public void load_save_unlocalized()
{
Lollipop.enter_uniprot_ptmlist(TestContext.CurrentContext.TestDirectory);
string uniprotPtmlist = Sweet.lollipop.input_files.FirstOrDefault(f => f.purpose == Purpose.PtmList).complete_path;
TheoreticalProteoformDatabase tpd = new TheoreticalProteoformDatabase();
tpd.ready_to_make_database(TestContext.CurrentContext.TestDirectory);
List <Modification> mods = PtmListLoader.ReadModsFromFile(uniprotPtmlist, out List <(Modification, string)> filteredModificationsWithWarnings).ToList();
foreach (Modification m in mods)
{
if (!Sweet.lollipop.modification_ranks.TryGetValue((double)m.MonoisotopicMass, out int x))
{
Sweet.lollipop.modification_ranks.Add((double)m.MonoisotopicMass, -1);
}
}
tpd.unlocalized_lookup = tpd.make_unlocalized_lookup(mods);
tpd.load_unlocalized_names(Path.Combine(TestContext.CurrentContext.TestDirectory, "Mods", "stored_mods.modnames"));
tpd.save_unlocalized_names(Path.Combine(TestContext.CurrentContext.TestDirectory, "Mods", "fake_stored_mods.modnames"));
Modification firstAcetyl = mods.FirstOrDefault(x => x.OriginalId.StartsWith("N-acetyl"));
Assert.AreNotEqual(firstAcetyl.OriginalId, tpd.unlocalized_lookup[firstAcetyl].id);
//Test amending
mods.AddRange(PtmListLoader.ReadModsFromFile(Path.Combine(TestContext.CurrentContext.TestDirectory, "Mods", "intact_mods.txt"), out filteredModificationsWithWarnings).OfType <Modification>());
Sweet.lollipop.modification_ranks = mods.DistinctBy(m => m.MonoisotopicMass).ToDictionary(m => (double)m.MonoisotopicMass, m => - 1);
tpd.unlocalized_lookup = tpd.make_unlocalized_lookup(mods.OfType <Modification>());
tpd.amend_unlocalized_names(Path.Combine(TestContext.CurrentContext.TestDirectory, "Mods", "fake_stored_mods.modnames"));
}
public void load_uniprot_ptmlist()
{
Sweet.lollipop = new Lollipop();
Lollipop.enter_uniprot_ptmlist(TestContext.CurrentContext.TestDirectory);
Assert.IsTrue(Sweet.lollipop.input_files.Any(f => f.purpose == Purpose.PtmList));
Sweet.lollipop = new Lollipop();
}
private void btn_downloadUniProtPtmList_Click(object sender, EventArgs e)
{
Lollipop.enter_uniprot_ptmlist(Environment.CurrentDirectory);
DisplayUtility.FillDataGridView(dgv_loadFiles, Sweet.lollipop.get_files(Sweet.lollipop.input_files, Lollipop.file_types[cmb_loadTable.SelectedIndex]).Select(f => new DisplayInputFile(f)));
DisplayInputFile.FormatInputFileTable(dgv_loadFiles, Lollipop.file_types[cmb_loadTable.SelectedIndex]);
btn_downloadUniProtPtmList.IsEnabled = false;
SetMakeDatabaseButton();
}
public void testProcessRawComponents()
{
Lollipop.correctionFactors = null;
Lollipop.raw_experimental_components.Clear(); //for if neucode test is run first
Func <string, IEnumerable <Component> > componentReader = c => new ExcelReader().read_components_from_xlsx(c, Lollipop.correctionFactors);
Lollipop.deconResultsFileNames = new System.ComponentModel.BindingList <string>();
Lollipop.deconResultsFileNames.Add("UnitTestFiles\\noisy.xlsx");
Lollipop.neucode_labeled = true;
Lollipop.process_raw_components(componentReader);
Assert.AreEqual(224, Lollipop.raw_experimental_components.Count);
}
public static void Main(string[] args)
{
Candy candy = new Candy(2.2, "ya", 7.4);
Lollipop lollipop = new Lollipop(2.2, "me", 5.5, 1.1, "good");
Chocolate chocolate = new Chocolate(2.1, "opl", 0.11, "milk", true, "quad");
//Gift gift = new Gift(new Candy[]{new Candy(1.1,"roflyan",2.1),new Lollipop(2,"asd",2.3,4.3,"der"), });
Gift gift = new Gift();
gift.Add(candy);
gift.Add(lollipop);
gift.Add(chocolate);
Sort.Bubble(gift);
Console.WriteLine(gift);
}
public void restore_lollipop_settings()
{
Lollipop defaults = new Lollipop();
StringBuilder builder = SaveState.save_method();
foreach (PropertyInfo property in typeof(Lollipop).GetProperties())
{
if (property.PropertyType == typeof(int))
{
property.SetValue(null, Convert.ToInt32(property.GetValue(null)) + 1);
Assert.AreEqual(Convert.ToInt32(property.GetValue(defaults)) + 1, Convert.ToInt32(property.GetValue(null))); //the int values were changed in the current program
}
else if (property.PropertyType == typeof(double))
{
property.SetValue(null, Convert.ToDouble(property.GetValue(null)) + 1);
Assert.AreEqual(Convert.ToDouble(property.GetValue(defaults)) + 1, Convert.ToDouble(property.GetValue(null))); //the double values were changed in the current program
}
else if (property.PropertyType == typeof(string))
{
property.SetValue(null, property.GetValue(null).ToString() + "hello");
Assert.AreEqual(property.GetValue(defaults).ToString() + "hello", Convert.ToDouble(property.GetValue(null)).ToString()); //the string values were changed in the current program
}
else if (property.PropertyType == typeof(decimal))
{
property.SetValue(null, Convert.ToDecimal(property.GetValue(null)) + 1);
Assert.AreEqual(Convert.ToDecimal(property.GetValue(defaults)) + 1, Convert.ToDecimal(property.GetValue(null))); //the decimal value were changed in the current program
}
else if (property.PropertyType == typeof(bool))
{
property.SetValue(null, !Convert.ToBoolean(property.GetValue(null)));
Assert.AreEqual(!Convert.ToBoolean(property.GetValue(defaults)), Convert.ToBoolean(property.GetValue(null))); //the bool value were changed in the current program
}
else
{
continue;
}
}
SaveState.open_method(builder.ToString());
foreach (PropertyInfo property in typeof(Lollipop).GetProperties())
{
if (property.PropertyType == typeof(int))
{
Assert.AreEqual(Convert.ToInt32(property.GetValue(defaults)), Convert.ToInt32(property.GetValue(null))); //the int values were changed back
}
else if (property.PropertyType == typeof(double))
{
Assert.AreEqual(Convert.ToDouble(property.GetValue(defaults)), Convert.ToDouble(property.GetValue(null))); //the double values were changed back
}
else if (property.PropertyType == typeof(string))
{
Assert.AreEqual(property.GetValue(defaults).ToString(), Convert.ToDouble(property.GetValue(null)).ToString()); //the string values were changed back
}
else if (property.PropertyType == typeof(decimal))
{
Assert.AreEqual(Convert.ToDecimal(property.GetValue(defaults)), Convert.ToDecimal(property.GetValue(null))); //the decimal value were changed back
}
else if (property.PropertyType == typeof(bool))
{
Assert.AreEqual(Convert.ToBoolean(property.GetValue(defaults)), Convert.ToBoolean(property.GetValue(null))); //the bool value were changed back
}
else
{
continue;
}
}
}
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.theoretical_database.ready_to_make_database(Environment.CurrentDirectory))
{
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);
}
else
{
MessageBoxResult d1 = 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", MessageBoxButton.OKCancel);
if (d1 == MessageBoxResult.OK)
{
Lollipop.enter_uniprot_ptmlist(Environment.CurrentDirectory);
if (loadResults.ReadyToRunTheGamut())
{
loadResults.RunTheGamut(true); // updates the dgvs
}
}
else
{
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 (BottomUpReader.bottom_up_PTMs_not_in_dictionary.Count() > 0)
{
warning_methods.Add("The following PTMs in the .mzid file were not matched with any PTMs in the theoretical database: ");
warning_methods.Add(string.Join(", ", BottomUpReader.bottom_up_PTMs_not_in_dictionary.Distinct()));
}
if (Sweet.lollipop.topdownReader.bad_topdown_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_topdown_ptms.Distinct()));
}
if (Sweet.lollipop.topdown_proteoforms.Count(t => !t.accepted) > 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.Where(t => !t.accepted).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);
}
