Java IntervalTree.put方法代码示例

import htsjdk.samtools.util.IntervalTree; //导入方法依赖的package包/类
private int processExon(IntervalTree<Block> intervalTree, int totalLength, GeneFeature feature,
                        int intronLength, int centerPosition, boolean forward) {
    int currentLength = 0;
    if (EXON_FEATURE_NAME.equalsIgnoreCase(feature.getFeature())) {
        Block exon = createExon(feature, intronLength);

        Iterator<IntervalTree.Node<Block>> nodeIterator = intervalTree.overlappers(exon.getStartIndex(),
                exon.getEndIndex());
        if (nodeIterator.hasNext()) {
            Block merged = exon;
            while (nodeIterator.hasNext()) {
                Block toMerge = nodeIterator.next().getValue();
                merged = mergeExons(merged, toMerge);
                currentLength = currentLength - calculateExonLength(toMerge, centerPosition, forward)
                              + calculateExonLength(merged, centerPosition, forward);
                nodeIterator.remove();
            }

            intervalTree.put(merged.getStartIndex(), merged.getEndIndex(), merged);
        } else {
            currentLength += calculateExonLength(exon, centerPosition, forward);
            intervalTree.put(exon.getStartIndex(), exon.getEndIndex(), exon);
        }
    }
    return totalLength + currentLength;
}
 

import htsjdk.samtools.util.IntervalTree; //导入方法依赖的package包/类
private IntervalTree<Annotation> retrieveTranscripts(Genomics genomics, StreamVariantsRequest request) {
  Stopwatch stopwatch = Stopwatch.createStarted();
  IntervalTree<Annotation> transcripts = new IntervalTree<>();
  Iterable<Annotation> transcriptIter =
      Paginator.Annotations.create(genomics, ShardBoundary.Requirement.OVERLAPS).search(
          new SearchAnnotationsRequest()
            .setAnnotationSetIds(transcriptSetIds)
            .setReferenceName(canonicalizeRefName(request.getReferenceName()))
            .setStart(request.getStart())
            .setEnd(request.getEnd()));
  for (Annotation annotation : transcriptIter) {
    transcripts.put(annotation.getStart().intValue(), annotation.getEnd().intValue(), annotation);
  }
  LOG.info(String.format("read %d transcripts in %s (%.2f / s)", transcripts.size(),
      stopwatch, (double)transcripts.size() / stopwatch.elapsed(TimeUnit.SECONDS)));
  return transcripts;
}
 

import htsjdk.samtools.util.IntervalTree; //导入方法依赖的package包/类
private void testOverlapping(List<Block> exons) {
    IntervalTree<Block> intervalTree = new IntervalTree<>();
    for (Block exon : exons) {
        Iterator<IntervalTree.Node<Block>> nodeIterator = intervalTree.overlappers(exon.getStartIndex(),
                                                                                   exon.getEndIndex());
        Assert.assertFalse("Should be no overlapping exons", nodeIterator.hasNext());
        intervalTree.put(exon.getStartIndex(), exon.getEndIndex(), exon);
    }
}
 

import htsjdk.samtools.util.IntervalTree; //导入方法依赖的package包/类
public IntervalTree getSCNVintervalTreeWithExtendBase(ArrayList<VarscanCNVFormat> SCNVlist, int extendBaseNumber){
     IntervalTree CNVIntervalTree = new IntervalTree();
     VarscanCNVFormat vscnv=null;
     for (int i = 0; i < SCNVlist.size(); i++) {
      vscnv=SCNVlist.get(i);
      CNVIntervalTree.put(Integer.parseInt(vscnv.getChr_start())-extendBaseNumber, Integer.parseInt(vscnv.getChr_stop())+extendBaseNumber, vscnv);
    }
     return CNVIntervalTree;
}
 

import htsjdk.samtools.util.IntervalTree; //导入方法依赖的package包/类
public IntervalTree getSCNVintervalTree(ArrayList<VarscanCNVFormat> SCNVlist){
     IntervalTree CNVIntervalTree = new IntervalTree();
     VarscanCNVFormat vscnv=null;
     for (int i = 0; i < SCNVlist.size(); i++) {
      vscnv=SCNVlist.get(i);
      CNVIntervalTree.put(Integer.parseInt(vscnv.getChr_start()), Integer.parseInt(vscnv.getChr_stop()), vscnv);
    }
     return CNVIntervalTree;
}
 

import htsjdk.samtools.util.IntervalTree; //导入方法依赖的package包/类
public IntervalTree getBEDIntervalTreeWithExtendBase(ArrayList<BED> SCNVlist, int extendBaseNumber){
     IntervalTree CNVIntervalTree = new IntervalTree();
     BED bed=null;
     for (int i = 0; i < SCNVlist.size(); i++) {
      bed=SCNVlist.get(i);
      CNVIntervalTree.put(bed.getChromStart()-extendBaseNumber, bed.getChromEnd()+extendBaseNumber, bed);
    }
     return CNVIntervalTree;
}