/**
* Recode the incoming object to a String, compacting it into a BCF2 string if the value is a
* list.
*
* @param value a String or List<String> to encode, or null
* @return a non-null string to encode
*/
private String javaStringToBCF2String(final Object value) {
if (value == null) return "";
else if (value instanceof List) {
final List<String> l = (List<String>) value;
return BCF2Utils.collapseStringList(l);
} else if (value.getClass().isArray()) {
final List<String> l = new ArrayList<String>();
Collections.addAll(l, (String[]) value);
return BCF2Utils.collapseStringList(l);
} else return (String) value;
}
@Override
public void encodeValue(
final BCF2Encoder encoder, final Object value, final BCF2Type type, final int minValues)
throws IOException {
int count = 0;
for (final Integer i : BCF2Utils.toList(Integer.class, value)) {
if (i != null) { // necessary because .,. => [null, null] in VC
encoder.encodeRawInt(i, type);
count++;
}
}
for (; count < minValues; count++) encoder.encodeRawMissingValue(type);
}
private BCF2FieldEncoder(
final VCFCompoundHeaderLine headerLine,
final Map<String, Integer> dict,
final BCF2Type staticType) {
this.headerLine = headerLine;
this.staticType = staticType;
final Integer offset = dict.get(getField());
if (offset == null)
throw new IllegalStateException(
"Format error: could not find string " + getField() + " in header as required by BCF");
this.dictionaryOffset = offset;
dictionaryOffsetType = BCF2Utils.determineIntegerType(offset);
}
@Override
public void encodeValue(
final BCF2Encoder encoder, final Object value, final BCF2Type type, final int minValues)
throws IOException {
int count = 0;
// TODO -- can be restructured to avoid toList operation
if (isAtomic) {
// fast path for fields with 1 fixed float value
if (value != null) {
encoder.encodeRawFloat((Double) value);
count++;
}
} else {
// handle generic case
final List<Double> doubles = BCF2Utils.toList(Double.class, value);
for (final Double d : doubles) {
if (d != null) { // necessary because .,. => [null, null] in VC
encoder.encodeRawFloat(d);
count++;
}
}
}
for (; count < minValues; count++) encoder.encodeRawMissingValue(type);
}
@Override
public BCF2Type getDynamicType(final Object value) {
return value == null
? BCF2Type.INT8
: BCF2Utils.determineIntegerType(BCF2Utils.toList(Integer.class, value));
}
@Override
public BCF2Type getDynamicType(final Object value) {
return value == null ? BCF2Type.INT8 : BCF2Utils.determineIntegerType((Integer) value);
}