public void TestReadIsotopes2()
{
var isotopeData = "<?xml version=\"1.0\"?>" + "<list xmlns=\"http://www.xml-cml.org/schema/cml2/core\""
+ " xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\""
+ " xsi:schemaLocation=\"http://www.xml-cml.org/schema/cml2/core ../../io/cml/data/cmlCore.xsd\">"
+ "" + " <isotopeList id=\"H\">"
+ " <isotope id=\"H1\" isotopeNumber=\"1\" elementType=\"H\">"
+ " <abundance dictRef=\"cdk:relativeAbundance\">100.0</abundance>"
+ " <scalar dictRef=\"cdk:exactMass\">1.00782504</scalar>"
+ " <scalar dictRef=\"cdk:atomicNumber\">1</scalar>" + " </isotope>"
+ " <isotope id=\"H2\" isotopeNumber=\"2\" elementType=\"H\">"
+ " <abundance dictRef=\"cdk:relativeAbundance\">0.015</abundance>"
+ " <scalar dictRef=\"cdk:exactMass\">2.01410179</scalar>"
+ " <scalar dictRef=\"cdk:atomicNumber\">1</scalar>" + " </isotope>"
+ " <isotope id=\"D2\" isotopeNumber=\"2\" elementType=\"D\">"
+ " <abundance dictRef=\"cdk:relativeAbundance\">0.015</abundance>"
+ " <scalar dictRef=\"cdk:exactMass\">2.01410179</scalar>"
+ " <scalar dictRef=\"cdk:atomicNumber\">1</scalar>" + " </isotope>"
+ " </isotopeList>" + "</list>";
IsotopeReader reader = new IsotopeReader(new MemoryStream(Encoding.UTF8.GetBytes(isotopeData)));
Assert.IsNotNull(reader);
var isotopes = reader.ReadIsotopes();
Assert.IsNotNull(isotopes);
Assert.AreEqual(3, isotopes.Count);
}
public void TestReadIsotopes()
{
IsotopeReader reader = new IsotopeReader(new MemoryStream(Encoding.UTF8.GetBytes("<?xml version=\"1.0\"?><list></list>")));
Assert.IsNotNull(reader);
var isotopes = reader.ReadIsotopes();
Assert.IsNotNull(isotopes);
Assert.AreEqual(0, isotopes.Count);
}
/// <summary>
/// Private constructor for the IsotopeFactory object.
/// </summary>
/// <exception cref="IOException">A problem with reading the isotopes.xml file</exception>
private XMLIsotopeFactory()
{
Trace.TraceInformation("Creating new IsotopeFactory");
// ObjIn in = null;
var errorMessage = $"There was a problem getting NCDK.Config.Data.isotopes.xml as a stream";
var configFile = "NCDK.Config.Data.isotopes.xml";
Debug.WriteLine($"Getting stream for {configFile}");
using (var reader = new IsotopeReader(ResourceLoader.GetAsStream(configFile)))
{
var isotopes = reader.ReadIsotopes();
foreach (var isotope in isotopes)
{
Add(isotope);
}
Debug.WriteLine($"Found #isotopes in file: {isotopes.Count}");
}
}
//private LoggingTool //logger;
/// <summary> Private constructor for the IsotopeFactory object.
///
/// </summary>
/// <exception cref="IOException"> A problem with reading the isotopes.xml
/// file
/// </exception>
/// <exception cref="OptionalDataException"> Unexpected data appeared in the isotope
/// ObjectInputStream
/// </exception>
/// <exception cref="ClassNotFoundException"> A problem instantiating the isotopes
/// </exception>
private IsotopeFactory(IChemObjectBuilder builder)
{
//logger = new LoggingTool(this);
//logger.info("Creating new IsotopeFactory");
System.IO.Stream ins = null;
// ObjIn in = null;
System.String errorMessage = "There was a problem getting org.openscience.cdk." + "config.isotopes.xml as a stream";
try
{
System.String configFile = "isotopes.xml";
//if (debug)
//logger.debug("Getting stream for ", 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);
//this.GetType().getClassLoader().getResourceAsStream(configFile);
}
catch (System.Exception exception)
{
//logger.error(errorMessage);
//logger.debug(exception);
throw new System.IO.IOException(errorMessage);
}
if (ins == null)
{
//logger.error(errorMessage);
throw new System.IO.IOException(errorMessage);
}
IsotopeReader reader = new IsotopeReader(ins, builder);
//in = new ObjIn(ins, new Config().aliasID(false));
//isotopes = (Vector) in.readObject();
isotopes = reader.readIsotopes();
//if (debug)
//logger.debug("Found #isotopes in file: ", isotopes.Count);
/* for (int f = 0; f < isotopes.size(); f++) {
* Isotope isotope = (Isotope)isotopes.elementAt(f);
* } What's this loop for?? */
majorIsotopes = System.Collections.Hashtable.Synchronized(new System.Collections.Hashtable());
}
//private LoggingTool //logger;
/// <summary> Private constructor for the IsotopeFactory object.
///
/// </summary>
/// <exception cref="IOException"> A problem with reading the isotopes.xml
/// file
/// </exception>
/// <exception cref="OptionalDataException"> Unexpected data appeared in the isotope
/// ObjectInputStream
/// </exception>
/// <exception cref="ClassNotFoundException"> A problem instantiating the isotopes
/// </exception>
private IsotopeFactory(IChemObjectBuilder builder)
{
//logger = new LoggingTool(this);
//logger.info("Creating new IsotopeFactory");
System.IO.Stream ins = null;
// ObjIn in = null;
System.String errorMessage = "There was a problem getting org.openscience.cdk." + "config.isotopes.xml as a stream";
try
{
System.String configFile = "isotopes.xml";
//if (debug)
//logger.debug("Getting stream for ", 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);
//this.GetType().getClassLoader().getResourceAsStream(configFile);
}
catch (System.Exception exception)
{
//logger.error(errorMessage);
//logger.debug(exception);
throw new System.IO.IOException(errorMessage);
}
if (ins == null)
{
//logger.error(errorMessage);
throw new System.IO.IOException(errorMessage);
}
IsotopeReader reader = new IsotopeReader(ins, builder);
//in = new ObjIn(ins, new Config().aliasID(false));
//isotopes = (Vector) in.readObject();
isotopes = reader.readIsotopes();
//if (debug)
//logger.debug("Found #isotopes in file: ", isotopes.Count);
/* for (int f = 0; f < isotopes.size(); f++) {
Isotope isotope = (Isotope)isotopes.elementAt(f);
} What's this loop for?? */
majorIsotopes = System.Collections.Hashtable.Synchronized(new System.Collections.Hashtable());
}
public void TestIsotopeReader_InputStream_IChemObjectBuilder()
{
IsotopeReader reader = new IsotopeReader(new MemoryStream(System.Array.Empty <byte>()));
Assert.IsNotNull(reader);
}
