public SeqSymmetry optimizeRequest(final SeqSpan span) {
final MutableSeqSymmetry query_sym = new SimpleMutableSeqSymmetry();
query_sym.addSpan(span);
SeqSymmetry optimized_sym = SeqUtils.exclusive(query_sym, this.requestSym, span.getBioSeq());
optimized_sym = SeqUtils.exclusive(optimized_sym, this.currentRequestSym, span.getBioSeq());
if (SeqUtils.hasSpan(optimized_sym)) {
return optimized_sym;
}
return null;
}
public boolean isLoaded(final SeqSpan span) {
final MutableSeqSymmetry query_sym = new SimpleMutableSeqSymmetry();
query_sym.addSpan(span);
final SeqSymmetry optimized_sym =
SeqUtils.exclusive(query_sym, this.requestSym, span.getBioSeq());
return !SeqUtils.hasSpan(optimized_sym);
}
public final void removeCurrentRequest(final SeqSpan span) {
for (int i = 0; i < this.currentRequestSym.getChildCount(); ++i) {
final SeqSymmetry sym = this.currentRequestSym.getChild(i);
if (span == sym.getSpan(span.getBioSeq())) {
this.currentRequestSym.removeChild(sym);
}
}
}
private static void writeOutChildren(
final DataOutputStream out,
final SymWithProps propsym,
final int min,
final int max,
final int childcount,
final SeqSymmetry sym,
final BioSeq seq)
throws IOException {
out.write(9);
if (propsym != null && propsym.getProperty("cds min") != null) {
out.write(propsym.getProperty("cds min").toString().getBytes());
} else {
out.write(Integer.toString(min).getBytes());
}
out.write(9);
if (propsym != null && propsym.getProperty("cds max") != null) {
out.write(propsym.getProperty("cds max").toString().getBytes());
} else {
out.write(Integer.toString(max).getBytes());
}
out.write(9);
out.write(48);
out.write(9);
out.write(Integer.toString(childcount).getBytes());
out.write(9);
final int[] blockSizes = new int[childcount];
final int[] blockStarts = new int[childcount];
for (int i = 0; i < childcount; ++i) {
final SeqSymmetry csym = sym.getChild(i);
final SeqSpan cspan = csym.getSpan(seq);
blockSizes[i] = cspan.getLength();
blockStarts[i] = cspan.getMin() - min;
}
for (int i = 0; i < childcount; ++i) {
out.write(Integer.toString(blockSizes[i]).getBytes());
out.write(44);
}
out.write(9);
for (int i = 0; i < childcount; ++i) {
out.write(Integer.toString(blockStarts[i]).getBytes());
out.write(44);
}
}
private static void writeOutFile(
final DataOutputStream out,
final BioSeq seq,
final SeqSpan span,
final SeqSymmetry sym,
final SymWithProps propsym)
throws IOException {
out.write(seq.getID().getBytes());
out.write(9);
final int min = span.getMin();
final int max = span.getMax();
out.write(Integer.toString(min).getBytes());
out.write(9);
out.write(Integer.toString(max).getBytes());
final int childcount = sym.getChildCount();
if (!span.isForward() || childcount > 0 || propsym != null) {
out.write(9);
if (propsym != null) {
if (propsym.getProperty("name") != null) {
out.write(((String) propsym.getProperty("name")).getBytes());
} else if (propsym.getProperty("id") != null) {
out.write(((String) propsym.getProperty("id")).getBytes());
}
}
out.write(9);
if (propsym != null && propsym.getProperty("score") != null) {
out.write(propsym.getProperty("score").toString().getBytes());
} else if (sym instanceof Scored) {
out.write(Float.toString(((Scored) sym).getScore()).getBytes());
} else {
out.write(48);
}
out.write(9);
if (span.isForward()) {
out.write(43);
} else {
out.write(45);
}
if (childcount > 0) {
writeOutChildren(out, propsym, min, max, childcount, sym, seq);
}
}
out.write(10);
}
@Override
public int getMax(final SeqSymmetry sym, final BioSeq seq) {
final SeqSpan span = sym.getSpan(seq);
return span.getMax();
}
@Override
public List<? extends SeqSymmetry> getRegion(final SeqSpan overlapSpan) throws Exception {
this.init();
final BioSeq seq = overlapSpan.getBioSeq();
if (!seq.equals(this.saveSeq) || this.saveSym == null) {
final Iterator<Map<Integer, List<List<Long>>>> binIter = this.getBinIter(seq.toString());
if (binIter == null) {
this.saveSym = new GraphSym(new int[0], new int[0], new float[0], this.featureName, seq);
} else {
final int[] xList = new int[32768];
for (int i = 0; i < 32768; ++i) {
xList[i] = i * 16384;
}
final int[] wList = new int[32768];
Arrays.fill(wList, 16384);
final float[] yList = new float[32768];
Arrays.fill(yList, 0.0f);
float largestY = Float.MIN_VALUE;
int indexLargest = -1;
while (binIter.hasNext()) {
final Map<Integer, List<List<Long>>> binWrapper = binIter.next();
final int binNo = binWrapper.keySet().iterator().next();
final int[] region = getRegion(binNo);
int yValue = 0;
for (final List<Long> chunkWrapper : binWrapper.get(binNo)) {
if (chunkWrapper != null) {
yValue +=
(int)
(getUncompressedLength(chunkWrapper.get(0), chunkWrapper.get(1))
* 16384L
/ (region[1] - region[0]));
}
}
if (1 + region[1] - region[0] == 16384
&& yValue > 0.0f
&& (yValue > largestY || indexLargest == -1)) {
indexLargest = region[0] / 16384;
largestY = yValue;
}
for (int j = region[0] / 16384; j < (region[1] + 1) / 16384; ++j) {
final float[] array = yList;
final int n = j;
array[n] += yValue;
}
}
indexLargest = -1;
if (indexLargest != -1) {
try {
final float realAvg =
this.getRealAvg(
new SimpleSeqSpan(indexLargest * 16384, (indexLargest + 1) * 16384, seq));
if (realAvg > 0.0f) {
final float ratio = realAvg / yList[indexLargest];
for (int k = 0; k < yList.length; ++k) {
final float[] array2 = yList;
final int n2 = k;
array2[n2] *= ratio;
}
}
} catch (Exception x) {
Logger.getLogger(this.getClass().getName())
.log(Level.SEVERE, "fail loading BAM segment " + this.uri, x);
}
}
this.saveSym = new GraphSym(xList, wList, yList, this.featureName, seq);
}
this.saveSeq = seq;
}
final List<SeqSymmetry> symList = new ArrayList<SeqSymmetry>();
symList.add(this.saveSym);
return symList;
}