Interface Itree

Method Details

• 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(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'