Beispiel #1
0
        public bool BuildPeptideSearchLibrary(CancelEventArgs e)
        {
            // Nothing to build, if now search files were specified
            if (!SearchFilenames.Any())
            {
                var libraries = SkylineWindow.Document.Settings.PeptideSettings.Libraries;
                if (!libraries.HasLibraries)
                {
                    return(false);
                }
                var libSpec = libraries.LibrarySpecs.FirstOrDefault(s => s.IsDocumentLibrary);
                return(libSpec != null && LoadPeptideSearchLibrary(libSpec));
            }

            double           cutOffScore;
            MessageBoxHelper helper = new MessageBoxHelper(WizardForm);

            if (!helper.ValidateDecimalTextBox(textCutoff, 0, 1.0, out cutOffScore))
            {
                e.Cancel = true;
                return(false);
            }
            ImportPeptideSearch.CutoffScore = cutOffScore;

            BiblioSpecLiteBuilder builder;

            try
            {
                builder = ImportPeptideSearch.GetLibBuilder(SkylineWindow.Document, SkylineWindow.DocumentFilePath, cbIncludeAmbiguousMatches.Checked);
            }
            catch (FileEx.DeleteException de)
            {
                MessageDlg.ShowException(this, de);
                return(false);
            }

            using (var longWaitDlg = new LongWaitDlg
            {
                Text = Resources.BuildPeptideSearchLibraryControl_BuildPeptideSearchLibrary_Building_Peptide_Search_Library,
                Message = Resources.BuildPeptideSearchLibraryControl_BuildPeptideSearchLibrary_Building_document_library_for_peptide_search_,
            })
            {
                // Disable the wizard, because the LongWaitDlg does not
                try
                {
                    ImportPeptideSearch.ClosePeptideSearchLibraryStreams(SkylineWindow.DocumentUI);
                    var status = longWaitDlg.PerformWork(WizardForm, 800,
                                                         monitor => LibraryManager.BuildLibraryBackground(SkylineWindow, builder, monitor, new LibraryManager.BuildState(null, null)));
                    if (status.IsError)
                    {
                        MessageDlg.ShowException(WizardForm, status.ErrorException);
                        return(false);
                    }
                }
                catch (Exception x)
                {
                    MessageDlg.ShowWithException(WizardForm, TextUtil.LineSeparate(string.Format(Resources.BuildPeptideSearchLibraryControl_BuildPeptideSearchLibrary_Failed_to_build_the_library__0__,
                                                                                                 Path.GetFileName(BiblioSpecLiteSpec.GetLibraryFileName(SkylineWindow.DocumentFilePath))), x.Message), x);
                    return(false);
                }
            }

            var docLibSpec = builder.LibrarySpec.ChangeDocumentLibrary(true);

            Settings.Default.SpectralLibraryList.Insert(0, docLibSpec);

            // Go ahead and load the library - we'll need it for
            // the modifications and chromatograms page.
            if (!LoadPeptideSearchLibrary(docLibSpec))
            {
                return(false);
            }

            var selectedIrtStandard = comboStandards.SelectedItem as IrtStandard;
            var addedIrts           = false;

            if (selectedIrtStandard != null && selectedIrtStandard != IrtStandard.NULL)
            {
                addedIrts = AddIrtLibraryTable(docLibSpec.FilePath, selectedIrtStandard);
            }

            var docNew = ImportPeptideSearch.AddDocumentSpectralLibrary(SkylineWindow.Document, docLibSpec);

            if (docNew == null)
            {
                return(false);
            }

            if (addedIrts)
            {
                docNew = ImportPeptideSearch.AddRetentionTimePredictor(docNew, docLibSpec);
            }

            SkylineWindow.ModifyDocument(Resources.BuildPeptideSearchLibraryControl_BuildPeptideSearchLibrary_Add_document_spectral_library, doc => docNew);

            if (!string.IsNullOrEmpty(builder.AmbiguousMatchesMessage))
            {
                MessageDlg.Show(WizardForm, builder.AmbiguousMatchesMessage);
            }
            return(true);
        }
        private bool BuildPeptideSearchLibrary(CancelEventArgs e)
        {
            // Nothing to build, if now search files were specified
            if (!SearchFilenames.Any())
            {
                var libraries = DocumentContainer.Document.Settings.PeptideSettings.Libraries;
                if (!libraries.HasLibraries)
                {
                    return(false);
                }
                var libSpec = libraries.LibrarySpecs.FirstOrDefault(s => s.IsDocumentLibrary);
                return(libSpec != null && LoadPeptideSearchLibrary(libSpec));
            }

            double           cutOffScore;
            MessageBoxHelper helper = new MessageBoxHelper(WizardForm);

            if (!helper.ValidateDecimalTextBox(textCutoff, 0, 1.0, out cutOffScore))
            {
                e.Cancel = true;
                return(false);
            }
            ImportPeptideSearch.CutoffScore = cutOffScore;

            BiblioSpecLiteBuilder builder;

            try
            {
                builder = ImportPeptideSearch.GetLibBuilder(DocumentContainer.Document, DocumentContainer.DocumentFilePath, cbIncludeAmbiguousMatches.Checked);
                builder.PreferEmbeddedSpectra = PreferEmbeddedSpectra;
            }
            catch (FileEx.DeleteException de)
            {
                MessageDlg.ShowException(this, de);
                return(false);
            }

            bool retry = false;

            do
            {
                using (var longWaitDlg = new LongWaitDlg
                {
                    Text = Resources.BuildPeptideSearchLibraryControl_BuildPeptideSearchLibrary_Building_Peptide_Search_Library,
                    Message = Resources.BuildPeptideSearchLibraryControl_BuildPeptideSearchLibrary_Building_document_library_for_peptide_search_,
                })
                {
                    // Disable the wizard, because the LongWaitDlg does not
                    try
                    {
                        ImportPeptideSearch.ClosePeptideSearchLibraryStreams(DocumentContainer.Document);
                        var status = longWaitDlg.PerformWork(WizardForm, 800,
                                                             monitor => LibraryManager.BuildLibraryBackground(DocumentContainer, builder, monitor, new LibraryManager.BuildState(null, null)));
                        if (status.IsError)
                        {
                            // E.g. could not find external raw data for MaxQuant msms.txt; ask user if they want to retry with "prefer embedded spectra" option
                            if (BiblioSpecLiteBuilder.IsLibraryMissingExternalSpectraError(status.ErrorException))
                            {
                                var response = ShowLibraryMissingExternalSpectraError(WizardForm, status.ErrorException);
                                if (response == UpdateProgressResponse.cancel)
                                {
                                    return(false);
                                }
                                else if (response == UpdateProgressResponse.normal)
                                {
                                    builder.PreferEmbeddedSpectra = true;
                                }

                                retry = true;
                            }
                            else
                            {
                                MessageDlg.ShowException(WizardForm, status.ErrorException);
                                return(false);
                            }
                        }
                    }
                    catch (Exception x)
                    {
                        MessageDlg.ShowWithException(WizardForm, TextUtil.LineSeparate(string.Format(Resources.BuildPeptideSearchLibraryControl_BuildPeptideSearchLibrary_Failed_to_build_the_library__0__,
                                                                                                     Path.GetFileName(BiblioSpecLiteSpec.GetLibraryFileName(DocumentContainer.DocumentFilePath))), x.Message), x);
                        return(false);
                    }
                }
            } while (retry);

            var docLibSpec = builder.LibrarySpec.ChangeDocumentLibrary(true);

            Settings.Default.SpectralLibraryList.Insert(0, docLibSpec);

            // Go ahead and load the library - we'll need it for
            // the modifications and chromatograms page.
            if (!LoadPeptideSearchLibrary(docLibSpec))
            {
                return(false);
            }

            var selectedIrtStandard = comboStandards.SelectedItem as IrtStandard;
            var addedIrts           = false;

            if (selectedIrtStandard != null && selectedIrtStandard != IrtStandard.EMPTY)
            {
                addedIrts = AddIrtLibraryTable(docLibSpec.FilePath, selectedIrtStandard);
            }

            var docNew = ImportPeptideSearch.AddDocumentSpectralLibrary(DocumentContainer.Document, docLibSpec);

            if (docNew == null)
            {
                return(false);
            }

            if (addedIrts)
            {
                docNew = ImportPeptideSearch.AddRetentionTimePredictor(docNew, docLibSpec);
            }

            DocumentContainer.ModifyDocumentNoUndo(doc => docNew);

            if (!string.IsNullOrEmpty(builder.AmbiguousMatchesMessage))
            {
                MessageDlg.Show(WizardForm, builder.AmbiguousMatchesMessage);
            }
            return(true);
        }