public RPChromosomeRegion getChromosomeBounds() { RPChromosomeRegion chromosomeBounds = chromosomeDataTree.getChromosomeBounds(); return chromosomeBounds; }
public RPChromosomeRegion getChromosomeBounds() { RPChromosomeRegion chromosomeBounds = chromosomeDataTree.getChromosomeBounds(); return chromosomeBounds; }
public RPChromosomeRegion getZoomLevelBounds(int zoomLevel) { RPChromosomeRegion chromosomeBounds = zoomLevels.getZoomLevelRPTree(zoomLevel).getChromosomeBounds(); return chromosomeBounds; }
public RPChromosomeRegion getZoomLevelBounds(int zoomLevel) { RPChromosomeRegion chromosomeBounds = zoomLevels.getZoomLevelRPTree(zoomLevel).getChromosomeBounds(); return chromosomeBounds; }
/** * Returns an iterator for zoom level records for all chromosome regions. * <p/> * Note: the BBFile can be BigBed or BigWig. * <p/> * Parameters: * zoomLevel - zoom level for data extraction; levels start at 1 * <p/> * Returns: * Iterator to provide BedFeature(s) for the requested chromosome region. * Error conditions: * 1) An empty iterator is returned if region has no data available */ public ZoomLevelIterator getZoomLevelIterator(int zoomLevel) { // check for valid zoom level if (zoomLevel < 1 || zoomLevel > zoomLevelCount) throw new RuntimeException("Error: ZoomLevelIterator zoom level is out of range\n"); // get the appropriate zoom level R+ zoom data index tree RPTree zoomDataTree = zoomLevels.getZoomLevelRPTree(zoomLevel); // get all regions bounds RPChromosomeRegion selectionRegion = zoomDataTree.getChromosomeBounds(); // compose an iterator boolean contained = true; //all regions are contained ZoomLevelIterator zoomIterator = new ZoomLevelIterator(fis, chromosomeIDTree, zoomDataTree, zoomLevel, selectionRegion, contained); return zoomIterator; }
/** * Returns an iterator for zoom level records for all chromosome regions. * <p/> * Note: the BBFile can be BigBed or BigWig. * <p/> * Parameters: * zoomLevel - zoom level for data extraction; levels start at 1 * <p/> * Returns: * Iterator to provide BedFeature(s) for the requested chromosome region. * Error conditions: * 1) An empty iterator is returned if region has no data available */ public ZoomLevelIterator getZoomLevelIterator(int zoomLevel) { // check for valid zoom level if (zoomLevel < 1 || zoomLevel > zoomLevelCount) throw new RuntimeException("Error: ZoomLevelIterator zoom level is out of range\n"); // get the appropriate zoom level R+ zoom data index tree RPTree zoomDataTree = zoomLevels.getZoomLevelRPTree(zoomLevel); // get all regions bounds RPChromosomeRegion selectionRegion = zoomDataTree.getChromosomeBounds(); // compose an iterator boolean contained = true; //all regions are contained ZoomLevelIterator zoomIterator = new ZoomLevelIterator(fis, chromosomeIDTree, zoomDataTree, zoomLevel, selectionRegion, contained); return zoomIterator; }
/** * Returns an iterator for BigBed features for all chromosome regions. * <p/> * Note: the BBFile type should be BigBed; else a null iterator is returned. * <p/> * Returns: * Iterator to provide BedFeature(s) for all chromosome regions. * Error conditions: * 1) An empty iterator is returned if region has no data available * 2) A null object is returned if the file is not BigBed.(see isBigBedFile method) */ public BigBedIterator getBigBedIterator() { if (!isBigBedFile()) return null; // get all region bounds RPChromosomeRegion selectionRegion = chromosomeDataTree.getChromosomeBounds(); // compose an iterator boolean contained = true; /// all regions are contained BigBedIterator bedIterator = new BigBedIterator(fis, chromosomeIDTree, chromosomeDataTree, selectionRegion, contained); return bedIterator; }
/** * Returns an iterator for zoom level records for all chromosome regions. * <p/> * Note: the BBFile can be BigBed or BigWig. * <p/> * Parameters: * zoomLevel - zoom level for data extraction; levels start at 1 * <p/> * Returns: * Iterator to provide BedFeature(s) for the requested chromosome region. * Error conditions: * 1) An empty iterator is returned if region has no data available */ synchronized public ZoomLevelIterator getZoomLevelIterator(int zoomLevel) { // check for valid zoom level if (zoomLevel < 1 || zoomLevel > zoomLevelCount) throw new RuntimeException("Error: ZoomLevelIterator zoom level is out of range\n"); // get the appropriate zoom level R+ zoom data index tree RPTree zoomDataTree = zoomLevels.getZoomLevelRPTree(zoomLevel); // get all regions bounds RPChromosomeRegion selectionRegion = zoomDataTree.getChromosomeBounds(); // compose an iterator boolean contained = true; //all regions are contained ZoomLevelIterator zoomIterator = new ZoomLevelIterator(fis, chromosomeIDTree, zoomDataTree, zoomLevel, selectionRegion, contained); return zoomIterator; }
/** * Returns an iterator for BigWig values for all chromosome regions. * <p/> * Note: the BBFile type should be BigWig; else a null iterator is returned. * <p/> * Returns: * Iterator to provide BedFeature(s) for all chromosome regions. * Error conditions: * 1) An empty iterator is returned if region has no data available * 2) A null object is returned if the file is not BigWig.(see isBigWigFile method) */ public BigWigIterator getBigWigIterator() { if (!isBigWigFile()) return null; // get all regions bounds RPChromosomeRegion selectionRegion = chromosomeDataTree.getChromosomeBounds(); // compose an iterator boolean contained = true; // all regions are contained BigWigIterator wigIterator = new BigWigIterator(fis, chromosomeIDTree, chromosomeDataTree, selectionRegion, contained); return wigIterator; }
/** * Returns an iterator for BigBed features for all chromosome regions. * <p/> * Note: the BBFile type should be BigBed; else a null iterator is returned. * <p/> * Returns: * Iterator to provide BedFeature(s) for all chromosome regions. * Error conditions: * 1) An empty iterator is returned if region has no data available * 2) A null object is returned if the file is not BigBed.(see isBigBedFile method) */ public BigBedIterator getBigBedIterator() { if (!isBigBedFile()) return null; // get all region bounds RPChromosomeRegion selectionRegion = chromosomeDataTree.getChromosomeBounds(); // compose an iterator boolean contained = true; /// all regions are contained BigBedIterator bedIterator = new BigBedIterator(fis, chromosomeIDTree, chromosomeDataTree, selectionRegion, contained); return bedIterator; }
/** * Returns an iterator for BigWig values for all chromosome regions. * <p/> * Note: the BBFile type should be BigWig; else a null iterator is returned. * <p/> * Returns: * Iterator to provide BedFeature(s) for all chromosome regions. * Error conditions: * 1) An empty iterator is returned if region has no data available * 2) A null object is returned if the file is not BigWig.(see isBigWigFile method) */ public BigWigIterator getBigWigIterator() { if (!isBigWigFile()) return null; // get all regions bounds RPChromosomeRegion selectionRegion = chromosomeDataTree.getChromosomeBounds(); // compose an iterator boolean contained = true; // all regions are contained BigWigIterator wigIterator = new BigWigIterator(fis, chromosomeIDTree, chromosomeDataTree, selectionRegion, contained); return wigIterator; }