[Biopython-dev] [Biopython (old issues only) - Bug #2489] (Closed) KDTree NN search without specifying radius

[redmine at redmine.open-bio.org]

Issue #2489 has been updated by Peter Cock.

Description updated
Status changed from New to Closed
% Done changed from 0 to 100

I'm going to close this since the relevant code was re-written and there has been no action on this issue since.

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Bug #2489: KDTree NN search without specifying radius
https://redmine.open-bio.org/issues/2489#change-15404

* Author: sam n
* Status: Closed
* Priority: Normal
* Assignee: Biopython Dev Mailing List
* Category: Main Distribution
* Target version: 1.45
* URL: 
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All the current searches in the KDTree require specifying a radius. If
you don't know what the radius is, you don't know how far to search without taking a typical estimate of the data set.

I just added a function to find the nearest neighbor to a coordinate
without specifying this radius up front.

I made the changes on the C++ side of Biopython's KDTree. 
It might be useful to other people so I will post the update, which is based on
http://www.google.com/codesearch?hl=en&q=+kdtree+show:b099E8j0eYY:M9X8aTw_p7E:Tn8Xj-OBPYY&sa=N&cd=4&ct=rc&cs_p=ftp://ftp.diku.dk/diku/users/martinz/tabu.tar.gz&cs_f=kdtree.c#first

However, I am not currently proficient in the Python C API, so someone else may
be able to write the interface in 3 minutes...

---Files--------------------------------
KDTree.cpp (19.4 KB)
KDTree.h (4.03 KB)


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