public object Clone()
{
var res = new InitialStates();
res._MTs = new List <MtRecord>(_MTs);
res._chromosomes = new List <ChromosomeRecord>(_chromosomes);
return(res);
}
public object Clone()
{
var res = new LaunchParameters();
if (Args != null)
{
res.Args = Args.Clone() as CliArgs;
}
if (Config != null)
{
res.Config = Config.Clone() as SimParams;
}
if (InitialStates != null)
{
res.InitialStates = InitialStates.Clone() as InitialStates;
}
if (PoleCoords != null)
{
res.PoleCoords = PoleCoords.Clone() as PoleCoordinates;
}
return(res);
}
internal String Apply(String workingDir)
{
if (Args == null)
{
throw new ApplicationException("Cannot launch simulation without CLI arguments");
}
CliArgs defaultArgs = new CliArgs();
String oldCellFile = Args.CellFile;
bool needCellFile = Args.Mode != LaunchMode.Help && Args.Mode != LaunchMode.Info;
String oldConfig = Args.ConfigFile;
bool needConfig = Args.Mode == LaunchMode.New || Args.Mode == LaunchMode.Continue || Args.Mode == LaunchMode.Restart;
String oldInitialFile = Args.InitialConditionsFile;
String oldPoleFile = Args.PoleCoordsFile;
try
{
//Settings file for results.
if (needCellFile || Args.CellFile != defaultArgs.CellFile)
{
Args.CellFile = ExtractFilename(workingDir, oldCellFile);
}
if (Args.Mode == LaunchMode.Fix)
{
return(Args.Export());
}
//Storing config.
if (needConfig || Args.ConfigFile != defaultArgs.ConfigFile)
{
if (Config == null)
{
throw new ApplicationException("Cannot launch simulation without config");
}
if (String.IsNullOrEmpty(Args.ConfigFile))
{
Args.ConfigFile = "mitosis.conf";
}
Args.ConfigFile = ExtractFilename(workingDir, oldConfig);
File.WriteAllText(Args.ConfigFile, Config.ExportAsProps());
}
//Storing initial states.
if (InitialStates != null)
{
if (String.IsNullOrEmpty(Args.InitialConditionsFile))
{
Args.InitialConditionsFile = "initial.xml";
}
Args.InitialConditionsFile = ExtractFilename(workingDir, Args.InitialConditionsFile);
File.WriteAllText(Args.InitialConditionsFile, InitialStates.ToString());
}
//Storing information about poles.
if (PoleCoords != null)
{
if (String.IsNullOrEmpty(Args.PoleCoordsFile))
{
Args.PoleCoordsFile = "poles.xml";
}
Args.PoleCoordsFile = ExtractFilename(workingDir, Args.PoleCoordsFile);
File.WriteAllText(Args.PoleCoordsFile, PoleCoords.ToString());
}
//Done, exporting.
return(Args.Export());
}
finally
{
Args.CellFile = oldCellFile;
Args.ConfigFile = oldConfig;
Args.InitialConditionsFile = oldInitialFile;
Args.PoleCoordsFile = oldPoleFile;
}
}