Tree edit distance using the Zhang Shasha algorithm

Project Description
## Zhang-Shasha: Tree edit distance in Python

## Installation

## Usage

## Specifying Custom Tree Formats

### Example

## References

Release History
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The `zss` module provides a function (`zss.distance`) that
computes the edit distance between the two given trees, as well as a small set
of utilities to make its use convenient.

If you’d like to learn more about how it works, see References below.

Brought to you by Tim Henderson (tim.tadh@gmail.com) and Steve Johnson (steve@steveasleep.com).

You can get `zss` and its soft requirements (
`editdist` and `numpy` >= 1.7) from PyPI:

pip install zss

Both modules are optional. `editdist` uses string edit distance to
compare node labels rather than a simple equal/not-equal check, and
`numpy` significantly speeds up the library. The only reason version
1.7 of `numpy` is required is that earlier versions have trouble
installing on current versions of Mac OS X.

You can install `zss` from the source code without dependencies in the
usual way:

python setup.py install

If you want to build the docs, you’ll need to install Sphinx >= 1.0.

To compare the distance between two trees, you need:

- A tree.
- Another tree.
- A node-node distance function. By default,
`zss`compares the edit distance between the nodes’ labels.`zss`currently only knows how to handle nodes with string labels. - Functions to let
`zss.distance`traverse your tree.

Here is an example using the library’s built-in default node structure and edit distance function

from zss import simple_distance, Node A = ( Node("f") .addkid(Node("a") .addkid(Node("h")) .addkid(Node("c") .addkid(Node("l")))) .addkid(Node("e")) ) B = ( Node("f") .addkid(Node("a") .addkid(Node("d")) .addkid(Node("c") .addkid(Node("b")))) .addkid(Node("e")) ) assert simple_distance(A, B) == 2

Specifying custom tree formats and distance metrics is easy. The
`zss.simple_distance` function takes 3 extra parameters besides the two tree
to compare:

`get_children`- a function to retrieve a list of children from a node.`get_label`- a function to retrieve the label object from a node.`label_dist`- a function to compute the non-negative integer distance between two node labels.

#!/usr/bin/env python import zss try: from editdist import distance as strdist except ImportError: def strdist(a, b): if a == b: return 0 else: return 1 def weird_dist(A, B): return 10*strdist(A, B) class WeirdNode(object): def __init__(self, label): self.my_label = label self.my_children = list() @staticmethod def get_children(node): return node.my_children @staticmethod def get_label(node): return node.my_label def addkid(self, node, before=False): if before: self.my_children.insert(0, node) else: self.my_children.append(node) return self A = ( WeirdNode("f") .addkid(WeirdNode("d") .addkid(WeirdNode("a")) .addkid(WeirdNode("c") .addkid(WeirdNode("b")) ) ) .addkid(WeirdNode("e")) ) B = ( WeirdNode("f") .addkid(WeirdNode("c") .addkid(WeirdNode("d") .addkid(WeirdNode("a")) .addkid(WeirdNode("b")) ) ) .addkid(WeirdNode("e")) ) dist = zss.simple_distance( A, B, WeirdNode.get_children, WeirdNode.get_label, weird_dist) print dist assert dist == 20

The algorithm used by `zss` is taken directly from the original paper by
Zhang and Shasha. If you would like to discuss the paper, or the the tree edit
distance problem (we have implemented a few other algorithms as well) please
email the authors.

approxlib by Dr. Nikolaus Augstent contains a good Java implementation of Zhang-Shasha as well as a number of other useful tree distance algorithms.

Kaizhong Zhang and Dennis Shasha. Simple fast algorithms for the editing distance between trees and related problems. SIAM Journal of Computing, 18:1245–1262, 1989. (the original paper)

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File Name & Checksum SHA256 Checksum Help | Version | File Type | Upload Date |
---|---|---|---|

zss-1.1.4.tar.gz (8.7 kB) Copy SHA256 Checksum SHA256 | – | Source | May 26, 2016 |