private static Converter ConverterFromArgs(string[] args)
{
Converter conv = new Converter();
conv.ReadFromSBML(args[0], Array.IndexOf(args, "-UseSBGN") != -1);
foreach (string arg in args)
{
// if dimensions{w,h} is in args
if (arg.IndexOf("}") == arg.Length - 1 && arg.Contains("-dimensions{"))
{
string dims = arg.Split(new string[] { "{", "}" }, StringSplitOptions.RemoveEmptyEntries)[1];
try
{
string[] dimArgs = dims.Split(',');
if (dimArgs.Length != 2)
{
throw new Exception("The number of arguments in -dimensions{w,h} is incorrect");
}
string width = dimArgs[0];
string height = dimArgs[1];
double w = parseDimToPoints(width);
double h = parseDimToPoints(height);
conv.specs.setDimensions(h, w, units.pts, units.pts);
}
catch (Exception e)
{
Console.WriteLine(e.Message);
}
}
}
return conv;
}
public MainForm()
{
conv = new Converter();
Hashtable fontTeXTable = getFonts();
if (fontTeXTable.Count != 0)
{
conv.fontTeXTable = fontTeXTable;
}
compileWithPdflatex = false;
nameChange += new fileNameChangeHandler(displayChange); // Used to change the sbml file loaded
compileWithPdfLaTeXChange += new compileToPdfChangeHandler(enableShowPDFCheckBox);
//Complete mainform initialization
InitializeComponent();
InitializeMyComponents(); // sets default values to UserAppDataRegistry values
setToolTips();
}
static void Main(string[] args)
{
//if (args.Length < 1 || args.Length > 2)
//{
// Console.WriteLine("Pass one or two arguments; the name of the SBML file and optionally, the output .tex file name");
// Environment.Exit(-1);
//}
//string fileName = args[0];
//Converter conv = new Converter(fileName);
//string outputFileName;
//if (args.Length == 1)
//{
// outputFileName = Path.Combine(Path.GetDirectoryName(fileName), Path.GetFileNameWithoutExtension(fileName) + ".tex");
//}
//else
//{
// outputFileName = args[1];
//}
//using (StreamWriter writer = new StreamWriter(outputFileName))
//{
// writer.WriteLine(conv.WriteFromLayout());
//}
//string fileName = "C:\\Users\\Si Yuan\\Desktop\\testcases\\CaMK-Activation.xml";
string fileName = @"C:\Users\Si yuan\Documents\SBML Models\linear1.xml"; ;
//string curDir = Directory.GetCurrentDirectory();
//string fontdatafile = curDir + "\\Fonts.txt";
Converter conv = new Converter(fileName, false);
string outputFileName = @"C:\Users\Si yuan\Desktop\test.tex";
using (StreamWriter writer = new StreamWriter(outputFileName))
{
writer.WriteLine(conv.WriteFromLayout());
}
//File.WriteAllBytes(outputFileName, conv.ToPDF());
}
public FileResult TikZ()
{
var converter = new Converter {Layout = CurrentLayout, specs = new RenderSpecs(CurrentLayout)};
var tex = converter.ToTex(CurrentLayout);
return new FileContentResult(System.Text.Encoding.UTF8.GetBytes(tex), "application/x-tex")
{
FileDownloadName="layout.tex"
};
}
public FileResult PDF()
{
var converter = new Converter { Layout = CurrentLayout };
Converter.LastCompileException = null;
var tex = converter.ToTex(CurrentLayout);
//var pdf = CompileTikZToPDF(tex);
//if (pdf == null || pdf.Length == 0)
//{
// return new FileContentResult(System.Text.Encoding.UTF8.GetBytes(LastMessage), "text/plain");
//}
var pdf = converter.ToPDF();
if (Converter.LastCompileException != null)
{
var errorMessage = Converter.LastCompileException.Message;
errorMessage += Environment.NewLine + Environment.NewLine + Converter.LastCompileException.StackTrace;
return new FileContentResult(System.Text.Encoding.UTF8.GetBytes(errorMessage), "text/plain");
}
return new FileContentResult(pdf, "application/pdf")
{
FileDownloadName = "layout.pdf"
};
}
/// <summary>
/// Convenience method for obtaining a PGF/TikZ
/// document. Returns a string of PGF/TikZ that
/// draws a specified set of rendering information
/// in the SBML file of the path passed. The
/// rendering may be replaced with SBGN default.
/// </summary>
/// <param name="filename">string indicating
/// path of the SBML file</param>
/// <param name="selectedLayoutNum">int indicating
/// which set of rendering information to use</param>
/// <param name="useSBGN">boolean indicating
/// whether the layout should be replaced by
/// SBGN default</param>
/// <returns></returns>
public static string ToTex(string filename, int selectedLayoutNum, Boolean useSBGN)
{
var conv = new Converter();
conv.ReadFromSBML(filename, useSBGN);
return conv.WriteFromLayout(selectedLayoutNum);
}
/// <summary>
/// Convenience method for obtaining a PGF/TikZ
/// document. Returns a string of PGF/TikZ that
/// draws the first set of rendering information
/// in the SBML file of the path passed.
/// </summary>
/// <param name="filename">string indicating path
/// of the SBML file</param>
/// <returns>string of PGF/TikZ commands</returns>
public static string ToTex(string filename)
{
var conv = new Converter(filename);
return conv.WriteFromLayout();
}
/// <summary>
/// Returns a <c>Converter</c> object with
/// <c>Layout</c> and <c>RenderSpecs</c>
/// for the SBML string passed. The
/// <c>Layout</c> may be overwritten with SBGN.
/// </summary>
/// <param name="sbmlContent">stroring of
/// SBML file contents</param>
/// <param name="useSBGN">boolean indicating
/// whether the layout should be replaced by
/// SBGN default</param>
/// <returns><c>Converter</c> with a
/// <c>Layout</c> and <c>RenderSpecs</c>
/// </returns>
public static Converter FromSBMLContent(string sbmlContent, bool useSBGN)
{
var converter = new Converter();
converter.ReadFromSBMLString(sbmlContent, useSBGN);
return converter;
}
