/// <summary> Reads a text based configuration file.
///
/// </summary>
/// <param name="builder">IChemObjectBuilder used to construct the IAtomType's.
/// </param>
/// <throws> IOException when a problem occured with reading from the InputStream </throws>
/// <returns> A Vector with read IAtomType's.
/// </returns>
public virtual System.Collections.ArrayList readAtomTypes(IChemObjectBuilder builder)
{
System.Collections.ArrayList atomTypes = System.Collections.ArrayList.Synchronized(new System.Collections.ArrayList(10));
if (ins == null)
{
// trying the default
//System.out.println("readAtomTypes getResourceAsStream:"
// + configFile);
//UPGRADE_ISSUE: Method 'java.lang.ClassLoader.getResourceAsStream' was not converted. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1000_javalangClassLoader'"
//UPGRADE_ISSUE: Method 'java.lang.Class.getClassLoader' was not converted. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1000_javalangClassgetClassLoader'"
ins = Assembly.GetExecutingAssembly().GetManifestResourceStream("NuGenCDKSharp." + configFile);
}
if (ins == null)
{
throw new System.IO.IOException("There was a problem getting the default stream: " + configFile);
}
// read the contents from file
//UPGRADE_TODO: The differences in the expected value of parameters for constructor 'java.io.BufferedReader.BufferedReader' may cause compilation errors. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1092'"
//UPGRADE_WARNING: At least one expression was used more than once in the target code. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1181'"
System.IO.StreamReader reader = new System.IO.StreamReader(new System.IO.StreamReader(ins, System.Text.Encoding.Default).BaseStream, new System.IO.StreamReader(ins, System.Text.Encoding.Default).CurrentEncoding, false, 1024);
SupportClass.Tokenizer tokenizer;
System.String string_Renamed;
while (true)
{
string_Renamed = reader.ReadLine();
if (string_Renamed == null)
{
break;
}
if (!string_Renamed.StartsWith("#"))
{
System.String name = "";
System.String rootType = "";
int atomicNumber = 0, colorR = 0, colorG = 0, colorB = 0;
double mass = 0.0, vdwaals = 0.0, covalent = 0.0;
tokenizer = new SupportClass.Tokenizer(string_Renamed, "\t ,;");
int tokenCount = tokenizer.Count;
if (tokenCount == 9)
{
name = tokenizer.NextToken();
rootType = tokenizer.NextToken();
System.String san = tokenizer.NextToken();
System.String sam = tokenizer.NextToken();
System.String svdwaals = tokenizer.NextToken();
System.String scovalent = tokenizer.NextToken();
System.String sColorR = tokenizer.NextToken();
System.String sColorG = tokenizer.NextToken();
System.String sColorB = tokenizer.NextToken();
try
{
//UPGRADE_TODO: The differences in the format of parameters for constructor 'java.lang.Double.Double' may cause compilation errors. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1092'"
mass = System.Double.Parse(sam);
//UPGRADE_TODO: The differences in the format of parameters for constructor 'java.lang.Double.Double' may cause compilation errors. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1092'"
vdwaals = System.Double.Parse(svdwaals);
//UPGRADE_TODO: The differences in the format of parameters for constructor 'java.lang.Double.Double' may cause compilation errors. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1092'"
covalent = System.Double.Parse(scovalent);
atomicNumber = System.Int32.Parse(san);
colorR = System.Int32.Parse(sColorR);
colorG = System.Int32.Parse(sColorG);
colorB = System.Int32.Parse(sColorB);
}
catch (System.FormatException nfe)
{
throw new System.IO.IOException("AtomTypeTable.ReadAtypes: " + "Malformed Number");
}
IAtomType atomType = builder.newAtomType(name, rootType);
atomType.AtomicNumber = atomicNumber;
atomType.setExactMass(mass);
atomType.VanderwaalsRadius = vdwaals;
atomType.CovalentRadius = covalent;
System.Drawing.Color color = System.Drawing.Color.FromArgb(colorR, colorG, colorB);
atomType.setProperty("org.openscience.cdk.renderer.color", color);
atomTypes.Add(atomType);
}
else
{
throw new System.IO.IOException("AtomTypeTable.ReadAtypes: " + "Wrong Number of fields");
}
}
} // end while
ins.Close();
return(atomTypes);
}
