public void TestEquals()
{
IResourceFormat a = (IResourceFormat)resourceFormat.GetType().GetConstructor(Type.EmptyTypes).Invoke(Array.Empty <object>());
IResourceFormat b = (IResourceFormat)resourceFormat.GetType().GetConstructor(Type.EmptyTypes).Invoke(Array.Empty <object>());
Assert.AreEqual(b, a);
}
public void TestGetFormat()
{
var filename = "NCDK.Data.Smiles.test2.smi";
Trace.TraceInformation("Testing: " + filename);
var ins = ResourceLoader.GetAsStream(filename);
EnumerableSMILESReader reader = new EnumerableSMILESReader(ins, ChemObjectBuilder.Instance);
IResourceFormat format = reader.Format;
Assert.IsTrue(format is SMILESFormat);
}
private void loadFormats()
{
if (formats == null)
{
formats = new System.Collections.ArrayList();
try
{
//logger.debug("Starting loading Formats...");
//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'"
//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'"
System.IO.StreamReader reader = new System.IO.StreamReader(Assembly.GetExecutingAssembly().GetManifestResourceStream("NuGenCDKSharp." + IO_FORMATS_LIST));//new System.IO.StreamReader(this.GetType().getClassLoader().getResourceAsStream(IO_FORMATS_LIST), System.Text.Encoding.Default).BaseStream, new System.IO.StreamReader(this.GetType().getClassLoader().getResourceAsStream(IO_FORMATS_LIST), System.Text.Encoding.Default).CurrentEncoding);
int formatCount = 0;
while (reader.Peek() != -1)
{
// load them one by one
System.String formatName = reader.ReadLine();
formatCount++;
try
{
//UPGRADE_ISSUE: Method 'java.lang.ClassLoader.loadClass' 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'"
ObjectHandle handle = System.Activator.CreateInstance("NuGenCDKSharp", formatName);
IResourceFormat format = (IResourceFormat)handle.Unwrap();//System.Activator.CreateInstance(//this.GetType().getClassLoader().loadClass(formatName));
if (format is IChemFormat)
{
formats.Add(format);
//logger.info("Loaded IChemFormat: " + format.GetType().FullName);
}
}
//UPGRADE_NOTE: Exception 'java.lang.ClassNotFoundException' was converted to 'System.Exception' which has different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1100'"
catch (System.Exception exception)
{
//logger.error("Could not find this IResourceFormat: ", formatName);
//logger.debug(exception);
}
//catch (System.Exception exception)
//{
// //logger.error("Could not load this IResourceFormat: ", 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);
}
}
}
private void LoadFormats()
{
if (formats == null)
{
formats = new List <IChemFormat>();
try
{
Debug.WriteLine("Starting loading Formats...");
var reader = new StreamReader(ResourceLoader.GetAsStream(typeof(IResourceFormat).Assembly, IO_FORMATS_LIST));
int formatCount = 0;
string formatName;
while ((formatName = reader.ReadLine()) != null)
{
// load them one by one
formatCount++;
try
{
var cls = typeof(IResourceFormat).Assembly.GetType(formatName);
if (cls != null)
{
IResourceFormat format = (IResourceFormat)cls.GetConstructor(Type.EmptyTypes).Invoke(Array.Empty <object>());
if (format is IChemFormat)
{
formats.Add((IChemFormat)format);
Trace.TraceInformation("Loaded IChemFormat: " + format.GetType().Name);
}
}
}
catch (ArgumentException exception)
{
Trace.TraceError($"Could not find this IResourceFormat: {formatName}");
Debug.WriteLine(exception);
}
catch (IOException exception)
{
Trace.TraceError($"Could not load this IResourceFormat: {formatName}");
Debug.WriteLine(exception);
}
}
Trace.TraceInformation("Number of loaded formats used in detection: ", formatCount);
}
catch (Exception exception)
{
Trace.TraceError($"Could not load this io format list: {IO_FORMATS_LIST}");
Debug.WriteLine(exception);
}
}
}
private static void ExpectFormat(string filename, IResourceFormat expectedFormat)
{
var ins = ResourceLoader.GetAsStream(filename);
Assert.IsNotNull(ins, $"Cannot find file: {filename}");
if (expectedFormat is IChemFormatMatcher)
{
factory.RegisterFormat((IChemFormatMatcher)expectedFormat);
}
ins = new BufferedStream(ins);
IChemFormat format = factory.GuessFormat(ins);
Assert.IsNotNull(format);
Assert.AreEqual(expectedFormat.FormatName, format.FormatName);
}
private void LoadFormats()
{
if (formats == null)
{
formats = new List <IChemFormat>();
try
{
Debug.WriteLine("Starting loading Formats...");
var reader = new StreamReader(ResourceLoader.GetAsStream(IO_FORMATS_LIST));
int formatCount = 0;
string formatName;
while ((formatName = reader.ReadLine()) != null)
{
// load them one by one
formatCount++;
try
{
System.Type formatClass = this.GetType().Assembly.GetType(formatName);
var getinstanceMethod = formatClass.GetProperty("Instance").GetGetMethod();
if (getinstanceMethod == null)
{
Trace.TraceError($"Could not find this IResourceFormat: {formatName}");
}
else
{
IResourceFormat format = (IResourceFormat)getinstanceMethod.Invoke(null, null);
if (format is IChemFormat)
{
formats.Add((IChemFormat)format);
Trace.TraceInformation("Loaded IChemFormat: " + format.GetType().Name);
}
}
}
catch (Exception exception)
{
Trace.TraceError($"Could not load this IResourceFormat: {formatName}");
Debug.WriteLine(exception);
}
}
Trace.TraceInformation("Number of loaded formats used in detection: ", formatCount);
}
catch (Exception exception)
{
Trace.TraceError($"Could not load this io format list: {IO_FORMATS_LIST}");
Debug.WriteLine(exception);
}
}
}
internal void ExpectReader(string filename, IResourceFormat expectedFormat, int expectedAtomCount, int expectedBondCount)
{
var ins = ResourceLoader.GetAsStream(filename);
Assert.IsNotNull(ins, "Cannot find file: " + filename);
if (expectedFormat is IChemFormatMatcher)
{
factory.RegisterFormat((IChemFormatMatcher)expectedFormat);
}
ISimpleChemObjectReader reader = factory.CreateReader(ins);
Assert.IsNotNull(reader);
Assert.AreEqual(((IChemFormat)expectedFormat).ReaderClassName, reader.GetType().FullName);
// now try reading something from it
IChemObject[] objects = { new ChemFile(), new ChemModel(), new AtomContainer(), new Reaction() };
bool read = false;
for (int i = 0; (i < objects.Length && !read); i++)
{
if (reader.Accepts(objects[i].GetType()))
{
IChemObject chemObject = reader.Read(objects[i]);
Assert.IsNotNull(chemObject, "Reader accepted a " + objects[i].GetType().Name + " but failed to read it");
AssertAtomCount(expectedAtomCount, chemObject);
AssertBondCount(expectedBondCount, chemObject);
read = true;
}
}
if (read)
{
// ok, reseting worked
}
else
{
Assert.Fail("Reading an IChemObject from the Reader did not work properly.");
}
}
public virtual void TestGetFormat()
{
IResourceFormat format = ChemObjectIOToTest.Format;
Assert.IsNotNull(format, "The IChemObjectIO.Format method returned null.");
}
public void SetResourceFormat(IResourceFormat format)
{
this.resourceFormat = format;
}
public void TestEquals_null()
{
IResourceFormat a = (IResourceFormat)resourceFormat.GetType().GetConstructor(Type.EmptyTypes).Invoke(Array.Empty <object>());
Assert.IsNotNull(a);
}
