private DataBag consumeBag(PushbackInputStream in, ResourceFieldSchema fieldSchema)
throws IOException {
if (fieldSchema == null) {
throw new IOException("Schema is null");
}
ResourceFieldSchema[] fss = fieldSchema.getSchema().getFields();
Tuple t;
int buf;
while ((buf = in.read()) != '{') {
if (buf == -1) {
throw new IOException("Unexpect end of bag");
}
}
if (fss.length != 1) throw new IOException("Only tuple is allowed inside bag schema");
ResourceFieldSchema fs = fss[0];
DataBag db = DefaultBagFactory.getInstance().newDefaultBag();
while (true) {
t = consumeTuple(in, fs);
if (t != null) db.add(t);
while ((buf = in.read()) != '}' && buf != ',') {
if (buf == -1) {
throw new IOException("Unexpect end of bag");
}
}
if (buf == '}') break;
}
return db;
}
@Override
public DataBag exec(Tuple input) throws IOException {
try {
DataBag bag = DefaultBagFactory.getInstance().newDefaultBag();
if (input == null || input.size() == 0) {
return bag; // an empty bag
}
if (this.fieldType == DataType.MAP) {
Tuple t = DefaultTupleFactory.getInstance().newTuple(1);
t.set(0, createMap(input));
bag.add(t);
} else {
bag.add(input);
}
return bag;
} catch (Exception e) {
throw new RuntimeException(
"Error while computing size in " + this.getClass().getSimpleName());
}
}
@Override
public DataBag exec(Tuple aInput) throws IOException {
// invalid value | 無効値
if (aInput == null) return DefaultBagFactory.getInstance().newDefaultBag();
// processing target | 処理対象
DataBag tTargetBag = DataType.toBag(aInput.get(0));
DataBag tComparableValueBag = DataType.toBag(aInput.get(1));
if (tTargetBag.size() == 0 || tComparableValueBag.size() == 0)
return DefaultBagFactory.getInstance().newDefaultBag();
Iterator<Tuple> tTargetBagIterator = tTargetBag.iterator();
Iterator<Tuple> tComparableValueBagIterator = tComparableValueBag.iterator();
ArrayList<Tuple> tProtoBag = new ArrayList<Tuple>();
Double tMaxValue = Double.NEGATIVE_INFINITY;
while (tComparableValueBagIterator.hasNext()) {
Tuple tCurrentTargetTuple = tTargetBagIterator.next();
Double tCurrentValue = DataType.toDouble(tComparableValueBagIterator.next().get(0));
if (tCurrentValue == null) continue;
// add a tuple to tProtoBag if the same as existing MaxValue
// 現 MaxValue と同じなら、タプルを tProtoBag に追加
if (tMaxValue.equals(tCurrentValue)) {
tProtoBag.add(tCurrentTargetTuple);
}
// clear tProtoBag if bigger than existing MaxValue and add a tuple to tProtoBag
// 現 MaxValue より大きいなら、tProtoBag をクリアし、タプルを tProtoBag に追加
else if (tMaxValue < tCurrentValue) {
tMaxValue = tCurrentValue;
tProtoBag.clear();
tProtoBag.add(tCurrentTargetTuple);
}
}
return DefaultBagFactory.getInstance().newDefaultBag(tProtoBag);
}
public DataBag exec(Tuple input) throws IOException {
DataBag output = DefaultBagFactory.getInstance().newDefaultBag();
if (input == null || input.size() == 0) return null;
try {
String seq = ((String) input.get(0));
// byte[] ba = ((DataByteArray) input.get(0)).get();
int distance = (Integer) input.get(1);
// int seqLength = SequenceString.numBases(ba);
// String seq = SequenceString.byteArrayToSequence(ba);
Set<String> neighbors = MetaUtils.generateAllNeighborsWithinDistance(seq, distance);
for (String n : neighbors) {
Tuple t = DefaultTupleFactory.getInstance().newTuple(1);
t.set(0, n);
output.add(t);
}
} catch (Exception e) {
System.err.println("HammingDistance: failed to process input; error - " + e.getMessage());
return null;
}
return output;
}