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<?php |
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/* |
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You may not change or alter any portion of this comment or credits of |
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supporting developers from this source code or any supporting source code |
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which is considered copyrighted (c) material of the original comment or credit |
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authors. |
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This program is distributed in the hope that it will be useful, but |
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WITHOUT ANY WARRANTY; without even the implied warranty of |
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. |
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*/ |
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/** |
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* Module: Pedigree |
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* |
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* @package XoopsModules\Pedigree |
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* @author XOOPS Module Development Team |
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* @copyright Copyright (c) 2001-2019 {@link https://xoops.org XOOPS Project} |
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* @license https://www.gnu.org/licenses/gpl-2.0.html GNU Public License |
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*/ |
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use Xmf\Request; |
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use XoopsModules\Pedigree; |
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ini_set('memory_limit', '32M'); |
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//require_once \dirname(__DIR__, 2) . '/mainfile.php'; |
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require_once __DIR__ . '/header.php'; |
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$moduleDirName = basename(__DIR__); |
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xoops_loadLanguage('main', $moduleDirName); |
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require_once XOOPS_ROOT_PATH . '/modules/' . $moduleDirName . '/include/common.php'; |
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$GLOBALS['xoopsOption']['template_main'] = 'pedigree_coi.tpl'; |
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require XOOPS_ROOT_PATH . '/header.php'; |
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//get module configuration |
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/** @var XoopsModuleHandler $moduleHandler */ |
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$moduleHandler = xoops_getHandler('module'); |
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$module = $moduleHandler->getByDirname($moduleDirName); |
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$configHandler = xoops_getHandler('config'); |
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$moduleConfig = $configHandler->getConfigsByCat(0, $module->getVar('mid')); |
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global $xoopsTpl, $xoopsDB, $moduleConfig; |
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//start kinship.php code -- help !! |
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/* ************************************************************************************* */ |
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/* |
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This program calculates the coefficient of inbreeding (IC, or COI, or F) |
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for the offspring of a couple of animals, given by their IDs (s=sire_ID&d=dam_ID), |
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or for a given animal given by its ID (a=animal_ID). |
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By default, all known ascendants are used. |
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However, maximum count of distinct ascendants is limited to $nb_maxi (default=600) |
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[higher values for $nb_maxi could lead to calculations ending in timeout], |
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or depth of tree can be limited to $nb_gen generations (default = 8). |
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*/ |
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/* ************************************************************************************* */ |
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if (!isset($verbose)) { |
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$verbose = 0; |
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} // don't display different steps of ICs calculation |
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if (!isset($detail)) { |
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$detail = 1; |
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} // don't display detail results [faster] |
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if (!isset($nb_maxi)) { |
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$nb_maxi = 600; |
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} // maximum count of distinct ascendants |
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if (!isset($nb_gen)) { |
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$nb_gen = 8; |
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} // maximum count of generations of ascendants |
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if (!isset($pedigree)) { |
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$pedigree = 0; |
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} // dont't display sketch pedigree [faster] |
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if (!isset($max_dist)) { // maximum length of implex loops |
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if ($nb_gen > 9) { |
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$max_dist = 14; |
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} else { |
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if (9 == $nb_gen) { |
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$max_dist = 17; |
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} else { |
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if (8 == $nb_gen) { |
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$max_dist = 18; |
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} else { |
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$max_dist = 99; |
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} |
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} |
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} |
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} |
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$empty = []; // an empty array |
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$sql1 = 'SELECT id, father, mother, roft FROM ' . $GLOBALS['xoopsDB']->prefix('pedigree_registry') . ' WHERE id '; |
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// input data arrays: |
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$IDs = $empty; |
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$fathers = $empty; |
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$mothers = $empty; |
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// working arrays: |
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$inds = $empty; |
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$marked = $empty; |
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$ICknown = $empty; |
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$deltaf = $empty; |
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$pater = $empty; |
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$mater = $empty; |
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$chrono = $empty; |
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// Coefficients of Inbreeding array (result): |
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$COIs = $empty; |
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/* ****************************** FUNCTIONS ********************************* */ |
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/** |
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* @return int |
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*/ |
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function chrono_sort() |
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{ |
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global $IDs, $inds, $fathers, $mothers, $chrono, $nl, $detail; |
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$impr = 0; |
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$modif = 1; |
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$nloop = 0; |
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$nba = count($IDs); |
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// print_r ($IDs) ; |
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// echo "<b>231 : $IDs[231] $fathers[231] $mothers[231] $chrono[231] $inds[231] </b><br>\n" ; |
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foreach ($IDs as $i => $v) { |
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$chrono[$i] = 1; |
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} // initialize all chronological ranks to 1 |
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$chrono[0] = 0; // except animal #0 (at 0 rank). |
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while ($modif && $nloop < 40) { |
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$modif = 0; |
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++$nloop; |
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for ($i = 1; $i < $nba; ++$i) { |
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$s = $fathers[$i]; |
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if ($s) { |
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$s = $inds[$s]; |
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} |
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$d = $mothers[$i]; |
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if ($d) { |
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$d = $inds[$d]; |
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} |
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if ($s && $chrono[$s] <= $chrono[$i]) { |
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$chrono[$s] = $chrono[$i] + 1; |
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$modif = 1; |
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} |
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if ($d && $chrono[$d] <= $chrono[$i]) { |
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$chrono[$d] = $chrono[$i] + 1; |
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$modif = 1; |
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} |
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} |
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} |
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if (40 == $nloop) { |
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die('Endless loop detected. Stopped.'); |
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} |
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array_multisort($chrono, $IDs, $fathers, $mothers); |
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$depth = $chrono[$nba - 1]; |
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//commentes out by JC |
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//if ($detail) echo "<br>Chronological ranking done : Pedigree stretched over <b>$depth</b> generations.<br>$nl" ; |
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if ($impr) { |
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echo "</center><pre>$nl $nl"; |
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foreach ($chrono as $i => $val) { |
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echo "<b>$i</b> : $val $IDs[$i] $fathers[$i] $mothers[$i] $nl"; |
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} |
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echo "</pre>$nl"; |
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die('</html>'); |
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} |
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$inds = array_flip($IDs); |
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return 0; |
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} |
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/** |
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* @param $s |
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* |
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* @return array |
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*/ |
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function fetch_record($s) |
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{ |
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global $database; |
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$r = $GLOBALS['xoopsDB']->queryF($database, $s); |
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$n = 0; |
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if ($r) { |
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$n = $GLOBALS['xoopsDB']->getRowsNum($r); |
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} |
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if (0 == $n) { |
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$record = ['0']; |
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} else { |
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$record = $GLOBALS['xoopsDB']->fetchBoth($r); |
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} |
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return $record; |
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} |
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/** |
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* @param $ind |
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* @param $gen |
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* |
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* @return int |
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*/ |
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function count_all($ind, $gen) |
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{ |
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global $inds, $nb_gen, $nb_all, $fathers, $mothers; |
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if ($ind) { |
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++$nb_all; |
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} |
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$s = $fathers[$ind]; |
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$d = $mothers[$ind]; |
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if ($s && $gen < $nb_gen) { |
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count_all($s, $gen + 1); |
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} |
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if ($d && $gen < $nb_gen) { |
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count_all($d, $gen + 1); |
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} |
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return 0; |
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} |
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/** |
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* @param $ch |
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* @param $niv |
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* |
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* @return int |
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*/ |
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function add_multi($ch, $niv) |
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{ |
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global $implx, $couls, $nl; |
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reset($implx); |
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$first = 1; |
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foreach ($implx as $im => $impl) { |
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if ($impl[0] == $ch || $impl[1] == $ch) { |
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if ($niv > 1 && $first) { |
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echo "<br>$nl"; |
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} else { |
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echo ' '; |
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} |
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$i = $im + 1; |
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$j = min($im, 6); |
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$c = $couls[$j]; |
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$first = 0; |
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echo '<span color=' . $c . ' size="+2"><b>*' . $i . '*</b></span>'; |
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} |
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} |
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return 0; |
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} |
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/** |
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* @param $ind |
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* @param $gen |
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* @param $class |
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* |
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* @return int |
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*/ |
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function output_animal($ind, $gen, $class) |
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{ |
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global $depth, $IDs, $fathers, $mothers, $nl; |
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if ($gen > $depth) { |
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return 0; |
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} |
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$cell_content = 'Ø'; |
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if ($ind || 0 == $gen) { |
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$ID = $IDs[$ind]; |
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$ani = set_name($ID); |
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$name = $ani[1]; |
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$name = $ID; |
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$cell_content = Pedigree\Utility::showParent($name) . $nl; |
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} |
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$rowspan = 1 << ($depth - $gen); |
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echo '<td rowspan=' . $rowspan . ' align="center" class="' . $class . '">' . $cell_content . "</td>$nl"; |
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if ($gen < $depth) { |
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$sire = 0; |
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if ($ind || 0 == $gen) { |
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$sire = $fathers[$ind]; |
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} |
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output_animal($sire, $gen + 1, '0'); |
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$dam = 0; |
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if ($ind || 0 == $gen) { |
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$dam = $mothers[$ind]; |
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} |
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output_animal($dam, $gen + 1, '1'); |
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} else { |
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echo "</tr><tr>$nl"; |
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} |
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return 0; |
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} |
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/** |
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* @return int |
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*/ |
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function SKETCH_PEDIGREE() |
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{ |
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global $nl, $detail, $depth, $IDs; |
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// print_r ($IDs) ; |
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echo $nl |
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. '<br>' |
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. $nl |
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. '<table border="3" cellpadding="4" width="85%"" cellpadding="0" cellspacing="0">' |
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. $nl |
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. '<tr><th colspan="10" align="center">SKETCH PEDIGREE OF COMMON PROGENY</th></tr>' |
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. $nl |
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. '<tr align="center" valign="middle"><th>Progeny</th><th>' |
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. _('Sire / Dam') |
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. '</th>'; |
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if ($depth >= 2) { |
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echo '<th>' . _('Grandparents') . '</th>' . $nl; |
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} |
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if ($depth >= 3) { |
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echo '<th>' . _('Great-Grandparents') . '</th>' . $nl; |
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} |
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if ($depth >= 4) { |
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echo '<th>3xGr. P.</th>' . $nl; |
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} |
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if ($depth >= 5) { |
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echo '<th>4xGr. P.</th>' . $nl; |
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} |
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if ($depth >= 6) { |
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echo '<th>5xGr. P.</th>' . $nl; |
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} |
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if ($depth >= 7) { |
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echo '<th>6xGr. P.</th>' . $nl; |
|
320
|
|
|
} |
|
321
|
|
|
echo '</tr><tr>'; |
|
322
|
|
|
output_animal(0, 0, '0'); /* output the sketch pedigree */ |
|
323
|
|
|
echo $nl . '</tr></table>' . $nl . '<p>' . $nl; |
|
324
|
|
|
|
|
325
|
|
|
return 0; |
|
326
|
|
|
} |
|
327
|
|
|
|
|
328
|
|
|
/** |
|
329
|
|
|
* @return int |
|
330
|
|
|
*/ |
|
331
|
|
|
function GENEALOGY() |
|
332
|
|
|
{ |
|
333
|
|
|
global $IDs, $fathers, $mothers, $inds, $nb_gen, $nb_maxi, $nbani, $nl, $sql1; |
|
334
|
|
|
$impr = 0; |
|
335
|
|
|
$fathers[0] = $IDs[1]; |
|
336
|
|
|
$mothers[0] = $IDs[2]; |
|
337
|
|
|
$fathers[1] = 0; |
|
338
|
|
|
$mothers[1] = 0; |
|
339
|
|
|
$fathers[2] = 0; |
|
340
|
|
|
$mothers[2] = 0; |
|
341
|
|
|
$last = 2; |
|
342
|
|
|
if ($impr) { |
|
343
|
|
|
echo "<!-- genealogy 'de cujus' (gener. 0) : $IDs[0] = $IDs[1] x $IDs[2] -->$nl"; |
|
344
|
|
|
} |
|
345
|
|
|
$generation = [$IDs[1], $IDs[2]]; // starting with first generation (sire and dam) |
|
346
|
|
|
$nbtot = 0; // count of total known ascendants within $nb_gen generations |
|
347
|
|
|
for ($nloop = 1, $tot = 2; $last <= $nb_maxi && $nloop <= $nb_gen; ++$nloop) { |
|
348
|
|
|
$nbtot += $tot; // count of total known ascendants within $nb_gen generations |
|
349
|
|
|
$nbani = $last; // count of distinct ascendants within $nb_gen generations |
|
350
|
|
|
$list = implode(',', array_unique($generation)); |
|
351
|
|
|
$generation = []; |
|
352
|
|
|
$tot = 0; |
|
353
|
|
|
if ($impr) { |
|
354
|
|
|
echo " [$list]$nl"; |
|
355
|
|
|
} |
|
356
|
|
|
|
|
357
|
|
|
// HERE IS FETCHED EACH TRIPLET [ID, sire_ID, dam_ID] : |
|
358
|
|
|
$r = $GLOBALS['xoopsDB']->queryF("$sql1 IN ($list)"); |
|
359
|
|
|
while (false !== ($rec = $GLOBALS['xoopsDB']->fetchBoth($r))) { |
|
360
|
|
|
$a = $rec[0] + 0; |
|
361
|
|
|
$s = $rec[1] + 0; |
|
362
|
|
|
$d = $rec[2] + 0; |
|
363
|
|
|
if (!isset($a)) { |
|
364
|
|
|
echo "ERROR : $a = $s x $d for list = '$list'<br>\n"; |
|
365
|
|
|
} |
|
366
|
|
|
if ($s) { |
|
367
|
|
|
++$tot; |
|
368
|
|
|
} |
|
369
|
|
|
if ($d) { |
|
370
|
|
|
++$tot; |
|
371
|
|
|
} |
|
372
|
|
|
$j = array_keys($IDs, $a); |
|
373
|
|
|
$j = $j[0]; |
|
374
|
|
|
$fathers[$j] = $s; |
|
375
|
|
|
$mothers[$j] = $d; |
|
376
|
|
|
if ($s && !in_array($s, $IDs)) { |
|
377
|
|
|
$i = ++$last; |
|
378
|
|
|
$IDs[$i] = $s; |
|
379
|
|
|
$fathers[$i] = 0; |
|
380
|
|
|
$mothers[$i] = 0; |
|
381
|
|
|
if ($s) { |
|
382
|
|
|
$generation[] = $s; |
|
383
|
|
|
} |
|
384
|
|
|
} |
|
385
|
|
|
if ($d && !in_array($d, $IDs)) { |
|
386
|
|
|
$i = ++$last; |
|
387
|
|
|
$IDs[$i] = $d; |
|
388
|
|
|
$fathers[$i] = 0; |
|
389
|
|
|
$mothers[$i] = 0; |
|
390
|
|
|
if ($s) { |
|
391
|
|
|
$generation[] = $d; |
|
392
|
|
|
} |
|
393
|
|
|
} |
|
394
|
|
|
if ($impr) { |
|
395
|
|
|
echo "<pre>genealogy ascendant (gener. $nloop) : $a = $s x $d [tot = $tot]$nl</pre>"; |
|
396
|
|
|
} |
|
397
|
|
|
} |
|
398
|
|
|
if (!count($generation)) { |
|
399
|
|
|
break; |
|
400
|
|
|
} |
|
401
|
|
|
} |
|
402
|
|
|
|
|
403
|
|
|
if ($nloop <= $nb_gen) { |
|
404
|
|
|
$nb_gen = $nloop; |
|
405
|
|
|
} // tree cut by $nb_maxi ! |
|
406
|
|
|
|
|
407
|
|
|
reset($IDs); |
|
408
|
|
|
$inds = array_flip($IDs); |
|
409
|
|
|
|
|
410
|
|
|
chrono_sort(); |
|
411
|
|
|
|
|
412
|
|
|
return $nbtot; |
|
413
|
|
|
} |
|
414
|
|
|
|
|
415
|
|
|
/** |
|
416
|
|
|
* @param $p |
|
417
|
|
|
* |
|
418
|
|
|
* @return int |
|
419
|
|
|
*/ |
|
420
|
|
|
function dist_p($p) |
|
421
|
|
|
{ |
|
422
|
|
|
global $IDs, $fathers, $mothers, $pater, $nb_gen, $detail, $nl; |
|
423
|
|
|
// Anim #P is the sire |
|
424
|
|
|
$listall = [$p]; |
|
425
|
|
|
$listnew = [$p]; |
|
426
|
|
|
$pater = []; |
|
427
|
|
|
$pater[$p] = 1; |
|
428
|
|
|
for ($nloop = 2; $nloop < ($nb_gen + 1); ++$nloop) { |
|
429
|
|
|
$liste = []; |
|
430
|
|
|
foreach ($listnew as $i) { |
|
431
|
|
|
$s = $fathers[$i]; |
|
432
|
|
|
$d = $mothers[$i]; |
|
433
|
|
|
if ($s && !$pater[$s]) { |
|
434
|
|
|
$pater[$s] = $nloop; |
|
435
|
|
|
} // least distance from $s to sire's progeny |
|
436
|
|
|
if ($d && !$pater[$d]) { |
|
437
|
|
|
$pater[$d] = $nloop; |
|
438
|
|
|
} // least distance from $d to sire's progeny |
|
439
|
|
|
if ($s) { |
|
440
|
|
|
$liste[] = $s; |
|
441
|
|
|
} |
|
442
|
|
|
if ($d) { |
|
443
|
|
|
$liste[] = $d; |
|
444
|
|
|
} |
|
445
|
|
|
} |
|
446
|
|
|
if (!count($liste)) { |
|
447
|
|
|
break; |
|
448
|
|
|
} |
|
449
|
|
|
//commented pout by jc |
|
450
|
|
|
//if (in_array ($IDs[2], $liste) && !$detail) |
|
451
|
|
|
//{ echo "<p>DAM is an ascendant (at $nloop generations) of SIRE. Stopped." ; |
|
452
|
|
|
// die ("</body></html>$nl") ; } |
|
453
|
|
|
$listnew = array_diff(array_unique($liste), $listall); |
|
454
|
|
|
/* $list1 = join (' ', $listall) ; $list2 = join ('+', $listnew) ; |
|
455
|
|
|
echo "<!-- P ($nloop) $list1/$list2 -->$nl" ; */ |
|
456
|
|
|
// $listall = array_merge($listall, $listnew); |
|
457
|
|
|
$listall[] = $listnew; |
|
458
|
|
|
} |
|
459
|
|
|
// $listall = call_user_func_array('array_merge', $listall); |
|
460
|
|
|
$listall = array_merge(...$listall); |
|
461
|
|
|
|
|
462
|
|
|
// Here $pater array contains list of all distinct ascendants of #P (including P himself) |
|
463
|
|
|
// Values of $pater are minimum distances to #P (in generations) +1 |
|
464
|
|
|
return 0; |
|
465
|
|
|
} |
|
466
|
|
|
|
|
467
|
|
|
/** |
|
468
|
|
|
* @param $m |
|
469
|
|
|
* |
|
470
|
|
|
* @return int |
|
471
|
|
|
*/ |
|
472
|
|
|
function dist_m($m) |
|
473
|
|
|
{ |
|
474
|
|
|
global $IDs, $fathers, $mothers, $mater, $nb_gen, $detail, $nl; |
|
475
|
|
|
// Anim #M is the dam |
|
476
|
|
|
$listall = [$m]; |
|
477
|
|
|
$listnew = [$m]; |
|
478
|
|
|
$mater = []; |
|
479
|
|
|
$mater[$m] = 1; |
|
480
|
|
|
for ($nloop = 2; $nloop <= ($nb_gen + 1); ++$nloop) { |
|
481
|
|
|
$liste = []; |
|
482
|
|
|
foreach ($listnew as $i) { |
|
483
|
|
|
$s = $fathers[$i]; |
|
484
|
|
|
$d = $mothers[$i]; |
|
485
|
|
|
if ($s && !isset($mater[$s])) { |
|
486
|
|
|
$mater[$s] = $nloop; |
|
487
|
|
|
} // least distance from $s to dam's progeny |
|
488
|
|
|
if ($d && !isset($mater[$d])) { |
|
489
|
|
|
$mater[$d] = $nloop; |
|
490
|
|
|
} // least distance from $d to dam's progeny |
|
491
|
|
|
// echo "I=" . $i . " MATER(I)=" . $mater[$i] . " NLOOP=" . $nloop . "<br>$nl" ; |
|
492
|
|
|
if ($s) { |
|
493
|
|
|
$liste[] = $s; |
|
494
|
|
|
} |
|
495
|
|
|
if ($d) { |
|
496
|
|
|
$liste[] = $d; |
|
497
|
|
|
} |
|
498
|
|
|
} |
|
499
|
|
|
if (!count($liste)) { |
|
500
|
|
|
break; |
|
501
|
|
|
} |
|
502
|
|
|
//commented out by jc |
|
503
|
|
|
//if (in_array ($IDs[1], $liste) && !$detail) |
|
504
|
|
|
// { echo "<p>SIRE is an ascendant (at $nloop generations) of DAM. Stopped." ; |
|
505
|
|
|
// die ("</body></html>$nl") ; } |
|
506
|
|
|
$listnew = array_diff(array_unique($liste), $listall); |
|
507
|
|
|
// $list1 = join (' ', $listall) ; $list2 = join ('+', $listnew) ; echo "M ($nloop) $list1/$list2 $nl" ; |
|
508
|
|
|
// $listall = array_merge($listall, $listnew); |
|
509
|
|
|
$listall[] = $listnew; |
|
510
|
|
|
} |
|
511
|
|
|
// $listall = call_user_func_array('array_merge', $listall); |
|
512
|
|
|
$listall = array_merge(...$listall); |
|
513
|
|
|
|
|
514
|
|
|
// Here $mater array contains list of all distinct ascendants of #M (including M herself) |
|
515
|
|
|
// Values of $mater are minimum distances to #M (in generations) +1 |
|
516
|
|
|
return 0; |
|
517
|
|
|
} |
|
518
|
|
|
|
|
519
|
|
|
/** |
|
520
|
|
|
* @return array |
|
521
|
|
|
*/ |
|
522
|
|
|
function calc_dist() /* Common Ascendants and their distances */ |
|
523
|
|
|
{ |
|
524
|
|
|
global $IDs, $fathers, $mothers, $nbanims, $pater, $mater, $empty, $nb_gen, $nl; |
|
525
|
|
|
global $dmax, $detail, $nb_gen; |
|
526
|
|
|
$distan = []; |
|
527
|
|
|
// dist_m (2) ; has already been called |
|
528
|
|
|
dist_p($fathers[0]); |
|
529
|
|
|
$dmax = 0; |
|
530
|
|
|
$impr = 0; |
|
531
|
|
|
$dmx = 7; |
|
532
|
|
|
if ($detail) { |
|
533
|
|
|
$dmx += 2; |
|
534
|
|
|
} |
|
535
|
|
|
// ksort ($pater) ; print_r ($pater) ; echo "<br>$nl" ; ksort ($mater) ; print_r ($mater) ; echo "<br>$nl" ; |
|
536
|
|
|
foreach ($pater as $i => $p) { |
|
537
|
|
|
if ($p) { |
|
538
|
|
|
$m = $mater[$i]; |
|
539
|
|
|
if ($m) { |
|
540
|
|
|
$di = $p + $m; |
|
541
|
|
|
if ($impr) { |
|
542
|
|
|
echo " $i : $p + $m = $di <br>$nl"; |
|
543
|
|
|
} |
|
544
|
|
|
if (!$dmax) { |
|
545
|
|
|
$dmax = $dmx + $di - ceil($di / 2.); |
|
546
|
|
|
} |
|
547
|
|
|
if ($di > ($dmax + 2)) { |
|
548
|
|
|
continue; |
|
549
|
|
|
} |
|
550
|
|
|
$distan[$i] = $di; |
|
551
|
|
|
} |
|
552
|
|
|
} |
|
553
|
|
|
} |
|
554
|
|
|
if (!$dmax) { |
|
555
|
|
|
$dmax = 2 * $nb_gen - 2; |
|
556
|
|
|
} |
|
557
|
|
|
|
|
558
|
|
|
return $distan; |
|
559
|
|
|
} |
|
560
|
|
|
|
|
561
|
|
|
/** |
|
562
|
|
|
* @param $p |
|
563
|
|
|
* @param $m |
|
564
|
|
|
* @param $a |
|
565
|
|
|
* @param $ndist |
|
566
|
|
|
* |
|
567
|
|
|
* @return int |
|
568
|
|
|
*/ |
|
569
|
|
|
function mater_side($p, $m, $a, $ndist) |
|
570
|
|
|
{ |
|
571
|
|
|
global $fathers, $mothers, $marked, $COIs, $deltaf, $ICknown, $verbose, $nl, $chrono, $paternal_rank, $max_dist; |
|
572
|
|
|
if (!$m || $ndist > $max_dist) { |
|
573
|
|
|
return 0; |
|
574
|
|
|
} |
|
575
|
|
|
if ($p == $m) { |
|
576
|
|
|
/* IMPLEX FOUND (node of consanguinity) { for Anim #A */ |
|
577
|
|
|
$already_known = $ICknown[$p]; |
|
578
|
|
|
} |
|
579
|
|
|
if (!$already_known) { |
|
580
|
|
|
CONSANG($p); |
|
581
|
|
|
} // MAIN RECURSION: |
|
582
|
|
|
$ICp = $COIs[$p]; // we need to know the IC of Parent for Wright's formula |
|
583
|
|
|
if ($verbose && !$already_known && $ICp > 0.001 * $verbose) { |
|
584
|
|
|
echo "IC of Animal $p is $ICp$nl"; |
|
585
|
|
|
} |
|
586
|
|
|
|
|
587
|
|
|
$incr = 1.0 / (1 << $ndist) * (1. + $ICp); // ******** applying WRIGHT's formula ******** |
|
588
|
|
|
|
|
589
|
|
|
// [Note: 1 << $ndist is equal to 2 power $ndist] |
|
590
|
|
|
$COIs[$a] += $incr; // incrementing the IC of AnimC |
|
591
|
|
|
if (0 == $a) { |
|
592
|
|
|
$deltaf[$p] += $incr; |
|
593
|
|
|
/* contribution of Anim #P to IC of Anim #0 */ // if ($verbose && $a == 0 && $incr > 0.0001*$verbose) |
|
594
|
|
|
// echo "Animal $p is contributing for " . substr ($deltaf[$p], 0, 10) . " to the IC of Animal $a$nl" ; |
|
595
|
|
|
} else { |
|
596
|
|
|
if (!$marked[$m] && $chrono[$m] < $paternal_rank) { |
|
597
|
|
|
mater_side($p, $fathers[$m], $a, $ndist + 1); |
|
598
|
|
|
mater_side($p, $mothers[$m], $a, $ndist + 1); |
|
599
|
|
|
} |
|
600
|
|
|
} |
|
601
|
|
|
|
|
602
|
|
|
return 0; |
|
603
|
|
|
} |
|
604
|
|
|
|
|
605
|
|
|
/** |
|
606
|
|
|
* @param $p |
|
607
|
|
|
* @param $m |
|
608
|
|
|
* @param $a |
|
609
|
|
|
* @param $pdist |
|
610
|
|
|
* @return int |
|
611
|
|
|
*/ |
|
612
|
|
|
function pater_side($p, $m, $a, $pdist) |
|
613
|
|
|
{ |
|
614
|
|
|
global $mater, $fathers, $mothers, $marked, $chrono, $paternal_rank; |
|
615
|
|
|
if (!$p) { |
|
616
|
|
|
return 0; |
|
617
|
|
|
} |
|
618
|
|
|
$paternal_rank = $chrono[$p]; |
|
619
|
|
|
$marked[$p] = 1; /* cut paternal side */ |
|
620
|
|
|
if ($a || isset($mater[$p])) { |
|
621
|
|
|
mater_side($p, $m, $a, $pdist); |
|
622
|
|
|
} |
|
623
|
|
|
pater_side($fathers[$p], $m, $a, $pdist + 1); |
|
624
|
|
|
pater_side($mothers[$p], $m, $a, $pdist + 1); |
|
625
|
|
|
$marked[$p] = 0; /* free paternal side */ |
|
626
|
|
|
|
|
627
|
|
|
return 0; |
|
628
|
|
|
} |
|
629
|
|
|
|
|
630
|
|
|
/** |
|
631
|
|
|
* @param $a |
|
632
|
|
|
* |
|
633
|
|
|
* @return int |
|
634
|
|
|
*/ |
|
635
|
|
|
function CONSANG($a) |
|
636
|
|
|
{ |
|
637
|
|
|
global $fathers, $mothers, $ICknown, $COIs, $nl; |
|
638
|
|
|
if (!$a || $ICknown[$a]) { |
|
639
|
|
|
return 0; |
|
640
|
|
|
} |
|
641
|
|
|
if (-1 == $a) { |
|
642
|
|
|
$a = 0; |
|
643
|
|
|
} // particular case : a= -1 means Anim #0 (to bypass above test) |
|
644
|
|
|
$IC_if_deadend = 0.0; // 0.0 means taht deadends are deemed to be total outcrosses... |
|
645
|
|
|
// if IC was already stored in the database for Aminal #A, it should be used here instead of 0.0 |
|
646
|
|
|
$p = $fathers[$a]; |
|
647
|
|
|
$m = $mothers[$a]; |
|
648
|
|
|
if (!$p || !$m) { |
|
649
|
|
|
$COIs[$a] = $IC_if_deadend; |
|
650
|
|
|
$ICknown[$a] = 2; |
|
651
|
|
|
|
|
652
|
|
|
return 0; |
|
653
|
|
|
} |
|
654
|
|
|
|
|
655
|
|
|
if ($verbose) { |
|
656
|
|
|
echo "</center><pre>$nl"; |
|
657
|
|
|
} |
|
658
|
|
|
pater_side($p, $m, $a, 1); // launch tree exploration |
|
659
|
|
|
if ($verbose) { |
|
660
|
|
|
echo "</pre><div style=\"text-align: center;\">$nl"; |
|
661
|
|
|
} |
|
662
|
|
|
|
|
663
|
|
|
$ICknown[$a] = 1; |
|
664
|
|
|
$p = $fathers[$a]; |
|
665
|
|
|
$m = $mothers[$a]; |
|
666
|
|
|
foreach ($fathers as $i => $pere) {/* siblings share the same COI value */ |
|
667
|
|
|
if ($i != $a && $pere == $p && $mothers[$i] == $m) { |
|
668
|
|
|
$COIs[$i] = $COIs[$a]; |
|
669
|
|
|
$ICknown[$i] = 1; |
|
670
|
|
|
} |
|
671
|
|
|
} |
|
672
|
|
|
|
|
673
|
|
|
// echo "<!-- COI($a) = $COIs[$a] $IDs[$a] ($fathers[$a] x $mothers[$a])-->$nl" ; |
|
674
|
|
|
return 0; |
|
675
|
|
|
} |
|
676
|
|
|
|
|
677
|
|
|
/** |
|
678
|
|
|
* @param $nb_gen |
|
679
|
|
|
* @param $nloop |
|
680
|
|
|
* |
|
681
|
|
|
* @return int |
|
682
|
|
|
*/ |
|
683
|
|
|
function boucle($nb_gen, $nloop) |
|
684
|
|
|
{ |
|
685
|
|
|
global $fathers, $mothers, $nbanims, $listing, $nl, $IDs; |
|
686
|
|
|
$nbtot = 0; |
|
687
|
|
|
$listing = ''; |
|
688
|
|
|
if ($nloop < ($nb_gen + 20)) { |
|
689
|
|
|
$nloop = $nb_gen + 20; |
|
690
|
|
|
} |
|
691
|
|
|
$list = [0 => 1]; |
|
692
|
|
|
//print_r($list); |
|
693
|
|
|
/* initialize list with Anim0 (rank = 1) */ |
|
694
|
|
|
for ($j = 1; $j < $nloop; ++$j) { |
|
695
|
|
|
$new = 0; |
|
696
|
|
|
foreach ($list as $i => $rank) { |
|
697
|
|
|
if (false !== ($s = $fathers[$i])) { |
|
698
|
|
|
if (!$list[$s]) { |
|
699
|
|
|
$new = 1; |
|
700
|
|
|
if ($j < $nb_gen) { |
|
701
|
|
|
++$nbtot; |
|
702
|
|
|
} |
|
703
|
|
|
} |
|
704
|
|
|
$list[$s] = $rank + 1; |
|
705
|
|
|
if ($j < $nb_gen) { |
|
706
|
|
|
++$nbtot; |
|
707
|
|
|
} |
|
708
|
|
|
if ($j > $nloop - 10) { |
|
709
|
|
|
$listing .= "Loop $j: Animal #$s " . $IDs[$s] . $nl; |
|
710
|
|
|
} |
|
711
|
|
|
} |
|
712
|
|
|
if (false !== ($d = $mothers[$i])) { |
|
713
|
|
|
if (!$list[$d]) { |
|
714
|
|
|
$new = 1; |
|
715
|
|
|
if ($j < $nb_gen) { |
|
716
|
|
|
++$nbtot; |
|
717
|
|
|
} |
|
718
|
|
|
} |
|
719
|
|
|
$list[$d] = $rank + 1; |
|
720
|
|
|
if ($j < $nb_gen) { |
|
721
|
|
|
++$nbtot; |
|
722
|
|
|
} |
|
723
|
|
|
if ($j > $nloop - 10) { |
|
724
|
|
|
$listing .= "Loop $j: Animal #$d " . $IDs[$d] . $nl; |
|
725
|
|
|
} |
|
726
|
|
|
} |
|
727
|
|
|
} |
|
728
|
|
|
if (!$new) { |
|
729
|
|
|
break; |
|
730
|
|
|
} |
|
731
|
|
|
} |
|
732
|
|
|
if ($new) { |
|
733
|
|
|
$nbtot = 0; |
|
734
|
|
|
} /* Endless loop detected (see listing) */ |
|
735
|
|
|
|
|
736
|
|
|
return $nbtot; |
|
737
|
|
|
} |
|
738
|
|
|
|
|
739
|
|
|
if (!function_exists('html_accents')) { |
|
740
|
|
|
/** |
|
741
|
|
|
* @param $string |
|
742
|
|
|
* @return mixed |
|
743
|
|
|
*/ |
|
744
|
|
|
function html_accents($string) |
|
745
|
|
|
{ |
|
746
|
|
|
return $string; |
|
747
|
|
|
} |
|
748
|
|
|
} |
|
749
|
|
|
|
|
750
|
|
|
/** |
|
751
|
|
|
* @param $ID |
|
752
|
|
|
* |
|
753
|
|
|
* @return array |
|
754
|
|
|
*/ |
|
755
|
|
|
function set_name($ID) |
|
756
|
|
|
{ |
|
757
|
|
|
// global $sql2, $sql2bis, $xoopsDB; |
|
758
|
|
|
$name = ' '; |
|
759
|
|
|
$ID = (int)$ID; |
|
760
|
|
|
$ani = []; |
|
761
|
|
|
if ($ID) { |
|
762
|
|
|
$sqlQuery = 'SELECT id, pname, roft FROM ' . $GLOBALS['xoopsDB']->prefix('pedigree_registry') . " WHERE id = '$ID'"; |
|
763
|
|
|
$queryResult = $GLOBALS['xoopsDB']->query($sqlQuery); |
|
764
|
|
|
$ani = $GLOBALS['xoopsDB']->fetchBoth($queryResult); |
|
765
|
|
|
/* |
|
766
|
|
|
$name = $ani[1]; |
|
767
|
|
|
if ($sql2bis) { // true for E.R.o'S. only |
|
768
|
|
|
$name = html_accents($name); |
|
769
|
|
|
//$affx = $ani[5] ; // affix-ID |
|
770
|
|
|
if ($affx) { |
|
771
|
|
|
$affix = fetch_record("$sql2bis '$affx'"); |
|
772
|
|
|
$type = $affix[1]; |
|
773
|
|
|
$affixe = html_accents($affix[0]); |
|
774
|
|
|
if ($type[0] === 'P') { |
|
775
|
|
|
$name = '<i>' . $affixe . '</i> ' . $name; |
|
776
|
|
|
} |
|
777
|
|
|
if ($type[0] === 'S') { |
|
778
|
|
|
$name = $name . ' <i>' . $affixe . '</i>'; |
|
779
|
|
|
} |
|
780
|
|
|
} |
|
781
|
|
|
$ani[1] = $name; |
|
782
|
|
|
} |
|
783
|
|
|
*/ |
|
784
|
|
|
} |
|
785
|
|
|
|
|
786
|
|
|
return $ani; |
|
787
|
|
|
} |
|
788
|
|
|
|
|
789
|
|
|
/** |
|
790
|
|
|
* @param $ems |
|
791
|
|
|
* |
|
792
|
|
|
* @return string |
|
793
|
|
|
*/ |
|
794
|
|
|
function Ems_($ems) |
|
795
|
|
|
{ |
|
796
|
|
|
if (function_exists('Ems')) { |
|
797
|
|
|
return Ems($ems); |
|
798
|
|
|
} |
|
799
|
|
|
if (!$ems) { |
|
800
|
|
|
return ' '; |
|
801
|
|
|
} |
|
802
|
|
|
$e = str_replace(' ', '+', $ems); |
|
803
|
|
|
$res = '<a href="#" style="text-decoration:none;" onClick="' . "window.open('http://www.somali.asso.fr/eros/decode_ems.php?$e'," . "'', 'resizable=no,width=570,height=370')" . '"' . "><b>$ems</b></a>"; |
|
804
|
|
|
|
|
805
|
|
|
return $res; |
|
806
|
|
|
} |
|
807
|
|
|
|
|
808
|
|
|
/** |
|
809
|
|
|
* @param $ID |
|
810
|
|
|
* |
|
811
|
|
|
* @return string |
|
812
|
|
|
*/ |
|
813
|
|
|
function one_animal($ID) |
|
814
|
|
|
{ |
|
815
|
|
|
global $xoopsDB; |
|
816
|
|
|
global $sex, $val, $sosa, $detail, $sql3; |
|
817
|
|
|
$content = ''; |
|
818
|
|
|
$sosa = 12; |
|
819
|
|
|
// echo '<div style="position:relative;float:right;width=2.0em;color=white;">' . $sosa . '</div>' ; |
|
820
|
|
|
$animal = set_name($ID); |
|
821
|
|
|
|
|
822
|
|
|
if (is_array($animal)) { |
|
823
|
|
|
[$ID, $name, $sex, $hd, $ems] = $animal; |
|
824
|
|
|
} |
|
825
|
|
|
$sqlQuery = 'SELECT SQL_CACHE COUNT(id) FROM ' . $GLOBALS['xoopsDB']->prefix('pedigree_registry') . " where father = '$ID' or mother = '$ID'"; |
|
826
|
|
|
$queryResult = $GLOBALS['xoopsDB']->queryF($sqlQuery); |
|
827
|
|
|
$nb = $GLOBALS['xoopsDB']->fetchBoth($queryResult); |
|
828
|
|
|
$nb_children = $nb[0]; |
|
829
|
|
|
if (0 == $nb_children) { |
|
830
|
|
|
$nb_children = _MA_PEDIGREE_COI_NO; |
|
831
|
|
|
} |
|
832
|
|
|
//$dogid = $animal[0]; |
|
833
|
|
|
$content .= '<tr><td><a href="dog.php?id=' . $ID . '">' . stripslashes($name) . '</a>'; |
|
834
|
|
|
// if ($nb_enf == 0) echo ' ø' ; |
|
835
|
|
|
if ($val) { |
|
836
|
|
|
$content .= $val; |
|
837
|
|
|
} |
|
838
|
|
|
if (1 == $sex) { |
|
839
|
|
|
$geslacht = '<img src="assets/images/female.gif">'; |
|
840
|
|
|
} |
|
841
|
|
|
if (0 == $sex) { |
|
842
|
|
|
$geslacht = '<img src="assets/images/male.gif">'; |
|
843
|
|
|
} |
|
844
|
|
|
$content .= '</td><td>' . $geslacht . '</td><td>' . $nb_children . _MA_PEDIGREE_COI_OFF . '</td></tr>'; |
|
845
|
|
|
|
|
846
|
|
|
return $content; |
|
847
|
|
|
} |
|
848
|
|
|
|
|
849
|
|
|
/* %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% MAIN %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% */ |
|
850
|
|
|
|
|
851
|
|
|
$nl = "\n"; // the newline character |
|
852
|
|
|
|
|
853
|
|
|
//edit by jc |
|
854
|
|
|
//$link = @mysqli_pconnect ($host, $database, $password) |
|
855
|
|
|
// or die ("<html><body>Connection to database failed.</body></html>") ; |
|
856
|
|
|
|
|
857
|
|
|
//$a = ''; |
|
858
|
|
|
$s = Request::getInt('s', 0, 'GET'); //_GET['s']; |
|
859
|
|
|
$d = Request::getInt('d', 0, 'GET'); //$_GET['d']; |
|
860
|
|
|
$detail = Request::getString('detail', '', 'GET'); //$_GET['detail']; |
|
861
|
|
|
|
|
862
|
|
|
if (isset($si)) { |
|
863
|
|
|
$s = Pedigree\Utility::findId($si); |
|
864
|
|
|
} |
|
865
|
|
|
if (isset($da)) { |
|
866
|
|
|
$d = Pedigree\Utility::findId($da); |
|
867
|
|
|
} |
|
868
|
|
|
//test for variables |
|
869
|
|
|
//echo "si=".$si." da=".$da." s=".$s." d=".$d; |
|
870
|
|
|
$utils = $GLOBALS['xoopsDB']->queryF("SELECT user(), date_format(now(),'%d-%b-%Y')"); |
|
871
|
|
|
[$who, $jourj] = $GLOBALS['xoopsDB']->fetchBoth($utils); |
|
872
|
|
|
|
|
873
|
|
|
if (isset($IC)) { |
|
874
|
|
|
$detail = -1; |
|
875
|
|
|
$a = $IC; |
|
876
|
|
|
} |
|
877
|
|
|
|
|
878
|
|
|
if (!isset($detail)) { |
|
879
|
|
|
$detail = 0; |
|
880
|
|
|
} |
|
881
|
|
|
|
|
882
|
|
|
if (!isset($a)) { |
|
883
|
|
|
if (isset($s) && !isset($d)) { |
|
884
|
|
|
$a = $s; |
|
885
|
|
|
$s = ''; |
|
886
|
|
|
} |
|
887
|
|
|
if (isset($d) && !isset($s)) { |
|
888
|
|
|
$a = $d; |
|
889
|
|
|
$d = ''; |
|
890
|
|
|
} |
|
891
|
|
|
} |
|
892
|
|
|
|
|
893
|
|
|
if (isset($a)) { |
|
894
|
|
|
$sqlQuery = 'SELECT id, father, mother, roft FROM ' . $GLOBALS['xoopsDB']->prefix('pedigree_registry') . " WHERE id = '$a'"; |
|
895
|
|
|
$queryResult = $GLOBALS['xoopsDB']->query($sqlQuery); |
|
896
|
|
|
$rowhond = $GLOBALS['xoopsDB']->fetchBoth($queryResult); |
|
897
|
|
|
$a = $rowhond['id']; |
|
898
|
|
|
$s = $rowhond['father']; |
|
899
|
|
|
$d = $rowhond['mother']; |
|
900
|
|
|
} |
|
901
|
|
|
$a += 0; |
|
902
|
|
|
$s += 0; |
|
903
|
|
|
$d += 0; // [IDs are numbers] |
|
904
|
|
|
|
|
905
|
|
|
$xoopsTpl->assign('ptitle', _MA_PEDIGREE_COI_CKRI); |
|
906
|
|
|
$xoopsTpl->assign('pcontent', strtr(_MA_PEDIGREE_COI_CKRI_CT, ['[animalType]' => $moduleConfig['animalType']])); |
|
907
|
|
|
|
|
908
|
|
|
if (!$s && !$d) { |
|
909
|
|
|
$error = _MA_PEDIGREE_COI_SPANF1 . $a . _MA_PEDIGREE_COI_SPANF2; |
|
910
|
|
|
$xoopsTpl->assign('COIerror', $error); |
|
911
|
|
|
} |
|
912
|
|
|
|
|
913
|
|
|
$maxn_ = 1000; |
|
914
|
|
|
$maxr_ = 9; |
|
915
|
|
|
|
|
916
|
|
|
$maxn = $maxn_; |
|
917
|
|
|
$maxr = $maxr_; |
|
918
|
|
|
$cinnamon = 0; |
|
919
|
|
|
$chocolat = 0; |
|
920
|
|
|
$dilution = 0; |
|
921
|
|
|
$sexlred = 0; |
|
922
|
|
|
|
|
923
|
|
|
$nivomin = -$maxr; /* Maximal depth of recursion (-10) */ |
|
924
|
|
|
$codec = 0; |
|
925
|
|
|
$gens = 4; /* 4 gens. for both pedigrees of couple */ |
|
926
|
|
|
$litter = 0; |
|
927
|
|
|
|
|
928
|
|
|
// echo "s:".$s."<br>"; |
|
929
|
|
|
// echo "d:".$d."<br>"; |
|
930
|
|
|
|
|
931
|
|
|
$codec1 = $d; |
|
932
|
|
|
$codec2 = $s; |
|
933
|
|
|
$val = ''; |
|
934
|
|
|
|
|
935
|
|
|
if (!$s && $d) { |
|
936
|
|
|
$codec1 = $d; |
|
937
|
|
|
$codec2 = 0; |
|
938
|
|
|
} |
|
939
|
|
|
if ($codec1 == $codec2) { |
|
940
|
|
|
$codec2 = 0; |
|
941
|
|
|
} |
|
942
|
|
|
|
|
943
|
|
|
$sqlQuery = 'SELECT father, mother, roft FROM ' . $GLOBALS['xoopsDB']->prefix('pedigree_registry') . " WHERE id = '$codec1'"; |
|
944
|
|
|
$queryResult = $GLOBALS['xoopsDB']->query($sqlQuery); |
|
945
|
|
|
$rowhond = $GLOBALS['xoopsDB']->fetchBoth($queryResult); |
|
946
|
|
|
$a1 = $rowhond['id']; |
|
947
|
|
|
$s1 = $rowhond['father']; |
|
948
|
|
|
$d1 = $rowhond['mother']; |
|
949
|
|
|
$sex1 = $rowhond['roft']; |
|
950
|
|
|
|
|
951
|
|
|
// echo "sqlquery:".$sqlQuery."<br>"; |
|
952
|
|
|
|
|
953
|
|
|
$sqlQuery = 'SELECT father, mother, roft FROM ' . $GLOBALS['xoopsDB']->prefix('pedigree_registry') . " WHERE id = '$codec2'"; |
|
954
|
|
|
$queryResult = $GLOBALS['xoopsDB']->query($sqlQuery); |
|
955
|
|
|
$rowhond = $GLOBALS['xoopsDB']->fetchBoth($queryResult); |
|
956
|
|
|
$a2 = $rowhond['id']; |
|
957
|
|
|
$s2 = $rowhond['father']; |
|
958
|
|
|
$d2 = $rowhond['mother']; |
|
959
|
|
|
$sex2 = $rowhond['roft']; |
|
960
|
|
|
|
|
961
|
|
|
// echo "sqlquery:".$sqlQuery."<br>"; |
|
962
|
|
|
|
|
963
|
|
|
//if ($sex1 == '0' && $sex2 == '1') { $a3 = $a1 ; $a1 = $a2 ; $a2 = $a3 ; } /* permute dam and sire */ |
|
964
|
|
|
$codec1 = $a1; |
|
965
|
|
|
$codec2 = $a2; |
|
966
|
|
|
if (!isset($s1) || !isset($d1) || !isset($s2) || !isset($d2)) { |
|
967
|
|
|
$xoopsTpl->assign('COIerror', _MA_PEDIGREE_COI_SGPU); |
|
968
|
|
|
} |
|
969
|
|
|
|
|
970
|
|
|
$title = strtr(_MA_PEDIGREE_FLD_FATH, ['[father]' => $moduleConfig['father']]) . ' (' . stripslashes(Pedigree\Utility::showParent($codec2)) . ')' . _MA_PEDIGREE_COI_AND . strtr(_MA_PEDIGREE_FLD_MOTH, ['[mother]' => $moduleConfig['mother']]) . ' (' . stripslashes( |
|
971
|
|
|
Pedigree\Utility::showParent($codec1) |
|
972
|
|
|
) . ')'; |
|
973
|
|
|
$content = stripslashes(one_animal($codec2)); |
|
974
|
|
|
$content .= stripslashes(one_animal($codec1)); |
|
975
|
|
|
$val = ''; |
|
976
|
|
|
$xoopsTpl->assign('SADtitle', $title); |
|
977
|
|
|
$xoopsTpl->assign('SADcontent', $content); |
|
978
|
|
|
$xoopsTpl->assign( |
|
979
|
|
|
'SADexplain', |
|
980
|
|
|
strtr(_MA_PEDIGREE_COI_SDEX, [ |
|
981
|
|
|
'[animalType]' => $moduleConfig['animalType'], |
|
982
|
|
|
'[animalTypes]' => $moduleConfig['animalTypes'], |
|
983
|
|
|
'[children]' => $moduleConfig['children'], |
|
984
|
|
|
]) |
|
985
|
|
|
); |
|
986
|
|
|
|
|
987
|
|
|
$de_cujus = 0; |
|
988
|
|
|
$sire_ID = Request::getInt('s', 0, 'GET'); //$_GET['s']; |
|
989
|
|
|
$dam_ID = Request::getInt('d', 0, 'GET'); //$_GET['d']; |
|
990
|
|
|
|
|
991
|
|
|
$rec = 'SELECT id FROM ' . $GLOBALS['xoopsDB']->prefix('pedigree_registry') . " WHERE father = '" . $sire_ID . "' AND mother = '" . $dam_ID . "' ORDER BY pname"; |
|
992
|
|
|
$result = $GLOBALS['xoopsDB']->query($rec); |
|
993
|
|
|
$content = ''; |
|
994
|
|
|
while (false !== ($row = $GLOBALS['xoopsDB']->fetchArray($result))) { |
|
995
|
|
|
$content .= one_animal($row['id']); |
|
996
|
|
|
} |
|
997
|
|
|
|
|
998
|
|
|
$xoopsTpl->assign( |
|
999
|
|
|
'COMtitle', |
|
1000
|
|
|
strtr(_MA_PEDIGREE_COI_COMTIT, [ |
|
1001
|
|
|
'[father]' => $moduleConfig['father'], |
|
1002
|
|
|
'[mother]' => $moduleConfig['mother'], |
|
1003
|
|
|
]) |
|
1004
|
|
|
); |
|
1005
|
|
|
$xoopsTpl->assign( |
|
1006
|
|
|
'COMexplain', |
|
1007
|
|
|
strtr(_MA_PEDIGREE_COI_COMEX, [ |
|
1008
|
|
|
'[animalType]' => $moduleConfig['animalType'], |
|
1009
|
|
|
'[children]' => $moduleConfig['children'], |
|
1010
|
|
|
]) |
|
1011
|
|
|
); |
|
1012
|
|
|
$xoopsTpl->assign('COMcontent', $content); |
|
1013
|
|
|
|
|
1014
|
|
|
if (!isset($nb_gen)) { |
|
1015
|
|
|
$nb_gen = 7; |
|
1016
|
|
|
if ($detail) { |
|
1017
|
|
|
$nb_gen = 9; |
|
1018
|
|
|
} |
|
1019
|
|
|
} elseif ($nb_gen < $pedigree) { |
|
1020
|
|
|
$nb_gen = $pedigree; |
|
1021
|
|
|
} |
|
1022
|
|
|
|
|
1023
|
|
|
$IDs = [$de_cujus + 0, $codec1 + 0, $codec2 + 0]; /* Structuring animal IDs into memory */ |
|
1024
|
|
|
|
|
1025
|
|
|
$nbanims = GENEALOGY(); // ************************************************************* // |
|
1026
|
|
|
|
|
1027
|
|
|
for ($i = 0; $i <= $nbanims; ++$i) { |
|
1028
|
|
|
$empty[$i] = 0; |
|
1029
|
|
|
} |
|
1030
|
|
|
|
|
1031
|
|
|
foreach ($fathers as $i => $a) { |
|
1032
|
|
|
if ($a) { |
|
1033
|
|
|
$fathers[$i] = $inds[$a]; |
|
1034
|
|
|
} |
|
1035
|
|
|
} /* Replace parents codes */ |
|
1036
|
|
|
foreach ($mothers as $i => $a) { |
|
1037
|
|
|
if ($a) { |
|
1038
|
|
|
$mothers[$i] = $inds[$a]; |
|
1039
|
|
|
} |
|
1040
|
|
|
} /* by their indices */ |
|
1041
|
|
|
|
|
1042
|
|
|
dist_m($mothers[0]); // set "$mater" array (list of all maternal ascendants), for Anim #0 |
|
1043
|
|
|
|
|
1044
|
|
|
/* Calculating CONSANGUINITY by dual (paternal & maternal) path method */ |
|
1045
|
|
|
$f = $empty; |
|
1046
|
|
|
$ICknown = $empty; |
|
1047
|
|
|
$deltaf = $empty; |
|
1048
|
|
|
$marked = $empty; |
|
1049
|
|
|
$SSDcor = $SSDsire = $SSDdam = ''; |
|
1050
|
|
|
|
|
1051
|
|
|
/****************** LAUNCHING ALL RECURSIONS ********************/ |
|
1052
|
|
|
/* */ |
|
1053
|
|
|
CONSANG(-1); /* [-1 is standing for de_cujus] |
|
1054
|
|
|
/* */ |
|
1055
|
|
|
/******************************************************************/ |
|
1056
|
|
|
|
|
1057
|
|
|
$nf = ceil(100 * $COIs[0]); |
|
1058
|
|
|
if ($nf >= 55) { |
|
1059
|
|
|
$w = _MA_PEDIGREE_COI_HUGE; |
|
1060
|
|
|
} else { |
|
1061
|
|
|
if ($nf >= 35) { |
|
1062
|
|
|
$w = _MA_PEDIGREE_COI_VHIG; |
|
1063
|
|
|
} else { |
|
1064
|
|
|
if ($nf >= 20) { |
|
1065
|
|
|
$w = _MA_PEDIGREE_COI_HIGH; |
|
1066
|
|
|
} else { |
|
1067
|
|
|
if ($nf >= 10) { |
|
1068
|
|
|
$w = _MA_PEDIGREE_COI_MEDI; |
|
1069
|
|
|
} else { |
|
1070
|
|
|
if ($nf >= 05) { |
|
|
|
|
|
|
1071
|
|
|
$w = _MA_PEDIGREE_COI_LOW; |
|
1072
|
|
|
} else { |
|
1073
|
|
|
if ($nf >= 02) { |
|
1074
|
|
|
$w = _MA_PEDIGREE_COI_VLOW; |
|
1075
|
|
|
} else { |
|
1076
|
|
|
if ($nf >= 01) { |
|
1077
|
|
|
$w = _MA_PEDIGREE_COI_VVLO; |
|
1078
|
|
|
} else { |
|
1079
|
|
|
$w = _MA_PEDIGREE_COI_TLTB; |
|
1080
|
|
|
} |
|
1081
|
|
|
} |
|
1082
|
|
|
} |
|
1083
|
|
|
} |
|
1084
|
|
|
} |
|
1085
|
|
|
} |
|
1086
|
|
|
} |
|
1087
|
|
|
$w = _MA_PEDIGREE_COI_TVI . ' ' . $w; |
|
1088
|
|
|
|
|
1089
|
|
|
$nb_all = 0; |
|
1090
|
|
|
count_all(0, 0); // count all ascendants in flat tree |
|
1091
|
|
|
|
|
1092
|
|
|
$nbmax = (2 << $nb_gen) - 2; |
|
1093
|
|
|
$asctc = _MA_PEDIGREE_COI_ASTC . $nb_gen . _MA_PEDIGREE_COI_ASTCGEN . $nbmax . ')'; |
|
1094
|
|
|
$ascuni = _MA_PEDIGREE_COI_ASDKA . $nb_gen . _MA_PEDIGREE_COI_ASGEN; |
|
1095
|
|
|
$xoopsTpl->assign('ASCtitle', _MA_PEDIGREE_COI_ACTIT); |
|
1096
|
|
|
$xoopsTpl->assign('ASCtc', $asctc); |
|
1097
|
|
|
$xoopsTpl->assign('ASCuni', $ascuni); |
|
1098
|
|
|
$xoopsTpl->assign('ASCall', $nb_all); |
|
1099
|
|
|
$xoopsTpl->assign('ASCani', $nbani); |
|
1100
|
|
|
$xoopsTpl->assign('ASCexplain', _MA_PEDIGREE_COI_ACEX); |
|
1101
|
|
|
|
|
1102
|
|
|
$f0 = mb_substr($COIs[0], 0, 8); |
|
1103
|
|
|
if (!$f0) { |
|
1104
|
|
|
$f0 = 'n.a.'; |
|
1105
|
|
|
} |
|
1106
|
|
|
$f1 = 100 * $f0; |
|
1107
|
|
|
|
|
1108
|
|
|
$xoopsTpl->assign( |
|
1109
|
|
|
'COItitle', |
|
1110
|
|
|
strtr(_MA_PEDIGREE_COI_COITIT, [ |
|
1111
|
|
|
'[father]' => $moduleConfig['father'], |
|
1112
|
|
|
'[mother]' => $moduleConfig['mother'], |
|
1113
|
|
|
]) |
|
1114
|
|
|
); |
|
1115
|
|
|
$xoopsTpl->assign('COIperc', $w); |
|
1116
|
|
|
$xoopsTpl->assign('COIval', $f1); |
|
1117
|
|
|
$xoopsTpl->assign( |
|
1118
|
|
|
'COIexplain', |
|
1119
|
|
|
strtr(_MA_PEDIGREE_COI_COIEX, [ |
|
1120
|
|
|
'[animalType]' => $moduleConfig['animalType'], |
|
1121
|
|
|
'[animalTypes]' => $moduleConfig['animalTypes'], |
|
1122
|
|
|
'[children]' => $moduleConfig['children'], |
|
1123
|
|
|
]) |
|
1124
|
|
|
); |
|
1125
|
|
|
$xoopsTpl->assign('COIcoi', _MA_PEDIGREE_COI_COI); |
|
1126
|
|
|
$dogid = Request::getInt('dogid', 0, 'GET'); |
|
1127
|
|
|
$query = 'UPDATE ' . $GLOBALS['xoopsDB']->prefix('pedigree_registry') . ' SET coi=' . $f1 . ' WHERE id = ' . $dogid; |
|
1128
|
|
|
$GLOBALS['xoopsDB']->queryF($query); |
|
1129
|
|
|
arsort($deltaf); |
|
1130
|
|
|
$j = 1; |
|
1131
|
|
|
foreach ($deltaf as $i => $v) { |
|
1132
|
|
|
if ($j > 12) { |
|
1133
|
|
|
break; |
|
1134
|
|
|
} |
|
1135
|
|
|
++$j; |
|
1136
|
|
|
$code = $IDs[$i]; |
|
1137
|
|
|
$v = mb_substr($v, 0, 7); |
|
1138
|
|
|
$animal = set_name($IDs[$i]); |
|
1139
|
|
|
$name = $animal[1]; |
|
1140
|
|
|
if (!$name) { |
|
1141
|
|
|
$name = $i . ' [' . $IDs[$i] . ']'; |
|
1142
|
|
|
} |
|
1143
|
|
|
if ($v > 0.0001 && $v < 1.0) { |
|
1144
|
|
|
$dogs[] = ['id' => $code, 'name' => stripslashes($name), 'coi' => 100 * $v]; |
|
1145
|
|
|
} |
|
1146
|
|
|
} |
|
1147
|
|
|
|
|
1148
|
|
|
$xoopsTpl->assign('TCAtitle', _MA_PEDIGREE_COI_TCATIT); |
|
1149
|
|
|
$xoopsTpl->assign('TCApib', _MA_PEDIGREE_COI_TCApib); |
|
1150
|
|
|
$xoopsTpl->assign('dogs', $dogs); |
|
1151
|
|
|
$xoopsTpl->assign( |
|
1152
|
|
|
'TCAexplain', |
|
1153
|
|
|
strtr(_MA_PEDIGREE_COI_TCAEX, [ |
|
1154
|
|
|
'[animalType]' => $moduleConfig['animalType'], |
|
1155
|
|
|
'[animalTypes]' => $moduleConfig['animalTypes'], |
|
1156
|
|
|
'[children]' => $moduleConfig['children'], |
|
1157
|
|
|
'[mother]' => $moduleConfig['mother'], |
|
1158
|
|
|
'[father]' => $moduleConfig['father'], |
|
1159
|
|
|
]) |
|
1160
|
|
|
); |
|
1161
|
|
|
|
|
1162
|
|
|
if ($detail) { |
|
1163
|
|
|
if ($verbose) { |
|
1164
|
|
|
$verbose = 0; |
|
1165
|
|
|
} |
|
1166
|
|
|
if (count($COIs) > 1) { |
|
1167
|
|
|
$ICs = $COIs; |
|
1168
|
|
|
arsort($ICs); |
|
1169
|
|
|
$j = 1; |
|
1170
|
|
|
foreach ($ICs as $i => $ic) { |
|
1171
|
|
|
if ($j > 12) { |
|
1172
|
|
|
break; |
|
1173
|
|
|
} |
|
1174
|
|
|
++$j; |
|
1175
|
|
|
$ID = $IDs[$i]; |
|
1176
|
|
|
$ani = set_name($ID); |
|
1177
|
|
|
$name = $ani[1]; |
|
1178
|
|
|
$ic = mb_substr($ic, 0, 6); |
|
1179
|
|
|
if ($ic > 0.125 && $i) { |
|
1180
|
|
|
$mia[] = ['id' => $ID, 'name' => stripslashes($name), 'coi' => 100 * $ic]; |
|
1181
|
|
|
} |
|
1182
|
|
|
} |
|
1183
|
|
|
} |
|
1184
|
|
|
$xoopsTpl->assign('MIAtitle', _MA_PEDIGREE_COI_MIATIT); |
|
1185
|
|
|
$xoopsTpl->assign('mia', $mia); |
|
1186
|
|
|
$xoopsTpl->assign('MIAexplain', strtr(_MA_PEDIGREE_COI_MIAEX, ['[animalType]' => $moduleConfig['animalType']])); |
|
1187
|
|
|
|
|
1188
|
|
|
if (!$ICknown[1]) { |
|
1189
|
|
|
$marked = $empty; |
|
1190
|
|
|
CONSANG(1); |
|
1191
|
|
|
} // Sire |
|
1192
|
|
|
if (!$ICknown[2]) { |
|
1193
|
|
|
$marked = $empty; |
|
1194
|
|
|
CONSANG(2); |
|
1195
|
|
|
} // Dam |
|
1196
|
|
|
$COR = 2.0 * $COIs[0] / sqrt((1. + $COIs[1]) * (1. + $COIs[2])); |
|
1197
|
|
|
$COR = mb_substr($COR, 0, 8); |
|
1198
|
|
|
if (!$COR) { |
|
1199
|
|
|
$COR = 'n.a.'; |
|
1200
|
|
|
} |
|
1201
|
|
|
$f1 = mb_substr($COIs[1], 0, 8); |
|
1202
|
|
|
$f2 = mb_substr($COIs[2], 0, 8); |
|
1203
|
|
|
if (!$f1) { |
|
1204
|
|
|
$f1 = 'n.a.'; |
|
1205
|
|
|
} |
|
1206
|
|
|
if (!$f2) { |
|
1207
|
|
|
$f2 = 'n.a.'; |
|
1208
|
|
|
} |
|
1209
|
|
|
$SSDcor = (100 * $COR); |
|
1210
|
|
|
$SSDsire = (100 * $f2); |
|
1211
|
|
|
$SSDdam = (100 * $f1); |
|
1212
|
|
|
} |
|
1213
|
|
|
|
|
1214
|
|
|
$xoopsTpl->assign( |
|
1215
|
|
|
'SSDtitle', |
|
1216
|
|
|
strtr(_MA_PEDIGREE_COI_SSDTIT, [ |
|
1217
|
|
|
'[father]' => $moduleConfig['father'], |
|
1218
|
|
|
'[mother]' => $moduleConfig['mother'], |
|
1219
|
|
|
]) |
|
1220
|
|
|
); |
|
1221
|
|
|
$xoopsTpl->assign('SSDcortit', _MA_PEDIGREE_COI_SSDcor); |
|
1222
|
|
|
$xoopsTpl->assign('SSDbsd', strtr(_MA_PEDIGREE_COI_SDDbsd, ['[father]' => $moduleConfig['father'], '[mother]' => $moduleConfig['mother']])); |
|
1223
|
|
|
$xoopsTpl->assign('SSDcor', $SSDcor); |
|
1224
|
|
|
|
|
1225
|
|
|
$xoopsTpl->assign('SSDS', _MA_PEDIGREE_COI_COI . _MA_PEDIGREE_FROM . strtr(_MA_PEDIGREE_FLD_FATH, ['[father]' => $moduleConfig['father']])); |
|
1226
|
|
|
$xoopsTpl->assign('SSDsire', $SSDsire); |
|
1227
|
|
|
$xoopsTpl->assign('SSDM', _MA_PEDIGREE_COI_COI . _MA_PEDIGREE_FROM . strtr(_MA_PEDIGREE_FLD_MOTH, ['[mother]' => $moduleConfig['mother']])); |
|
1228
|
|
|
$xoopsTpl->assign('SSDdam', $SSDdam); |
|
1229
|
|
|
|
|
1230
|
|
|
// echo "SSDsire : ".$SSDsire."<br>"; |
|
1231
|
|
|
// echo "SSDdam : ".$SSDdam."<br>"; |
|
1232
|
|
|
// print_r($COIs); |
|
1233
|
|
|
|
|
1234
|
|
|
$xoopsTpl->assign( |
|
1235
|
|
|
'SSDexplain', |
|
1236
|
|
|
strtr(_MA_PEDIGREE_COI_SSDEX, [ |
|
1237
|
|
|
'[father]' => $moduleConfig['father'], |
|
1238
|
|
|
'[mother]' => $moduleConfig['mother'], |
|
1239
|
|
|
'[animalType]' => $moduleConfig['animalTypes'], |
|
1240
|
|
|
]) |
|
1241
|
|
|
); |
|
1242
|
|
|
$xoopsTpl->assign('TNXtitle', _MA_PEDIGREE_COI_TNXTIT); |
|
1243
|
|
|
$xoopsTpl->assign('TNXcontent', _MA_PEDIGREE_COI_TNXCON); |
|
1244
|
|
|
$xoopsTpl->assign('Name', _MA_PEDIGREE_FLD_NAME); |
|
1245
|
|
|
$xoopsTpl->assign('Gender', _MA_PEDIGREE_FLD_GEND); |
|
1246
|
|
|
$xoopsTpl->assign('Children', strtr(_MA_PEDIGREE_FLD_PUPS, ['[children]' => $moduleConfig['children']])); |
|
1247
|
|
|
|
|
1248
|
|
|
//add data to smarty template |
|
1249
|
|
|
$xoopsTpl->assign('explain', _MA_PEDIGREE_EXPLAIN); |
|
1250
|
|
|
|
|
1251
|
|
|
//comments and footer |
|
1252
|
|
|
require XOOPS_ROOT_PATH . '/footer.php'; |
|
1253
|
|
|
|
mambax7 /
pedigree
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