Java Chromosome.getIndex方法代码示例

import org.broad.igv.feature.Chromosome; //导入方法依赖的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; //导入方法依赖的package包/类
public void unsafeRefreshChromosomes(SuperAdapter superAdapter) {

        if (chrBox1.getSelectedIndex() == 0 || chrBox2.getSelectedIndex() == 0) {
            chrBox1.setSelectedIndex(0);
            chrBox2.setSelectedIndex(0);
            MatrixType matrixType = (MatrixType) displayOptionComboBox.getSelectedItem();
            if (MatrixType.isPearsonType(matrixType)) {
                // can't do pearson's genomewide
                displayOptionComboBox.setSelectedIndex(0);
                superAdapter.unsafeDisplayOptionComboBoxActionPerformed();
            }
        }

        Chromosome chr1 = (Chromosome) chrBox1.getSelectedItem();
        Chromosome chr2 = (Chromosome) chrBox2.getSelectedItem();

        Chromosome chrX = chr1.getIndex() < chr2.getIndex() ? chr1 : chr2;
        Chromosome chrY = chr1.getIndex() < chr2.getIndex() ? chr2 : chr1;

        superAdapter.unsafeUpdateHiCChromosomes(chrX, chrY);
        setNormalizationDisplayState(superAdapter.getHiC());

        updateThumbnail(superAdapter.getHiC());
    }
 

import org.broad.igv.feature.Chromosome; //导入方法依赖的package包/类
private void unsafeSave1DTrackToWigFile(Chromosome chromosomeForPosition, PrintWriter printWriter,
                                        int binStartPosition) {
    // todo could crash with custom chromosomes - so make sure this doesn't get called on those chromosomes
    int resolution = getZoom().getBinSize();
    for (Chromosome chromosome : chromosomeHandler.getChromosomeArrayWithoutAllByAll()) {
        Matrix matrix = null;
        if (displayOption == MatrixType.OBSERVED) {
            matrix = dataset.getMatrix(chromosomeForPosition, chromosome);
        } else if (displayOption == MatrixType.CONTROL) {
            matrix = controlDataset.getMatrix(chromosomeForPosition, chromosome);
        }

        if (matrix == null) continue;

        MatrixZoomData zd = matrix.getZoomData(currentZoom);
        printWriter.println("fixedStep chrom=chr" + chromosome.getName().replace("chr", "")
                + " start=1 step=" + resolution + " span=" + resolution);

        int[] regionIndices;
        if (chromosomeForPosition.getIndex() < chromosome.getIndex()) {
            regionIndices = new int[]{binStartPosition, binStartPosition, 0, chromosome.getLength()};
        } else {
            regionIndices = new int[]{0, chromosome.getLength(), binStartPosition, binStartPosition};
        }

        zd.dump1DTrackFromCrossHairAsWig(printWriter, binStartPosition,
                chromosomeForPosition.getIndex() == chromosome.getIndex(), regionIndices,
                normalizationType, displayOption);
    }
}
 

import org.broad.igv.feature.Chromosome; //导入方法依赖的package包/类
private void initializeCleanedChromosomesList(List<Chromosome> chromosomes) {
    cleanedChromosomes.clear();
    for (Chromosome c : chromosomes) {
        String cleanName = cleanUpName(c.getName());
        Chromosome cleanChromosome = new Chromosome(c.getIndex(), cleanName, c.getLength());
        cleanedChromosomes.add(cleanChromosome);
    }
}
 

import org.broad.igv.feature.Chromosome; //导入方法依赖的package包/类
/**
 * @param handler
 */
public void initialize(Chromosome chr1, Chromosome chr2, HiCZoom zoom, ChromosomeHandler handler) {
    allRegionsForChr.clear();
    boundariesOfCustomChromosomeX.clear();
    boundariesOfCustomChromosomeY.clear();

    populateRegions(chr1, handler, boundariesOfCustomChromosomeX, zoom);
    if (chr1.getIndex() != chr2.getIndex()) {
        populateRegions(chr2, handler, boundariesOfCustomChromosomeY, zoom);
    } else {
        boundariesOfCustomChromosomeY.addAll(boundariesOfCustomChromosomeX);
    }
}
 

import org.broad.igv.feature.Chromosome; //导入方法依赖的package包/类
private void populateRegions(Chromosome chr, ChromosomeHandler handler, List<Integer> boundaries, HiCZoom zoom) {
    int chrIndex = chr.getIndex();
    Pair<List<MotifAnchor>, List<MotifAnchor>> allRegionsInfo = getAllRegionsFromSubChromosomes(handler, chr);

    if (allRegionsInfo != null) {
        allRegionsForChr.put(chrIndex, allRegionsInfo);
        List<MotifAnchor> translatedRegions = allRegionsInfo.getSecond();
        for (MotifAnchor anchor : translatedRegions) {
            boundaries.add(anchor.getX2() / zoom.getBinSize());
        }
    }
}
 

import org.broad.igv.feature.Chromosome; //导入方法依赖的package包/类
private static List<MotifAnchor> extractAllGenes(BufferedReader reader, ChromosomeHandler handler) {
    List<MotifAnchor> genes = new ArrayList<>();

    String nextLine;
    try {
        while ((nextLine = reader.readLine()) != null) {
            String[] values = nextLine.split("\\s+");
            if (values.length == 4 || values.length == 16) {  // 16 is refGene official format
                Chromosome chr = handler.getChromosomeFromName(values[2]);
                // refGene contains contigs as well, ignore these genes
                if (chr != null) {
                    int chrIndex = chr.getIndex();
                    // 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.length==4) ? values[1].trim() : values[12].trim();
                    MotifAnchor gene = new MotifAnchor(chrIndex, txStart, txEnd, name);
                    genes.add(gene);
                }
            }
        }
    } catch (Exception e) {
        System.err.println("Gene database not properly formatted");
        System.exit(50);
    }
    if (genes.size() == 0) {
        System.err.println("Gene database not properly formatted");
        System.exit(51);
    }

    return genes;
}
 

import org.broad.igv.feature.Chromosome; //导入方法依赖的package包/类
public static ArrayList<ContactRecord> createWholeGenomeRecords(Dataset dataset, ChromosomeHandler handler,
                                                                HiCZoom zoom, boolean includeIntra) {
    ArrayList<ContactRecord> recordArrayList = new ArrayList<>();
    int addX = 0;
    int addY = 0;
    for (Chromosome c1 : handler.getChromosomeArrayWithoutAllByAll()) {
        for (Chromosome c2 : handler.getChromosomeArrayWithoutAllByAll()) {
            if (c1.getIndex() < c2.getIndex() || (c1.equals(c2) && includeIntra)) {
                Matrix matrix = dataset.getMatrix(c1, c2);
                if (matrix != null) {
                    MatrixZoomData zd = matrix.getZoomData(zoom);
                    if (zd != null) {
                        Iterator<ContactRecord> iter = zd.contactRecordIterator();
                        while (iter.hasNext()) {
                            ContactRecord cr = iter.next();
                            int binX = cr.getBinX() + addX;
                            int binY = cr.getBinY() + addY;
                            recordArrayList.add(new ContactRecord(binX, binY, cr.getCounts()));
                        }
                    }
                }
            }
            addY += c2.getLength() / zoom.getBinSize() + 1;
        }
        addX += c1.getLength() / zoom.getBinSize() + 1;
        addY = 0;
    }
    return recordArrayList;
}
 

import org.broad.igv.feature.Chromosome; //导入方法依赖的package包/类
public static HiCDataPoint[] liftDataArrayFromAsm(HiCDataSource dataSource, HiC hic, Chromosome chromosome, int binX1, int binX2, HiCGridAxis gridAxis, double scaleFactor, WindowFunction windowFunction) {
        HiCZoom zoom = hic.getZoom();
        // get aggregate scaffold handler
        AssemblyScaffoldHandler aFragHandler = AssemblyHeatmapHandler.getSuperAdapter().getAssemblyStateTracker().getAssemblyHandler();

        final int binSize = zoom.getBinSize();
        long actualBinSize = (long) binSize;
        if (chromosome.getIndex() == 0) {
            actualBinSize = 1000 * actualBinSize;
        }

        List<Scaffold> xAxisAggregateScaffolds = aFragHandler.getIntersectingAggregateFeatures(
                (long) (actualBinSize * binX1 * HiCGlobals.hicMapScale), (long) (actualBinSize * binX2 * HiCGlobals.hicMapScale));

        List<HiCDataPoint> modifiedDataPoints = new ArrayList<>();

        int x1pos, x2pos;
        for (Scaffold xScaffold : xAxisAggregateScaffolds) {
            x1pos = (int) (xScaffold.getOriginalStart() / HiCGlobals.hicMapScale);
            x2pos = (int) (xScaffold.getOriginalEnd() / HiCGlobals.hicMapScale);

            // have to case long because of thumbnail, maybe fix thumbnail instead

            if (xScaffold.getCurrentStart() < actualBinSize * binX1 * HiCGlobals.hicMapScale) {
                if (!xScaffold.getInvertedVsInitial()) {
                    x1pos = (int) ((xScaffold.getOriginalStart() + actualBinSize * binX1 * HiCGlobals.hicMapScale - xScaffold.getCurrentStart()) / HiCGlobals.hicMapScale);
                } else {
                    x2pos = (int) ((xScaffold.getOriginalStart() - actualBinSize * binX1 * HiCGlobals.hicMapScale + xScaffold.getCurrentEnd()) / HiCGlobals.hicMapScale);
                }
            }

            if (xScaffold.getCurrentEnd() > actualBinSize * binX2 * HiCGlobals.hicMapScale) {
                if (!xScaffold.getInvertedVsInitial()) {
                    x2pos = (int) ((xScaffold.getOriginalStart() + actualBinSize * binX2 * HiCGlobals.hicMapScale - xScaffold.getCurrentStart()) / HiCGlobals.hicMapScale);
                } else {
                    x1pos = (int) ((xScaffold.getOriginalStart() - actualBinSize * binX2 * HiCGlobals.hicMapScale + xScaffold.getCurrentEnd()) / HiCGlobals.hicMapScale);
                }
            }

            HiCDataPoint[] dataArray = dataSource.getData(chromosome, (int) (x1pos / actualBinSize), (int) (x2pos / actualBinSize), gridAxis, scaleFactor, windowFunction);

            for (HiCDataPoint point : dataArray) {
                int newStart;
                int newEnd;
                int newBin;
                if (!xScaffold.getInvertedVsInitial()) {
                    newStart = (int) ((xScaffold.getCurrentStart() + HiCGlobals.hicMapScale * point.getGenomicStart() - xScaffold.getOriginalStart()) / HiCGlobals.hicMapScale);
                    newBin = (int) ((xScaffold.getCurrentStart() + HiCGlobals.hicMapScale * point.getBinNumber() * binSize - xScaffold.getOriginalStart()) / HiCGlobals.hicMapScale / binSize);
                } else {
                    newStart = (int) ((xScaffold.getCurrentEnd() - HiCGlobals.hicMapScale * point.getGenomicEnd() + xScaffold.getOriginalStart()) / HiCGlobals.hicMapScale);
                    newBin = (int) ((xScaffold.getCurrentEnd() - HiCGlobals.hicMapScale * point.getBinNumber() * binSize + xScaffold.getOriginalStart()) / HiCGlobals.hicMapScale / binSize - 1);
                }
                newEnd = newStart + point.getGenomicEnd() - point.getGenomicStart();
//                newBin=newStart/binSize;
                if (point instanceof HiCCoverageDataSource.CoverageDataPoint) {
                    HiCCoverageDataSource.CoverageDataPoint covPoint = (HiCCoverageDataSource.CoverageDataPoint) point;
                    modifiedDataPoints.add(new HiCCoverageDataSource.CoverageDataPoint(newStart / binSize, newStart, newEnd, covPoint.value));
                }
//                else if (point instanceof HiCDataAdapter.DataAccumulator) { // not working quite as supposed to, seems like does not remove prev? confusing...
//                    HiCDataAdapter.DataAccumulator accumPoint = (HiCDataAdapter.DataAccumulator) point;
//                    HiCDataAdapter.DataAccumulator newAccumPoint = new HiCDataAdapter.DataAccumulator((double) newBin, accumPoint.width, newStart, newEnd);
//                    newAccumPoint.nPts = accumPoint.nPts;
//                    newAccumPoint.weightedSum = accumPoint.weightedSum;
//                    newAccumPoint.max = accumPoint.max;
//                    modifiedDataPoints.add(newAccumPoint);
//                    //if(accumPoint.getBinNumber()!=(double)newBin) System.out.println(accumPoint.getBinNumber()+" "+(double)newBin); // why do these not match?
//                }
            }
        }

        HiCDataPoint[] points = new HiCDataPoint[modifiedDataPoints.size()];
        for (int i = 0; i < points.length; i++) {
            points[i] = modifiedDataPoints.get(i);
        }
        return points;
    }
 

import org.broad.igv.feature.Chromosome; //导入方法依赖的package包/类
/**
 * Dumps the matrix.  Does more argument checking, thus this should not be called outside of this class.
 *
 * @throws java.io.IOException   In case of problems writing out matrix
 */
private void dumpMatrix() throws IOException {

    Chromosome chromosome1 = chromosomeHandler.getChromosomeFromName(chr1);
    Chromosome chromosome2 = chromosomeHandler.getChromosomeFromName(chr2);

    Matrix matrix = dataset.getMatrix(chromosome1, chromosome2);
    if (matrix == null) {
        System.err.println("No reads in " + chr1 + " " + chr2);
        return;
    }

    if (chromosome2.getIndex() < chromosome1.getIndex()) {
        regionIndices = new int[]{regionIndices[2], regionIndices[3], regionIndices[0], regionIndices[1]};
    }

    MatrixZoomData zd = matrix.getZoomData(zoom);
    if (zd == null) {
        System.err.println("Unknown resolution: " + zoom);
        System.err.println("This data set has the following bin sizes (in bp): ");
        for (int zoomIdx = 0; zoomIdx < dataset.getNumberZooms(HiC.Unit.BP); zoomIdx++) {
            System.err.print(dataset.getZoom(HiC.Unit.BP, zoomIdx).getBinSize() + " ");
        }
        System.err.println("\nand the following bin sizes (in frag): ");
        for (int zoomIdx = 0; zoomIdx < dataset.getNumberZooms(HiC.Unit.FRAG); zoomIdx++) {
            System.err.print(dataset.getZoom(HiC.Unit.FRAG, zoomIdx).getBinSize() + " ");
        }
        System.exit(13);
    }


    ExpectedValueFunction df = null;
    if (MatrixType.isExpectedValueType(matrixType)) {
        df = dataset.getExpectedValues(zd.getZoom(), norm);
        if (df == null) {
            System.err.println(matrixType + " not available at " + chr1 + " " + zoom + " " + norm);
            System.exit(14);
        }
    }
    zd.dump(pw, les, norm, matrixType, useRegionIndices, regionIndices, df, dense);

}
 

import org.broad.igv.feature.Chromosome; //导入方法依赖的package包/类
private boolean isInterChromosomal() {
    Chromosome chr1 = (Chromosome) chrBox1.getSelectedItem();
    Chromosome chr2 = (Chromosome) chrBox2.getSelectedItem();
    return chr1.getIndex() != chr2.getIndex();
}