Package org.snpeff.interval.tree

Class IntervalForest

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

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void add​(java.util.Collection<? extends Marker> intervals)
      Add all intervals
      void add​(Marker interval)
      Add an interval
      void add​(Markers intervals)
      Add all intervals
      void build()
      Build all trees
      java.lang.String getName()  
      Itree getOrCreateTree​(java.lang.String id)
      Get (or create) an interval tree for ID
      Itree getOrCreateTreeChromo​(java.lang.String chromo)
      Get (or create) an interval tree based for "chromo" (chromosome name)
      Itree getTree​(java.lang.String key)
      Get an interval tree using an ID
      Itree getTreeChromo​(java.lang.String chromo)
      Get an interval tree using a chromosome name
      boolean hasTree​(java.lang.String chromo)
      Is the tree 'chromo' available?
      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.
      java.util.Iterator<Itree> iterator()  
      java.util.Collection<java.lang.String> keySet()  
      protected Itree newItree()
      Create new tree.
      Markers query​(Marker marker)
      Query all intervals that intersect with 'interval'
      Markers query​(Markers marker)
      Query all intervals that intersect with any interval in 'intervals'
      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'
      void setDebug​(boolean debug)  
      void setName​(java.lang.String name)  
      int size()  
      Markers stab​(java.lang.String chromo, int point)
      Obtain all intervals that intersect with 'point'
      Markers stab​(Marker marker)
      Obtain all intervals that intersect with 'marker.start'
      java.lang.String toString()  

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

      • Methods inherited from interface java.lang.Iterable

        forEach, spliterator

    • Constructor Detail

      • IntervalForest

        public IntervalForest()

      • IntervalForest

        public IntervalForest​(Markers markers)

    • Method Detail

      • add

        public void add​(java.util.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 java.lang.String getName()

      • getOrCreateTree

        public Itree getOrCreateTree​(java.lang.String id)
        Get (or create) an interval tree for ID

      • getOrCreateTreeChromo

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

      • getTree

        public Itree getTree​(java.lang.String key)
        Get an interval tree using an ID

      • getTreeChromo

        public Itree getTreeChromo​(java.lang.String chromo)
        Get an interval tree using a chromosome name

      • hasTree

        public boolean hasTree​(java.lang.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 java.util.Iterator<Itree> iterator()
        Specified by:
        iterator in interface java.lang.Iterable<Itree>

      • keySet

        public java.util.Collection<java.lang.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​(java.lang.String name)

      • size

        public int size()

      • stab

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

      • stab

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

      • toString

        public java.lang.String toString()
        Overrides:
        toString in class java.lang.Object