Uses of Interface
org.snpeff.interval.tree.Itree

Packages that use Itree

Package	Description
org.snpeff.interval.tree
org.snpeff.snpEffect.testCases.unity

Uses of Itree in org.snpeff.interval.tree

Classes in org.snpeff.interval.tree that implement Itree

Modifier and Type	Class	Description
class	IntervalTree	An Interval Tree is essentially a map from intervals to objects, which can be queried for all data associated with a particular interval of point
class	IntervalTreeArray	Interval tree structure using arrays This is slightly faster than the new IntervalTree implementation
class	IntervalTreeOri	An Interval Tree is essentially a map from intervals to objects, which can be queried for all data associated with a particular interval of point

Methods in org.snpeff.interval.tree that return Itree

Modifier and Type	Method	Description
Itree	IntervalForest.getOrCreateTree(java.lang.String id)	Get (or create) an interval tree for ID
Itree	IntervalForest.getOrCreateTreeChromo(java.lang.String chromo)	Get (or create) an interval tree based for "chromo" (chromosome name)
Itree	IntervalForest.getTree(java.lang.String key)	Get an interval tree using an ID
Itree	IntervalForest.getTreeChromo(java.lang.String chromo)	Get an interval tree using a chromosome name
protected Itree	IntervalForest.newItree()	Create new tree.

Methods in org.snpeff.interval.tree that return types with arguments of type Itree

Modifier and Type	Method	Description
java.util.Iterator<Itree>	IntervalForest.iterator()

Uses of Itree in org.snpeff.snpEffect.testCases.unity

Methods in org.snpeff.snpEffect.testCases.unity that return Itree

Modifier and Type	Method	Description
protected Itree	TestCasesIntervalTree.newItree(Markers markers)
protected Itree	TestCasesIntervalTreeArray.newItree(Markers markers)
protected Itree	TestCasesIntervalTreeOri.newItree(Markers markers)

Methods in org.snpeff.snpEffect.testCases.unity with parameters of type Itree

Modifier and Type	Method	Description
protected int	TestCasesIntervalTree.compareQuery(Marker m, Itree intTree)	Perform a query using 'naive' lookup and interval forest.