new public static IEnumerable <string> GetUsageOptions()
{
IEnumerable <string> options = FusionFlags.GetUsageOptions();
List <string> additionalOptions = new List <string>();
List <string> symmetries = SymmetryBuilderFactory.GetKnownSymmetryNames().Where(sym => !sym.StartsWith("C")).ToList();
// architecture options
additionalOptions.Add(GetFormattedOptionString("-arch <architecture>", "desired symmetry architecture, options are:"));
additionalOptions.Add(GetFormattedOptionString("", symmetries.Aggregate((a, b) => a + ", " + b)));
// axis1 options
additionalOptions.Add(GetFormattedOptionString("-axis1 <axis>", "first axis name corresponding to selected architecture"));
foreach (string symmetry in symmetries)
{
additionalOptions.Add(GetFormattedOptionString("", String.Format("\t{0} available in architecture {1}", GetAxesOptionsString(symmetry), symmetry)));
}
// axis2 options
additionalOptions.Add(GetFormattedOptionString("-axis2 <axis>", "first axis name corresponding to selected architecture"));
foreach (string symmetry in symmetries)
{
additionalOptions.Add(GetFormattedOptionString("", String.Format("\t{0} available in architecture {1}", GetAxesOptionsString(symmetry), symmetry)));
}
// oligomer selection
additionalOptions.Add(GetFormattedOptionString("-regex_oligomer1 <regex>", "oligomer1 pdb search pattern"));
additionalOptions.Add(GetFormattedOptionString("-regex_oligomer2 <regex>", "oligomer2 pdb search pattern"));
return(options.Concat(additionalOptions));
}
public override bool ParseArgs(string[] args)
{
if (args.FirstOrDefault() != InstanceBaseFlag)
{
return(false);
}
if (!base.ParseArgs(args))
{
return(false);
}
for (int i = 0; i < args.Length; i++)
{
if (args[i] == "-arch")
{
Architecture = args[i + 1];
if (!SymmetryBuilderFactory.GetKnownSymmetryNames().Contains(Architecture))
{
Console.WriteLine("Unknown '-arch' value - allowed values are:");
Console.Write(SymmetryBuilderFactory.GetKnownSymmetryNames().Aggregate("", (a, b) => a + "\n\t" + b));
Console.WriteLine();
return(false);
}
i++;
continue;
}
if (args[i] == "-regex_oligomer1")
{
OligomerRegex1 = args[i + 1];
i++;
continue;
}
if (args[i] == "-regex_oligomer2")
{
OligomerRegex2 = args[i + 1];
i++;
continue;
}
if (args[i] == "-axis1")
{
UnitId1 = args[i + 1];
i++;
continue;
}
if (args[i] == "-axis2")
{
UnitId2 = args[i + 1];
i++;
continue;
}
}
if (Architecture == null || !SymmetryBuilderFactory.GetKnownSymmetryNames().Contains(Architecture))
{
Console.WriteLine("Mandatory '-arch' flag missing or invalid - allowed values are:");
Console.Write(SymmetryBuilderFactory.GetKnownSymmetryNames().Aggregate("", (a, b) => a + "\n\t" + b));
Console.WriteLine();
return(false);
}
if (UnitId1 == null || !SymmetryBuilderFactory.GetSymmetryUnitIds(Architecture).Contains(UnitId1))
{
Console.WriteLine("Mandatory '-axis1' flag is missing or invalid - allowed values are:");
Console.Write(SymmetryBuilderFactory.GetSymmetryUnitIds(Architecture).Aggregate("", (a, b) => a + "\n\t" + b));
return(false);
}
if (UnitId2 == null || !SymmetryBuilderFactory.GetSymmetryUnitIds(Architecture).Contains(UnitId2))
{
Console.WriteLine("Mandatory '-axis1' flag is missing or invalid - allowed values are:");
Console.Write(SymmetryBuilderFactory.GetSymmetryUnitIds(Architecture).Aggregate("", (a, b) => a + "\n\t" + b));
return(false);
}
return(true);
}