Index (dsh-bio-range 3.0 API)

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A

AbstractRangeTree<C extends Comparable,V> - Class in org.dishevelled.bio.range.entrytree: Abstract implementation of range tree.
AbstractRangeTree<C extends Comparable> - Class in org.dishevelled.bio.range.tree: Abstract implementation of range tree.
AbstractRangeTree() - Constructor for class org.dishevelled.bio.range.entrytree.AbstractRangeTree
AbstractRangeTree() - Constructor for class org.dishevelled.bio.range.tree.AbstractRangeTree

C

center(Range<C>) - Static method in class org.dishevelled.bio.range.Ranges: Return the center of the specified range.
CenteredRangeTree<C extends Comparable,V> - Class in org.dishevelled.bio.range.entrytree: Centered range tree.
CenteredRangeTree<C extends Comparable> - Class in org.dishevelled.bio.range.tree: Centered range tree.
closed(N, N) - Static method in class org.dishevelled.bio.range.rtree.RangeGeometries: Create and return a new rectangle geometry from the specified closed range [lower..upper].
closedOpen(N, N) - Static method in class org.dishevelled.bio.range.rtree.RangeGeometries: Create and return a new rectangle geometry from the specified closed open range [lower..upper).
contains(C) - Method in class org.dishevelled.bio.range.entrytree.AbstractRangeTree
contains(C) - Method in interface org.dishevelled.bio.range.entrytree.RangeTree: Return true if the specified location intersects with any range entries in this range tree.
contains(C) - Method in class org.dishevelled.bio.range.tree.AbstractRangeTree
contains(C) - Method in interface org.dishevelled.bio.range.tree.RangeTree: Return true if the specified location intersects with any ranges in this range tree.
count(C) - Method in class org.dishevelled.bio.range.entrytree.AbstractRangeTree
count(C) - Method in interface org.dishevelled.bio.range.entrytree.RangeTree: Return the number of range entries in this range tree at the specified location.
count(C) - Method in class org.dishevelled.bio.range.tree.AbstractRangeTree
count(C) - Method in interface org.dishevelled.bio.range.tree.RangeTree: Return the number of ranges in this range tree at the specified location.
count(Range<C>) - Method in class org.dishevelled.bio.range.entrytree.AbstractRangeTree
count(Range<C>) - Method in interface org.dishevelled.bio.range.entrytree.RangeTree: Return the number of range entries in this range tree that intersect the specified query range.
count(Range<C>) - Method in class org.dishevelled.bio.range.tree.AbstractRangeTree
count(Range<C>) - Method in interface org.dishevelled.bio.range.tree.RangeTree: Return the number of ranges in this range tree that intersect the specified query range.
create(Iterable<Range<C>>) - Static method in class org.dishevelled.bio.range.tree.CenteredRangeTree: Create and return a new range tree from the specified ranges.
create(Iterable<Range<C>>) - Static method in class org.dishevelled.bio.range.tree.RangeList: Create and return a new range tree from the specified ranges.
create(Iterable<RangeTree.Entry<C, V>>) - Static method in class org.dishevelled.bio.range.entrytree.CenteredRangeTree: Create and return a new range tree from the specified range entries.
create(List<Range<C>>, List<V>) - Static method in class org.dishevelled.bio.range.entrytree.CenteredRangeTree: Create and return a new range tree from the specified ranges and values.

E

equals(Object) - Method in class org.dishevelled.bio.range.entrytree.RangeEntry

G

getRange() - Method in class org.dishevelled.bio.range.entrytree.RangeEntry
getRange() - Method in interface org.dishevelled.bio.range.entrytree.RangeTree.Entry: Return the range for this range tree entry.
getValue() - Method in class org.dishevelled.bio.range.entrytree.RangeEntry
getValue() - Method in interface org.dishevelled.bio.range.entrytree.RangeTree.Entry: Return the value for this range tree entry.

H

hashCode() - Method in class org.dishevelled.bio.range.entrytree.RangeEntry

I

intersect(Range<C>) - Method in class org.dishevelled.bio.range.entrytree.CenteredRangeTree
intersect(Range<C>) - Method in interface org.dishevelled.bio.range.entrytree.RangeTree: Return the range entries in this range tree that intersect the specified query range, if any.
intersect(Range<C>) - Method in class org.dishevelled.bio.range.tree.CenteredRangeTree
intersect(Range<C>) - Method in class org.dishevelled.bio.range.tree.RangeList
intersect(Range<C>) - Method in interface org.dishevelled.bio.range.tree.RangeTree: Return the ranges in this range tree that intersect the specified query range, if any.
intersect(Range<C>, Range<C>) - Static method in class org.dishevelled.bio.range.Ranges: Return true if the specified ranges intersect.
intersect(Iterable<Range<C>>) - Method in class org.dishevelled.bio.range.tree.AbstractRangeTree
intersect(Iterable<Range<C>>) - Method in interface org.dishevelled.bio.range.tree.RangeTree: Return the intersection of the ranges in this range tree with the specified query list of ranges as intersecting pairs of ranges, if any.
intersects(Range<C>) - Method in class org.dishevelled.bio.range.entrytree.AbstractRangeTree
intersects(Range<C>) - Method in interface org.dishevelled.bio.range.entrytree.RangeTree: Return true if the specified query range intersects with any range entries in this range tree.
intersects(Range<C>) - Method in class org.dishevelled.bio.range.tree.AbstractRangeTree
intersects(Range<C>) - Method in interface org.dishevelled.bio.range.tree.RangeTree: Return true if the specified query range intersects with any ranges in this range tree.
intersects(Iterable<Range<C>>) - Method in class org.dishevelled.bio.range.entrytree.AbstractRangeTree
intersects(Iterable<Range<C>>) - Method in interface org.dishevelled.bio.range.entrytree.RangeTree: Return true if any range in the specified query list of ranges intersects with any range entries in this range tree.
intersects(Iterable<Range<C>>) - Method in class org.dishevelled.bio.range.tree.AbstractRangeTree
intersects(Iterable<Range<C>>) - Method in interface org.dishevelled.bio.range.tree.RangeTree: Return true if any range in the specified query list of ranges intersects with any ranges in this range tree.
isEmpty() - Method in class org.dishevelled.bio.range.entrytree.AbstractRangeTree
isEmpty() - Method in interface org.dishevelled.bio.range.entrytree.RangeTree: Return true if the number of range entries in this range tree is zero.
isEmpty() - Method in class org.dishevelled.bio.range.tree.AbstractRangeTree
isEmpty() - Method in class org.dishevelled.bio.range.tree.RangeList
isEmpty() - Method in interface org.dishevelled.bio.range.tree.RangeTree: Return true if the number of ranges in this range tree is zero.
isGreaterThan(Range<C>, C) - Static method in class org.dishevelled.bio.range.Ranges: Return true if the specified range is strictly greater than the specified value.
isLessThan(Range<C>, C) - Static method in class org.dishevelled.bio.range.Ranges: Return true if the specified range is strictly less than the specified value.

O

open(N, N) - Static method in class org.dishevelled.bio.range.rtree.RangeGeometries: Create and return a new rectangle geometry from the specified open range (lower..upper).
openClosed(N, N) - Static method in class org.dishevelled.bio.range.rtree.RangeGeometries: Create and return a new rectangle geometry from the specified open closed range (lower..upper]
orderingByLowerEndpoint() - Static method in class org.dishevelled.bio.range.Ranges: Return an ordering by lower endpoint over ranges.
orderingByUpperEndpoint() - Static method in class org.dishevelled.bio.range.Ranges: Return an ordering by upper endpoint over ranges.
org.dishevelled.bio.range - package org.dishevelled.bio.range: Guava ranges for genomics.
org.dishevelled.bio.range.entrytree - package org.dishevelled.bio.range.entrytree: Range tree composed of entries.
org.dishevelled.bio.range.rtree - package org.dishevelled.bio.range.rtree: Range R-Tree/R*-tree.
org.dishevelled.bio.range.tree - package org.dishevelled.bio.range.tree: Range tree.

Q

query(C) - Method in class org.dishevelled.bio.range.entrytree.AbstractRangeTree
query(C) - Method in interface org.dishevelled.bio.range.entrytree.RangeTree: Return the range entries in this range tree at the specified location, if any.
query(C) - Method in class org.dishevelled.bio.range.tree.AbstractRangeTree
query(C) - Method in interface org.dishevelled.bio.range.tree.RangeTree: Return the ranges in this range tree at the specified location, if any.

R

range(Range<N>) - Static method in class org.dishevelled.bio.range.rtree.RangeGeometries: Create and return a new rectangle geometry from the specified range.
RangeEntry<C extends Comparable,V> - Class in org.dishevelled.bio.range.entrytree: Implementation of RangeTree.Entry.
RangeEntry(Range<C>, V) - Constructor for class org.dishevelled.bio.range.entrytree.RangeEntry: Create a new range entry with the specified range and value.
RangeGeometries - Class in org.dishevelled.bio.range.rtree: Geometries for use in building R-Trees and R*-Trees from Guava ranges.
RangeList<C extends Comparable> - Class in org.dishevelled.bio.range.tree: Range list.
Ranges - Class in org.dishevelled.bio.range: Utility methods on ranges.
RangeTree<C extends Comparable,V> - Interface in org.dishevelled.bio.range.entrytree: Range tree composed of entries.
RangeTree<C extends Comparable> - Interface in org.dishevelled.bio.range.tree: Range tree.
RangeTree.Entry<C extends Comparable,V> - Interface in org.dishevelled.bio.range.entrytree: Entry in a range tree.
reverseOrderingByLowerEndpoint() - Static method in class org.dishevelled.bio.range.Ranges: Return a reverse ordering by lower endpoint over ranges.
reverseOrderingByUpperEndpoint() - Static method in class org.dishevelled.bio.range.Ranges: Return a reverse ordering by upper endpoint over ranges.

S

singleton(N) - Static method in class org.dishevelled.bio.range.rtree.RangeGeometries: Create and return a new point geometry from the specified singleton value.
size() - Method in class org.dishevelled.bio.range.entrytree.CenteredRangeTree
size() - Method in interface org.dishevelled.bio.range.entrytree.RangeTree: Return the number of range entries in this range tree.
size() - Method in class org.dishevelled.bio.range.tree.CenteredRangeTree
size() - Method in class org.dishevelled.bio.range.tree.RangeList
size() - Method in interface org.dishevelled.bio.range.tree.RangeTree: Return the number of ranges in this range tree.

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