final String zzB(String paramString) {
String[] arrayOfString1 = paramString.split("\n");
if (arrayOfString1.length == 0) {
return "";
}
zza localzza = new zza();
PriorityQueue localPriorityQueue = new PriorityQueue(this.zztK, new Comparator() {});
for (int i = 0; i < arrayOfString1.length; i++) {
String[] arrayOfString2 = zzbx.zzD(arrayOfString1[i]);
if (arrayOfString2.length >= this.zztJ) {
zzbz.zza(arrayOfString2, this.zztK, this.zztJ, localPriorityQueue);
}
}
Iterator localIterator = localPriorityQueue.iterator();
for (; ; ) {
if (localIterator.hasNext()) {
zzbz.zza localzza1 = (zzbz.zza) localIterator.next();
try {
localzza.write(this.zztM.zzz(localzza1.zztR));
} catch (IOException localIOException) {
zzb.e("Error while writing hash to byteStream", localIOException);
}
}
}
return localzza.toString();
}
public void PQOrdering() {
PriorityQueue<String> pq = new PriorityQueue<String>();
pq.add("5");
pq.add("3");
pq.add("1");
pq.add("2");
pq.add("4");
pq.add("6");
System.out.println("Unordered: " + pq); // Unordered: [1, 2, 3, 5, 4, 6]
Iterator<String> itr = pq.iterator();
System.out.print("Unordered Itr: ");
while (itr.hasNext()) {
System.out.print(itr.next() + ", "); // Unordered Itr: 1, 2, 3, 5, 4, 6,
}
System.out.println("");
System.out.print("Unordered Arrays: ");
Object[] obj = pq.toArray();
for (Object o : obj) {
System.out.print(o + ", "); // Unordered Arrays: 1, 2, 3, 5, 4, 6,
}
// To order a PQ
System.out.print("\nOrdered:");
while (!pq.isEmpty()) {
System.out.print(pq.poll() + ", "); // Ordered: 1, 2, 3, 4, 5, 6,
}
System.out.println("********************************************");
}
/**
* Transfer all the jobs in the queue of a SchedulingAlgorithm to another, such as when switching
* to another algorithm in the GUI
*
* @param otherAlg The other algorithm to transfer to.
*/
public void transferJobsTo(SchedulingAlgorithm otherAlg) {
Iterator<Process> iter = pQ.iterator();
while (iter.hasNext()) {
otherAlg.addJob(iter.next());
iter.remove();
}
}
public String solve() {
PriorityQueue<Neighbor> copy = new PriorityQueue<Neighbor>(neighbors);
// Mencari jumlah masing-masing kelas pada priority queue Neighbor
Iterator<Neighbor> itr = copy.iterator();
while (itr.hasNext()) {
Neighbor n = itr.next();
boolean found = false;
int j = 0;
while ((j < classes.size()) && !found) {
// Jika kelas yang sama sudah ada, maka counter hanya akan bertambah
if (data.get(n.index).get(data.get(n.index).size() - 1).equals(classes.get(j).classData)) {
classes.get(j).addCounter();
found = true;
} else {
j++;
}
}
// Jika kelas belum ada pada list, maka kelas akan ditambahkan
if (!found) {
DataClass newData = new DataClass(data.get(n.index).get(data.get(n.index).size() - 1));
classes.add(newData);
}
}
classes.sort(
new Comparator<DataClass>() {
@Override
public int compare(DataClass d1, DataClass d2) {
return (d1.count <= d2.count ? 1 : -1);
}
});
return classes.get(0).classData;
}
@Override
public void draw() {
// Lock the state
try {
lock.acquire();
} catch (InterruptedException e) {
e.printStackTrace();
}
// Only draw if we are playing the replay
if (playing) {
background(25);
// Mark whether or not we draw a frame
boolean drewframe = false;
// Loop through all frame
for (Iterator<UpdatePacket> it = frameQueue.iterator(); it.hasNext(); ) {
UpdatePacket u = it.next();
// Only draw if it matches the current time
if (!(u.timestamp == timeline.getTime())) continue;
// Draw stuff
for (int i = 0; i < u.numRects; i++) {
fill(color(u.rectColors[i][0], u.rectColors[i][1], u.rectColors[i][2]));
rect(
(float) u.rectVals[i][0],
(float) u.rectVals[i][1],
(float) u.rectVals[i][2],
(float) u.rectVals[i][3]);
}
// Remember this frame
lastFrame.add(u);
// Signal a frame was drawn
drewframe = true;
}
// Check of no frame was drawn
if (!drewframe) {
// Draw the previous frame
for (UpdatePacket u : lastFrame) {
for (int i = 0; i < u.numRects; i++) {
fill(color(u.rectColors[i][0], u.rectColors[i][1], u.rectColors[i][2]));
rect(
(float) u.rectVals[i][0],
(float) u.rectVals[i][1],
(float) u.rectVals[i][2],
(float) u.rectVals[i][3]);
}
}
// Clear the previous frame
lastFrame.clear();
}
// Step the time-line
timeline.step();
}
// Unlock the state
lock.release();
}
@Override
protected void map(LongWritable key, Text value, Context context)
throws IOException, InterruptedException {
Configuration conf = context.getConfiguration();
Integer k = Integer.valueOf(conf.get("krecords"));
// _log.info("Threshold =>" + threshold);
PriorityQueue<UniformData> sortedQueue =
new PriorityQueue<UniformData>(k, new UniformDataComparator());
String[] tokens = value.toString().split(",");
Long id = Long.valueOf(tokens[2].trim());
Double score = Double.valueOf(tokens[1]);
if (_isFirst) {
UniformData record = new UniformData(id, score);
sortedQueue.add(record);
_max = score;
_counter++;
_isFirst = false;
} else {
if (_counter <= k) {
score = Utils.calculateScore(tokens);
if (score > _max) {
UniformData record = new UniformData(id, score);
sortedQueue.add(record);
_max = record.getScore();
_counter++;
// _log.info("Worst Threshold =>" + threshold+" for top-k/counter =>"+counter);
}
} else {
List<UniformData> records = new ArrayList<UniformData>(sortedQueue);
if (records.size() > 0) {
if (records.get(k - 1).getScore() > _max) {
UniformData record = new UniformData(id, score);
sortedQueue.add(record);
_max = records.get(k - 1).getScore();
_counter++;
// _log.info("Worst Threshold =>" + threshold+" for after k+1 =>"+counter);
}
}
}
}
Iterator<UniformData> recIter = sortedQueue.iterator();
Integer kRecords = 0;
while (recIter.hasNext()) {
UniformData record = recIter.next();
DoubleWritable scoreWR = new DoubleWritable(record.getScore());
context.write(scoreWR, record);
if (kRecords == k) {
break;
}
kRecords++;
}
}
/**
* Removes one instance of the given message from the queue.
*
* @return true if removed, false if not. If false is returned, the message may be currently being
* dispatched.
*/
public boolean remove(T message) {
lock.lock();
try {
Iterator<DelayedMessage> iterator = queue.iterator();
while (iterator.hasNext()) {
DelayedMessage next = iterator.next();
if (next.message.equals(message)) {
iterator.remove();
return true;
}
}
return false;
} finally {
lock.unlock();
}
}
@Override
public int advance(int targetDocId) {
if (currentDocId == Constants.EOF) {
return Constants.EOF;
}
if (targetDocId < minDocId) {
targetDocId = minDocId;
} else if (targetDocId > maxDocId) {
currentDocId = Constants.EOF;
return currentDocId;
}
long start = System.nanoTime();
// Remove iterators that are before the target document id from the queue
Iterator<IntPair> iterator = queue.iterator();
while (iterator.hasNext()) {
IntPair pair = iterator.next();
if (pair.getLeft() < targetDocId) {
iterator.remove();
iteratorIsInQueue[pair.getRight()] = false;
}
}
// Advance all iterators that are not in the queue to the target document id
for (int i = 0; i < docIdIterators.length; i++) {
if (!iteratorIsInQueue[i]) {
int nextDocId = docIdIterators[i].advance(targetDocId);
if (nextDocId != Constants.EOF) {
pointers[i].setLeft(nextDocId);
queue.add(pointers[i]);
}
iteratorIsInQueue[i] = true;
}
}
// Return the first element
if (queue.size() > 0) {
currentDocId = queue.peek().getLeft();
} else {
currentDocId = Constants.EOF;
}
long end = System.nanoTime();
timeMeasure.addAndGet(end - start);
return currentDocId;
}
public void printElementsQueue(PriorityQueue<Patient> queueToPrint, String name) {
Patient patientQueuing = null;
Iterator<Patient> iter = queueToPrint.iterator();
String a = "[";
while (iter.hasNext()) {
Patient elementInQueue = iter.next();
if (elementInQueue instanceof Patient) {
patientQueuing = elementInQueue;
a = a + patientQueuing.getId() + ", ";
}
}
if (a.length() > 2)
System.out.println(
"" + this.getId() + " " + name + ": " + a.substring(0, a.length() - 2) + "]");
}
/** Method to clear the Collection. */
public synchronized void clear() {
if (ownerOP != null && !delegate.isEmpty()) {
// Cascade delete
if (SCOUtils.hasDependentElement(ownerMmd)) {
Iterator iter = delegate.iterator();
while (iter.hasNext()) {
ownerOP.getExecutionContext().deleteObjectInternal(iter.next());
}
}
}
delegate.clear();
makeDirty();
if (ownerOP != null && !ownerOP.getExecutionContext().getTransaction().isActive()) {
ownerOP.getExecutionContext().processNontransactionalUpdate();
}
}
public static void align(
Graph graph,
SAMRecord rec,
Node recNode,
ReferenceSequence sequence,
SAMProgramRecord programRecord,
int offset,
AlleleCoverageCutoffs alleleCoverageCutoffs,
boolean correctBases,
boolean useSequenceQualities,
int MAXIMUM_TOTAL_COVERAGE,
int MAX_HEAP_SIZE)
throws Exception {
int i;
AlignHeapNode curAlignHeapNode = null;
AlignHeapNode nextAlignHeapNode = null;
AlignHeapNode bestAlignHeapNode = null;
AlignHeap heap = null;
String read = null; // could be cs
String readBases = null; // always nt
String qualities = null; // could be cq
SRMAUtil.Space space = SRMAUtil.Space.NTSPACE;
ListIterator<NodeRecord> iter = null;
AlignHeapNodeComparator comp = null;
int alignmentStart = -1;
int numStartNodesAdded = 0;
boolean strand = rec.getReadNegativeStrandFlag(); // false -> forward, true -> reverse
String softClipStartBases = null;
String softClipStartQualities = null;
String softClipEndBases = null;
String softClipEndQualities = null;
// Debugging stuff
String readName = rec.getReadName();
assert SRMAUtil.Space.COLORSPACE != space;
// Get space
read = (String) rec.getAttribute("CS");
if (null == read) {
// Use base space
space = SRMAUtil.Space.NTSPACE;
} else {
// assumes CS and CQ are always in sequencing order
space = SRMAUtil.Space.COLORSPACE;
}
// Get read and qualities
if (space == SRMAUtil.Space.NTSPACE) {
byte tmpRead[] = rec.getReadString().getBytes();
byte tmpQualities[] = rec.getBaseQualityString().getBytes();
// Reverse once
if (strand) { // reverse
SAMRecordUtil.reverseArray(tmpRead);
SAMRecordUtil.reverseArray(tmpQualities);
}
read = new String(tmpRead);
readBases = new String(tmpRead);
qualities = new String(tmpQualities);
// Reverse again
if (strand) { // reverse
SAMRecordUtil.reverseArray(tmpRead);
SAMRecordUtil.reverseArray(tmpQualities);
}
} else {
byte tmpRead[] = rec.getReadString().getBytes();
// Reverse once
if (strand) { // reverse
SAMRecordUtil.reverseArray(tmpRead);
}
readBases = new String(tmpRead);
// Reverse again
if (strand) { // reverse
SAMRecordUtil.reverseArray(tmpRead);
}
read = SRMAUtil.normalizeColorSpaceRead(read);
qualities = (String) rec.getAttribute("CQ");
// Some aligners include a quality value for the adapter. A quality value
// IMHO should not be given for an unobserved (assumed) peice of data. Trim
// the first quality in this case
if (qualities.length() == 1 + read.length()) { // trim the first quality
qualities = qualities.substring(1);
}
}
// Reverse back
if (readBases.length() <= 0) {
throw new Exception("Error. The current alignment has no bases.");
}
if (read.length() <= 0) {
throw new Exception("Error. The current alignment has no bases.");
}
if (qualities.length() <= 0) {
throw new Exception("Error. The current alignment has no qualities.");
}
if (readBases.length() != read.length()) {
if (space == SRMAUtil.Space.COLORSPACE) {
throw new Exception(
"Error. The current alignment's read bases length does not match the length of the colors in the CS tag ["
+ rec.getReadName()
+ "].");
} else {
throw new Exception("Error. Internal error: readBases.length() != read.length()");
}
}
// Deal with soft-clipping
// - save the soft clipped sequence for latter
{
List<CigarElement> cigarElements = null;
cigarElements = rec.getCigar().getCigarElements();
CigarElement e1 = cigarElements.get(0); // first
CigarElement e2 = cigarElements.get(cigarElements.size() - 1); // last
// Soft-clipped
if (CigarOperator.S == e1.getOperator()) {
if (space == SRMAUtil.Space.COLORSPACE) {
throw new Exception(
"Error. Soft clipping with color-space data not currently supported.");
}
int l = e1.getLength();
if (strand) { // reverse
softClipStartBases = readBases.substring(readBases.length() - l);
softClipStartQualities = qualities.substring(qualities.length() - l);
readBases = readBases.substring(0, readBases.length() - l);
read = read.substring(0, read.length() - l);
qualities = qualities.substring(0, qualities.length() - l);
} else {
softClipStartBases = readBases.substring(0, l - 1);
softClipStartQualities = qualities.substring(0, l - 1);
readBases = readBases.substring(l);
read = read.substring(l);
qualities = qualities.substring(l);
}
}
if (CigarOperator.S == e2.getOperator()) {
if (space == SRMAUtil.Space.COLORSPACE) {
throw new Exception(
"Error. Soft clipping with color-space data not currently supported.");
}
int l = e2.getLength();
if (strand) { // reverse
softClipEndBases = readBases.substring(0, l - 1);
softClipEndQualities = qualities.substring(0, l - 1);
readBases = readBases.substring(l);
read = read.substring(l);
qualities = qualities.substring(l);
} else {
softClipEndBases = readBases.substring(readBases.length() - l);
softClipEndQualities = qualities.substring(qualities.length() - l);
readBases = readBases.substring(0, readBases.length() - l);
read = read.substring(0, read.length() - l);
qualities = qualities.substring(0, qualities.length() - l);
}
}
}
// Remove mate pair information
Align.removeMateInfo(rec);
comp =
new AlignHeapNodeComparator(
(strand) ? AlignHeap.HeapType.MAXHEAP : AlignHeap.HeapType.MINHEAP);
// Bound by original alignment if possible
bestAlignHeapNode =
Align.boundWithOriginalAlignment(
rec,
graph,
recNode,
comp,
strand,
read,
qualities,
readBases,
space,
sequence,
alleleCoverageCutoffs,
useSequenceQualities,
MAXIMUM_TOTAL_COVERAGE,
MAX_HEAP_SIZE);
/*
System.err.println("readName="+rec.getReadName());
if(null != bestAlignHeapNode) {
System.err.println("\nFOUND BEST:" + rec.toString());
}
else {
System.err.println("\nNOT FOUND (BEST): " + rec.toString());
}
Align.updateSAM(rec, programRecord, bestAlignHeapNode, space, read, qualities, softClipStartBases, softClipStartQualities, softClipEndBases, softClipEndQualities, strand, correctBases);
return;
*/
heap = new AlignHeap((strand) ? AlignHeap.HeapType.MAXHEAP : AlignHeap.HeapType.MINHEAP);
// Add start nodes
if (strand) { // reverse
alignmentStart = rec.getAlignmentEnd();
for (i = alignmentStart + offset; alignmentStart - offset <= i; i--) {
int position = graph.getPriorityQueueIndexAtPositionOrBefore(i);
PriorityQueue<Node> startNodeQueue = graph.getPriorityQueue(position);
if (0 != position && null != startNodeQueue) {
Iterator<Node> startNodeQueueIter = startNodeQueue.iterator();
while (startNodeQueueIter.hasNext()) {
Node startNode = startNodeQueueIter.next();
int f = passFilters(graph, startNode, alleleCoverageCutoffs, MAXIMUM_TOTAL_COVERAGE);
if (0 == f) {
heap.add(
new AlignHeapNode(
null,
startNode,
startNode.coverage,
read.charAt(0),
qualities.charAt(0),
useSequenceQualities,
space));
} else if (f < 0) {
return;
}
if (startNode.position < i) {
i = startNode.position;
}
numStartNodesAdded++;
}
}
}
} else {
alignmentStart = rec.getAlignmentStart();
for (i = alignmentStart - offset; i <= alignmentStart + offset; i++) {
int position = graph.getPriorityQueueIndexAtPositionOrGreater(i);
PriorityQueue<Node> startNodeQueue = graph.getPriorityQueue(position);
if (0 != position && null != startNodeQueue) {
Iterator<Node> startNodeQueueIter = startNodeQueue.iterator();
while (startNodeQueueIter.hasNext()) {
Node startNode = startNodeQueueIter.next();
int f = passFilters(graph, startNode, alleleCoverageCutoffs, MAXIMUM_TOTAL_COVERAGE);
if (0 == f) {
heap.add(
new AlignHeapNode(
null,
startNode,
startNode.coverage,
read.charAt(0),
qualities.charAt(0),
useSequenceQualities,
space));
} else if (f < 0) {
return;
}
if (i < startNode.position) {
i = startNode.position;
}
numStartNodesAdded++;
}
}
}
}
if (numStartNodesAdded == 0) {
throw new Exception("Did not add any start nodes!");
}
// Get first node off the heap
curAlignHeapNode = heap.poll();
while (null != curAlignHeapNode) {
if (MAX_HEAP_SIZE <= heap.size()) {
// too many to consider
return;
}
// System.err.println("strand:" + strand + "\tsize:" + heap.size() + "\talignmentStart:" +
// alignmentStart + "\toffset:" + offset + "\treadOffset:" + curAlignHeapNode.readOffset);
// System.err.print("size:" + heap.size() + ":" + curAlignHeapNode.readOffset + ":" +
// curAlignHeapNode.score + ":" + curAlignHeapNode.alleleCoverageSum + ":" +
// curAlignHeapNode.startPosition + "\t");
// curAlignHeapNode.node.print(System.err);
// System.err.print("\rposition:" + curAlignHeapNode.node.position + "\treadOffset:" +
// curAlignHeapNode.readOffset);
// Remove all non-insertions with the same contig/pos/read-offset/type/base and lower score
nextAlignHeapNode = heap.peek();
while (Node.INSERTION != curAlignHeapNode.node.type
&& null != nextAlignHeapNode
&& 0 == comp.compare(curAlignHeapNode, nextAlignHeapNode)) {
if (curAlignHeapNode.score < nextAlignHeapNode.score
|| (curAlignHeapNode.score == nextAlignHeapNode.score
&& curAlignHeapNode.alleleCoverageSum < nextAlignHeapNode.alleleCoverageSum)) {
// Update current node
curAlignHeapNode = heap.poll();
} else {
// Ignore next node
heap.poll();
}
nextAlignHeapNode = heap.peek();
}
nextAlignHeapNode = null;
// Check if the alignment is complete
if (curAlignHeapNode.readOffset == read.length() - 1) {
// All read bases examined, store if has the best alignment.
// System.err.print(curAlignHeapNode.alleleCoverageSum + ":" + curAlignHeapNode.score +
// ":");
// System.err.print(curAlignHeapNode.startPosition + ":");
// curAlignHeapNode.node.print(System.err);
if (null == bestAlignHeapNode
|| bestAlignHeapNode.score < curAlignHeapNode.score
|| (bestAlignHeapNode.score == curAlignHeapNode.score
&& bestAlignHeapNode.alleleCoverageSum < curAlignHeapNode.alleleCoverageSum)) {
bestAlignHeapNode = curAlignHeapNode;
}
} else if (null != bestAlignHeapNode && curAlignHeapNode.score < bestAlignHeapNode.score) {
// ignore, under the assumption that scores can only become more negative.
} else {
if (strand) { // reverse
// Go to all the "prev" nodes
iter = curAlignHeapNode.node.prev.listIterator();
} else { // forward
// Go to all "next" nodes
iter = curAlignHeapNode.node.next.listIterator();
}
while (iter.hasNext()) {
NodeRecord next = iter.next();
int f =
passFilters(
graph, next.node, next.coverage, alleleCoverageCutoffs, MAXIMUM_TOTAL_COVERAGE);
if (0 == f) {
heap.add(
new AlignHeapNode(
curAlignHeapNode,
next.node,
next.coverage,
read.charAt(curAlignHeapNode.readOffset + 1),
qualities.charAt(curAlignHeapNode.readOffset + 1),
useSequenceQualities,
space));
} else if (f < 0) {
return;
}
}
iter = null;
}
// Get next node
curAlignHeapNode = heap.poll();
}
// Recover alignment
Align.updateSAM(
rec,
sequence,
programRecord,
bestAlignHeapNode,
space,
read,
qualities,
softClipStartBases,
softClipStartQualities,
softClipEndBases,
softClipEndQualities,
strand,
correctBases);
}
