public void ApplyQonverterSettings(IDictionary<Analysis, QonverterSettings> qonverterSettings)
{
clearData();
setControlsWhenDatabaseLocked(true);
var workerThread = new BackgroundWorker()
{
WorkerReportsProgress = true,
WorkerSupportsCancellation = true
};
workerThread.DoWork += (s, e) =>
{
var qonverter = new Qonverter();
qonverter.QonversionProgress += progressMonitor.UpdateProgress;
foreach (var item in qonverterSettings)
qonverter.SettingsByAnalysis[(int) item.Key.Id] = item.Value.ToQonverterSettings();
//qonverter.LogQonversionDetails = true;
qonverter.Reset(Text);
qonverter.Qonvert(Text);
};
workerThread.RunWorkerCompleted += (s, e) =>
{
if (e.Result is Exception)
{
Program.HandleException(e.Result as Exception);
setControlsWhenDatabaseLocked(false);
return;
}
lock (session)
{
var sessionFactory = DataModel.SessionFactoryFactory.CreateSessionFactory(Text, new SessionFactoryConfig { WriteSqlToConsoleOut = true });
session = sessionFactory.OpenSession();
//session.CreateSQLQuery("PRAGMA temp_store=MEMORY").ExecuteUpdate();
_layoutManager.SetSession(session);
// delete old filters since they are not valid with different qonverter settings
session.CreateSQLQuery("DELETE FROM FilterHistory").ExecuteUpdate();
session.Clear();
if (basicFilter == null)
basicFilter = new DataFilter()
{
MaximumQValue = 0.02,
MinimumDistinctPeptides = 2,
MinimumSpectra = 2,
MinimumAdditionalPeptides = 1,
GeneLevelFiltering = false,
DistinctMatchFormat = new DistinctMatchFormat
{
IsChargeDistinct = true,
IsAnalysisDistinct = false,
AreModificationsDistinct = true,
ModificationMassRoundToNearest = 1.0m
}
};
basicFilterControl.DataFilter = basicFilter;
viewFilter = basicFilter;
session.Close();
sessionFactory.Close();
}
progressMonitor = new ProgressMonitor();
progressMonitor.ProgressUpdate += progressMonitor_ProgressUpdate;
basicFilterControl = new BasicFilterControl();
basicFilterControl.BasicFilterChanged += basicFilterControl_BasicFilterChanged;
basicFilterControl.ShowQonverterSettings += ShowQonverterSettings;
dataFilterPopup = new Popup(basicFilterControl) { FocusOnOpen = true };
dataFilterPopup.Closed += dataFilterPopup_Closed;
new Thread(() => OpenFiles(new List<string> { Text }, null)).Start();
};
workerThread.RunWorkerAsync();
}
void openToolStripMenuItem_Click(object sender, EventArgs e)
{
List<string> fileNames;
TreeNode treeStructure = null;
if (sender == openToolStripMenuItem)
{
var ofd = new OpenFileDialog
{
Filter = "IDPicker DB|*.idpDB",
Multiselect = true,
SupportMultiDottedExtensions = true
};
var folderHistory = FolderHistoryInterface.GetRecentFolders();
if (folderHistory.Any() && Directory.Exists(folderHistory.Last()))
ofd.InitialDirectory = folderHistory.First();
if (ofd.ShowDialog() == DialogResult.OK)
{
fileNames = ofd.FileNames.ToList();
if (fileNames.Any())
{
var baseDirectory = Path.GetDirectoryName(fileNames[0]);
foreach (var file in fileNames)
if (Path.GetDirectoryName(file) != baseDirectory)
baseDirectory = null;
if (baseDirectory != null)
FolderHistoryInterface.AddFolderToHistory(baseDirectory);
}
}
else return;
}
else
{
var fileTypeList = new List<string>
{
"IDPicker files|*.idpDB;*.mzid;*.pepXML;*.pep.xml;*.xml;*.dat",
"Importable files|*.mzid;*.pepXML;*.pep.xml;*.xml;*.dat",
"MzIdentML files|*.mzid;*.xml",
"PepXML files|*.pepXML;*.pep.xml;*.xml",
"Mascot files|*.dat",
//"IDPicker XML|*.idpXML",
"IDPicker DB|*.idpDB",
"All files|*.*"
};
var openFileDialog = new IDPOpenDialog(fileTypeList);
if (openFileDialog.ShowDialog() == DialogResult.OK)
{
fileNames = openFileDialog.GetFileNames().Distinct().ToList();
if (session != null && sender == importToolStripMenuItem)
treeStructure = openFileDialog.GetTreeStructure(session);
else
treeStructure = openFileDialog.GetTreeStructure();
if (!fileNames.Any())
return;
}
else return;
}
clearData();
progressMonitor = new ProgressMonitor();
progressMonitor.ProgressUpdate += progressMonitor_ProgressUpdate;
basicFilterControl = new BasicFilterControl();
basicFilterControl.BasicFilterChanged += basicFilterControl_BasicFilterChanged;
basicFilterControl.ApplyFilterChanges += basicFilterControl_ApplyFilterChanges;
basicFilterControl.ShowQonverterSettings += ShowQonverterSettings;
dataFilterPopup = new Popup(basicFilterControl) {FocusOnOpen = true};
dataFilterPopup.Closed += dataFilterPopup_Closed;
breadCrumbControl.ClearBreadcrumbs();
if (session != null)
{
if (sender == importToolStripMenuItem)
{
//add current session to file list
var idpDbFilepath = session.Connection.GetDataSource();
if (!fileNames.Contains(idpDbFilepath))
fileNames.Add(idpDbFilepath);
}
clearSession();
}
//System.Data.SQLite.SQLiteConnection.ClearAllPools();
new Thread(() => { OpenFiles(fileNames, treeStructure); }).Start();
}
public IDPickerForm (IList<string> args)
{
InitializeComponent();
toolStripStatusLabel.Text = "Initializing...";
Thread.CurrentThread.Priority = ThreadPriority.AboveNormal;
this.args = args;
defaultDataFilter = new DataFilter();
manager = new Manager(dockPanel)
{
ShowChromatogramListForNewSources = false,
ShowSpectrumListForNewSources = false,
OpenFileUsesCurrentGraphForm = true,
};
progressMonitor = new ProgressMonitor();
progressMonitor.ProgressUpdate += progressMonitor_ProgressUpdate;
if (Program.IsHeadless)
Load += IDPickerForm_Load;
else
Shown += IDPickerForm_Load;
basicFilterControl = new BasicFilterControl();
basicFilterControl.BasicFilterChanged += basicFilterControl_BasicFilterChanged;
basicFilterControl.ApplyFilterChanges += basicFilterControl_ApplyFilterChanges;
basicFilterControl.ShowQonverterSettings += ShowQonverterSettings;
dataFilterPopup = new Popup(basicFilterControl) { FocusOnOpen = true };
dataFilterPopup.Closed += dataFilterPopup_Closed;
breadCrumbControl = new BreadCrumbControl() { Dock = DockStyle.Fill };
breadCrumbControl.BreadCrumbClicked += breadCrumbControl_BreadCrumbClicked;
breadCrumbPanel.Controls.Add(breadCrumbControl);
fragmentationStatisticsForm = new FragmentationStatisticsForm(this);
fragmentationStatisticsForm.Show(dockPanel, DockState.DockBottomAutoHide);
fragmentationStatisticsForm.AutoHidePortion = 0.5;
peakStatisticsForm = new PeakStatisticsForm(this);
peakStatisticsForm.Show(dockPanel, DockState.DockBottomAutoHide);
peakStatisticsForm.AutoHidePortion = 0.5;
distributionStatisticsForm = new DistributionStatisticsForm(this);
distributionStatisticsForm.Show(dockPanel, DockState.DockBottomAutoHide);
distributionStatisticsForm.AutoHidePortion = 0.5;
reassignPSMsForm = new RescuePSMsForm(this);
reassignPSMsForm.Show(dockPanel, DockState.DockBottomAutoHide);
reassignPSMsForm.AutoHidePortion = 0.5;
ptmAttestationForm = new PTMAttestationForm(this);
ptmAttestationForm.Show(dockPanel, DockState.DockBottomAutoHide);
ptmAttestationForm.AutoHidePortion = 0.5;
spectrumTableForm = new SpectrumTableForm();
spectrumTableForm.Show(dockPanel, DockState.DockLeft);
spectrumTableForm.AutoHidePortion = 0.5;
proteinTableForm = new ProteinTableForm();
proteinTableForm.Show(dockPanel, DockState.DockTop);
proteinTableForm.AutoHidePortion = 0.5;
peptideTableForm = new PeptideTableForm();
peptideTableForm.Show(dockPanel, DockState.DockTop);
peptideTableForm.AutoHidePortion = 0.5;
proteinTableForm.Activate();
modificationTableForm = new ModificationTableForm();
modificationTableForm.Show(dockPanel, DockState.Document);
modificationTableForm.AutoHidePortion = 0.5;
analysisTableForm = new AnalysisTableForm();
analysisTableForm.Show(dockPanel, DockState.Document);
analysisTableForm.AutoHidePortion = 0.5;
filterHistoryForm = new FilterHistoryForm();
filterHistoryForm.Show(dockPanel, DockState.Document);
filterHistoryForm.AutoHidePortion = 0.5;
spectrumTableForm.SpectrumViewFilter += handleViewFilter;
spectrumTableForm.SpectrumViewVisualize += spectrumTableForm_SpectrumViewVisualize;
spectrumTableForm.FinishedSetData += handleFinishedSetData;
spectrumTableForm.StartingSetData += handleStartingSetData;
proteinTableForm.ProteinViewFilter += handleViewFilter;
proteinTableForm.ProteinViewVisualize += proteinTableForm_ProteinViewVisualize;
proteinTableForm.FinishedSetData += handleFinishedSetData;
proteinTableForm.StartingSetData += handleStartingSetData;
peptideTableForm.PeptideViewFilter += handleViewFilter;
peptideTableForm.FinishedSetData += handleFinishedSetData;
peptideTableForm.StartingSetData += handleStartingSetData;
modificationTableForm.ModificationViewFilter += handleViewFilter;
modificationTableForm.FinishedSetData += handleFinishedSetData;
modificationTableForm.StartingSetData += handleStartingSetData;
analysisTableForm.AnalysisViewFilter += handleViewFilter;
analysisTableForm.FinishedSetData += handleFinishedSetData;
analysisTableForm.StartingSetData += handleStartingSetData;
filterHistoryForm.LoadPersistentDataFilter += handleLoadPersistentDataFilter;
//filterHistoryForm.FinishedSetData += handleFinishedSetData;
//filterHistoryForm.StartingSetData += handleStartingSetData;
// hide DockPanel before initializing layout manager
dockPanel.Visible = false;
dockPanel.ShowDocumentIcon = true;
persistentForms = new IPersistentForm[]
{
proteinTableForm,
peptideTableForm,
spectrumTableForm,
analysisTableForm,
filterHistoryForm
};
_layoutManager = new LayoutManager(this, dockPanel, persistentForms);
// load last or default location and size
_layoutManager.LoadMainFormSettings();
// certain features are only enabled for development builds
if (Application.ExecutablePath.Contains("build-nt-x86"))
{
// provide SQL logging for development builds
logForm = new LogForm();
logForm.AutoHidePortion = 0.25;
Console.SetOut(logForm.LogWriter);
developerToolStripMenuItem.ForeColor = SystemColors.MenuBar;
}
else
{
Console.SetOut(TextWriter.Null);
developerToolStripMenuItem.Visible = false;
}
/*spyEventLogForm = new SpyEventLogForm();
spyEventLogForm.AddEventSpy(new EventSpy("proteinTableForm", proteinTableForm));
spyEventLogForm.AddEventSpy(new EventSpy("peptideTableForm", peptideTableForm));
spyEventLogForm.AddEventSpy(new EventSpy("spectrumTableForm", spectrumTableForm));
spyEventLogForm.AddEventSpy(new EventSpy("modificationTableForm", modificationTableForm));
spyEventLogForm.Show(dockPanel, DockState.DockBottomAutoHide);*/
}