本文整理了Java中org.broad.igv.bbfile.ZoomLevelIterator类的一些代码示例，展示了ZoomLevelIterator类的具体用法。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类的具体详情如下：
包路径：org.broad.igv.bbfile.ZoomLevelIterator
类名称：ZoomLevelIterator

ZoomLevelIterator介绍

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代码示例

代码示例来源：origin: igvteam/igv

private int getHitRegion(RPChromosomeRegion hitRegion, boolean contained) {
  int hitCount = 0;
  // check if new hit list is needed
  // Note: getHitList will reset mLeafItemIndex to 0, the beginning of new hit list
  if (leafHitList == null) {   //|| mLeafItemIndex >= mLeafHitList.size()){
    hitCount = getHitList(hitRegion, contained);
    if (hitCount == 0)
      return 0;   // no hit data found
  } else {
    hitCount = leafHitList.size() - leafItemIndex;
    if (hitCount == 0)
      return 0;   // hit list exhausted
  }
  // Perform a block read for starting base of selection region - use first leaf hit
  dataBlockRead = getDataBlock(leafItemIndex++);
  // try next item - probably intersection issue
  // Note: recursive call until a block is valid or hit list exhuasted
  if (!dataBlockRead)
    hitCount = getHitRegion(hitRegion, contained);
  return hitCount;
}

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: pcingola/SnpEff

public int setSelectionRegion(RPChromosomeRegion selectionRegion,
               boolean contained) {
  this.selectionRegion = selectionRegion;
  isContained = contained;
  // set up hit list and first data block read
  leafHitList = null;    // Must nullify existing hit list first!
  int hitCount = getHitRegion(selectionRegion, contained);
  if (hitCount == 0)   // no hits - no point in fetching data
    throw new RuntimeException("No wig data found in the selection region");
  // Ready for next() data extraction
  return hitCount;
}

代码示例来源：origin: edu.toronto.cs.savant/savant-core

ZoomLevelIterator zoomIterator = new ZoomLevelIterator(fis, chromosomeIDTree,
    zoomDataTree, zoomLevel, selectionRegion, contained);

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

public int setSelectionRegion(RPChromosomeRegion selectionRegion,
               boolean contained) {
  this.selectionRegion = selectionRegion;
  isContained = contained;
  // set up hit list and first data block read
  leafHitList = null;    // Must nullify existing hit list first!
  int hitCount = getHitRegion(selectionRegion, contained);
  if (hitCount == 0)   // no hits - no point in fetching data
    throw new RuntimeException("No wig data found in the selection region");
  // Ready for next() data extraction
  return hitCount;
}

代码示例来源：origin: pcingola/SnpEff

ZoomLevelIterator zoomIterator = new ZoomLevelIterator(fis, chromosomeIDTree,
    zoomDataTree, zoomLevel, selectionRegion, contained);

代码示例来源：origin: edu.toronto.cs.savant/savant-core

private int getHitRegion(RPChromosomeRegion hitRegion, boolean contained) {
  int hitCount = 0;
  // check if new hit list is needed
  // Note: getHitList will reset mLeafItemIndex to 0, the beginning of new hit list
  if (leafHitList == null) {   //|| mLeafItemIndex >= mLeafHitList.size()){
    hitCount = getHitList(hitRegion, contained);
    if (hitCount == 0)
      return 0;   // no hit data found
  } else {
    hitCount = leafHitList.size() - leafItemIndex;
    if (hitCount == 0)
      return 0;   // hit list exhausted
  }
  // Perform a block read for starting base of selection region - use first leaf hit
  dataBlockRead = getDataBlock(leafItemIndex++);
  // try next item - probably intersection issue
  // Note: recursive call until a block is valid or hit list exhuasted
  if (!dataBlockRead)
    hitCount = getHitRegion(hitRegion, contained);
  return hitCount;
}

代码示例来源：origin: igvteam/igv

if (zlIter.hasNext()) {
  while (zlIter.hasNext()) {
    ZoomDataRecord rec = zlIter.next();
    values[nValues++] = (rec.getMeanVal());
    if (nValues >= 10000) {

代码示例来源：origin: edu.toronto.cs.savant/savant-core

public int setSelectionRegion(RPChromosomeRegion selectionRegion,
               boolean contained) {
  this.selectionRegion = selectionRegion;
  isContained = contained;
  // set up hit list and first data block read
  leafHitList = null;    // Must nullify existing hit list first!
  int hitCount = getHitRegion(selectionRegion, contained);
  if (hitCount == 0)   // no hits - no point in fetching data
    throw new RuntimeException("No wig data found in the selection region");
  // Ready for next() data extraction
  return hitCount;
}

代码示例来源：origin: igvteam/igv

/**
 * Returns an iterator for zoom level records for all chromosome regions.
 * <p/>
 * Note: the BBFile can be BigBed or BigWig.
 * <p/>
 * Parameters:
 * zoomLevel - zoom level for data extraction; levels start at 1
 * <p/>
 * Returns:
 * Iterator to provide BedFeature(s) for the requested chromosome region.
 * Error conditions:
 * 1) An empty iterator is returned if region has no data available
 */
synchronized public ZoomLevelIterator getZoomLevelIterator(int zoomLevel) {
  // check for valid zoom level
  if (zoomLevel < 1 || zoomLevel > zoomLevelCount)
    throw new RuntimeException("Error: ZoomLevelIterator zoom level is out of range\n");
  // get the appropriate zoom level R+ zoom data index tree
  RPTree zoomDataTree = zoomLevels.getZoomLevelRPTree(zoomLevel);
  // get all regions bounds
  RPChromosomeRegion selectionRegion = zoomDataTree.getChromosomeBounds();
  // compose an iterator
  boolean contained = true;   //all regions are contained
  ZoomLevelIterator zoomIterator = new ZoomLevelIterator(fis, chromosomeIDTree,
      zoomDataTree, zoomLevel, selectionRegion, contained);
  return zoomIterator;
}

代码示例来源：origin: pcingola/SnpEff

private int getHitRegion(RPChromosomeRegion hitRegion, boolean contained) {
  int hitCount = 0;
  // check if new hit list is needed
  // Note: getHitList will reset mLeafItemIndex to 0, the beginning of new hit list
  if (leafHitList == null) {   //|| mLeafItemIndex >= mLeafHitList.size()){
    hitCount = getHitList(hitRegion, contained);
    if (hitCount == 0)
      return 0;   // no hit data found
  } else {
    hitCount = leafHitList.size() - leafItemIndex;
    if (hitCount == 0)
      return 0;   // hit list exhausted
  }
  // Perform a block read for starting base of selection region - use first leaf hit
  dataBlockRead = getDataBlock(leafItemIndex++);
  // try next item - probably intersection issue
  // Note: recursive call until a block is valid or hit list exhuasted
  if (!dataBlockRead)
    hitCount = getHitRegion(hitRegion, contained);
  return hitCount;
}

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;
  chunkEnd = (Math.min(region.getEnd(), wItem.getChromEnd()) - region.getStart() - 1) / windowSize;

代码示例来源：origin: igvteam/igv

int hitCount = getHitRegion(selectionRegion, contained);
if (hitCount == 0) {
  empty = true;

代码示例来源：origin: edu.toronto.cs.savant/savant-core

/**
 * Returns an iterator for zoom level records for all chromosome regions.
 * <p/>
 * Note: the BBFile can be BigBed or BigWig.
 * <p/>
 * Parameters:
 * zoomLevel - zoom level for data extraction; levels start at 1
 * <p/>
 * Returns:
 * Iterator to provide BedFeature(s) for the requested chromosome region.
 * Error conditions:
 * 1) An empty iterator is returned if region has no data available
 */
public ZoomLevelIterator getZoomLevelIterator(int zoomLevel) {
  // check for valid zoom level
  if (zoomLevel < 1 || zoomLevel > zoomLevelCount)
    throw new RuntimeException("Error: ZoomLevelIterator zoom level is out of range\n");
  // get the appropriate zoom level R+ zoom data index tree
  RPTree zoomDataTree = zoomLevels.getZoomLevelRPTree(zoomLevel);
  // get all regions bounds
  RPChromosomeRegion selectionRegion = zoomDataTree.getChromosomeBounds();
  // compose an iterator
  boolean contained = true;   //all regions are contained
  ZoomLevelIterator zoomIterator = new ZoomLevelIterator(fis, chromosomeIDTree,
      zoomDataTree, zoomLevel, selectionRegion, contained);
  return zoomIterator;
}

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);
      }
    }
  }
}

代码示例来源：origin: pcingola/SnpEff

int hitCount = getHitRegion(selectionRegion, contained);
if (hitCount == 0) {
  empty = true;

代码示例来源：origin: pcingola/SnpEff

/**
 * Returns an iterator for zoom level records for all chromosome regions.
 * <p/>
 * Note: the BBFile can be BigBed or BigWig.
 * <p/>
 * Parameters:
 * zoomLevel - zoom level for data extraction; levels start at 1
 * <p/>
 * Returns:
 * Iterator to provide BedFeature(s) for the requested chromosome region.
 * Error conditions:
 * 1) An empty iterator is returned if region has no data available
 */
public ZoomLevelIterator getZoomLevelIterator(int zoomLevel) {
  // check for valid zoom level
  if (zoomLevel < 1 || zoomLevel > zoomLevelCount)
    throw new RuntimeException("Error: ZoomLevelIterator zoom level is out of range\n");
  // get the appropriate zoom level R+ zoom data index tree
  RPTree zoomDataTree = zoomLevels.getZoomLevelRPTree(zoomLevel);
  // get all regions bounds
  RPChromosomeRegion selectionRegion = zoomDataTree.getChromosomeBounds();
  // compose an iterator
  boolean contained = true;   //all regions are contained
  ZoomLevelIterator zoomIterator = new ZoomLevelIterator(fis, chromosomeIDTree,
      zoomDataTree, zoomLevel, selectionRegion, contained);
  return zoomIterator;
}

代码示例来源：origin: edu.toronto.cs.savant/savant-core

int hitCount = getHitRegion(selectionRegion, contained);
if (hitCount == 0) {
  empty = true;

代码示例来源：origin: igvteam/igv

ZoomLevelIterator zoomIterator = new ZoomLevelIterator(fis, chromosomeIDTree,
    zoomDataTree, zoomLevel, selectionRegion, contained);