EDIT

<?php

require_once('cdm/cdm_api.php');

function tagNameParts($name, $numOfNameTokens){

    $out = '<span class="name">';

    $token = strtok($name, " \n\t");

    $i = 0;

    $noSpace = true;

    while($token != false){

        if($i == $numOfNameTokens){

            $out .= '</span> <span class="authors">';

            $noSpace = true;

        }

        $out .= ($noSpace?'':' ').$token;

        $noSpace = false;

        $token = strtok(" \n\t");

        $i++;

    }

    return $out.'</span>';

}

/**

 * Renders the full name string (complete scientific name including the author team)

 *  

 * @param NameTO $nameTO the taxon name

 */

function theme_cdm_name(NameTO $nameTO){

    //TODO: how to respect the different subtypes of eu.etaxonomy.cdm.model.name.TaxonNameBase ?

    return cdm_taggedtext2html($nameTO->taggedName, 'span');

}

/**

 * Renders the given TaxonTO. The $enclosingTag (if not set false)

 * will get the following class attributes:

 * - name

 * - acceptet (only if $ptaxon is an accepted name)

 * 

 * @param TaxonTO $taxon

 * @param boolean $noSecundum defaults to false. If set to true the secundum part is omitted.

 * @param string $enclosingTag defaults to span.

 * @param boolean $showNomRef whether to dispülay the nomenclatural reference

 * @return string of XHTML

 * 

 * usage: taxon_detail, theme_ptname_link

 */

function theme_cdm_taxon(TaxonTO $taxon, $noSecundum = true ,$enclosingTag = 'span', $showNomRef = false){

    /* TODO: port me

    $refSecundum = false;

    if(!$noSecundum && $taxon->ref){

        $refSecundum = str_trunk($ptaxon->ref, 40, '...');

    }

	*/

    $out = theme('cdm_name', $taxon)

	    .($refSecundum ? '&nbsp;<span class="secundum">sec. '.$refSecundum.'</span>': '')

	    .$ptaxon->namePhrase;

    /* TODO: port me

    if($showNomRef){

        $out .= (str_beginsWith($ptaxon->nomRef, 'in') || trim($ptaxon->nomRef) == '' ? ' ':', ').theme('cdm_nomRef',$taxon);

    }

    if($enclosingTag){

        $out = '<'.$enclosingTag.' class="name'.($ptaxon->isAccepted()?' accepted':'').'"><!-- ['.$ptaxon->nameId.'|'.$ptaxon->refId.'] -->'.$out.'</'.$enclosingTag.'>';

    }

    */

    return $out;

}

/**

 * Renders a link to the taxon detail page for the given $taxon 

 *

 * @param TaxonTO $taxon

 */

function theme_cdm_taxon_link(TaxonTO $taxon, $fragment = '', $showNomRef = false){

    if($fragment){

        $fragment = '#'.$fragment;

    }

    if(!$taxon->isAccepted) { 

        $out = 'ERROR: theme_cdm_taxon_link() not accepted ptname; status:'.$taxon->status.$out;

    }

    $out = l(theme('cdm_taxon', $taxon, true, false), 'taxon', array('class'=>'accepted'), "uuid=$taxon->uuid", $fragment);

    if($showNomRef){

       $out .=' '.theme('cdm_nomRef', $ptaxon);

    }

	return $out;

}

//TODO: port everything below

/**

 * Renders a list of synonyms including misapplied names which are related to the 

 * given TAXIC_PTaxon.

 *

 * @param TAXIC_PTaxon $ptaxon

 * @param boolean $recursive default is false. Whether to crawl recursively into the

 * three of relations

 * 

 * usage taxon_detail.php.inc

 */

function render_synonyms(TAXIC_PTaxon $ptaxon, $recursive = false, $showNotes = false){

    $_debug = false;

    $is_higher_rank = $ptaxon->rankId < 60;

    $out = false;

    $last_relQualifierId = false;

    $last_was_heterotypic = false;

    $last_basionym_nameId = false;

    $is_other_basionym = false;

    $synonyms = findSynonyms($ptaxon->nameId, $ptaxon->refId, false, $recursive);

    foreach($synonyms AS $relpt){ // -- relations loop

      // whether this is the first entry in the lsit

      $is_first_entry = $out === false;

      // whether the current taxon has another basionym than the last one

      $is_other_basionym = $last_basionym_nameId !== false  

        && ($last_basionym_nameId !== $relpt->basionymNameId)

        && $relpt->relQualifierId != 3;

      // whether the current taxon has another name ralation than the last one

      $is_other_relQualifierId = $last_relQualifierId !== false && ($last_relQualifierId !== $relpt->relQualifierId);

      //is here the end of list of homotypic end of heterotypic subsection?  

      //$end_of_section = ($last_relQualifierId !== false && $is_other_basionym);

      $end_of_section = !$is_first_entry && $is_other_basionym || $is_other_relQualifierId && $relpt->relQualifierId == 3 /* misaplied */;

      // name relations declared as synomyn (id=2) are assumed to be heterotypic

      $is_heterotypic = $relpt->relQualifierId == 6 || ($relpt->relQualifierId == 2 && !$is_other_basionym && $last_was_heterotypic);

      // DELETE ME? $is_heterotypic = $relpt->relQualifierId == 6 || ($relpt->relQualifierId == 2 && !$is_other_basionym);

      $is_homotypic = $relpt->relQualifierId == 7 || $relpt->relQualifierId == 101 || $relpt->relQualifierId == 103;

      // is this taxon homotypic to a previously printed heterotypic taxon, so is should be

      // an intented subelement and re-taged as homotypic 

      $is_subelement = $is_heterotypic && !$is_other_basionym && !$is_first_entry;

      $is_the_basionym = $is_homotypic && !$last_basionym_nameId;

      if($is_first_entry){ 

        $out = '<ul>'.chr(10).'<li class="blank_line"></li>'.chr(10); 

           if($is_heterotypic){

             if($_debug) $out .= '<li><span style="color:blue; font-size: 80%;">renderTypeDesignations before first entry which is heterotypic]</span></li>';

             $out .= renderTypeDesignations($ptaxon->nameId, '', $is_higher_rank ); 

             $out .= '<li class="blank_line"></li>'.chr(10);

           }

      }

      /*$out .= '<li><span style="color:blue; font-size: 80%;">last: '

				.$last_basionym_nameId.' !== '.$relpt->basionymNameId.' '.$relpt->fullName

                .'</span></li>';

		*/      

      //DEBUG $out .= '<pre>'.print_r($relpt, true).'</pre>';

      if($is_other_basionym){

        if($_debug) $out .= '<li><span style="color:blue; font-size: 80%;">renderTypeDesignations 1 (relID: '.$last_relQualifierId.' for '.$last_basionym_nameId.')</span></li>';

        $out .= renderTypeDesignations($last_basionym_nameId, ($last_was_heterotypic ? 'subelement' : ''), $is_higher_rank ); 

        //$out .= renderTypeDesignations($last_basionym_nameId, '', $is_higher_rank ); 

      }

      if($end_of_section){

          // find type information          

          $out .= '<li class="blank_line"></li>'.chr(10);

      }

      if($is_subelement){

          // all those taxa which are homotypic to the preceeding basionym are to be

          // displayed as homotypic

          $relpt->relQualifierId = 7;

          $cssClass = 'subelement';

      } else {

          $cssClass = '';

      }

      $out .= render_related_ptname($relpt, 'li', $cssClass, $showNotes).chr(10);

       // remember last synonyms properties for next round

      $last_relQualifierId = $relpt->relQualifierId;

      $last_basionym_name = $relpt->basionymFullName;

      $last_basionym_nameId = $relpt->basionymNameId;

      $last_was_heterotypic = $is_heterotypic;

    } // END relations loop

    if($is_the_basionym){

       if($_debug) $out .= '<li><span style="color:blue; font-size: 80%;">renderTypeDesignations 0 for '.$relpt->nameId.'</span></li>';

        $out .= renderTypeDesignations($relpt->nameId, '', $is_higher_rank);

    } else 

    // TypeDesignations for the last item

    if($is_other_basionym || !$last_was_heterotypic){

        if($_debug) $out .= '<li><span style="color:blue; font-size: 80%;">renderTypeDesignations 2 for '.$last_basionym_nameId.'</span></li>';

        $out .= renderTypeDesignations($last_basionym_nameId, '', $is_higher_rank);

    } else

    // In case the given PTaxon had no synonyms ...

     if($last_basionym_nameId === false || $last_relQualifierId == 7){

        if($_debug) $out .= '<li><span style="color:blue; font-size: 80%;">renderTypeDesignations 3 for'.$ptaxon->nameId.'; last_basionym_nameId = '.$last_basionym_nameId.'</span></li>';

        $out .= renderTypeDesignations($ptaxon->nameId, '', $is_higher_rank);

    } else {

      $out .= '<li class="blank_line"></li>'.chr(10).'</ul>';

    }

    return $out;

}

// -------------------- END function render_synonyms()

function render_homonyms(TAXIC_TaxonName $taxon){

  $homonyms = getLaterHomonyms($taxon);

  $out = '';

  foreach($homonyms as $homnym){

    $out .= '<li class="homonym">[non '.$homnym->authors.', '.$homnym->nomRef.']'.render_notes($homnym).'</li>';

  }

  if($out){

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

  }

  return $out;

}

/**

 * render_related_ptname() is used by render_synonyms()

 * @param TAXIC_PTaxon $relPTaxon

 * @param String $enclosingTag 

 */

function render_related_ptname($relPTaxon, $enclosingTag = 'li', $cssClass = '', $showNotes = false){

    $cssClass .= ' '.str_replace(' ', '_', $relPTaxon->relQualifier);

    switch($relPTaxon->relQualifierId){

        case 7  :

        case 101  :

        case 103  : // homotypic-synonym

            $relSign = '≡';

            break;

        case 3  :   // misapplied_name

            $relSign = '-';

            break;

        case 8  :   // invalid_designation

            $relSign = '-';

            break;

        default : 

            $relSign = '=';

            break;

    }

    //$relSign .= $relPTaxon->relQualifierId;

    $out = '';

    if($relPTaxon->relQualifierId == 3){

        // special look for misapplied_names

        $relatedToName = ''; // only used in HTML comment

        $sensuPart = ' sensu '.$relPTaxon->ref;

        if($relPTaxon->relInversion){

            $namePart = ($relPTaxon->isAccepted()? render_ptname_link($relPTaxon) : render_ptname($relPTaxon));

            $out = $relPTaxon->relQualifier.' '.$namePart.' '.$sensuPart;

        } else {

            $namePart = '„'.trim($relPTaxon->name).'“';

            if($relPTaxon->relPTaxon->name){

                // only used in HTML comment!!

                $relatedToName = trim($relPTaxon->relPTaxon->name); 

            }

            $out .= $namePart.'</span>'.$sensuPart;

        }

    } else {

        $relatedToName = ($relPTaxon->relPTaxon ? $relPTaxon->relPTaxon->name : false);

        if($relPTaxon->isAccepted()) {

            $out .= render_ptname_link($relPTaxon, null, true);

        } else {

            $out .= render_ptname($relPTaxon, true ,'span', true);

        }

    } // END else special look for misapplied_names

    $notes = ($showNotes && showNotes() ? render_notes($relPTaxon) : '');

    $out =  '<'.$enclosingTag.' class="'.$cssClass.'"><!-- '.$relPTaxon->relQualifier.' '.$relatedToName.'-->'

			.'<a name="'.$relPTaxon->nameId.'_'.$relPTaxon->refId.'" ></a><span class="relation_sign">'.$relSign.'</span> '

            .$out . $notes

            .'</'.$enclosingTag.'>';

    return $out;

}

/**

 * @param TAXIC_PTaxon $ptname

 */

$NOMREFSET_COUNTER = 0;

function render_nomRef($ptname){

  global $conf;

  global $NOMREFSET_COUNTER;

  $NOMREFSET_COUNTER += 1;

    if(count($protoploges = $ptname->getProtologues()) > 0){

		$prot = $protoploges[0];

		// FIXME: protologues are really a list of links. treat only the first

		if(is_file($conf['abs_media_path'].$conf['protologue_path'].$prot.".png")){

    	  $nomrefLink = '<span class="nomref"><a href="'.$conf['protologue_path'].$prot.'.png" rel="lightbox[nomrefset'.$NOMREFSET_COUNTER.']" title="&lt;a href=&quot;'.$conf['protologue_quality_path'].$prot.'.tif&quot;&gt;High Quality Scan&lt;/a&gt;">'.trim($ptname->nomRef).'</a></span>';

		} else {

		  $nomrefLink = '<span class="nomref"><a href="'.$conf['protologue_path'].$prot.'001.png" rel="lightbox[nomrefset'.$NOMREFSET_COUNTER.']" title="&lt;a href=&quot;'.$conf['protologue_quality_path'].$prot.'.tif&quot;&gt;High Quality Scan&lt;/a&gt;">'.trim($ptname->nomRef).'</a></span>';	  

          // check in filesystem if there are more pages as JPGs. TIFFs can cope with 8 pages per file, so no need for that

          $i=2;

          while (is_file($conf['abs_media_path'].$conf['protologue_path'].$prot.str_pad($i, 3, '0', STR_PAD_LEFT).".png")){

          	$nomrefLink = $nomrefLink."   <a href='".$conf['protologue_path'].$prot.str_pad($i, 3, '0', STR_PAD_LEFT).".png' rel='lightbox[nomrefset".$NOMREFSET_COUNTER."]'></a>";

          	$i++;

          }

		}

        return $nomrefLink;

    } else {

        return '<span class="nomref">'.trim($ptname->nomRef).'</span>';

    }

}

function renderTypeDesignations($nameId, $cssClass = '', $togglebox = false, $separator = '<br />' , $enclosingTag = 'li'){

  $typeDesignations = getTypeDesignations($nameId);

  if(count($typeDesignations) > 0){

    $out = ''; 

    foreach($typeDesignations as $td){

      if(strlen($out) > 0){

        $out .= $separator.chr(10);

      }

      $out .= $td['TypeStatus'].' - '.html_entity_decode($td['TypePhrase']);

    }

    if($togglebox){

       $out = '<div class="tbox_toggler">&nbsp;</div><div class="tbox_content">'.$out.'</div>';

    } 

    return '<'.$enclosingTag.' class="type_designation'.($cssClass ? ' '.$cssClass : '' ).'">'

  		.$out.'</'.$enclosingTag.'>'.chr(10);

  }

}

/**

 * render a numeric pager

 */

function renderNumPager($numOfPages, $activePage, $maxPagerItems, $linkUrlBase){

    if ($activePage > $maxPagerItems - 2){

        // shift visible pager items

        $begin = $activePage - floor($maxPagerItems / 2);

        $end   = min($activePage + ceil($maxPagerItems / 2), $numOfPages);

    } else {

        $begin = 1; 

        $end   = min($numOfPages, $maxPagerItems);

    }

    // hide the pager if there is only one page:

    if($begin == $end)

        return;

    echo '<ul class="paging numeric">';

    if ($activePage > 10){

	    echo '<li><a href="', $linkUrlBase, $activePage - 10, '" title="backward 10 pages">&laquo;</a></li>';

    }

    if ($activePage > 1){

	    echo '<li><a href="', $linkUrlBase, $activePage - 1, '" title="previuos">&lt;</a></li>';

    }

	for ($pn = $begin; $pn <= $end ; ++$pn) {

		if($pn != $activePage){

		     echo '<li><a href="'.$linkUrlBase.$pn.'">'. $pn. '</a></li>';

		} else {

			echo '<li class="active">'.$pn.'</li>';

		}

	} 

    if ($activePage < $numOfPages){

	    echo '<li><a href="', $linkUrlBase, $activePage + 1, '" title="next">&gt;</a></li>';

    }

    if ($activePage < $numOfPages - 9){

	    echo '<li><a href="', $linkUrlBase, $activePage + 10, '" title="forward 10 pages">&raquo;</a></li>';

    }

    if($numOfPages > 0){

        echo '<li> (of '.$numOfPages.' pages)</li>';

    }

    echo '</ul>';

}

/**

 * @param TAXIC_TaxonName $taxon

 */

function render_notes(TAXIC_TaxonName $taxon){

    if(!showNotes()){

      return;

    }

    $notes = array();

    if($taxon->nameNotes && trim($taxon->nameNotes)){

      $notes['Name Notes'] = $taxon->nameNotes;

    }

    if($taxon->nomRefNotes && trim($taxon->nomRefNotes)){

      $notes['Nomenclatural Ref. Notes'] = $taxon->nomRefNotes;

    }

    if($taxon instanceof TAXIC_PTaxon){

      if($taxon->nameNotes && trim($taxon->conceptNotes)){

        $notes['Taxon Concept Notes'] = $taxon->conceptNotes;

      }

      if($taxon->refNotes && trim($taxon->refNotes)){

        $notes['Concept Reference Notes'] = $taxon->refNotes;

      }

    }

    if(count($notes) > 0){

      $out = '<span class="note_toggler"><img src="themes/cichorieae/note_gray.gif" /><div class="note">';

      $out .= '<div class="title"><div class="close" title="close"><img src="themes/cichorieae/close.gif" /></div>Notes on '.render_name($taxon).'</div><div class="content">';

      foreach(array_keys($notes) as $title){

        $out .= render_notes_entry($title, $notes[$title]);

      }

      return $out.'</div></div></span>';

    } else {

      return;

    }

}

function render_notes_entry($title, $note){

    return '<h4>'.$title.'</h4><p>'.htmlspecialchars($note).'</p>'.chr(10);

}