EDIT

 * Copyright (C) 2007 EDIT

 * European Distributed Institute of Taxonomy

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

 *

 * The contents of this file are subject to the Mozilla Public License Version 1.1

 * See http://www.mozilla.org/MPL/MPL-1.1.html for the full license terms.

 */

		//$out .=  theme('cdm_footnote_key', $a, $a->footnoteListKey, (isset($out)? ',' : ''));

		$out .=  theme('cdm_footnote_key', $a, (isset($out)? ',' : ''));

	}

	return theme('cdm_footnotes', $footnoteListKey . '-annotations', $enclosingTag);

	$out = '<span class="footnote-key footnote-key-'.$footnoteKey->keyStr.' member-of-footnotes-'.$footnoteKey->footnoteListKey.'">'.$separator

	.'<a href="#footnote-'.$footnoteKey->keyStr.'">'.$footnoteKey->keyStr.'</a>'

	.'</span>';

	return $out;

	_add_js_footnotes();

	$out = '<span class="footnote footnote-'.$footnoteKey.'"><a name="footnote-'.$footnoteKey.'"></a><span class="footnote-anchor">'.$footnoteKey.'.</span>&nbsp;'.$footnoteText.'</span>';

	return $out;

	if (is_array($footnote_list)){

		foreach ($footnote_list as $element){

			if ($element == $footnote){

				$result = true;

			}

	 * 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/footnotes.js');

				if ($element->language->representation_L10n){

					$key = '<b>' . $element->language->representation_L10n . '</b>';

					$key .= (strlen($element->area->titleCache)>0) ? ' (' . $element->area->titleCache . ')' : '';

				}

				// adding footnotes sources

				if($element->name){

				  $rendered_element_list .= (strlen($rendered_element_list) > 0 ? ', ': '') . $element->name . $sourcesFootnoteKeyList;

			  }

			}

			if ($key){

			 $common_name_out .= (strlen($common_name_out) > 0 ? '; ': '') . $key . ': ' . $rendered_element_list;

			}else{

			  $common_name_out .= (strlen($common_name_out) > 0 ? '; ': '') . $rendered_element_list;

	$common_name_out = "<div class=common_names_as_common_names> $common_name_out </div>";

  $out_array[] = $text_data_out;

	$common_name_out_text_data = '<div class=common_names_as_text_data>' . theme('cdm_descriptionElementArray', $out_array, $element->feature) . '</div>';

	return $common_name_out;

	//return $common_name_out . theme('cdm_descriptionElementArray', $out_array, $element->feature);

	//return "<div class=common_names> $common_name_out $common_name_out_text_data";

	//	$descriptionElementCount = cdm_ws_get(CDM_WS_PORTAL_TAXON_DESCRIPTIONS_ELEMENTSBYTYPE, array($taxon->uuid, 'IndividualsAssociation'), "count=true");

	//	if($descriptionElementCount->Integer < 0) { //DEBUG HACK

	// ### sending the same query twice is faster than two different ones, $descriptionElements will be retrieved again in the specimens page

	$descriptionElementCount = is_array($descriptionElements) ? count($descriptionElements) : 0;

		$hideTabs[] = theme('cdm_taxonpage_tab', 'Specimens');

	}

  					drupal_set_message('The \'FeatureTree\' for the generation of natural language representations is not configured correctly, please select a \'FeatureTree\' in the '.l('CDM Dataportal Settings', 'admin/settings/cdm_dataportal/layout'), 'warning');

  	array($taxon, $media));

	$descriptionElements = cdm_ws_get(CDM_WS_PORTAL_TAXON_DESCRIPTIONS_ELEMENTSBYTYPE, array($taxon->uuid, 'IndividualsAssociation') );

	//collect media (fieldObjectMedia, derivedUnitMedia) and add as fields

	foreach($descriptionElements as $descriptionElement) {

		if($descriptionElement->associatedSpecimenOrObservation){

			$descriptionElement->_fieldObjectMedia = cdm_ws_get(CDM_WS_DERIVEDUNIT_FACADE, array($descriptionElement->associatedSpecimenOrObservation->uuid, 'fieldObjectMedia') );

			$descriptionElement->_derivedUnitMedia = cdm_ws_get(CDM_WS_DERIVEDUNIT_FACADE, array($descriptionElement->associatedSpecimenOrObservation->uuid, 'derivedUnitMedia') );

			//	  	$derivedUnitFacde = cdm_ws_get(CDM_WS_DERIVEDUNIT_FACADE, array($descriptionElement->associatedSpecimenOrObservation->uuid) );

			//	  	$descriptionElement->_titleCache = $derivedUnitFacde->titleCache;

		}

	}

	if(variable_get('cdm_dataportal_map_openlayers', 1)){

		$occurrenceQuery = cdm_ws_get(CDM_WS_GEOSERVICE_OCCURRENCEMAP, $taxon->uuid);

		$occurrenceQuery = $occurrenceQuery->String;

		$out .= get_openlayers_map(variable_get('cdm_dataportal_geoservice_display_width', false), $occurrenceQuery);

	}

	if($descriptionElements){

		$out_specimenList = '<table class="specimens">';

		$i = 1;

		foreach($descriptionElements as $descriptionElement) {

			$i++;

			if($descriptionElement->associatedSpecimenOrObservation){

				$mediaList = array();

				if(is_array($descriptionElement->_fieldObjectMedia)){

					$mediaList = array_merge($mediaList, $descriptionElement->_fieldObjectMedia);

				}

				if(is_array($descriptionElement->_derivedUnitMedia)){

					$mediaList = array_merge($mediaList, $descriptionElement->_derivedUnitMedia);

				}

				$li = '<tr class="descriptionElement descriptionElement_IndividualsAssociation '.($i%2?'odd':'even').'"><td>' . $descriptionElement->associatedSpecimenOrObservation->titleCache;

				if(count($mediaList) > 0){

					$gallery_settings = getGallerySettings(CDM_DATAPORTAL_SPECIMEN_GALLERY_NAME);

					$gallery_name =  $descriptionElement->associatedSpecimenOrObservation->uuid;

					$captionElements = array('#uri'=>t('open media'));

					$gallery_html = theme(

					$mediaList,

					$gallery_name ,

					$gallery_settings['cdm_dataportal_media_maxextend'],

					$gallery_settings['cdm_dataportal_media_cols'],

					$gallery_settings['cdm_dataportal_media_maxRows'],

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

				} else {

					$gallery_html = '';

				}

				$li .= '</td><td>'.$gallery_html.'</td></tr>';

				$out_specimenList .= $li;

			}

		}

		$out_specimenList .= '</table>';

	}

	$out .= drupal_get_form('specimens_search_form');

	//$test = specimens_table($descriptionElements);

	//$out .= $test;

	$out .= $out_specimenList;

function specimens_search_form() {

	//form select options

	$form['specimens_search_options'] = array(

    '#type' => 'value',

    '#value' => array(t('No sort'), t('Name'), t('CatalogNumber'), t('Gallery'))

	);

	//the form

	$form['specimens_search'] = array(

    '#title' => t('Speciments sort'),

	  '#type' => 'fieldset',

	  '#description' => t('Select your sort criteria.'),

	  '#collapsible' => TRUE,

    '#collapsed' => FALSE

	);

	//criteria

	$form['specimens_search']['first_criteria'] = array(

    '#title' => t('First criteria'),

    '#type' => 'select',

    '#options' => $form['specimens_search_options']['#value']

	);

	$form['specimens_search']['second_criteria'] = array(

    '#title' => t('Second criteria'),

    '#type' => 'select',

    '#options' => $form['specimens_search_options']['#value']

	);

	$form['specimens_search']['third_criteria'] = array(

    '#title' => t('Third criteria'),

    '#type' => 'select',

    '#options' => $form['specimens_search_options']['#value']

	);

	//submit button

	$form['specimens_search']['submit'] = array(

    '#type' => 'submit',

    '#value' => t('Sort')

	);

	/*

	//from properties

	$form['#method'] = 'post';

	$form['#action'] = 'http://example.com/?q=foo/bar';

	$form['#attributes'] = array(

    'enctype' => 'multipart/form-data',

    'target' => 'name_of_target_frame'

	);

	$form['#prefix'] = '<div class="my-form-class">';

	$form['#suffix'] = '</div>';

	*/

	//returning value

	return $form;

}

	//if(!isset($synomymie->homotypicSynonymsByHomotypicGroup[0])){

	//}

	if($synomymie->homotypicSynonymsByHomotypicGroup){

    $out .= theme('cdm_homotypicSynonymyGroup', $synomymie->homotypicSynonymsByHomotypicGroup);

	//render name relationships

	$name_rels_to_show = variable_get('name_relationships_to_show', null);

	$skip = array();

	if($name_rels_to_show){

		foreach ($name_rels_to_show as $key => $value){

			if ($value === 0){

				$skip[] = $key;

			}

		}

		if (sizeof($name_rels_to_show) != sizeof($skip)){

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

			$out .= theme('cdm_nameRelationships', $nameRelationships, $skip);

		}

	}

	/*

	 if(variable_get(CDM_DATAPORTAL_DISPLAY_NAME_RELATIONSHIPS, CDM_DATAPORTAL_DISPLAY_NAME_RELATIONSHIPS_DEFAULT)){

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

	 // TODO is it correct to skip relationsFromThisName since all relationships are to be understood as 'is .... of'

	 if(variable_get('cdm_dataportal_name_relations_skiptype_basionym', 1)){

	 $skip = array(UUID_BASIONYM);

	 }

	 $out .= theme('cdm_nameRelationships', $nameRelationships, $skip);

	 }

	 */

	$hasImages = isset($media[0]);

	if($hasImages){

		//

		$maxExtend = 150;

		$cols = 3;

		$maxRows = false;

		$alternativeMediaUri = null;

		$captionElements = array('title', 'rights', '#uri'=>t('open Image'));

		$gallery_name = $taxon->uuid;

		$mediaLinkType = 'LIGHTBOX';

		$gallery_settings = getGallerySettings(CDM_DATAPORTAL_MEDIA_GALLERY_NAME);

		$out = '<div class="image-gallerie">';

		$out .= theme('cdm_media_gallerie', $media,

		$gallery_name,

		$gallery_settings['cdm_dataportal_media_maxextend'],

		$gallery_settings['cdm_dataportal_media_cols'],

		0, // ignore maxrows settings

		$captionElements,

		$mediaLinkType,

		null);

		$out .= '</div>';

	}else{

		$out = 'No images available.';

	}

	return $out;

	$flashLink = isset($media[0]);

	if($flashLink){

		$taggedName = $taxon->name->taggedName;

		$nameArray = array();

		foreach($taggedName as $taggedText){

			if($taggedText->type == 'name'){

				$nameArray[] = $taggedText->text;

			}

		}

		$query = join("%5F", $nameArray) . '%20AND%20EditWP6%20AND%20jpg';

		$out = '

	}else{

		$out = 'No images available.';

	}

	return $out;