mambax7 / pedigree

coi.php

<?php

For compatibility and reusability of your code, PSR1 recommends that a file should introduce either new symbols (like classes, functions, etc.) or have side-effects (like outputting something, or including other files), but not both at the same time. The first symbol is defined on line 99 and the first side effect is on line 2.

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

require_once dirname(dirname(__DIR__)) . '/mainfile.php';

/*

43% of this comment could be valid code. Did you maybe forget this after debugging?

if (file_exists(XOOPS_ROOT_PATH . "/modules/" . $xoopsModule->dirname() . "/language/" . $xoopsConfig['language'] . "/main.php")) {
    require_once XOOPS_ROOT_PATH . "/modules/" . $xoopsModule->dirname() . "/language/" . $xoopsConfig['language'] . "/main.php";
} else {
    include_once XOOPS_ROOT_PATH . "/modules/" . $xoopsModule->dirname() . "/language/english/main.php";
}
*/

xoops_loadLanguage('main', basename(dirname(__DIR__)));

require_once(XOOPS_ROOT_PATH . "/modules/" . $xoopsModule->dirname() . "/include/functions.php");

$xoopsOption['template_main'] = "pedigree_coi.tpl";
include XOOPS_ROOT_PATH . '/header.php';

//get module configuration
$module_handler =& xoops_gethandler('module');
$module         =& $module_handler->getByDirname("pedigree");
$config_handler =& xoops_gethandler('config');
$moduleConfig   =& $config_handler->getConfigsByCat(0, $module->getVar('mid'));

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) {
        $max_dist = 14;
    } else {
        if ($nb_gen == 9) {
            $max_dist = 17;
        } else {
            if ($nb_gen == 8) {
                $max_dist = 18;
            } else {
                $max_dist = 99;
            }
        }
    }
}

$empty = array(); // an empty array
$sql1  = "select ID, father, mother, roft from " . $xoopsDB->prefix("pedigree_tree") . " 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) ;

50% of this comment could be valid code. Did you maybe forget this after debugging?

    // echo "<b>231 : $IDs[231] $fathers[231] $mothers[231] $chrono[231] $inds[231] </b><br />\n" ;

50% of this comment could be valid code. Did you maybe forget this after debugging?

    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;
                $modif      = 1;
            }
        }
    }
    if ($nloop == 40) {
        die ("Endless loop detected. Stopped.");
    }
    array_multisort($chrono, $IDs, $fathers, $mothers);
    $depth = $chrono[$nba - 1];
    //commentes out by JC
    //if ($detail) echo "<br />Chronological ranking done : Pedigree stretched over <b>$depth</b> generations.<br />$nl" ;

64% of this comment could be valid code. Did you maybe forget this after debugging?

    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>");
    }
    $inds = array_flip($IDs);

    return 0;
}

/**
 * @param $s
 *
 * @return array
 */
function fetch_record($s)
{
    /** @var XoopsMySQLDatabase */
    global $xoopsDB;
    $r = $xoopsDB->query($s);
    $n = 0;
    if ($r) {
        $n = $xoopsDB->getRowsNum($r);
    }
    if ($n == 0) {
        $record = array('0');
    } else {
        $record = $xoopsDB->fetchBoth($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 '<font color=' . $c . ' size="+2"><b>*' . $i . '*</b></font>';
        }
    }

    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 || $gen == 0) {
        $ID           = $IDs[$ind];
        $ani          = set_name($ID);
        $name         = $ani[1];
        $name         = $ID;
        $cell_content = showparent($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 || $gen == 0) {
            $sire = $fathers[$ind];
        }
        output_animal($sire, $gen + 1, "0");
        $dam = 0;
        if ($ind || $gen == 0) {
            $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) ;

50% of this comment could be valid code. Did you maybe forget this after debugging?

    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;
    global $xoopsDB;

Use of global functionality is not recommended; it makes your code harder to test, and less reusable.

    $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";
    }
    $generation = array($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
        $list       = join(',', array_unique($generation));
        $generation = array();
        $tot        = 0;
        if ($impr) {
            echo "    [$list]$nl";
        }

        // HERE IS FETCHED EACH TRIPLET [ID, sire_ID, dam_ID] :
        $r = $xoopsDB->query("$sql1 IN ($list)");
        while ($rec = $xoopsDB->fetchBoth($r)) {
            $a = $rec[0] + 0;
            $s = $rec[1] + 0;
            $d = $rec[2] + 0;
            if (!$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
    $listall   = array($p);
    $listnew   = array($p);
    $pater     = array();
    $pater[$p] = 1;
    for ($nloop = 2; $nloop < ($nb_gen + 1); ++$nloop) {
        $liste = array();
        foreach ($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)

70% of this comment could be valid code. Did you maybe forget this after debugging?

        //{ echo "<p>DAM is an ascendant (at $nloop generations) of SIRE.  Stopped." ;

58% of this comment could be valid code. Did you maybe forget this after debugging?

        // die ("</body></html>$nl") ; }

60% of this comment could be valid code. Did you maybe forget this after debugging?

        $listnew = array_diff(array_unique($liste), $listall);
        /* $list1 = join (' ', $listall) ; $list2 = join ('+', $listnew) ;

48% of this comment could be valid code. Did you maybe forget this after debugging?

             echo "<!-- P ($nloop) $list1/$list2 -->$nl" ; */
        $listall = array_merge($listall, $listnew);
    }
    // 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
    $listall   = array($m);
    $listnew   = array($m);
    $mater     = array();
    $mater[$m] = 1;
    for ($nloop = 2; $nloop <= ($nb_gen + 1); ++$nloop) {
        $liste = array();
        foreach ($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" ;

37% of this comment could be valid code. Did you maybe forget this after debugging?

            if ($s) {
                $liste[] = $s;
            }
            if ($d) {
                $liste[] = $d;
            }
        }
        if (!count($liste)) {
            break;
        }
        //commented out by jc
        //if (in_array ($IDs[1], $liste) && !$detail)

70% of this comment could be valid code. Did you maybe forget this after debugging?

        // { echo "<p>SIRE is an ascendant (at $nloop generations) of DAM.  Stopped." ;

50% of this comment could be valid code. Did you maybe forget this after debugging?

        //  die ("</body></html>$nl") ; }

60% of this comment could be valid code. Did you maybe forget this after debugging?

        $listnew = array_diff(array_unique($liste), $listall);
        // $list1 = join (' ', $listall) ; $list2 = join ('+', $listnew) ; echo "M ($nloop) $list1/$list2 $nl" ;

48% of this comment could be valid code. Did you maybe forget this after debugging?

        $listall = array_merge($listall, $listnew);
    }
    // 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;
    $distan = array();
    // dist_m (2) ;   has already been called
    dist_p($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" ;

50% of this comment could be valid code. Did you maybe forget this after debugging?

    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 */ {
        $already_known = isset($ICknown[$p]) ? $ICknown[$p] : 0;

        if (!$already_known) {
            CONSANG($p);
        }  // MAIN RECURSION:
        $ICp = isset($COIs[$p]) ? $COIs[$p] : 0;                    // 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] = isset($COIs[$a]) ? $COIs[$a] : 0;
        $COIs[$a] += $incr;  // incrementing the IC of AnimC
        if ($a == 0) {
            $deltaf[$p] += $incr;
        }
        /* contribution of Anim #P to IC of Anim #0 */
        // if ($verbose && $a == 0 && $incr > 0.0001*$verbose)

46% of this comment could be valid code. Did you maybe forget this after debugging?

        //    echo "Animal $p is contributing for " . substr ($deltaf[$p], 0, 10) . " to the IC of Animal $a$nl" ;

52% of this comment could be valid code. Did you maybe forget this after debugging?

    } 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 (isset($mater[$p]) || $a) {
        mater_side($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 || isset($ICknown[$a])) {
        return 0;
    }
    if ($a == -1) {
        $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 (isset($verbose)) {
        echo "</center><pre>$nl";
    }
    pater_side($p, $m, $a, 1);  // launch tree exploration
    if (isset($verbose)) {
        echo "</pre><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]    = isset($COIs[$a]) ? $COIs[$a] : 0;
            $ICknown[$i] = 1;
        }
    }
    // echo "<!-- COI($a) = $COIs[$a] $IDs[$a] ($fathers[$a] x $mothers[$a])-->$nl" ;

50% of this comment could be valid code. Did you maybe forget this after debugging?

    return 0;
}

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

    return $nbtot;
}

/**
 * @param $ID
 *
 * @return array
 */
function set_name($ID)
{
    global $sql2, $sql2bis, $xoopsDB;
    $name = ' ';
    $ani  = array();
    if ($ID) {
        $sqlquery    = "SELECT ID, NAAM, roft from " . $xoopsDB->prefix("pedigree_tree") . " where ID = '$ID'";
        $queryresult = $xoopsDB->query($sqlquery);
        $ani         = $xoopsDB->fetchBoth($queryresult);
//        $name        = $ani[1];

60% of this comment could be valid code. Did you maybe forget this after debugging?

        if ($sql2bis) {  // true for E.R.o'S. only
            $name = html_accents($name);
            //$affx = $ani[5] ;  // affix-ID

55% of this comment could be valid code. Did you maybe forget this after debugging?

            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;

Use of global functionality is not recommended; it makes your code harder to test, and less reusable.

    global $sex, $val, $sosa, $detail, $sql3;
    $sosa    = 12;
    $content = '';
    // echo '<div style="position:relative;float:right;width=2.0em;color=white;">' . $sosa . '</div>' ;

36% of this comment could be valid code. Did you maybe forget this after debugging?

    $animal = set_name($ID);
    list ($ID, $name, $sex/*, $hd, $ems*/) = $animal;

67% of this comment could be valid code. Did you maybe forget this after debugging?

    $sqlquery    = "select SQL_CACHE count(ID) from " . $xoopsDB->prefix("pedigree_tree") . " where father = '$ID' or mother = '$ID'";
    $queryresult = $xoopsDB->($sqlquery);

This code did not parse for me. Apparently, there is an error somewhere around this line:

Syntax error, unexpected '(', expecting T_STRING or T_VARIABLE or '{' or '$'

    $nb          = $xoopsDB->fetchBoth($queryresult);
    $nb_children = $nb[0];
    if ($nb_children == 0) {
        $nb_children = _MA_PEDIGREE_COI_NO;
    }
//    $dogid = $animal[0];

60% of this comment could be valid code. Did you maybe forget this after debugging?

    $content .= "<tr><td><a href=\"dog.php?id=" . $ID . "\">" . stripslashes($name) . "</a>";
    // if ($nb_enf == 0) echo ' &oslash;' ;

50% of this comment could be valid code. Did you maybe forget this after debugging?

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

    return $content;
}

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

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

//edit by jc

44% of this comment could be valid code. Did you maybe forget this after debugging?

//$link = @mysql_pconnect ($host, $database, $password)
//   or   die ("<html><body>Connection to database failed.</body></html>") ;
$s      = $_GET['s'];
$d      = $_GET['d'];
$detail = $_GET['detail'];

if (isset($si)) {
    $s = findid($si);
}
if (isset($da)) {
    $d = findid($da);
}
//test for variables

46% of this comment could be valid code. Did you maybe forget this after debugging?

//echo "si=".$si." da=".$da." s=".$s." d=".$d;
$utils = $xoopsDB->query("select user(), date_format(now(),'%d-%b-%Y')");
list ($who, $jourj) = $xoopsDB->fetchBoth($utils);

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

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

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

if (isset($a)) {
    $sqlquery    = "select ID, father, mother, roft from " . $xoopsDB->prefix("pedigree_tree") . " where ID  = '$a'";
    $queryresult = $xoopsDB->query($sqlquery);
    $rowhond     = $xoopsDB->fetchBoth($queryresult);
    $a           = $rowhond['ID'];
    $s           = $rowhond['father'];
    $d           = $rowhond['mother'];
} else {
    $a = 0;
}
$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, array('[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 />";

53% of this comment could be valid code. Did you maybe forget this after debugging?

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

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

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

$sqlquery    = "select ID, father, mother, roft from " . $xoopsDB->prefix("pedigree_tree") . " where ID  = '$codec1'";
$queryresult = $xoopsDB->query($sqlquery);
$rowhond     = $xoopsDB->fetchBoth($queryresult);
$a1          = $rowhond['ID'];
$s1          = $rowhond['father'];
$d1          = $rowhond['mother'];
$sex1        = $rowhond['roft'];

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

56% of this comment could be valid code. Did you maybe forget this after debugging?

$sqlquery    = "select ID, father, mother, roft from " . $xoopsDB->prefix("pedigree_tree") . " where ID  = '$codec2'";
$queryresult = $xoopsDB->query($sqlquery);
$rowhond     = $xoopsDB->fetchBoth($queryresult);
$a2          = $rowhond['ID'];
$s2          = $rowhond['father'];
$d2          = $rowhond['mother'];
$sex2        = $rowhond['roft'];

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

56% of this comment could be valid code. Did you maybe forget this after debugging?

//if ($sex1 == '0' && $sex2 == '1') { $a3 = $a1 ; $a1 = $a2 ; $a2 = $a3 ; }   /* permute dam and sire */

36% of this comment could be valid code. Did you maybe forget this after debugging?

$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, array('[father]' => $moduleConfig['father'])) . " (" . stripslashes(showparent($codec2)) . ")" . _MA_PEDIGREE_COI_AND . strtr(
        _MA_PEDIGREE_FLD_MOTH,
        array('[mother]' => $moduleConfig['mother'])
    ) . " (" . stripslashes(showparent($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, array('[animalType]' => $moduleConfig['animalType'], '[animalTypes]' => $moduleConfig['animalTypes'], '[children]' => $moduleConfig['children']))
);

$de_cujus = 0;
$sire_ID  = $_GET['s'];
$dam_ID   = $_GET['d'];
$rec      = "select ID from " . $xoopsDB->prefix("pedigree_tree") . " WHERE father = '" . $sire_ID . "' and mother = '" . $dam_ID . "' order by NAAM";
$result   = $xoopsDB->query($rec);
$content  = "";
while ($row = $xoopsDB->fetchArray($result)) {
    $content .= one_animal($row['ID']);
}

$xoopsTpl->assign("COMtitle", strtr(_MA_PEDIGREE_COI_COMTIT, array('[father]' => $moduleConfig['father'], '[mother]' => $moduleConfig['mother'])));
$xoopsTpl->assign("COMexplain", strtr(_MA_PEDIGREE_COI_COMEX, array('[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;
}

$IDs = array($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;

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

$nf = ceil(100 * (isset($COIs[0]) ? $COIs[0] : 0));
if ($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);

$f0 = substr((isset($COIs[0]) ? $COIs[0] : 0), 0, 8);
if (!$f0) {
    $f0 = "n.a.";
}
$f1 = 100 * $f0;

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

$xoopsTpl->assign("TCAtitle", _MA_PEDIGREE_COI_TCATIT);
$xoopsTpl->assign("TCApib", _MA_PEDIGREE_COI_TCApib);
$xoopsTpl->assign("dogs", isset($dogs) ? $dogs : 0);
$xoopsTpl->assign(
    "TCAexplain",
    strtr(
        _MA_PEDIGREE_COI_TCAEX,
        array(
            '[animalType]'  => $moduleConfig['animalType'],
            '[animalTypes]' => $moduleConfig['animalTypes'],
            '[children]'    => $moduleConfig['children'],
            '[mother]'      => $moduleConfig['mother'],
            '[father]'      => $moduleConfig['father']
        )
    )
);

if ($detail) {
    if (!isset ($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);
            $name = isset($ani[1]) ? $ani[1] : '';
            $ic   = substr($ic, 0, 6);
            if ($ic > 0.125 && $i) {
                $mia[] = array('id' => $ID, 'name' => stripslashes($name), 'coi' => (100 * $ic));
            }
        }
    }
    $xoopsTpl->assign("MIAtitle", _MA_PEDIGREE_COI_MIATIT);
    $xoopsTpl->assign("mia", isset($mia) ? $mia : 0);
    $xoopsTpl->assign("MIAexplain", strtr(_MA_PEDIGREE_COI_MIAEX, array('[animalType]' => $moduleConfig['animalType'])));

    if (!$ICknown[1]) {
        $marked = $empty;
        CONSANG(1);
    }    // Sire
    if (!$ICknown[2]) {
        $marked = $empty;
        CONSANG(2);
    }    // Dam

50% of this comment could be valid code. Did you maybe forget this after debugging?

//    $COR = 2.0 * $COIs[0] / sqrt((1. + $COIs[1]) * (1. + $COIs[2]));
    $COR = 2.0 * (isset($COIs[0]) ? $COIs[0] : 0) / sqrt((1. + (isset($COIs[1]) ? $COIs[1] : 0)) * (1. + (isset($COIs[2]) ? $COIs[2] : 0)));
    $COR = substr($COR, 0, 8);
    if (!$COR) {
        $COR = "n.a.";
    }
    $f1 = substr((isset($COIs[1]) ? $COIs[1] : 0), 0, 8);
    $f2 = substr((isset($COIs[2]) ? $COIs[2] : 0), 0, 8);
    if (!$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, array('[father]' => $moduleConfig['father'], '[mother]' => $moduleConfig['mother'])));
$xoopsTpl->assign("SSDcortit", _MA_PEDIGREE_COI_SSDcor);
$xoopsTpl->assign("SSDbsd", strtr(_MA_PEDIGREE_COI_SDDbsd, array('[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, array('[father]' => $moduleConfig['father'])));
$xoopsTpl->assign("SSDsire", $SSDsire);
$xoopsTpl->assign("SSDM", _MA_PEDIGREE_COI_COI . _MA_PEDIGREE_FROM . strtr(_MA_PEDIGREE_FLD_MOTH, array('[mother]' => $moduleConfig['mother'])));
$xoopsTpl->assign("SSDdam", $SSDdam);

// echo "SSDsire : ".$SSDsire."<br />";

54% of this comment could be valid code. Did you maybe forget this after debugging?

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

$xoopsTpl->assign("SSDexplain", strtr(_MA_PEDIGREE_COI_SSDEX, array('[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, array('[children]' => $moduleConfig['children'])));

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

//comments and footer
include XOOPS_ROOT_PATH . "/footer.php";