/**
 * Documentation for this function.
 */
 function onMakeFinalPDB()
 {
     $context = getContext();
     $newModel = $_SESSION['models'][$context['newModel']];
     $oldModel = $_SESSION['models'][$newModel['parent']];
     $newPDB = $_SESSION['dataDir'] . '/' . MP_DIR_MODELS . '/' . $newModel['pdb'];
     $oldPDB = $_SESSION['dataDir'] . '/' . MP_DIR_MODELS . '/' . $oldModel['pdb'];
     $url = $_SESSION['dataURL'] . '/' . MP_DIR_MODELS . '/' . $newModel['pdb'];
     // Put our money where our mouth is and calculate that new PDB file
     $all_changes = $context['sswingChanges'];
     $usercnit = $_REQUEST['cnit'];
     // Remove changes for residues that weren't selected
     foreach ($all_changes as $k => $v) {
         $res = substr($k, 0, 9);
         if (!isset($usercnit[$res])) {
             unset($all_changes[$k]);
         } else {
             $changed_res[$res] = $res;
         }
         // used below for the lab notebook
     }
     // Make PDB file
     pdbSwapCoords($oldPDB, $newPDB, $all_changes);
     // Make up the lab notebook entry
     $text = "The following residues were automatically refit by SSWING, creating {$newModel['pdb']} from {$oldModel['pdb']}:\n<ul>\n";
     foreach ($changed_res as $res) {
         $text .= "<li>{$res}</li>\n";
     }
     $text .= "</ul>\n";
     $text .= "<p>You can now <a href='{$url}'>download the optimized and annotated PDB file</a> (" . formatFilesize(filesize($newPDB)) . ").</p>\n";
     $entryNum = addLabbookEntry("Refit sidechains with SSWING to get {$newModel['pdb']}", $text, "{$oldModel['id']}|{$newModel['id']}", 'auto');
     $ctx = array('labbookEntry' => $entryNum);
     pageGoto("generic_done.php", $ctx);
 }

 public function handle($path, Application $app)
 {
     $files = array();
     $folders = array();
     $list = $this->filesystem->listContents($path);
     $ignored = array(".", "..", ".DS_Store", ".gitignore", ".htaccess");
     foreach ($list as $entry) {
         if (in_array($entry['basename'], $ignored)) {
             continue;
         }
         $fullfilename = $this->filesystem->getAdapter()->applyPathPrefix($entry['path']);
         if (!$app['filepermissions']->authorized(realpath($fullfilename))) {
             continue;
         }
         if ($entry['type'] === 'file') {
             try {
                 $url = $this->filesystem->url($entry['path']);
             } catch (\Exception $e) {
                 $url = $entry['path'];
             }
             // Ugh, for some reason the foldername for the theme is included twice. Why?
             // For now we 'fix' this with an ugly hack, replacing it. :-/
             // TODO: dig into Filesystem and figure out why this happens.
             $pathsegments = explode('/', $entry['path']);
             if (!empty($pathsegments[0])) {
                 $url = str_replace('/' . $pathsegments[0] . '/' . $pathsegments[0] . '/', '/' . $pathsegments[0] . '/', $url);
             }
             $files[$entry['path']] = array('path' => $entry['dirname'], 'filename' => $entry['basename'], 'newpath' => $entry['path'], 'relativepath' => $entry['path'], 'writable' => true, 'readable' => false, 'type' => isset($entry['extension']) ? $entry['extension'] : '', 'filesize' => formatFilesize($entry['size']), 'modified' => date("Y/m/d H:i:s", $entry['timestamp']), 'permissions' => 'public', 'url' => $url);
             /***** Extra checks for files that can be resolved via PHP urlopen functions *****/
             try {
                 $files[$entry['path']]['permissions'] = $this->filesystem->getVisibility($entry['path']);
             } catch (\Exception $e) {
             }
             if (is_readable($fullfilename)) {
                 $files[$entry['path']]['readable'] = true;
                 if (!empty($entry['extension']) && in_array($entry['extension'], array('gif', 'jpg', 'png', 'jpeg'))) {
                     $size = getimagesize($fullfilename);
                     $files[$entry['path']]['imagesize'] = sprintf("%s × %s", $size[0], $size[1]);
                 }
                 $files[$entry['path']]['permissions'] = \utilphp\util::full_permissions($fullfilename);
             }
         }
         if ($entry['type'] == 'dir') {
             $folders[$entry['path']] = array('path' => $entry['dirname'], 'foldername' => $entry['basename'], 'newpath' => $entry['path'], 'modified' => date("Y/m/d H:i:s", $entry['timestamp']), 'writable' => true);
             /***** Extra checks for files that can be resolved via PHP urlopen functions *****/
             if (is_readable($fullfilename)) {
                 if (!is_writable($fullfilename)) {
                     $folders[$entry['path']]['writable'] = false;
                 }
             }
         }
     }
     ksort($files);
     ksort($folders);
     return array($files, $folders);
 }

 function displayMap($context)
 {
     echo $this->pageHeader("Map {$context['mapName']} added");
     echo "<p>The following electron density maps are now available:\n";
     echo "<ul>\n";
     foreach ($_SESSION['edmaps'] as $map) {
         $mapPath = "{$_SESSION['dataDir']}/" . MP_DIR_EDMAPS . "/{$map}";
         echo "<li><b>{$map}</b> (" . formatFilesize(filesize($mapPath)) . ")</li>\n";
     }
     echo "</ul>\n</p>\n";
     echo "<p>" . makeEventForm("onReturn");
     echo "<input type='submit' name='cmd' value='Continue &gt;'>\n</form></p>\n";
     echo $this->pageFooter();
 }

            $my_uploader->set_path($path);
            if ($my_uploader->upload('file')) {
                $my_uploader->save_file();
            }
            if ($my_uploader->upload_failed()) {
                $error = $my_uploader->get_error();
            }
            $image_file = $path . $my_uploader->fileinfo('filename');
            if (!file_exists($image_file)) {
                $error = $lang->phrase('admin_cms_file_does_not_exist');
            }
            $image_file = str_replace(realpath($config['fpath']) . DIRECTORY_SEPARATOR, '', $image_file);
            $image_file = str_replace(DIRECTORY_SEPARATOR, '/', $image_file);
        }
    }
    $filesize = formatFilesize(ini_maxupload());
    $htmlhead .= '<script type="text/javascript" src="templates/editor/wysiwyg-popup.js"></script>';
    echo head(' onLoad="loadImage();"');
    ?>
<form method="post" action="admin.php?action=cms&amp;job=doc_insert_image&amp;wysiwyg=<?php 
    echo $wysiwyg;
    ?>
" enctype="multipart/form-data">
<table class="border" border="0" cellspacing="0" cellpadding="4" align="center" style="width: 700px;">
	<tr>
		<td class="obox" colspan="3"><?php 
    echo $lang->phrase('admin_wysiwyg_upload_x');
    ?>
</td>
	</tr>
	<tr class="mbox">

function exec_query_form($query = '')
{
    global $db;
    $tables = $db->list_tables();
    ?>
<form name="form" method="post" action="admin.php?action=db&job=query2">
 <table class="border" border="0" cellspacing="0" cellpadding="4" align="center">
  <tr> 
   <td class="obox" colspan="2"><b>Execute Queries</b></td>
  </tr>
  <tr> 
	<td class="mbox" width="90%">
	<span style="float: right;">semicolon-separated list</span><strong>Queries:</strong>
	<textarea name="query" id="query" rows="10" cols="90" class="texteditor" style="width: 100%; height: 200px;"><?php 
    echo iif(!empty($query), $query);
    ?>
</textarea>
	</td>
	<td class="mbox" width="10%">
	<strong>Tables:</strong>
	<div style="overflow: scroll; height: 200px; width: 150px; border: 1px solid #336699; padding: 2px;">
	<?php 
    foreach ($tables as $table) {
        ?>
	<a href="javascript:InsertTags('query', '`<?php 
        echo $table;
        ?>
`', '');"><?php 
        echo $table;
        ?>
</a><br />
	<?php 
    }
    ?>
	</div>
	</td>
  </tr>
  <tr> 
   <td class="ubox" colspan="2" align="center"><input type="submit" name="Submit" value="Submit"></td> 
  </tr>
 </table>
</form>
<br />
<?php 
    if (empty($query)) {
        ?>
<form name="form" method="post" action="admin.php?action=db&amp;job=query2&amp;type=1" enctype="multipart/form-data">
 <table class="border" border="0" cellspacing="0" cellpadding="4" align="center">
  <tr> 
   <td class="obox"><b>Import SQL File</b></td>
  </tr>
  <tr>
  	<td class="mbox">
  	<input type="file" name="upload" size="80" /><br />
  	<span class="stext">Allowed file types: .sql, .zip - Maximum file size: <?php 
        echo formatFilesize(ini_maxupload());
        ?>
</span>
  	</td>
  </tr>
  <tr> 
   <td class="ubox" align="center"><input type="submit" name="Submit" value="Submit"></td> 
  </tr>
 </table>
</form>
<br />
<?php 
    }
}

    }
    $delobj = $scache->load('components');
    $delobj->delete();
    $db->query('UPDATE ' . $db->pre . 'component SET active = "' . $act . '" WHERE id = ' . $id, __LINE__, __FILE__);
    viscacha_header('Location: admin.php?action=cms&job=com');
} elseif ($job == 'com_add') {
    echo head();
    ?>
<form name="form" method="post" action="admin.php?action=cms&job=com_add2" enctype="multipart/form-data">
 <table class="border" border="0" cellspacing="0" cellpadding="4" align="center">
  <tr> 
   <td class="obox" colspan="2">Import a new Component</td>
  </tr>
  <tr> 
   <td class="mbox" width="50%"><em>Either</em> upload a file:<br /><span class="stext">Compressed file (.zip) containing the component. Maximum file size: <?php 
    echo formatFilesize(ini_maxupload());
    ?>
. You should install only components from confidential sources!</td>
   <td class="mbox" width="50%"><input type="file" name="upload" size="40" /></td> 
  </tr>
  <tr>
   <td class="mbox"><em>or</em> select a file from the server:<br /><span class="stext">Path starting from the Viscacha-root-directory: <?php 
    echo $config['fpath'];
    ?>
</span></td>
   <td class="mbox"><input type="text" name="server" size="50" /></td>
  </tr>
  <tr>
   <td class="mbox">Delete file after import:</td>
   <td class="mbox"><input type="checkbox" name="delete" value="1" checked="checked" /></td>
  </tr>

//.........这里部分代码省略.........
    // ------------------------------------
    $action_colspan = 1;
    if ($net2ftp_settings["functionuse_view"] == "yes") {
        $action_colspan++;
    }
    if ($net2ftp_settings["functionuse_edit"] == "yes") {
        $action_colspan++;
    }
    if ($net2ftp_settings["functionuse_update"] == "yes") {
        $action_colspan++;
    }
    // Total nr of columns
    $total_colspan = $action_colspan + 9;
    // ------------------------------------
    // Name, Type, Size, ...
    // Determine the sort criteria and direction (ascending/descending)
    // ------------------------------------
    $sortArray["dirfilename"]["text"] = __("Name");
    $sortArray["type"]["text"] = __("Type");
    $sortArray["size"]["text"] = __("Size");
    $sortArray["owner"]["text"] = __("Owner");
    $sortArray["group"]["text"] = __("Group");
    $sortArray["permissions"]["text"] = __("Perms");
    $sortArray["mtime"]["text"] = __("Mod Time");
    $icon_directory = $net2ftp_globals["application_rootdir_url"] . "/skins/" . $net2ftp_globals["skin"] . "/images/mime";
    // Loop over all the sort possibilities
    while (list($key, $value) = each($sortArray)) {
        // The list is sorted by the current $key
        // Print the icon representing the current sortorder
        // Print the link to sort using the other sortorder
        if ($net2ftp_globals["sort"] == $key) {
            // Ascending
            if ($net2ftp_globals["sortorder"] == "ascending") {
                $sortArray[$key]["title"] = __("Click to sort by %1\$s in descending order", $value["text"]);
                $sortArray[$key]["onclick"] = "do_sort('" . $key . "','descending');";
                $icon = "ascend.png";
                $alt = __("Ascending order");
            } else {
                $sortArray[$key]["title"] = __("Click to sort by %1\$s in ascending order", $value["text"]);
                $sortArray[$key]["onclick"] = "do_sort('" . $key . "','ascending');";
                $icon = "descend.png";
                $alt = __("Descending order");
            }
        } else {
            $sortArray[$key]["title"] = __("Click to sort by %1\$s in ascending order", $value["text"]);
            $sortArray[$key]["onclick"] = "do_sort('" . $key . "','ascending');";
            $icon = "";
            $alt = "";
        }
        // The icon to be printed is determined above
        // Now, print the full HTML depending on the browser agent, version and platform
        if ($icon != "") {
            if ($net2ftp_globals["browser_agent"] == "IE" && ($net2ftp_globals["browser_version"] == "5.5" || $net2ftp_globals["browser_version"] == "6") && $net2ftp_globals["browser_platform"] == "Win") {
                $sortArray[$key]["icon"] = "<img src=\"{$icon_directory}/spacer.gif\"   alt=\"{$alt}\" style=\"border: 0px; width: 16px; height: 16px; filter: progid:DXImageTransform.Microsoft.AlphaImageLoader(src='{$icon_directory}/{$icon}', sizingMethod='scale');\" />\n";
            } else {
                $sortArray[$key]["icon"] = "<img src=\"{$icon_directory}/{$icon}\"        alt=\"{$alt}\" style=\"border: 0px; width: 16px; height: 16px;\" />\n";
            }
        } else {
            $sortArray[$key]["icon"] = "";
        }
    }
    // ------------------------------------
    // popup - FormAndFieldname
    // ------------------------------------
    if (isset($_POST["FormAndFieldName"]) == true) {
        $FormAndFieldName = validateGenericInput($_POST["FormAndFieldName"]);
    } else {
        $FormAndFieldName = "";
    }
    // ------------------------------------
    // Action URL
    // Used for Up, Subdirectories, Files (download + actions)
    // ------------------------------------
    $action_url = printPHP_SELF("actions");
    // ------------------------------------
    // Data transfer statistics
    // Print this only if the consumption statistics are available (logging must be on, using a MySQL database)
    // ------------------------------------
    if (isset($net2ftp_globals["consumption_ipaddress_datatransfer"]) == true || isset($net2ftp_globals["consumption_ftpserver_datatransfer"]) == true) {
        $print_consumption = true;
        $consumption_ipaddress_datatransfer = formatFilesize($net2ftp_globals["consumption_ipaddress_datatransfer"]);
        $consumption_ftpserver_datatransfer = formatFilesize($net2ftp_globals["consumption_ftpserver_datatransfer"]);
    } else {
        $print_consumption = false;
    }
    // ------------------------------------
    // HTTP URL
    // ------------------------------------
    $list_files_tmp[1]["dirfilename_url"] = "";
    $httplink = ftp2http($directory, $list_files_tmp, "no");
    // -------------------------------------------------------------------------
    // Print the output - part 2
    // -------------------------------------------------------------------------
    if ($net2ftp_globals["state2"] == "main") {
        setStatus(6, 10, __("Printing the list of directories and files"));
        require_once $net2ftp_globals["application_skinsdir"] . "/" . $net2ftp_globals["skin"] . "/browse_main.template.php";
    } elseif ($net2ftp_globals["state2"] == "popup") {
        require_once $net2ftp_globals["application_skinsdir"] . "/" . $net2ftp_globals["skin"] . "/browse_popup.template.php";
    }
}

 /**
  * string get_error(int error_code);
  * 
  * Gets the correct error message for language set by constructor
  * 
  * @param error_code		(int) error code
  * 
  */
 function get_error($error_code = '')
 {
     global $lang;
     $error_message = array();
     $error_code = (int) $error_code;
     if (!$this->max_image_height) {
         $this->max_image_height = $lang->phrase('upload_unspecified');
     }
     if (!$this->max_image_width) {
         $this->max_image_width = $lang->phrase('upload_unspecified');
     }
     $aft = implode(", ", $this->acceptable_file_types);
     $mfs = formatFilesize($this->max_filesize);
     $pathfile = $this->path . $this->file["name"];
     if (is_object($lang)) {
         $lang->assign('this', $this);
         $lang->assign('aft', $aft);
         $lang->assign('mfs', $mfs);
         $lang->assign('pathfile', $pathfile);
         $error_message[0] = $lang->phrase('upload_error_noupload');
         $error_message[1] = $lang->phrase('upload_error_maxfilesize');
         $error_message[2] = $lang->phrase('upload_error_maximagesize');
         $error_message[3] = $lang->phrase('upload_error_wrongfiletype');
         $error_message[4] = $lang->phrase('upload_error_fileexists');
         $error_message[5] = $lang->phrase('upload_error_noaccess');
     } else {
         $error_message[0] = 'Es wurde keine Datei hochgeladen';
         $error_message[1] = 'Zugriff verweigert. Konnte Datei nicht zu "{%this->path}" kopieren.';
         $error_message[2] = 'Nur {$aft} Dateien dürfen hochgeladen werden.';
         $error_message[3] = 'Maximale Dateigrösse überschritten. Datei darf nicht grösser als {$mfs} sein.';
         $error_message[4] = 'Maximale Bildgrösse überschritten. Bild darf nicht grösser als {%this->max_image_width} x {%this->max_image_height} Pixel sein.';
         $error_message[5] = 'Datei "{$pathfile}" existiert bereits.';
     }
     // for backward compatability:
     $this->errors[$error_code] = $error_message[$error_code];
     return $error_message[$error_code];
 }

function exec_query_form($query = '')
{
    global $db, $lang;
    $tables = $db->list_tables();
    $lang->assign('maxfilesize', formatFilesize(ini_maxupload()));
    ?>
<script type="text/javascript" src="templates/editor/bbcode.js"></script>
<form name="form" method="post" action="admin.php?action=db&job=query2">
 <table class="border" border="0" cellspacing="0" cellpadding="4" align="center">
  <tr>
   <td class="obox" colspan="2"><?php 
    echo $lang->phrase('admin_db_execute_queries');
    ?>
</td>
  </tr>
  <tr>
	<td class="mbox" width="90%">
	<span style="float: right;"><?php 
    echo $lang->phrase('admin_db_semicolon_sep_list');
    ?>
</span><strong><?php 
    echo $lang->phrase('admin_db_queries');
    ?>
</strong>
	<textarea name="query" id="query" rows="10" cols="90" class="texteditor" style="width: 100%; height: 200px;"><?php 
    echo iif(!empty($query), $query);
    ?>
</textarea>
	</td>
	<td class="mbox" width="10%">
	<strong><?php 
    echo $lang->phrase('admin_db_tables');
    ?>
</strong>
	<div style="overflow: scroll; height: 200px; width: 150px; border: 1px solid #336699; padding: 2px;">
	<?php 
    foreach ($tables as $table) {
        ?>
	<a href="javascript:InsertTags('query', '`<?php 
        echo $table;
        ?>
`', '');"><?php 
        echo $table;
        ?>
</a><br />
	<?php 
    }
    ?>
	</div>
	</td>
  </tr>
  <tr>
   <td class="ubox" colspan="2" align="center"><input type="submit" name="Submit" value="<?php 
    echo $lang->phrase('admin_db_form_submit');
    ?>
"></td>
  </tr>
 </table>
</form>
<br />
<?php 
    if (empty($query)) {
        ?>
<form name="form" method="post" action="admin.php?action=db&amp;job=query2&amp;type=1" enctype="multipart/form-data">
 <table class="border" border="0" cellspacing="0" cellpadding="4" align="center">
  <tr>
   <td class="obox"><b><?php 
        echo $lang->phrase('admin_db_import_sql_file');
        ?>
</b></td>
  </tr>
  <tr>
  	<td class="mbox">
  	<input type="file" name="upload" size="80" /><br />
  	<span class="stext"><?php 
        echo $lang->phrase('admin_db_allowed_filetypes_max_filesize');
        ?>
</span>
  	</td>
  </tr>
  <tr>
   <td class="ubox" align="center"><input type="submit" name="Submit" value="<?php 
        echo $lang->phrase('admin_db_form_submit');
        ?>
"></td>
  </tr>
 </table>
</form>
<br />
<?php 
    }
}

    echo "<table width=100%>\n";
    echo "<tr>\n";
    echo "<td><b>Session ID</b></td>\n";
    echo "<td><a href='" . basename($_SERVER['PHP_SELF']) . "?sort=last'><b>Last touched</b></a></td>\n";
    echo "<td><a href='" . basename($_SERVER['PHP_SELF']) . "?sort=ttl'><b>Time to live</b></a></td>\n";
    echo "<td><a href='" . basename($_SERVER['PHP_SELF']) . "?sort=size'><b>Size on disk</b></a></td>\n";
    echo "<td><!-- space for Debug cmd --></td>\n";
    echo "<td><!-- space for Enter cmd --></td>\n";
    echo "<td><!-- space for Destroy cmd --></td>\n";
    echo "</tr>\n";
    foreach ($sessList as $sess) {
        echo "<tr>\n";
        echo "<td>{$sess['id']}</td>\n";
        echo "<td>" . formatMinutesElapsed(time() - $sess['last']) . " ago</td>\n";
        echo "<td>" . formatHoursElapsed($sess['ttl']) . "</td>\n";
        echo "<td>" . formatFilesize($sess['size']) . "</td>\n";
        echo "<td><a href='../viewdebug.php?" . MP_SESSION_NAME . "={$sess['id']}' target='_blank'>Debug</a></td>\n";
        echo "<td><a href='../index.php?" . MP_SESSION_NAME . "={$sess['id']}'>Enter</a></td>\n";
        // We use basename() to get "index.php" instead of the full path,
        // which is subject to corruption with URL forwarding thru kinemage.
        echo "<td><a href='" . basename($_SERVER['PHP_SELF']) . "?cmd=Destroy&target={$sess['id']}'>Destroy</a></td>\n";
        echo "</tr>\n";
    }
    echo "</table>\n";
} else {
    echo "<center><i>No live sessions found on disk.</i></center>\n";
}
?>
</body>
</html>

runJiffiloop($pdb, $pdbPrefix, $fragfiller_args);
//reduceNoBuild($pdb, $outpath);
setProgress($tasks, 'notebook');
//$kinout = $_SESSION['dataDir'].'/'.MP_DIR_MODELS.'/'.$kinpath;
//$kinurl = $_SESSION['dataURL'].'/'.MP_DIR_MODELS.'/'.$kinpath;
// have to scan MP_DIR_MODELS directory for all outputted loop files.
$gapCount = 0;
$pdbFiles = listDir($pdbDir);
$pdbEntries = "<p>You can now use the following links to download multi-model PDB files for each filled gap.</p>\n";
foreach ($pdbFiles as $pdbName) {
    //echo "For $pdbName\n";
    if (preg_match("/" . $modelID . ".*\\.[0-9]*-[0-9]*\\.pdb/", $pdbName)) {
        //echo "Found $pdbName\n";
        $filledPdbFile = $_SESSION['dataDir'] . '/' . MP_DIR_MODELS . '/' . $pdbName;
        $pdburl = $_SESSION['dataURL'] . '/' . MP_DIR_MODELS . '/' . $pdbName;
        $pdbEntries .= "<p>File <a href='{$pdburl}'>{$pdbName}</a> (" . formatFilesize(filesize($filledPdbFile)) . ").</p>\n";
        $gapCount += 1;
    } else {
        if (preg_match("/.kin/", $pdbName)) {
            // because JiffiLoop puts all output files in one directory, this moves the output kin to the kin directory.
            //echo "kin file name: ".$pdbName."\n";
            $origKinFile = $_SESSION['dataDir'] . '/' . MP_DIR_MODELS . '/' . $pdbName;
            $newKinFile = $kinDir . '/' . $pdbName;
            rename($origKinFile, $newKinFile);
            $jiffiKin = $pdbName;
        }
    }
}
//$pdbout = $_SESSION['dataDir'].'/'.MP_DIR_MODELS.'/'.$pdbpath;
//$pdburl = $_SESSION['dataURL'].'/'.MP_DIR_MODELS.'/'.$pdbpath;
$entry = "Jiffiloop was run on {$model['pdb']}; {$gapCount} JiffiLoop PDB files were found. If there are no files shown here, JiffiLoop likely crashed; please contact the developers.\n";

 function makeFileCommands($path, $url)
 {
     $s = '';
     $s .= "<td><small>" . formatFilesize(filesize($path)) . "</small></td>";
     $lcPath = strtolower($path);
     // Kinemages
     if (endsWith($lcPath, ".kin")) {
         $s .= "<td><small><a href='viewtext.php?{$_SESSION['sessTag']}&file={$path}&mode=plain' target='_blank'>plain text</a></small></td>";
         $s .= "<td></td>";
         //$s .= "<td><small><a href='viewtext.php?$_SESSION[sessTag]&file=$path&mode=kin' target='_blank'>highlighted</a></small></td>";
         $s .= "<td><small><a href='viewking.php?{$_SESSION['sessTag']}&url={$url}' target='_blank'>in KiNG</a></small></td>";
     } elseif (endsWith($lcPath, ".kin.gz")) {
         $s .= "<td></td>";
         $s .= "<td><small><a href='viewking.php?{$_SESSION['sessTag']}&url={$url}' target='_blank'>in KiNG</a></small></td>";
         $s .= "<td></td>";
     } elseif (endsWith($path, "H.pdb")) {
         $s .= "<td><small><a href='viewtext.php?{$_SESSION['sessTag']}&file={$path}&mode=plain' target='_blank'>plain text</a></small></td>";
         $s .= "<td><small><a href='download_trimmed.php?{$_SESSION['sessTag']}&file={$path}'>without H</a></small></td>";
         $s .= "<td><small><a href='viewpdbking.php?{$_SESSION['sessTag']}&url={$url}' target='_blank'>in KiNG</a></small></td>";
     } elseif (endsWith($path, ".pdb")) {
         $s .= "<td><small><a href='viewtext.php?{$_SESSION['sessTag']}&file={$path}&mode=plain' target='_blank'>plain text</a></small></td>";
         $s .= "<td></td>";
         $s .= "<td><small><a href='viewpdbking.php?{$_SESSION['sessTag']}&url={$url}' target='_blank'>in KiNG</a></small></td>";
     } elseif (endsWith($lcPath, ".table")) {
         $s .= "<td></td>";
         $s .= "<td><small><a href='viewtable.php?{$_SESSION['sessTag']}&file={$path}' target='_blank'>as table</a></small></td>";
         $s .= "<td></td>";
     } elseif (endsWith($lcPath, ".html")) {
         $s .= "<td><small><a href='viewtext.php?{$_SESSION['sessTag']}&file={$path}&mode=plain' target='_blank'>plain text</a></small></td>";
         $s .= "<td><small><a href='viewtext.php?{$_SESSION['sessTag']}&file={$path}&mode=html' target='_blank'>as HTML</a></small></td>";
         $s .= "<td></td>";
     } elseif (endsWith($lcPath, ".pdf")) {
         $s .= "<td></td>";
         $s .= "<td></td>";
         $s .= "<td></td>";
     } elseif (endsWith($lcPath, ".gz") || endsWith($lcPath, ".tgz") || endsWith($lcPath, ".zip")) {
         $s .= "<td></td>";
         $s .= "<td></td>";
         $s .= "<td></td>";
     } else {
         $s .= "<td><small><a href='viewtext.php?{$_SESSION['sessTag']}&file={$path}&mode=plain' target='_blank'>plain text</a></small></td>";
         $s .= "<td></td>";
         $s .= "<td></td>";
     }
     $s .= "<td align='right'><small><a href='{$url}'><img src='img/download.gif'> Download</a></small></td>";
     return $s;
 }

 public function files($path, Silex\Application $app, Request $request)
 {
     $files = array();
     $folders = array();
     $basefolder = __DIR__ . "/../../../../";
     $path = stripTrailingSlash(str_replace("..", "", $path));
     $currentfolder = realpath($basefolder . $path);
     if (is_writable($currentfolder)) {
         // Define the "Upload here" form.
         $form = $app['form.factory']->createBuilder('form')->add('FileUpload', 'file', array('label' => __("Upload a file to this folder:")))->getForm();
         // Handle the upload.
         if ($request->isMethod('POST')) {
             $form->bind($request);
             if ($form->isValid()) {
                 $files = $request->files->get($form->getName());
                 /* Make sure that Upload Directory is properly configured and writable */
                 $filename = $files['FileUpload']->getClientOriginalName();
                 $files['FileUpload']->move($currentfolder, $filename);
                 echo "path: {$path}";
                 $app['session']->getFlashBag()->set('info', __("File '%file%' was uploaded successfully.", array('%file%' => $filename)));
                 // Add the file to our stack..
                 $app['stack']->add($path . "/" . $filename);
             } else {
                 $app['session']->getFlashBag()->set('error', __("File '%file%' could not be uploaded.", array('%file%' => $filename)));
             }
             return redirect('files', array('path' => $path));
         }
         $formview = $form->createView();
     } else {
         // Folder not writable, don't show an upload.
         $formview = false;
     }
     $ignored = array(".", "..", ".DS_Store", ".gitignore", ".htaccess");
     // Get the pathsegments, so we can show the path..
     $pathsegments = array();
     $cumulative = "";
     if (!empty($path)) {
         foreach (explode("/", $path) as $segment) {
             $cumulative .= $segment . "/";
             $pathsegments[$cumulative] = $segment;
         }
     }
     if (file_exists($currentfolder)) {
         $d = dir($currentfolder);
         while (false !== ($entry = $d->read())) {
             if (in_array($entry, $ignored)) {
                 continue;
             }
             $fullfilename = $currentfolder . "/" . $entry;
             if (is_file($fullfilename)) {
                 $files[$entry] = array('path' => $path, 'filename' => $entry, 'newpath' => $path . "/" . $entry, 'writable' => is_writable($fullfilename), 'readable' => is_readable($fullfilename), 'type' => getExtension($entry), 'filesize' => formatFilesize(filesize($fullfilename)), 'modified' => date("Y/m/d H:i:s", filemtime($fullfilename)), 'permissions' => \util::full_permissions($fullfilename));
                 if (in_array(getExtension($entry), array('gif', 'jpg', 'png', 'jpeg'))) {
                     $size = getimagesize($fullfilename);
                     $files[$entry]['imagesize'] = sprintf("%s × %s", $size[0], $size[1]);
                 }
             }
             if (is_dir($fullfilename)) {
                 $folders[$entry] = array('path' => $path, 'foldername' => $entry, 'newpath' => $path . "/" . $entry, 'writable' => is_writable($fullfilename), 'modified' => date("Y/m/d H:i:s", filemtime($fullfilename)));
             }
         }
         $d->close();
     } else {
         $app['session']->getFlashBag()->set('error', __("Folder '%s' could not be found, or is not readable.", array('%s' => $path)));
     }
     $app['twig']->addGlobal('title', __("Files in %s", array('%s' => $path)));
     // Make sure the files and folders are sorted properly.
     ksort($files);
     ksort($folders);
     // Select the correct template to render this. If we've got 'CKEditor' in the title, it's a dialog
     // from CKeditor to insert a file..
     if (!$request->query->has('CKEditor')) {
         $twig = 'files.twig';
     } else {
         $twig = 'files_ck.twig';
     }
     return $app['render']->render($twig, array('path' => $path, 'files' => $files, 'folders' => $folders, 'pathsegments' => $pathsegments, 'form' => $formview));
 }

 /**
  * Ajax helper function to facilitate the selection of files from the images/
  * folder.
  *
  */
 public static function ext_fileSelector()
 {
     global $PIVOTX;
     $PIVOTX['session']->minLevel(PIVOTX_UL_NORMAL);
     $path = $PIVOTX['paths']['upload_base_path'];
     $url = $PIVOTX['paths']['upload_base_url'];
     if (empty($path) || empty($url)) {
         echo "Can't continue: paths not set..";
         die;
     }
     $breadcrumbs = array("<a href='#' onclick=\"fileSelectorChangefolder('')\">" . basename($path) . "</a>");
     if (!empty($_POST['folder'])) {
         $folder = fixPath($_POST['folder']) . "/";
         $path .= $folder;
         $url .= $folder;
         $incrementalpath = "";
         foreach (explode("/", $folder) as $item) {
             if (!empty($item)) {
                 $incrementalpath = $incrementalpath . $item . "/";
                 $breadcrumbs[] = sprintf("<a href='#' onclick=\"fileSelectorChangefolder('%s')\">%s</a>", $incrementalpath, $item);
             }
         }
     }
     $breadcrumbs = implode(" &raquo; ", $breadcrumbs);
     $files = array();
     $folders = array();
     $d = dir($path);
     while (false !== ($filename = $d->read())) {
         if (strpos($filename, '.thumb.') !== false || strpos($filename, '._') !== false || $filename == ".DS_Store" || $filename == "Thumbs.db" || $filename == "." || $filename == ".." || $filename == ".svn") {
             // Skip this one..
             continue;
         }
         if (is_file($path . $filename)) {
             $files[$filename]['link'] = $url . urlencode($filename);
             $files[$filename]['name'] = trimText($filename, 50);
             $ext = strtolower(getExtension($filename));
             $files[$filename]['ext'] = $ext;
             $files[$filename]['bytesize'] = filesize($path . "/" . $filename);
             $files[$filename]['size'] = formatFilesize($files[$filename]['bytesize']);
             if (in_array($ext, array('gif', 'jpg', 'jpeg', 'png'))) {
                 $dim = getimagesize($path . "/" . $filename);
                 $files[$filename]['dimension'] = sprintf('%s &#215; %s', $dim[0], $dim[1]);
                 $files[$filename]['image_type'] = $ext;
             }
             $files[$filename]['path'] = $folder . $filename;
         }
         if (is_dir($path . $filename)) {
             $folders[$filename] = array('link' => $url . urlencode($filename), 'name' => trimText($filename, 50), 'path' => $folder . $filename);
         }
     }
     $d->close();
     ksort($folders);
     ksort($files);
     echo "<div id='fileselector'>";
     printf("<p><strong>%s:</strong> %s </p>", __("Current path"), $breadcrumbs);
     foreach ($folders as $folder) {
         printf("<div class='folder'><a href='#' onclick=\"fileSelectorChangefolder('%s'); return false;\">%s</a></div>", addslashes($folder['path']), $folder['name']);
     }
     foreach ($files as $file) {
         if ($PIVOTX['config']->get('fileselector_thumbs') && !empty($file['image_type'])) {
             $height = getDefault($PIVOTX['config']->get('fileselector_thumbs_height'), 40);
             $link_text = sprintf("<img src='%sincludes/timthumb.php?h=%s&amp;src=%s' alt='%s' title='%s'>", $PIVOTX['paths']['pivotx_url'], $height, $file['path'], $file['name'], $file['name']);
             $extra_style = "style='height: {$height}px; margin-bottom: 5px;'";
         } else {
             $link_text = $file['name'];
             $extra_style = "";
         }
         printf("<div class='file' {$extra_style}><a href='#' onclick=\"fileSelectorChoose('%s'); return false;\">%s</a> <span>(%s%s)</span></div>", addslashes($file['path']), $link_text, $file['size'], !empty($file['dimension']) ? " - " . $file['dimension'] . " px" : "");
     }
     echo "</div>";
     //echo "<pre>\n"; print_r($folders); echo "</pre>";
     //echo "<pre>\n"; print_r($files); echo "</pre>";
 }

    $newModel['history'] = "Derived from {$model['pdb']} by Reduce -nobuild9999 -nuclear";
}
$newModel['isUserSupplied'] = $model['isUserSupplied'];
$newModel['isReduced'] = true;
$_SESSION['models'][$newModel['id']] = $newModel;
$_SESSION['bgjob']['modelID'] = $newModel['id'];
$_SESSION['lastUsedModelID'] = $newModel['id'];
// this is now the current model
$hcount = countReduceChanges($outpath);
setProgress($tasks, 'notebook');
$pdb = $_SESSION['dataDir'] . '/' . MP_DIR_MODELS . '/' . $outname;
$url = $_SESSION['dataURL'] . '/' . MP_DIR_MODELS . '/' . $outname;
$entry = "Reduce was run on {$model['pdb']} to add and optimize missing hydrogens, resulting in {$newModel['pdb']}.\n";
if ($hcount) {
    $entry .= "{$hcount['found']} hydrogens were found in the original model, and {$hcount['add']} hydrogens were added.\n";
    if ($hcount['std']) {
        $entry .= "{$hcount['std']} H were repositioned to standardize bond lengths.\n";
    }
    if ($hcount['adj']) {
        $entry .= "The positions of {$hcount['adj']} hydrogens were adjusted to optimize H-bonding.\n";
    }
}
$entry .= "Asn/Gln/His flips were not optimized.\n";
$entry .= "<p>You can now <a href='{$url}'>download the annotated PDB file</a> (" . formatFilesize(filesize($pdb)) . ").</p>\n";
$_SESSION['bgjob']['labbookEntry'] = addLabbookEntry("Added H with -nobuild9999 to get {$newModel['pdb']}", $entry, "{$modelID}|{$newModel['id']}", "auto", "add_h.png");
setProgress($tasks, null);
############################################################################
// Clean up and go home
unset($_SESSION['bgjob']['processID']);
$_SESSION['bgjob']['endTime'] = time();
$_SESSION['bgjob']['isRunning'] = false;