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 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 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...
}
