public bool Equal_in_standard_way(Obo_networkTable_line_class other)
{
bool equal = ((this.Id.Equals(other.Id)) &&
(this.Parent_id.Equals(other.Parent_id)));
return(equal);
}
public Obo_networkTable_line_class Deep_copy()
{
Obo_networkTable_line_class copy = (Obo_networkTable_line_class)this.MemberwiseClone();
copy.Id = (string)this.Id.Clone();
copy.Name = (string)this.Name.Clone();
copy.Parent_id = (string)this.Parent_id.Clone();
copy.Parent_name = (string)this.Parent_name.Clone();
return(copy);
}
private void Remove_duplicates()
{
NetworkTable = Obo_networkTable_line_class.Order_in_standard_way(NetworkTable);
int sigNW_length = NetworkTable.Length;
Obo_networkTable_line_class obo_networkTable_line;
List <Obo_networkTable_line_class> new_sigNW = new List <Obo_networkTable_line_class>();
for (int indexSigNW = 0; indexSigNW < sigNW_length; indexSigNW++)
{
obo_networkTable_line = NetworkTable[indexSigNW];
if ((indexSigNW == 0) ||
(!obo_networkTable_line.Equal_in_standard_way(NetworkTable[indexSigNW - 1])))
{
new_sigNW.Add(obo_networkTable_line);
}
}
}
private void Add_to_networkTable(Obo_networkTable_line_class[] add_networkTable)
{
int add_length = add_networkTable.Length;
int this_length = this.NetworkTable.Length;
int new_length = add_length + this_length;
Obo_networkTable_line_class[] new_networkTable = new Obo_networkTable_line_class[new_length];
int indexNew = -1;
for (int indexThis = 0; indexThis < this_length; indexThis++)
{
indexNew++;
new_networkTable[indexNew] = this.NetworkTable[indexThis].Deep_copy();
}
for (int indexAdd = 0; indexAdd < add_length; indexAdd++)
{
indexNew++;
new_networkTable[indexNew] = add_networkTable[indexAdd].Deep_copy();
}
this.NetworkTable = new_networkTable;
}
private Obo_networkTable_line_class[] Read_obo_file()
{
Obo_networkTable_private_readOptions_class readOptions = new Obo_networkTable_private_readOptions_class();
StreamReader reader = new StreamReader(readOptions.Complete_file_name);
string input_line;
bool new_term = false;
string id = "error";
string name = "error";
string parent_id = "error";
string parent_name = "error";
string[] splitString;
string[] parent_id_parent_name;
Obo_interaction_type_enum interaction_type;
StringBuilder sb;
int splitString_length;
bool continue_reading = true;
bool new_parent = false;
bool at_least_one_line_added = false;
bool end_of_term = false;
bool is_obsolete = false;
List <Obo_networkTable_line_class> networkTable_list = new List <Obo_networkTable_line_class>();
Obo_networkTable_line_class new_networkTable_line;
Dictionary <string, bool> added_scps_dict = new Dictionary <string, bool>();
while (((input_line = reader.ReadLine()) != null) && (continue_reading))
{
#region Get split stings
splitString = input_line.Split(':');
splitString_length = splitString.Length;
if ((splitString_length > 2) && (!splitString[0].Equals("synonym")) && (!splitString[0].Equals("xref")) && (!splitString[0].Equals("def")))
{
sb = new StringBuilder();
for (int indexS = 1; indexS < splitString_length; indexS++)
{
splitString[indexS] = splitString[indexS].Replace("{", "").Replace("}", "");
if (indexS > 1)
{
sb.AppendFormat(":");
}
sb.AppendFormat(splitString[indexS]);
}
splitString = new string[] { splitString[0], sb.ToString() };
}
#endregion
#region Set every turn default values
parent_id = Global_class.Empty_entry;
parent_name = Global_class.Empty_entry;
interaction_type = Obo_interaction_type_enum.E_m_p_t_y;
new_parent = false;
#endregion
if (String.IsNullOrEmpty(splitString[0]))
{
end_of_term = true;
}
else
{
switch (splitString[0])
{
case Obo_networkTable_private_readOptions_class.New_term_marker:
new_term = true;
is_obsolete = false;
break;
case Obo_networkTable_private_readOptions_class.Id_marker:
id = Text_class.Remove_space_comma_semicolon_colon_from_end_and_beginning_of_text(splitString[1]);
break;
case Obo_networkTable_private_readOptions_class.Namespace_marker:
break;
case Obo_networkTable_private_readOptions_class.Name_marker:
name = Text_class.Remove_space_comma_semicolon_colon_from_end_and_beginning_of_text(splitString[1]);
break;
case Obo_networkTable_private_readOptions_class.Is_a_marker:
parent_id_parent_name = splitString[1].Split(Obo_networkTable_private_readOptions_class.Parent_id_parent_name_separator);
parent_id = Text_class.Remove_space_comma_semicolon_colon_from_end_and_beginning_of_text(parent_id_parent_name[0]);
if (parent_id_parent_name.Length == 2)
{
parent_name = Text_class.Remove_space_comma_semicolon_colon_from_end_and_beginning_of_text(parent_id_parent_name[1]);
}
interaction_type = Obo_interaction_type_enum.Is_a;
new_parent = true;
break;
case Obo_networkTable_private_readOptions_class.Part_of_marker:
parent_id_parent_name = splitString[1].Split(Obo_networkTable_private_readOptions_class.Parent_id_parent_name_separator);
parent_id = Text_class.Remove_space_comma_semicolon_colon_from_end_and_beginning_of_text(parent_id_parent_name[0]);
parent_name = Text_class.Remove_space_comma_semicolon_colon_from_end_and_beginning_of_text(parent_id_parent_name[1]);
interaction_type = Obo_interaction_type_enum.Part_of;
new_parent = true;
break;
case Obo_networkTable_private_readOptions_class.End_reading_marker:
continue_reading = false;
break;
case Obo_networkTable_private_readOptions_class.Is_obsolete_marker:
is_obsolete = true;
break;
default:
break;
}
}
if (new_term)
{
new_term = false;
id = (string)Global_class.Empty_entry.Clone();
name = (string)Global_class.Empty_entry.Clone();
at_least_one_line_added = false;
end_of_term = false;
}
else if ((new_parent) && (!is_obsolete))
{
new_networkTable_line = new Obo_networkTable_line_class(id, name);
new_networkTable_line.Parent_id = (string)parent_id.Clone();
new_networkTable_line.Parent_name = (string)parent_name.Clone();
new_networkTable_line.Interaction_type = interaction_type;
networkTable_list.Add(new_networkTable_line);
at_least_one_line_added = true;
}
else if ((end_of_term) && (!at_least_one_line_added) && (!is_obsolete))
{
if (!added_scps_dict.ContainsKey(name))
{
new_networkTable_line = new Obo_networkTable_line_class(id, name);
networkTable_list.Add(new_networkTable_line);
at_least_one_line_added = true;
}
else
{
throw new Exception("Process name already exists");
}
}
}
return(networkTable_list.ToArray());
}
