public void OkDialog()
{
var helper = new MessageBoxHelper(this);
int numDecoys;
if (!helper.ValidateNumberTextBox(textNumberOfDecoys, 0, null, out numDecoys))
{
return;
}
int numComparableGroups = RefinementSettings.SuggestDecoyCount(_document);
if (numComparableGroups == 0)
{
helper.ShowTextBoxError(textNumberOfDecoys, Resources.GenerateDecoysError_No_peptide_precursor_models_for_decoys_were_found_);
return;
}
if (!Equals(DecoysMethod, DecoyGeneration.SHUFFLE_SEQUENCE) && numComparableGroups < numDecoys)
{
helper.ShowTextBoxError(textNumberOfDecoys,
Resources.GenerateDecoysDlg_OkDialog_The_number_of_peptides__0__must_be_less_than_the_number_of_peptide_precursor_models_for_decoys__1___or_use_the___2___decoy_generation_method_,
null, numComparableGroups, DecoyGeneration.SHUFFLE_SEQUENCE);
return;
}
_numDecoys = numDecoys;
DialogResult = DialogResult.OK;
}
public GenerateDecoysDlg(SrmDocument document)
{
_document = document;
InitializeComponent();
Icon = Resources.Skyline;
// Set initial decoys number
textNumberOfDecoys.Text = RefinementSettings.SuggestDecoyCount(document).ToString(LocalizationHelper.CurrentCulture);
// Fill method type combo box
comboDecoysGenerationMethod.Items.AddRange(DecoyGeneration.Methods.Cast <object>().ToArray());
comboDecoysGenerationMethod.SelectedIndex = 0;
}
protected override void DoTest()
{
// DDA with IDs and alignment
string filePathDda = TestFilesDir.GetTestPath(@"DDA\Bereman_5proteins_spikein_decoys.sky.zip");
RunUI(() => SkylineWindow.OpenSharedFile(filePathDda));
var doc = WaitForDocumentLoaded();
int expectedDecoys = RefinementSettings.SuggestDecoyCount(doc);
RunDlg <GenerateDecoysDlg>(() => SkylineWindow.ShowGenerateDecoysDlg(), decoysDlg =>
{
decoysDlg.DecoysMethod = DecoyGeneration.SHUFFLE_SEQUENCE;
decoysDlg.OkDialog();
});
doc = WaitForDocumentChange(doc);
Assert.AreEqual(expectedDecoys, doc.Peptides.Count(p => p.IsDecoy));
ImportResultsFiles(DDA_FILES.Select(s => GetDataFile("DDA", s)).Select(MsDataFileUri.Parse));
RunUI(() =>
{
SkylineWindow.SaveDocument();
SkylineWindow.ArrangeGraphsTiled();
SkylineWindow.ShowAlignedPeptideIDTimes(true);
SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SequenceTree.SelectedNode.FirstNode;
});
// Random nature of decoys makes it hard to make this very deterministic
// But eventually we should see some peptides without IDs of their own
// All peptides should have aligned IDs, if they don't have a single ID,
// since it might be the only ID
int countWithIds = 0, countTotal = 0;
while (countWithIds < 20 || countTotal - 4 < countWithIds)
{
WaitForGraphs();
RunUI(() =>
{
foreach (var graphChromatogram in SkylineWindow.GraphChromatograms)
{
countTotal++;
int countIds = graphChromatogram.RetentionMsMs != null
? graphChromatogram.RetentionMsMs.Length
: 0;
if (countIds != 1)
{
Assert.IsNotNull(graphChromatogram.AlignedRetentionMsMs);
Assert.AreNotEqual(0, graphChromatogram.AlignedRetentionMsMs.Length);
}
if (countIds > 0)
{
ValidateTimeRange(graphChromatogram, graphChromatogram.RetentionMsMs, 6, 90);
countWithIds++;
}
else
{
ValidateTimeRange(graphChromatogram, graphChromatogram.AlignedRetentionMsMs, 6, 90);
}
}
var nextNode = SkylineWindow.SequenceTree.SelectedNode.NextNode;
if (nextNode != null)
{
SkylineWindow.SequenceTree.SelectedNode = nextNode;
}
});
}
// DIA with DDA IDs
string filePathDia = TestFilesDir.GetTestPath(@"DIA\Hoofnagle_QE_DIA_targeted_decoys.sky.zip");
RunUI(() => SkylineWindow.OpenSharedFile(filePathDia));
doc = WaitForDocumentLoaded();
expectedDecoys = RefinementSettings.SuggestDecoyCount(doc);
RunDlg <GenerateDecoysDlg>(() => SkylineWindow.ShowGenerateDecoysDlg(), decoysDlg =>
{
decoysDlg.DecoysMethod = DecoyGeneration.REVERSE_SEQUENCE;
decoysDlg.OkDialog();
});
doc = WaitForDocumentChange(doc);
Assert.AreEqual(expectedDecoys, doc.Peptides.Count(p => p.IsDecoy));
ImportResultsFiles(DIA_FILES.Select(s => GetDataFile("DIA", s)).Select(MsDataFileUri.Parse));
RunUI(() =>
{
SkylineWindow.SaveDocument();
SkylineWindow.ArrangeGraphsTiled();
SkylineWindow.ShowOtherRunPeptideIDTimes(true);
SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SequenceTree.SelectedNode.FirstNode;
});
for (int i = 0; i < 6; i++)
{
WaitForGraphs();
RunUI(() =>
{
foreach (var graphChromatogram in SkylineWindow.GraphChromatograms)
{
Assert.IsNull(graphChromatogram.RetentionMsMs);
Assert.IsNull(graphChromatogram.AlignedRetentionMsMs);
Assert.IsNotNull(graphChromatogram.UnalignedRetentionMsMs);
Assert.AreNotEqual(0, graphChromatogram.UnalignedRetentionMsMs.Length);
ValidateTimeRange(graphChromatogram, graphChromatogram.UnalignedRetentionMsMs, 8, 120);
}
SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SequenceTree.SelectedNode.NextNode;
});
}
// DIA with IRT values
string filePathDiaIrt = TestFilesDir.GetTestPath(@"DIA-iRT\AQUA4_Human_picked_napedro2_full_rescore_iRT_decoys.sky.zip");
RunUI(() => SkylineWindow.OpenSharedFile(filePathDiaIrt));
doc = WaitForDocumentLoaded();
expectedDecoys = RefinementSettings.SuggestDecoyCount(doc);
RunDlg <GenerateDecoysDlg>(() => SkylineWindow.ShowGenerateDecoysDlg(), decoysDlg =>
{
decoysDlg.DecoysMethod = DecoyGeneration.SHUFFLE_SEQUENCE;
decoysDlg.OkDialog();
});
doc = WaitForDocumentChange(doc);
Assert.AreEqual(expectedDecoys, doc.Peptides.Count(p => p.IsDecoy));
ImportResultsFile(GetDataFile("DIA-iRT", IRT_FILES[0]));
RunUI(() =>
{
SkylineWindow.SaveDocument();
SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SequenceTree.SelectedNode.FirstNode;
});
for (int i = 0; i < 6; i++)
{
WaitForGraphs();
RunUI(() =>
{
foreach (var graphChromatogram in SkylineWindow.GraphChromatograms)
{
Assert.IsNull(graphChromatogram.RetentionMsMs);
Assert.IsNull(graphChromatogram.AlignedRetentionMsMs);
Assert.IsNull(graphChromatogram.UnalignedRetentionMsMs);
Assert.IsTrue(graphChromatogram.PredictedRT.HasValue);
ValidateTimeRange(graphChromatogram, new [] { graphChromatogram.PredictedRT.Value }, 8, 135);
}
SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SequenceTree.SelectedNode.NextNode;
});
}
}
