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<?php
//
// Copyright 2010-2016, Julian Catchen <jcatchen@illinois.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/>.
//
require_once("Locus.php");
class Catalog {
var $db; // Hash of database statement handles.
var $display; // An array of form variables necessary to write URLs.
var $params; // An array of parameters to fetch our results from the database.
var $queries; // An array of SQL queries.
var $loci; // Array of groups objects.
var $num_loci; // Total number of groups, after filtering
function Catalog($db, $batch_id, $display_params) {
$this->db = $db;
$this->batch = $batch_id;
$this->display = $display_params;
$this->queries = array();
$this->params = array();
$this->loci = array();
$this->num_loci = 0;
$this->prepare_queries();
}
function prepare_queries() {
$query =
"SELECT allele FROM catalog_alleles " .
"WHERE batch_id=? AND tag_id=?";
if (!($this->db['allele_sth'] = $this->db['dbh']->prepare($query)))
write_db_error($this->db['dbh'], __FILE__, __LINE__);
$query =
"SELECT col, rank_1, rank_2 FROM catalog_snps " .
"WHERE batch_id=? AND tag_id=? ORDER BY col";
if (!($this->db['snp_sth'] = $this->db['dbh']->prepare($query)))
write_db_error($this->db['dbh'], __FILE__, __LINE__);
$query =
"SELECT samples.id, samples.sample_id, samples.type, file, tag_id, allele " .
"FROM matches " .
"JOIN samples ON (matches.sample_id=samples.id) " .
"WHERE matches.batch_id=? AND catalog_id=? ORDER BY samples.id";
if (!($this->db['mat_sth'] = $this->db['dbh']->prepare($query)))
write_db_error($this->db['dbh'], __FILE__, __LINE__);
$query =
"SELECT COUNT(tag_id) as count FROM catalog_index " .
"WHERE batch_id=?";
$query .= $this->apply_query_filters();
$this->queries['tag_count'] = $query;
$query =
"SELECT catalog_index.tag_id as tag_id, chr, bp, snps, alleles, parents, progeny, valid_progeny, " .
"seq, marker, max_pct, ratio, ests, pe_radtags, blast_hits, external_id " .
"FROM catalog_index " .
"JOIN catalog_tags ON (catalog_index.cat_id=catalog_tags.id) " .
"LEFT JOIN catalog_annotations ON " .
"(" .
"catalog_index.batch_id=catalog_annotations.batch_id AND " .
"catalog_index.tag_id=catalog_annotations.catalog_id" .
") " .
"WHERE catalog_index.batch_id=?";
$query .= $this->apply_query_filters();
$this->queries['tag'] = $query;
}
function prepare_filter_parameters() {
$this->params[] = &$this->batch;
$typestr = "i";
$filters = $this->display['filter_type'];
if (!isset($filters)) {
array_unshift($param, $typestr);
return;
}
foreach ($filters as $filter) {
if ($filter == "snps") {
$this->params[] = &$this->display['filter_snps_l'];
$this->params[] = &$this->display['filter_snps_u'];
$typestr .= "ii";
} else if ($filter == "alle") {
$this->params[] = &$this->display['filter_alle_l'];
$this->params[] = &$this->display['filter_alle_u'];
$typestr .= "ii";
} else if ($filter == "pare") {
$this->params[] = &$this->display['filter_pare_l'];
$this->params[] = &$this->display['filter_pare_u'];
$typestr .= "ii";
} else if ($filter == "prog") {
$this->params[] = &$this->display['filter_prog'];
$typestr .= "i";
} else if ($filter == "vprog") {
$this->params[] = &$this->display['filter_vprog'];
$typestr .= "i";
} else if ($filter == "lnl") {
$this->params[] = &$this->display['filter_lnl_l'];
$this->params[] = &$this->display['filter_lnl_u'];
$typestr .= "ii";
} else if ($filter == "cata") {
$this->params[] = &$this->display['filter_cata'];
$typestr .= "i";
} else if ($filter == "gcnt") {
$this->params[] = &$this->display['filter_gcnt'];
$typestr .= "i";
} else if ($filter == "ref") {
$this->params[] = &$this->display['filter_ref'];
$typestr .= "i";
} else if ($filter == "loc") {
$this->params[] = &$this->display['filter_chr'];
$this->params[] = &$this->display['filter_sbp'];
$this->params[] = &$this->display['filter_ebp'];
$typestr .= "sii";
} else if ($filter == "mark") {
$this->params[] = &$this->display['filter_mark'];
}
}
array_unshift($this->params, $typestr);
}
function apply_query_filters() {
$sql_filters =
array("cata" => "(catalog_index.tag_id = ?)",
"alle" => "(alleles >= ? AND alleles <= ?)",
"snps" => "(snps >= ? AND snps <= ?)",
"pare" => "(parents >= ? AND parents <= ?)",
"prog" => "(progeny >= ?)",
"vprog" => "(valid_progeny >= ?)",
"lnl" => "(lnl >= ? AND lnl <= ?)",
"mark" => "(marker LIKE ?)",
"est" => "(ests > 0)",
"pe" => "(pe_radtags > 0)",
"blast" => "(blast_hits > 0)",
"gcnt" => "(geno_cnt >= ?)",
"ref" => "(catalog_index.type = ?)",
"loc" => "(catalog_index.chr = ? && catalog_index.bp >= ? && catalog_index.bp <= ?)");
$filters = $this->display['filter_type'];
if (count($filters) > 0) {
$query = " AND ";
while (count($filters) > 0) {
$filter = array_shift($filters);
$query .= $sql_filters[$filter];
$query .= count($filters) > 0 ? " AND " : "";
}
}
return $query;
}
function &loci() {
return $this->loci;
}
function &locus($id) {
return $this->loci[$id];
}
function num_loci() {
return $this->num_loci;
}
function determine_count() {
if (!($this->db['tag_count_sth'] = $this->db['dbh']->prepare($this->queries['tag_count'])))
write_db_error($this->db['dbh'], __FILE__, __LINE__);
$this->prepare_filter_parameters();
array_unshift($this->params, $this->db['tag_count_sth']);
call_user_func_array("mysqli_stmt_bind_param", $this->params);
array_shift($this->params);
if (!$this->db['tag_count_sth']->execute())
write_db_error($this->db['tag_count_sth'], __FILE__, __LINE__);
$res = $this->db['tag_count_sth']->get_result();
$row = $res->fetch_assoc();
$this->num_loci = $row['count'];
}
function populate($start_group, $num_groups) {
//
// We only want to load genes between $start_gene and $end_gene.
//
$this->queries['tag'] .= " LIMIT " . $start_group . ", " . $num_groups;
if (!($this->db['tag_sth'] = $this->db['dbh']->prepare($this->queries['tag'])))
write_db_error($this->db['dbh'], __FILE__, __LINE__);
$this->prepare_filter_parameters();
//
// Fetch the results and populate the array of groups.
//
array_unshift($this->params, $this->db['tag_sth']);
call_user_func_array("mysqli_stmt_bind_param", $this->params);
array_shift($this->params);
if (!$this->db['tag_sth']->execute())
write_db_error($this->db['tag_sth'], __FILE__, __LINE__);
$res = $this->db['tag_sth']->get_result();
while ($row = $res->fetch_assoc()) {
$locus = new Locus();
$locus->id = $row['tag_id'];
$locus->annotation = $row['external_id'];
$locus->chr = $row['chr'];
$locus->bp = $row['bp'];
$locus->marker = $row['marker'];
$locus->seq = $row['seq'];
$locus->num_alleles = $row['alleles'];
$locus->num_snps = $row['snps'];
$locus->num_parents = $row['parents'];
$locus->num_progeny = $row['progeny'];
$locus->valid_progeny = $row['valid_progeny'];
$locus->num_ests = $row['ests'];
$locus->num_pe_tags = $row['pe_radtags'];
$locus->num_blast = $row['blast_hits'];
//
// Fetch SNPs and Alleles
//
if (!$this->db['snp_sth']->bind_param("ii", $this->batch, $locus->id))
write_db_error($db['snp_sth'], __FILE__, __LINE__);
if (!$this->db['snp_sth']->execute())
write_db_error($db['snp_sth'], __FILE__, __LINE__);
$snp_res = $this->db['snp_sth']->get_result();
while ($snp_row = $snp_res->fetch_assoc()) {
$locus->snps .= $snp_row['col'] . "," . $snp_row['rank_1'] . ">" . $snp_row['rank_2'] . ";";
}
$locus->snps = substr($locus->snps, 0, -1);
if (!$this->db['all_sth']->bind_param("ii", $this->batch, $locus->id))
write_db_error($db['all_sth'], __FILE__, __LINE__);
if (!$this->db['all_sth']->execute())
write_db_error($db['all_sth'], __FILE__, __LINE__);
$all_res = $this->db['all_sth']->get_result();
while ($all_row = $all_res->fetch_assoc()) {
$locus->alleles .= $all_row['allele'] . ";";
}
$locus->alleles = substr($locus->alleles, 0, -1);
//
// Add genotypes
//
if (!$this->db['mat_sth']->bind_param("ii", $this->batch, $locus->id))
write_db_error($db['mat_sth'], __FILE__, __LINE__);
if (!$this->db['mat_sth']->execute())
write_db_error($db['mat_sth'], __FILE__, __LINE__);
$gen_res = $this->db['mat_sth']->get_result();
while ($gen_row = $gen_res->fetch_assoc())
$locus->add_genotype($gen_row['id'], $gen_row['file'], $gen_row['allele']);
$this->loci[$row['tag_id']] = $locus;
}
}
}
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