mambax7 / pedigree

coi.php

<?php
/*
 You may not change or alter any portion of this comment or credits of
 supporting developers from this source code or any supporting source code
 which is considered copyrighted (c) material of the original comment or credit
 authors.

 This program 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.
 */

/**
 * Module: Pedigree
 *
 * @package   XoopsModules\Pedigree
 * @author    XOOPS Module Development Team
 * @copyright Copyright (c) 2001-2019 {@link https://xoops.org XOOPS Project}
 * @license   https://www.gnu.org/licenses/gpl-2.0.html GNU Public License
 */

use Xmf\Request;
use XoopsModules\Pedigree;

ini_set('memory_limit', '32M');

//require_once  \dirname(__DIR__, 2) . '/mainfile.php';
require_once __DIR__ . '/header.php';
$moduleDirName = basename(__DIR__);
xoops_loadLanguage('main', $moduleDirName);
require_once XOOPS_ROOT_PATH . '/modules/' . $moduleDirName . '/include/common.php';

$GLOBALS['xoopsOption']['template_main'] = 'pedigree_coi.tpl';
require XOOPS_ROOT_PATH . '/header.php';

//get module configuration
/** @var XoopsModuleHandler $moduleHandler */
$moduleHandler = xoops_getHandler('module');
$module        = $moduleHandler->getByDirname($moduleDirName);
$configHandler = xoops_getHandler('config');
$moduleConfig  = $configHandler->getConfigsByCat(0, $module->getVar('mid'));

The method getConfigsByCat() does not exist on XoopsObjectHandler. It seems like you code against a sub-type of XoopsObjectHandler such as XoopsPersistableObjectHandler.

global $xoopsTpl, $xoopsDB, $moduleConfig;

//start kinship.php code -- help !!
/* ************************************************************************************* */
/*
     This program calculates the coefficient of inbreeding (IC, or COI, or F)
     for the offspring of a couple of animals, given by their IDs (s=sire_ID&d=dam_ID),
     or for a given animal given by its ID (a=animal_ID).

     By default, all known ascendants are used.
     However, maximum count of distinct ascendants is limited to $nb_maxi (default=600)
              [higher values for $nb_maxi could lead to calculations ending in timeout],
              or depth of tree can be limited to $nb_gen generations (default = 8).
*/
/* ************************************************************************************* */

if (!isset($verbose)) {
    $verbose = 0;
} // don't display different steps of ICs calculation
if (!isset($detail)) {
    $detail = 1;
} // don't display detail results [faster]
if (!isset($nb_maxi)) {
    $nb_maxi = 600;
} // maximum count of distinct ascendants
if (!isset($nb_gen)) {
    $nb_gen = 8;
} // maximum count of generations of ascendants
if (!isset($pedigree)) {
    $pedigree = 0;
} // dont't display sketch pedigree [faster]
if (!isset($max_dist)) { // maximum length of implex loops
    if ($nb_gen > 9) {
        $max_dist = 14;
    } else {
        if (9 == $nb_gen) {
            $max_dist = 17;
        } else {
            if (8 == $nb_gen) {
                $max_dist = 18;
            } else {
                $max_dist = 99;
            }
        }
    }
}

$empty = []; // an empty array
$sql1  = 'SELECT id, father, mother, roft FROM ' . $GLOBALS['xoopsDB']->prefix('pedigree_registry') . ' WHERE id ';

// input data arrays:
$IDs     = $empty;
$fathers = $empty;
$mothers = $empty;

// working arrays:
$inds    = $empty;
$marked  = $empty;
$ICknown = $empty;
$deltaf  = $empty;
$pater   = $empty;
$mater   = $empty;
$chrono  = $empty;

// Coefficients of Inbreeding array (result):
$COIs = $empty;

/* ******************************  FUNCTIONS  ********************************* */

/**
 * @return int
 */
function chrono_sort()
{
    global $IDs, $inds, $fathers, $mothers, $chrono, $nl, $detail;
    $impr  = 0;
    $modif = 1;
    $nloop = 0;
    $nba   = count($IDs);
    // print_r ($IDs) ;
    // echo "<b>231 : $IDs[231] $fathers[231] $mothers[231] $chrono[231] $inds[231] </b><br>\n" ;
    foreach ($IDs as $i => $v) {
        $chrono[$i] = 1;
    } // initialize all chronological ranks to 1
    $chrono[0] = 0; // except animal #0 (at 0 rank).
    while ($modif && $nloop < 40) {
        $modif = 0;
        ++$nloop;
        for ($i = 1; $i < $nba; ++$i) {
            $s = $fathers[$i];
            if ($s) {
                $s = $inds[$s];
            }
            $d = $mothers[$i];
            if ($d) {
                $d = $inds[$d];
            }
            if ($s && $chrono[$s] <= $chrono[$i]) {
                $chrono[$s] = $chrono[$i] + 1;
                $modif      = 1;
            }
            if ($d && $chrono[$d] <= $chrono[$i]) {
                $chrono[$d] = $chrono[$i] + 1;
                $modif      = 1;
            }
        }
    }
    if (40 == $nloop) {
        die('Endless loop detected. Stopped.');

Using exit here is not recommended.

    }
    array_multisort($chrono, $IDs, $fathers, $mothers);
    $depth = $chrono[$nba - 1];

The assignment to $depth is dead and can be removed.

    //commentes out by JC
    //if ($detail) echo "<br>Chronological ranking done : Pedigree stretched over <b>$depth</b> generations.<br>$nl" ;
    if ($impr) {
        echo "</center><pre>$nl $nl";
        foreach ($chrono as $i => $val) {
            echo "<b>$i</b> : $val $IDs[$i] $fathers[$i] $mothers[$i] $nl";
        }
        echo "</pre>$nl";
        die('</html>');

Using exit here is not recommended.

    }
    $inds = array_flip($IDs);

    return 0;
}

/**
 * @param $s
 *
 * @return array
 */
function fetch_record($s)
{
    global $database;
    $r = $GLOBALS['xoopsDB']->queryF($database, $s);
    $n = 0;
    if ($r) {
        $n = $GLOBALS['xoopsDB']->getRowsNum($r);
    }
    if (0 == $n) {
        $record = ['0'];
    } else {
        $record = $GLOBALS['xoopsDB']->fetchBoth($r);
    }

    return $record;
}

/**
 * @param $ind
 * @param $gen
 *
 * @return int
 */
function count_all($ind, $gen)
{
    global $inds, $nb_gen, $nb_all, $fathers, $mothers;
    if ($ind) {
        ++$nb_all;
    }
    $s = $fathers[$ind];
    $d = $mothers[$ind];
    if ($s && $gen < $nb_gen) {
        count_all($s, $gen + 1);
    }
    if ($d && $gen < $nb_gen) {
        count_all($d, $gen + 1);
    }

    return 0;
}

/**
 * @param $ch
 * @param $niv
 *
 * @return int
 */
function add_multi($ch, $niv)
{
    global $implx, $couls, $nl;
    reset($implx);
    $first = 1;
    foreach ($implx as $im => $impl) {
        if ($impl[0] == $ch || $impl[1] == $ch) {
            if ($niv > 1 && $first) {
                echo "<br>$nl";
            } else {
                echo '&nbsp;&nbsp;&nbsp;';
            }
            $i     = $im + 1;
            $j     = min($im, 6);
            $c     = $couls[$j];
            $first = 0;
            echo '<span color=' . $c . ' size="+2"><b>*' . $i . '*</b></span>';
        }
    }

    return 0;
}

/**
 * @param $ind
 * @param $gen
 * @param $class
 *
 * @return int
 */
function output_animal($ind, $gen, $class)
{
    global $depth, $IDs, $fathers, $mothers, $nl;
    if ($gen > $depth) {
        return 0;
    }
    $cell_content = '&Oslash;';
    if ($ind || 0 == $gen) {
        $ID           = $IDs[$ind];
        $ani          = set_name($ID);
        $name         = $ani[1];

The assignment to $name is dead and can be removed.

        $name         = $ID;
        $cell_content = Pedigree\Utility::showParent($name) . $nl;
    }
    $rowspan = 1 << ($depth - $gen);
    echo '<td rowspan=' . $rowspan . ' align="center" class="' . $class . '">' . $cell_content . "</td>$nl";
    if ($gen < $depth) {
        $sire = 0;
        if ($ind || 0 == $gen) {
            $sire = $fathers[$ind];
        }
        output_animal($sire, $gen + 1, '0');
        $dam = 0;
        if ($ind || 0 == $gen) {
            $dam = $mothers[$ind];
        }
        output_animal($dam, $gen + 1, '1');
    } else {
        echo "</tr><tr>$nl";
    }

    return 0;
}

/**
 * @return int
 */
function SKETCH_PEDIGREE()
{
    global $nl, $detail, $depth, $IDs;
    // print_r ($IDs) ;
    echo $nl
         . '<br>'
         . $nl
         . '<table border="3" cellpadding="4" width="85%"" cellpadding="0" cellspacing="0">'
         . $nl
         . '<tr><th colspan="10" align="center">SKETCH &nbsp; PEDIGREE &nbsp; OF COMMON PROGENY</th></tr>'
         . $nl
         . '<tr align="center" valign="middle"><th>Progeny</th><th>'
         . _('Sire / Dam')
         . '</th>';
    if ($depth >= 2) {
        echo '<th>' . _('Grandparents') . '</th>' . $nl;
    }
    if ($depth >= 3) {
        echo '<th>' . _('Great-Grandparents') . '</th>' . $nl;
    }
    if ($depth >= 4) {
        echo '<th>3xGr. P.</th>' . $nl;
    }
    if ($depth >= 5) {
        echo '<th>4xGr. P.</th>' . $nl;
    }
    if ($depth >= 6) {
        echo '<th>5xGr. P.</th>' . $nl;
    }
    if ($depth >= 7) {
        echo '<th>6xGr. P.</th>' . $nl;
    }
    echo '</tr><tr>';
    output_animal(0, 0, '0'); /* output the sketch pedigree */
    echo $nl . '</tr></table>' . $nl . '<p>' . $nl;

    return 0;
}

/**
 * @return int
 */
function GENEALOGY()
{
    global $IDs, $fathers, $mothers, $inds, $nb_gen, $nb_maxi, $nbani, $nl, $sql1;
    $impr       = 0;
    $fathers[0] = $IDs[1];
    $mothers[0] = $IDs[2];
    $fathers[1] = 0;
    $mothers[1] = 0;
    $fathers[2] = 0;
    $mothers[2] = 0;
    $last       = 2;
    if ($impr) {
        echo "<!-- genealogy 'de cujus' (gener. 0) : $IDs[0] = $IDs[1] x $IDs[2] -->$nl";
    }
    $generation = [$IDs[1], $IDs[2]]; // starting with first generation (sire and dam)
    $nbtot      = 0; // count of total known ascendants within $nb_gen generations
    for ($nloop = 1, $tot = 2; $last <= $nb_maxi && $nloop <= $nb_gen; ++$nloop) {
        $nbtot      += $tot; // count of total known ascendants within $nb_gen generations
        $nbani      = $last; // count of    distinct ascendants within $nb_gen generations
        $list       = implode(',', array_unique($generation));
        $generation = [];
        $tot        = 0;
        if ($impr) {
            echo "    [$list]$nl";
        }

        // HERE IS FETCHED EACH TRIPLET [ID, sire_ID, dam_ID] :
        $r = $GLOBALS['xoopsDB']->queryF("$sql1 IN ($list)");
        while (false !== ($rec = $GLOBALS['xoopsDB']->fetchBoth($r))) {
            $a = $rec[0] + 0;
            $s = $rec[1] + 0;
            $d = $rec[2] + 0;
            if (!isset($a)) {
                echo "ERROR : $a = $s x $d for list = '$list'<br>\n";
            }
            if ($s) {
                ++$tot;
            }
            if ($d) {
                ++$tot;
            }
            $j           = array_keys($IDs, $a);
            $j           = $j[0];
            $fathers[$j] = $s;
            $mothers[$j] = $d;
            if ($s && !in_array($s, $IDs)) {
                $i           = ++$last;
                $IDs[$i]     = $s;
                $fathers[$i] = 0;
                $mothers[$i] = 0;
                if ($s) {
                    $generation[] = $s;
                }
            }
            if ($d && !in_array($d, $IDs)) {
                $i           = ++$last;
                $IDs[$i]     = $d;
                $fathers[$i] = 0;
                $mothers[$i] = 0;
                if ($s) {
                    $generation[] = $d;
                }
            }
            if ($impr) {
                echo "<pre>genealogy ascendant (gener. $nloop) : $a = $s x $d  [tot = $tot]$nl</pre>";
            }
        }
        if (!count($generation)) {
            break;
        }
    }

    if ($nloop <= $nb_gen) {
        $nb_gen = $nloop;
    } // tree cut by $nb_maxi !

    reset($IDs);
    $inds = array_flip($IDs);

    chrono_sort();

    return $nbtot;
}

/**
 * @param $p
 *
 * @return int
 */
function dist_p($p)
{
    global $IDs, $fathers, $mothers, $pater, $nb_gen, $detail, $nl;
    // Anim #P is the sire
    $listall   = [$p];
    $listnew   = [$p];
    $pater     = [];
    $pater[$p] = 1;
    for ($nloop = 2; $nloop < ($nb_gen + 1); ++$nloop) {
        $liste = [];
        foreach ($listnew as $i) {
            $s = $fathers[$i];
            $d = $mothers[$i];
            if ($s && !$pater[$s]) {
                $pater[$s] = $nloop;
            } // least distance from $s to sire's progeny
            if ($d && !$pater[$d]) {
                $pater[$d] = $nloop;
            } // least distance from $d to sire's progeny
            if ($s) {
                $liste[] = $s;
            }
            if ($d) {
                $liste[] = $d;
            }
        }
        if (!count($liste)) {
            break;
        }
        //commented pout by jc
        //if (in_array ($IDs[2], $liste) && !$detail)
        //{ echo "<p>DAM is an ascendant (at $nloop generations) of SIRE.  Stopped." ;
        // die ("</body></html>$nl") ; }
        $listnew = array_diff(array_unique($liste), $listall);
        /* $list1 = join (' ', $listall) ; $list2 = join ('+', $listnew) ;
             echo "<!-- P ($nloop) $list1/$list2 -->$nl" ; */
        //        $listall = array_merge($listall, $listnew);
        $listall[] = $listnew;
    }
    //    $listall = call_user_func_array('array_merge', $listall);
    $listall = array_merge(...$listall);

The assignment to $listall is dead and can be removed.

    // Here $pater array contains list of all distinct ascendants of #P (including P himself)
    // Values of $pater are minimum distances to #P (in generations) +1
    return 0;
}

/**
 * @param $m
 *
 * @return int
 */
function dist_m($m)
{
    global $IDs, $fathers, $mothers, $mater, $nb_gen, $detail, $nl;
    // Anim #M is the dam
    $listall   = [$m];
    $listnew   = [$m];
    $mater     = [];
    $mater[$m] = 1;
    for ($nloop = 2; $nloop <= ($nb_gen + 1); ++$nloop) {
        $liste = [];
        foreach ($listnew as $i) {
            $s = $fathers[$i];
            $d = $mothers[$i];
            if ($s && !isset($mater[$s])) {
                $mater[$s] = $nloop;
            } // least distance from $s to dam's progeny
            if ($d && !isset($mater[$d])) {
                $mater[$d] = $nloop;
            } // least distance from $d to dam's progeny
            // echo "I=" . $i . " MATER(I)=" . $mater[$i] . " NLOOP=" . $nloop . "<br>$nl" ;
            if ($s) {
                $liste[] = $s;
            }
            if ($d) {
                $liste[] = $d;
            }
        }
        if (!count($liste)) {
            break;
        }
        //commented out by jc
        //if (in_array ($IDs[1], $liste) && !$detail)
        // { echo "<p>SIRE is an ascendant (at $nloop generations) of DAM.  Stopped." ;
        //  die ("</body></html>$nl") ; }
        $listnew = array_diff(array_unique($liste), $listall);
        // $list1 = join (' ', $listall) ; $list2 = join ('+', $listnew) ; echo "M ($nloop) $list1/$list2 $nl" ;
        //        $listall = array_merge($listall, $listnew);
        $listall[] = $listnew;
    }
    //    $listall = call_user_func_array('array_merge', $listall);
    $listall = array_merge(...$listall);

The assignment to $listall is dead and can be removed.

    // Here $mater array contains list of all distinct ascendants of #M (including M herself)
    // Values of $mater are minimum distances to #M (in generations) +1
    return 0;
}

/**
 * @return array
 */
function calc_dist() /* Common Ascendants and their distances */
{
    global $IDs, $fathers, $mothers, $nbanims, $pater, $mater, $empty, $nb_gen, $nl;
    global $dmax, $detail, $nb_gen;
    $distan = [];
    // dist_m (2) ;   has already been called
    dist_p($fathers[0]);
    $dmax = 0;
    $impr = 0;
    $dmx  = 7;
    if ($detail) {
        $dmx += 2;
    }
    // ksort ($pater) ; print_r ($pater) ; echo "<br>$nl" ; ksort ($mater) ; print_r ($mater) ; echo "<br>$nl" ;
    foreach ($pater as $i => $p) {
        if ($p) {
            $m = $mater[$i];
            if ($m) {
                $di = $p + $m;
                if ($impr) {
                    echo " $i : $p + $m = $di <br>$nl";
                }
                if (!$dmax) {
                    $dmax = $dmx + $di - ceil($di / 2.);
                }
                if ($di > ($dmax + 2)) {
                    continue;
                }
                $distan[$i] = $di;
            }
        }
    }
    if (!$dmax) {
        $dmax = 2 * $nb_gen - 2;
    }

    return $distan;
}

/**
 * @param $p
 * @param $m
 * @param $a
 * @param $ndist
 *
 * @return int
 */
function mater_side($p, $m, $a, $ndist)
{
    global $fathers, $mothers, $marked, $COIs, $deltaf, $ICknown, $verbose, $nl, $chrono, $paternal_rank, $max_dist;
    if (!$m || $ndist > $max_dist) {
        return 0;
    }
    if ($p == $m) {
        /* IMPLEX FOUND (node of consanguinity) { for Anim #A */
        $already_known = $ICknown[$p];
    }
    if (!$already_known) {

The variable $already_known does not seem to be defined for all execution paths leading up to this point.

        CONSANG($p);
    } // MAIN RECURSION:
    $ICp = $COIs[$p]; // we need to know the IC of Parent for Wright's formula
    if ($verbose && !$already_known && $ICp > 0.001 * $verbose) {
        echo "IC of Animal $p is $ICp$nl";
    }

    $incr = 1.0 / (1 << $ndist) * (1. + $ICp); // ******** applying WRIGHT's formula ********

    // [Note:  1 << $ndist is equal to 2 power $ndist]
    $COIs[$a] += $incr; // incrementing the IC of AnimC
    if (0 == $a) {
        $deltaf[$p] += $incr;
        /* contribution of Anim #P to IC of Anim #0 */ // if ($verbose && $a == 0 && $incr > 0.0001*$verbose)
        //    echo "Animal $p is contributing for " . substr ($deltaf[$p], 0, 10) . " to the IC of Animal $a$nl" ;
    } else {
        if (!$marked[$m] && $chrono[$m] < $paternal_rank) {
            mater_side($p, $fathers[$m], $a, $ndist + 1);
            mater_side($p, $mothers[$m], $a, $ndist + 1);
        }
    }

    return 0;
}

/**
 * @param $p
 * @param $m
 * @param $a
 * @param $pdist
 * @return int
 */
function pater_side($p, $m, $a, $pdist)
{
    global $mater, $fathers, $mothers, $marked, $chrono, $paternal_rank;
    if (!$p) {
        return 0;
    }
    $paternal_rank = $chrono[$p];
    $marked[$p]    = 1; /* cut paternal side */
    if ($a || isset($mater[$p])) {
        mater_side($p, $m, $a, $pdist);
    }
    pater_side($fathers[$p], $m, $a, $pdist + 1);
    pater_side($mothers[$p], $m, $a, $pdist + 1);
    $marked[$p] = 0; /* free paternal side */

    return 0;
}

/**
 * @param $a
 *
 * @return int
 */
function CONSANG($a)
{
    global $fathers, $mothers, $ICknown, $COIs, $nl;
    if (!$a || $ICknown[$a]) {
        return 0;
    }
    if (-1 == $a) {
        $a = 0;
    } // particular case : a= -1 means Anim #0 (to bypass above test)
    $IC_if_deadend = 0.0; // 0.0 means taht deadends are deemed to be total outcrosses...
    // if IC was already stored in the database for Aminal #A, it should be used here instead of 0.0
    $p = $fathers[$a];
    $m = $mothers[$a];
    if (!$p || !$m) {
        $COIs[$a]    = $IC_if_deadend;
        $ICknown[$a] = 2;

        return 0;
    }

    if ($verbose) {

The variable $verbose seems to be never defined.

        echo "</center><pre>$nl";
    }
    pater_side($p, $m, $a, 1); // launch tree exploration
    if ($verbose) {
        echo "</pre><div style=\"text-align: center;\">$nl";
    }

    $ICknown[$a] = 1;
    $p           = $fathers[$a];
    $m           = $mothers[$a];
    foreach ($fathers as $i => $pere) {/* siblings share the same COI value */
        if ($i != $a && $pere == $p && $mothers[$i] == $m) {
            $COIs[$i]    = $COIs[$a];
            $ICknown[$i] = 1;
        }
    }

    // echo "<!-- COI($a) = $COIs[$a] $IDs[$a] ($fathers[$a] x $mothers[$a])-->$nl" ;
    return 0;
}

/**
 * @param $nb_gen
 * @param $nloop
 *
 * @return int
 */
function boucle($nb_gen, $nloop)
{
    global $fathers, $mothers, $nbanims, $listing, $nl, $IDs;
    $nbtot   = 0;
    $listing = '';
    if ($nloop < ($nb_gen + 20)) {
        $nloop = $nb_gen + 20;
    }
    $list = [0 => 1];
    //print_r($list);
    /* initialize list with Anim0 (rank = 1) */
    for ($j = 1; $j < $nloop; ++$j) {
        $new = 0;
        foreach ($list as $i => $rank) {
            if (false !== ($s = $fathers[$i])) {
                if (!$list[$s]) {
                    $new = 1;
                    if ($j < $nb_gen) {
                        ++$nbtot;
                    }
                }
                $list[$s] = $rank + 1;
                if ($j < $nb_gen) {
                    ++$nbtot;
                }
                if ($j > $nloop - 10) {
                    $listing .= "Loop $j: Animal #$s " . $IDs[$s] . $nl;
                }
            }
            if (false !== ($d = $mothers[$i])) {
                if (!$list[$d]) {
                    $new = 1;
                    if ($j < $nb_gen) {
                        ++$nbtot;
                    }
                }
                $list[$d] = $rank + 1;
                if ($j < $nb_gen) {
                    ++$nbtot;
                }
                if ($j > $nloop - 10) {
                    $listing .= "Loop $j: Animal #$d " . $IDs[$d] . $nl;
                }
            }
        }
        if (!$new) {
            break;
        }
    }
    if ($new) {

The variable $new does not seem to be defined for all execution paths leading up to this point.

        $nbtot = 0;
    } /* Endless loop detected (see listing) */

    return $nbtot;
}

if (!function_exists('html_accents')) {
    /**
     * @param $string
     * @return mixed
     */
    function html_accents($string)
    {
        return $string;
    }
}

/**
 * @param $ID
 *
 * @return array
 */
function set_name($ID)
{
    //    global $sql2, $sql2bis, $xoopsDB;
    $name = ' ';

The assignment to $name is dead and can be removed.

    $ID   = (int)$ID;
    $ani  = [];
    if ($ID) {
        $sqlQuery    = 'SELECT id, pname, roft FROM ' . $GLOBALS['xoopsDB']->prefix('pedigree_registry') . " WHERE id = '$ID'";
        $queryResult = $GLOBALS['xoopsDB']->query($sqlQuery);
        $ani         = $GLOBALS['xoopsDB']->fetchBoth($queryResult);
        /*
        $name        = $ani[1];
        if ($sql2bis) { // true for E.R.o'S. only
            $name = html_accents($name);
            //$affx = $ani[5] ;  // affix-ID
            if ($affx) {
                $affix  = fetch_record("$sql2bis '$affx'");
                $type   = $affix[1];
                $affixe = html_accents($affix[0]);
                if ($type[0] === 'P') {
                    $name = '<i>' . $affixe . '</i>&nbsp;' . $name;
                }
                if ($type[0] === 'S') {
                    $name = $name . '&nbsp;<i>' . $affixe . '</i>';
                }
            }
            $ani[1] = $name;
        }
               */
    }

    return $ani;
}

/**
 * @param $ems
 *
 * @return string
 */
function Ems_($ems)
{
    if (function_exists('Ems')) {
        return Ems($ems);
    }
    if (!$ems) {
        return '&nbsp;';
    }
    $e   = str_replace(' ', '+', $ems);
    $res = '<a href="#" style="text-decoration:none;" onClick="' . "window.open('http://www.somali.asso.fr/eros/decode_ems.php?$e'," . "'', 'resizable=no,width=570,height=370')" . '"' . "><b>$ems</b></a>";

    return $res;
}

/**
 * @param $ID
 *
 * @return string
 */
function one_animal($ID)
{
    global $xoopsDB;
    global $sex, $val, $sosa, $detail, $sql3;
    $content = '';
    $sosa    = 12;
    // echo '<div style="position:relative;float:right;width=2.0em;color=white;">' . $sosa . '</div>' ;
    $animal = set_name($ID);

    if (is_array($animal)) {

The condition is_array($animal) is always true.

        [$ID, $name, $sex, $hd, $ems] = $animal;
    }
    $sqlQuery    = 'SELECT SQL_CACHE COUNT(id) FROM ' . $GLOBALS['xoopsDB']->prefix('pedigree_registry') . " where father = '$ID' or mother = '$ID'";
    $queryResult = $GLOBALS['xoopsDB']->queryF($sqlQuery);
    $nb          = $GLOBALS['xoopsDB']->fetchBoth($queryResult);
    $nb_children = $nb[0];
    if (0 == $nb_children) {
        $nb_children = _MA_PEDIGREE_COI_NO;
    }
    //$dogid = $animal[0];
    $content .= '<tr><td><a href="dog.php?id=' . $ID . '">' . stripslashes($name) . '</a>';

The variable $name does not seem to be defined for all execution paths leading up to this point.

    // if ($nb_enf == 0) echo ' ø' ;
    if ($val) {
        $content .= $val;
    }
    if (1 == $sex) {
        $geslacht = '<img src="assets/images/female.gif">';
    }
    if (0 == $sex) {
        $geslacht = '<img src="assets/images/male.gif">';
    }
    $content .= '</td><td>' . $geslacht . '</td><td>' . $nb_children . _MA_PEDIGREE_COI_OFF . '</td></tr>';

The variable $geslacht does not seem to be defined for all execution paths leading up to this point.

    return $content;
}

/* %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%  MAIN  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% */

$nl = "\n"; // the newline character

//edit by jc
//$link = @mysqli_pconnect ($host, $database, $password)
//   or   die ("<html><body>Connection to database failed.</body></html>") ;

//$a = '';
$s      = Request::getInt('s', 0, 'GET'); //_GET['s'];
$d      = Request::getInt('d', 0, 'GET'); //$_GET['d'];
$detail = Request::getString('detail', '', 'GET'); //$_GET['detail'];

if (isset($si)) {
    $s = Pedigree\Utility::findId($si);
}
if (isset($da)) {
    $d = Pedigree\Utility::findId($da);
}
//test for variables
//echo "si=".$si." da=".$da." s=".$s." d=".$d;
$utils = $GLOBALS['xoopsDB']->queryF("SELECT user(), date_format(now(),'%d-%b-%Y')");
[$who, $jourj] = $GLOBALS['xoopsDB']->fetchBoth($utils);

if (isset($IC)) {
    $detail = -1;
    $a      = $IC;
}

if (!isset($detail)) {
    $detail = 0;
}

if (!isset($a)) {
    if (isset($s) && !isset($d)) {
        $a = $s;
        $s = '';
    }
    if (isset($d) && !isset($s)) {
        $a = $d;
        $d = '';
    }
}

if (isset($a)) {
    $sqlQuery    = 'SELECT id, father, mother, roft FROM ' . $GLOBALS['xoopsDB']->prefix('pedigree_registry') . " WHERE id  = '$a'";
    $queryResult = $GLOBALS['xoopsDB']->query($sqlQuery);
    $rowhond     = $GLOBALS['xoopsDB']->fetchBoth($queryResult);
    $a           = $rowhond['id'];
    $s           = $rowhond['father'];
    $d           = $rowhond['mother'];
}
$a += 0;
$s += 0;
$d += 0; // [IDs are numbers]

$xoopsTpl->assign('ptitle', _MA_PEDIGREE_COI_CKRI);
$xoopsTpl->assign('pcontent', strtr(_MA_PEDIGREE_COI_CKRI_CT, ['[animalType]' => $moduleConfig['animalType']]));

if (!$s && !$d) {
    $error = _MA_PEDIGREE_COI_SPANF1 . $a . _MA_PEDIGREE_COI_SPANF2;
    $xoopsTpl->assign('COIerror', $error);
}

$maxn_ = 1000;
$maxr_ = 9;

$maxn     = $maxn_;
$maxr     = $maxr_;
$cinnamon = 0;
$chocolat = 0;
$dilution = 0;
$sexlred  = 0;

$nivomin = -$maxr; /* Maximal depth of recursion (-10) */
$codec   = 0;
$gens    = 4; /* 4 gens. for both pedigrees of couple */
$litter  = 0;

// echo "s:".$s."<br>";
// echo "d:".$d."<br>";

$codec1 = $d;
$codec2 = $s;
$val    = '';

if (!$s && $d) {
    $codec1 = $d;
    $codec2 = 0;
}
if ($codec1 == $codec2) {
    $codec2 = 0;
}

$sqlQuery    = 'SELECT father, mother, roft FROM ' . $GLOBALS['xoopsDB']->prefix('pedigree_registry') . " WHERE id  = '$codec1'";
$queryResult = $GLOBALS['xoopsDB']->query($sqlQuery);
$rowhond     = $GLOBALS['xoopsDB']->fetchBoth($queryResult);
$a1          = $rowhond['id'];
$s1          = $rowhond['father'];
$d1          = $rowhond['mother'];
$sex1        = $rowhond['roft'];

// echo "sqlquery:".$sqlQuery."<br>";

$sqlQuery    = 'SELECT father, mother, roft FROM ' . $GLOBALS['xoopsDB']->prefix('pedigree_registry') . " WHERE id  = '$codec2'";
$queryResult = $GLOBALS['xoopsDB']->query($sqlQuery);
$rowhond     = $GLOBALS['xoopsDB']->fetchBoth($queryResult);
$a2          = $rowhond['id'];
$s2          = $rowhond['father'];
$d2          = $rowhond['mother'];
$sex2        = $rowhond['roft'];

// echo "sqlquery:".$sqlQuery."<br>";

//if ($sex1 == '0' && $sex2 == '1') { $a3 = $a1 ; $a1 = $a2 ; $a2 = $a3 ; }   /* permute dam and sire */
$codec1 = $a1;
$codec2 = $a2;
if (!isset($s1) || !isset($d1) || !isset($s2) || !isset($d2)) {
    $xoopsTpl->assign('COIerror', _MA_PEDIGREE_COI_SGPU);
}

$title   = strtr(_MA_PEDIGREE_FLD_FATH, ['[father]' => $moduleConfig['father']]) . ' (' . stripslashes(Pedigree\Utility::showParent($codec2)) . ')' . _MA_PEDIGREE_COI_AND . strtr(_MA_PEDIGREE_FLD_MOTH, ['[mother]' => $moduleConfig['mother']]) . ' (' . stripslashes(
        Pedigree\Utility::showParent($codec1)
    ) . ')';
$content = stripslashes(one_animal($codec2));
$content .= stripslashes(one_animal($codec1));
$val     = '';
$xoopsTpl->assign('SADtitle', $title);
$xoopsTpl->assign('SADcontent', $content);
$xoopsTpl->assign(
    'SADexplain',
    strtr(_MA_PEDIGREE_COI_SDEX, [
        '[animalType]'  => $moduleConfig['animalType'],
        '[animalTypes]' => $moduleConfig['animalTypes'],
        '[children]'    => $moduleConfig['children'],
    ])
);

$de_cujus = 0;
$sire_ID  = Request::getInt('s', 0, 'GET'); //$_GET['s'];
$dam_ID   = Request::getInt('d', 0, 'GET'); //$_GET['d'];

$rec     = 'SELECT id FROM ' . $GLOBALS['xoopsDB']->prefix('pedigree_registry') . " WHERE father = '" . $sire_ID . "' AND mother = '" . $dam_ID . "' ORDER BY pname";
$result  = $GLOBALS['xoopsDB']->query($rec);
$content = '';
while (false !== ($row = $GLOBALS['xoopsDB']->fetchArray($result))) {
    $content .= one_animal($row['id']);
}

$xoopsTpl->assign(
    'COMtitle',
    strtr(_MA_PEDIGREE_COI_COMTIT, [
        '[father]' => $moduleConfig['father'],
        '[mother]' => $moduleConfig['mother'],
    ])
);
$xoopsTpl->assign(
    'COMexplain',
    strtr(_MA_PEDIGREE_COI_COMEX, [
        '[animalType]' => $moduleConfig['animalType'],
        '[children]'   => $moduleConfig['children'],
    ])
);
$xoopsTpl->assign('COMcontent', $content);

if (!isset($nb_gen)) {
    $nb_gen = 7;
    if ($detail) {
        $nb_gen = 9;
    }
} elseif ($nb_gen < $pedigree) {
    $nb_gen = $pedigree;
}

$IDs = [$de_cujus + 0, $codec1 + 0, $codec2 + 0]; /* Structuring animal IDs into memory */

$nbanims = GENEALOGY(); // ************************************************************* //

for ($i = 0; $i <= $nbanims; ++$i) {
    $empty[$i] = 0;
}

foreach ($fathers as $i => $a) {
    if ($a) {
        $fathers[$i] = $inds[$a];
    }
} /* Replace parents codes */
foreach ($mothers as $i => $a) {
    if ($a) {
        $mothers[$i] = $inds[$a];
    }
} /*   by  their  indices  */

dist_m($mothers[0]); // set "$mater" array (list of all maternal ascendants), for Anim #0

/* Calculating CONSANGUINITY by dual (paternal & maternal) path method */
$f       = $empty;
$ICknown = $empty;
$deltaf  = $empty;
$marked  = $empty;
$SSDcor  = $SSDsire = $SSDdam = '';

/******************  LAUNCHING ALL RECURSIONS  ********************/
/*                                                                */
CONSANG(-1); /* [-1 is standing for de_cujus]
/*                                                                */
/******************************************************************/

$nf = ceil(100 * $COIs[0]);
if ($nf >= 55) {
    $w = _MA_PEDIGREE_COI_HUGE;
} else {
    if ($nf >= 35) {
        $w = _MA_PEDIGREE_COI_VHIG;
    } else {
        if ($nf >= 20) {
            $w = _MA_PEDIGREE_COI_HIGH;
        } else {
            if ($nf >= 10) {
                $w = _MA_PEDIGREE_COI_MEDI;
            } else {
                if ($nf >= 05) {
                    $w = _MA_PEDIGREE_COI_LOW;
                } else {
                    if ($nf >= 02) {
                        $w = _MA_PEDIGREE_COI_VLOW;
                    } else {
                        if ($nf >= 01) {
                            $w = _MA_PEDIGREE_COI_VVLO;
                        } else {
                            $w = _MA_PEDIGREE_COI_TLTB;
                        }
                    }
                }
            }
        }
    }
}
$w = _MA_PEDIGREE_COI_TVI . ' ' . $w;

$nb_all = 0;
count_all(0, 0); // count all ascendants in flat tree

$nbmax  = (2 << $nb_gen) - 2;
$asctc  = _MA_PEDIGREE_COI_ASTC . $nb_gen . _MA_PEDIGREE_COI_ASTCGEN . $nbmax . ')';
$ascuni = _MA_PEDIGREE_COI_ASDKA . $nb_gen . _MA_PEDIGREE_COI_ASGEN;
$xoopsTpl->assign('ASCtitle', _MA_PEDIGREE_COI_ACTIT);
$xoopsTpl->assign('ASCtc', $asctc);
$xoopsTpl->assign('ASCuni', $ascuni);
$xoopsTpl->assign('ASCall', $nb_all);
$xoopsTpl->assign('ASCani', $nbani);
$xoopsTpl->assign('ASCexplain', _MA_PEDIGREE_COI_ACEX);

$f0 = mb_substr($COIs[0], 0, 8);
if (!$f0) {
    $f0 = 'n.a.';
}
$f1 = 100 * $f0;

$xoopsTpl->assign(
    'COItitle',
    strtr(_MA_PEDIGREE_COI_COITIT, [
        '[father]' => $moduleConfig['father'],
        '[mother]' => $moduleConfig['mother'],
    ])
);
$xoopsTpl->assign('COIperc', $w);
$xoopsTpl->assign('COIval', $f1);
$xoopsTpl->assign(
    'COIexplain',
    strtr(_MA_PEDIGREE_COI_COIEX, [
        '[animalType]'  => $moduleConfig['animalType'],
        '[animalTypes]' => $moduleConfig['animalTypes'],
        '[children]'    => $moduleConfig['children'],
    ])
);
$xoopsTpl->assign('COIcoi', _MA_PEDIGREE_COI_COI);
$dogid = Request::getInt('dogid', 0, 'GET');
$query = 'UPDATE ' . $GLOBALS['xoopsDB']->prefix('pedigree_registry') . ' SET coi=' . $f1 . ' WHERE id = ' . $dogid;
$GLOBALS['xoopsDB']->queryF($query);
arsort($deltaf);
$j = 1;
foreach ($deltaf as $i => $v) {
    if ($j > 12) {
        break;
    }
    ++$j;
    $code   = $IDs[$i];
    $v      = mb_substr($v, 0, 7);
    $animal = set_name($IDs[$i]);
    $name   = $animal[1];
    if (!$name) {
        $name = $i . ' [' . $IDs[$i] . ']';
    }
    if ($v > 0.0001 && $v < 1.0) {
        $dogs[] = ['id' => $code, 'name' => stripslashes($name), 'coi' => 100 * $v];
    }
}

$xoopsTpl->assign('TCAtitle', _MA_PEDIGREE_COI_TCATIT);
$xoopsTpl->assign('TCApib', _MA_PEDIGREE_COI_TCApib);
$xoopsTpl->assign('dogs', $dogs);
$xoopsTpl->assign(
    'TCAexplain',
    strtr(_MA_PEDIGREE_COI_TCAEX, [
        '[animalType]'  => $moduleConfig['animalType'],
        '[animalTypes]' => $moduleConfig['animalTypes'],
        '[children]'    => $moduleConfig['children'],
        '[mother]'      => $moduleConfig['mother'],
        '[father]'      => $moduleConfig['father'],
    ])
);

if ($detail) {
    if ($verbose) {
        $verbose = 0;
    }
    if (count($COIs) > 1) {
        $ICs = $COIs;
        arsort($ICs);
        $j = 1;
        foreach ($ICs as $i => $ic) {
            if ($j > 12) {
                break;
            }
            ++$j;
            $ID   = $IDs[$i];
            $ani  = set_name($ID);
            $name = $ani[1];
            $ic   = mb_substr($ic, 0, 6);
            if ($ic > 0.125 && $i) {
                $mia[] = ['id' => $ID, 'name' => stripslashes($name), 'coi' => 100 * $ic];
            }
        }
    }
    $xoopsTpl->assign('MIAtitle', _MA_PEDIGREE_COI_MIATIT);
    $xoopsTpl->assign('mia', $mia);
    $xoopsTpl->assign('MIAexplain', strtr(_MA_PEDIGREE_COI_MIAEX, ['[animalType]' => $moduleConfig['animalType']]));

    if (!$ICknown[1]) {
        $marked = $empty;
        CONSANG(1);
    } // Sire
    if (!$ICknown[2]) {
        $marked = $empty;
        CONSANG(2);
    } // Dam
    $COR = 2.0 * $COIs[0] / sqrt((1. + $COIs[1]) * (1. + $COIs[2]));
    $COR = mb_substr($COR, 0, 8);
    if (!$COR) {
        $COR = 'n.a.';
    }
    $f1 = mb_substr($COIs[1], 0, 8);
    $f2 = mb_substr($COIs[2], 0, 8);
    if (!$f1) {
        $f1 = 'n.a.';
    }
    if (!$f2) {
        $f2 = 'n.a.';
    }
    $SSDcor  = (100 * $COR);
    $SSDsire = (100 * $f2);
    $SSDdam  = (100 * $f1);
}

$xoopsTpl->assign(
    'SSDtitle',
    strtr(_MA_PEDIGREE_COI_SSDTIT, [
        '[father]' => $moduleConfig['father'],
        '[mother]' => $moduleConfig['mother'],
    ])
);
$xoopsTpl->assign('SSDcortit', _MA_PEDIGREE_COI_SSDcor);
$xoopsTpl->assign('SSDbsd', strtr(_MA_PEDIGREE_COI_SDDbsd, ['[father]' => $moduleConfig['father'], '[mother]' => $moduleConfig['mother']]));
$xoopsTpl->assign('SSDcor', $SSDcor);

$xoopsTpl->assign('SSDS', _MA_PEDIGREE_COI_COI . _MA_PEDIGREE_FROM . strtr(_MA_PEDIGREE_FLD_FATH, ['[father]' => $moduleConfig['father']]));
$xoopsTpl->assign('SSDsire', $SSDsire);
$xoopsTpl->assign('SSDM', _MA_PEDIGREE_COI_COI . _MA_PEDIGREE_FROM . strtr(_MA_PEDIGREE_FLD_MOTH, ['[mother]' => $moduleConfig['mother']]));
$xoopsTpl->assign('SSDdam', $SSDdam);

// echo "SSDsire : ".$SSDsire."<br>";
// echo "SSDdam : ".$SSDdam."<br>";
// print_r($COIs);

$xoopsTpl->assign(
    'SSDexplain',
    strtr(_MA_PEDIGREE_COI_SSDEX, [
        '[father]'     => $moduleConfig['father'],
        '[mother]'     => $moduleConfig['mother'],
        '[animalType]' => $moduleConfig['animalTypes'],
    ])
);
$xoopsTpl->assign('TNXtitle', _MA_PEDIGREE_COI_TNXTIT);
$xoopsTpl->assign('TNXcontent', _MA_PEDIGREE_COI_TNXCON);
$xoopsTpl->assign('Name', _MA_PEDIGREE_FLD_NAME);
$xoopsTpl->assign('Gender', _MA_PEDIGREE_FLD_GEND);
$xoopsTpl->assign('Children', strtr(_MA_PEDIGREE_FLD_PUPS, ['[children]' => $moduleConfig['children']]));

//add data to smarty template
$xoopsTpl->assign('explain', _MA_PEDIGREE_EXPLAIN);

//comments and footer
require XOOPS_ROOT_PATH . '/footer.php';