/usr/share/stacks/php/Locus.php is in stacks-web 1.35-1ubuntu1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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//
// Copyright 2010, Julian Catchen <jcatchen@uoregon.edu>
//
// This file is part of Stacks.
//
// Stacks 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.
//
// Stacks is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
// GNU General Public License for more details.
//
// You should have received a copy of the GNU General Public License
// along with Stacks. If not, see <http://www.gnu.org/licenses/>.
//
class Locus {
var $id;
var $seq;
var $annotation;
var $chr;
var $bp;
var $snps;
var $alleles;
var $genotypes; // Array of samples that possess this locus
var $num_parents;
var $num_progeny;
var $num_snps;
var $num_alleles;
var $num_ests;
var $num_pe_tags;
var $num_blast;
var $valid_progeny;
var $marker;
function Locus() {
$this->genotypes = array();
$this->annotation = "";
$this->chr = "";
$this->bp = 0;
$this->marker = "";
$this->snps = "";
$this->alleles = "";
$this->num_parents = 0;
$this->num_progeny = 0;
$this->valid_progeny = 0;
$this->num_alleles = 0;
$this->num_snps = 0;
$this->num_ests = 0;
$this->num_pe_tags = 0;
$this->num_blast = 0;
}
function &genotypes() {
return $this->genotypes;
}
function &genotype($id) {
if (isset($this->genotypes[$id]))
return $this->genotypes[$id];
else
return NULL;
}
function add_genotype($id, $file, $allele) {
$a = array('file' => $file,
'allele' => $allele,
'tag_id' => $id);
if (!isset($this->genotypes[$file]))
$this->genotypes[$file] = array();
array_push($this->genotypes[$file], $a);
}
}
?>
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