Interface Itree

    • Method Summary

      All Methods Instance Methods Abstract Methods 
      Modifier and Type Method Description
      void add​(Marker interval)
      Add an interval object to the interval tree's list
      void add​(Markers markers)
      Add all intervals to interval tree's list
      void build()
      Build the interval tree to reflect the list of intervals.
      Markers getIntervals()  
      boolean isEmpty()  
      boolean isInSync()
      Is the tree 'in sync'? If false, the tree must be 'build()' before the next query
      void load​(java.lang.String fileName, Genome genome)
      Load intervals from file
      Markers query​(Interval interval)
      Perform an interval query, returning the intervals that intersect with 'interval'
      int size()
      Size: number of entries in this tree
      Markers stab​(int point)
      Perform a stabbing query, returning the interval objects
      • Methods inherited from interface java.lang.Iterable

        forEach, iterator, spliterator
    • Method Detail

      • add

        void add​(Marker interval)
        Add an interval object to the interval tree's list
      • add

        void add​(Markers markers)
        Add all intervals to interval tree's list
      • build

        void build()
        Build the interval tree to reflect the list of intervals. Must not run if this is currently in sync
      • getIntervals

        Markers getIntervals()
      • isEmpty

        boolean isEmpty()
      • isInSync

        boolean isInSync()
        Is the tree 'in sync'? If false, the tree must be 'build()' before the next query
      • load

        void load​(java.lang.String fileName,
                  Genome genome)
        Load intervals from file
      • query

        Markers query​(Interval interval)
        Perform an interval query, returning the intervals that intersect with 'interval'
        Returns:
        All intervals that intersect 'interval'
      • size

        int size()
        Size: number of entries in this tree
      • stab

        Markers stab​(int point)
        Perform a stabbing query, returning the interval objects
        Returns:
        All intervals intersecting 'point'