// All of the Private Data Type Parsing functions assume previous validation for null, empty, or comment lines
private ComplexFileData ParseComplex(string line)
{
ComplexFileData cd = new ComplexFileData();
// split the complex by the '.' character
string[] complex_strings = line.Split(
new[] { "." },
StringSplitOptions.RemoveEmptyEntries);
// parse the info for each molecule in the complex
for (int i = 0; i < complex_strings.Length; ++i)
{
cd.molecules.Add(ParseMolecule(complex_strings[i]));
}
return(cd);
}
/// <summary>
/// Parses a list of file-lines, line by line, for seed species data
/// Generally, expected to be called third in file parsing
/// Seed species are species present at the beginning of the simulation
/// </summary>
/// <param name="info"> The strings (file lines) to parse for data</param>
/// <param name="fdata"> The BNGL File data object that holds parsed data</param>
/// <returns>0(int) for successfull completion</returns>
private int ParseSeedSpecies(List <string> info, BNGLFileData fdata)
{
foreach (string s in info)
{
int rp = s.IndexOf(")"); // assuming the following layout:
// [molecule]"(" [binding-sites] ")" [numerical value]
ComplexFileData cd = ParseComplex(s.Substring(0, rp + 1));
string iv_string = s.Substring(rp + 1).Trim();
// Check that a value was specified for the seed species
if (String.IsNullOrEmpty(iv_string))
{
Debug.LogError(String.Format("{0} Seed Species is missing a value.\n{1}", fileErrorMsg, s));
return(-1);
}
SeedSpeciesFileData ssd = new SeedSpeciesFileData();
ssd.complex = cd;
float n = 0;
bool isNum = float.TryParse(iv_string, out n);
if (isNum) // A number was specified as the initial value for this seed species
{
ssd.initialValue = n;
}
else // A parameter was specified as the initial value for this seed species
{
// Check that the specified parameter was specified and parsed
if (!fdata.parameters.ContainsKey(iv_string))
{
Debug.LogError(String.Format("{0} A Seed Species referenced an undefined parameter.\n{1}", fileErrorMsg, s));
return(-1);
}
ssd.initialValue = fdata.parameters[iv_string];
}
fdata.seedSpecies.Add(ssd);
}
return(0);
}
