protected override Parameters AddParameters(INetworkData ndata)
{
Boolean undirected = CheckDataUndirected(ndata);
Boolean connected = CheckDataConnected(ndata);
var valuesList = new List <String>()
{
"Network \t Density", "Network \t Average node connectivity", "Network \t Node connectivity", "Network \t Edge connectivity", "Network \t Diameter", "Network \t Radius", "Node \t Degree", "Node \t Out-degree", "Node \t Degree centrality", "Node \t In-degree centrality", "Node \t Out-degree centrality", "Node \t Closeness centrality", "Node \t Betweenness centrality", "Node \t Average neighbor degree", "Node \t Clustering coefficient", "Edge \t Betweenness centrality"
};
string[] values = UpdateParameterPropertyValues(valuesList, undirected, connected);
string[] directedOrNot = { undirected ? "Undirected" : "Directed" };
Parameters parameters = new Parameters();
parameters.AddParameterGroup(new Parameter[] { new MultiChoiceParam("Properties", new int[0] {
})
{
Values = values,
Help = "Please select here the properties that should be calculated."
} }, "", false);
parameters.AddParameterGroup(new Parameter[] { new SingleChoiceParam("Graph type")
{
Values = directedOrNot,
Visible = false,
} }, "", false);
return(parameters);
}
/// <summary>
/// Create the parameters for the GUI with default of 'Code file' and 'Executable'. Includes buttons
/// for preview downloads of 'Parameters' for development purposes.
/// Overwrite this function to provide custom parameters.
/// </summary>
public virtual Parameters GetParameters(ref string errString)
{
Parameters parameters = new Parameters();
parameters.AddParameterGroup(SpecificParameters(ref errString), "Specific", false);
var parametersPreviewButton = Utils.ParametersPreviewButton(parameters);
parameters.AddParameterGroup(new Parameter[] { ExecutableParam(), parametersPreviewButton }, "Generic", false);
return(parameters);
}
/// <summary>
/// Create the parameters for the GUI with default of specific 'Code file' parameter and generic 'Executable'.
/// Includes buttons /// for preview downloads of 'Data' and 'Parameters' for development purposes.
/// Overwrite <see cref="SpecificParameters"/> to add specific parameter. Overwrite this function for full control.
/// </summary>
/// <param name="mdata"></param>
/// <param name="errString"></param>
/// <returns></returns>
public virtual Parameters GetParameters(IMatrixData mdata, ref string errString)
{
Parameters parameters = new Parameters();
parameters.AddParameterGroup(SpecificParameters(mdata, ref errString), "specific", false);
var previewButton = Utils.DataPreviewButton(mdata);
var parametersPreviewButton = Utils.ParametersPreviewButton(parameters);
parameters.AddParameterGroup(new Parameter[] { ExecutableParam(), previewButton, parametersPreviewButton }, "generic", false);
return(parameters);
}
public void TestGroupedParameters()
{
Parameters parameters = new Parameters();
parameters.AddParameterGroup(new Parameter[] { new StringParam("myname", "myvalue") }, "grp1", false);
parameters.AddParameterGroup(new Parameter[] { new IntParam("some int", 42) }, "grp2", true);
Parameters parameters2 = parameters.ToXmlAndBack();
Assert.AreEqual("myvalue", parameters2.GetSubGroupAt(0).GetParam <string>("myname").Value);
Assert.AreEqual(42, parameters.GetSubGroupAt(1).GetParam <int>("some int").Value);
Assert.AreEqual("myvalue", parameters2.GetParam <string>("myname").Value);
}
public Parameters GetParameters(INetworkData ndata, ref string errString)
{
Parameters parameters = AddParameters(ndata);
parameters.AddParameterGroup(new Parameter[] { new FileParam(CodeLabel)
{
Filter = CodeFilter
} }, "specific", false);
parameters.AddParameterGroup(new Parameter[] { new FileParam(InterpreterLabel)
{
Filter = InterpreterFilter
} }, "generic", false);
return(parameters);
}
public virtual Parameters GetParameters(IMatrixData mdata, ref string errString)
{
Parameters parameters = new Parameters
(
PECAParameters.GetWorkingDir()
);
parameters.AddParameterGroup(PECAParameters.GetAboutData(), "About Data", false);
parameters.AddParameterGroup(PECAParameters.SelectData(mdata), "Select Data", true);
parameters.AddParameterGroup(PECAParameters.GetMCMCParams(), "MCMC Parameters", false);
return(parameters);
}
/// <summary>
/// Create the parameters for the GUI with default of generic 'Executable', 'Code file' and 'Additional arguments' parameters.
/// Includes buttons for preview downloads of 'Data' and 'Parameters' for development purposes.
/// Overwrite <see cref="SpecificParameters"/> to add specific parameter. Overwrite this function for full control.
/// </summary>
public virtual Parameters GetParameters(IMatrixData data, ref string errString)
{
Parameters parameters = new Parameters();
var specificParameters = SpecificParameters(data, ref errString);
if (!string.IsNullOrEmpty(errString))
{
return(null);
}
parameters.AddParameterGroup(specificParameters, "Specific", false);
var previewButton = Utils.DataPreviewButton(data);
var parametersPreviewButton = Utils.ParametersPreviewButton(parameters);
parameters.AddParameterGroup(new Parameter[] { ExecutableParam(), previewButton, parametersPreviewButton }, "Generic", false);
return(parameters);
}
//public string HelpOutput { get; }
//public string[] HelpSupplTables { get; }
//public int NumSupplTables { get; }
//public string[] HelpDocuments { get; }
//public int NumDocuments { get; }
public override Parameters GetParameters(IMatrixData mdata, ref string errString)
{
Parameters parameters = new Parameters
(
PECAParameters.GetWorkingDir()
);
parameters.AddParameterGroup(PECAParameters.GetAboutData(), "About Data", false);
parameters.AddParameterGroup(PECAParameters.GetFeatures(), "Features", false);
parameters.AddParameterGroup(PECAParameters.GetModule(), PECAParameters.network + " Info", false);
parameters.AddParameterGroup(PECAParameters.SelectConditionalData(mdata), "Select Data", true);
parameters.AddParameterGroup(PECAParameters.GetMCMCParams(), "MCMC Parameters", false);
return(parameters);
}
//public string HelpOutput { get; }
//public string[] HelpSupplTables { get; }
//public int NumSupplTables { get; }
//public string[] HelpDocuments { get; }
//public int NumDocuments { get; }
public override Parameters GetParameters(IMatrixData mdata, ref string errString)
{
string[] expSeriesNames = new string[] { PECAParameters.pecaRSeries1, PECAParameters.pecaRSeries2 };
string[] expSeriesHelp = new string[] { "mRNA Data", "'artificial' protein expressions" };
Parameters parameters = new Parameters
(
PECAParameters.GetWorkingDir()
);
parameters.AddParameterGroup(PECAParameters.GetAboutDataWithTP(), "About Data", false);
parameters.AddParameterGroup(PECAParameters.GetFeatures(), "Features", false);
parameters.AddParameterGroup(PECAParameters.GetConditionalModule(), "Gene Set Analysis", false);
parameters.AddParameterGroup(PECAParameters.SelectMultipleData(mdata, expSeriesNames, expSeriesHelp), "Select Data", true);
parameters.AddParameterGroup(PECAParameters.GetMCMCParams(), "MCMC Parameters", false);
return(parameters);
}
//public string HelpOutput { get; }
//public string[] HelpSupplTables { get; }
//public int NumSupplTables { get; }
//public string[] HelpDocuments { get; }
//public int NumDocuments { get; }
public override Parameters GetParameters(IMatrixData mdata, ref string errString)
{
string[] expSeriesNames = new string[] { PECAParameters.pecaPSSeries1, PECAParameters.pecaPSSeries2, PECAParameters.pecaPSSeries3 };
string[] expSeriesHelp = new string[] { "mRNA Data", "the channel representing degradation of pre-existing proteins", "the channel representing synthesis of new proteins" };
Parameters parameters = new Parameters
(
PECAParameters.GetWorkingDir()
);
parameters.AddParameterGroup(PECAParameters.GetAboutDataWithTP(), "About Data", false);
parameters.AddParameterGroup(PECAParameters.GetFeatures(), "Features", false);
parameters.AddParameterGroup(PECAParameters.GetConditionalModule(), "Gene Set Analysis", false);
parameters.AddParameterGroup(PECAParameters.SelectMultipleData(mdata, expSeriesNames, expSeriesHelp), "Select Data", true);
parameters.AddParameterGroup(PECAParameters.GetMCMCParams(), "MCMC Parameters", false);
return(parameters);
}
public void TestGroupedParameters()
{
var parameters = new Parameters();
parameters.AddParameterGroup(new Parameter[] {new StringParam("myname", "myvalue")}, "grp1", false);
parameters.AddParameterGroup(new Parameter[] {new IntParam("some int", 42)}, "grp2", true);
var parameters2 = parameters.ToXmlAndBack();
Assert.AreEqual("myvalue", parameters2.GetSubGroupAt(0).GetParam<string>("myname").Value);
Assert.AreEqual(42, parameters.GetSubGroupAt(1).GetParam<int>("some int").Value);
Assert.AreEqual("myvalue", parameters2.GetParam<string>("myname").Value);
}
