EDIT

<?php

// $Id$

/*

 * Copyright (C) 2007 EDIT

 * European Distributed Institute of Taxonomy 

 * http://www.e-taxonomy.eu

 */

function _add_js_thickbox(){

   // ---- jQuery ThickBox:

  /*

   * bug: compat-1.0.js && thickbox.js line 237 .trigger("unload")

   * -> event is not triggered because of problems with compat-1.0.js'

   * see INSTALL.txt

   * 

   */

  drupal_add_js(drupal_get_path('module', 'cdm_dataportal').'/js/thickbox.js');

  drupal_add_css(drupal_get_path('module', 'cdm_dataportal').'/js/cdm_thickbox.css');

}

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, $displayNomRef = true){

    //TODO: - take the different subtypes of eu.etaxonomy.cdm.model.name.TaxonNameBase into account?

    $class = ''; //name'; //($nameTO->secUuid ? 'taxon' : 'taxonname');  

    if(!$nameTO){

      return '<span class="error">Invalid NameTO</span>';      

    }

    $hasNomRef = $nameTO->nomenclaturalReference->fullCitation;

    //FIXME class="'.$class.' below seems to be unused

    if(!$nameTO->taggedName || !count($nameTO->taggedName)){

      $out .= '<span class="'.$class.'">'.$nameTO->fullname.'</span>';

    } else {

      $skip = $hasNomRef ? array('reference') : array();

      $out .= '<span class="'.$class.'">'.cdm_taggedtext2html($nameTO->taggedName, 'span', ' ', $skip).'</span>';

    }

    if($displayNomRef && $hasNomRef){

      $out .= (str_beginsWith($nameTO->nomenclaturalReference->fullCitation, 'in') ? ' ':', ');

      $out .= theme('cdm_nomenclaturalReferenceSTO', $nameTO->nomenclaturalReference);

    }

    if($nameTO->status){

      $out .= ', '.cdm_dataportal_t($nameTO->status);

    }

    return $out;

}

/**

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

 * will get the following class attributes:

 * - name

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

 * 

 * @param TaxonTO $taxon

 * @param boolean $displayNomRef whether to display the nomenclatural reference

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

 * @param string $enclosingTag defaults to span.

 * @return string of XHTML

 * 

 * usage: taxon_detail, theme_ptname_link

 */

function theme_cdm_taxon($taxonTO, $displayNomRef = true, $noSecundum = true, $enclosingTag = 'span'){

    $refSecundum = false;

    if(!$noSecundum){  

      $ref_sec = cdm_ws_get(CDM_WS_SIMPLE_REFERENCE ,$taxonTO->secUuid);

      if($ref_sec){

        $refSecundum = str_trunk($ref_sec->fullcitation, 40, '...');

      }

    }

    $out  = theme('cdm_name', $taxonTO->name, $displayNomRef);

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

	  //TODO:   .$ptaxon->namePhrase; 

    if($enclosingTag){

        $out = '<'.$enclosingTag.' class="taxon'.($taxonTO->accepted === true ? ' accepted':'').'">'.$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, $fragment = NULL, $showNomRef = true){

    if($fragment){

        $fragment = '#'.$fragment;

    }

    if(!$taxon->accepted) { 

        $out = 'ERROR: theme_cdm_taxon_link() - taxon is not accepted';

    }

    $name_html = theme('cdm_taxon', $taxonTO, false, true, '');

    $out = l($name_html, cdm_dataportal_taxon_path($taxonTO->uuid), array('class'=>'accepted'), '', $fragment, FALSE, TRUE);

    if($showNomRef){

       $out .=' '.theme('cdm_nomenclaturalReferenceSTO', $taxonTO->name->nomenclaturalReference);

    }

	return $out;

}

function theme_cdm_related_taxon($taxonSTO, $reltype_uuid = '', $displayNomRef = true){

  $relsign = '';

  $name_prefix = '';

  $name_postfix = '';

  switch ($reltype_uuid){

    case UUID_HOMOTYPIC_SYNONYM_OF: 

      $relsign = '≡';

      break;

    case UUID_MISAPPLIED_NAME_FOR: 

    case UUID_INVALID_DESIGNATION_FOR:

      $relsign = '–'; // – — −

      $name_prefix = '"';

      $name_postfix = '"';

      break;

    default : 

      $relsign = '=';

  }

  $out = '<span class="relation_sign">'.$relsign.'</span>'.$name_prefix.theme('cdm_taxon',$taxonSTO, $displayNomRef).$name_postfix;

  return $out;

}

function theme_select_secuuid($element) {

  $default_uuid = variable_get($element['#varname'], false);

  $tree = cdm_taxontree_build_tree(null, false); // get root nodes

  $secUuids = array();

  foreach($tree as $node){

    $secUuids[] = $node->secUuid;

  }

  cdm_api_secref_cache_prefetch($secUuids);

  theme('cdm_taxontree_add_scripts');

  drupal_add_js('$(document).ready(function() {$(\'ul.cdm_taxontree\').cdm_taxontree(

  {

    widget:                 true,

    element_name:           \''.$element['#varname'].'\',  // 

    multiselect:            '.($element['#multiple']?'true':'false').',         //

  }

  );});', 'inline');

  $out  = '<div class="cdm_taxontree_widget">';

  $out .= '<div class="taxontree">'.theme('cdm_taxontree', $tree, NULL, FALSE, 'cdm_taxontree_node_reference').'</div>';

  $out .= $element['#children'].'<div style="clear: both;" /></div>';

  return theme(

    'form_element',

    array(

      '#title' => $element['#title'],

      '#description' => $element['#description'],

      '#id' => $element['#id'],

      '#required' => $element['#required'],

      '#error' => $element['#error'],

    ),

    $out

  );

}

function theme_cdm_dynabox($label, $content_url, $theme, $enclosingtag = 'li'){

  $cdm_proxy_url = url('cdm_api/proxy/'.urlencode($content_url)."/$theme");

  $out .= '<li class="dynabox"><span class="label">'.$label.'</span>';

  $out .= '<ul class="dynabox_content" title="'.$cdm_proxy_url.'"><li><img class="loading" src="'.drupal_get_path('module', 'cdm_dataportal').'/images/loading_circle_grey_16.gif" style="display:none;"></li></ul>';

  return $out;

}

function theme_cdm_listof_taxa($taxonSTOs){

  drupal_add_js(drupal_get_path('module', 'cdm_dataportal').'/js/cdm_dynabox.js');

  drupal_add_css(drupal_get_path('module', 'cdm_dataportal').'/cdm_dataportal.css');

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

  foreach($taxonSTOs as $taxon){

    if(_cdm_dataportal_acceptetByCurrentView($taxon)){

      $out .= '<li>'.theme('cdm_taxon_link', $taxon).'</li>';

    } else {

      $out .= theme('cdm_dynabox', theme('cdm_name', $taxon->name), cdm_compose_url(CDM_WS_ACCEPTED_TAXON, array($taxon->uuid)), 'cdm_listof_taxa');

    }

  }

  $out .= '</ul>';

  return $out;

}

function theme_cdm_alternative_taxa($taxonSTOs){

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

  foreach($taxonSTOs as $taxon){

    $out .= '<li>'.theme('cdm_taxon_link', $taxon).'</li>';

  }

  $out .= '</ul>';

  return $out;

}

function theme_cdm_credits(){

  $secRef_array = _cdm_dataportal_currentSecRef_array();

  return '<span class="sec_reference_citation">'.$secRef_array['citation'].'</span>'

  .( $secRef_array['year'] ? ' <span class="year">'.$secRef_array['year'].'</span>' : '')

  .( $secRef_array['authorship'] ? '<div class="author">'.$secRef_array['authorship'].'</div>' : '');

}

function theme_cdm_fullreference($referenceTO){

  $out = $referenceTO->authorship;

  if($referenceTO->fullCitation){

    $out .= ' '.$referenceTO->fullCitation;

  }

  if($referenceTO->microReference){

    $out .= ' : '.$referenceTO->microReference;

  }

  if($referenceTO->year){

    $out .= '. '.$referenceTO->year;

  }

  return $out;

}

/**

 * Enter description here...

 *

 * @param unknown_type $referenceSTO a referenceSTO or referenceTO instance

 * @param unknown_type $cssClass

 * @param unknown_type $separator

 * @param unknown_type $enclosingTag

 * @return unknown

 */

function theme_cdm_nomenclaturalReferenceSTO($referenceSTO, $cssClass = '', $separator = '<br />' , $enclosingTag = 'li'){

  if(isset($referenceSTO->microReference)){

    // well it is a ReferenceTO

    $nomref_citation = theme('cdm_fullreference', $referenceSTO);

  } else {

    // it is ReferenceSTO

    $nomref_citation = $referenceSTO->fullCitation; 

  }

  _add_js_thickbox();

  // find media representations for inline display and high quality for download

  // assuming that there is only one protologue per name only the first media is used 

  /* TODO currently it is assumed that high quality representations are tiffs

   * which is only true for the cichoriea portal

   */

  if( count($referenceSTO->media[0]->representations) > 0 ){

    foreach($referenceSTO->media[0]->representations as $representation){

      $mimeType = $representation->mimeType;

      if(($mimeType == 'image/png' || $mimeType == 'image/jpeg' || $mimeType == 'image/gif')

        && count($representation->representationParts) > 0){

        $representation_inline = $representation;

      } else if($representation->mimeType == 'image/tiff'

        && count($representation->representationParts) > 0){

        $representation_highquality = $representation;

      }

    }

  }

  if($representation_inline) {

    $attributes = array('class'=>'thickbox', 'rel'=>'protologues-'.$referenceSTO->uuid);

    for($i = 0; $part = $representation_inline->representationParts[$i]; $i++){

      if($i == 0){        

        $out = l($nomref_citation, $part->uri, $attributes, NULL, NULL, TRUE);

      } else {

        $out .= l('', $part->uri, $attributes, NULL, NULL, TRUE);              

      }

    }

  } else {

    // no media available, so display just the citation string

    $out =  $nomref_citation;

  }

  return $out;  

}

function theme_cdm_taxon_page($taxonTO){

  $out = '';

  $out .= theme('cdm_homotypicSynonyms', $taxonTO->homotypicSynonyms, $taxonTO->typeDesignations, $taxonTO->nameTypeDesignations);

  foreach($taxonTO->heterotypicSynonymyGroups as $hs_group){

    $out .= theme('cdm_heterotypicSynonymyGroup', $hs_group);

  }

  $out .= theme('cdm_taxonRelations', $taxonTO->taxonRelations);

  return $out;

}

function theme_cdm_homotypicSynonyms($synonymRelationshipTOs, $specimenTypeDesignations = false, $nameTypeDesignations = false){

  $out = '';

  $out = '<ul class="homotypicSynonyms">';

  foreach($synonymRelationshipTOs as $synonym){

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

  }

  if($specimenTypeDesignations){

    $out .= theme('cdm_typedesignations', $specimenTypeDesignations, $nameTypeDesignations);

  }

  $out .= '</ul>';

  return $out;

}

function theme_cdm_heterotypicSynonymyGroup($homotypicGroupTO){

  $out = '';  

  $out = '<ul class="heterotypicSynonymyGroup">';

  $is_first_entry = true;

  foreach($homotypicGroupTO->taxa as $taxonSTO){

    if($is_first_entry){

      $is_first_entry = false;

      // is first list entry

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

    } else {

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

    }

  }

  if(isset($homotypicGroupTO->typeDesignations)){

    $out .= theme('cdm_typedesignations', $homotypicGroupTO->typeDesignations);

  }

  $out .= '</ul>';

  return $out;

}

/**

 * renders misapplied names and invalid designations. 

 * Both relation types are currently treated the same!

 *

 * @param unknown_type $TaxonRelationshipTOs

 * @return unknown

 */

function theme_cdm_taxonRelations($TaxonRelationshipTOs){

  drupal_add_js(drupal_get_path('module', 'cdm_dataportal').'/js/cluetip/jquery.cluetip.js');

  drupal_add_js(drupal_get_path('module', 'cdm_dataportal').'/js/jquery.dimensions.js');

  drupal_add_js(drupal_get_path('module', 'cdm_dataportal').'/js/cluetip/jquery.hoverIntent.js');

  drupal_add_css(drupal_get_path('module', 'cdm_dataportal').'/js/cluetip/jquery.cluetip.css');

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

      $('.cluetip').css({color: '#0062C2'}).cluetip({

        splitTitle: '|',

        showTitle: true,

        activation: 'hover',

        arrows: true,

        dropShadow: false,

        cluetipClass: 'rounded'

      });

    });", 'inline');

  // aggregate misapplied named having the same fullname:

  $misapplied = array();

  foreach($TaxonRelationshipTOs as $taxonRelation){

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

      $sensu_reference_list = cdm_ws_get(CDM_WS_SIMPLE_REFERENCE ,$taxonRelation->taxon->secUuid);

      $sensu_reference = $sensu_reference_list[0];

      $name = $taxonRelation->taxon->name->fullname;

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

        $misapplied[$name] = '<span class="misapplied">'.theme('cdm_related_taxon',$taxonRelation->taxon, UUID_MISAPPLIED_NAME_FOR, false).'</span>';

      } else {

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

      }

      $misapplied[$name] .= '&nbsp;<span class="sensu cluetip no-print" title="|sensu '.htmlspecialchars(theme('cdm_fullreference',$sensu_reference )).'|">sensu '

      .$sensu_reference->authorship.'</span>'

      .'<span class="reference only-print">sensu '.theme('cdm_fullreference',$sensu_reference ).'</span>'

      ;

    }

  }

  // generate output

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

  foreach($misapplied as $misapplied_name){

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

  }

  $out .= '</ul>';

  return $out;

}

function theme_cdm_typedesignations($specimenTypeDesignations, $nameTypeDesignations = array()){

  $out = '<ul class="typeDesignations">';

  foreach($nameTypeDesignations as $ntd){

    $out .= '<li class="nameTypeDesignation"><span class="status">'.$ntd->status->text.'</span> - '.theme('cdm_name', $ntd->typeSpecies, false);

    $out .= theme('cdm_typedesignations', $ntd->typeSpecimens);

    $out .= '</li>';

  }    

  foreach($specimenTypeDesignations as $std){

    $out .= '<li class="specimenTypeDesignation">';

    $out .= '<span class="status">'.$std->status->text.'</span> - '.$std->typeSpecimen->specimenLabel;

    $out .= theme('cdm_specimen', $std->typeSpecimen);

    $out .= '</li>';

  }

  $out .= '</ul>';

  return $out;

}

function theme_cdm_specimen($specimen){

  // rights, 

  //$specimen->specimenLabel

  //$specimen->uuid

  _add_js_thickbox();

  $out = '';

  if(isset($specimen->media[0])){

    $image_url = drupal_get_path('module', 'cdm_dataportal').'/images/external_link.gif';

    // thickbox has problems reading the first url parameter, so a litte hack is needed here:

    // adding a meningless patameter &tb_hack=1& ....

    $out .= '&nbsp;<a href="#TB_inline?tb_hack=1&width=300&amp;height=330&amp;inlineId=specimen_media_'.$specimen->uuid.'" class="thickbox">'

    .'<img src="'.$image_url.'" title="'.t('Show media').'" /></a>';

    $out .= '<div id="specimen_media_'.$specimen->uuid.'" class="tickbox_content"><table>';

    $media_row = '<tr class="media_data">';

    $meta_row = '<tr class="meta_data">';

    foreach($specimen->media as $media){

      foreach($media->representations as $representation){

        //TODO this this is PART 2/2 of a HACK - select preferred representation by mimetype and size

        //      

        if(true || $representation->mimeType == 'image/jpeg'){

          foreach($representation->representationParts as $part){

            // get media uri conversion rules if the module is installed and activated

            if(module_exists('cdm_mediauri')){

              $muris = cdm_mediauri_conversion($part->uri);

            }

            // --- handle media preview rules

            if(isset($muris['preview'])){    

              $a_child = '<img src="'.$muris['preview']['uri'].'" class="preview" '

                .($muris['preview']['size_x'] ? 'width="'.$muris['preview']['size_x'].'"' : '')

                .($muris['preview']['size_y'] ? 'width="'.$muris['preview']['size_y'].'"' : '')

                .'/>';

            } else {

              $a_child = '<img src="'.$image_url.'" />';

            }

            // --- handle web application rules

            $webapp = '';

            if(isset($muris['webapp'])){

              if($muris['webapp']['embed_html']){

                // embed in same page

                $webapp = $muris['webapp']['embed_html'];  

              } else {

                $webapp = l(t('web application'), $muris['webapp']['uri']);            

              }

            }

            $media_row .= '<td><a href="'.$part->uri.'" target="'.$part->uuid.'">'.$a_child.'</a></td>';

            $meta_row .= '<td><span class="label">'.check_plain($specimen->specimenLabel).'</span><div class="webapp">'.$webapp.'</div></td>';

          } // END parts

          //TODO this is PART 2/2 of a hack

          break;

        } // END representations

      } // END media

    }

    $out .= $media_row.'</tr>';

    $out .= $meta_row.'</tr>';

    $out .= '</div></table>';

  }

  return $out;

}

function theme_cdm_search_results($resultPageSTO, $path, $parameters){

  drupal_set_title(t('Search Results'));

  $out = '';

  if(count($resultPageSTO->results) > 0){

    $out = theme('cdm_listof_taxa', $resultPageSTO->results);

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

  } else {

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

  }

  return $out;

}

function theme_cdm_pager(&$resultPageSTO, $path, $parameters, $neighbors = 2){

  $out = '';

  if ($resultPageSTO->totalPageCount > 1) {

    $viewportsize = $neighbors * 2 + 1; 

    $out .= '<div class="pager">';

    if($resultPageSTO->pageNumber > 1){

      $out .= theme('cdm_pager_link', t('« first'), 1,  $resultPageSTO, $path, $parameters, array('class' => 'pager-first'));

      $out .= theme('cdm_pager_link', t('‹ previous'), $resultPageSTO->pageNumber - 1, $resultPageSTO, $path, $parameters, array('class' => 'pager-previous'));

    }

    if($resultPageSTO->totalPageCount <= $viewportsize || $resultPageSTO->pageNumber <= $neighbors){

      $first_number = 1;

    } else if($resultPageSTO->pageNumber >= $resultPageSTO->totalPageCount - $neighbors){

      $first_number = $resultPageSTO->totalPageCount - $viewportsize;

    } else {

      $first_number = $resultPageSTO->pageNumber - $neighbors;

    }

    if($first_number > 1){

      $out .= '<div class="pager-list-dots-left">...</div>';

    }

    for($i = $first_number; $i < $first_number + $viewportsize; $i++){

      $out .= theme('cdm_pager_link', $i, $i,  $resultPageSTO, $path, $parameters, array('class' => 'pager-first'));

    }

    if($i < $resultPageSTO->totalPageCount){

      $out .= '<div class="pager-list-dots-right">...</div>';

    }

    if($resultPageSTO->pageNumber < $resultPageSTO->totalPageCount){

      $out .= theme('cdm_pager_link', t('next ›'), $resultPageSTO->pageNumber + 1, $resultPageSTO, $path, $parameters, array('class' => 'pager-next'));

      $out .= theme('cdm_pager_link', t('last »'), $resultPageSTO->totalPageCount, $resultPageSTO, $path, $parameters, array('class' => 'pager-last'));

    }

    $out .= '</div>';

    return $out;

  }

}

function theme_cdm_pager_link($text, $linkPageNumber, &$resultPageSTO, $path, $parameters = array(), $attributes) {

  $out = '';

  if ($linkPageNumber == $resultPageSTO->pageNumber) {

    $out = '<strong>'.$text.'</strong>';

  } else {

    // <a class="pager-next active" title="Go to page 3" href="/node?page=2">3</a>

    $parameters['page'] = $linkPageNumber;

    $out = l($text, $path, $attributes, compose_url_prameterstr($parameters));

  }

  return $out;

}