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本文整理了Java中org.broad.igv.bbfile.ZoomDataRecord.getChromEnd()
方法的一些代码示例,展示了ZoomDataRecord.getChromEnd()
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。ZoomDataRecord.getChromEnd()
方法的具体详情如下:
包路径:org.broad.igv.bbfile.ZoomDataRecord
类名称:ZoomDataRecord
方法名:getChromEnd
暂无
代码示例来源:origin: igvteam/igv
int genomeEnd = genome.getGenomeCoordinate(chr, rec.getChromEnd());
scores.add(new BasicScore(genomeStart, genomeEnd, value));
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: org.opencb.biodata/biodata-tools
wItem = zoomIterator.next();
chunkStart = (Math.max(region.getStart(), wItem.getChromStart()) - region.getStart()) / windowSize;
chunkEnd = (Math.min(region.getEnd(), wItem.getChromEnd()) - region.getStart() - 1) / windowSize;
for (int chunk = chunkStart; chunk <= chunkEnd; chunk++) {
length = Math.min(wItem.getChromEnd() - region.getStart(), chunk * windowSize + windowSize)
- Math.max(wItem.getChromStart() - region.getStart(), chunk * windowSize);
chunks[chunk] += (wItem.getMeanVal() * length);
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);
}
}
}
}
本文整理了Java中org.broad.igv.bbfile.ZoomDataRecord.getChromEnd()方法的一些代码示例,展示了ZoomDataRecord.getChromEnd()
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