EDIT

/**

 * Returns HTML for misapplied names and invalid designations.

 *

 * Both relation types are currently treated the same!

 *

 * @param array $variables

 *   An associative array containing:

 *   - taxonRelationships

 *   - focusedTaxon

 *

 * @ingroup themeable

 *

 * @return string

 *    the rendered html

 */

function theme_cdm_taxonRelationships($variables) {

  $taxonRelationships = $variables['taxonRelationships'];

  $focusedTaxon = $variables['focusedTaxon'];

  if (!$taxonRelationships) {

    return null;

  }

  RenderHints::pushToRenderStack('taxonRelationships');

  $footnoteListKey = 'taxonRelationships';

  RenderHints::setFootnoteListKey($footnoteListKey);

  $misapplied = array();

  $joinedAuthorTeams = array();

  $taxon_relationship_types = variable_get(CDM_TAXON_RELATIONSHIP_TYPES, unserialize(CDM_TAXON_RELATIONSHIP_TYPES_DEFAULT));

  // Aggregate misapplied names having the same fullname:

  foreach ($taxonRelationships as $taxonRelation) {

    if (in_array($taxonRelation->type->uuid, $taxon_relationship_types)) {

      if ($taxonRelation->type->uuid == UUID_MISAPPLIED_NAME_FOR || $taxonRelation->type->uuid == UUID_INVALID_DESIGNATION_FOR) {

        $name = $taxonRelation->fromTaxon->name->titleCache;

        if(isset($taxonRelation->fromTaxon->sec)) {

          // taxa not always are have a sec reference (e.g. doubtful taxa)

          $authorteam = cdm_ws_get(CDM_WS_REFERENCE_AUTHORTEAM, $taxonRelation->fromTaxon->sec->uuid);

          $authorteam = $authorteam->titleCache;

        }

        if (!isset($misapplied[$name])) {

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

          $misapplied[$name]['out'] = cdm_related_taxon($taxonRelation->fromTaxon, UUID_MISAPPLIED_NAME_FOR);

        }

        else {

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

          // being rendered explicitly.

          $misapplied[$name]['out'] = uuid_anchor($taxonRelation->fromTaxon->uuid, $misapplied[$name]['out']);

        }

        // Collect all authors for this fullname.

        if (isset($authorteam)) {

          $misapplied[$name]['authorteam'][$authorteam] = '';

          $joinedAuthorTeams[$authorteam] = 'sensu ' . theme('cdm_reference', array('reference' => $taxonRelation->fromTaxon->sec));

        }

      }

      else {

        // All relationsship types but misapplied_name_for

        // invalid_designation_for.

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

      }

    }

  }

  // Sort the joinedAuthorTeams and create footnotes and footnotekeys.

  ksort($joinedAuthorTeams);

  foreach ($joinedAuthorTeams as $authorteam => $sensuCitation) {

    $footnoteKey = FootnoteManager::addNewFootnote($footnoteListKey, $sensuCitation);

    $joinedAuthorTeams[$authorteam] = '<span class="sensu">sensu '

      . $authorteam

      . theme('cdm_footnote_key', array('footnoteKey' => $footnoteKey))

      . '</span>';

  }

  // ---- Generate output ---- //

  $out = '<div class="taxon-relationships">';

  if (is_array($misapplied) && count($misapplied) > 0) {

    $out .= '<ul class="misapplied">';

    foreach ($misapplied as $misapplied_name) {

      $out .= '<li class="synonym"><span class="misapplied">' . $misapplied_name['out'] . ' </span>';

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

        // Fill authors with the renderedFootnoteKey and sorting 'em.

        foreach ($misapplied_name['authorteam'] as $authorteam => &$renderedFootnoteKey) {

          $renderedFootnoteKey = $joinedAuthorTeams[$authorteam];

        }

        ksort($misapplied_name['authorteam']);

        $out .= join('; ', $misapplied_name['authorteam']);

      }

      $out .= '</li>';

    }

    $out .= '</ul>';

  }

  if (isset($taxon_relationships_lines) && is_array($taxon_relationships_lines) && count($taxon_relationships_lines) > 0) {

    $out .= '<ul class="taxonRelationships">';

    foreach ($taxon_relationships_lines as $taxon_relationship_line) {

      $out .= '<li class="synonym">' . $taxon_relationship_line . '</li>';

    }

    $out .= '</ul>';

  }

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

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

// AK: why splitting footnotes at the sensu string ??? this is weired and hacky

//     TODO remove below dead code

//   $tr_footnotes_exploded = explode('sensu', $tr_footnotes);

//   $tr_footnotes_aux = '';

//   foreach ($tr_footnotes_exploded as $element) {

//     $tr_footnotes_aux .= $element;

//   }

  $out .= '<ul class="footnotes">' . $footnotes . '</ul>';

  $out .= '</div>';

  RenderHints::popFromRenderStack();

  return $out;

}

/**

 * Renders a representation of the given taxon relationship.

 *

 * According name relationships are also being rendered.

 *

 * @param unknown_type $taxonRelationship

 * @param boolean $doLinkTaxon

 *     whether to create a link to the related taxon

 * @param boolean $inverse

 *     whether the $taxonRelationship should be treaded as invers relation

 *

 * @return void|string

 */

function cdm_taxonRelationship($taxonRelationship, $doLinkTaxon = FALSE, $inverse = FALSE) {

  // Validate object.

  if (!(isset($taxonRelationship->toTaxon) && isset($taxonRelationship->fromTaxon) && isset($taxonRelationship->type))) {

    return null;

  }

  $taxonRelationType = $taxonRelationship->type;

  if ($inverse) {

    $toTaxon = $taxonRelationship->fromTaxon;

    $relsign = $taxonRelationType->inverseRepresentation_L10n_abbreviatedLabel;

    $reltype_representation = $taxonRelationType->inverseRepresentation_L10n;

  }

  else {

    $toTaxon = $taxonRelationship->toTaxon;

    $relsign = $taxonRelationType->representation_L10n_abbreviatedLabel;

    $reltype_representation = $taxonRelationType->representation_L10n;

  }

  return cdm_related_taxon($toTaxon, NULL, $relsign, $reltype_representation, $taxonRelationship->doubtful, $doLinkTaxon);

}

/**

 * Renders a representation of the given taxon relationship.

 *

 * According name relationships are also being rendered.

 *

 * @param $taxon

 *  The CDM TaxonBase entity

 * @param $reltype_uuid

 *  The UUID of the TaxonRelationshipType

 * @param $relsign

 *  Optional. Can be  used to override the internal decision strategy on finding a suitable icon for the relationship

 * @param $reltype_representation

 *   Optional: Defines the value for the title attribute of the html element enclosing the relsign

 * @param $doubtful

 *   TODO

 * @param $doLinkTaxon

 *   The taxon will be rendered as clickable link when true.

 *

 * @return string

 *   Markup for the taxon relationship.

 */

function cdm_related_taxon($taxon, $reltype_uuid = NULL, $relsign = NULL, $reltype_representation = NULL, $doubtful=false, $doLinkTaxon = FALSE) {

  static $relsign_homo = '≡';

  static $relsign_hetero = '=';

  static $relsign_invalid = '–';

  static $nom_status_invalid_type_uuids =  array(

      UUID_NOMENCLATURALSTATUS_TYPE_INVALID,

      UUID_NOMENCLATURALSTATUS_TYPE_NUDUM,

      UUID_NOMENCLATURALSTATUS_TYPE_COMBINATIONINVALID,

      UUID_NOMENCLATURALSTATUS_TYPE_PROVISIONAL

  );

  // 'taxonRelationships';

  $footnoteListKey = NULL;

  $skip_tags = array();

  $is_invalid = false;

  if (!$relsign) {

    switch ($reltype_uuid) {

      case UUID_HETEROTYPIC_SYNONYM_OF:

      case UUID_SYNONYM_OF:

        $relsign = $relsign_hetero;

        break;

      case UUID_HOMOTYPIC_SYNONYM_OF:

        $relsign = $relsign_homo;

        break;

      case UUID_MISAPPLIED_NAME_FOR:

      case UUID_INVALID_DESIGNATION_FOR:

        $skip_tags[] = 'authors';

        $is_invalid = true;

        $relsign = $relsign_invalid;

        break;

      default:

        $relsign = $relsign_invalid;

    }

  }

  if($doubtful) {

    $relsign = '?' . $relsign;

  }

  /*

  Names with status invalid or nudum are to be displayed with the

  $relsign_invalid, these names appear at the end of all names in their

  homotypic group (ordered correctly by the java cdm_lib).

  */

  if (isset($taxon->name->status) && is_array($taxon->name->status)) {

    foreach ($taxon->name->status as $status) {

      if (in_array($status->type->uuid , $nom_status_invalid_type_uuids)) {

        $relsign = $relsign_invalid;

        break;

      }

    }

  }

  // Now rendering starts ..

  RenderHints::pushToRenderStack('related_taxon');

  if (isset($taxon->name->nomenclaturalReference)) {

    $referenceUri = url(path_to_reference($taxon->name->nomenclaturalReference->uuid));

  }

  $taxonUri = '';

  if ($doLinkTaxon) {

    $taxonUri = url(path_to_taxon($taxon->uuid, "synonymy"));

  }

  // Printing the taxonName and the handling the special case of annotations.

  if (!isset($referenceUri)) {

    $referenceUri = FALSE;

  }

  $out_taxon_part = render_taxon_or_name($taxon, $taxonUri, $referenceUri, TRUE, FALSE, $skip_tags, $is_invalid);

  $taxon_footnotes = theme('cdm_annotations_as_footnotekeys',

       array('cdmBase_list' => array(

         $taxon->name,

         $taxon,

       ),

       'footnote_list_key' => $footnoteListKey)

  );

  $homonyms = cdm_name_relationships_of($taxon);

  $out = '<span class="relation_sign" title="' . $reltype_representation . '">' . $relsign . '</span>'

      . $out_taxon_part . $taxon_footnotes . ' '  . $homonyms;

  $out = uuid_anchor($taxon->uuid, $out);

  RenderHints::popFromRenderStack();

  return $out;

}