public static <T> Iterator<T> iterator(Class<T> class1, final Object value) {
if (value == null) {
return Collections.EMPTY_LIST.iterator();
}
if (Boon.isArray(value)) {
final int length = Arry.len(value);
return new Iterator<T>() {
int i = 0;
@Override
public boolean hasNext() {
return i < length;
}
@Override
public T next() {
if (i >= length) throw new NoSuchElementException("No more properties");
T next = (T) BeanUtils.idx(value, i);
i++;
return next;
}
@Override
public void remove() {}
};
} else if (Typ.isCollection(value.getClass())) {
return ((Collection<T>) value).iterator();
} else {
return (Iterator<T>) Collections.singleton(value).iterator();
}
}
@SuppressWarnings("unchecked")
public SpectrumIterator() {
try {
it = new Ms2QueryIterator();
} catch (FileNotFoundException e) {
// do nothing
it = Collections.EMPTY_LIST.iterator();
}
}
/**
* Iterator type that can combine multiple iterators into one logical iterator.
*
* @author Abe White
*/
public abstract class MultiIterator implements Iterator {
private static final int PAST_END = -1;
private Iterator _itr = Collections.EMPTY_LIST.iterator();
private Iterator _last = null;
private int _index = 0;
public boolean hasNext() {
setIterator();
return _itr.hasNext();
}
public Object next() {
setIterator();
return _itr.next();
}
public void remove() {
setIterator();
_last.remove();
}
/**
* Implement this method to return the iterator at the <code>index</code>th position in the list
* of iterators to process. Indexing starts at 0 and will proceed upward linearly, never repeating
* the same index. Return null to indicate that there are no more iterators to process. You may
* return null to index 0, in which case this iterator will act like an iterator over an empty
* collection.
*/
protected abstract Iterator newIterator(int index);
/** Sets internal iterator to the iterator to use for processing. */
private void setIterator() {
// if already iterated through all, nothing to do
if (_index == PAST_END) return;
// always remove from the last iterator used
_last = _itr;
// find next iterator with a value
Iterator newItr = _itr;
while (newItr != null && !newItr.hasNext()) newItr = newIterator(_index++);
// switch current iter if needed
if (newItr != null && _itr != newItr) _itr = newItr;
else if (newItr == null) _index = PAST_END;
}
}
/**
* Assign the right TARGET if found.
*
* @param iArgs Parameters to bind
* @return true if the target has been recognized, otherwise false
*/
protected boolean assignTarget(final Map<Object, Object> iArgs) {
parameters = iArgs;
if (parsedTarget == null) return true;
if (iArgs != null && iArgs.size() > 0 && compiledFilter != null)
compiledFilter.bindParameters(iArgs);
if (target == null) {
if (parsedTarget.getTargetClasses() != null) searchInClasses();
else if (parsedTarget.getTargetIndexValues() != null) {
target =
new IndexValuesIterator(
parsedTarget.getTargetIndexValues(), parsedTarget.isTargetIndexValuesAsc());
} else if (parsedTarget.getTargetClusters() != null) searchInClusters();
else if (parsedTarget.getTargetRecords() != null) {
if (!lazyIteration && parsedTarget.getTargetQuery() != null) {
// EXECUTE THE QUERY TO ALLOW DISTRIB EXECUTION
target =
((Iterable<? extends OIdentifiable>)
getDatabase()
.command(new OCommandSQL(parsedTarget.getTargetQuery()))
.execute(iArgs))
.iterator();
} else if (parsedTarget.getTargetRecords() instanceof OIterableRecordSource) {
target = ((OIterableRecordSource) parsedTarget.getTargetRecords()).iterator(iArgs);
} else {
target = parsedTarget.getTargetRecords().iterator();
}
} else if (parsedTarget.getTargetVariable() != null) {
final Object var = getContext().getVariable(parsedTarget.getTargetVariable());
if (var == null) {
target = Collections.EMPTY_LIST.iterator();
return true;
} else if (var instanceof OIdentifiable) {
final ArrayList<OIdentifiable> list = new ArrayList<OIdentifiable>();
list.add((OIdentifiable) var);
target = list.iterator();
} else if (var instanceof Iterable<?>)
target = ((Iterable<? extends OIdentifiable>) var).iterator();
} else return false;
}
return true;
}
synchronized Iterator<Mutation> getFeatures(String trackKey, String chr, int start, int end)
throws IOException {
if (currentRange == null || !currentRange.contains(chr, start, end)) {
Iterator<Feature> features = tribbleFeatureSource.getFeatures(chr, start, end);
while (features.hasNext()) {
Mutation feat = (Mutation) features.next();
String thisKey = feat.getSampleId();
List<Mutation> keyFeatures = featureMap.get(thisKey);
if (keyFeatures == null) {
keyFeatures = new ArrayList<Mutation>();
featureMap.put(thisKey, keyFeatures);
}
keyFeatures.add(feat);
currentRange = new Range(chr, start, end);
}
}
List<Mutation> featureList = featureMap.get(trackKey);
return featureList == null ? Collections.EMPTY_LIST.iterator() : featureList.iterator();
}
public ListIterator childrenFolded() {
if (isFolded()) {
return Collections.EMPTY_LIST.listIterator();
}
return childrenUnfolded();
}
public ListIterator childrenUnfolded() {
return children != null ? children.listIterator() : Collections.EMPTY_LIST.listIterator();
}
/**
* return a sub list of this list
*
* @param fromIndex start index
* @param toIndex end index
* @return a list
*/
public List subList(int fromIndex, int toIndex) {
if (this.collection != null) return ((List) this.collection).subList(fromIndex, toIndex);
return Collections.EMPTY_LIST.subList(fromIndex, toIndex);
}
/**
* return a list iterator over the list
*
* @param index
* @return an instance of ListIterator
*/
public ListIterator listIterator(int index) {
if (this.collection != null) return ((List) this.collection).listIterator(index);
return Collections.EMPTY_LIST.listIterator(index);
}
