private void Generate_parent_child_network()
{
if (Options.Report)
{
Report_class.WriteLine("{0}: Generate hierarchical parent child MBCO network", typeof(Mbc_enrichment_pipeline_class).Name);
}
Mbco_parentChild_nw.Generate_by_reading_safed_obo_file();
}
private void Generate_leave_out_scp_network()
{
if (Options.Report)
{
Report_class.WriteLine("{0}: Generate SCP networks", typeof(Mbc_enrichment_pipeline_class).Name);
}
Dictionary <string, int> processName_processLevel_dict = Mbco_parentChild_nw.Get_processName_level_dictionary_after_setting_process_level();
Leave_out_class leave_out = new Leave_out_class();
leave_out.Generate_by_reading_safed_file();
Leave_out_scp_network_for_dynamicEnrichment_analysis.Options.Consider_scp_interactions_between_signaling_processes = this.Options.Consider_interactions_between_signalingSCPs_for_dyanmicEnrichment;
Leave_out_scp_network_for_dynamicEnrichment_analysis.Options.Top_quantile_of_considered_SCP_interactions_per_level = this.Options.Top_quantile_of_scp_interactions_for_dynamicEnrichment_per_level;
Leave_out_scp_network_for_dynamicEnrichment_analysis.Generate_scp_scp_network_from_leave_out(leave_out);
Leave_out_scp_network_for_dynamicEnrichment_analysis.Scp_nw.Nodes.Set_processLevel_for_all_nodes_based_on_dictionary(processName_processLevel_dict);
Leave_out_scp_network_for_dynamicEnrichment_visualization.Options.Consider_scp_interactions_between_signaling_processes = this.Options.Consider_interactions_between_signalingSCPs_for_dyanmicEnrichment;
Leave_out_scp_network_for_dynamicEnrichment_visualization.Options.Top_quantile_of_considered_SCP_interactions_per_level = this.Options.Top_quantile_of_scp_interactions_for_visualization_of_dynamicEnrichment_per_level;
Leave_out_scp_network_for_dynamicEnrichment_visualization.Generate_scp_scp_network_from_leave_out(leave_out);
Leave_out_scp_network_for_dynamicEnrichment_visualization.Scp_nw.Transform_into_undirected_single_network_and_set_all_widths_to_one();
Leave_out_scp_network_for_dynamicEnrichment_visualization.Scp_nw.Nodes.Set_processLevel_for_all_nodes_based_on_dictionary(processName_processLevel_dict);
}