private static void PastePeptides(PasteDlg pasteDlg, BackgroundProteome.DuplicateProteinsFilter duplicateProteinsFilter,
bool addUnmatched, bool addFiltered)
{
RunDlg <FilterMatchedPeptidesDlg>(pasteDlg.PastePeptides, filterMatchedPeptidesDlg =>
{
filterMatchedPeptidesDlg.DuplicateProteinsFilter = duplicateProteinsFilter;
filterMatchedPeptidesDlg.AddUnmatched = addUnmatched;
filterMatchedPeptidesDlg.AddFiltered = addFiltered;
filterMatchedPeptidesDlg.OkDialog();
});
}
private static void PasteTransitions(PasteDlg pasteDlg, BackgroundProteome.DuplicateProteinsFilter duplicateProteinsFilter,
bool addUnmatched, bool addFiltered)
{
RunUI(() => pasteDlg.IsMolecule = false); // Make sure it's ready for peptides, not small molecules
RunDlg <FilterMatchedPeptidesDlg>(pasteDlg.PasteTransitions, filterMatchedPeptidesDlg =>
{
// Make sure we only count each peptide once for the FilterMatchedPeptidesDlg.
Assert.AreEqual(NUM_UNMATCHED_EXPECTED, filterMatchedPeptidesDlg.UnmatchedCount);
filterMatchedPeptidesDlg.DuplicateProteinsFilter = duplicateProteinsFilter;
filterMatchedPeptidesDlg.AddUnmatched = addUnmatched;
filterMatchedPeptidesDlg.AddFiltered = addFiltered;
filterMatchedPeptidesDlg.OkDialog();
});
}
private static void VerifyTransitionListError(PasteDlg insertTransDlg, string insertListText,
object oldValue, object newValue, object containsValue, int row, int col, int replacements = 0)
{
string pasteText = oldValue != null && newValue != null?
insertListText.Replace(oldValue.ToString(), newValue.ToString()) :
insertListText;
SetClipboardText(pasteText);
insertTransDlg.PasteTransitions();
insertTransDlg.OkDialog();
if (containsValue != null)
{
AssertEx.AreComparableStrings(containsValue.ToString(), insertTransDlg.ErrorText, replacements);
}
Assert.AreEqual(row, insertTransDlg.SelectedGridRow);
Assert.AreEqual(col, insertTransDlg.SelectedGridColumn);
insertTransDlg.ClearRows();
}
protected override void DoTest()
{
// Formerly this little .sky file would not update its (unsearchable) protein metdata on load
RunUI(() => SkylineWindow.OpenFile(TestFilesDir.GetTestPath("Mutant Peptides with Braf AG A00Y - Cut Down.sky")));
var doc = WaitForDocumentLoaded();
var nodeProt = doc.MoleculeGroups.First();
var metadata = nodeProt.ProteinMetadata;
Assert.IsFalse(metadata.NeedsSearch());
RunUI(() => SkylineWindow.OpenFile(TestFilesDir.GetTestPath("ProteinMetadataFunctionalTests.sky")));
doc = WaitForDocumentLoaded();
nodeProt = doc.MoleculeGroups.First();
metadata = nodeProt.ProteinMetadata;
// Examine the various View | Targets | By* modes
foreach (ProteinMetadataManager.ProteinDisplayMode mode in Enum.GetValues(typeof(ProteinMetadataManager.ProteinDisplayMode)))
{
ProteinMetadataManager.ProteinDisplayMode arg = mode;
RunUI(() => SkylineWindow.UpdateTargetsDisplayMode(arg)); // This should alter the text displayed by the node in the sequence tree view
WaitForConditionUI(() =>
{
var displayText = SkylineWindow.SequenceTree.GetSequenceNodes().First().Text;
if (arg != ProteinMetadataManager.ProteinDisplayMode.ByName &&
Equals(displayText, GetDisplayText(ProteinMetadataManager.ProteinDisplayMode.ByName, metadata)))
{
return(false);
}
return(Equals(displayText, GetDisplayText(arg, metadata)));
});
}
// Examine the various Edit | Refine | Sort Proteins | By* modes
Assert.AreEqual("YIL075C", nodeProt.Name); // unsorted
foreach (ProteinMetadataManager.ProteinDisplayMode mode in Enum.GetValues(typeof(ProteinMetadataManager.ProteinDisplayMode)))
{
string expectedTopName = null;
switch (mode)
{
case ProteinMetadataManager.ProteinDisplayMode.ByName:
expectedTopName = "YAL003W";
RunUI(() => SkylineWindow.sortProteinsByNameToolStripMenuItem_Click(null, null));
break;
case ProteinMetadataManager.ProteinDisplayMode.ByAccession:
expectedTopName = TestSmallMolecules ? "ZZZTESTINGNONPROTEOMICMOLECULEGROUP" : "YFL038C";
RunUI(() => SkylineWindow.sortProteinsByAccessionToolStripMenuItem_Click(null, null));
break;
case ProteinMetadataManager.ProteinDisplayMode.ByPreferredName:
RunUI(() => SkylineWindow.sortProteinsByPreferredNameToolStripMenuItem_Click(null, null));
expectedTopName = TestSmallMolecules ? "ZZZTESTINGNONPROTEOMICMOLECULEGROUP" : "YAL016W";
break;
case ProteinMetadataManager.ProteinDisplayMode.ByGene:
RunUI(() => SkylineWindow.sortProteinsByGeneToolStripMenuItem_Click(null, null));
expectedTopName = TestSmallMolecules ? "ZZZTESTINGNONPROTEOMICMOLECULEGROUP" : "YGL234W";
break;
}
var actualTopName = WaitForDocumentLoaded().MoleculeGroups.First().Name.ToUpperInvariant();
Assert.AreEqual(expectedTopName, actualTopName);
}
// Now paste in our fake fasta test data, and handle it with our fake webaccess handler
var protdbLoader = SkylineWindow.BackgroundProteomeManager;
protdbLoader.FastaImporter = new WebEnabledFastaImporter(new CommonTest.FastaImporterTest.PlaybackProvider());
var treeLoader = SkylineWindow.ProteinMetadataManager;
treeLoader.FastaImporter = new WebEnabledFastaImporter(new CommonTest.FastaImporterTest.PlaybackProvider());
const int maxEntries = 5;
var fastaText = CommonTest.FastaImporterTest.GetFastaTestText(maxEntries); // Just get the first few
SetClipboardTextUI(fastaText);
var pasteDlg = ShowDialog <PasteDlg>(SkylineWindow.ShowPasteFastaDlg); // Show the paste dialog
RunDlg <EmptyProteinsDlg>(() => // Anticpate the EmptyProteinsDialog as a side effect
{
pasteDlg.PasteFasta(); // Doing this in pastDlg...
pasteDlg.OkDialog();
},
dlg =>
{
Assert.AreEqual(maxEntries, dlg.EmptyProteins);
dlg.KeepEmptyProteins();
dlg.OkDialog(); // ... will cause EmptyProteinsDlg to pop up, so OK it.
});
// Check that IPI:IPI00197700.1 got an accession number P04638
WaitForCondition(() => SkylineWindow.Document.MoleculeGroups.Any(pg => Equals("IPI:IPI00197700.1", pg.Name)));
doc = WaitForDocumentLoaded();
nodeProt = doc.MoleculeGroups.First(pg => Equals("IPI:IPI00197700.1", pg.Name));
Assert.AreEqual("P04638", nodeProt.ProteinMetadata.Accession);
// Now make our fake fasta into a protdb file, and check statement completion against that
const string basename = "fake.fasta";
var protdbPath = TestFilesDir.GetTestPath(basename + ProteomeDb.EXT_PROTDB);
var fastapath = TestFilesDir.GetTestPath(basename);
using (StreamWriter outfile = new StreamWriter(fastapath))
{
outfile.Write(CommonTest.FastaImporterTest.GetFastaTestText()); // write them all
}
BackgroundProteomeTest.CreateBackgroundProteome(protdbPath, basename, fastapath);
doc = WaitForDocumentChange(doc);
// Test for getting accession info from protdb
RunUI(() =>
{
SequenceTree sequenceTree = SkylineWindow.SequenceTree;
SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SequenceTree.Nodes[SkylineWindow.SequenceTree.Nodes.Count - 1]; // Select the creation node
sequenceTree.BeginEdit(false);
// ReSharper disable LocalizableElement
sequenceTree.StatementCompletionEditBox.TextBox.Text = "NP_313205";
// ReSharper restore LocalizableElement
sequenceTree.CommitEditBox(false);
});
doc = WaitForDocumentChange(doc);
nodeProt = doc.MoleculeGroups.First(pg => Equals("NP_313205", pg.Name));
Assert.AreEqual("P0A7T9", nodeProt.ProteinMetadata.Accession);
var snapshot = SkylineWindow.Document;
// Test for getting protein from protdb by preferredName
const string uniRef100A5Di11 = "UniRef100_A5DI11";
const string a5Di11 = "A5DI11";
RunUI(() =>
{
SequenceTree sequenceTree = SkylineWindow.SequenceTree;
SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SequenceTree.Nodes[SkylineWindow.SequenceTree.Nodes.Count - 1]; // Select the creation node
sequenceTree.BeginEdit(false);
// ReSharper disable LocalizableElement
sequenceTree.StatementCompletionEditBox.TextBox.Text = "EF2_PICGU"; // PreferredName for UniRef100_A5DI11
// ReSharper restore LocalizableElement
sequenceTree.CommitEditBox(false);
});
WaitForCondition(() => SkylineWindow.Document.MoleculeGroups.Any(pg => Equals(uniRef100A5Di11, pg.Name)));
doc = WaitForDocumentChange(doc);
nodeProt = doc.MoleculeGroups.First(pg => Equals(uniRef100A5Di11, pg.Name));
Assert.AreEqual(a5Di11, nodeProt.ProteinMetadata.Accession);
// Paste in some junk and make sure we handle the View Targets By* gracefully
const string badname = "badname";
RunUI(() =>
{
SequenceTree sequenceTree = SkylineWindow.SequenceTree;
SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SequenceTree.Nodes[SkylineWindow.SequenceTree.Nodes.Count - 1]; // Select the creation node
sequenceTree.BeginEdit(false);
sequenceTree.StatementCompletionEditBox.TextBox.Text = badname;
sequenceTree.CommitEditBox(false);
});
doc = WaitForDocumentChange(doc);
var nodeText = SkylineWindow.SequenceTree.GetSequenceNodes().Last(n => !SrmDocument.IsSpecialNonProteomicTestDocNode(n.DocNode)).Text;
var failsafe = String.Format(Resources.PeptideGroupTreeNode_ProteinModalDisplayText__name___0__, badname); // As in PeptideGroupTreeNode.cs
Assert.AreEqual(failsafe, nodeText);
// Revert those changes, so we can insert another way
Assert.IsTrue(SkylineWindow.SetDocument(snapshot, doc));
WaitForCondition(() => !SkylineWindow.Document.MoleculeGroups.Any(pg => Equals(uniRef100A5Di11, pg.Name)));
doc = SkylineWindow.Document;
// Test for pasting accession number in protein paste dialog, and having it populate with correct name
SetClipboardTextUI(a5Di11);
PasteDlg pasteProteinsDlgA = ShowDialog <PasteDlg>(SkylineWindow.ShowPasteProteinsDlg);
RunUI(() =>
{
var selectedNode = SkylineWindow.SequenceTree.Nodes[SkylineWindow.SequenceTree.Nodes.Count - 1];
SkylineWindow.SequenceTree.SelectedNode = selectedNode;
pasteProteinsDlgA.SelectedPath = SkylineWindow.SequenceTree.SelectedPath;
pasteProteinsDlgA.PasteProteins();
});
OkDialog(pasteProteinsDlgA, pasteProteinsDlgA.OkDialog);
WaitForCondition(() => SkylineWindow.Document.MoleculeGroups.Any(pg => Equals(uniRef100A5Di11, pg.Name)));
doc = WaitForDocumentChange(doc);
nodeProt = doc.MoleculeGroups.First(pg => Equals(uniRef100A5Di11, pg.Name));
Assert.AreEqual(a5Di11, nodeProt.ProteinMetadata.Accession);
// See what happens when you paste in a gene name shared by a couple of proteins
const string dupeGene = "Apoa2";
const string ipi00197700 = "IPI:IPI00197700.1";
SetClipboardTextUI(dupeGene);
PasteDlg pasteProteinsDlgB = ShowDialog <PasteDlg>(SkylineWindow.ShowPasteProteinsDlg);
RunUI(() =>
{
var selectedNode = SkylineWindow.SequenceTree.Nodes[SkylineWindow.SequenceTree.Nodes.Count - 1];
SkylineWindow.SequenceTree.SelectedNode = selectedNode;
pasteProteinsDlgB.SelectedPath = SkylineWindow.SequenceTree.SelectedPath;
pasteProteinsDlgB.PasteProteins();
});
OkDialog(pasteProteinsDlgB, pasteProteinsDlgB.OkDialog);
WaitForCondition(() => SkylineWindow.Document.MoleculeGroups.Any(pg => Equals(ipi00197700, pg.Name)));
doc = WaitForDocumentChange(doc);
nodeProt = doc.MoleculeGroups.First(pg => Equals(ipi00197700, pg.Name));
Assert.AreEqual(dupeGene, nodeProt.ProteinMetadata.Gene);
// Test for pasting in protein PasteDlg with sequence and metadata - metadata values are same as DocumentGrid column names
const string pasteProteinName = "Protein";
const string pasteProteinDescription = "Description";
const string pasteProteinAccession = "Accession";
const string pasteProteinPreferredName = "PreferredName";
const string pasteProteinGene = "Gene";
const string pasteProteinSpecies = "Species";
var pasteProteinText = String.Join("\t", pasteProteinName, pasteProteinDescription,
"MFEQFDLDSELLASINK IGYTKPTSIQELVIPQAMV", pasteProteinAccession, pasteProteinPreferredName, // Note the whitespace embedded in the sequence - UI should deal with that
pasteProteinGene, pasteProteinSpecies);
SetClipboardTextUI(pasteProteinText);
PasteDlg pasteProteinsDlg = ShowDialog <PasteDlg>(SkylineWindow.ShowPasteProteinsDlg);
RunUI(() =>
{
var selectedNode = SkylineWindow.SequenceTree.Nodes[SkylineWindow.SequenceTree.Nodes.Count - 1];
SkylineWindow.SequenceTree.SelectedNode = selectedNode;
pasteProteinsDlg.SelectedPath = SkylineWindow.SequenceTree.SelectedPath;
pasteProteinsDlg.PasteProteins();
});
OkDialog(pasteProteinsDlg, pasteProteinsDlg.OkDialog);
WaitForCondition(() => SkylineWindow.Document.MoleculeGroups.Any(pg => Equals(pasteProteinName, pg.Name)));
doc = WaitForDocumentChange(doc);
nodeProt = doc.MoleculeGroups.First(pg => Equals(pasteProteinName, pg.Name));
Assert.AreEqual(pasteProteinAccession, nodeProt.ProteinMetadata.Accession);
// Verify DocumentGrid's use of protein metadata - last line should agree with var pasteProteinText
var documentGrid = ShowDialog <DocumentGridForm>(() => SkylineWindow.ShowDocumentGrid(true));
RunUI(() => documentGrid.ChooseView(Resources.SkylineViewContext_GetDocumentGridRowSources_Proteins));
WaitForCondition(() => (documentGrid.RowCount > 0)); // Let it initialize
foreach (var colName in new[]
{
pasteProteinAccession,
pasteProteinPreferredName,
pasteProteinGene,
pasteProteinSpecies
})
{ // Column content should match column name, for pasteProteinText as input
string value = null;
string name = colName;
RunUI(() =>
{
var col = documentGrid.FindColumn(PropertyPath.Parse(name));
value =
documentGrid.DataGridView.Rows[documentGrid.RowCount - 1].Cells[col.Index].Value.ToString();
});
Assert.AreEqual(colName, value);
}
}
protected override void DoTest()
{
const double precursorMzAtZNeg2 = 242.0373281;
const double productMzAtZNeg2 = 213.5097436;
const double precursorCE = 1.23;
const double precursorDT = 2.34;
const double highEnergyDtOffset = -.012;
const double slens = 6.789;
const double coneVoltage = 7.89;
const double compensationVoltage = 8.901;
const double declusteringPotential = 9.012;
const double precursorRT = 3.45;
const double precursorRTWindow = 4.567;
const string note = "noted!";
var docEmpty = SkylineWindow.Document;
TestLabelsNoFormulas();
TestPrecursorTransitions();
TestTransitionListArrangementAndReporting();
string line1 = "MyMolecule\tMyMol\tMyFrag\tC34H12O4\tC34H3O\t" + precursorMzAtZNeg2 + "\t" + productMzAtZNeg2 + "\t-2\t-2\tlight\t" +
precursorRT + "\t" + precursorRTWindow + "\t" + precursorCE + "\t" + note + "\t" + precursorDT + "\t" + highEnergyDtOffset + "\t" + slens + "\t" + coneVoltage +
"\t" + compensationVoltage + "\t" + declusteringPotential; // Legit
const string line2start = "\r\nMyMolecule2\tMyMol2\tMyFrag2\tCH12O4\tCH3O\t";
const string line3 = "\r\nMyMolecule2\tMyMol2\tMyFrag2\tCH12O4\tCHH500000000\t\t\t1\t1";
const string line4 = "\r\nMyMolecule3\tMyMol3\tMyFrag3\tH2\tH\t\t\t1\t1";
// Provoke some errors
TestError(line1.Replace("C34H12O4", "C77H12O4"), // mz and formula disagree
String.Format(Resources.PasteDlg_ReadPrecursorOrProductColumns_Error_on_line__0___Precursor_m_z__1__does_not_agree_with_value__2__as_calculated_from_ion_formula_and_charge_state__delta____3___Transition_Settings___Instrument___Method_match_tolerance_m_z____4_____Correct_the_m_z_value_in_the_table__or_leave_it_blank_and_Skyline_will_calculate_it_for_you_,
1, (float)precursorMzAtZNeg2, 500.0373, 258, docEmpty.Settings.TransitionSettings.Instrument.MzMatchTolerance));
TestError(line1.Replace("C34H3", "C76H3"), // mz and formula disagree
String.Format(Resources.PasteDlg_ReadPrecursorOrProductColumns_Error_on_line__0___Product_m_z__1__does_not_agree_with_value__2__as_calculated_from_ion_formula_and_charge_state__delta____3___Transition_Settings___Instrument___Method_match_tolerance_m_z____4_____Correct_the_m_z_value_in_the_table__or_leave_it_blank_and_Skyline_will_calculate_it_for_you_,
1, (float)productMzAtZNeg2, 465.5097, 252, docEmpty.Settings.TransitionSettings.Instrument.MzMatchTolerance));
var badcharge = Transition.MAX_PRODUCT_CHARGE + 1;
TestError(line1 + line2start + "\t\t1\t" + badcharge, // Excessively large charge for product
String.Format(Resources.Transition_Validate_Product_ion_charge__0__must_be_non_zero_and_between__1__and__2__,
badcharge, -Transition.MAX_PRODUCT_CHARGE, Transition.MAX_PRODUCT_CHARGE));
badcharge = 120;
TestError(line1 + line2start + "\t\t" + badcharge + "\t1", // Insanely large charge for precursor
String.Format(Resources.Transition_Validate_Precursor_charge__0__must_be_non_zero_and_between__1__and__2__,
badcharge, -TransitionGroup.MAX_PRECURSOR_CHARGE, TransitionGroup.MAX_PRECURSOR_CHARGE));
TestError(line1 + line2start + "\t\t1\t", // No mz or charge for product
String.Format(Resources.PasteDlg_ValidateEntry_Error_on_line__0___Product_needs_values_for_any_two_of__Formula__m_z_or_Charge_, 2));
TestError(line1 + line2start + "19\t5", // Precursor Formula and m/z don't make sense together
String.Format(Resources.PasteDlg_ValidateEntry_Error_on_line__0___Precursor_formula_and_m_z_value_do_not_agree_for_any_charge_state_, 2));
TestError(line1 + line2start + "\t5\t1", // Product Formula and m/z don't make sense together
String.Format(Resources.PasteDlg_ValidateEntry_Error_on_line__0___Product_formula_and_m_z_value_do_not_agree_for_any_charge_state_, 2));
TestError(line1 + line2start + "\t", // No mz or charge for precursor or product
String.Format(Resources.PasteDlg_ValidateEntry_Error_on_line__0___Precursor_needs_values_for_any_two_of__Formula__m_z_or_Charge_, 2));
TestError(line1 + line3, // Insanely large molecule
string.Format(Resources.CustomIon_Validate_The_mass_of_the_custom_ion_exceeeds_the_maximum_of__0_, CustomIon.MAX_MASS));
TestError(line1 + line4, // Insanely small molecule
string.Format(Resources.CustomIon_Validate_The_mass_of_the_custom_ion_is_less_than_the_minimum_of__0__, CustomIon.MIN_MASS));
TestError(line1 + line2start + +precursorMzAtZNeg2 + "\t" + productMzAtZNeg2 + "\t-2\t-2\t\t\t" + precursorRTWindow + "\t" + precursorCE + "\t" + precursorDT + "\t" + highEnergyDtOffset, // Explicit retention time window without retention time
Resources.Peptide_ExplicitRetentionTimeWindow_Explicit_retention_time_window_requires_an_explicit_retention_time_value_);
for (int withSpecials = 2; withSpecials-- > 0;)
{
// By default we don't show drift or other exotic columns
var columnOrder = (withSpecials == 0) ? null : new[]
{
PasteDlg.SmallMoleculeTransitionListColumnHeaders.moleculeGroup,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.namePrecursor,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.nameProduct,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.formulaPrecursor,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.formulaProduct,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.mzPrecursor,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.mzProduct,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.chargePrecursor,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.chargeProduct,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.labelType,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.rtPrecursor,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.rtWindowPrecursor,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.cePrecursor,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.note,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.dtPrecursor,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.dtHighEnergyOffset,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.slens,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.coneVoltage,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.compensationVoltage,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.declusteringPotential,
};
// Take a legit full paste and mess with each field in turn
string[] fields = { "MyMol", "MyPrecursor", "MyProduct", "C12H9O4", "C6H4O2", "217.049535420091", "108.020580420091", "1", "1", "heavy", "123", "5", "25", "this is a note", "7", "9", "88.5", "99.6", "77.3", "66.2" };
string[] badfields = { "", "", "", "123", "123", "fish", "-345", "cat", "pig", "12", "frog", "hamster", "boston", "foosball", "greasy", "mumble", "gumdrop", "dingle", "gorse", "AHHHHHRGH" };
var expectedErrors = new List <string>()
{
Resources.PasteDlg_ShowNoErrors_No_errors, Resources.PasteDlg_ShowNoErrors_No_errors, Resources.PasteDlg_ShowNoErrors_No_errors, // No name, no problem
BioMassCalc.MONOISOTOPIC.FormatArgumentExceptionMessage(badfields[3]),
BioMassCalc.MONOISOTOPIC.FormatArgumentExceptionMessage(badfields[4]),
string.Format(Resources.PasteDlg_ReadPrecursorOrProductColumns_Invalid_m_z_value__0_, badfields[5]),
string.Format(Resources.PasteDlg_ReadPrecursorOrProductColumns_Invalid_m_z_value__0_, badfields[6]),
string.Format(Resources.PasteDlg_ReadPrecursorOrProductColumns_Invalid_charge_value__0_, badfields[7]),
string.Format(Resources.PasteDlg_ReadPrecursorOrProductColumns_Invalid_charge_value__0_, badfields[8]),
string.Format(Resources.SrmDocument_ReadLabelType_The_isotope_modification_type__0__does_not_exist_in_the_document_settings, badfields[9]),
string.Format(Resources.PasteDlg_ReadPrecursorOrProductColumns_Invalid_retention_time_value__0_, badfields[10]),
string.Format(Resources.PasteDlg_ReadPrecursorOrProductColumns_Invalid_retention_time_window_value__0_, badfields[11]),
string.Format(Resources.PasteDlg_ReadPrecursorOrProductColumns_Invalid_collision_energy_value__0_, badfields[12]),
null // Notes are freeform, so any value is fine
};
if (withSpecials > 0)
{
var s = expectedErrors.Count;
expectedErrors.Add(
string.Format(Resources.PasteDlg_ReadPrecursorOrProductColumns_Invalid_drift_time_value__0_, badfields[s++]));
expectedErrors.Add(
string.Format(Resources.PasteDlg_ReadPrecursorOrProductColumns_Invalid_drift_time_high_energy_offset_value__0_, badfields[s++]));
expectedErrors.Add(
string.Format(Resources.PasteDlg_ReadPrecursorOrProductColumns_Invalid_S_Lens_value__0_, badfields[s++]));
expectedErrors.Add(
string.Format(Resources.PasteDlg_ReadPrecursorOrProductColumns_Invalid_cone_voltage_value__0_, badfields[s++]));
expectedErrors.Add(
string.Format(Resources.PasteDlg_ReadPrecursorOrProductColumns_Invalid_compensation_voltage__0_, badfields[s++]));
expectedErrors.Add(
string.Format(Resources.PasteDlg_ReadPrecursorOrProductColumns_Invalid_declustering_potential__0_, badfields[s++]));
}
expectedErrors.Add(Resources.PasteDlg_ShowNoErrors_No_errors); // N+1'th pass is unadulterated
for (var bad = 0; bad < expectedErrors.Count(); bad++)
{
var line = "";
for (var f = 0; f < expectedErrors.Count() - 1; f++)
{
line += ((bad == f) ? badfields[f] : fields[f]).Replace(".", LocalizationHelper.CurrentCulture.NumberFormat.NumberDecimalSeparator) + "\t";
}
if (!string.IsNullOrEmpty(expectedErrors[bad]))
{
TestError(line, expectedErrors[bad], columnOrder);
}
}
}
// Now load the document with a legit paste
TestError(line1 + line2start + "\t\t1\t1", String.Empty);
var docOrig = WaitForDocumentChange(docEmpty);
var testTransitionGroups = docOrig.MoleculeTransitionGroups.ToArray();
Assert.AreEqual(2, testTransitionGroups.Count());
var transitionGroup = testTransitionGroups[0];
var precursor = docOrig.Molecules.First();
var product = transitionGroup.Transitions.First();
Assert.AreEqual(precursorCE, transitionGroup.ExplicitValues.CollisionEnergy);
Assert.AreEqual(precursorDT, transitionGroup.ExplicitValues.DriftTimeMsec);
Assert.AreEqual(slens, transitionGroup.ExplicitValues.SLens);
Assert.AreEqual(coneVoltage, transitionGroup.ExplicitValues.ConeVoltage);
Assert.AreEqual(compensationVoltage, transitionGroup.ExplicitValues.CompensationVoltage);
Assert.AreEqual(declusteringPotential, transitionGroup.ExplicitValues.DeclusteringPotential);
Assert.AreEqual(note, product.Annotations.Note);
Assert.AreEqual(highEnergyDtOffset, transitionGroup.ExplicitValues.DriftTimeHighEnergyOffsetMsec.Value, 1E-7);
Assert.AreEqual(precursorRT, precursor.ExplicitRetentionTime.RetentionTime);
Assert.AreEqual(precursorRTWindow, precursor.ExplicitRetentionTime.RetentionTimeWindow);
Assert.IsTrue(ReferenceEquals(transitionGroup.TransitionGroup, product.Transition.Group));
Assert.AreEqual(precursorMzAtZNeg2, BioMassCalc.CalculateIonMz(precursor.CustomIon.MonoisotopicMass, transitionGroup.PrecursorCharge), 1E-7);
Assert.AreEqual(productMzAtZNeg2, BioMassCalc.CalculateIonMz(product.GetIonMass(), product.Transition.Charge), 1E-7);
// Does that produce the expected transition list file?
TestTransitionListOutput(docOrig, "PasteMoleculeTinyTest.csv", "PasteMoleculeTinyTestExpected.csv", ExportFileType.IsolationList);
// Does serialization of imported values work properly?
AssertEx.Serializable(docOrig);
// Reset
RunUI(() =>
{
SkylineWindow.NewDocument(true);
docOrig = SkylineWindow.Document;
});
// Now a proper user data set
var pasteDlg = ShowDialog <PasteDlg>(SkylineWindow.ShowPasteTransitionListDlg);
PasteDlg dlg = pasteDlg;
RunUI(() =>
{
dlg.IsMolecule = true;
dlg.SetSmallMoleculeColumns(null); // Reset column headers to default selection and order
});
// Formerly SetExcelFileClipboardText(TestFilesDir.GetTestPath("MoleculeTransitionList.xlsx"),"sheet1",6,false); but TeamCity doesn't like that
SetCsvFileClipboardText(TestFilesDir.GetTestPath("MoleculeTransitionList.csv"));
RunUI(pasteDlg.PasteTransitions);
OkDialog(pasteDlg, pasteDlg.OkDialog);
var pastedDoc = WaitForDocumentChange(docOrig);
AssertEx.Serializable(pastedDoc);
RunUI(() => SkylineWindow.SaveDocument(TestFilesDir.GetTestPath("PasteMolecules.Sky")));
var paths = new []
{
"13417_02_WAA283_3805_071514" + ExtensionTestContext.ExtWatersRaw,
"13417_03_WAA283_3805_071514" + ExtensionTestContext.ExtWatersRaw,
"13418_02_WAA283_3805_071514" + ExtensionTestContext.ExtWatersRaw,
"13418_03_WAA283_3805_071514" + ExtensionTestContext.ExtWatersRaw,
};
var doc = SkylineWindow.Document;
RunUI(() => SkylineWindow.ChangeSettings(doc.Settings.
ChangeTransitionSettings(
doc.Settings.TransitionSettings.ChangeInstrument(
doc.Settings.TransitionSettings.Instrument.ChangeMzMatchTolerance(0.6))), true));
PasteMoleculesTestImportResults(paths);
var importDoc = SkylineWindow.Document;
var transitionCount = importDoc.MoleculeTransitionCount;
var tranWithResults = importDoc.MoleculeTransitions.Count(tran => tran.HasResults);
var tranWithPeaks = importDoc.MoleculeTransitions.Count(tran =>
{
for (int i = 0; i < 4; i++)
{
if (tran.GetPeakCountRatio(i) > 0)
{
return(true);
}
}
return(false);
});
// PauseTest(); // Pretty pictures!
Assert.AreEqual(98, transitionCount);
Assert.AreEqual(98, tranWithResults);
Assert.AreEqual(90, tranWithPeaks);
// Does that produce the expected transition list file?
TestTransitionListOutput(importDoc, "PasteMoleculeTest.csv", "PasteMoleculeTestExpected.csv", ExportFileType.List);
// Verify that MS1 filtering works properly
var pasteText =
"Steryl esters [ST0102],12:0 Cholesteryl ester,C39H68O2NH4,1\r\n" +
"Steryl esters [ST0102],14:0 Cholesteryl ester,C41H72O2NH4,1\r\n" +
"Steryl esters [ST0102],14:1 Cholesteryl ester,C41H70O2NH4,1\r\n" +
"Steryl esters [ST0102],15:1 Cholesteryl ester,C42H72O2NH4,1";
var columnOrderB = new[]
{
PasteDlg.SmallMoleculeTransitionListColumnHeaders.moleculeGroup,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.namePrecursor,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.formulaPrecursor,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.chargePrecursor,
};
// Doc is set for MS1 filtering, precursor transitions, charge=1, two peaks, should show M and M+1, M+2 after filter is invoked by changing to 3 peaks
RunUI(() => SkylineWindow.OpenFile(TestFilesDir.GetTestPath("small_molecule_missing_m1.sky")));
WaitForDocumentLoaded();
TestError(pasteText, String.Empty, columnOrderB);
var docB = SkylineWindow.Document;
Assert.AreEqual(4, docB.MoleculeTransitionCount); // Initial import is faithful to what's pasted
var transitionSettingsUI = ShowDialog <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
RunUI(() =>
{
transitionSettingsUI.SelectedTab = TransitionSettingsUI.TABS.FullScan;
transitionSettingsUI.Peaks = 3;
});
OkDialog(transitionSettingsUI, transitionSettingsUI.OkDialog);
docB = WaitForDocumentChange(docB);
Assert.AreEqual(12, docB.MoleculeTransitionCount);
// Verify that we can import heavy/light pairs
var columnOrderC = new[]
{
PasteDlg.SmallMoleculeTransitionListColumnHeaders.moleculeGroup,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.namePrecursor,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.formulaPrecursor,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.mzProduct,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.chargePrecursor,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.chargeProduct,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.labelType,
};
pasteText =
"A,27-HC,C36H57N2O3,135,1,1,light\r\n" +
"A,27-HC,C36H57N2O3,181,1,1,light\r\n" +
"A,27-HC,C36H57N2O3,367,1,1,light\r\n" +
"A,27-HC,C36H51H'6N2O3,135,1,1,heavy\r\n" +
"A,27-HC,C36H51H'6N2O3,181,1,1,heavy\r\n" +
"A,27-HC,C36H51H'6N2O3,215,1,1,heavy\r\n";
RunUI(() =>
{
SkylineWindow.NewDocument(true);
});
TestError(pasteText, String.Empty, columnOrderC);
var docC = SkylineWindow.Document;
Assert.AreEqual(1, docC.MoleculeGroupCount);
Assert.AreEqual(1, docC.MoleculeCount);
Assert.AreEqual(2, docC.MoleculeTransitionGroupCount);
}
private static void VerifyTransitionListError(PasteDlg insertTransDlg, string insertListText,
object oldValue, object newValue, int row, int col)
{
VerifyTransitionListError(insertTransDlg, insertListText, oldValue, newValue, newValue, row, col);
}
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
var docB = SkylineWindow.Document;
OkDialog(peptideSettingsUI, peptideSettingsUI.OkDialog);
WaitForDocumentChange(docB);
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);
}
}
}
