public void results_decoy_dataframe_with_something() { Sweet.lollipop = new Lollipop(); Sweet.lollipop.input_files.Add(ConstructorsForTesting.InputFile("fake.txt", Labeling.NeuCode, Purpose.Identification, "n", "s", "1", "1", "1")); //0 ExperimentalProteoform e = ConstructorsForTesting.ExperimentalProteoform("E1"); e.linked_proteoform_references = new List <Proteoform>(new List <Proteoform> { ConstructorsForTesting.make_a_theoretical() }); e.ptm_set = e.linked_proteoform_references.Last().ptm_set; ProteoformFamily f = new ProteoformFamily(e); f.construct_family(); Sweet.lollipop.decoy_proteoform_communities.Add("Decoy1", new ProteoformCommunity()); Sweet.lollipop.decoy_proteoform_communities["Decoy1"].families = new List <ProteoformFamily> { f }; var time_stamp = Sweet.time_stamp(); var directory = TestContext.CurrentContext.TestDirectory; ResultsSummaryGenerator.save_all(TestContext.CurrentContext.TestDirectory, time_stamp, Sweet.lollipop.TusherAnalysis1 as IGoAnalysis, Sweet.lollipop.TusherAnalysis1 as TusherAnalysis); Assert.IsTrue(File.Exists(Path.Combine(directory, "decoy_experimental_results_" + time_stamp + ".tsv"))); var lines = File.ReadAllLines(Path.Combine(directory, "decoy_experimental_results_" + time_stamp + ".tsv")); Assert.AreEqual(2, lines.Length); }
private void btn_save_Click(object sender, EventArgs e) { if (!Directory.Exists(SaveState.lollipop.results_folder)) { return; } string timestamp = SaveState.time_stamp(); ResultsSummaryGenerator.save_all(SaveState.lollipop.results_folder, timestamp); ((ProteoformSweet)MdiParent).save_all_plots(SaveState.lollipop.results_folder, timestamp); }
public void saveall() { SaveState.lollipop = new Lollipop(); ExperimentalProteoform e = ConstructorsForTesting.ExperimentalProteoform("asdf"); SaveState.lollipop.qVals.Add(e.quant); GoTermNumber g = new GoTermNumber(new GoTerm("id", "desc", Aspect.BiologicalProcess), 0, 0, 0, 0); g.by = -1; SaveState.lollipop.goTermNumbers.Add(g); ResultsSummaryGenerator.save_all(TestContext.CurrentContext.TestDirectory, SaveState.time_stamp()); }
private void btn_save_Click(object sender, RoutedEventArgs e) { if (!Directory.Exists(Sweet.lollipop.results_folder)) { return; } string timestamp = Sweet.time_stamp(); ResultsSummaryGenerator.save_all(Sweet.lollipop.results_folder, timestamp, get_go_analysis(), get_tusher_analysis()); MDIParent.save_all_plots(Sweet.lollipop.results_folder, timestamp); using (StreamWriter file = new StreamWriter(System.IO.Path.Combine(Sweet.lollipop.results_folder, "presets_" + timestamp + ".xml"))) file.WriteLine(Sweet.save_method()); }
public void saveall() { Sweet.lollipop = new Lollipop(); ExperimentalProteoform e = ConstructorsForTesting.ExperimentalProteoform("asdf"); Sweet.lollipop.qVals.Add(e.quant); GoTermNumber g = new GoTermNumber(new GoTerm("id", "desc", Aspect.BiologicalProcess), 0, 0, 0, 0); g.by = -1; Sweet.lollipop.TusherAnalysis1.GoAnalysis.goTermNumbers.Add(g); Sweet.lollipop.topdown_proteoforms = new List <TopDownProteoform>() { ConstructorsForTesting.TopDownProteoform("td1", 1000, 10) }; ResultsSummaryGenerator.save_all(TestContext.CurrentContext.TestDirectory, Sweet.time_stamp(), Sweet.lollipop.TusherAnalysis1 as IGoAnalysis, Sweet.lollipop.TusherAnalysis1 as TusherAnalysis); }
public bool full_run() { clear_lists(); if (!SaveState.lollipop.theoretical_database.ready_to_make_database(Environment.CurrentDirectory)) { if (SaveState.lollipop.get_files(SaveState.lollipop.input_files, Purpose.ProteinDatabase).Count() <= 0) { MessageBox.Show("Please list at least one protein database.", "Full Run"); return(false); } else { DialogResult d = MessageBox.Show("No PTM list is listed.\n\nWill now download the default PTM list from UniProt and use it for the Full Run.", "Full Run", MessageBoxButtons.OKCancel); if (d == DialogResult.OK) { SaveState.lollipop.enter_uniprot_ptmlist(); if (loadDeconvolutionResults.ReadyToRunTheGamut()) { loadDeconvolutionResults.RunTheGamut(); // updates the dgvs } } else { return(false); } } } if (SaveState.lollipop.results_folder == "") { DialogResult d = MessageBox.Show("Choose a results folder for this Full Run?", "Full Run", MessageBoxButtons.YesNoCancel); if (d == DialogResult.Yes) { FolderBrowserDialog folderBrowser = new FolderBrowserDialog(); DialogResult dr = folderBrowser.ShowDialog(); if (dr == DialogResult.OK) { string temp_folder_path = folderBrowser.SelectedPath; SaveState.lollipop.results_folder = temp_folder_path; loadDeconvolutionResults.InitializeParameterSet(); // updates the textbox } else if (dr == DialogResult.Cancel) { return(false); } } else if (d == DialogResult.Cancel) { return(false); } } Cursor = Cursors.WaitCursor; foreach (ISweetForm sweet in forms) { if (sweet.ReadyToRunTheGamut()) { sweet.RunTheGamut(); } } string timestamp = SaveState.time_stamp(); ResultsSummaryGenerator.save_all(SaveState.lollipop.results_folder, timestamp); save_all_plots(SaveState.lollipop.results_folder, timestamp); Cursor = Cursors.Default; return(true); }
public Stopwatch full_run() { forms[1].ClearListsTablesFigures(true); // clear forms following load deconvolution results MessageBoxResult d3 = MessageBox.Show("Use presets for this Full Run?", "Full Run", MessageBoxButton.YesNoCancel); if (d3 == MessageBoxResult.Yes) { bool?dr = methodFileOpen.ShowDialog(); if (dr == true) { string filepath = methodFileOpen.FileName; MessageBoxResult d4 = MessageBox.Show("Add files at the listed paths if they still exist?", "Full Run", MessageBoxButton.YesNoCancel); if (d4 == MessageBoxResult.Cancel) { return(null); } if (!open_method(filepath, File.ReadAllLines(filepath), d4 == MessageBoxResult.Yes)) { return(null); } ; } else if (dr == false) { return(null); } } else if (d3 == MessageBoxResult.Cancel) { return(null); } loadResults.FillTablesAndCharts(); // updates the filelists in form // Check that there are input files if (Sweet.lollipop.input_files.Count == 0) { MessageBox.Show("Please load in deconvolution result files in order to use load and run.", "Full Run"); return(null); } // Check that theoretical database(s) are present if (Sweet.lollipop.get_files(Sweet.lollipop.input_files, Purpose.ProteinDatabase).Count() <= 0) { MessageBox.Show("Please list at least one protein database.", "Full Run"); return(null); } // Option to choose a result folder if (Sweet.lollipop.results_folder == "") { MessageBoxResult d2 = MessageBox.Show("Choose a results folder for this Full Run?", "Full Run", MessageBoxButton.YesNoCancel); if (d2 == MessageBoxResult.Yes) { System.Windows.Forms.FolderBrowserDialog folderBrowser = new System.Windows.Forms.FolderBrowserDialog(); System.Windows.Forms.DialogResult dr = folderBrowser.ShowDialog(); if (dr == System.Windows.Forms.DialogResult.OK) { string temp_folder_path = folderBrowser.SelectedPath; Sweet.lollipop.results_folder = temp_folder_path; loadResults.InitializeParameterSet(); // updates the textbox } else if (dr == System.Windows.Forms.DialogResult.Cancel) { return(null); } } else if (d2 == MessageBoxResult.Cancel) { return(null); } } else { MessageBoxResult d2 = MessageBox.Show("Would you like to save results of this Full Run to " + Sweet.lollipop.results_folder + "?", "Full Run", MessageBoxButton.YesNoCancel); if (d2 == MessageBoxResult.No) { Sweet.lollipop.results_folder = ""; } else if (d2 == MessageBoxResult.Cancel) { return(null); } } //Run the program Mouse.OverrideCursor = Cursors.Wait; Stopwatch stopwatch = new Stopwatch(); stopwatch.Start(); foreach (ISweetForm sweet in forms) { if (sweet.ReadyToRunTheGamut()) { sweet.RunTheGamut(true); } } // Save the results resultsSummary.InitializeParameterSet(); if (Sweet.lollipop.results_folder != "") { string timestamp = Sweet.time_stamp(); ResultsSummaryGenerator.save_all(Sweet.lollipop.results_folder, timestamp, resultsSummary.get_go_analysis(), resultsSummary.get_tusher_analysis()); save_all_plots(Sweet.lollipop.results_folder, timestamp); using (StreamWriter file = new StreamWriter(Path.Combine(Sweet.lollipop.results_folder, "presets_" + timestamp + ".xml"))) file.WriteLine(Sweet.save_method()); } List <string> warning_methods = new List <string>() { "Warning:" }; if (Sweet.lollipop.bottomupReader.bad_ptms.Count > 0) { warning_methods.Add("The following PTMs in the bottom-up file were not matched with any PTMs in the theoretical database: "); warning_methods.Add(string.Join(", ", Sweet.lollipop.bottomupReader.bad_ptms.Distinct())); } if (Sweet.lollipop.topdownReader.bad_ptms.Count > 0) { warning_methods.Add("Top-down proteoforms with the following modifications were not matched to a modification in the theoretical PTM list: "); warning_methods.Add(string.Join(", ", Sweet.lollipop.topdownReader.bad_ptms.Distinct())); } if (Sweet.lollipop.topdown_proteoforms_no_theoretical.Count() > 0) { warning_methods.Add("Top-down proteoforms with the following accessions were not matched to a theoretical proteoform in the theoretical database: "); warning_methods.Add(string.Join(", ", Sweet.lollipop.topdown_proteoforms_no_theoretical.Select(t => t.accession.Split('_')[0]).Distinct())); } if (warning_methods.Count > 1) { MessageBox.Show(String.Join("\n\n", warning_methods)); } // Program ran successfully stopwatch.Stop(); Mouse.OverrideCursor = null; return(stopwatch); }