ZoomLevelIterator zoomIterator = new ZoomLevelIterator(fis, chromosomeIDTree, zoomDataTree, zoomLevel, selectionRegion, contained);
ZoomLevelIterator zoomIterator = new ZoomLevelIterator(fis, chromosomeIDTree, zoomDataTree, zoomLevel, selectionRegion, contained);
/** * 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 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; }
ZoomLevelIterator zoomIterator = new ZoomLevelIterator(fis, chromosomeIDTree, zoomDataTree, zoomLevel, selectionRegion, contained);
ZoomLevelIterator zoomIterator = new ZoomLevelIterator(fis, chromosomeIDTree, zoomDataTree, zoomLevel, selectionRegion, contained);
ZoomLevelIterator zoomIterator = new ZoomLevelIterator(fis, chromosomeIDTree, zoomDataTree, zoomLevel, selectionRegion, contained);