent);
}
}
Assert.AreEqual(5, maxTran);
AssertEx.Serializable(docIsotopesP1, AssertEx.Cloned); // Express any failure in terms of XML diffs
// Use 10%, and check that 15N modifications all have M-1
const float minPercent2 = 5;
var docIsotopesP2 = docIsotopesP1.ChangeSettings(docIsotopesP1.Settings.ChangeTransitionFullScan(fs =>
fs.ChangePrecursorIsotopes(FullScanPrecursorIsotopes.Percent, minPercent2, enrichments)));
docCheckPoints.Add(docIsotopesP2);
foreach (var nodeGroup in docIsotopesP2.MoleculeTransitionGroups)
{
var firstChild = (TransitionDocNode) nodeGroup.Children[0];
if (nodeGroup.TransitionGroup.LabelType.Name.EndsWith("15N"))
Assert.AreEqual(-1, firstChild.Transition.MassIndex);
else
Assert.AreNotEqual(-1, firstChild.Transition.MassIndex);
}
AssertEx.Serializable(docIsotopesP2, AssertEx.Cloned);
// Use lower enrichment of 13C, and verify that this add M-1 for 13C labeled precursors
var enrichmentsLow13C = enrichments.ChangeEnrichment(new IsotopeEnrichmentItem(BioMassCalc.C13, 0.9));
var docIsotopesLow13C = docIsotopesP1.ChangeSettings(docIsotopesP1.Settings.ChangeTransitionFullScan(fs =>
fs.ChangePrecursorIsotopes(FullScanPrecursorIsotopes.Percent, minPercent2, enrichmentsLow13C)));
tranGroupsNew = docIsotopesLow13C.MoleculeTransitionGroups.ToArray();
for (int i = 0; i < tranGroupsOld.Length; i++)
{
var nodeGroup = tranGroupsNew[i];
if (!Equals(nodeGroup.TransitionGroup.LabelType.Name, "heavy"))
Assert.AreSame(tranGroupsOld[i].IsotopeDist, nodeGroup.IsotopeDist);
else
{
var firstChild = (TransitionDocNode)nodeGroup.Children[0];
Assert.IsTrue(firstChild.Transition.MassIndex < 0);
}
}
AssertEx.Serializable(docIsotopesLow13C, AssertEx.Cloned); // Express any failure as XML diffs
// Use 0%, and check that everything has M-1 and lower
var enrichmentsLow = enrichmentsLow13C.ChangeEnrichment(new IsotopeEnrichmentItem(BioMassCalc.N15, 0.97));
var docIsotopesLowP0 = docIsotopesP1.ChangeSettings(docIsotopesP1.Settings.ChangeTransitionFullScan(fs =>
fs.ChangePrecursorIsotopes(FullScanPrecursorIsotopes.Percent, 0, enrichmentsLow)));
docCheckPoints.Add(docIsotopesLowP0);
foreach (var nodeGroup in docIsotopesLowP0.MoleculeTransitionGroups)
{
Assert.AreEqual(nodeGroup.IsotopeDist.CountPeaks, nodeGroup.Children.Count);
var firstChild = (TransitionDocNode)nodeGroup.Children[0];
if (nodeGroup.TransitionGroup.LabelType.IsLight)
Assert.AreEqual(-1, firstChild.Transition.MassIndex);
else
Assert.IsTrue(-1 > firstChild.Transition.MassIndex);
}
AssertEx.Serializable(docIsotopesLowP0, AssertEx.Cloned);
// Test a document with variable and heavy modifications, which caused problems for
// the original implementation
var docVariable = ResultsUtil.DeserializeDocument("HeavyVariable.sky", GetType());
Assert.IsFalse(docVariable.MoleculeTransitionGroups.Any(nodeGroup => nodeGroup.IsotopeDist == null));
foreach (var nodeGroup in docVariable.MoleculeTransitionGroups)
{
var isotopePeaks = nodeGroup.IsotopeDist;
Assert.IsNotNull(isotopePeaks);
// The peaks should always includ at least M-1
Assert.IsTrue(isotopePeaks.MassIndexToPeakIndex(0) > 0);
// Precursor mass and m/z values are expected to match exactly (well, within XML roundtrip tolerance anyway)
Assert.AreEqual(nodeGroup.PrecursorMz, nodeGroup.IsotopeDist.GetMZI(0), SequenceMassCalc.MassTolerance);
// Check isotope distribution masses
for (int i = 1; i < isotopePeaks.CountPeaks; i++)
{
int massIndex = isotopePeaks.PeakIndexToMassIndex(i);
Assert.IsTrue(isotopePeaks.GetMZI(massIndex - 1) < isotopePeaks.GetMZI(massIndex));
double massDelta = GetMassDelta(isotopePeaks, massIndex);
bool containsSulfur = nodeGroup.TransitionGroup.Peptide.IsCustomIon
? (nodeGroup.CustomIon.Formula.IndexOfAny("S".ToCharArray()) != -1)
: (nodeGroup.TransitionGroup.Peptide.Sequence.IndexOfAny("CM".ToCharArray()) != -1);
if (massIndex == 0)
{
double expectedDelta = (isotopePeaks.GetProportionI(massIndex - 1) == 0
? GetMassDelta(isotopePeaks, massIndex + 1)
: 1.0017);
Assert.AreEqual(expectedDelta, massDelta, 0.001);
}
else if (!containsSulfur || massIndex == 1)
{
Assert.AreEqual(c13Delta, massDelta, 0.001);
}
else
{
Assert.AreEqual(1.00075, massDelta, 0.001);
}
}
}
docCheckPoints.Add(docVariable);
}
private void DoFullScanFilterTest(RefinementSettings.ConvertToSmallMoleculesMode asSmallMolecules,
out List<SrmDocument> docCheckpoints, bool centroided = false)
{
docCheckpoints = new List<SrmDocument>();
TestSmallMolecules = false; // We test small molecules explicitly
var testFilesDir = new TestFilesDir(TestContext, ZIP_FILE);
string docPath = testFilesDir.GetTestPath("BSA_Protea_label_free_20100323_meth3_multi.sky");
var expectedPepCount = 7;
var expectedTransGroupCount = 7;
var expectedTransCount = 49;
var doc = InitFullScanDocument(docPath, 2, ref expectedPepCount, ref expectedTransGroupCount, ref expectedTransCount, asSmallMolecules);
if (centroided && ExtensionTestContext.CanImportThermoRaw)
{
const double ppm20 = 20.0;
doc = doc.ChangeSettings(doc.Settings.ChangeTransitionFullScan(fs =>
fs.ChangePrecursorResolution(FullScanMassAnalyzerType.centroided, ppm20, 0)));
}
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[] {new MsDataFilePath(rawPath)})});
SrmDocument docResults = docContainer.ChangeMeasuredResults(measuredResults, 3, 3, 21);
docCheckpoints.Add(docResults);
// Refilter allowing multiple precursors per spectrum
SrmDocument docMulti = doc.ChangeSettings(doc.Settings.ChangeTransitionFullScan(
fs => fs.ChangeAcquisitionMethod(FullScanAcquisitionMethod.DIA, new IsolationScheme("Test", 2))));
AssertEx.Serializable(docMulti, AssertEx.DocumentCloned);
// Release data cache file
Assert.IsTrue(docContainer.SetDocument(docMulti, docResults));
// And remove it
FileEx.SafeDelete(Path.ChangeExtension(docPath, ChromatogramCache.EXT));
docCheckpoints.Add(docContainer.ChangeMeasuredResults(measuredResults, 6, 6, 38));
// Import full scan Orbi-Velos data
docPath = testFilesDir.GetTestPath("BSA_Protea_label_free_20100323_meth3_long_acc_template.sky");
expectedPepCount = 3;
expectedTransGroupCount = 3;
expectedTransCount = 21;
doc = InitFullScanDocument(docPath, 1, ref expectedPepCount, ref expectedTransGroupCount, ref expectedTransCount, asSmallMolecules);
docCheckpoints.Add(doc);
Assert.AreEqual(FullScanMassAnalyzerType.orbitrap, doc.Settings.TransitionSettings.FullScan.ProductMassAnalyzer);
// Make sure saving this type of document works
AssertEx.Serializable(doc, AssertEx.DocumentCloned);
Assert.IsTrue(docContainer.SetDocument(doc, docContainer.Document));
rawPath = testFilesDir.GetTestPath("ah_20101029r_BSA_CID_FT_centroid_3uscan_3" +
ExtensionTestContext.ExtThermoRaw);
measuredResults = new MeasuredResults(new[] { new ChromatogramSet("Accurate", new[] { rawPath }) });
docCheckpoints.Add(docContainer.ChangeMeasuredResults(measuredResults, 3, 3, 21));
// Import LTQ data with MS1 and MS/MS
docPath = testFilesDir.GetTestPath("BSA_Protea_label_free_20100323_meth3_test4.sky");
expectedPepCount = 3;
expectedTransGroupCount = 4;
expectedTransCount = 32;
doc = InitFullScanDocument(docPath, 3, ref expectedPepCount, ref expectedTransGroupCount, ref expectedTransCount, asSmallMolecules);
Assert.AreEqual(FullScanMassAnalyzerType.none, doc.Settings.TransitionSettings.FullScan.ProductMassAnalyzer);
Assert.AreEqual(FullScanMassAnalyzerType.none, doc.Settings.TransitionSettings.FullScan.PrecursorMassAnalyzer);
docCheckpoints.Add(doc);
var docBoth = doc.ChangeSettings(doc.Settings.ChangeTransitionFullScan(fs =>
fs.ChangeAcquisitionMethod(FullScanAcquisitionMethod.Targeted, null)
.ChangePrecursorResolution(FullScanMassAnalyzerType.qit, TransitionFullScan.DEFAULT_RES_QIT, null)));
docCheckpoints.Add(docBoth);
AssertEx.Serializable(docBoth, AssertEx.DocumentCloned);
Assert.IsTrue(docContainer.SetDocument(docBoth, docContainer.Document));
string dataPath = testFilesDir.GetTestPath("klc_20100329v_Protea_Peptide_Curve_200fmol_uL_tech1.mzML");
var listResults = new List<ChromatogramSet>
{
new ChromatogramSet("MS1 and MS/MS", new[] { dataPath }),
};
measuredResults = new MeasuredResults(listResults.ToArray());
docCheckpoints.Add(docContainer.ChangeMeasuredResults(measuredResults, expectedPepCount, expectedTransGroupCount, expectedTransCount-6));
// The mzML was filtered for the m/z range 410 to 910.
foreach (var nodeTran in docContainer.Document.PeptideTransitions)
{
Assert.IsTrue(nodeTran.HasResults);
Assert.IsNotNull(nodeTran.Results[0]);
if (410 > nodeTran.Mz || nodeTran.Mz > 910)
Assert.IsTrue(nodeTran.Results[0][0].IsEmpty);
else
Assert.IsFalse(nodeTran.Results[0][0].IsEmpty);
}
// Import LTQ data with MS1 and MS/MS using multiple files for a single replicate
listResults.Add(new ChromatogramSet("Multi-file", new[]
{
testFilesDir.GetTestPath("both_DRV.mzML"),
testFilesDir.GetTestPath("both_KVP.mzML"),
}));
measuredResults = new MeasuredResults(listResults.ToArray());
docCheckpoints.Add(docContainer.ChangeMeasuredResults(measuredResults, expectedPepCount - 1, expectedTransGroupCount-1, expectedTransCount-6));
int indexResults = listResults.Count - 1;
foreach (var nodeTran in docContainer.Document.PeptideTransitions)
{
Assert.IsTrue(nodeTran.HasResults);
Assert.AreEqual(listResults.Count, nodeTran.Results.Count);
var peptide = nodeTran.Transition.Group.Peptide;
// DRV without FASTA sequence should not have data for non-precursor transitions
if (!peptide.Sequence.StartsWith("DRV") || !peptide.Begin.HasValue)
{
Assert.IsNotNull(nodeTran.Results[indexResults]);
Assert.IsFalse(nodeTran.Results[indexResults][0].IsEmpty);
}
else if (nodeTran.Transition.IonType != IonType.precursor)
Assert.IsNull(nodeTran.Results[indexResults]);
else
{
// Random, bogus peaks chosen in both files
Assert.IsNotNull(nodeTran.Results[indexResults]);
Assert.AreEqual(2, nodeTran.Results[indexResults].Count);
Assert.IsFalse(nodeTran.Results[indexResults][0].IsEmpty);
Assert.IsFalse(nodeTran.Results[indexResults][1].IsEmpty);
}
}
if (asSmallMolecules == RefinementSettings.ConvertToSmallMoleculesMode.masses_only)
return; // Can't work with isotope distributions when we don't have ion formulas
// Verify handling of bad request for vendor centroided data - out-of-range PPM
docPath = testFilesDir.GetTestPath("Yeast_HI3 Peptides_test.sky");
expectedPepCount = 2;
expectedTransGroupCount = 2;
expectedTransCount = 2;
doc = InitFullScanDocument(docPath, 2, ref expectedPepCount, ref expectedTransGroupCount, ref expectedTransCount, asSmallMolecules);
Assert.AreEqual(FullScanMassAnalyzerType.none, doc.Settings.TransitionSettings.FullScan.ProductMassAnalyzer);
Assert.AreEqual(FullScanMassAnalyzerType.none, doc.Settings.TransitionSettings.FullScan.PrecursorMassAnalyzer);
var docBad = doc;
AssertEx.ThrowsException<InvalidDataException>(() =>
docBad.ChangeSettings(docBad.Settings.ChangeTransitionFullScan(fs =>
fs.ChangePrecursorIsotopes(FullScanPrecursorIsotopes.Count, 1, IsotopeEnrichments.DEFAULT)
.ChangePrecursorResolution(FullScanMassAnalyzerType.centroided, 50 * 1000, 400))),
string.Format(Resources.TransitionFullScan_ValidateRes_Mass_accuracy_must_be_between__0__and__1__for_centroided_data_,
TransitionFullScan.MIN_CENTROID_PPM,TransitionFullScan.MAX_CENTROID_PPM));
// Verify relationship between PPM and resolving power
const double ppm = 20.0; // Should yield same filter width as resolving power 50,000 in TOF
var docNoCentroid = doc.ChangeSettings(doc.Settings.ChangeTransitionFullScan(fs =>
fs.ChangePrecursorIsotopes(FullScanPrecursorIsotopes.Count, 1, IsotopeEnrichments.DEFAULT)
.ChangePrecursorResolution(FullScanMassAnalyzerType.centroided, ppm, 0)));
AssertEx.Serializable(docNoCentroid, AssertEx.DocumentCloned);
Assert.IsTrue(docContainer.SetDocument(docNoCentroid, docContainer.Document));
const double mzTest = 400.0;
var filterWidth = docNoCentroid.Settings.TransitionSettings.FullScan.GetPrecursorFilterWindow(mzTest);
Assert.AreEqual(mzTest * 2.0 * ppm * 1E-6, filterWidth);
// Verify handling of bad request for vendor centroided data - ask for centroiding in mzML
const string fileName = "S_2_LVN.mzML";
var filePath = testFilesDir.GetTestPath(fileName);
AssertEx.ThrowsException<AssertFailedException>(() =>
{
listResults = new List<ChromatogramSet> { new ChromatogramSet("rep1", new[] {new MsDataFilePath(filePath, null, true)}), };
docContainer.ChangeMeasuredResults(new MeasuredResults(listResults.ToArray()), 1, 1, 1);
},
string.Format(Resources.NoCentroidedDataException_NoCentroidedDataException_No_centroided_data_available_for_file___0_____Adjust_your_Full_Scan_settings_, fileName));
// Import FT data with only MS1
docPath = testFilesDir.GetTestPath("Yeast_HI3 Peptides_test.sky");
expectedPepCount = 2;
expectedTransGroupCount = 2;
expectedTransCount = 2;
doc = InitFullScanDocument(docPath, 2, ref expectedPepCount, ref expectedTransGroupCount, ref expectedTransCount, asSmallMolecules);
Assert.AreEqual(FullScanMassAnalyzerType.none, doc.Settings.TransitionSettings.FullScan.ProductMassAnalyzer);
Assert.AreEqual(FullScanMassAnalyzerType.none, doc.Settings.TransitionSettings.FullScan.PrecursorMassAnalyzer);
var docMs1 = doc.ChangeSettings(doc.Settings.ChangeTransitionFullScan(fs =>
fs.ChangePrecursorIsotopes(FullScanPrecursorIsotopes.Count, 1, IsotopeEnrichments.DEFAULT)
.ChangePrecursorResolution(FullScanMassAnalyzerType.tof, 50 * 1000, null)));
Assert.AreEqual(filterWidth, docMs1.Settings.TransitionSettings.FullScan.GetPrecursorFilterWindow(mzTest));
docMs1 = doc.ChangeSettings(doc.Settings.ChangeTransitionFullScan(fs =>
fs.ChangePrecursorIsotopes(FullScanPrecursorIsotopes.Count, 1, IsotopeEnrichments.DEFAULT)
.ChangePrecursorResolution(FullScanMassAnalyzerType.ft_icr, 50 * 1000, mzTest)));
AssertEx.Serializable(docMs1, AssertEx.DocumentCloned);
Assert.IsTrue(docContainer.SetDocument(docMs1, docContainer.Document));
const string rep1 = "rep1";
listResults = new List<ChromatogramSet>
{
new ChromatogramSet(rep1, new[] {filePath}),
};
measuredResults = new MeasuredResults(listResults.ToArray());
docCheckpoints.Add(docContainer.ChangeMeasuredResults(measuredResults, 1, 1, 1));
// Because of the way the mzML files were filtered, all of the LVN peaks should be present
// in the first replicate, and all of the NVN peaks should be present in the other.
foreach (var nodeTranGroup in docContainer.Document.MoleculeTransitionGroups)
{
foreach (var docNode in nodeTranGroup.Children)
{
var nodeTran = (TransitionDocNode) docNode;
Assert.IsTrue(nodeTran.HasResults);
Assert.AreEqual(1, nodeTran.Results.Count);
if ((nodeTran.Transition.Group.Peptide.IsCustomIon
? nodeTranGroup.CustomIon.Name
: nodeTran.Transition.Group.Peptide.Sequence).StartsWith("LVN"))
Assert.IsFalse(nodeTran.Results[0][0].IsEmpty);
else
Assert.IsTrue(nodeTran.Results[0][0].IsEmpty);
}
}
const string rep2 = "rep2";
listResults.Add(new ChromatogramSet(rep2, new[] {testFilesDir.GetTestPath("S_2_NVN.mzML")}));
measuredResults = new MeasuredResults(listResults.ToArray());
docCheckpoints.Add(docContainer.ChangeMeasuredResults(measuredResults, 1, 1, 1));
// Because of the way the mzML files were filtered, all of the LVN peaks should be present
// in the first replicate, and all of the NVN peaks should be present in the other.
foreach (var nodeTranGroup in docContainer.Document.MoleculeTransitionGroups)
{
foreach (var docNode in nodeTranGroup.Children)
{
var nodeTran = (TransitionDocNode) docNode;
Assert.IsTrue(nodeTran.HasResults);
Assert.AreEqual(2, nodeTran.Results.Count);
if ((nodeTran.Transition.Group.Peptide.IsCustomIon
? nodeTranGroup.CustomIon.Name
: nodeTran.Transition.Group.Peptide.Sequence).StartsWith("LVN"))
Assert.IsTrue(nodeTran.Results[1][0].IsEmpty);
else
Assert.IsFalse(nodeTran.Results[1][0].IsEmpty);
}
}
// Chromatograms should be present in the cache for a number of isotopes.
var docMs1Isotopes = docContainer.Document.ChangeSettings(doc.Settings
.ChangeTransitionFullScan(fs => fs.ChangePrecursorIsotopes(FullScanPrecursorIsotopes.Count,
3, IsotopeEnrichments.DEFAULT))
.ChangeTransitionFilter(filter => filter.ChangeIonTypes(new[] {IonType.precursor})));
docCheckpoints.Add(docMs1Isotopes);
AssertEx.IsDocumentState(docMs1Isotopes, null, 2, 2, 2 ); // Need to reset auto-manage for transitions
var refineAutoSelect = new RefinementSettings { AutoPickChildrenAll = PickLevel.transitions };
docMs1Isotopes = refineAutoSelect.Refine(docMs1Isotopes);
AssertEx.IsDocumentState(docMs1Isotopes, null, 2, 2, 6);
AssertResult.IsDocumentResultsState(docMs1Isotopes, rep1, 1, 1, 0, 3, 0);
AssertResult.IsDocumentResultsState(docMs1Isotopes, rep2, 1, 1, 0, 3, 0);
docCheckpoints.Add(docMs1Isotopes);
// Add M-1 transitions, and verify that they have chromatogram data also, but
// empty peaks in all cases
var docMs1All = docMs1Isotopes.ChangeSettings(docMs1Isotopes.Settings
.ChangeTransitionFullScan(fs => fs.ChangePrecursorIsotopes(FullScanPrecursorIsotopes.Percent,
0, IsotopeEnrichments.DEFAULT))
.ChangeTransitionIntegration(i => i.ChangeIntegrateAll(false))); // For compatibility with v2.5 and earlier
docCheckpoints.Add(docMs1All);
AssertEx.IsDocumentState(docMs1All, null, 2, 2, 10);
AssertResult.IsDocumentResultsState(docMs1All, rep1, 1, 1, 0, 4, 0);
AssertResult.IsDocumentResultsState(docMs1All, rep2, 1, 1, 0, 4, 0);
var ms1AllTranstions = docMs1All.MoleculeTransitions.ToArray();
var tranM1 = ms1AllTranstions[0];
Assert.AreEqual(-1, tranM1.Transition.MassIndex);
Assert.IsTrue(tranM1.Results[0] != null && tranM1.Results[1] != null);
Assert.IsTrue(tranM1.Results[0][0].IsEmpty && tranM1.Results[1][0].IsEmpty);
tranM1 = ms1AllTranstions[5];
Assert.AreEqual(-1, tranM1.Transition.MassIndex);
Assert.IsTrue(tranM1.Results[0] != null && tranM1.Results[1] != null);
Assert.IsTrue(tranM1.Results[0][0].IsEmpty && tranM1.Results[1][0].IsEmpty);
}
protected override void DoTest()
{
// This test is quite specific to the input data set - needs results for all nodes to export the list. Shut off the special non-proteomic test mode, otherwise you 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;
// For now, CSV files are produced with invariant culture because some manufacturers do not handle internationalized CSVs.
_cultureInfo = CultureInfo.InvariantCulture;
_fieldSeparator = TextUtil.GetCsvSeparator(_cultureInfo);
string isolationWidth = string.Format(_cultureInfo, "Narrow (~{0:0.0} m/z)", 1.3);
const double slens = 1.234;
// Load document which is already configured for DDA, and contains data for scheduling
string standardDocumentFile = TestFilesDir.GetTestPath("BSA_Protea_label_free_meth3.sky");
RunUI(() => { SkylineWindow.OpenFile(standardDocumentFile); });
WaitForDocumentLoaded();
if (SmallMoleculeTestMode != RefinementSettings.ConvertToSmallMoleculesMode.none)
{
ConvertDocumentToSmallMolecules(SmallMoleculeTestMode, AsSmallMoleculesNegative);
WaitForDocumentLoaded();
}
var t46 = 46.790;
var t39 = 39.900;
var halfWin = 1.0;
if (AsExplicitRetentionTimes)
{
const double timeOffset = 10; // To verify that explicit retention times are in use
const double winOffset = .4;
RunUI(() => SkylineWindow.ModifyDocument("Convert to explicit retention times", document =>
{
var refine = new RefinementSettings();
return refine.ConvertToExplicitRetentionTimes(document, timeOffset, winOffset);
}));
t46 += timeOffset;
t39 += timeOffset;
halfWin += winOffset*0.5;
}
// Conversion to negative charge states shifts the masses
var mzFirst = AsSmallMoleculesNegative ? 580.304419 : 582.318971;
var mzLast = AsSmallMoleculesNegative ? 442.535467 : 444.55002;
var zFirst = AsSmallMoleculesNegative ? -2 : 2;
var zLast = AsSmallMoleculesNegative ? -3 : 3;
var ceFirst = AsSmallMoleculesNegative ? 20.3 : 20.4;
var ceLast = AsSmallMoleculesNegative ? 16.2 : 19.2;
double? slensA = null;
double? slensB = null;
if (WithSLens)
{
slensA = slens;
slensB = ThermoMassListExporter.DEFAULT_SLENS;
}
// Export Agilent unscheduled DDA list.
ExportIsolationList(
"AgilentUnscheduledDda.csv",
ExportInstrumentType.AGILENT_TOF, FullScanAcquisitionMethod.None, ExportMethodType.Standard,
AgilentIsolationListExporter.GetDdaHeader(_fieldSeparator),
FieldSeparate("True", mzFirst, 20, zFirst, "Preferred", 0, string.Empty, isolationWidth, ceFirst),
FieldSeparate("True", mzLast, 20, zLast, "Preferred", 0, string.Empty, isolationWidth, ceLast));
// Export Agilent scheduled DDA list.
ExportIsolationList(
"AgilentScheduledDda.csv",
ExportInstrumentType.AGILENT_TOF, FullScanAcquisitionMethod.None, ExportMethodType.Scheduled,
AgilentIsolationListExporter.GetDdaHeader(_fieldSeparator),
FieldSeparate("True", mzFirst, 20, zFirst, "Preferred", t46, 2*halfWin, isolationWidth, ceFirst),
FieldSeparate("True", mzLast, 20, zLast, "Preferred", t39, 2*halfWin, isolationWidth, ceLast));
// Export Thermo unscheduled DDA list.
const double nce = ThermoQExactiveIsolationListExporter.NARROW_NCE;
bool AsSmallMolecules = (SmallMoleculeTestMode != RefinementSettings.ConvertToSmallMoleculesMode.none);
bool AsSmallMoleculeMasses = (SmallMoleculeTestMode == RefinementSettings.ConvertToSmallMoleculesMode.masses_only);
var peptideA = AsSmallMolecules
? (AsSmallMoleculeMasses ? "Ion [1164.639040/1165.343970] (light)" : (AsSmallMoleculesNegative ? "LVNELTEFAK(-H2) (light)" : "LVNELTEFAK(+H2) (light)"))
: "LVNELTEFAK (light)";
var peptideB = AsSmallMolecules
? (AsSmallMoleculeMasses ? "Ion [1333.651707/1334.400621] (light)" : (AsSmallMoleculesNegative ? "IKNLQSLDPSH(-H3) (light)" : "IKNLQSLDPSH(+H3) (light)"))
: "IKNLQS[+80.0]LDPSH (light)";
var polarity = AsSmallMoleculesNegative ? "Negative" : "Positive";
var thermoQExactiveIsolationListExporter = new ThermoQExactiveIsolationListExporter(SkylineWindow.Document)
{
UseSlens = WithSLens
};
ExportIsolationList(
"ThermoUnscheduledDda.csv",
ExportInstrumentType.THERMO_Q_EXACTIVE, FullScanAcquisitionMethod.None, ExportMethodType.Standard,
thermoQExactiveIsolationListExporter.GetHeader(_fieldSeparator),
FieldSeparate(mzFirst, string.Empty, string.Empty, Math.Abs(zFirst), polarity, string.Empty, string.Empty, nce, slensA, peptideA),
FieldSeparate(mzLast, string.Empty, string.Empty, Math.Abs(zLast), polarity, string.Empty, string.Empty, nce, slensB, peptideB));
// Export Thermo scheduled DDA list.
if (!AsSmallMoleculesNegative) // .skyd file chromatograms are not useful in this conversion due to mass shift
ExportIsolationList(
"ThermoScheduledDda.csv",
ExportInstrumentType.THERMO_Q_EXACTIVE, FullScanAcquisitionMethod.None, ExportMethodType.Scheduled,
thermoQExactiveIsolationListExporter.GetHeader(_fieldSeparator),
FieldSeparate(mzFirst, string.Empty, string.Empty, Math.Abs(zFirst), polarity, t46 - halfWin, t46 + halfWin, nce, slensA, peptideA),
FieldSeparate(mzLast, string.Empty, string.Empty, Math.Abs(zLast), polarity, t39 - halfWin, t39 + halfWin, nce, slensB, peptideB));
// Export Agilent unscheduled Targeted list.
ExportIsolationList(
"AgilentUnscheduledTargeted.csv",
ExportInstrumentType.AGILENT_TOF, FullScanAcquisitionMethod.Targeted, ExportMethodType.Standard,
AgilentIsolationListExporter.GetTargetedHeader(_fieldSeparator),
FieldSeparate("True", mzFirst, zFirst, 0, string.Empty, isolationWidth, ceFirst, string.Empty),
FieldSeparate("True", mzLast, zLast, 0, string.Empty, isolationWidth, ceLast, string.Empty));
// Export Agilent scheduled Targeted list.
if (!AsSmallMoleculesNegative) // .skyd file chromatograms are not useful in this conversion due to mass shift
ExportIsolationList(
"AgilentScheduledTargeted.csv",
ExportInstrumentType.AGILENT_TOF, FullScanAcquisitionMethod.Targeted, ExportMethodType.Scheduled,
AgilentIsolationListExporter.GetTargetedHeader(_fieldSeparator),
FieldSeparate("True", mzFirst, zFirst, t46, 2*halfWin, isolationWidth, ceFirst, string.Empty),
FieldSeparate("True", mzLast, zLast, t39, 2*halfWin, isolationWidth, ceLast, string.Empty));
// Export Thermo unscheduled Targeted list.
ExportIsolationList(
"ThermoUnscheduledTargeted.csv",
ExportInstrumentType.THERMO_Q_EXACTIVE, FullScanAcquisitionMethod.Targeted, ExportMethodType.Standard,
thermoQExactiveIsolationListExporter.GetHeader(_fieldSeparator),
FieldSeparate(mzFirst, string.Empty, string.Empty, Math.Abs(zFirst), polarity, string.Empty, string.Empty, nce, slensA, peptideA),
FieldSeparate(mzLast, string.Empty, string.Empty, Math.Abs(zLast), polarity, string.Empty, string.Empty, nce, slensB, peptideB));
// Export Thermo scheduled Targeted list.
if (!AsSmallMoleculesNegative) // .skyd file chromatograms are not useful in this conversion due to mass shift
ExportIsolationList(
"ThermoScheduledTargeted.csv",
ExportInstrumentType.THERMO_Q_EXACTIVE, FullScanAcquisitionMethod.Targeted, ExportMethodType.Scheduled,
thermoQExactiveIsolationListExporter.GetHeader(_fieldSeparator),
FieldSeparate(mzFirst, string.Empty, string.Empty, Math.Abs(zFirst), polarity, t46 - halfWin, t46 + halfWin, nce, slensA, peptideA),
FieldSeparate(mzLast, string.Empty, string.Empty, Math.Abs(zLast), polarity, t39 - halfWin, t39 + halfWin, nce, slensB, peptideB));
// Export Thermo Fusion unscheduled Targeted list.
var thermoFusionMassListExporter = new ThermoFusionMassListExporter(SkylineWindow.Document)
{
UseSlens = WithSLens
};
ExportIsolationList(
"FusionUnscheduledTargeted.csv",
ExportInstrumentType.THERMO_FUSION, FullScanAcquisitionMethod.Targeted, ExportMethodType.Standard,
thermoFusionMassListExporter.GetHeader(_fieldSeparator),
FieldSeparate(mzFirst, zFirst, string.Empty, string.Empty, nce),
FieldSeparate(mzLast, zLast, string.Empty, string.Empty, nce));
// Export Thermo Fusion scheduled Targeted list.
if (!AsSmallMoleculesNegative) // .skyd file chromatograms are not useful in this conversion due to mass shift
ExportIsolationList(
"FusionScheduledTargeted.csv",
ExportInstrumentType.THERMO_FUSION, FullScanAcquisitionMethod.Targeted, ExportMethodType.Scheduled,
thermoFusionMassListExporter.GetHeader(_fieldSeparator),
FieldSeparate(mzFirst, zFirst, t46 - halfWin, t46 + halfWin, nce, slensA),
FieldSeparate(mzLast, zLast, t39 - halfWin, t39 + halfWin, nce, slensB));
string fragmentsFirst;
if (!AsSmallMolecules || AsExplicitRetentionTimes)
fragmentsFirst = FieldSeparate("582.3190", "951.4782", "595.3086", "708.3927", "837.4353", "1017.5251");
else if (!AsSmallMoleculesNegative)
fragmentsFirst = FieldSeparate("582.3190", "595.3086", "708.3927", "837.4353", "951.4782", "1017.5251");
else
fragmentsFirst = FieldSeparate("580.3044", "595.3097", "708.3938", "837.4364", "951.4793", "1017.5262");
string fragmentsLast;
if (!AsSmallMolecules || AsExplicitRetentionTimes)
fragmentsLast = FieldSeparate("444.5500", "496.7443", "340.1615", "406.8553", "609.7794", "545.7319");
else if (!AsSmallMoleculesNegative)
fragmentsLast = FieldSeparate("340.1615", "406.8553", "444.5500", "455.1885", "488.7104", "496.7443");
else
fragmentsLast = FieldSeparate("340.1626", "406.8564", "442.5355", "455.1896", "488.7115", "496.7454");
var rtFirst = !AsExplicitRetentionTimes
? FieldSeparate("45.8", "47.8")
: FieldSeparate("55.6", "58.0");
var rtLast = !AsExplicitRetentionTimes
? FieldSeparate("38.9", "40.9")
: FieldSeparate("48.7", "51.1");
var trapCeFirstTrap = !AsSmallMoleculesNegative
? FieldSeparate("21.2", "27.9")
: FieldSeparate("21.2", "27.8");
var trapCeLastTrap = !AsSmallMoleculesNegative
? FieldSeparate("17.3", "23.0")
: FieldSeparate("17.2", "23.0");
var trapCeFirstTransfer = !AsSmallMoleculesNegative
? FieldSeparate("26.2", "32.9")
: FieldSeparate("26.2", "32.8");
var trapCeLastTransfer = !AsSmallMoleculesNegative
? FieldSeparate("22.3", "28.0")
: FieldSeparate("22.2", "28.0");
// Export Waters Synapt (trap region) unscheduled Targeted list
ExportIsolationList(
"WatersTrapUnscheduledTargeted.mrm",
ExportInstrumentType.WATERS_SYNAPT_TRAP, FullScanAcquisitionMethod.Targeted, ExportMethodType.Standard,
WatersIsolationListExporter.GetHeader(_fieldSeparator),
FieldSeparate(0, "0.0", "30.0", mzFirst.ToString("0.0000", CultureInfo.InvariantCulture), fragmentsFirst, trapCeFirstTrap, "2.0", "2.0", 30, "0.0000", 0, 199),
FieldSeparate(0, "0.0", "30.0", mzLast.ToString("0.0000", CultureInfo.InvariantCulture), fragmentsLast, trapCeLastTrap, "2.0", "2.0", 30, "0.0000", 0, 199));
// Export Waters Synapt (trap region) scheduled Targeted list
ExportIsolationList(
"WatersTrapScheduledTargeted.mrm",
ExportInstrumentType.WATERS_SYNAPT_TRAP, FullScanAcquisitionMethod.Targeted, ExportMethodType.Scheduled,
WatersIsolationListExporter.GetHeader(_fieldSeparator),
FieldSeparate(0, rtFirst, mzFirst.ToString("0.0000", CultureInfo.InvariantCulture), fragmentsFirst, trapCeFirstTrap, "2.0", "2.0", 30, "0.0000", 0, 199),
FieldSeparate(0, rtLast, mzLast.ToString("0.0000", CultureInfo.InvariantCulture), fragmentsLast, trapCeLastTrap, "2.0", "2.0", 30, "0.0000", 0, 199));
// Export Waters Synapt (transfer region) unscheduled Targeted list
ExportIsolationList(
"WatersTransferUnscheduledTargeted.mrm",
ExportInstrumentType.WATERS_SYNAPT_TRANSFER, FullScanAcquisitionMethod.Targeted, ExportMethodType.Standard,
WatersIsolationListExporter.GetHeader(_fieldSeparator),
FieldSeparate(0, "0.0", "30.0", mzFirst.ToString("0.0000", CultureInfo.InvariantCulture), fragmentsFirst, "4.0", "4.0", trapCeFirstTransfer, 30, "0.0000", 0, 199),
FieldSeparate(0, "0.0", "30.0", mzLast.ToString("0.0000", CultureInfo.InvariantCulture), fragmentsLast, "4.0", "4.0", trapCeLastTransfer, 30, "0.0000", 0, 199));
// Export Waters Synapt (transfer region) scheduled Targeted list
ExportIsolationList(
"WatersTransferScheduledTargeted.mrm",
ExportInstrumentType.WATERS_SYNAPT_TRANSFER, FullScanAcquisitionMethod.Targeted, ExportMethodType.Scheduled,
WatersIsolationListExporter.GetHeader(_fieldSeparator),
FieldSeparate(0, rtFirst, mzFirst.ToString("0.0000", CultureInfo.InvariantCulture), fragmentsFirst, "4.0", "4.0", trapCeFirstTransfer, 30, "0.0000", 0, 199),
FieldSeparate(0, rtLast, mzLast.ToString("0.0000", CultureInfo.InvariantCulture), fragmentsLast, "4.0", "4.0", trapCeLastTransfer, 30, "0.0000", 0, 199));
// Export Waters Xevo unscheduled Targeted list
ExportIsolationList(
"WatersXevoUnscheduledTargeted.mrm",
ExportInstrumentType.WATERS_XEVO_QTOF, FullScanAcquisitionMethod.Targeted, ExportMethodType.Standard,
WatersIsolationListExporter.GetHeader(_fieldSeparator),
FieldSeparate(0, "0.0", "30.0", mzFirst.ToString("0.0000", CultureInfo.InvariantCulture), fragmentsFirst, trapCeFirstTrap, 30, "0.0000", 0, 199),
FieldSeparate(0, "0.0", "30.0", mzLast.ToString("0.0000", CultureInfo.InvariantCulture), fragmentsLast, trapCeLastTrap, 30, "0.0000", 0, 199));
// Export Waters Xevo scheduled Targeted list
ExportIsolationList(
"WatersXevoScheduledTargeted.mrm",
ExportInstrumentType.WATERS_XEVO_QTOF, FullScanAcquisitionMethod.Targeted, ExportMethodType.Scheduled,
WatersIsolationListExporter.GetHeader(_fieldSeparator),
FieldSeparate(0, rtFirst, mzFirst.ToString("0.0000", CultureInfo.InvariantCulture), fragmentsFirst, trapCeFirstTrap, 30, "0.0000", 0, 199),
FieldSeparate(0, rtLast, mzLast.ToString("0.0000", CultureInfo.InvariantCulture), fragmentsLast, trapCeLastTrap, 30, "0.0000", 0, 199));
// Check error if analyzer is not set correctly.
CheckMassAnalyzer(ExportInstrumentType.AGILENT_TOF, FullScanMassAnalyzerType.tof);
CheckMassAnalyzer(ExportInstrumentType.THERMO_Q_EXACTIVE, FullScanMassAnalyzerType.orbitrap);
}
/* TODO bspratt drift time libs for small molecules
[TestMethod]
public void WatersImsMsePredictedDriftTimesChromatogramTestAsSmallMolecules()
{
WatersImsMseChromatogramTest(DriftFilterType.predictor, true);
}
[TestMethod]
public void WatersImsMseLibraryDriftTimesChromatogramTestAsSmallMolecules()
{
WatersImsMseChromatogramTest(DriftFilterType.library, true);
}
*/
private void WatersImsMseChromatogramTest(DriftFilterType mode,
RefinementSettings.ConvertToSmallMoleculesMode asSmallMolecules = RefinementSettings.ConvertToSmallMoleculesMode.none)
{
string subdir = (asSmallMolecules == RefinementSettings.ConvertToSmallMoleculesMode.none) ? null : asSmallMolecules.ToString();
var testFilesDir = new TestFilesDir(TestContext, ZIP_FILE, subdir);
TestSmallMolecules = false; // Don't need that extra magic node
bool withDriftTimePredictor = (mode == DriftFilterType.predictor); // Load the doc that has a drift time predictor?
bool withDriftTimeFilter = (mode != DriftFilterType.none); // Perform drift time filtering? (either with predictor, or with bare times in blib file)
string docPath;
SrmDocument document = InitWatersImsMseDocument(testFilesDir, withDriftTimePredictor ? "single_with_driftinfo.sky" : "single_no_driftinfo.sky", asSmallMolecules, out docPath);
AssertEx.IsDocumentState(document, (withDriftTimePredictor || (asSmallMolecules != RefinementSettings.ConvertToSmallMoleculesMode.none)) ? 1 : 0, 1, 1, 1, 8); // Drift time lib load bumps the doc version
var docContainer = new ResultsTestDocumentContainer(document, docPath);
var doc = docContainer.Document;
var docOriginal = doc;
string testModeStr = withDriftTimePredictor ? "with drift time predictor" : "without drift time info";
if (withDriftTimeFilter && !withDriftTimePredictor)
{
// Use the bare drift times in the spectral library
var librarySpec = new BiblioSpecLiteSpec("drift test",
testFilesDir.GetTestPath("mse-mobility.filtered-scaled.blib"));
doc = doc.ChangeSettings(
doc.Settings.ChangePeptideLibraries(lib => lib.ChangeLibrarySpecs(new[] { librarySpec })).
ChangePeptidePrediction(p => p.ChangeLibraryDriftTimesResolvingPower(100)).
ChangePeptidePrediction(p => p.ChangeUseLibraryDriftTimes(true))
);
testModeStr = "with drift times from spectral library";
}
var listChromatograms = new List<ChromatogramSet>();
// A small subset of the QC_HDMSE_02_UCA168_3495_082213 data set (RT 21.5-22.5) from Will Thompson
const string path = @"waters-mobility.mz5";
listChromatograms.Add(AssertResult.FindChromatogramSet(doc, new MsDataFilePath(path)) ??
new ChromatogramSet(Path.GetFileName(path).Replace('.', '_'), new[] { path }));
var docResults = doc.ChangeMeasuredResults(new MeasuredResults(listChromatograms));
Assert.IsTrue(docContainer.SetDocument(docResults, docOriginal, true));
docContainer.AssertComplete();
document = docContainer.Document;
float tolerance = (float)document.Settings.TransitionSettings.Instrument.MzMatchTolerance;
double maxHeight = 0;
var results = document.Settings.MeasuredResults;
Assert.AreEqual(1, document.MoleculePrecursorPairs.Count());
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, testModeStr);
var chromGroup = chromGroupInfo[0];
var expectedPeaks = ((asSmallMolecules == RefinementSettings.ConvertToSmallMoleculesMode.masses_only) ? 6 : 5);
Assert.AreEqual(withDriftTimeFilter ? 3 : expectedPeaks, chromGroup.NumPeaks, testModeStr); // This will be higher if we don't filter on DT
foreach (var tranInfo in chromGroup.TransitionPointSets)
{
maxHeight = Math.Max(maxHeight, tranInfo.MaxIntensity);
}
}
Assert.AreEqual(withDriftTimeFilter? 5226 : 20075 , maxHeight, 1, testModeStr); // Without DT filtering, this will be much greater
// 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(21.94865, (double)nodePep.GetMeasuredRetentionTime(0), .0001, testModeStr);
Assert.AreEqual(1.0, (double)nodePep.GetPeakCountRatio(0), 0.0001, testModeStr);
nPeptides++;
}
}
Assert.AreEqual(1, nPeptides);
if (withDriftTimePredictor || withDriftTimeFilter)
{
// Verify that the .imdb pr .blib file goes out in the share zipfile
for (int complete = 0; complete <= 1; complete++)
{
var sharePath = testFilesDir.GetTestPath(complete==1?"share_complete.zip":"share_minimized.zip");
var share = new SrmDocumentSharing(document, docPath, sharePath, complete==1);
using (var longWaitDlg = new LongWaitDlg
{
// ReSharper disable once LocalizableElement
Text = "unit test WatersImsTest -- sharing document",
})
{
longWaitDlg.PerformWork(null, 1000, share.Share);
Assert.IsFalse(longWaitDlg.IsCanceled);
}
var files = share.ListEntries().ToArray();
Assert.IsTrue(files.Contains(withDriftTimePredictor ? "scaled.imdb" : "mse-mobility.filtered-scaled.blib"));
// And round trip it to make sure we haven't left out any new features in minimized imdb or blib files
using (var longWaitDlg = new LongWaitDlg
{
// ReSharper disable once LocalizableElement
Text = "unit test WatersImsTest",
})
{
longWaitDlg.PerformWork(null, 1000, share.Extract);
Assert.IsFalse(longWaitDlg.IsCanceled);
}
using (TextReader reader = new StreamReader(share.DocumentPath))
{
XmlSerializer documentSerializer = new XmlSerializer(typeof(SrmDocument));
var document2 = (SrmDocument) documentSerializer.Deserialize(reader);
Assert.IsNotNull(document2);
var im = document.Settings.GetIonMobilities(new MsDataFilePath(path));
var pep = document2.Molecules.First();
foreach (TransitionGroupDocNode nodeGroup in pep.Children)
{
double windowDT;
var centerDriftTime = document.Settings.PeptideSettings.Prediction.GetDriftTime(
pep, nodeGroup, im, out windowDT);
Assert.AreEqual(3.86124, centerDriftTime.DriftTimeMsec(false) ?? 0, .0001, testModeStr);
Assert.AreEqual(0.077224865797235934, windowDT, .0001, testModeStr);
}
}
}
}
// Release file handles
docContainer.Release();
testFilesDir.Dispose();
string cachePath = ChromatogramCache.FinalPathForName(docPath, null);
FileEx.SafeDelete(cachePath);
}
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();
});
if (AsSmallMolecules)
{
return; // Too peptide-centric from here to end of test
}
FindNode("IHGFDLAAINLQR");
RestoreViewOnScreen(8);
WaitForCondition(15*60*1000, () => SkylineWindow.Document.Settings.MeasuredResults.IsLoaded); // 10 minutes
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 ConvertDocumentToSmallMolecules(RefinementSettings.ConvertToSmallMoleculesMode mode = RefinementSettings.ConvertToSmallMoleculesMode.formulas,
bool invertCharges = false, bool ignoreDecoys = false)
{
WaitForDocumentLoaded();
RunUI(() => SkylineWindow.ModifyDocument("Convert to small molecules", document =>
{
var refine = new RefinementSettings();
return refine.ConvertToSmallMolecules(document, mode, invertCharges, ignoreDecoys);
}));
}
private void ExportWithExplicitCollisionEnergyValues(string pathList)
{
var original = SkylineWindow.Document;
var refine = new RefinementSettings();
var document = refine.ConvertToSmallMolecules(original);
for (var loop = 0; loop < 2; loop++)
{
SkylineWindow.SetDocument(document, SkylineWindow.Document);
var exportMethodDlg = ShowDialog<ExportMethodDlg>(() => SkylineWindow.ShowExportMethodDialog(ExportFileType.List));
RunUI(() =>
{
exportMethodDlg.InstrumentType = ExportInstrumentType.THERMO_QUANTIVA;
exportMethodDlg.OptimizeType = ExportOptimize.CE;
exportMethodDlg.MethodType = ExportMethodType.Standard;
});
RunUI(() => exportMethodDlg.OkDialog(pathList));
WaitForClosedForm(exportMethodDlg);
var actual = File.ReadAllLines(pathList);
if (loop == 1)
{
// Explicit CE values
Assert.AreEqual(document.MoleculeTransitionCount+1, actual.Length); // Should be just one line per transition, and a header
break;
}
else
{
Assert.AreEqual(document.MoleculeTransitionCount*11 + 1, actual.Length); // Multiple steps, and a header
}
// Change the current document to use explicit CE values, verify that this changes the output
var ce = 1;
for (bool changing = true; changing; )
{
changing = false;
foreach (var peptideGroupDocNode in document.MoleculeGroups)
{
var pepGroupPath = new IdentityPath(IdentityPath.ROOT, peptideGroupDocNode.Id);
foreach (var nodePep in peptideGroupDocNode.Molecules)
{
var pepPath = new IdentityPath(pepGroupPath, nodePep.Id);
foreach (var nodeTransitionGroup in nodePep.TransitionGroups)
{
if (!nodeTransitionGroup.ExplicitValues.CollisionEnergy.HasValue)
{
var tgPath = new IdentityPath(pepPath, nodeTransitionGroup.Id);
document = (SrmDocument)document.ReplaceChild(tgPath.Parent,
nodeTransitionGroup.ChangeExplicitValues(nodeTransitionGroup.ExplicitValues.ChangeCollisionEnergy(ce++)));
changing = true;
break;
}
}
}
if (changing)
break;
}
}
}
SkylineWindow.SetDocument(original, SkylineWindow.Document);
}
public static SrmDocument ChangeAutoManageChildren(SrmDocument document, PickLevel which, bool autoPick)
{
var refine = new RefinementSettings { AutoPickChildrenAll = which, AutoPickChildrenOff = !autoPick };
return refine.Refine(document);
}
