public CommandLineUI(string[] args, CommandStatusWriter consoleOut)
{
_commandArgs = new CommandArgs(consoleOut, false);
if (!_commandArgs.ParseArgs(args))
{
consoleOut.WriteLine(Resources.CommandLine_Run_Exiting___);
return;
}
Program.UnitTest = Program.FunctionalTest = true;
Program.TestExceptions = new List <Exception>();
Program.NoSaveSettings = true;
Program.DisableJoining = _commandArgs.ImportDisableJoining;
Program.NoAllChromatogramsGraph = _commandArgs.NoAllChromatogramsGraph;
Settings.Default.AutoShowAllChromatogramsGraph = !_commandArgs.HideAllChromatogramsGraph;
LocalizationHelper.InitThread();
// Run test in new thread (Skyline on main thread).
Program.Init();
Settings.Default.SrmSettingsList[0] = SrmSettingsList.GetDefault();
// Reset defaults with names from resources for testing different languages
Settings.Default.BackgroundProteomeList[0] = BackgroundProteomeList.GetDefault();
Settings.Default.DeclusterPotentialList[0] = DeclusterPotentialList.GetDefault();
Settings.Default.RetentionTimeList[0] = RetentionTimeList.GetDefault();
Settings.Default.ShowStartupForm = false;
var threadTest = new Thread(Run);
LocalizationHelper.InitThread(threadTest);
threadTest.Start();
Program.Main();
threadTest.Join();
}
public void SettingsChangeNotDoc()
{
SrmDocument docFasta = CreateMixedDoc();
SrmSettings settings = docFasta.Settings;
// Change declustering potential, collision energy, and retention time
var regressions = new DeclusterPotentialList();
regressions.AddDefaults();
var dpRegress = regressions["SCIEX"];
var collisions = new CollisionEnergyList();
collisions.AddDefaults();
var ceRegress = collisions["SCIEX"];
var calc = Settings.Default.RTScoreCalculatorList.GetDefaults().First();
var rtRegress = new RetentionTimeRegression("Test", calc, 3.5, 10.4, 12.8,
new MeasuredRetentionTime[0]);
SrmSettings settings2 = settings.ChangePeptidePrediction(p => p.ChangeRetentionTime(rtRegress)).
ChangeTransitionPrediction(p => p.ChangeCollisionEnergy(ceRegress).ChangeDeclusteringPotential(dpRegress));
SrmDocument docFasta2 = docFasta.ChangeSettings(settings2);
AssertEx.IsDocumentState(docFasta2, docFasta.RevisionIndex + 1, 3, 111, 352);
Assert.AreSame(docFasta.Children, docFasta2.Children);
Assert.AreNotEqual(docFasta.Settings, docFasta2.Settings);
// Change auto-select toggles
SrmSettings settings3 = settings.ChangePeptideFilter(f => f.ChangeAutoSelect(false)).
ChangeTransitionFilter(f => f.ChangeAutoSelect(false));
SrmDocument docFasta3 = docFasta.ChangeSettings(settings3);
AssertEx.IsDocumentState(docFasta3, docFasta.RevisionIndex + 1, 3, 111, 352);
Assert.AreSame(docFasta.Children, docFasta3.Children);
Assert.AreNotEqual(docFasta.Settings, docFasta3.Settings);
}
public void SettingsChangeNotDoc()
{
SrmDocument docFasta = CreateMixedDoc();
SrmSettings settings = docFasta.Settings;
// Change declustering potential, collision energy, and retention time
var regressions = new DeclusterPotentialList();
regressions.AddDefaults();
var dpRegress = regressions["ABI"];
var collisions = new CollisionEnergyList();
collisions.AddDefaults();
var ceRegress = collisions["ABI 4000 QTrap"];
var calc = Settings.Default.RTScoreCalculatorList.GetDefaults().First();
var rtRegress = new RetentionTimeRegression("Test", calc, 3.5, 10.4, 12.8,
new MeasuredRetentionTime[0]);
SrmSettings settings2 = settings.ChangePeptidePrediction(p => p.ChangeRetentionTime(rtRegress)).
ChangeTransitionPrediction(p => p.ChangeCollisionEnergy(ceRegress).ChangeDeclusteringPotential(dpRegress));
SrmDocument docFasta2 = docFasta.ChangeSettings(settings2);
AssertEx.IsDocumentState(docFasta2, docFasta.RevisionIndex + 1, 3, 111, 352);
Assert.AreSame(docFasta.Children, docFasta2.Children);
Assert.AreNotEqual(docFasta.Settings, docFasta2.Settings);
// Change auto-select toggles
SrmSettings settings3 = settings.ChangePeptideFilter(f => f.ChangeAutoSelect(false)).
ChangeTransitionFilter(f => f.ChangeAutoSelect(false));
SrmDocument docFasta3 = docFasta.ChangeSettings(settings3);
AssertEx.IsDocumentState(docFasta3, docFasta.RevisionIndex + 1, 3, 111, 352);
Assert.AreSame(docFasta.Children, docFasta3.Children);
Assert.AreNotEqual(docFasta.Settings, docFasta3.Settings);
}
