Class BigBedIterator

  • All Implemented Interfaces:
    java.util.Iterator<BedFeature>

    public class BigBedIterator
    extends java.lang.Object
    implements java.util.Iterator<BedFeature>
    Created by IntelliJ IDEA. User: martind Date: Apr 5, 2010 Time: 3:10:26 PM To change this template use File | Settings | File Templates.
    • Constructor Detail

      • BigBedIterator

        public BigBedIterator​(SeekableStream fis,
                              BPTree chromIDTree,
                              RPTree chromDataTree,
                              RPChromosomeRegion selectionRegion,
                              boolean contained)
        Constructor for a BigBed iterator over the specified chromosome region Parameters: fis - file input stream handle chromIDTree - B+ index tree returns chromomosme ID's for chromosome names chromDataTree - R+ chromosome data locations 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
      • BigBedIterator

        public BigBedIterator()
    • Method Detail

      • hasNext

        public boolean hasNext()
        Specified by:
        hasNext in interface java.util.Iterator<BedFeature>
      • next

        public BedFeature 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.
        Specified by:
        next in interface java.util.Iterator<BedFeature>
      • remove

        public void remove()
        Specified by:
        remove in interface java.util.Iterator<BedFeature>
      • setSelectionRegion

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

        public boolean isContained()
      • getChromosomeIDTree

        public BPTree getChromosomeIDTree()
      • getChromosomeDataTree

        public RPTree getChromosomeDataTree()