private void loadReaders()
{
if (formats == null)
{
formats = new List <IChemFormatMatcher>();
//System.Collections.ArrayList.Synchronized(new System.Collections.ArrayList(10));
try
{
//logger.debug("Starting loading Readers...");
Stream stm = Assembly.GetExecutingAssembly().GetManifestResourceStream("NuGenCDKSharp." + IO_FORMATS_LIST);
System.IO.StreamReader reader = new System.IO.StreamReader(stm);
int formatCount = 0;
while (reader.Peek() != -1)
{
// load them one by one
System.String formatName = reader.ReadLine();
formatCount++;
try
{
ObjectHandle handle = System.Activator.CreateInstance("NuGenCDKSharp", formatName);
IChemFormatMatcher format = (IChemFormatMatcher)handle.Unwrap();
formats.Add(format);
//logger.info("Loaded IO format: " + format.GetType().FullName);
}
catch (System.Exception exception)
{
//logger.error("Could not find this ChemObjectReader: ", formatName);
//logger.debug(exception);
}
}
//logger.info("Number of loaded formats used in detection: ", formatCount);
}
catch (System.Exception exception)
{
//logger.error("Could not load this io format list: ", IO_FORMATS_LIST);
//logger.debug(exception);
}
}
}
public void TestBug2153298()
{
var filename = "NCDK.Data.ASN.PubChem.cid1145.xml";
var ins = ResourceLoader.GetAsStream(filename);
Assert.IsNotNull(ins, "Cannot find file: " + filename);
IChemFormatMatcher realFormat = (IChemFormatMatcher)PubChemCompoundXMLFormat.Instance;
factory.RegisterFormat(realFormat);
// ok, if format ok, try instantiating a reader
ins = ResourceLoader.GetAsStream(filename);
ISimpleChemObjectReader reader = factory.CreateReader(ins);
Assert.IsNotNull(reader);
Assert.AreEqual(((IChemFormat)PubChemCompoundXMLFormat.Instance).ReaderClassName, reader.GetType().FullName);
// now try reading something from it
IAtomContainer molecule = (IAtomContainer)reader.Read(builder.NewAtomContainer());
Assert.IsNotNull(molecule);
Assert.AreNotSame(0, molecule.Atoms.Count);
Assert.AreNotSame(0, molecule.Bonds.Count);
}
public virtual void SetChemFormatMatcher(IChemFormatMatcher matcher)
{
base.SetChemFormat(matcher);
this.matcher = matcher;
}
/// <summary>
/// Registers a format for detection.
/// </summary>
public void RegisterFormat(IChemFormatMatcher format)
{
formats.Add(format);
}
/// <summary> Registers a format for detection.</summary>
public virtual void registerFormat(IChemFormatMatcher format)
{
formats.Add(format);
}
/// <summary> Registers a format for detection.</summary>
public virtual void registerFormat(IChemFormatMatcher format)
{
formats.Add(format);
}
/// <summary> Creates a String of the Class name of the <code>IChemObject</code> reader
/// for this file format. The input is read line-by-line
/// until a line containing an identifying string is
/// found.
///
/// <p>The ReaderFactory detects more formats than the CDK
/// has Readers for.
///
/// <p>This method is not able to detect the format of gziped files.
/// Use <code>guessFormat(InputStream)</code> instead for such files.
///
/// </summary>
/// <throws> IOException if an I/O error occurs </throws>
/// <throws> IllegalArgumentException if the input is null </throws>
/// <summary>
/// </summary>
/// <seealso cref="guessFormat(InputStream)">
/// </seealso>
public virtual IChemFormat guessFormat(StreamReader input)
{
if (input == null)
{
throw new System.ArgumentException("input cannot be null");
}
// make a copy of the header
char[] header = new char[this.headerLength];
//UPGRADE_ISSUE: Method 'java.io.BufferedReader.markSupported' was not converted. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1000'"
//if (!input.markSupported())
//{
// //logger.error("Mark not supported");
// throw new System.ArgumentException("input must support mark");
//}
//int pos = this.headerLength;//input.mark(this.headerLength);
input.Read(header, 0, this.headerLength);
input.BaseStream.Seek(0, SeekOrigin.Begin);
//UPGRADE_ISSUE: Constructor 'java.io.BufferedReader.BufferedReader' was not converted. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1000_javaioBufferedReaderBufferedReader_javaioReader'"
System.IO.StringReader buffer = new StringReader(new System.String(header));
/* Search file for a line containing an identifying keyword */
System.String line = null;
int lineNumber = 1;
while ((line = buffer.ReadLine()) != null)
{
//logger.debug(lineNumber + ": ", line);
for (int i = 0; i < formats.Count; i++)
{
IChemFormatMatcher cfMatcher = (IChemFormatMatcher)formats[i];
if (cfMatcher.matches(lineNumber, line))
{
//logger.info("Detected format: ", cfMatcher.FormatName);
return(cfMatcher);
}
}
lineNumber++;
}
//logger.warn("Now comes the tricky and more difficult ones....");
//UPGRADE_ISSUE: Constructor 'java.io.BufferedReader.BufferedReader' was not converted. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1000_javaioBufferedReaderBufferedReader_javaioReader'"
buffer = new StringReader(new System.String(header));
line = buffer.ReadLine();
// is it a XYZ file?
SupportClass.Tokenizer tokenizer = new SupportClass.Tokenizer(line.Trim());
try
{
int tokenCount = tokenizer.Count;
if (tokenCount == 1)
{
System.Int32.Parse(tokenizer.NextToken());
// if not failed, then it is a XYZ file
return(null);// new org.openscience.cdk.io.formats.XYZFormat();
}
else if (tokenCount == 2)
{
System.Int32.Parse(tokenizer.NextToken());
if ("Bohr".ToUpper().Equals(tokenizer.NextToken().ToUpper()))
{
return(null);// new org.openscience.cdk.io.formats.XYZFormat();
}
}
}
catch (System.FormatException exception)
{
//logger.info("No, it's not a XYZ file");
}
//logger.warn("File format undetermined");
return(null);
}
/// <summary>
/// Registers a format for detection.
/// </summary>
public void RegisterFormat(IChemFormatMatcher format)
{
formatFactory.RegisterFormat(format);
}