Examples of org.broad.igv.feature.Chromosome

org.broad.igv.feature.Chromosome
Simple representation of a chromosome. Basically a name, length, and optionally a list of cytobands. @author jrobinso


    public long getNominalLength() {
        if (nominalLength < 0) {
            nominalLength = 0;
            for (String chrName : getLongChromosomeNames()) {
                Chromosome chr = getChromosome(chrName);
                nominalLength += chr.getLength();
            }
        }
        return nominalLength;
    }

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        try {
            pw = new PrintWriter(file);
            for (String chr : genome.getAllChromosomeNames()) {


                Chromosome chromosome = genome.getChromosome(chr);
                pw.println(chromosome.getName() + "\t" + chromosome.getLength());


            }
        } finally {
            if (pw != null) pw.close();
        }

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                String[] tokens = Globals.whitespacePattern.split(nextLine);
                if (tokens.length >= 2) {
                    String chr = tokens[0];
                    int length = Integer.parseInt(tokens[1]);
                    chromosomes.add(new Chromosome(idx, chr, length));
                    idx++;
                } else {
                    log.info("Unexpected # of tokens at line: " + nextLine);
                }

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    public int getChrLength(String chr) {
        if (chr.equals(Globals.CHR_ALL)) {
            return (int) (genome.getNominalLength() / 1000);
        } else {
            Chromosome c = genome.getChromosome(chr);
            return c == null ? 0 : c.getLength();
        }
    }

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        int wgBinSize = sizeInKB / 700;
        int wgBinCount = sizeInKB / wgBinSize + 1;


        //Chromosome bins
        for (String chr : genome.getAllChromosomeNames()) {
            Chromosome c = genome.getChromosome(chr);
            int len = c.getLength();
            int nBins = len / binSize + 1;
            List<LocusScore> ampBins = new ArrayList(nBins);
            List<LocusScore> delBins = new ArrayList(nBins);
            for (int i = 0; i < nBins; i++) {
                int start = i * binSize;

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                    // Divide total count by window size.  This is the average count per
                    // base over the window,  so for example 30x coverage remains 30x irrespective of window size.
                    int bucketStartPosition = entry.getKey() * windowSize;
                    int bucketEndPosition = bucketStartPosition + windowSize;
                    if (genome != null) {
                        Chromosome chromosome = genome.getChromosome(chr);
                        if (chromosome != null) {
                            bucketEndPosition = Math.min(bucketEndPosition, chromosome.getLength());
                        }
                    }
                    int bucketSize = bucketEndPosition - bucketStartPosition;


                    final Counter counter = entry.getValue();

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            throw e;
        }
        visitedChromosomes.add(chr);




        Chromosome c = genome.getChromosome(chr);
        if (c == null) {
            log.warn("Chromosome: " + chr + " not found in .genome file.  Skipping.");
            skippedChromosomes.add(chr);
        } else {


            chromosomes.add(chr);


            log.info("Processing chromosome " + chr);
            if (zoomLevels != null) {
                for (Zoom zl : zoomLevels) {
                    zl.close();
                }
            }
            if (rawData != null) {
                rawData.close();
            }


            currentChr = chr;
            currentChrLength = c.getLength();
            zoomLevels = new Zoom[getNZoom() + 1];
            for (int z = 0; z <= getNZoom(); z++) {
                zoomLevels[z] = new Zoom(chr, z, currentChrLength);
            }

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    public int getChrLength(String chr) {
        if (chr.equals(Globals.CHR_ALL)) {
            return (int) (genome.getNominalLength() / 1000);
        } else {
            Chromosome c = genome.getChromosome(chr);
            return c == null ? 0 : c.getLength();
        }
    }

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    }


    public List<LocusScore> getSummaryScoresForRange(String chr, int startLocation, int endLocation, int zoom) {


        Chromosome chromosome = genome.getChromosome(chr);


        String tmp = chrNameMap.get(chr);
        String querySeq = tmp == null ? chr : tmp;


        // If we are in gene list view bypass caching.
        if (Globals.isHeadless() || FrameManager.isGeneListMode() || FrameManager.isExomeMode()) {
            return getSummaryScores(querySeq, startLocation, endLocation, zoom);
        } else {


            ArrayList scores = new ArrayList();


            // TODO -- this whole section could be computed once and stored,  it is only a function of the genome, chr, and zoom level.
            double tileWidth = 0;
            if (chr.equals(Globals.CHR_ALL)) {
                tileWidth = (genome.getNominalLength() / 1000.0);
            } else {
                if (chromosome != null) {
                    tileWidth = chromosome.getLength() / ((int) Math.pow(2.0, zoom));
                }
            }
            if (tileWidth == 0) {
                return null;
            }

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        if (chrName.equals("All")) {
            // TODO -- remove the hardcoded unit divider ("1000")
            return (int) (genome.getNominalLength() / 1000);
        } else {
            Chromosome chromosome = genome.getChromosome(chrName);
            if (chromosome == null) {
                log.error("Null chromosome: " + chrName);
                if (genome.getChromosomes().size() == 0) {
                    return 1;
                } else {
                    return genome.getChromosomes().iterator().next().getLength();
                }
            }
            return chromosome.getLength();
        }
    }

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