public void ConvertDocumentToSmallMolecules(RefinementSettings.ConvertToSmallMoleculesMode mode = RefinementSettings.ConvertToSmallMoleculesMode.formulas,
RefinementSettings.ConvertToSmallMoleculesChargesMode invertCharges = RefinementSettings.ConvertToSmallMoleculesChargesMode.none,
bool ignoreDecoys = false)
{
var doc = WaitForDocumentLoaded();
RunUI(() => SkylineWindow.ModifyDocument("Convert to small molecules", document =>
{
var refine = new RefinementSettings();
var path = Path.GetDirectoryName(SkylineWindow.DocumentFilePath);
var smallMolDoc = refine.ConvertToSmallMolecules(document, path, mode, invertCharges, ignoreDecoys);
CheckConsistentLibraryInfo(smallMolDoc);
return(smallMolDoc);
}));
WaitForDocumentChange(doc);
var newDocFileName =
SkylineWindow.DocumentFilePath.Contains(BiblioSpecLiteSpec.DotConvertedToSmallMolecules) ?
SkylineWindow.DocumentFilePath :
SkylineWindow.DocumentFilePath.Replace(".sky", BiblioSpecLiteSpec.DotConvertedToSmallMolecules + ".sky");
RunUI(() => SkylineWindow.SaveDocument(newDocFileName));
WaitForCondition(() => File.Exists(newDocFileName));
RunUI(() => SkylineWindow.OpenFile(newDocFileName));
WaitForDocumentLoaded();
CheckConsistentLibraryInfo();
Thread.Sleep(1000);
}
public void DoTestExportIsolationList(RefinementSettings.ConvertToSmallMoleculesMode asSmallMolecules,
bool asExplicitRetentionTimes = false, RefinementSettings.ConvertToSmallMoleculesChargesMode negativeCharges = RefinementSettings.ConvertToSmallMoleculesChargesMode.none, bool withSLens = false)
{
if (asSmallMolecules != RefinementSettings.ConvertToSmallMoleculesMode.none && !RunSmallMoleculeTestVersions)
{
Console.Write(MSG_SKIPPING_SMALLMOLECULE_TEST_VERSION);
return;
}
SmallMoleculeTestMode = asSmallMolecules;
AsSmallMoleculesNegativeMode = negativeCharges;
AsSmallMoleculesNegative = negativeCharges != RefinementSettings.ConvertToSmallMoleculesChargesMode.none;
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 (SmallMoleculeTestMode != RefinementSettings.ConvertToSmallMoleculesMode.none)
{
TestDirectoryName = "AsSmallMolecules_" + SmallMoleculeTestMode;
}
if (AsSmallMoleculesNegative)
{
TestDirectoryName += "_Negative_" + AsSmallMoleculesNegativeMode;
}
if (WithSLens)
{
TestDirectoryName += "WithSLens";
}
RunFunctionalTest();
}
