<?php

/**
 * @file
 * Bartik's theme implementation to display a node.
 *
 * Available variables:
 * - $title: the (sanitized) title of the node.
 * - $content: An array of node items. Use render($content) to print them all,
 *   or print a subset such as render($content['field_example']). Use
 *   hide($content['field_example']) to temporarily suppress the printing of a
 *   given element.
 * - $user_picture: The node author's picture from user-picture.tpl.php.
 * - $date: Formatted creation date. Preprocess functions can reformat it by
 *   calling format_date() with the desired parameters on the $created variable.
 * - $name: Themed username of node author output from theme_username().
 * - $node_url: Direct URL of the current node.
 * - $display_submitted: Whether submission information should be displayed.
 * - $submitted: Submission information created from $name and $date during
 *   template_preprocess_node().
 * - $classes: String of classes that can be used to style contextually through
 *   CSS. It can be manipulated through the variable $classes_array from
 *   preprocess functions. The default values can be one or more of the
 *   following:
 *   - node: The current template type; for example, "theming hook".
 *   - node-[type]: The current node type. For example, if the node is a
 *     "Blog entry" it would result in "node-blog". Note that the machine
 *     name will often be in a short form of the human readable label.
 *   - node-teaser: Nodes in teaser form.
 *   - node-preview: Nodes in preview mode.
 *   The following are controlled through the node publishing options.
 *   - node-promoted: Nodes promoted to the front page.
 *   - node-sticky: Nodes ordered above other non-sticky nodes in teaser
 *     listings.
 *   - node-unpublished: Unpublished nodes visible only to administrators.
 * - $title_prefix (array): An array containing additional output populated by
 *   modules, intended to be displayed in front of the main title tag that
 *   appears in the template.
 * - $title_suffix (array): An array containing additional output populated by
 *   modules, intended to be displayed after the main title tag that appears in
 *   the template.
 *
 * Other variables:
 * - $node: Full node object. Contains data that may not be safe.
 * - $type: Node type; for example, story, page, blog, etc.
 * - $comment_count: Number of comments attached to the node.
 * - $uid: User ID of the node author.
 * - $created: Time the node was published formatted in Unix timestamp.
 * - $classes_array: Array of html class attribute values. It is flattened
 *   into a string within the variable $classes.
 * - $zebra: Outputs either "even" or "odd". Useful for zebra striping in
 *   teaser listings.
 * - $id: Position of the node. Increments each time it's output.
 *
 * Node status variables:
 * - $view_mode: View mode; for example, "full", "teaser".
 * - $teaser: Flag for the teaser state (shortcut for $view_mode == 'teaser').
 * - $page: Flag for the full page state.
 * - $promote: Flag for front page promotion state.
 * - $sticky: Flags for sticky post setting.
 * - $status: Flag for published status.
 * - $comment: State of comment settings for the node.
 * - $readmore: Flags true if the teaser content of the node cannot hold the
 *   main body content.
 * - $is_front: Flags true when presented in the front page.
 * - $logged_in: Flags true when the current user is a logged-in member.
 * - $is_admin: Flags true when the current user is an administrator.
 *
 * Field variables: for each field instance attached to the node a corresponding
 * variable is defined; for example, $node->body becomes $body. When needing to
 * access a field's raw values, developers/themers are strongly encouraged to
 * use these variables. Otherwise they will have to explicitly specify the
 * desired field language; for example, $node->body['en'], thus overriding any
 * language negotiation rule that was previously applied.
 *
 * @see template_preprocess()
 * @see template_preprocess_node()
 * @see template_process()
 */
?>
<div id="node-<?php print $node->nid; ?>" class="<?php print $classes; ?> clearfix"<?php print $attributes; ?>>

  <?php print render($title_prefix); ?>
  <?php if (!$page): ?>
    <h2<?php print $title_attributes; ?>>
      <a href="<?php print $node_url; ?>"><?php print $title; ?></a>
    </h2>
  <?php endif; ?>
  <?php print render($title_suffix); ?>

  <div class="content clearfix"<?php print $content_attributes; ?>>
    <?php
      // We hide the comments and links now so that we can render them later.
      hide($content['comments']);
      hide($content['links']);
    ?>

    <table>
      <tr><th>Human-Readable Name</th><td><?php print $node->db_name; ?></td></tr>
      <tr><th>Database Path</th><td><?php print $node->db_path; ?></td></tr>
      <tr><th>Database Type</th><td><?php print $node->db_dbtype; ?></td></tr>
<?php if ($node->linkout->none === FALSE ) { ?>
      <tr><th>FASTA Header Format</th><td><?php print $node->linkout->regex_type; ?></td></tr>
      <tr><th>External Database</th><td><?php print $node->linkout->db_id->name; ?></td></tr>
      <tr><th>RegEx</th><td><?php print $node->linkout->regex; ?></td></tr>
      <tr><th>Link-out Type</th><td><?php print $node->linkout->type; ?></td></tr>
<?php } ?>
      <tr><th>Whole Genome Viewer</th><td><?php print ($node->cvitjs_enabled) ? 'Enabled' : 'Disabled'; ?></td></tr>
    </table>


    <?php
      if ($node->cvitjs_enabled) {

        print '<h3>Whole Genome Viewer</h3>';

        $conf_section = blast_ui_get_cvit_conf_text('data.'.$node->db_name);

        if (!$conf_section) {

          print '<div class="messages warning">There is no section for this genome target defined in the CViTjs
            configuration file. <strong>No genome visualization will be shown until you define a
            configuration section, "[data.'.$form_state['values']['db_name'].']", at '
            .l('Admin > Tripal > Extensions > Tripal BLAST > BLAST UI', 'admin/tripal/extension/tripal_blast')
            .'</strong>.</div>';
        }
        else {
          print '<h4>Configuration</h4>'
            . '<pre>'.$conf_section.'</pre>';
        }
    }
    ?>
    <?php
      // Add in any remaining content
      print render($content);
    ?>
  </div>

</div>