EDIT

function tagged_text_new($tag_type, $text = null){

  $tt = new stdClass();

  $tt->type = $tag_type;

  $tt->text = $text;

  return $tt;

}

 * from the webservice and the original entry in the TaggedText array will be

 * Tagged text where the type starts with 'PLACEHOLDER_' will be added to the markup as plain text whereas the

 * taggedText->type wrapped in curly brackets: '{'. $tt->text . '}' is used as text.

 * see tagged_text_extract_secref()

 *

 *   The markup.

      if(str_beginsWith($tt->type, 'PLACEHOLDER_')){

        $out .=  '{'. $tt->type . '}';

      } else {

        $out .= '<' . $tag . ' class="' . $class_attr . '">'

          . t('@text', array('@text' => $tt->text))

          . '</' . $tag . '>'

          . $glue;

        }

      $was_separator = $is_separator;

    }

    $i++;

  }

  return $out;

}

/**

 * Converts an array of TaggedText items into corresponding plain text string

 *

 * Each item is provided with a class attribute which is set to the key of the

 * TaggedText item.

 *

 * @param array $taggedtxt

 *   Array with text items to convert.

 * @param array $skiptags

 *   Array of tag names to skip

 *

 * @return string

 *   The plain text

 */

function cdm_tagged_text_to_string(array $taggedtxt, $skiptags = array()) {

  $out = '';

  $was_separator = false;

  $i = 0;

  foreach ($taggedtxt as $tt) {

    if (!in_array($tt->type, $skiptags) && $tt->text) {

      $is_last = $i + 1 == count($taggedtxt);

      $is_separator = is_tagged_text_sepatator_type($tt->type);

      $glue = !$is_separator && !$was_separator && !$is_last ? ' ' : '';

      $out .= t('@text', array('@text' => $tt->text)) . $glue;

/**

 * Extracts the tagged text for sec references with separator and citation detail from a tagged text array.

 * @param $tagged_text

 *    The tagged text to operate on

 * @param string $ref_tag_type

 *    The tagtype for a secreference is "secReference", but "relSecReference" is also used in case of relationships.

 * @param bool $replace_with_placeholder

 *    Indicates the method to add a empty placeholder tagged text alement as relpacement for the extrated tagged text

 *    elements.

 * @return array

 */

function tagged_text_extract_secref(&$tagged_text, $ref_tag_type = "secReference", $replace_with_placeholder = false) {

    $extract_pos = null;

      if ($tagged_text[$i + 1]->type == $ref_tag_type && $tagged_text[$i]->type == "separator"){

        if($replace_with_placeholder){

          // text must not be null, see cdm_tagged_text_to_markup()

          $tagged_text[$i] = tagged_text_new("PLACEHOLDER_" . $ref_tag_type, "PLACEHOLDER_" . $ref_tag_type);

        } else {

          unset($tagged_text[$i]);

        }

        // also get the microreference which could be in $tagged_text[$i + 3]

        if(isset($tagged_text[$i + 3])  && $tagged_text[$i + 2]->type == "separator" && $tagged_text[$i + 3]->type == $ref_tag_type){

          unset($tagged_text[$i + 2]);

          unset($tagged_text[$i + 3]);

  $tagged_text = array_values($tagged_text); // re-index array to make it continuous again

function tagged_text_extract_nomstatus(&$tagged_text) {

  $secref_tagged_text = tagged_text_extract_secref($taggedTitle);

  $nom_status_tagged_text = tagged_text_extract_nomstatus($taggedTitle);

  $footnote_list_key = 'taxon_relationships';

  RenderHints::setFootnoteListKey($footnote_list_key);

  $joined_sensu_refs = array();

  //  - show only the author team as short citation for the sec reference

  //  - show the according reference as footnote to this short citation

          // using name tags + author as full name key

          $full_name_key = join(' ', cdm_tagged_text_values($taxon_relation->taggedText, array('name', 'authors')));

          // Render the first name found as representative for all others.

          //###OLD: $misapplied[$name]['out'] = cdm_related_taxon($taxon_relation->fromTaxon, UUID_MISAPPLIED_NAME_FOR);

          $sensu_tagged_text = tagged_text_extract_secref($taxon_relation->taggedText, "secReference", true);

          $relsec_tagged_text = tagged_text_extract_secref($taxon_relation->taggedText, "relSecReference", true);

          if (isset($sensu_tagged_text[1])) {

            array_shift($sensu_tagged_text); // remove first element which contains the "sensu", this will be added later in this code

            $sensu_citation_short_markup = cdm_tagged_text_to_markup($sensu_tagged_text);

            $sensu_citation_short = cdm_tagged_text_to_string($sensu_tagged_text);

            $sensu_uuid = $sensu_tagged_text[0]->entityReference->uuid;

            $misapplied[$full_name_key]['sensu_uuids'][] = $sensu_uuid;

            if (!isset($joined_sensu_refs[$sensu_uuid])) {

              $joined_sensu_refs[$sensu_uuid] = array(

                'short_citation' => $sensu_citation_short,

                'markup' => $sensu_citation_short_markup // to be expanded later as short_citation + footnote key

              );

            }

            if (isset($relsec_tagged_text[1])) {

              array_shift($relsec_tagged_text); // remove first element which contains the "err. sec", this will be added later in this code

              $relsec_citation_short_markup = cdm_tagged_text_to_markup($relsec_tagged_text);

              $relsec_citation_short = cdm_tagged_text_to_string($relsec_tagged_text);

              $relsec_uuid = $relsec_tagged_text[0]->entityReference->uuid;

              $misapplied[$full_name_key]['relsec_uuids'][] = $relsec_uuid;

              if (!isset($joined_sensu_refs[$relsec_uuid])) {

                $joined_sensu_refs[$relsec_uuid] = array(

                  'short_citation' => $relsec_citation_short,

                  'markup' => $relsec_citation_short_markup // to be expanded later as short_citation + footnote key

                );

            if (!isset($misapplied[$full_name_key]['out'])) {

              $misapplied[$full_name_key]['out'] = cdm_tagged_text_to_markup($taxon_relation->taggedText);

            } else {

              // We need to add the anchors for all of the other misapplied names not

              // being rendered explicitly.

              $misapplied[$full_name_key]['out'] = uuid_anchor($taxon_relation->taxonUuid, $misapplied[$full_name_key]['out']);

            }

          } else {

            RenderHints::pushToRenderStack('other_taxon_relationship');

            // All relationship types except misapplied_name_for and invalid_designation_for.

            $taxon_relationships_lines[] = cdm_taxonRelationship($taxon_relation, TRUE, _is_invers_taxonRelationship($taxon_relation, $focusedTaxon));

          RenderHints::popFromRenderStack();

    } // END loop over $taxonRelationshipsDTO->relations

  // Sort the $joined_sensu_refs and create footnotes and footnote keys.

  uasort($joined_sensu_refs, function($a, $b) {

    if ($a['short_citation'] == $b['short_citation']) {

      return 0;

    return ($a['short_citation'] < $b['short_citation']) ? -1 : 1;

  });

  foreach ($joined_sensu_refs as $sensu_uuid => $sensu_strings) {

    $footnote_key = '';

    if(!empty($sensu_strings)) {

      $sensu_reference = cdm_ws_get(CDM_WS_REFERENCE, $sensu_uuid);

      if(!$sensu_reference){

        drupal_set_message("Problem fetching sensu reference with uuid " . $sensu_uuid, 'error');

      }

      $footnote_key = FootnoteManager::addNewFootnote($footnote_list_key, $sensu_reference->titleCache);

      $footnote_key = theme('cdm_footnote_key', array('footnoteKey' => $footnote_key));

    $joined_sensu_refs[$sensu_uuid]['markup'] = '<span class="sensu">' . $sensu_strings['markup'] . $footnote_key . '</span>';

    ksort($misapplied); // order the misapplied by scientific name

      $misapplied_name_markup = $misapplied_name['out'];

      if (isset($misapplied_name['sensu_uuids'])) {

        $sensu_refs_with_fkey = array();

        foreach ($misapplied_name['sensu_uuids'] as $sensu_uuid) {

          $sensu_refs_with_fkey[$joined_sensu_refs[$sensu_uuid]['short_citation']] = $joined_sensu_refs[$sensu_uuid]['markup'];

        }

        ksort($sensu_refs_with_fkey);

        $sensu_refs_with_fkey_markup = join('; ', $sensu_refs_with_fkey);

        $misapplied_name_markup = str_replace('{PLACEHOLDER_secReference}', ' sensu ' . $sensu_refs_with_fkey_markup, $misapplied_name_markup);

      }

      if (isset($misapplied_name['relsec_uuids'])) {

        $relsec_refs_with_fkey = array();

        foreach ($misapplied_name['relsec_uuids'] as $relsec_uuid) {

          $relsec_refs_with_fkey[$joined_sensu_refs[$relsec_uuid]['short_citation']] = $joined_sensu_refs[$relsec_uuid]['markup'];

        ksort($relsec_refs_with_fkey);

        $relsec_refs_with_fkey_markup = join('; ', $relsec_refs_with_fkey);

        $misapplied_name_markup = str_replace('{PLACEHOLDER_relSecReference}', ', err. sec. ' . $relsec_refs_with_fkey_markup, $misapplied_name_markup);

      $out .= '<li class="synonym"><span class="misapplied">' . $misapplied_name_markup . ' </span>';

  $footnotes = theme('cdm_footnotes', array('footnoteListKey' => $footnote_list_key, 'enclosingTag' => 'li'));

  $footnotes .= theme('cdm_annotation_footnotes', array('footnoteListKey' => $footnote_list_key, 'enclosingTag' => 'li'));

     *

     * TODO 1b) Der Buchlink verweist auf den Protolog von N. blancoi Blume – der hat ja aber gerade nichts mit dieser Namensanwendung zu tun (also: Protologbildlinks müssen bei MAN weggelassen werden oder der Link muss nach dem <non Blume>

eingefügt werden)