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]);
}
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 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);
}
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_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_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_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_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_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 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 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 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"));
}