EDIT

function _is_invers_taxonRelationship($taxonRelationship, $focusedTaxon){

  return $taxonRelationship->fromTaxon->uuid == $focusedTaxon->uuid;

}

	$out .= '<li class="synonym">'.cdm_related_taxon($taxon, UUID_HOMOTYPIC_SYNONYM_OF).'</li>';

			$out .= '<li class="firstentry synonym">'.cdm_related_taxon($synonym, UUID_HETEROTYPIC_SYNONYM_OF).'</li>';

			$out .= '<li class="synonym">'.cdm_related_taxon($synonym, UUID_HOMOTYPIC_SYNONYM_OF).'</li>';

			$out .= '<li class="synonym">'.cdm_related_taxon($taxon, UUID_HOMOTYPIC_SYNONYM_OF).'</li>';

		$out .= '<li class="synonym">'.cdm_related_taxon($synonym, UUID_HOMOTYPIC_SYNONYM_OF).'</li>';

    $out .= theme('cdm_taxonRelationships', $taxonRelationships, $taxon);

  $showThumbnails = $_SESSION['pageoptions']['searchtaxa']['showThumbnails'];

  if( !is_numeric($showThumbnails)){

    $showThumbnails = 1;

  }

  $setSessionUri = url('cdm_api/setvalue/session', "var=[pageoption][searchtaxa][showThumbnails]&val=");

  drupal_add_js('$(document).ready(function() {

  drupal_set_title(t('Search results'));

  $out = ''; //l('Advanced Search', '/cdm_dataportal/search');

  $out = '<div class="page_options"><form name="pageoptions"><input id="showThumbnails" type="checkbox" name="showThumbnails" '.($showThumbnails == 1? 'checked="checked"': '').'> '.t('Show Thumbnails').'</form></div>';

  if(count($pager->records) > 0){

      $out .= '<div id="search_results">';

    $out .= theme('cdm_list_of_taxa', $pager->records);

    $out .= '</div>';

    $out .= theme('cdm_pager', $pager, $path, $parameters);

  } else {

    $out = '<h4 class="error">Sorry, no matching entries found.</h4>';

  }

  return $out;

function theme_cdm_taxonRelationships($taxonRelationships, $focusedTaxon){

  if(!$taxonRelationships){

    return;

  }

  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;

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

          $authorteam = $author_team->titleCache;

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

            $misapplied[$name]['out'] =

              '<span class="misapplied">'

              .cdm_related_taxon($taxonRelation->fromTaxon, UUID_MISAPPLIED_NAME_FOR).

              '</span>';

          }

          // collect all authors for this fullname

          if(isset($authorteam)){

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

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

          }

          } else {

            // all relationsship types but misapplied_name_for invalid_designation_for

             $taxonRelationshipsLines[] = cdm_taxonRelationship($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', $footnoteKey).'</span>';

  }

  // generate output

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

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

      foreach($misapplied as $misapplied_name){

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

        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(is_array($taxonRelationshipsLines) && count($taxonRelationshipsLines) >0 ){

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

      foreach($taxonRelationshipsLines as $taxonRelationshipLine){

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

      }

      $out .= '</ul>';

  }

  $tr_footnotes = theme('cdm_footnotes', $footnoteListKey, 'li');

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

  $tr_footnotes_aux = '';

  foreach ($tr_footnotes_exploded as $element){

    $tr_footnotes_aux .= $element;

  }

  $out .= '<ul>' . $tr_footnotes_aux . '</ul>';

  //$out .= '</ul>';

  RenderHints::popFromRenderStack();

  return $out;

  RenderHints::pushToRenderStack('acceptedFor');

  $out = '';

  if(isset($_REQUEST['acceptedFor'])){

    $synonym = cdm_ws_get(CDM_WS_PORTAL_TAXON, $_REQUEST['acceptedFor']);

    if($synonym){

      $out .= '<span class="acceptedFor">';

      $out .= t('is accepted for ');

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

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

      }

      $out .= theme('cdm_taxonName', $synonym->name, null, $referenceUri);

      $out .= theme('cdm_annotations_as_footnotekeys', $synonym);

      $out .= '</span>';

    }

  }

  RenderHints::popFromRenderStack();

  return $out;

  RenderHints::pushToRenderStack('list_of_taxa');

  $form_name = 'search_gallery';

  //$default_values = unserialize(CDM_DATAPORTAL_GALLERY_SETTINGS);

  $showMedia_taxa = $gallery_settings['cdm_dataportal_show_taxon_thumbnails'];

  $showMedia_synonyms = $gallery_settings['cdm_dataportal_show_synonym_thumbnails'];

  //$showMedia_taxa = variable_get('cdm_dataportal_findtaxa_show_taxon_thumbnails', 1);

  //$showMedia_synonyms = variable_get('cdm_dataportal_findtaxa_show_synonym_thumbnails', 0);

  $classification_uuid = get_taxonomictree_uuid_selected();

  // .. well, for sure not as performant as before, but better than nothing.

  $synonym_uuids = array();

  foreach($records as $taxon){

    if($taxon->class != "Taxon"){

      if(!array_key_exists($taxon->uuid, $synonym_uuids)){

        $synonym_uuids[$taxon->uuid] = $taxon->uuid;

      }

    }

  }

  // batch service not jet implemented:

  // $table_of_accepted = cdm_ws_property(CDM_WS_PORTAL_TAXON_ACCEPTED, join(',', $synonym_uuids));

  // thus ...

  $table_of_accepted = array();

  foreach($synonym_uuids as $synUuid){

    $table_of_accepted[$synUuid] = cdm_ws_get(CDM_WS_PORTAL_TAXON_ACCEPTED, array($synUuid, $classification_uuid));

  }

  $out = '<ul class="cdm_names" style="background-image: none;">';

  foreach($records as $taxon){

    // its a Taxon

    if($taxon->class == "Taxon"){

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

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

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

      }

      $out .= '<li class="Taxon">'.theme('cdm_taxonName', $taxon->name, $taxonUri, $referenceUri);

      $out .= theme('cdm_annotations_as_footnotekeys', $taxon);

      if($showMedia_taxa){

        $out .= theme('cdm_taxon_list_thumbnails', $taxon);

      }

      $out .= '</li>';

    } else {

      // its a synonym

      $uuid = $taxon->uuid;

      $acceptedTaxa = $table_of_accepted[$uuid];

      if(count($acceptedTaxa) == 1){

        $acceptedTaxon = $acceptedTaxa[0];

        $taxonUri = theme('cdm_uri_to_synonym', $taxon->uuid, $acceptedTaxon->uuid, 'synonymy');

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

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

        }

        $out .= '<li class="Synonym">'.theme('cdm_taxonName', $taxon->name, $taxonUri, $referenceUri);

        $out .= theme('cdm_annotations_as_footnotekeys', $taxon);

        if($showMedia_synonyms){

          $out .= theme('cdm_taxon_list_thumbnails', $acceptedTaxon);

        }

        $out .= '</li>';

      } else {

        //TODO avoid using Ajax in the cdm_dynabox .... why?

        //TODO add media

        $out .= cdm_dynabox(

          theme('cdm_taxonName', $taxon->name, null, null, false),

          cdm_compose_url(CDM_WS_PORTAL_TAXON_ACCEPTED, array($taxon->uuid, $classification_uuid)),

          'cdm_list_of_taxa',

          'Click for accepted taxon');

      }

    }

  }

  $out .= '</ul>';

  RenderHints::popFromRenderStack();

  return $out;

/**

 * renders a representation of the given taxon relationship.

 * According name relatinships are also being rendered.

 *

 *

 * @param unknown_type $taxon

 * @param unknown_type $reltype_uuid

 * @param unknown_type $taxonRelationType

 * @param unknown_type $doLinkTaxon

 */

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

  // validate object

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

    return;

  }

  $reltype_uuid = $taxonRelationship->type->uuid;

  $taxonRelationType = $taxonRelationship->type;

  $reltype_representation = '';

  if($inverse) {

    $taxon = $taxonRelationship->toTaxon;

    $relsign = $taxonRelationType->inverseRepresentation_L10n_abbreviatedLabel;

    $reltype_representation = $taxonRelationType->inverseRepresentation_L10n;

  } else {

    $taxon = $taxonRelationship->fromTaxon;

    $relsign = $taxonRelationType->representation_L10n_abbreviatedLabel;

    $reltype_representation = $taxonRelationType->representation_L10n;

  }

  return cdm_related_taxon($taxon, null, $relsign, $reltype_representation, $doLinkTaxon);

}

/**

* renders a representation of the given taxon relationship.

* According name relatinships are also being rendered.

*

*

* @param unknown_type $taxon

* @param unknown_type $reltype_uuid

* @param unknown_type $taxonRelationType

* @param unknown_type $doLinkTaxon

*/

function cdm_related_taxon($taxon, $reltype_uuid = null, $relsign = null, $reltype_representation = null, $doLinkTaxon = false){

  static $relsign_homo = '≡';

  static $relsign_hetero = '=';

  static $relsign_invalid = '–';

  $name_prefix = '';

  $name_postfix = '';

  $skiptags = array();

  if(!$relsign) {

    $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:

        $skiptags[] = 'authors';

        $relsign = $relsign_invalid;

        $name_prefix = '"';

        $name_postfix = '"';

        break;

      default :

        $relsign = $relsign_invalid;

    }

  }

  /*

   * 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 ( is_array($taxon->name->status)) {

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

      if ($status->type->uuid == UUID_NOMENCLATURALSTATUS_TYPE_INVALID || $status->type->uuid == UUID_NOMENCLATURALSTATUS_TYPE_NUDUM){

        $relsign = $relsign_invalid;

      }

    }

  }

  // now rendering starts ..

  RenderHints::pushToRenderStack('related_taxon');

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

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

  }

  if($doLinkTaxon){

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

  }

  //printing the taxonName and the handling the special case of annotations

  $nameHtml = theme('cdm_taxonName', $taxon->name, $taxonUri, $referenceUri, true, false, $skiptags);

  $special_annotations_array = array();

  $special_annotations_array[] = $taxon->name;

  $special_annotations_array[] = $taxon;

  $nameHtml .= theme('cdm_annotations_as_footnotekeys', $special_annotations_array);

  //later homonym or trated as later homonym AND bloking names

  $from_name_relations = cdm_ws_get(CDM_WS_PORTAL_TAXON_FROM_NAMERELATIONS, $taxon->uuid);

  $to_name_relations = cdm_ws_get(CDM_WS_PORTAL_TAXON_TO_NAMERELATIONS, $taxon->uuid);

  //first the FROM RELS

  if ($from_name_relations){

    foreach($from_name_relations as $element){

      switch ($element->type->representation_L10n){

        case 'later homonym for':

          if(isset($name_relations_html)){

            $name_relations_html .= ' nec ' . l($element->toName->titleCache . ' ' .  substr($element->toName->nomenclaturalReference->datePublished->start, 0, 4),

                'cdm_dataportal/name/' . $element->toName->uuid . '/' . $taxon->uuid . '/' . $element->toName->taxonBases[0]->uuid);

          }else{

            $name_relations_html = ' non ' . l($element->toName->titleCache . ' ' .  substr($element->toName->nomenclaturalReference->datePublished->start, 0, 4),

            . ' ' . $element->toName->datePublished->start;

          }

          break;

        case 'treated as later homonym for':

          if(isset($name_relations_html)){

            $name_relations_html = ' nec ' . l($element->toName->titleCache . ' ' .  substr($element->toName->nomenclaturalReference->datePublished->start, 0, 4),

          }else{

            $name_relations_html = ' non ' . l($element->toName->titleCache . ' ' .  substr($element->toName->nomenclaturalReference->datePublished->start, 0, 4),

                             'cdm_dataportal/name/' . $element->toName->uuid);

          }

          break;

      }

    }

    //second the TO RELS

    if ($to_name_relations){

      foreach($to_name_relations as $element){

        switch ($element->type->representation_L10n){

          case 'blocking name for':

            if(isset($name_relations_html) ){

              $name_relations_html .= ' nec ' . l($element->fromName->titleCache . ' ' .  substr($element->fromName->nomenclaturalReference->datePublished->start, 0, 4),

            }else{

              $name_relations_html = ' non ' . l($element->fromName->titleCache . ' ' .  substr($element->fromName->nomenclaturalReference->datePublished->start, 0, 4),

              . ' ' . $element->fromName->datePublished->start;

            }

            break;

        }

      }

    }

    if(isset($name_relations_html)){

      $name_relations_html = '['. $name_relations_html .']';

    }

  }

  $out = '<span class="relation_sign" title="' . $reltype_representation . '">'.$relsign.'</span>'.$name_prefix . $nameHtml . $name_postfix . $name_relations_html;

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

  RenderHints::popFromRenderStack();

  return $out;

  $gallery_settings = getGallerySettings(CDM_DATAPORTAL_SEARCH_GALLERY_NAME);

  $showCaption = $gallery_settings['cdm_dataportal_show_thumbnail_captions'];

  if($showCaption){

    $captionElements = array('title', 'rights');

  }

  $gallery_name = $taxon->uuid;

   $mediaQueryParameters = array("type"=>"ImageFile");

  $galleryLinkUri = path_to_taxon($taxon->uuid).'/images';

  // cdm_dataportal_show_media = ???? TODO

  $selectShowMedia = variable_get('cdm_dataportal_show_media', 0);

  if ($selectShowMedia == 0){

    $mediaList = cdm_ws_get(CDM_WS_PORTAL_TAXON_MEDIA, array($taxon->uuid), queryString( $mediaQueryParameters ));

  }else{

    $mediaList = cdm_ws_get(CDM_WS_PORTAL_TAXON_SUBTREE_MEDIA, array($taxon->uuid), queryString( $mediaQueryParameters ));

  }

  $out .= theme('cdm_media_gallerie', $mediaList, $gallery_name ,

      $gallery_settings['cdm_dataportal_media_maxextend'],

      $gallery_settings['cdm_dataportal_media_cols'],

      $gallery_settings['cdm_dataportal_media_maxRows'],

      $captionElements, 'LIGHTBOX', null, $galleryLinkUri);

  return $out;