intervaltree 0.14.0

Interval Tree implementations.


To use this package, run the following command in your project's root directory:

intervaltree

intervaltree provides 3 implementations of an interval tree structure:

  1. Augmented AVL tree
  2. Augmented Splay tree
  3. Implicit Interval Tree

A classic Red-Black tree is not included but would be welcomed.

In addition to the package module itself, which includes a "BasicInterval" struct and an "overlaps" function, the package includes 3 sub-modules, one for each of the tree types listed above:

intervaltree.avltree intervaltree.splaytree intervaltree.iitree

Simply include intervaltree.<treetype> in your code.

Overview

Each tree is implemented as a container type. So, in addition to [start,end) interval coordinates, it may contain other data.

API (unstable until 1.0.0)

Encapsulating Struct, templated on "IntervalType", containing ValueType IntervalType or a pointer to it (in the case of IITree)

Operations implemented in various combinations across the 3 tree types: insert remove find findOverlapsWith findMin

Planned: ForwardRange interface

Brief discussion of interval trees and relative tradeoffs

https://en.wikipedia.org/wiki/Interval_tree

https://en.wikipedia.org/wiki/Red%E2%80%93blacktree https://en.wikipedia.org/wiki/AVLtree https://en.wikipedia.org/wiki/Splay_tree https://github.com/lh3/cgranges

Red-Black trees are relatively well-balanced, but not perfectly so. Insertion is fastest; query is slightly slower than AVL tree due to imperfect balance, but it is a good compromise and widely used.

AVL trees are more well-balanced than Red-Black trees. This makes insertion slightly slower, but provides the fastest amortized lookups.

Splay trees "splay" the most recently accessed node to the top/root of the tree, so they may become extremely unbalanced. However, this imbalance provides an implicit caching effect when the next insertion, deletion, or lookup is very close in coordinate space to the most recently accessed node. In sequential queries, one may need only to descend a single node from the root. This means for sequentially ordered operations, it can beat the perfectly balanced AVL tree. Random access, on the other hand, can be extremely poor.

Implicit Interval Trees (IIT) store the entire tree in a compact linear array sorted by start position. They were created by Heng Li and implemented as the "cgranges" C library. This library is intended for genome applications, and includes a "contig" parameter. The IIT structure excels at both sequential and random access, with the disadvantage that it must be reindexed (resorted) after any/all inserts or deletes, so it works best with static trees.

Credits

AVL tree based on attractivechaos' klib https://github.com/attractivechaos/klib Splay tree is my own implementation IITree is a D wrapper around Heng Li's cgranges C library, which is included as source https://github.com/lh3/cgranges

Authors:
  • James S Blachly, MD
Dependencies:
emsi_containers
Versions:
0.14.0 2019-Nov-16
0.13.2 2019-Sep-14
0.13.1 2019-Aug-24
0.13.0 2019-Aug-24
0.12.0 2019-Aug-14
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