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);
}
private MBCO_association_line_class[] Generate_new_mbco_association_lines_by_merging_neighboring_scps_for_one_level(Ontology_enrichment_line_class[] sameSampleLevel_mbco_enrich_lines_standard)
{
int level = sameSampleLevel_mbco_enrich_lines_standard[0].ProcessLevel;
int sameSample_length = sameSampleLevel_mbco_enrich_lines_standard.Length;
Ontology_enrichment_line_class onto_enrich_line;
List <string> scpNames_list = new List <string>();
for (int indexE = 0; indexE < sameSample_length; indexE++)
{
onto_enrich_line = sameSampleLevel_mbco_enrich_lines_standard[indexE];
if (onto_enrich_line.ProcessLevel != level)
{
throw new System.Exception("more than one level");
}
if ((indexE != 0) &&
(!onto_enrich_line.Equal_complete_sample(sameSampleLevel_mbco_enrich_lines_standard[indexE - 1])))
{
throw new Exception("More than one sample");
}
scpNames_list.Add(onto_enrich_line.Scp_name);
}
if (scpNames_list.Distinct().ToArray().Length != scpNames_list.Count)
{
throw new Exception();
}
Dictionary <string, string[]> scpNames_scpUnionNames_dict = Leave_out_scp_network_for_dynamicEnrichment_analysis.Generate_scpNames_scpUnionNames_dict_with_indicated_numbers_of_combined_scps(this.Options.Numbers_of_merged_scps_for_dynamicEnrichment_per_level[level], scpNames_list.ToArray());
string[] scpNames = scpNames_scpUnionNames_dict.Keys.ToArray();
string scpName;
string[] scpUnionNames;
string scpUnionName;
int scpUnionNames_length;
int scpNames_length = scpNames.Length;
scpNames = scpNames.OrderBy(l => l).ToArray();
this.MBCO_association.Order_by_processName_symbol();
int mbco_length = this.MBCO_association.MBCO_associations.Length;
int indexMBCO = 0;
int stringCompare = -2;
MBCO_association_line_class mbc_association_line;
MBCO_association_line_class scpUnion_mbc_association_line;
List <MBCO_association_line_class> scpUnion_mbc_association_list = new List <MBCO_association_line_class>();
for (int indexScp = 0; indexScp < scpNames_length; indexScp++)
{
scpName = scpNames[indexScp];
stringCompare = -2;
while ((indexMBCO < mbco_length) && (stringCompare <= 0))
{
mbc_association_line = this.MBCO_association.MBCO_associations[indexMBCO];
stringCompare = mbc_association_line.ProcessName.CompareTo(scpName);
if (stringCompare < 0)
{
indexMBCO++;
}
else if (stringCompare == 0)
{
scpUnionNames = scpNames_scpUnionNames_dict[scpName];
scpUnionNames_length = scpUnionNames.Length;
for (int indexUnion = 0; indexUnion < scpUnionNames_length; indexUnion++)
{
scpUnionName = scpUnionNames[indexUnion];
scpUnion_mbc_association_line = new MBCO_association_line_class();
scpUnion_mbc_association_line.ProcessID = "SCP union";
scpUnion_mbc_association_line.ProcessName = (string)scpUnionName.Clone();
scpUnion_mbc_association_line.ProcessLevel = mbc_association_line.ProcessLevel;
scpUnion_mbc_association_line.Symbol = (string)mbc_association_line.Symbol.Clone();
scpUnion_mbc_association_line.Parent_processName = "SCP union";
scpUnion_mbc_association_list.Add(scpUnion_mbc_association_line);
}
indexMBCO++;
}
}
}
List <MBCO_association_line_class> final_scpUnion_mbc_association_list = new List <MBCO_association_line_class>();
scpUnion_mbc_association_list = scpUnion_mbc_association_list.OrderBy(l => l.ProcessName).ThenBy(l => l.Symbol).ToList();
int scpUnion_length = scpUnion_mbc_association_list.Count;
for (int indexScpUnion = 0; indexScpUnion < scpUnion_length; indexScpUnion++)
{
mbc_association_line = scpUnion_mbc_association_list[indexScpUnion];
if ((indexScpUnion == 0) ||
(!mbc_association_line.ProcessName.Equals(scpUnion_mbc_association_list[indexScpUnion - 1].ProcessName)) ||
(!mbc_association_line.Symbol.Equals(scpUnion_mbc_association_list[indexScpUnion - 1].Symbol)))
{
final_scpUnion_mbc_association_list.Add(mbc_association_line);
}
}
return(final_scpUnion_mbc_association_list.ToArray());
}
