Class BigWigIterator

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

    public class BigWigIterator
    extends java.lang.Object
    implements java.util.Iterator<WigItem>
    Created by IntelliJ IDEA. User: martind Date: Apr 13, 2010 Time: 12:34:16 PM To change this template use File | Settings | File Templates.
    • Constructor Detail

      • BigWigIterator

        public BigWigIterator​(SeekableStream fis,
                              BPTree chromIDTree,
                              RPTree chromDataTree,
                              RPChromosomeRegion selectionRegion,
                              boolean contained)
        Constructor for a BigWig iterator over the specified chromosome region

        Parameters: fis - file input stream handle chromIDTree - B+ chromosome index tree provides chromosome ID's for chromosome names chromDataTree - R+ chromosome data locations tree selectionRegion - chromosome region for selection of Wig feature extraction consists of: startChromID - ID of start chromosome startBase - starting base position for values endChromID - ID of end chromosome endBase - ending base position for values contained - specifies wig values must be contained by region, if true; else return any intersecting region values

      • BigWigIterator

        public BigWigIterator()
        Constructor for an "empty" iterator
    • Method Detail

      • hasNext

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

        public WigItem next()
        Method returns the current Wig item and advances to the next Wig record.

        Returns: Wig item for current BigWig data record.

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

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

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

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

        public boolean isContained()
      • getChromosomeIDTree

        public BPTree getChromosomeIDTree()
      • getChromosomeDataTree

        public RPTree getChromosomeDataTree()