//JAVA TO C# CONVERTER TODO TASK: Most Java annotations will not have direct .NET equivalent attributes:
//ORIGINAL LINE: @Requires("! strings.isEmpty()") @Ensures("result.isIntegerType()") private final org.broadinstitute.variant.bcf2.BCF2Type encodeStringsByRef(final Collection<String> strings) throws IOException
//JAVA TO C# CONVERTER WARNING: Method 'throws' clauses are not available in .NET:
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
private BCF2Type encodeStringsByRef(ICollection <string> strings)
{
//JAVA TO C# CONVERTER WARNING: The original Java variable was marked 'final':
//ORIGINAL LINE: final List<Integer> offsets = new ArrayList<Integer>(strings.size());
IList <int?> offsets = new List <int?>(strings.Count);
// iterate over strings until we find one that needs 16 bits, and break
foreach (String string in strings)
{
//JAVA TO C# CONVERTER WARNING: The original Java variable was marked 'final':
//ORIGINAL LINE: final Integer got = stringDictionaryMap.get(string);
int?got = stringDictionaryMap[string];
if (got == null)
{
throw new IllegalStateException("Format error: could not find string " + string + " in header as required by BCF");
}
//JAVA TO C# CONVERTER WARNING: The original Java variable was marked 'final':
//ORIGINAL LINE: final int offset = got;
int offset = got;
offsets.Add(offset);
}
//JAVA TO C# CONVERTER WARNING: The original Java variable was marked 'final':
//ORIGINAL LINE: final org.broadinstitute.variant.bcf2.BCF2Type type = org.broadinstitute.variant.bcf2.BCF2Utils.determineIntegerType(offsets);
BCF2Type type = BCF2Utils.determineIntegerType(offsets);
encoder.encodeTyped(offsets, type);
return(type);
}
//JAVA TO C# CONVERTER TODO TASK: Most Java annotations will not have direct .NET equivalent attributes:
//ORIGINAL LINE: @Ensures("encodeStream.size() > old(encodeStream.size())") public final void encodeTypedInt(final int v) throws java.io.IOException
//JAVA TO C# CONVERTER WARNING: Method 'throws' clauses are not available in .NET:
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
public void encodeTypedInt(int v)
{
//JAVA TO C# CONVERTER WARNING: The original Java variable was marked 'final':
//ORIGINAL LINE: final org.broadinstitute.variant.bcf2.BCF2Type type = org.broadinstitute.variant.bcf2.BCF2Utils.determineIntegerType(v);
BCF2Type type = BCF2Utils.determineIntegerType(v);
encodeTypedInt(v, type);
}
// ----------------------------------------------------------------------
//
// Constructor
//
// ----------------------------------------------------------------------
//JAVA TO C# CONVERTER TODO TASK: Most Java annotations will not have direct .NET equivalent attributes:
//ORIGINAL LINE: @Requires({"headerLine != null", "dict != null"}) private BCF2FieldEncoder(final Bio.VCF.VCFCompoundHeaderLine headerLine, final java.util.Map<String, Integer> dict, final org.broadinstitute.variant.bcf2.BCF2Type staticType)
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
private BCF2FieldEncoder(VCFCompoundHeaderLine headerLine, IDictionary <string, int?> dict, BCF2Type staticType)
{
this.headerLine = headerLine;
this.staticType = staticType;
//JAVA TO C# CONVERTER WARNING: The original Java variable was marked 'final':
//ORIGINAL LINE: final Integer offset = dict.get(getField());
int?offset = dict[Field];
if (offset == null)
{
throw new IllegalStateException("Format error: could not find string " + Field + " in header as required by BCF");
}
this.dictionaryOffset = offset;
dictionaryOffsetType = BCF2Utils.determineIntegerType(offset);
}
//JAVA TO C# CONVERTER WARNING: Method 'throws' clauses are not available in .NET:
//ORIGINAL LINE: public void start(final BCF2Encoder encoder, final org.broadinstitute.variant.variantcontext.VariantContext vc) throws java.io.IOException
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
public override void start(BCF2Encoder encoder, VariantContext vc)
{
// the only value that is dynamic are integers
//JAVA TO C# CONVERTER WARNING: The original Java variable was marked 'final':
//ORIGINAL LINE: final java.util.List<Integer> values = new java.util.ArrayList<Integer>(vc.getNSamples());
IList <int?> values = new List <int?>(vc.NSamples);
foreach (Genotype g in vc.Genotypes)
{
foreach (Object i in BCF2Utils.toList(g.getExtendedAttribute(Field, null)))
{
if (i != null) // we know they are all integers
{
values.Add((int?)i);
}
}
}
encodingType = BCF2Utils.determineIntegerType(values);
base.start(encoder, vc);
}
//JAVA TO C# CONVERTER TODO TASK: Most Java annotations will not have direct .NET equivalent attributes:
//ORIGINAL LINE: @Requires("arg != null") private final org.broadinstitute.variant.bcf2.BCF2Type determineBCFType(final Object arg)
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
private BCF2Type determineBCFType(object arg)
{
//JAVA TO C# CONVERTER WARNING: The original Java variable was marked 'final':
//ORIGINAL LINE: final Object toType = arg instanceof List ? ((List)arg).get(0) : arg;
object toType = arg is IList ? ((IList)arg)[0] : arg;
if (toType is int?)
{
return(BCF2Utils.determineIntegerType((int?)toType));
}
else if (toType is string)
{
return(BCF2Type.CHAR);
}
else if (toType is double?)
{
return(BCF2Type.FLOAT);
}
else
{
throw new System.ArgumentException("No native encoding for Object of type " + arg.GetType().Name);
}
}
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
//ORIGINAL LINE: public org.broadinstitute.variant.bcf2.BCF2Type getDynamicType(final Object value)
public override BCF2Type getDynamicType(object value)
{
return(value == null ? BCF2Type.INT8 : BCF2Utils.determineIntegerType(toList(typeof(int?), value)));
}
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
//ORIGINAL LINE: public org.broadinstitute.variant.bcf2.BCF2Type getDynamicType(final Object value)
public override BCF2Type getDynamicType(object value)
{
return(value == null ? BCF2Type.INT8 : BCF2Utils.determineIntegerType((int[])value));
}
