/**
* This uses a fixed window size and is much faster
*
* @param cpg Must be streamed in serially.
*/
protected void streamCpgFixedWind(Cpg[] cpg) {
int newPos = cpg[0].chromPos;
Logger.getLogger(Logger.GLOBAL_LOGGER_NAME).fine(String.format("Found Cpg: %d\n", newPos));
// Add this Cpg to the head of the queue
window.add(cpg);
if (useSummarizers) {
for (int t = 0; t < this.numTables(); t++) {
methSummarizer.get(t).streamCpg(cpg[t]);
methSummarizerFw.get(t).streamCpg(cpg[t]);
methSummarizerRev.get(t).streamCpg(cpg[t]);
}
}
// Remove cpgs from the tail
boolean done = false;
Cpg[] endCpg, secondCpg;
// while (!done && ((endCpg = window.peek()) != null))
// {
// if ((newPos - endCpg[0].chromPos) < this.walkParams.maxScanningWindSize)
// {
// done = true;
// }
while (!done && (window.size() > 1)) {
endCpg = window.get(0);
secondCpg = window.get(1);
if ((newPos - secondCpg[0].chromPos) < this.walkParams.minScanningWindSize) {
done = true;
} else {
window.remove();
if (useSummarizers) {
for (int t = 0; t < this.numTables(); t++) {
methSummarizer.get(t).removeCpg(endCpg[t]);
methSummarizerFw.get(t).removeCpg(endCpg[t]);
methSummarizerRev.get(t).removeCpg(endCpg[t]);
}
}
}
}
// System.err.printf("\tFixed wind checking %s (id=%d)\n",this.windStr(),this.hashCode());
// And process the window
if ((window.size() >= walkParams.minScanningWindCpgs)
&& ((CpgWalker.windEnd(window, false) - CpgWalker.windStart(window, false))
>= walkParams.minScanningWindSize)) {
// System.err.println("\t\t Sufficient Cpgs: " + window.size());
// double mean = this.methSummarizer.getValMean(true);
// System.err.println("\t\t Mean meth=" + mean);
// if (mean < 0.7)
// System.out.println(MethylDbUtils.bedLine("chr11", windStart(), windEnd(), ".", mean));
this.processWindow(this.window, true);
} else {
// System.err.println("\t\t Not enough Cpgs");
}
}
