Editable interval tree data structure for Python 2 and 3
Project description
intervaltree
A mutable, self-balancing interval tree for Python 2 and 3. Queries may be by point, by range overlap, or by range envelopment.
This library was designed to allow tagging text and time intervals, where the intervals include the lower bound but not the upper bound.
Installing
pip install intervaltree
Features
Supports Python 2.6+ and Python 3.2+
Initializing
blank tree = IntervalTree()
from an iterable of Interval objects (tree = IntervalTree(intervals))
from an iterable of tuples (tree = IntervalTree.from_tuples(interval_tuples))
Insertions
tree[begin:end] = data
tree.add(interval)
tree.addi(begin, end, data)
Deletions
tree.remove(interval) (raises ValueError if not present)
tree.discard(interval) (quiet if not present)
tree.removei(begin, end, data) (short for tree.remove(Interval(begin, end, data)))
tree.discardi(begin, end, data) (short for tree.discard(Interval(begin, end, data)))
tree.remove_overlap(point)
tree.remove_overlap(begin, end) (removes all overlapping the range)
tree.remove_envelop(begin, end) (removes all enveloped in the range)
Overlap queries
tree[point]
tree[begin:end]
tree.search(point)
tree.search(begin, end)
Envelop queries
tree.search(begin, end, strict=True)
Membership queries
interval_obj in tree (this is fastest, O(1))
tree.containsi(begin, end, data)
tree.overlaps(point)
tree.overlaps(begin, end)
Iterable
for interval_obj in tree:
tree.items()
Sizing
len(tree)
tree.is_empty()
not tree
tree.begin() (the begin coordinate of the leftmost interval)
tree.end() (the end coordinate of the rightmost interval)
Set-like operations
union
result_tree = tree.union(iterable)
result_tree = tree1 | tree2
tree.update(iterable)
tree |= other_tree
difference
result_tree = tree.difference(iterable)
result_tree = tree1 - tree2
tree.difference_update(iterable)
tree -= other_tree
intersection
result_tree = tree.intersection(iterable)
result_tree = tree1 & tree2
tree.intersection_update(iterable)
tree &= other_tree
symmetric difference
result_tree = tree.symmetric_difference(iterable)
result_tree = tree1 ^ tree2
tree.symmetric_difference_update(iterable)
tree ^= other_tree
comparison
tree1.issubset(tree2) or tree1 <= tree2
tree1 <= tree2
tree1.issuperset(tree2) or tree1 > tree2
tree1 >= tree2
tree1 == tree2
Restructuring
chop(begin, end) (slice intervals and remove everything between begin and end)
slice(point) (slice intervals at point)
split_overlaps() (slice at all interval boundaries)
Copying and typecasting
IntervalTree(tree) (Interval objects are same as those in tree)
tree.copy() (Interval objects are shallow copies of those in tree)
set(tree) (can later be fed into IntervalTree())
list(tree) (ditto)
Pickle-friendly
Automatic AVL balancing
Examples
Getting started
>>> from intervaltree import Interval, IntervalTree >>> t = IntervalTree() >>> t IntervalTree()
Adding intervals - any object works!
>>> t[1:2] = "1-2" >>> t[4:7] = (4, 7) >>> t[5:9] = {5: 9}
Query by point
The result of a query is a set object, so if ordering is important,you must sort it first.>>> sorted(t[6]) [Interval(4, 7, (4, 7)), Interval(5, 9, {5: 9})] >>> sorted(t[6])[0] Interval(4, 7, (4, 7))
Query by range
Note that ranges are inclusive of the lower limit, but non-inclusive of the upper limit. So:
>>> sorted(t[2:4]) []
But:
>>> sorted(t[1:5]) [Interval(1, 2, '1-2'), Interval(4, 7, (4, 7))]
Accessing an Interval object
>>> iv = Interval(4, 7, (4, 7)) >>> iv.begin 4 >>> iv.end 7 >>> iv.data (4, 7) >>> begin, end, data = iv >>> begin 4 >>> end 7 >>> data (4, 7)
Constructing from lists of intervals
We could have made a similar tree this way:
>>> ivs = [(1, 2), (4, 7), (5, 9)] >>> t = IntervalTree( ... Interval(begin, end, "%d-%d" % (begin, end)) for begin, end in ivs ... )
Or, if we don’t need the data fields:
>>> t2 = IntervalTree(Interval(*iv) for iv in ivs)
Removing intervals
>>> t.remove( Interval(1, 2, "1-2") ) >>> sorted(t) [Interval(4, 7, '4-7'), Interval(5, 9, '5-9')] >>> t.remove( Interval(500, 1000, "Doesn't exist")) # raises ValueError Traceback (most recent call last): ValueError >>> t.discard(Interval(500, 1000, "Doesn't exist")) # quietly does nothing >>> del t[5] # same as t.remove_overlap(5) >>> t IntervalTree()
We could also empty a tree entirely:
>>> t2.clear() >>> t2 IntervalTree()
Or remove intervals that overlap a range:
>>> t = IntervalTree([ ... Interval(0, 10), ... Interval(10, 20), ... Interval(20, 30), ... Interval(30, 40)]) >>> t.remove_overlap(25, 35) >>> sorted(t) [Interval(0, 10), Interval(10, 20)]
We can also remove only those intervals completely enveloped in a range:
>>> t.remove_envelop(5, 20) >>> sorted(t) [Interval(0, 10)]
Chopping
We could also chop out parts of the tree:
>>> t = IntervalTree([Interval(0, 10)]) >>> t.chop(3, 7) >>> sorted(t) [Interval(0, 3), Interval(7, 10)]
To modify the new intervals’ data fields based on which side of the interval is being chopped:
>>> def datafunc(iv, islower): ... oldlimit = iv[islower] ... return "oldlimit: {0}, islower: {1}".format(oldlimit, islower) >>> t = IntervalTree([Interval(0, 10)]) >>> t.chop(3, 7, datafunc) >>> sorted(t)[0] Interval(0, 3, 'oldlimit: 10, islower: True') >>> sorted(t)[1] Interval(7, 10, 'oldlimit: 0, islower: False')
Slicing
You can also slice intervals in the tree without removing them:
>>> t = IntervalTree([Interval(0, 10), Interval(5, 15)]) >>> t.slice(3) >>> sorted(t) [Interval(0, 3), Interval(3, 10), Interval(5, 15)]
You can also set the data fields, for example, re-using datafunc() from above:
>>> t = IntervalTree([Interval(5, 15)]) >>> t.slice(10, datafunc) >>> sorted(t)[0] Interval(5, 10, 'oldlimit: 15, islower: True') >>> sorted(t)[1] Interval(10, 15, 'oldlimit: 5, islower: False')
Future improvements
See the issue tracker on GitHub.
Based on
Eternally Confuzzled’s AVL tree
Wikipedia’s Interval Tree
Heavily modified from Tyler Kahn’s Interval Tree implementation in Python (GitHub project)
Incorporates modifications by konstantint
Copyright
Chaim-Leib Halbert, 2013-2015
Modifications, Konstantin Tretyakov, 2014
Licensed under the Apache License, version 2.0.
The source code for this project is at https://github.com/chaimleib/intervaltree
Change log
Version 2.0.4
Fix: Issue #27: README incorrectly showed using a comma instead of a colon when querying the IntervalTree: it showed tree[begin, end] instead of tree[begin:end]
Version 2.0.3
Fix: README showed using + operator for setlike union instead of the correct | operator
Removed tests from release package to speed up installation; to get the tests, download from GitHub
Version 2.0.2
Fix: Issue #20: performance enhancement for large trees. IntervalTree.search() made a copy of the entire boundary_table resulting in linear search time. The sortedcollections package is now the sole install dependency
Version 2.0.1
Fix: Issue #26: failed to prune empty Node after a rotation promoted contents of s_center
Version 2.0.0
IntervalTree now supports the full collections.MutableSet API
Added:
__delitem__ to IntervalTree
Interval comparison methods lt(), gt(), le() and ge() to Interval, as an alternative to the comparison operators, which are designed for sorting
IntervalTree.from_tuples(iterable)
IntervalTree.clear()
IntervalTree.difference(iterable)
IntervalTree.difference_update(iterable)
IntervalTree.union(iterable)
IntervalTree.intersection(iterable)
IntervalTree.intersection_update(iterable)
IntervalTree.symmetric_difference(iterable)
IntervalTree.symmetric_difference_update(iterable)
IntervalTree.chop(a, b)
IntervalTree.slice(point)
Deprecated IntervalTree.extend() – use update() instead
Internal improvements:
More verbose tests with progress bars
More tests for comparison and sorting behavior
Code in the README is included in the unit tests
Fixes
BACKWARD INCOMPATIBLE: On ranged queries where begin >= end, the query operated on the overlaps of begin. This behavior was documented as expected in 1.x; it is now changed to be more consistent with the definition of Intervals, which are half-open.
Issue #25: pruning empty Nodes with staggered descendants could result in invalid trees
Sorting Intervals and numbers in the same list gathered all the numbers at the beginning and the Intervals at the end
IntervalTree.overlaps() and friends returned None instead of False
Maintainers: make install-testpypi failed because the pip was missing a --pre flag
Version 1.1.1
Removed requirement for pyandoc in order to run functionality tests.
Version 1.1.0
Added ability to use Interval.distance_to() with points, not just Intervals
Added documentation on return types to IntervalTree and Interval
Interval.__cmp__() works with points too
Fix: IntervalTree.score() returned maximum score of 0.5 instead of 1.0. Now returns max of subscores instead of avg
Internal improvements:
Development version numbering scheme, based on git describe the “building towards” release is appended after a hyphen, eg. 1.0.2-37-g2da2ef0-1.10. The previous tagged release is 1.0.2, and there have been 37 commits since then, current tag is g2da2ef0, and we are getting ready for a 1.1.0 release
Optimality tests added
Interval overlap tests for ranges, Intervals and points added
Version 1.0.2
Version 1.0.1
Fix: pip install failure because of failure to generate README.rst
Version 1.0.0
Renamed from PyIntervalTree to intervaltree
Speed improvements for adding and removing Intervals (~70% faster than 0.4)
Bug fixes:
BACKWARD INCOMPATIBLE: len() of an Interval is always 3, reverting to default behavior for namedtuples. In Python 3, len returning a non-integer raises an exception. Instead, use Interval.length(), which returns 0 for null intervals and end - begin otherwise. Also, if the len() === 0, then not iv is True.
When inserting an Interval via __setitem__ and improper parameters given, all errors were transformed to IndexError
split_overlaps did not update the boundary_table counts
Internal improvements:
More robust local testing tools
Long series of interdependent tests have been separated into sections
Version 0.4
Faster balancing (~80% faster)
Bug fixes:
Double rotations were performed in place of a single rotation when presented an unbalanced Node with a balanced child.
During single rotation, kept referencing an unrotated Node instead of the new, rotated one
Version 0.3.3
Made IntervalTree crash if inited with a null Interval (end <= begin)
IntervalTree raises ValueError instead of AssertionError when a null Interval is inserted
Version 0.3.2
Support for Python 3.2+ and 2.6+
Changed license from LGPL to more permissive Apache license
Merged changes from https://github.com/konstantint/PyIntervalTree to https://github.com/chaimleib/PyIntervalTree
Interval now inherits from a namedtuple. Benefits: should be faster. Drawbacks: slight behavioural change (Intervals not mutable anymore).
Added float tests
Use setup.py for tests
Automatic testing via travis-ci
Removed dependency on six
Interval improvements:
Intervals without data have a cleaner string representation
Intervals without data are pickled more compactly
Better hashing
Intervals are ordered by begin, then end, then by data. If data is not orderable, sorts by type(data)
Bug fixes:
Fixed crash when querying empty tree
Fixed missing close parenthesis in examples
Made IntervalTree crash earlier if a null Interval is added
Internals:
New test directory
Nicer display of data structures for debugging, using custom test/pprint.py (Python 2.6, 2.7)
More sensitive exception handling
Local script to test in all supported versions of Python
Added IntervalTree.score() to measure how optimally a tree is structured
Version 0.2.3
Slight changes for inclusion in PyPI.
Some documentation changes
Added tests
Bug fix: interval addition via [] was broken in Python 2.7 (see http://bugs.python.org/issue21785)
Added intervaltree.bio subpackage, adding some utilities for use in bioinformatics
Version 0.2.2b
Forked from https://github.com/MusashiAharon/PyIntervalTree
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