Class ZoomLevelIterator

  • Direct Known Subclasses:
    ZoomLevelIterator.EmptyIterator

    public class ZoomLevelIterator
    extends java.lang.Object
    Created by IntelliJ IDEA. User: martind Date: Apr 16, 2010 Time: 4:19:29 PM To change this template use File | Settings | File Templates.
    • Constructor Detail

      • ZoomLevelIterator

        public ZoomLevelIterator()
        Default constructor. This is provided to support return of a subclassed "empty" iterator
      • ZoomLevelIterator

        public ZoomLevelIterator​(SeekableStream fis,
                                 BPTree chromIDTree,
                                 RPTree zoomDataTree,
                                 int zoomLevel,
                                 RPChromosomeRegion selectionRegion,
                                 boolean contained)
        Constructs a zoom level iterator over the specified chromosome region

        Parameters: fis - file input stream handle chromIDTree - B+ index tree returns chromId for chromosome name key zoomLevelTree - zoom level R+ chromosome index tree zoomLevel - zoom level represented by the R+ tree selectionRegion - chromosome region for selection of Bed feature extraction consists of: startChromID - ID of start chromosome startBase - starting base position for features endChromID - ID of end chromosome endBase - starting base position for features contained - specifies bed features must be contained by region, if true; else return any intersecting region features

    • Method Detail

      • hasNext

        public boolean hasNext()
      • next

        public ZoomDataRecord next()
        Method returns the current bed feature and advances to the next bed record.

        Returns: Bed feature for current BigBed data record.

        Note: If "next" method is called when a "next item" does not exist, an UnsupportedOperationException will be thrown.

      • remove

        public void remove()
      • getZoomLevel

        public int getZoomLevel()
      • setSelectionRegion

        public int setSelectionRegion​(RPChromosomeRegion selectionRegion,
                                      boolean contained)
      • isContained

        public boolean isContained()
      • getChromosomeIDTree

        public BPTree getChromosomeIDTree()
      • getZoomDataTree

        public RPTree getZoomDataTree()