Package org.snpeff.interval.tree

Class IntervalForest

java.lang.Object
org.snpeff.interval.tree.IntervalForest
All Implemented Interfaces:
Serializable, Iterable<Itree>
public class IntervalForest extends Object implements Serializable, Iterable<Itree>
A set of interval trees (e.g. one per chromosome, one per transcript ID, etc)
Author:
pcingola
See Also:

  • Constructor Details

    • IntervalForest

      public IntervalForest()

    • IntervalForest

      public IntervalForest(Markers markers)

  • Method Details

    • add

      public void add(Collection<? extends Marker> intervals)
      Add all intervals

    • add

      public void add(Marker interval)
      Add an interval

    • add

      public void add(Markers intervals)
      Add all intervals

    • build

      public void build()
      Build all trees

    • getName

      public String getName()

    • getOrCreateTree

      public Itree getOrCreateTree(String id)
      Get (or create) an interval tree for ID

    • getOrCreateTreeChromo

      public Itree getOrCreateTreeChromo(String chromo)
      Get (or create) an interval tree based for "chromo" (chromosome name)

    • getTree

      public Itree getTree(String key)
      Get an interval tree using an ID

    • getTreeChromo

      public Itree getTreeChromo(String chromo)
      Get an interval tree using a chromosome name

    • hasTree

      public boolean hasTree(String chromo)
      Is the tree 'chromo' available?

    • intersect

      public Markers intersect(Markers markers)
      Return the intersection of 'markers' and this IntervalForest For each marker 'm' in 'markers' - query the tree to get all markers intersecting 'm' - create a new interval which is the intersection of 'm' with all the resutls from the previous query.

    • iterator

      public Iterator<Itree> iterator()
      Specified by:
      iterator in interface Iterable<Itree>

    • keySet

      public Collection<String> keySet()

    • newItree

      protected Itree newItree()
      Create new tree. In oder to change the implementation, only this method should be changed.

    • query

      public Markers query(Marker marker)
      Query all intervals that intersect with 'interval'

    • query

      public Markers query(Markers marker)
      Query all intervals that intersect with any interval in 'intervals'

    • queryUnique

      public Markers queryUnique(Markers markers)
      Query unique intervals that intersect with any interval in 'markers' I.e.: Return a set of intervals that intersects (at least once) with any interval in 'markers'

    • setDebug

      public void setDebug(boolean debug)

    • setName

      public void setName(String name)

    • size

      public int size()

    • stab

      public Markers stab(Marker marker)
      Obtain all intervals that intersect with 'marker.start'

    • stab

      public Markers stab(String chromo, int point)
      Obtain all intervals that intersect with 'point'

    • toString

      public String toString()
      Overrides:
      toString in class Object