/usr/share/stacks/php/stacks

<?php
//
// Copyright 2010-2015, Julian Catchen <jcatchen@illinois.edu>
//
// This file is part of Stacks.
//
// Stacks is free software: you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
// the Free Software Foundation, either version 3 of the License, or
// (at your option) any later version.
//
// Stacks is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
// GNU General Public License for more details.
//
// You should have received a copy of the GNU General Public License
// along with Stacks.  If not, see <http://www.gnu.org/licenses/>.
//

function write_header($page_title) {
    global $version, $site_title; 
    global $root_path, $img_path;

    echo <<< EOQ
<!DOCTYPE html>
<html>
<head>
  <meta charset="utf-8">
  <title>$site_title: $page_title</title>
  <link rel="stylesheet" type="text/css" href="$root_path/stacks.css" />
  <script type="text/javascript" src="$root_path/stacks.js"></script>
  <script type="text/javascript" src="$root_path/annotate.js"></script>
  <script type="text/javascript" src="$root_path/export.js"></script>
</head>

<body>
<div class="main" style="width: 95%;">
<div id="header">
<h1><a href="$root_path/"><img src="$img_path/stacks_logo_rev_small.png" /></a></h1>
<p>
  <a href="http://catchenlab.life.illinois.edu/stacks/">version 

EOQ;

    include("version.php");
    echo <<< EOQ
  </a>
</p>
</div>

EOQ;
}

function write_compact_header($page_title) {
    global $root_path, $css_path, $site_title, $js_path;

    echo <<< EOQ
<?xml version="1.0" encoding="iso-8859-1"?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
    "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">

<head>
  <title>$site_title: $page_title</title>
  <link rel="stylesheet" type="text/css" href="$root_path/stacks.css" />
  <script type="text/javascript" src="$root_path/stacks.js"></script>
  <script type="text/javascript" src="$root_path/annotate.js"></script>
</head>

<body>

EOQ;
}

function write_footer() {

    echo <<< EOQ
<div class="footer">
  <div style="float: left;">
    last updated: 
EOQ;

    include("last_modified.php");

    echo <<< EOQ
  </div>
</div>

</body>
</html>

EOQ;
}

function write_compact_footer() {

    echo <<< EOQ

</body>
</html>

EOQ;
}

function print_scale($max_len) {
    if ($max_len == 0) return "";

    $class = array("light_scale", "dark_scale");
    $str   = "";
    $c     = 0;

    $str .= "<span class=\"" . $class[$c % 2] . "\">";
    for ($i = 0; $i < $max_len; $i++) {
      
        $str .= $i % 10;

        if (($i + 1) % 10 == 0) {
            $c++;
            $str .= "</span><span class=\"". $class[$c % 2] . "\">";
        }
    }
    $str .= "</span>";

    return $str;
}

function print_snps($tag_id, $consensus, $seq, $snps, $wrap) {
    global $display_len;

    $str     = "";
    $start   = 0;
    $snp_cnt = count($snps);

    while (count($snps)) {
        $snp = array_shift($snps);
        $con = substr($consensus, $snp['col'], 1);
        $end = $snp['col'];

        $s    = substr($seq, $start, $end - $start);
        $str .= $s;
        $s    = substr($seq, $end, 1);

        if ($con == $s)
            $str .= "<span id=\"${tag_id}_$snp[col]\" class=\"rank_1\">$s</span>";
        else if ($s == "N")
            $str .= "$s";
        else
            $str .= "<span id=\"${tag_id}_$snp[col]\" class=\"rank_2\">$s</span>";

        $start = $end + 1;
    }

    if ($snp_cnt > 0) {
        $s    = substr($seq, $start);
        $str .= $s;
    } else {
        $str  = $consensus;
    }

    if ($wrap == false || strlen($consensus) <= $display_len) 
        return $str;

    //
    // Add line breaks to the sequence
    //
    $s   = "";
    $nuc = 0;
    $pos = 0;
    $len = strlen($str);
    while ($len > $display_len) {
        for ($pos = 0, $nuc = 0; $pos < $display_len && $nuc < $len; $nuc++, $pos++) {
            if ($str[$nuc] == '<') {
                do { $nuc++; } while ($str[$nuc] != '>');
                $pos--;
            }
        }	
        $s  .= substr($str, 0, $nuc) . "<br />\n";
        $str = substr($str, $nuc);
        $pos = 0;
        $nuc = 0;
        $len = strlen($str);
    }
    $s .= $str;

    return $s;
}

function print_snps_errs($consensus, $sequence, $snps, $cat_snps) {
    $str = "";
    $con = str_split($consensus);
    $seq = str_split($sequence);

    for ($i = 0; $i < count($con); $i++) {
        // Is a SNP defined in this column?
        if (isset($snps[$i])) {
            if ($con[$i] == $seq[$i])
                $str .= "<span class=\"rank_1\">$seq[$i]</span>";
            else if ($seq[$i] == "N")
                $str .= "$seq[$i]";
            else
                $str .= "<span class=\"rank_2\">$seq[$i]</span>";

        } else if (isset($cat_snps[$i])) {
            $str .= "<span class=\"cat_snp\">$seq[$i]</span>";
        } else {
            // Does this nucleotide equal the consensus nucleotide at position $i?
            if ($con[$i] == $seq[$i] || $seq[$i] == "N")
                $str .= $seq[$i];
            else
                $str .= "<span class=\"err\">$seq[$i]</span>";
        }
    }

    return $str;
}

function generate_key_element_select($name, $elements, $selected_key, $javascript) {
    $script_code = "";

    if (strlen($javascript) > 0) {
        $script_code = " onchange=\"$javascript\"";
    }

    $ctl = "  <select id=\"$name\" name=\"$name\"" . $script_code . ">\n";

    foreach ($elements as $key => $element) {

        if ($key == $selected_key) 
            $ctl .= "  <option selected=\"selected\" value=\"$key\">$element</option>\n";
        else
            $ctl .= "  <option value=\"$key\">$element</option>\n";
    }

    $ctl .= "  </select>\n";

    return $ctl;
}

function generate_element_select($name, $elements, $selected_ele, $change_js, $blur_js = "") {
    $script_code = "";

    if (strlen($change_js) > 0 && strlen($blur_js) > 0) {
        $script_code = " onchange=\"$change_js\" onblur=\"$blur_js\"";
    } else if (strlen($change_js) > 0) {
        $script_code = " onchange=\"$change_js\"";
    } else if (strlen($blur_js) > 0) {
        $script_code = " onblur=\"$blur_js\"";
    }

    $ctl = "  <select id=\"$name\" name=\"$name\"" . $script_code . ">\n";

    foreach ($elements as $element) {

        if ($element == $selected_ele) 
            $ctl .= "  <option selected=\"selected\">$element</option>\n";
        else
            $ctl .= "  <option>$element</option>\n";
    }

    $ctl .= "  </select>\n";

    return $ctl;
}

function print_bp($bp) {

  // Convert the location to be in megabases
  if ($bp > 1000000)
      $bp = sprintf("%.02fMb", $bp / 1000000);
  else if ($bp > 1000)
    $bp = sprintf("%.1fKb", $bp / 1000);
  else 
    $bp = sprintf("%dbp", $bp);

  return $bp;
}

?>
stacks-web 1.35-1ubuntu1 / usr / share / stacks / php / stacks_functions.php
