jeetsukumaran

#include <iostream>
#include <vector>

int main(int, char* []) {
    std::vector<int> a(10000000, 10);
    std::vector<int> b;
    b.reserve(10000000);
    b.insert(b.end(), a.begin(), a.end());
}

jeetsukumaran

#! /bin/sh

BUILD_TYPE="release"
PROGRAM_LABEL=""
for arg in $@
do
    if [[ $arg = debug ]]
    then
        BUILD_TYPE="debug"
    elif [[ $arg = profil* ]]

jeetsukumaran

#! /usr/bin/env python

import re
import dendropy as dpy

BEAST_NODE_INFO_PATTERN = re.compile(r'(.+?)=({.+?,.+?}|.+?)(,|$)')

BEAST_SUMMARY_TREE_NODE_FIELDS = [
        'height',
        'height_median',

jeetsukumaran

#! /usr/bin/env python

import dendropy
from dendropy import treesplit
from dendropy.interop import paup

trees = dendropy.TreeList.get_from_path('smallwt.nex', 'nexus')
taxa = trees.taxon_set
tax_labels, bipartitions, bipartition_counts, bipartition_freqs = paup.bipartitions("weightedtrees.taxa.nex", "weightedtrees.nex", use_tree_weights=True)
split_dists_paup = paup.build_split_distribution(bipartition_counts,

jeetsukumaran

#! /bin/bash

if [[ -z $1 ]]
then
    if [[ -z $VIMRUNTIME ]]
    then
        VIMRUNTIME=$HOME/.vim
    fi
else
    VIMRUNTIME="$1"

jeetsukumaran

#! /usr/bin/env python

###############################################################################
##
##  Copyright 2011 Jeet Sukumaran.
##
##  This program is free software; you can redistribute it and/or modify
##  it under the terms of the GNU General Public License as published by
##  the Free Software Foundation; either version 3 of the License, or
##  (at your option) any later version.

jeetsukumaran

#! /usr/bin/env python

from dendropy.interop import ncbi

entrez = ncbi.Entrez(generate_labels=True,
            label_num_desc_components=2,
            label_separator='_',
            exclude_gbnum_from_label=True,
            sort_taxa_by_label=True)

jeetsukumaran

#! /usr/bin/env python

import os
import sys
import dendropy

src_filepath = sys.argv[1]
full_data = dendropy.DnaCharacterMatrix.get_from_path(src_filepath, 'nexus')
items = full_data.character_subsets.items()
basename = os.path.splitext(os.path.basename(src_filepath))[0]

jeetsukumaran

#! /bin/bash

if [[ -z $1 ]]
then
    echo "require version number (e.g. "2.2.4") as argument"
    exit
fi
VERSION="$1"
NOW=$(date +"%Y%b%d")
SRC="satesrc-v$VERSION-$NOW"

jeetsukumaran

#! /bin/bash

compose_name() {
    if [[ $(which git 2> /dev/null) ]]
    then
        STATUS=$(git status 2>/dev/null)
        if [[ -z $STATUS ]]
        then
            return
        fi