public void cytoscape_script_nothing_selected() { string message = CytoscapeScript.write_cytoscape_script(new List <ProteoformFamily>(), Sweet.lollipop.target_proteoform_community.families, TestContext.CurrentContext.TestDirectory, "", "test", null, false, false, CytoscapeScript.color_scheme_names[0], Lollipop.edge_labels[0], Lollipop.node_labels[0], CytoscapeScript.node_label_positions[0], Lollipop.node_positioning[0], 2, false, Lollipop.gene_name_labels[1]); }
public void cytoscape_script_from_topdown() { Sweet.lollipop = new Lollipop(); ProteoformCommunity community = TestProteoformFamilies.construct_community_with_td_proteoforms(-1); Sweet.lollipop.target_proteoform_community = community; TopDownProteoform td = ConstructorsForTesting.TopDownProteoform("ASDF", 1000, 50); td.gene_name = new GeneName(new List <Tuple <string, string> > { new Tuple <string, string>("genename", "genename") }); ProteoformFamily fam = new ProteoformFamily(td); fam.construct_family(); CytoscapeScript.write_cytoscape_script(new List <ProteoformFamily>() { fam }, new List <ProteoformFamily>() { fam }, TestContext.CurrentContext.TestDirectory, "", "test", null, false, false, CytoscapeScript.color_scheme_names[0], Lollipop.edge_labels[0], Lollipop.node_labels[0], CytoscapeScript.node_label_positions[0], Lollipop.node_positioning[0], 2, true, Lollipop.gene_name_labels[1]); string[] edge_lines = File.ReadAllLines(Path.Combine(TestContext.CurrentContext.TestDirectory, CytoscapeScript.edge_file_prefix + "test" + CytoscapeScript.edge_file_extension)); HashSet <string> shared_pf_names_edges = new HashSet <string>(); for (int i = 1; i < edge_lines.Length; i++) { if (edge_lines[i] == "") { break; } string[] line = edge_lines[i].Split(new char[] { '\t' }); shared_pf_names_edges.Add(line[0]); shared_pf_names_edges.Add(line[2]); } string[] node_lines = File.ReadAllLines(Path.Combine(TestContext.CurrentContext.TestDirectory, CytoscapeScript.node_file_prefix + "test" + CytoscapeScript.node_file_extension)); HashSet <string> shared_pf_names_nodes = new HashSet <string>(); for (int i = 1; i < node_lines.Length; i++) { if (node_lines[i] == "") { break; } string[] line = node_lines[i].Split(new char[] { '\t' }); shared_pf_names_nodes.Add(line[0]); } Assert.True(shared_pf_names_nodes.All(name => shared_pf_names_edges.Contains(name))); Assert.True(shared_pf_names_edges.All(name => shared_pf_names_nodes.Contains(name))); Assert.AreEqual(2, shared_pf_names_nodes.Count); Assert.AreEqual(2, shared_pf_names_edges.Count); }
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"); }
public void test_write_families_regular_display() { TheoreticalProteoform t = ConstructorsForTesting.make_a_theoretical(); ExperimentalProteoform e = ConstructorsForTesting.ExperimentalProteoform("E1"); ProteoformRelation et = new ProteoformRelation(e, t, ProteoformComparison.ExperimentalTheoretical, 0, TestContext.CurrentContext.TestDirectory); et.peak = new DeltaMassPeak(et, new HashSet <ProteoformRelation> { et }); et.peak.Accepted = true; e.relationships.Add(et); t.relationships.Add(et); e.agg_intensity = 999.99; e.quant.TusherValues1.numeratorIntensitySum = 444.44m; e.quant.TusherValues1.denominatorIntensitySum = 333.33m; e.quant.intensitySum = 777.77m; List <ProteoformFamily> f = new List <ProteoformFamily> { new ProteoformFamily(e) }; f.First().construct_family(); string message = CytoscapeScript.write_cytoscape_script(f, f, TestContext.CurrentContext.TestDirectory, "", "test", null, false, false, CytoscapeScript.color_scheme_names[0], Lollipop.edge_labels[0], Lollipop.node_labels[0], CytoscapeScript.node_label_positions[0], Lollipop.node_positioning[0], 2, false, Lollipop.gene_name_labels[1]); Assert.True(File.Exists(Path.Combine(TestContext.CurrentContext.TestDirectory, CytoscapeScript.script_file_prefix + "test" + CytoscapeScript.script_file_extension))); Assert.True(File.Exists(Path.Combine(TestContext.CurrentContext.TestDirectory, CytoscapeScript.style_file_prefix + "test" + CytoscapeScript.style_file_extension))); Assert.True(File.Exists(Path.Combine(TestContext.CurrentContext.TestDirectory, CytoscapeScript.node_file_prefix + "test" + CytoscapeScript.node_file_extension))); Assert.True(File.Exists(Path.Combine(TestContext.CurrentContext.TestDirectory, CytoscapeScript.edge_file_prefix + "test" + CytoscapeScript.edge_file_extension))); //Check that the style xml is all there List <string> vizProperties = new List <string>(); using (XmlReader xml = XmlReader.Create(Path.Combine(TestContext.CurrentContext.TestDirectory, CytoscapeScript.style_file_prefix + "test" + CytoscapeScript.style_file_extension))) { while (xml.Read()) { switch (xml.NodeType) { case XmlNodeType.Element: if (xml.Name == "visualProperty") { vizProperties.Add(xml.GetAttribute("name")); } break; } } } Assert.AreEqual(CytoscapeScript.default_styles.Keys.Where(s => s.StartsWith("NETWORK")).Count(), vizProperties.Where(s => s.StartsWith("NETWORK")).Count()); Assert.AreEqual(CytoscapeScript.default_styles.Keys.Where(s => s.StartsWith("NODE")).Count(), vizProperties.Where(s => s.StartsWith("NODE")).Count()); Assert.AreEqual(CytoscapeScript.default_styles.Keys.Where(s => s.StartsWith("EDGE")).Count(), vizProperties.Where(s => s.StartsWith("EDGE")).Count()); Assert.AreEqual(CytoscapeScript.default_styles.Keys.Where(s => !s.StartsWith("NETWORK") && !s.StartsWith("NODE") && !s.StartsWith("EDGE")).Count(), vizProperties.Where(s => !s.StartsWith("NETWORK") && !s.StartsWith("NODE") && !s.StartsWith("EDGE")).Count()); Assert.AreEqual(CytoscapeScript.default_styles.Keys.Count, vizProperties.Count); Assert.True(message.StartsWith("Finished")); }
private void btn_buildAllQuantifiedFamilies_Click(object sender, EventArgs e) { string time_stamp = SaveState.time_stamp(); tb_recentTimeStamp.Text = time_stamp; string message = CytoscapeScript.write_cytoscape_script(SaveState.lollipop.target_proteoform_community.families, SaveState.lollipop.target_proteoform_community.families, SaveState.lollipop.family_build_folder_path, "", time_stamp, true, cb_redBorder.Checked, cb_boldLabel.Checked, cmbx_colorScheme.SelectedItem.ToString(), cmbx_nodeLabel.SelectedItem.ToString(), cmbx_edgeLabel.SelectedItem.ToString(), cmbx_nodeLabelPositioning.SelectedItem.ToString(), cmbx_nodeLayout.SelectedItem.ToString(), SaveState.lollipop.deltaM_edge_display_rounding, cb_geneCentric.Checked, cmbx_geneLabel.SelectedItem.ToString()); MessageBox.Show(message, "Cytoscape Build"); }
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_buildFamiliesWithSignificantChange_Click(object sender, EventArgs e) { List <ProteoformFamily> families = SaveState.lollipop.getInterestingFamilies(SaveState.lollipop.satisfactoryProteoforms, SaveState.lollipop.minProteoformFoldChange, SaveState.lollipop.minProteoformFDR, SaveState.lollipop.minProteoformIntensity).Distinct().ToList(); string time_stamp = SaveState.time_stamp(); tb_recentTimeStamp.Text = time_stamp; string message = CytoscapeScript.write_cytoscape_script(families, SaveState.lollipop.target_proteoform_community.families, SaveState.lollipop.family_build_folder_path, "", time_stamp, true, 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(), SaveState.lollipop.deltaM_edge_display_rounding, cb_geneCentric.Checked, cmbx_geneLabel.SelectedItem.ToString()); MessageBox.Show(message, "Cytoscape Build"); }
private void btn_buildFamiliesAllGO_Click(object sender, EventArgs e) { Aspect a = (Aspect)cmbx_goAspect.SelectedItem; List <ProteoformFamily> go_families = SaveState.lollipop.getInterestingFamilies(SaveState.lollipop.goTermNumbers.Where(n => n.Aspect == a).Distinct().ToList(), SaveState.lollipop.target_proteoform_community.families); string time_stamp = SaveState.time_stamp(); tb_recentTimeStamp.Text = time_stamp; string message = CytoscapeScript.write_cytoscape_script(go_families, SaveState.lollipop.target_proteoform_community.families, SaveState.lollipop.family_build_folder_path, "", time_stamp, true, 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(), SaveState.lollipop.deltaM_edge_display_rounding, cb_geneCentric.Checked, cmbx_geneLabel.SelectedItem.ToString()); MessageBox.Show(message, "Cytoscape Build"); }
private void btn_buildFromSelectedGoTerms_Click(object sender, EventArgs e) { List <GoTermNumber> selected_gos = (DisplayUtility.get_selected_objects(dgv_goAnalysis).Select(o => (GoTermNumber)o)).ToList(); List <ProteoformFamily> selected_families = SaveState.lollipop.getInterestingFamilies(selected_gos, SaveState.lollipop.target_proteoform_community.families).Distinct().ToList(); string time_stamp = SaveState.time_stamp(); tb_recentTimeStamp.Text = time_stamp; string message = CytoscapeScript.write_cytoscape_script(selected_families, SaveState.lollipop.target_proteoform_community.families, SaveState.lollipop.family_build_folder_path, "", time_stamp, true, 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(), SaveState.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 void test_write_families_no_experimentals_which_shouldnt_happen() { List <ProteoformFamily> f = new List <ProteoformFamily> { new ProteoformFamily(ConstructorsForTesting.make_a_theoretical()) }; f.First().construct_family(); string message = CytoscapeScript.write_cytoscape_script(f, f, TestContext.CurrentContext.TestDirectory, "", "test", null, false, false, CytoscapeScript.color_scheme_names[0], Lollipop.edge_labels[0], Lollipop.node_labels[0], CytoscapeScript.node_label_positions[0], Lollipop.node_positioning[0], 2, false, Lollipop.gene_name_labels[1]); Assert.True(message.Contains("Error")); }
public void nodes_table_gives_meaningful_unmodified_theoreticals() { Proteoform p = ConstructorsForTesting.make_a_theoretical(); ProteoformFamily f = new ProteoformFamily(p); f.construct_family(); string node_table = CytoscapeScript.get_cytoscape_nodes_tsv(new List <ProteoformFamily> { f }, null, CytoscapeScript.color_scheme_names[0], Lollipop.edge_labels[0], Lollipop.node_labels[0], Lollipop.node_positioning[0], 2, f.theoretical_proteoforms, false, Lollipop.gene_name_labels[1]); Assert.True(node_table.Contains(CytoscapeScript.unmodified_theoretical_label)); Assert.AreNotEqual(f.theoretical_proteoforms[0].accession, CytoscapeScript.get_proteoform_shared_name(p, Lollipop.node_labels[0], 2)); }
public void nodes_table_gives_meaningful_topdown() { TopDownProteoform t = ConstructorsForTesting.TopDownProteoform("ACC", 999.99, 50); ProteoformFamily f = new ProteoformFamily(t); f.construct_family(); string node_table = CytoscapeScript.get_cytoscape_nodes_tsv(new List <ProteoformFamily> { f }, null, CytoscapeScript.color_scheme_names[0], Lollipop.edge_labels[0], Lollipop.node_labels[0], Lollipop.node_positioning[0], 2, f.theoretical_proteoforms, false, Lollipop.gene_name_labels[1]); Assert.True(node_table.Contains("ACC")); Assert.True(node_table.Contains("999.99")); }
public void cytoscape_edges_and_nodes_match() { Sweet.lollipop = new Lollipop(); ProteoformCommunity community = TestProteoformFamilies.construct_two_families_with_potentially_colliding_theoreticals(); Sweet.lollipop.target_proteoform_community = community; IEnumerable <TheoreticalProteoform> theoreticals = community.families.SelectMany(f => f.theoretical_proteoforms); string edges = CytoscapeScript.get_cytoscape_edges_tsv(community.families, Lollipop.edge_labels[0], Lollipop.node_labels[0], 2, theoreticals, false, Lollipop.gene_name_labels[1]); string[] lines = edges.Split(new char[] { '\n' }); HashSet <string> shared_pf_names_edges = new HashSet <string>(); for (int i = 1; i < lines.Length; i++) { if (lines[i] == "") { break; } string[] line = lines[i].Split(new char[] { '\t' }); shared_pf_names_edges.Add(line[0]); shared_pf_names_edges.Add(line[2]); } string nodes = CytoscapeScript.get_cytoscape_nodes_tsv(community.families, null, CytoscapeScript.color_scheme_names[0], Lollipop.edge_labels[0], Lollipop.node_labels[0], Lollipop.node_positioning[0], 2, theoreticals, false, Lollipop.gene_name_labels[1]); lines = nodes.Split(new char[] { '\n' }); HashSet <string> shared_pf_names_nodes = new HashSet <string>(); for (int i = 1; i < lines.Length; i++) { if (lines[i] == "") { break; } string[] line = lines[i].Split(new char[] { '\t' }); shared_pf_names_nodes.Add(line[0]); } Assert.True(shared_pf_names_nodes.All(name => shared_pf_names_edges.Contains(name))); Assert.True(shared_pf_names_edges.All(name => shared_pf_names_nodes.Contains(name))); Assert.AreEqual(9, shared_pf_names_nodes.Count); //both families }
public void cytoscape_script_from_subset_of_families() { Sweet.lollipop = new Lollipop(); ProteoformCommunity community = TestProteoformFamilies.construct_two_families_with_potentially_colliding_theoreticals(); Sweet.lollipop.target_proteoform_community = community; CytoscapeScript.write_cytoscape_script(new List <ProteoformFamily> { community.families[0] }, community.families, TestContext.CurrentContext.TestDirectory, "", "test", null, false, false, CytoscapeScript.color_scheme_names[0], Lollipop.edge_labels[0], Lollipop.node_labels[0], CytoscapeScript.node_label_positions[0], Lollipop.node_positioning[0], 2, false, Lollipop.gene_name_labels[1]); string[] edge_lines = File.ReadAllLines(Path.Combine(TestContext.CurrentContext.TestDirectory, CytoscapeScript.edge_file_prefix + "test" + CytoscapeScript.edge_file_extension)); HashSet <string> shared_pf_names_edges = new HashSet <string>(); for (int i = 1; i < edge_lines.Length; i++) { if (edge_lines[i] == "") { break; } string[] line = edge_lines[i].Split(new char[] { '\t' }); shared_pf_names_edges.Add(line[0]); shared_pf_names_edges.Add(line[2]); } string[] node_lines = File.ReadAllLines(Path.Combine(TestContext.CurrentContext.TestDirectory, CytoscapeScript.node_file_prefix + "test" + CytoscapeScript.node_file_extension)); HashSet <string> shared_pf_names_nodes = new HashSet <string>(); for (int i = 1; i < node_lines.Length; i++) { if (node_lines[i] == "") { break; } string[] line = node_lines[i].Split(new char[] { '\t' }); shared_pf_names_nodes.Add(line[0]); } Assert.True(shared_pf_names_nodes.All(name => shared_pf_names_edges.Contains(name))); Assert.True(shared_pf_names_edges.All(name => shared_pf_names_nodes.Contains(name))); Assert.AreEqual(community.families.First().proteoforms.Count, shared_pf_names_nodes.Count); }
public void cytoscape_script_from_theoreticals() { Sweet.lollipop = new Lollipop(); Sweet.lollipop.gene_centric_families = false; ProteoformCommunity community = TestProteoformFamilies.construct_two_families_with_potentially_colliding_theoreticals(false); Sweet.lollipop.target_proteoform_community = community; CytoscapeScript.write_cytoscape_script(community.families.SelectMany(f => f.theoretical_proteoforms.Where(t => t.ExpandedProteinList.Select(p => p.FullName).Contains(TestProteoformFamilies.p1_fullName))).ToArray(), community.families, TestContext.CurrentContext.TestDirectory, "", "test", null, false, false, CytoscapeScript.color_scheme_names[0], Lollipop.edge_labels[0], Lollipop.node_labels[0], CytoscapeScript.node_label_positions[0], Lollipop.node_positioning[0], 2, false, Lollipop.gene_name_labels[1]); string[] edge_lines = File.ReadAllLines(Path.Combine(TestContext.CurrentContext.TestDirectory, CytoscapeScript.edge_file_prefix + "test" + CytoscapeScript.edge_file_extension)); HashSet <string> shared_pf_names_edges = new HashSet <string>(); for (int i = 1; i < edge_lines.Length; i++) { if (edge_lines[i] == "") { break; } string[] line = edge_lines[i].Split(new char[] { '\t' }); shared_pf_names_edges.Add(line[0]); shared_pf_names_edges.Add(line[2]); } string[] node_lines = File.ReadAllLines(Path.Combine(TestContext.CurrentContext.TestDirectory, CytoscapeScript.node_file_prefix + "test" + CytoscapeScript.node_file_extension)); HashSet <string> shared_pf_names_nodes = new HashSet <string>(); for (int i = 1; i < node_lines.Length; i++) { if (node_lines[i] == "") { break; } string[] line = node_lines[i].Split(new char[] { '\t' }); shared_pf_names_nodes.Add(line[0]); } Assert.True(shared_pf_names_nodes.All(name => shared_pf_names_edges.Contains(name))); Assert.True(shared_pf_names_edges.All(name => shared_pf_names_nodes.Contains(name))); Assert.AreEqual(5, shared_pf_names_nodes.Count); //only the first family }
public void nodes_table_gives_meaningful_experimentals() { ExperimentalProteoform e = ConstructorsForTesting.ExperimentalProteoform("E1"); e.agg_intensity = 999.99; e.agg_mass = 888.88; e.agg_rt = 777.77; ProteoformFamily f = new ProteoformFamily(e); f.construct_family(); string node_table = CytoscapeScript.get_cytoscape_nodes_tsv(new List <ProteoformFamily> { f }, null, CytoscapeScript.color_scheme_names[0], Lollipop.edge_labels[0], Lollipop.node_labels[0], Lollipop.node_positioning[0], 2, f.theoretical_proteoforms, false, Lollipop.gene_name_labels[1]); Assert.True(node_table.Contains("E1")); Assert.True(node_table.Contains("999.99")); }
public void cytoscape_script_from_gotermnumber() { ProteoformCommunity community = TestProteoformFamilies.construct_two_families_with_potentially_colliding_theoreticals(); SaveState.lollipop.target_proteoform_community = community; CytoscapeScript.write_cytoscape_script(new GoTermNumber[] { new GoTermNumber(TestProteoformFamilies.p1_goterm, 0, 0, 0, 0) }, community.families, TestContext.CurrentContext.TestDirectory, "", "test", false, false, false, CytoscapeScript.color_scheme_names[0], Lollipop.edge_labels[0], Lollipop.node_labels[0], CytoscapeScript.node_label_positions[0], Lollipop.node_positioning[0], 2, false, Lollipop.gene_name_labels[1]); string[] edge_lines = File.ReadAllLines(Path.Combine(TestContext.CurrentContext.TestDirectory, CytoscapeScript.edge_file_prefix + "test" + CytoscapeScript.edge_file_extension)); HashSet <string> shared_pf_names_edges = new HashSet <string>(); for (int i = 1; i < edge_lines.Length; i++) { if (edge_lines[i] == "") { break; } string[] line = edge_lines[i].Split(new char[] { '\t' }); shared_pf_names_edges.Add(line[0]); shared_pf_names_edges.Add(line[2]); } string[] node_lines = File.ReadAllLines(Path.Combine(TestContext.CurrentContext.TestDirectory, CytoscapeScript.node_file_prefix + "test" + CytoscapeScript.node_file_extension)); HashSet <string> shared_pf_names_nodes = new HashSet <string>(); for (int i = 1; i < node_lines.Length; i++) { if (node_lines[i] == "") { break; } string[] line = node_lines[i].Split(new char[] { '\t' }); shared_pf_names_nodes.Add(line[0]); } Assert.True(shared_pf_names_nodes.All(name => shared_pf_names_edges.Contains(name))); Assert.True(shared_pf_names_edges.All(name => shared_pf_names_nodes.Contains(name))); Assert.AreEqual(9, shared_pf_names_nodes.Count); //both families this time because they all have the same stuff... }
public void nodes_table_gives_meaningful_modified_theoreticals2() { ModificationMotif motif; ModificationMotif.TryGetMotif("K", out motif); Modification m = new Modification("id", _modificationType: "modtype", _target: motif, _locationRestriction: "Anywhere.", _monoisotopicMass: 1); Proteoform p = ConstructorsForTesting.make_a_theoretical(); ProteoformFamily f = new ProteoformFamily(p); f.construct_family(); string node_table = CytoscapeScript.get_cytoscape_nodes_tsv(new List <ProteoformFamily> { f }, null, CytoscapeScript.color_scheme_names[0], Lollipop.edge_labels[0], Lollipop.node_labels[0], Lollipop.node_positioning[0], 2, f.theoretical_proteoforms, false, Lollipop.gene_name_labels[1]); Assert.True(node_table.Contains(CytoscapeScript.modified_theoretical_label)); Assert.AreNotEqual(f.theoretical_proteoforms[0].accession, CytoscapeScript.get_proteoform_shared_name(p, Lollipop.node_labels[0], 2)); }
public void nodes_table_gives_meaningful_modified_theoreticals2() { ModificationMotif motif; ModificationMotif.TryGetMotif("K", out motif); ModificationWithMass m = new ModificationWithMass("oxidation", new Tuple <string, string>("", ""), motif, ModificationSites.K, 1, new Dictionary <string, IList <string> >(), new List <double>(), new List <double>(), ""); Proteoform p = ConstructorsForTesting.make_a_theoretical(); ProteoformFamily f = new ProteoformFamily(p); f.construct_family(); string node_table = CytoscapeScript.get_cytoscape_nodes_tsv(new List <ProteoformFamily> { f }, false, CytoscapeScript.color_scheme_names[0], Lollipop.edge_labels[0], Lollipop.node_labels[0], Lollipop.node_positioning[0], 2, f.theoretical_proteoforms, false, Lollipop.gene_name_labels[1]); Assert.True(node_table.Contains(CytoscapeScript.modified_theoretical_label)); Assert.AreNotEqual(f.theoretical_proteoforms[0].accession, CytoscapeScript.get_proteoform_shared_name(p, Lollipop.node_labels[0], 2)); }
public void cytoscape_improper_build_folder() { TheoreticalProteoform t = ConstructorsForTesting.make_a_theoretical(); ExperimentalProteoform e = ConstructorsForTesting.ExperimentalProteoform("E1"); ProteoformRelation et = new ProteoformRelation(e, t, ProteoformComparison.ExperimentalTheoretical, 0, TestContext.CurrentContext.TestDirectory); e.agg_intensity = 999.99; e.quant.TusherValues1.numeratorIntensitySum = 444.44m; e.quant.TusherValues1.denominatorIntensitySum = 333.33m; e.quant.intensitySum = 777.77m; List <ProteoformFamily> f = new List <ProteoformFamily> { new ProteoformFamily(e) }; f.First().construct_family(); string message = CytoscapeScript.write_cytoscape_script(f, f, "", "", "test", null, false, false, CytoscapeScript.color_scheme_names[0], Lollipop.edge_labels[0], Lollipop.node_labels[0], CytoscapeScript.node_label_positions[0], Lollipop.node_positioning[0], 2, false, Lollipop.gene_name_labels[1]); Assert.False(message.StartsWith("Finished")); }