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_buildAllFamilies_Click(object sender, RoutedEventArgs e)
{
string time_stamp = Sweet.time_stamp();
tb_recentTimeStamp.Text = time_stamp;
string message = CytoscapeScript.write_cytoscape_script(Sweet.lollipop.target_proteoform_community.families, Sweet.lollipop.target_proteoform_community.families, Sweet.lollipop.family_build_folder_path, "", time_stamp, (bool)ck_cb_buildAsQuantitative ? MDIParent.resultsSummary.get_go_analysis() : null, (bool)cb_redBorder.IsChecked, (bool)cb_boldLabel.IsChecked, "Smarties", cmbx_edgeLabel.SelectedItem.ToString(), cmbx_nodeLabel.SelectedItem.ToString(), cmbx_nodeLabelPositioning.SelectedItem.ToString(), cmbx_nodeLayout.SelectedItem.ToString(), Sweet.lollipop.deltaM_edge_display_rounding, (bool)ck_cb_geneCentric, cmbx_geneLabel.SelectedItem.ToString());//data binding
MessageBox.Show(message, "Cytoscape Build");
}
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());
}
private void btn_buildAllFamilies_Click(object sender, EventArgs e)
{
string time_stamp = Sweet.time_stamp();
tb_recentTimeStamp.Text = time_stamp;
string message = CytoscapeScript.write_cytoscape_script(Sweet.lollipop.target_proteoform_community.families, Sweet.lollipop.target_proteoform_community.families,
Sweet.lollipop.family_build_folder_path, "", time_stamp,
cb_buildAsQuantitative.Checked ? (MdiParent as ProteoformSweet).resultsSummary.get_go_analysis() : null, cb_redBorder.Checked, cb_boldLabel.Checked,
cmbx_colorScheme.SelectedItem.ToString(), cmbx_edgeLabel.SelectedItem.ToString(), cmbx_nodeLabel.SelectedItem.ToString(), cmbx_nodeLabelPositioning.SelectedItem.ToString(), cmbx_nodeLayout.SelectedItem.ToString(), Sweet.lollipop.deltaM_edge_display_rounding,
cb_geneCentric.Checked, cmbx_geneLabel.SelectedItem.ToString());
MessageBox.Show(message, "Cytoscape Build");
}
private void btn_buildSelectedFamilies_Click(object sender, RoutedEventArgs e)
{
string time_stamp = Sweet.time_stamp();
tb_recentTimeStamp.Text = time_stamp;
object[] selected = DisplayUtility.get_selected_objects(dgv_main);
string message = CytoscapeScript.write_cytoscape_script(selected, Sweet.lollipop.target_proteoform_community.families,
Sweet.lollipop.family_build_folder_path, "", time_stamp,
(bool)cb_buildAsQuantitative.IsChecked ? (this.MDIParent as ProteoformSweet).resultsSummary.get_go_analysis() : null, (bool)cb_redBorder.IsChecked, (bool)cb_boldLabel.IsChecked,
cmbx_colorScheme.SelectedItem.ToString(), cmbx_edgeLabel.SelectedItem.ToString(), cmbx_nodeLabel.SelectedItem.ToString(), cmbx_nodeLabelPositioning.SelectedItem.ToString(), cmbx_nodeLayout.SelectedItem.ToString(), Sweet.lollipop.deltaM_edge_display_rounding,
(bool)cb_geneCentric.IsChecked, cmbx_geneLabel.SelectedItem.ToString(), (bool)ck_cb_scale_nodes);
MessageBox.Show(message, "Cytoscape Build");
}
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);
}
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);
}