[Biopython-dev] Fwd: [biopython] trie - reducing memory use (#19)

[Peter Cock]

Who's the best person to review this Bio.Trie change?

Peter

---------- Forwarded message ----------
From: timwintle
<reply+i-1763187-df3c67d017837136f6a3b53ee6b9afec9716ab9b at reply.github.com>
Date: Wed, Sep 28, 2011 at 11:34 AM
Subject: [biopython] trie - reducing memory use (#19)
To: Peter Cock <p.j.a.cock at googlemail.com>


This adds space for static 1-charater strings which are used for
transitions in the trie implementation - which avoids multiple
allocations for the same string.

Over a large (dense) set of 8-character strings, I observed memory use
reduced from 388M to 283M after this change.

You can merge this Pull Request by running:

 git pull https://github.com/timwintle/biopython trie-memory-use

Or you can view, comment on it, or merge it online at:

 https://github.com/biopython/biopython/pull/19

-- Commit Summary --

* Pre-allocation of single char strings
* Removing old functions

-- File Changes --

M Bio/trie.c (113)
M Bio/triemodule.c (1)

-- Patch Links --

 https://github.com/biopython/biopython/pull/19.patch
 https://github.com/biopython/biopython/pull/19.diff

--
Reply to this email directly or view it on GitHub:
https://github.com/biopython/biopython/pull/19