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org.broad.igv.bbfile.ZoomLevelIterator.hasNext()方法的使用及代码示例

转载 作者：知者 更新时间：2024-03-16 10:29:31 26 4
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本文整理了Java中org.broad.igv.bbfile.ZoomLevelIterator.hasNext()方法的一些代码示例，展示了ZoomLevelIterator.hasNext()的具体用法。这些代码示例主要来源于Github/Stackoverflow/Maven等平台，是从一些精选项目中提取出来的代码，具有较强的参考意义，能在一定程度帮忙到你。ZoomLevelIterator.hasNext()方法的具体详情如下：
包路径：org.broad.igv.bbfile.ZoomLevelIterator
类名称：ZoomLevelIterator
方法名：hasNext

ZoomLevelIterator.hasNext介绍

暂无

代码示例

代码示例来源：origin: igvteam/igv

lowestResHeader.getZoomLevel(), firstChr, 0, lastChr, Integer.MAX_VALUE, false);
while (zlIter.hasNext()) {
  ZoomDataRecord rec = zlIter.next();

代码示例来源：origin: igvteam/igv

protected List<LocusScore> getZoomSummaryScores(String chr, int start, int end, int zoom) {
  Chromosome c = genome.getChromosome(chr);
  if (c == null) return null;
  double nBins = Math.pow(2, zoom);
  double scale = c.getLength() / (nBins * 700);
  BBZoomLevelHeader zlHeader = getZoomLevelForScale(scale);
  if (zlHeader == null) return null;
  int bbLevel = zlHeader.getZoomLevel();
  int reductionLevel = zlHeader.getReductionLevel();
  // If we are at the highest precomputed resolution compare to the requested resolution.  If they differ
  // by more than a factor of 2 compute "on the fly"
  String tmp = chrNameMap.get(chr);
  String querySeq = tmp == null ? chr : tmp;
  if (reader.isBigBedFile() || bbLevel > 1 || (bbLevel == 1 && (reductionLevel / scale) < 2)) {
    ArrayList<LocusScore> scores = new ArrayList(1000);
    ZoomLevelIterator zlIter = reader.getZoomLevelIterator(bbLevel, querySeq, start, querySeq, end, false);
    while (zlIter.hasNext()) {
      ZoomDataRecord rec = zlIter.next();
      float v = getValue(rec);
      BasicScore bs = new BasicScore(rec.getChromStart(), rec.getChromEnd(), v);
      scores.add(bs);
    }
    return scores;
  } else {
    // No precomputed scores for this resolution level
    return null;
  }
}

代码示例来源：origin: igvteam/igv

if (zlIter.hasNext()) {
  while (zlIter.hasNext()) {
    ZoomDataRecord rec = zlIter.next();
    values[nValues++] = (rec.getMeanVal());

代码示例来源：origin: org.opencb.biodata/biodata-tools

ZoomDataRecord wItem;
int length, chunkStart, chunkEnd;
while (zoomIterator.hasNext()) {
  wItem = zoomIterator.next();
  chunkStart = (Math.max(region.getStart(), wItem.getChromStart()) - region.getStart()) / windowSize;

代码示例来源：origin: igvteam/igv

@Test
public void testBigBed() throws IOException {
  String path = TestUtils.DATA_DIR + "bb/chr21.refseq.bb";
  BBFileReader bbReader = new BBFileReader(path);
  BBFileHeader bbFileHdr = bbReader.getBBFileHeader();
  assertTrue(bbFileHdr.isBigBed());
  String chr = "chr21";
  int start = 26490012;
  int end = 42182827;
  for (BBZoomLevelHeader header : bbReader.getZoomLevels().getZoomLevelHeaders()) {
    assertNotNull(header);
    ZoomLevelIterator zlIter = bbReader.getZoomLevelIterator(header.getZoomLevel(), chr, start, chr, end, false);
    while (zlIter.hasNext()) {
      ZoomDataRecord rec = zlIter.next();
      int n = rec.getBasesCovered();
      if (n > 0) {
        assertEquals(chr, rec.getChromName());
        assertTrue(rec.getChromEnd() >= start && rec.getChromStart() <= end);
      }
    }
  }
}

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