public Mbc_enrichment_pipeline_class()
{
Options = new Mbc_enrichment_pipeline_options_class();
Mbco_parentChild_nw = new MBCO_obo_network_class();
Leave_out_scp_network_for_dynamicEnrichment_analysis = new Leave_out_scp_scp_network_class();
Leave_out_scp_network_for_dynamicEnrichment_visualization = new Leave_out_scp_scp_network_class();
}
public void Add_ancestors_of_missing_levels(MBCO_obo_network_class mbco_obo_network_parent_child)
{
MBCO_obo_network_class mbco_obo_network_child_parent = mbco_obo_network_parent_child.Deep_copy_mbco_obo_nw();
mbco_obo_network_child_parent.Transform_into_child_parent_direction();
MBCO_obo_network_class current_mbco_obo_network;
int[] levels_in_scp = this.Scp_nw.Nodes.Get_all_levels();
int levels_in_scp_length = levels_in_scp.Length;
int level_in_scp;
int max_level_in_scp = -1;
for (int indexLevelScp = 0; indexLevelScp < levels_in_scp_length; indexLevelScp++)
{
level_in_scp = levels_in_scp[indexLevelScp];
if ((max_level_in_scp == -1) ||
(max_level_in_scp < level_in_scp))
{
max_level_in_scp = level_in_scp;
}
}
int[] levels_in_mbco = mbco_obo_network_child_parent.Nodes.Get_all_levels();
int[] add_levels_preliminary = Overlap_class.Get_part_of_list1_but_not_of_list2(levels_in_mbco, levels_in_scp);
List <int> add_levels_list = new List <int>();
foreach (int add_level_preliminary in add_levels_preliminary)
{
if ((add_level_preliminary < max_level_in_scp) && (add_level_preliminary != 0))
{
add_levels_list.Add(add_level_preliminary);
}
}
int[] add_levels = add_levels_list.ToArray();
add_levels = add_levels.OrderByDescending(l => l).ToArray();
int add_length = add_levels.Length;
int add_level;
string[] add_parents;
string[] children;
string[] keep_nodes;
for (int indexAdd = 0; indexAdd < add_length; indexAdd++)
{
add_level = add_levels[indexAdd];
level_in_scp = add_level + 1;
children = this.Scp_nw.Nodes.Get_all_nodeNames_of_indicated_levels(level_in_scp);
add_parents = mbco_obo_network_child_parent.Get_all_parents_if_direction_is_child_parent(children);
current_mbco_obo_network = mbco_obo_network_parent_child.Deep_copy_mbco_obo_nw();
keep_nodes = Array_class.Get_ordered_union(add_parents, children);
current_mbco_obo_network.Keep_only_input_nodeNames(keep_nodes);
this.Scp_nw.Merge_this_network_with_other_network(current_mbco_obo_network);
}
}
private Dictionary <string, bool> Generate_dictionary_with_all_signaling_processes()
{
Dictionary <string, bool> signaling_processes_dict = new Dictionary <string, bool>();
MBCO_obo_network_class mbco_obo_nw = new MBCO_obo_network_class();
mbco_obo_nw.Generate_by_reading_safed_obo_file();
string[] signaling_processes = mbco_obo_nw.Get_all_offspring_if_direction_is_parent_child("Cellular communication");
signaling_processes = signaling_processes.OrderBy(l => l).ToArray();
foreach (string signaling_process in signaling_processes)
{
signaling_processes_dict.Add(signaling_process, true);
}
return(signaling_processes_dict);
}
public void Generate(Network_class process_nw, Color_enum[] rotation_colors)
{
this.Process_nw = process_nw.Deep_copy();
this.Process_nw.Transform_into_undirected_double_network();
this.Rotation_colors = rotation_colors;
this.Rotation_colors_length = this.Rotation_colors.Length;
this.Already_considered_neighbors = new Dictionary <int, bool>();
NodeIndex_colorIndex_dict = new Dictionary <int, int>();
Color_lines_list = new List <yed_node_color_line_class>();
MBCO_obo_network_class mbc_obo_parent_child = new MBCO_obo_network_class();
mbc_obo_parent_child.Generate_by_reading_safed_obo_file();
ProcessName_siblingNames_dict = mbc_obo_parent_child.Get_processName_siblings_dictionary_if_direction_is_parent_child();
}
