An interval tree data structure
Project description
# itree
`itree` is an interval tree data structure based on a self-balancing AVL binary search tree tree.
Suitable for use with sequence features in bioinformatics.
## Getting Started
* **Construction**
Creating an interval tree object:
```python
>>> import itree
>>> t = itree.ITree()
```
* **Insertion**
Any item inserted into an interval tree must contain "start" and "end" attributes as integers.
```python
>>> import collections
>>> i = collections.namedtuple('MyInterval', ['start','end'])
>>> t.insert(i(1,15))
>>> t.insert(i(3,20))
>>> t.insert(i(4,20))
>>> t.insert(i(5,15))
>>> t.insert(i(6,7))
```
* **Search**
Search for all intervals overlapping a given interval
```python
>>> t.search(i(1,4))
[MyInterval(start=3, end=20), MyInterval(start=4, end=20), MyInterval(start=1, end=15)]
```
* **Removal**
Remove an interval exactly matching the given interval by its `start` and `end` attributes (but not necessarily the
same object).
```python
>>> t.pstring()
┌–(1,15)
–(3,20)
┌–(4,20)
└–(5,15)
└–(6,7)
>>> t.remove(i(1,15))
>>> t.pstring()
┌–(3,20)
└–(4,20)
–(5,15)
└–(6,7)
```
The `pstring` method is mostly for debugging, but here we illustrate the rebalancing of the tree.
`itree` is an interval tree data structure based on a self-balancing AVL binary search tree tree.
Suitable for use with sequence features in bioinformatics.
## Getting Started
* **Construction**
Creating an interval tree object:
```python
>>> import itree
>>> t = itree.ITree()
```
* **Insertion**
Any item inserted into an interval tree must contain "start" and "end" attributes as integers.
```python
>>> import collections
>>> i = collections.namedtuple('MyInterval', ['start','end'])
>>> t.insert(i(1,15))
>>> t.insert(i(3,20))
>>> t.insert(i(4,20))
>>> t.insert(i(5,15))
>>> t.insert(i(6,7))
```
* **Search**
Search for all intervals overlapping a given interval
```python
>>> t.search(i(1,4))
[MyInterval(start=3, end=20), MyInterval(start=4, end=20), MyInterval(start=1, end=15)]
```
* **Removal**
Remove an interval exactly matching the given interval by its `start` and `end` attributes (but not necessarily the
same object).
```python
>>> t.pstring()
┌–(1,15)
–(3,20)
┌–(4,20)
└–(5,15)
└–(6,7)
>>> t.remove(i(1,15))
>>> t.pstring()
┌–(3,20)
└–(4,20)
–(5,15)
└–(6,7)
```
The `pstring` method is mostly for debugging, but here we illustrate the rebalancing of the tree.
Project details
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
itree-0.0.2.tar.gz
(6.5 kB
view hashes)
Built Distribution
itree-0.0.2-py3-none-any.whl
(8.0 kB
view hashes)