Java Chromosome类代码示例

import org.broad.igv.feature.Chromosome; //导入依赖的package包/类
/**
 * Alternate constructor for defining a minimal genome, usually from parsing a chrom.sizes file.
 *
 * @param id
 * @param chromosomes
 */
public Genome(String id, List<Chromosome> chromosomes) {
    this.id = id;
    this.displayName = id;
    this.chrAliasTable = new HashMap<String, String>();
    this.sequence = null;

    chromosomeNames = new ArrayList<String>(chromosomes.size());
    chromosomeMap = new LinkedHashMap<String, Chromosome>(chromosomes.size());
    for (Chromosome chromosome : chromosomes) {
        chromosomeNames.add(chromosome.getName());
        chromosomeMap.put(chromosome.getName(), chromosome);
    }
    initializeChromosomeAliases();

}
 

import org.broad.igv.feature.Chromosome; //导入依赖的package包/类
/**
 * Return the nucleotide sequence on the + strand for the genomic interval.  This method can return null
 * if sequence is not available.
 *
 * @param chr
 * @param start start position in "zero-based" coordinates
 * @param end   end position
 * @return sequence, or null if not available
 * @api
 */
public byte[] getSequence(String chr, int start, int end) {

    if (sequence == null) {
        return null;
    }

    Chromosome c = getChromosome(chr);
    if (c == null) {
        return null;
    }
    end = Math.min(end, c.getLength());
    if (end <= start) {
        return null;
    }
    return sequence.getSequence(chr, start, end);
}
 

import org.broad.igv.feature.Chromosome; //导入依赖的package包/类
/**
 * Export a "chrom.sizes" file for the specified genome
 *
 * @param directory output directory
 * @param genome
 * @throws FileNotFoundException
 */
public static void exportChromSizes(File directory, Genome genome) throws FileNotFoundException {


    String fn = genome.getId() + ".chrom.sizes";
    File file = new File(directory, fn);
    PrintWriter pw = null;

    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();
    }

}
 

import org.broad.igv.feature.Chromosome; //导入依赖的package包/类
/**
 *
 * @param trackId
 * @param dataset
 * @param genome
 */
public DatasetDataSource(String trackId, Dataset dataset, Genome genome) {
    super(genome);
    this.trackId = trackId;
    this.dataset = dataset;

    // TODO -- remove this "instanceof" hack
    if (genome.getHomeChromosome().equals(Globals.CHR_ALL)) {
        if (dataset instanceof IGVDataset) {
            genomeSummaryData = ((IGVDataset) dataset).getGenomeSummary();
        } else {
            genomeSummaryData = new GenomeSummaryData(genome, new String[]{trackId});
            for (Chromosome chr : genome.getChromosomes()) {
                int[] startLocations = dataset.getStartLocations(chr.getName());
                if (!chr.getName().equals(Globals.CHR_ALL) && (startLocations != null) && (startLocations.length > 0)) {
                    Map<String, float[]> dMap = new HashMap<String, float[]>();
                    dMap.put(trackId, dataset.getData(trackId, chr.getName()));
                    genomeSummaryData.addData(chr.getName(), startLocations, dMap);
                }
            }
        }
    }
}
 

import org.broad.igv.feature.Chromosome; //导入依赖的package包/类
private static int getChromosomeLength(String chrName) {
    Genome genome = getGenome();

    if (genome == null) {
        return 1;
    }

    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();
    }
}
 

import org.broad.igv.feature.Chromosome; //导入依赖的package包/类
private void setChromosomesFromBroadcast(String chrXName, String chrYName) {
    if (!chrXName.equals(xContext.getChromosome().getName()) || !chrYName.equals(yContext.getChromosome().getName())) {
        Chromosome chrX = chromosomeHandler.getChromosomeFromName(chrXName);
        Chromosome chrY = chromosomeHandler.getChromosomeFromName(chrYName);

        if (chrX == null || chrY == null) {
            //System.out.println("Most probably origin is a different species saved location or sync/link between two different species maps.");
            return;
        }

        this.xContext = new Context(chrX);
        this.yContext = new Context(chrY);
        superAdapter.setSelectedChromosomesNoRefresh(chrX, chrY);
        refreshEigenvectorTrackIfExists();
    }
}
 

import org.broad.igv.feature.Chromosome; //导入依赖的package包/类
private void safeSave1DTrackToWigFile(final Chromosome chromosomeForPosition, final File outputWigFile,
                                      final int binStartPosition) {
    superAdapter.getMainWindow().executeLongRunningTask(new Runnable() {
        @Override
        public void run() {
            try {
                PrintWriter printWriter = new PrintWriter(outputWigFile);
                unsafeSave1DTrackToWigFile(chromosomeForPosition, printWriter, binStartPosition);
                printWriter.close();
                if (outputWigFile.exists() && outputWigFile.length() > 0) {
                    // TODO this still doesn't add to the resource tree / load annotation dialog box
                    //superAdapter.getTrackLoadAction();
                    //getResourceTree().add1DCustomTrack(outputWigFile);
                    HiC.this.unsafeLoadTrack(outputWigFile.getAbsolutePath());
                    LoadAction loadAction = superAdapter.getTrackLoadAction();
                    loadAction.checkBoxesForReload(outputWigFile.getName());
                }
            } catch (Exception e) {
                System.err.println("Unable to generate and save 1D HiC track");
            }
        }
    }, "Saving_1D_track_as_wig");

}
 

import org.broad.igv.feature.Chromosome; //导入依赖的package包/类
private static List<Chromosome> getIndicesFromSubChromosomes(final ChromosomeHandler handler, Chromosome chromosome) {
    final List<Chromosome> indices = new ArrayList<>();
    if (handler.isCustomChromosome(chromosome)) {
        GenomeWideList<MotifAnchor> regions = handler.getListOfRegionsInCustomChromosome(chromosome.getIndex());
        regions.processLists(new FeatureFunction<MotifAnchor>() {
            @Override
            public void process(String chr, List<MotifAnchor> featureList) {
                if (featureList.size() > 0) {
                    Chromosome chromosomeN = handler.getChromosomeFromName(chr);
                    if (chromosomeN != null) {
                        indices.add(chromosomeN);
                    }
                }
            }
        });
    } else {
        indices.add(chromosome);
    }
    return indices;
}
 

import org.broad.igv.feature.Chromosome; //导入依赖的package包/类
/**
 * For each given chromosome name, find its equivalent Chromosome object
 *
 * @param chromosomesSpecified by strings
 * @param handler as Chromosome objects
 * @return the specified Chromosomes corresponding to the given strings
 */
public static ChromosomeHandler stringToChromosomes(Set<String> chromosomesSpecified,
                                                    ChromosomeHandler handler) {
    List<Chromosome> chromosomes = new ArrayList<>();
    chromosomes.add(0, null);

    for (String strKey : chromosomesSpecified) {
        boolean chrFound = false;
        for (Chromosome chrKey : handler.getChromosomeArray()) {
            if (equivalentChromosome(strKey, chrKey)) {
                chromosomes.add(chrKey);
                chrFound = true;
                break;
            }
        }
        if (!chrFound) {
            System.err.println("Chromosome " + strKey + " not found");
        }
    }
    return new ChromosomeHandler(chromosomes);
}
 

import org.broad.igv.feature.Chromosome; //导入依赖的package包/类
public double[] getEigenvector(Chromosome chr, HiCZoom zoom, int number, NormalizationType type) {

        String key = chr.getName() + "_" + zoom.getKey() + "_" + number + "_" + type;
        if (!eigenvectorCache.containsKey(key)) {

            double[] eigenvector;
            //eigenvector = reader.readEigenvector(chr.getName(), zoom, number, type.toString());

            ExpectedValueFunction df = getExpectedValues(zoom, type);
            Matrix m = getMatrix(chr, chr);
            MatrixZoomData mzd = m.getZoomData(zoom);
            if (df != null && mzd.getPearsons(df) != null) {
                eigenvector = mzd.computeEigenvector(df, number);
            } else {
                eigenvector = new double[0];
            }

            eigenvectorCache.put(key, eigenvector);
        }

        return eigenvectorCache.get(key);

    }
 

import org.broad.igv.feature.Chromosome; //导入依赖的package包/类
public static GenomeWideList<MotifAnchor> extractAllAnchorsFromAllFeatures(Feature2DList features, final ChromosomeHandler handler) {

        final GenomeWideList<MotifAnchor> extractedAnchorList = new GenomeWideList<>();
        features.processLists(new FeatureFunction() {
            @Override
            public void process(String chr, List<Feature2D> feature2DList) {
                for (Feature2D f : feature2DList) {
                    Chromosome chrom = handler.getChromosomeFromName((f.getChr1()));
                    extractedAnchorList.addFeature(chrom.getName(), new MotifAnchor(chrom.getIndex(), f.getStart1(), f.getEnd1()));
                    chrom = handler.getChromosomeFromName((f.getChr2()));
                    extractedAnchorList.addFeature(chrom.getName(), new MotifAnchor(chrom.getIndex(), f.getStart2(), f.getEnd2()));
                }
            }
        });

        mergeAndExpandSmallAnchors(extractedAnchorList, getMinSizeForExpansionFromGUI());

        return extractedAnchorList;
    }
 

import org.broad.igv.feature.Chromosome; //导入依赖的package包/类
private static void addToList(String chr1Name, String chr2Name, ChromosomeHandler handler, String nextLine,
                              Feature2DList newList, boolean useFeature2DWithMotif, Feature2D.FeatureType featureType,
                              int start1, int end1, int start2, int end2, Color c, Map<String, String> attrs) {
    Chromosome chr1 = handler.getChromosomeFromName(chr1Name);
    Chromosome chr2 = handler.getChromosomeFromName(chr2Name);
    if (chr1 == null || chr2 == null) {
        handleError(nextLine);
        return;
    }

    // Convention is chr1 is lowest "index". Swap if necessary
    if (useFeature2DWithMotif) {
        if (chr1.getIndex() <= chr2.getIndex()) {
            newList.add(chr1.getIndex(), chr2.getIndex(), new Feature2DWithMotif(featureType, chr1Name, chr1.getIndex(), start1, end1, chr2Name, chr2.getIndex(), start2, end2, c, attrs));
        } else {
            newList.add(chr2.getIndex(), chr1.getIndex(), new Feature2DWithMotif(featureType, chr2Name, chr2.getIndex(), start2, end2, chr1Name, chr1.getIndex(), start1, end1, c, attrs));
        }
    } else {
        if (chr1.getIndex() <= chr2.getIndex()) {
            newList.add(chr1.getIndex(), chr2.getIndex(), new Feature2D(featureType, chr1Name, start1, end1, chr2Name, start2, end2, c, attrs));
        } else {
            newList.add(chr2.getIndex(), chr1.getIndex(), new Feature2D(featureType, chr2Name, start2, end2, chr1Name, start1, end1, c, attrs));
        }
    }
}
 

import org.broad.igv.feature.Chromosome; //导入依赖的package包/类
public static Map<String, GeneLocation> getLocationMap(BufferedReader reader, ChromosomeHandler handler) throws IOException {
    Map<String, GeneLocation> geneLocationHashMap = new HashMap<>();

    String nextLine;
    while ((nextLine = reader.readLine()) != null) {
        String[] values = nextLine.split("\\s+");
        if (values.length == 4 || values.length == 16) {  // 16 is refGene official format

            // transcript start; for 4 column format, just position-1
            int txStart = (values.length==4) ? Integer.valueOf(values[3].trim())-1 : Integer.valueOf(values[4].trim());
            // transcript end; for 4 column format, just position+1
            //int txEnd = (values.length==4) ? Integer.valueOf(values[3].trim())+1 : Integer.valueOf(values[5].trim());
            String name = values[1].trim();
            String name2 = (values.length==4) ? values[0].trim() : values[12].trim();
            Chromosome chr = handler.getChromosomeFromName(values[2]);
            GeneLocation location = new GeneLocation(chr, txStart);
            geneLocationHashMap.put(name2.toLowerCase(), location);
            geneLocationHashMap.put(name.trim().toLowerCase(), location);
        }
    }
    return geneLocationHashMap;
}
 

import org.broad.igv.feature.Chromosome; //导入依赖的package包/类
/**
 * Representation of MatrixZoomData used for preprocessing
 *
 * @param chr1             index of first chromosome  (x-axis)
 * @param chr2             index of second chromosome
 * @param binSize          size of each grid bin in bp
 * @param blockColumnCount number of block columns
 * @param zoom             integer zoom (resolution) level index.  TODO Is this needed?
 */
MatrixZoomDataPP(Chromosome chr1, Chromosome chr2, int binSize, int blockColumnCount, int zoom, boolean isFrag) {

    this.tmpFiles = new ArrayList<>();
    this.blockNumbers = new HashSet<>(1000);

    this.sum = 0;
    this.chr1 = chr1;
    this.chr2 = chr2;
    this.binSize = binSize;
    this.blockColumnCount = blockColumnCount;
    this.zoom = zoom;
    this.isFrag = isFrag;

    // Get length in proper units
    Chromosome longChr = chr1.getLength() > chr2.getLength() ? chr1 : chr2;
    int len = isFrag ? fragmentCalculation.getNumberFragments(longChr.getName()) : longChr.getLength();

    int nBinsX = len / binSize + 1;

    blockBinCount = nBinsX / blockColumnCount + 1;
    blocks = new LinkedHashMap<>(blockColumnCount * blockColumnCount);
}
 

import org.broad.igv.feature.Chromosome; //导入依赖的package包/类
/**
 * Add an observed distance.  This is called for each pair in the data set
 *
 * @param chrIdx index of chromosome where observed, so can increment count
 * @param bin1   Position1 observed in units of "bins"
 * @param bin2   Position2 observed in units of "bins"
 */
public void addDistance(Integer chrIdx, int bin1, int bin2, double weight) {

    // Ignore NaN values    TODO -- is this the right thing to do?
    if (Double.isNaN(weight)) return;

    int dist;
    Chromosome chr = chromosomesMap.get(chrIdx);
    if (chr == null) return;

    Double count = chromosomeCounts.get(chrIdx);
    if (count == null) {
        chromosomeCounts.put(chrIdx, weight);
    } else {
        chromosomeCounts.put(chrIdx, count + weight);
    }
    dist = Math.abs(bin1 - bin2);


    actualDistances[dist] += weight;

}