Package org.broad.igv.feature.genome

Examples of org.broad.igv.feature.genome.ChromosomeCoordinate

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                s = Math.max(0.0, s);
                String chr = null;
                if (isWholeGenomeView()) {
                    Genome genome = GenomeManager.getInstance().getCurrentGenome();
                    ChromosomeCoordinate start = genome.getChromosomeCoordinate((int) s);
                    ChromosomeCoordinate end = genome.getChromosomeCoordinate((int) e);

                    chr = start.getChr();
                    s = start.getCoordinate();
                    e = end.getCoordinate();
                    if (end.getChr() != start.getChr()) {
                        e = genome.getChromosome(start.getChr()).getLength();
                    }
                } else {
                    chr = frame.getChrName();
                }
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        List<LocusScore> wgScores = ds.getSummaryScores(Globals.CHR_ALL, 0, Integer.MAX_VALUE, 0);
        for (LocusScore score : wgScores) {

            int genomeStart = score.getStart();
            ChromosomeCoordinate stCoord = genome.getChromosomeCoordinate(genomeStart);
            ChromosomeCoordinate endCoord = genome.getChromosomeCoordinate(score.getEnd());

            // Skip "edge" bins that include data from 2 chromosomes.  We don't know the expected value for these.
            if (stCoord.getChr().equals(endCoord.getChr())) {
                String chrName = stCoord.getChr();
                double ev = expectedValues.get(chrName);
                assertEquals(ev, score.getScore(), 0.001);
            }
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        int maxDistance = (int) (this.scale) * 2;

        // Convert from All view chr coordinates
        if (chr.equals("All")) {

            ChromosomeCoordinate chrCoordinate = GenomeManager.getInstance().getCurrentGenome().getChromosomeCoordinate(location);
            chr = chrCoordinate.getChr();
            location = chrCoordinate.getCoordinate();
            maxDistance = maxDistance * 1000;
        }

        int index = findIndex(chr, y, location, maxDistance);

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