Exemple #1
0
        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();
        }
Exemple #2
0
        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();
        }
Exemple #3
0
        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);*/
        }