"branching out" to tripal module only repo

theme/tripal_subthemes/tripal_analysis_blast_theme/css/tripal_analysis_blast.css

@@ -1,33 +0,0 @@
-#tripal_analysis_blast-table {
-   width: 100%;
-	overflow:auto;
-}
-#tripal_analysis_blast-table td {
-  text-align: left;
-}
-#tripal_analysis_blast-table .tripal-table-even-row {
-   border-top: 0px solid #CCCCCC;
-   border-bottom: 0px solid #CCCCCC;
-}
-#tripal_analysis_blast-table .tripal-table-odd-row {
-   border-top: 0px solid #CCCCCC;
-   border-bottom: 0px solid #CCCCCC;
-}
-#tripal_analysis_blast-table .tripal_analysis_blast-result-first-row {
-   border-top: 1px solid #CCCCCC;
-}
-#tripal_analysis_blast-table .tripal_analysis_blast-result-last-row {
-   border-bottom: 1px solid #CCCCCC;
-}
-
-.tripal_analysis_blast-info-hsp-desc {
-	background-color: #FFFFFF;
-	border:0px solid #CCC5AE;
-	display:none;
-	overflow:auto;
-   width: 100%;
-}
-.tripal_analysis_blast-info-hsp-desc pre{
-	background-color: #FFFFFF;
-   border:none;
-}

theme/tripal_subthemes/tripal_analysis_blast_theme/js/tripal_analysis_blast.js

@@ -1,183 +0,0 @@
-
-if (Drupal.jsEnabled) {
-   
-   $(document).ready(function(){
-	   // If Anlaysis admin page is shown, get the settings for selected database
-	   if ($("#edit-blastdb")[0]) {
-		   tripal_update_regex($("#edit-blastdb")[0]);
-		   tripal_set_genbank_style();
-	   }
-      // hide the alignment information on the blast results box
-      $(".tripal_analysis_blast-info-hsp-desc").hide();
-
-   });
-  
-   //------------------------------------------------------------
-   // Update the blast results based on the user selection
-   function tripal_update_blast(link,db_id){
-      tripal_startAjax();
-      $.ajax({
-         url: link.href,
-         dataType: 'json',
-         type: 'POST',
-         success: function(data){         
-            $("#blast_db_" + db_id).html(data.update);
-            $(".tripal_analysis_blast-info-hsp-desc").hide();
-            tripal_stopAjax();
-         }
-      });
-      return false;
-   }
-
-   //------------------------------------------------------------
-   // Update the blast results based on the user selection
-   function tripal_blast_toggle_alignment(analysis_id,hit_id){
-      var alignment_box = $("#tripal_analysis_blast-info-hsp-desc-"+analysis_id+"-"+hit_id);
-      var toggle_img = $("#tripal_analysis_blast-info-toggle-image-"+analysis_id+"-"+hit_id);
-	   var icon_url = toggle_img.attr("src");
-
-
-      if (alignment_box.is(':visible')) {
-         alignment_box.fadeOut('fast');
-	      var changed_icon_url = icon_url.replace(/arrow_d.png/,"arrow_r.png");
-	      toggle_img.attr("src", changed_icon_url);
-	   } else {
-         var width = alignment_box.parent().width();
-         alignment_box.css("width", width+'px');
-         alignment_box.fadeIn('slow');
-	      var icon_url = icon_url.replace(/arrow_r.png/,"arrow_d.png");
-	      toggle_img.attr("src", icon_url);
-	   }
-      return false;
-   }
-   
-   //------------------------------------------------------------
-   // Update regular expression for selected database
-   function tripal_update_regex(options){
-	   // Get the dbname from DOM
-	   var index = options.selectedIndex;
-	   var dbid = options[index].value;
-
-	   // Form the link for the following ajax call	   
-      var baseurl = tripal_get_base_url();
-      var link = baseurl + '/tripal_blast_regex/' + dbid;
-	   
-	   // Make ajax call to retrieve regular expressions
-	   $.ajax( {
-			url : link,
-			dataType : 'json',
-			type : 'POST',
-			success : tripal_set_parser,
-		});
-	}
-   
-   // Set parser for the admin page
-   function tripal_set_parser(data) {
-	   // Set title if it exists
-	   if (data.name) {
-			$("#edit-displayname").val(data.name);
-	   } else {
-			$("#edit-displayname").val("");
-	   }
-		
-	   // If genbank_style is TRUE, check the Genbank style box, clear all regular expressions, and disable
-	   // the text fields
-	   if (data.genbank_style == 1) {
-		   $("#edit-gb-style-parser").attr("checked", true);
-		   $("#edit-hit-id").val("");
-		   $("#edit-hit-def").val("");
-		   $("#edit-hit-accession").val("");
-		
-	   // Otherwise, uncheck the Genbank style box and set the regular expressions
-	   } else {
-			$("#edit-gb-style-parser").attr("checked", false);
-			if (data.reg1) {
-				$("#edit-hit-id").val(data.reg1);			
-			// Show default hit-id parser if it's not set
-			} else {
-				$("#edit-hit-id").val("^(.*?)\s.*$");
-			}
-			if (data.reg2) {
-				$("#edit-hit-def").val(data.reg2);
-			// Show default hit-def parser if it's not set
-			} else {
-				$("#edit-hit-def").val("^.*?\s(.*)$");
-			}
-			if (data.reg3) {
-				$("#edit-hit-accession").val(data.reg3);			
-			// Show default hit-accession parser if it's not set
-			} else {
-				$("#edit-hit-accession").val("^(.*?)\s.*$");
-			}
-		}
-		tripal_set_genbank_style();  
-   }
-   // ------------------------------------------------------------
-   // Use genbank style parser. Hide regular expression text feilds
-   function tripal_set_genbank_style (){
-	  // Disable regular expressions if genbank style parser is used (checked)
-	  if ($("#edit-gb-style-parser").is(":checked")) {
-		  $("#edit-hit-id-wrapper > label").css("color", "grey");
-		  $("#edit-hit-def-wrapper > label").css("color", "grey");
-		  $("#edit-hit-accession-wrapper > label").css("color", "grey");
-		  $("#edit-hit-id").attr('disabled', 'disabled');
-		  $("#edit-hit-def").attr('disabled', 'disabled');
-		  $("#edit-hit-accession").attr('disabled', 'disabled');
-	  } else {
-		  $("#edit-hit-id-wrapper > label").css("color", "black");
-		  $("#edit-hit-def-wrapper > label").css("color", "black");
-		  $("#edit-hit-accession-wrapper > label").css("color", "black");
-		  $("#edit-hit-id").removeAttr('disabled');
-		  $("#edit-hit-def").removeAttr('disabled');
-		  $("#edit-hit-accession").removeAttr('disabled');
-	  }
-   }
-   // -------------------------------------------------------------
-   // Function that toggles the blast droppable subbox content
-   function tripal_set_blast_subbox(db_id){
-	  
-	  $('.blast-hit-arrow-icon').hover(
-	     function() {
-	        $(this).css("cursor", "pointer");
-	     },
-	     function() {
-	        $(this).css("cursor", "pointer");
-	     }
-	  );
-     $('.blast-hit-arrow-icon').click(function() {
-	        
-     });
-   }
-   
-   	//------------------------------------------------------------
-	// Update the blast best hit report for selected page and sorting
-	function tripal_update_best_hit_report(obj, analysis_id, sort, descending, per_page){
-		var page = obj.selectedIndex + 1;
-		var baseurl = location.href.substring(0,location.href.lastIndexOf('/tripal_blast_report/'));
-		var link = baseurl + '/tripal_blast_report/' + analysis_id + "/" + page + "/" + sort + "/" + descending + "/" + per_page;
-
-		tripal_startAjax();
-		$.ajax({
-			url: link,
-			dataType: 'html',
-			type: 'POST',
-			success: function(data){
-				var d = document.createElement('div');
-				d.innerHTML = data;
-				var divs = d.getElementsByTagName("div");
-				for (var i = 0; i < divs.length; i ++) {
-					if (divs[i].getAttribute('id') == 'blast-hits-report') {	
-						var report_table = document.getElementById('blast-hits-report');
-						report_table.innerHTML = divs[i].innerHTML;
-						var table_breport = document.getElementById('tripal_blast_report_table');
-						var sel = document.getElementById('tripal_blast_report_page_selector');
-						sel.options[page - 1].selected = true;
-						tripal_stopAjax();
-					}
-				}
-			}
-		});
-		
-		return false;
-	}
-}

theme/tripal_subthemes/tripal_analysis_blast_theme/node-chado_analysis_blast.tpl.php

@@ -1,100 +0,0 @@
-<?php
-// Purpose: This template provides the layout of the organism node (page)
-//   using the same templates used for the various feature content blocks.
-//
-// To Customize the Featture Node Page:
-//   - This Template: customize basic layout and which elements are included
-//   - Using Panels: Override the node page using Panels3 and place the blocks
-//       of content as you please. This method requires no programming. See
-//       the Tripal User Guide for more details
-//   - Block Templates: customize the content/layout of each block of stock 
-//       content. These templates are found in the tripal_stock subdirectory
-//
-// Variables Available:
-//   - $node: a standard object which contains all the fields associated with
-//       nodes including nid, type, title, taxonomy. It also includes stock
-//       specific fields such as stock_name, uniquename, stock_type, synonyms,
-//       properties, db_references, object_relationships, subject_relationships,
-//       organism, etc.
-//   NOTE: For a full listing of fields available in the node object the
-//       print_r $node line below or install the Drupal Devel module which 
-//       provides an extra tab at the top of the node page labelled Devel
-?>
-
-<?php
- //uncomment this line to see a full listing of the fields avail. to $node
- //print '<pre>'.print_r($variables,TRUE).'</pre>';
-drupal_add_css('./tripal-node-templates.css');
-
-$node = $variables['node'];
-$organism = $variables['node']->organism;
-?>
-
-<?php if ($teaser) { 
-  include('tripal_analysis_blast/tripal_analysis_blast_teaser.tpl.php'); 
-} else { ?>
-
-<script type="text/javascript">
-if (Drupal.jsEnabled) {
-   $(document).ready(function() {
-      // hide all tripal info boxes at the start
-      $(".tripal-info-box").hide();
- 
-      // iterate through all of the info boxes and add their titles
-      // to the table of contents
-      $(".tripal-info-box-title").each(function(){
-        var parent = $(this).parent();
-        var id = $(parent).attr('id');
-        var title = $(this).text();
-        $('#tripal_analysis_blast_toc_list').append('<li><a href="#'+id+'" class="tripal_analysis_blast_toc_item">'+title+'</a></li>');
-      });
-
-      // when a title in the table of contents is clicked, then
-      // show the corresponding item in the details box
-      $(".tripal_analysis_blast_toc_item").click(function(){
-         $(".tripal-info-box").hide();
-         href = $(this).attr('href');
-         $(href).fadeIn('slow');
-         // we want to make sure our table of contents and the details
-         // box stay the same height
-         $("#tripal_analysis_blast_toc").height($(href).parent().height());
-         return false;
-      }); 
-
-      // we want the base details to show up when the page is first shown 
-      // unless the user specified a specific block
-      var block = window.location.href.match(/[\?|\&]block=(.+?)\&/)
-      if(block == null){
-         block = window.location.href.match(/[\?|\&]block=(.+)/)
-      }
-      if(block != null){
-         $("#tripal_analysis_blast-"+block[1]+"-box").show();
-      } else {
-         $("#tripal_analysis_blast-base-box").show();
-      }
-
-      $("#tripal_analysis_blast_toc").height($("#tripal_analysis_blast-base-box").parent().height());
-      
-   });
-}
-</script>
-
-
-<div id="tripal_analysis_blast_details" class="tripal_details">
-
-   <!-- Basic Details Theme -->
-   <?php include('tripal_analysis_blast/tripal_analysis_blast_base.tpl.php'); ?>
-
-   <?php print $content ?>
-</div>
-
-<!-- Table of contents -->
-<div id="tripal_analysis_blast_toc" class="tripal_toc">
-   <div id="tripal_analysis_blast_toc_title" class="tripal_toc_title">Resources</i></div>
-   <span id="tripal_analysis_blast_toc_desc" class="tripal_toc_desc"></span>
-   <ul id="tripal_analysis_blast_toc_list" class="tripal_toc_list">
-
-   </ul>
-</div>
-
-<?php } ?>

theme/tripal_subthemes/tripal_analysis_blast_theme/tripal_analysis_blast/tripal_analysis_blast_base.tpl.php

@@ -1,78 +0,0 @@
-<?php
-$node = $variables['node'];
-$analysis = $variables['node']->analysis;
-
-// the description is a text field so we want to expand that
-$analysis = tripal_core_expand_chado_vars($analysis,'field','analysis.description');
-
-// get the blast data 
-$blast = $node->analysis->tripal_analysis_blast;
-
-//dpm($analysis);
-
-?>
-<div id="tripal_analysis_blast-base-box" class="tripal_analysis_blast-info-box tripal-info-box">
-  <div class="tripal_analysis_blast-info-box-title tripal-info-box-title">Blast Analysis Details</div>
-  <div class="tripal_analysis_blast-info-box-desc tripal-info-box-desc"></div>
-   <table id="tripal_analysis_blast-table-base" class="tripal_analysis_blast-table tripal-table tripal-table-vert">
-      <tr class="tripal_analysis_blast-table-odd-row tripal-table-even-row">
-        <th>Analysis Name</th>
-        <td><?php print $analysis->name; ?></td>
-      </tr>
-      <tr class="tripal_analysis_blast-table-odd-row tripal-table-odd-row">
-        <th nowrap>Software</th>
-        <td><?php 
-          print $analysis->program; 
-          if($analysis->programversion){
-             print " (" . $analysis->programversion . ")"; 
-          }
-          if($analysis->algorithm){
-             print ". " . $analysis->algorithm; 
-          }
-          ?>
-        </td>
-      </tr>
-      <tr class="tripal_analysis_blast-table-odd-row tripal-table-even-row">
-        <th nowrap>Source</th>
-        <td><?php 
-          if($analysis->sourceuri){
-             print "<a href=\"$analysis->sourceuri\">$analysis->sourcename</a>"; 
-          } else {
-             print $analysis->sourcename; 
-          }
-          if($analysis->sourceversion){
-             print " (" . $analysis->sourceversion . ")"; 
-          }
-          ?>
-          </td>
-      </tr>
-      <tr class="tripal_analysis_blast-table-odd-row tripal-table-odd-row">
-        <th nowrap>Date performed</th>
-        <td><?php print preg_replace("/^(\d+-\d+-\d+) .*/","$1",$analysis->timeexecuted); ?></td>
-      </tr>
-      <tr class="tripal_analysis_blast-table-odd-row tripal-table-even-row">
-        <th nowrap>Description</th>
-        <td><?php print $analysis->description; ?></td>
-      </tr> 
-      <tr class="tripal_analysis_blast-table-even-row tripal-table-odd-row">
-        <th nowrap>Database</th>
-        <td><?php print $blast->db->name ?></td>
-      </tr> 
-      <tr class="tripal_analysis_blast-table-even-row tripal-table-even-row">
-        <th nowrap>Blast Arguments</th>
-        <td><?php print $blast->blastparameters ?></td>
-      </tr>  
-      <tr class="tripal_analysis_blast-table-odd-row tripal-table-odd-row">
-        <th>Report</th>
-        <td>
-        	<?php 
-        		if ($analysis->blast_report) {					
-        			print "<a href=$analysis->blast_report>View the best hit report</a>";
-        		} else {
-        			print "not available";
-        		}
-        	?>
-        	</td>
-      </tr>       	                                
-   </table>   
-</div>

theme/tripal_subthemes/tripal_analysis_blast_theme/tripal_analysis_blast/tripal_analysis_blast_report.tpl.php

@@ -1,123 +0,0 @@
-<?php
-$report  = $variables['report_object'];
-$hits = $report->hits;
-?>
-
-<style type="text/css">
-#tripal_blast_report_current_page {
-	float: right;
-	margin-bottom: 5px;
-	margin-right: 20px;
-}
-#tripal_blast_report_pager {
-	float: right;
-	margin-bottom: 10px;
-	margin-right: 20px;
-}
-#tripal_blast_report_per_page {
-	float: left;
-	margin-bottom: 10px;
-}
-</style>
-
-<div id="tripal_ajaxLoading" style="display:none">
-	<div id="loadingText">Loading...</div>
-	<img src="<?php print url("sites/all/themes/theme_tripal/images/ajax-loader.gif") ?>">
-</div>
-
-<div id="blast-hits-report">
-	<strong>Analysis Date: </strong><?php print $report->time?> (<a href=<?php print $report->url ?>><?php print $report->name ?></a>)<br>
-	There are <strong><?php print $report->counter ?></strong> records. 
-	<div id=tripal_blast_report_current_page>page <strong><?php print $report->currentpage ?></strong> of <strong><?php print $report->no_page ?></strong>
-	</div>
-	
-	<table id="tripal_analysi_blast-report-table" class="tripal_analysis_blast-table tripal-table tripal-table-horz">
-		<tr class="tripal_analysis_blast-table-odd-row tripal-table-odd-row">
-			<th nowrap><?php if ($report->sort == 0) {print $report->symbol;} ?>
-				<a href=<?php print $report->byQuery ?>>Query</a>
-			</th>
-			<th nowrap><?php if ($report->sort == 1) {print $report->symbol;} ?>
-				<a href=<?php print $report->byMatchName ?>>Match Name</a>
-			</th>
-			<th nowrap><?php if ($report->sort == 2) {print $report->symbol;} ?>
-				<a href=<?php print $report->byDescription ?>>Description</a>
-			</th>
-			<th nowrap><?php if ($report->sort == 3) {print $report->symbol;} ?>
-				<a href=<?php print $report->byEvalue ?>>E-value</a>
-			</th>
-			<th nowrap><?php if ($report->sort == 4) {print $report->symbol;} ?>
-				<a href=<?php print $report->byIdentity ?>>%Identity</a>
-			</th>
-			<th nowrap><?php if ($report->sort == 5) {print $report->symbol;} ?>
-				<a href=<?php print $report->byLength ?>>Length</a>
-			</th>
-		</tr>
-		
-		<?php foreach($hits AS $hit) {?>
-		<tr class="<?php print $hit->class ?>">
-		                           <td nowrap><a href=<?php print $hit->q_url ?>><?php print $hit->query ?></a></td>
-		                           <td nowrap><a href=<?php print $hit->urlprefix.$hit->match ?> target=_blank><?php print $hit->match ?></td>
-		                           <td><?php print $hit->desc ?></td>
-		                           <td nowrap><?php print $hit->evalue ?></td>
-		                           <td nowrap><?php print $hit->identity ?></td>
-		                           <td nowrap><?php print $hit->length ?></td>
-		                         </tr>
-		<?php } ?>	
-			
-	</table>
-			<div id="tripal_blast_report_per_page">Show	
-				<?php 
-				$per_page = $report->per_page;
-				$path = $report->path;
-				if ($per_page == 10) {?>
-					<strong>10</strong> | 
-				<?php } else { 
-					$url_path = url($path."10");
-				?>	
-					<a href=<?php print $url_path ?>>10</a> | 
-				<?php } 
-				if ($per_page == 20) {
-				?>
-					<strong>20</strong> | 
-				<?php } else {
-					$url_path = url($path."20");
-				?>
-					<a href=<?php print $url_path ?>>20</a> | 
-				<?php } 
-				if ($per_page == 50) {
-				?>
-					<strong>50</strong> | 
-				<?php } else {
-					$url_path = url($path."50");
-				?>
-					<a href=<?php print $url_path ?>>50</a> | 
-				<?php }
-				if ($per_page == 100) {
-				?>
-					<strong>100</strong> | 
-				<?php } else {
-					$url_path = url($path."100");
-				?>
-					<a href=<?php print $url_path ?>>100</a> | 
-				<?php }
-				if ($per_page == 200) {
-				?>
-					<strong>200</strong> | 
-				<?php } else {
-					$url_path = url($path."200");
-				?>
-			   	<a href=<?php print $url_path ?>>200</a>
-				<?php } ?>
-				
-				records per page
-		</div>
-		<div id=tripal_blast_report_pager>page
-			<select id=tripal_blast_report_page_selector onChange="tripal_update_best_hit_report(this, <?php print $report->analysis_id ?>,<?php print $report->sort ?>, <?php print $report->descending ?>, <?php print $report->per_page ?>)">
-			<?php  for ($i = 1; $i <= $report->no_page; $i ++) { ?>
-				<option value=<?php print $i ?>><?php print $i ?></option>
-			<?php } ?>	                           
-			</select>
-		</div>
-</div>
-			
-	

theme/tripal_subthemes/tripal_analysis_blast_theme/tripal_analysis_blast/tripal_analysis_blast_teaser.tpl.php

@@ -1,53 +0,0 @@
-<?php
-$node = $variables['node'];
-$analysis = $variables['node']->analysis;
-
-// the description is a text field so we want to expand that
-$analysis = tripal_core_expand_chado_vars($analysis,'field','analysis.description');
-
-
-?>
-<div id="tripal_analysis-base-box" class="tripal_analysis-info-box tripal-info-box">
-  <div class="tripal_analysis-info-box-title tripal-info-box-title">Details</div>
-   <table id="tripal_analysis-table-base" class="tripal_analysis-table tripal-table tripal-table-vert">
-      <tr class="tripal_analysis-table-odd-row tripal-table-even-row">
-        <th>Analysis Name</th>
-        <td><?php print $analysis->name; ?></td>
-      </tr>
-      <tr class="tripal_analysis-table-odd-row tripal-table-odd-row">
-        <th nowrap>Software</th>
-        <td><?php 
-          print $analysis->program; 
-          if($analysis->programversion){
-             print " (" . $analysis->programversion . ")"; 
-          }
-          if($analysis->algorithm){
-             print ". " . $analysis->algorithm; 
-          }
-          ?>
-        </td>
-      </tr>
-      <tr class="tripal_analysis-table-odd-row tripal-table-even-row">
-        <th nowrap>Source</th>
-        <td><?php 
-          if($analysis->sourceuri){
-             print "<a href=\"$analysis->sourceuri\">$analysis->sourcename</a>"; 
-          } else {
-             print $analysis->sourcename; 
-          }
-          if($analysis->sourceversion){
-             print " (" . $analysis->sourceversion . ")"; 
-          }
-          ?>
-          </td>
-      </tr>
-      <tr class="tripal_analysis-table-odd-row tripal-table-odd-row">
-        <th nowrap>Date performed</th>
-        <td><?php print preg_replace("/^(\d+-\d+-\d+) .*/","$1",$analysis->timeexecuted); ?></td>
-      </tr>
-      <tr class="tripal_analysis-table-odd-row tripal-table-even-row">
-        <th nowrap>Description</th>
-        <td><?php print $analysis->description; ?></td>
-      </tr>             	                                
-   </table>   
-</div>

theme/tripal_subthemes/tripal_analysis_blast_theme/tripal_analysis_blast_theme.info

@@ -1,10 +0,0 @@
-name = Tripal Subtheme: Blast Analysis
-description = A tripal subtheme for tripal analysis blast module
-version = 6.x-0.3.1b
-core = 6.x
-engine = phptemplate
-base theme = tripal
-
-stylesheets[all][] = css/tripal_analysis_blast.css
-
-scripts[] = js/tripal_analysis_blast.js

theme/tripal_subthemes/tripal_analysis_blast_theme/tripal_feature/tripal_feature_blast_results.tpl.php

@@ -1,111 +0,0 @@
-<?php
-$feature  = $variables['node']->feature;
-$blast_results_list = $feature->tripal_analysis_blast->blast_results_list;
-
-?>
-<div id="tripal_ajaxLoading" style="display:none">
-	<div id="loadingText">Loading...</div>
-	<img src="sites/all/themes/theme_tripal/images/ajax-loader.gif">
-</div>
-
-<?php 
-if(count($blast_results_list) > 0){
-   foreach ($blast_results_list as $blast_result) {
-	  $hits_array = $blast_result->hits_array;
-	  $db = $blast_result->db;
-     $analysis = $blast_result->analysis;
-?>
-<div id="blast_db_<?php print $db->db_id ?>">
-<div id="tripal_analysis_blast-results-<?php print "$db->db_id" ?>-box" class="tripal_analysis_blast-box tripal-info-box">
-	<div class="tripal-info-box-title tripal_analysis_blast-info-box-title"><?php if ($db->displayname) {print $db->displayname;} else {print $db->name . "Homologs";} ?></div>
-	<div class="tripal-info-box-desc tripal_analysis_blast-info-box-desc">
-	<strong>Analysis Date: </strong><?php print preg_replace("/^(\d+-\d+-\d+) .*/","$1",$analysis->timeexecuted) . " (<a href=".url("node/$analysis->nid").">$analysis->name</a>)"?><br>
-	<!--Query: <?php print "$blast_result->xml_tag"?><br>-->
-	
-	<?php 
-   if($blast_result->max != 10){    
-      $url = url("tripal_top_blast/$feature->feature_id/$db->db_id/10");
-		?><span><a onclick="return tripal_update_blast(this,<?php print $db->db_id?>)" href="<?php print $url ?>">Show Best 10 Hits</a></span><?php
-	} else { 
-		?><span>Best 10 Hits Shown</span><?php
-	} 
-	
-	if($blast_result->number_hits <= 10){ 
-	} 
-   else if ($blast_result->max != 25) { 
-  	   $url = url("tripal_top_blast/$feature->feature_id/$db->db_id/25"); 	
-		?><span> | <a onclick="return tripal_update_blast(this,<?php print"$db->db_id"?>)" href="<?php print $url ?>">Show Best 25 Hits</a></span><?php
-	}else {
-		?><span> | Best 25 Hits Shown</span><?php
-	} 
-	
-	if($blast_result->number_hits <= 25){
-	} 
-   else if ($blast_result->max != 0) {
-	   $url = url("tripal_top_blast/$feature->feature_id/$db->db_id/all"); 		
-		?><span> | <a onclick="return tripal_update_blast(this, <?php print $db->db_id ?>)" href="<?php print $url ?>">Show All Hits</a> </span><?php
-	} else {
-		?><span> | All Hits Shown</span><?php
-	} 
-   ?>
-	<br><br><span>Click a description for more details</span>
-   </div>
-	<table id="tripal_analysis_blast-table" class="tripal-table tripal-table-horz tripal_analysis_blast-table">
-		<tr>
-         <th>&nbsp;</th>
-			<th nowrap>Match Name</th>
-			<th nowrap>E value</th>
-			<th nowrap>Identity</th>
-			<th nowrap>Description</th>
-		</tr>
-		
-		<?php 
-      $i = 0; 
-      if(sizeof($hits_array)==0){?>
-        <tr>
-          <td colspan="5">    
-            <div class="tripal-no-results">There are no matches against <?php print $db->name?> for this <?php print $feature->type_id->name?>.</div> 
-          </td>
-        </tr><?php
-      }
-		foreach($hits_array AS $hit) { 
-         $class = 'tripal-table-odd-row tripal_analysis_blast-table-odd-row';
-         if($i % 2 == 0 ){
-            $class = 'tripal-table-even-row tripal_analysis_blast-table-odd-row';
-         }?>
-         <tr class="<?php print $class ?> tripal_analysis_blast-result-first-row">
-            <td><?php print $i+1 ?>.</td>
-		      <?php if ($hit['hit_url']) { ?>
-			      <td><a href="<?php print $hit['hit_url']?>" target="_blank"><?php print $hit['hit_name']?></a></td>
-		      <?php } else {?>
-			      <td><?php print $hit['hit_name'] ?></td>
-		      <?php } ?>
-			   <td nowrap><?php print $hit['best_evalue']?></td>
-			   <td nowrap><?php  print $hit['percent_identity']?></td>
-			   <td><?php print $hit['description']?></td>
-		   </tr>
-	      <tr class="<?php print $class ?>">
-		      <td colspan=5>
-			      <a class="blast-hit-arrow-icon" onclick="return tripal_blast_toggle_alignment(<?php print $analysis->analysis_id ?>,<?php print $i?>)"><img id="tripal_analysis_blast-info-toggle-image-<?php print $analysis->analysis_id ?>-<?php print $i?>" src=<?php print $hit['arrowr_url']?> align="top"> View Alignment</a>
-			      <div class="tripal_analysis_blast-info-hsp-title"></div>
-		      </td>
-	      </tr>
-	      <tr class="<?php print $class ?> tripal_analysis_blast-result-last-row">
-		      <td colspan=5>
-		      <?php 
-		      $hsps_array = $hit['hsp'];
-		      foreach ($hsps_array AS $hsp) { ?>
-			      <div class="tripal_analysis_blast-info-hsp-desc" id="tripal_analysis_blast-info-hsp-desc-<?php print $analysis->analysis_id ?>-<?php print $i?>">
-				      &nbsp;HSP <?php  print $hsp['hsp_num'] ?>
-				      <pre>Score: <?php print $hsp['bit_score'] ?> bits (<?php print $hsp['score'] ?>), Expect = <?php print $hsp['evalue'] ?><br>Identity = <?php print sprintf("%d/%d (%.2f%%)", $hsp['identity'], $hsp['align_len'], $hsp['identity']/$hsp['align_len']*100) ?>, Postives = <?php print sprintf("%d/%d (%.2f%%)", $hsp['positive'], $hsp['align_len'], $hsp['positive']/$hsp['align_len']*100)?>, Query Frame = <?php print $hsp['query_frame']?></a><br><br></a>Query: <?php print sprintf("%4d", $hsp['query_from'])?> <?php print $hsp['qseq'] ?> <?php print sprintf("%d", $hsp['query_to']); ?><br>            <?php print $hsp['midline'] ?><br>Sbjct: <?php print sprintf("%4d", $hsp['hit_from']) ?> <?php print $hsp['hseq']?> <?php print sprintf("%d",$hsp['hit_to']) ?></pre><br>
-			      </div>
-		      <?php } ?>
-		      </td>
-	      </tr>		
-         <?php $i++;
-	   } ?>
-	</table>
-</div>
-</div>
-  <?php } ?>
-<?php } ?>

theme/tripal_subthemes/tripal_analysis_go_theme/css/tripal_analysis_go.css

@@ -1,17 +0,0 @@
-
-.tripal_go-info-box, .tripal_go_summary-info-box {
-   margin-top: 10px;
-   margin-left: 0px;
-   margin-right: 0px;
-   margin-bottom: 0px;
-   padding-top: 0px;
-   padding-left: 0px;
-   padding-bottom: 0px;
-   padding-right: 0px;
-   border-collapse: collapse;
-   z-index: 10;
-}
-
-.tripal_go_summary-info-box .tripal_cv_tree {
-   border-collapse: separate;
-}

theme/tripal_subthemes/tripal_analysis_go_theme/js/tripal_analysis_go.js

@@ -1,52 +0,0 @@
-
-
-if (Drupal.jsEnabled) {
-
-
-   $(document).ready(function() {
-       // Select default GO analysis when available
-       var selectbox = $('#edit-tripal-analysis-go-select');
-       if(selectbox.length > 0){ 
-    	   var option = document.getElementById("analysis_id_for_go_report");
-    	   if (option) {
-    		   var options = document.getElementsByTagName('option');
-    		   var index = 0;
-    		   for (index = 0; index < options.length; index ++) {
-    			   if (options[index].value == option.value) {
-    				   break;
-    			   }
-    		   }
-    		   selectbox[0].selectedIndex = index;
-    		   tripal_analysis_go_org_charts(option.value);
-    	// Otherwise, show the first option by default
-    	   } else {
-    		   selectbox[0].selectedIndex = 1;
-    		   tripal_analysis_go_org_charts(selectbox.val());
-    	   }
-       }
-   });
-
-
-   function tripal_analysis_go_org_charts(item){
-      if(!item){
-         $("#tripal_analysis_go_org_charts").html('');
-         return false;
-      }
-      // Form the link for the following ajax call 
-      baseurl = tripal_get_base_url();      
-      var link = baseurl + '?q=tripal_analysis_go_org_charts/' + item;
-      tripal_startAjax();
-      $.ajax({
-           url: link,
-           dataType: 'json',
-           type: 'POST',
-           success: function(data){
-             $("#tripal_analysis_go_org_charts").html(data[0]);
-             tripal_cv_init_chart();
-             tripal_cv_init_tree();
-             tripal_stopAjax();
-           }
-      });
-      return false;
-   }
-}

theme/tripal_subthemes/tripal_analysis_go_theme/tripal_analysis_go_theme

@@ -1,10 +0,0 @@
-name = Tripal Subtheme: GO Analysis
-description = A tripal subtheme for tripal analysis go module
-version = 6.x-0.3.1b
-core = 6.x
-engine = phptemplate
-base theme = tripal
-
-stylesheets[all][] = css/tripal_analysis_go.css
-
-scripts[] = js/tripal_analysis_go.js

theme/tripal_subthemes/tripal_analysis_go_theme/tripal_feature/tripal_feature_go_terms.tpl.php

@@ -1,35 +0,0 @@
-<?php
-$feature = $variables['node']->feature;
-$terms = $feature->tripal_analysis_go->terms;
-?>
-<div id="tripal_feature-go_terms-box" class="tripal_feature-info-box tripal-info-box">
-  <div class="tripal_feature-info-box-title tripal-info-box-title">GO Assignments</div>
-  <div class="tripal_feature-info-box-desc tripal-info-box-desc">This <?php print $feature->type_id->name ?> is annotated with the following GO terms.</div>
-  <?php if(count($terms) > 0){ ?>
-  <table id="tripal_feature-go_terms-table" class="tripal_feature-table tripal-table tripal-table-horz">
-    <tr>
-      <th>Category</th>
-      <th>Term Accession</th>
-      <th>Term Name</th>
-    </tr>
-    <?php
-    $i = 0; 
-    foreach ($terms as $term){
-      $class = 'tripal_feature-table-odd-row tripal-table-odd-row';
-      if($i % 2 == 0 ){
-         $class = 'tripal_feature-table-odd-row tripal-table-even-row';
-      }
-      ?>
-      <tr class="<?php print $class ?>">
-        <td><?php print $term->cvname ?></td>
-        <td>GO:<?php print $term->accession?></td>
-        <td><span title="<?php print $term->definition ?>"><?php print $term->goterm ?></span></td>
-      </tr>
-      <?php
-      $i++;  
-    } ?>
-  </table>
-  <?php } else { ?>
-    <div class="tripal-no-results">There are no GO terms for this feature</div> 
-  <?php }?>
-</div>

theme/tripal_subthemes/tripal_analysis_go_theme/tripal_organism/tripal_organism_go_summary.tpl.php

@@ -1,35 +0,0 @@
-<?php
-  $organism = $node->organism;
-  $form = $organism->tripal_analysis_go->select_form['form'];
-  $has_results = $organism->tripal_analysis_go->select_form['has_results'];
-?>
-<div id="tripal_organism-go_summary-box" class="tripal_organism-info-box tripal-info-box">
-  <div  class="tripal_organism-info-box-title tripal-info-box-title">GO Analysis Reports</div>
-  <?php 
-     if($has_results){
-        print $form;
-     } else {
-       ?><div class="tripal-no-results">
-           There are no GO reports available
-           <?php if(user_access('access administration pages')){ ?>
-              <p><br>Administrators, to view a GO report you must:
-              <ul>
-                 <li>load GO assignments and associate them to features and a corresponding analysis</li>
-                 <li>Set the <a href="<?php print url('admin/tripal/tripal_cv/cvtermpath');?>">cvtermpath</a> for the 'biological process', 'molecular_function' and 'cellular_component' vocabularies.</li>
-                 <li>Populate the <a href="<?php print url('admin/tripal/tripal_mviews');?>">go_count_analysis</a> materialized view</li>
-              </ul> </p>
-           <?php }?>
-         </div><?php
-     }
-  ?>
-  <div id="tripal_analysis_go_org_charts"></div>    
-  <div id="tripal_cv_cvterm_info_box">
-      <a href="#" onclick="$('#tripal_cv_cvterm_info_box').hide()" style="float: right">Close [X]</a>
-      <div>Term Information</div>
-      <div id="tripal_cv_cvterm_info"></div>
-   </div>
-   <div id="tripal_ajaxLoading" style="display:none">
-     <div id="loadingText">Loading...</div>
-   </div>
-</div>
-

theme/tripal_subthemes/tripal_analysis_interpro_theme/css/tripal_analysis_interpro.css

@@ -1,44 +0,0 @@
-
-.tripal_interpro-info-box {
-   margin-top: 10px;
-   margin-left: 0px;
-   margin-right: 0px;
-   margin-bottom: 0px;
-   padding-top: 0px;
-   padding-left: 0px;
-   padding-bottom: 0px;
-   padding-right: 0px;
-   border-collapse: collapse;
-   z-index: 10;
-}
-
-.tripal_interpro_results_table {
-   margin-left: auto;
-   margin-right: auto;
-}
-
-.tripal_interpro_results_table tbody {
-    border-top: none;
-}
-
-.tripal_interpro_results_table tbody tr td table{
-   background: #FFFFFF;
-}
-
-.tripal_interpro_results_table tbody tr td table tr{
-   background: #FFFFFF;
-}
-
-.tripal_interpro_results_table tbody tr td table tr td{
-   background: #FFFFFF;
-}
-/* feature node sepcific template */
-.tripal_feature_interpro-results-table {
-   padding-top: 10px;
-   padding-bottom: 10px;
-}
-.tripal_feature-interpro_results_subtitle{
-   padding-top: 10px;
-   padding-bottom: 10px;
-   font-weight: bold;
-}

theme/tripal_subthemes/tripal_analysis_interpro_theme/js/tripal_analysis_interpro.js

@@ -1,29 +0,0 @@
-if (Drupal.jsEnabled) {
-   
-   $(document).ready(function(){
-	   var fontcolor = $(".interpro_results_table tbody tr td table tbody tr td b a").parent().prev().css('color');
-	   // Disable the hyperlink for sequences in the interpro box
-	   $(".tripal_interpro_results_table tbody tr td table tbody tr td b a").removeAttr('href');
-	   $(".tripal_interpro_results_table tbody tr td table tbody tr td b a").css('font-weight','normal');
-	   $(".tripal_interpro_results_table tbody tr td table tbody tr td b a").css('text-decoration','none');
-	   $(".tripal_interpro_results_table tbody tr td table tbody tr td b a").css('color',fontcolor);
-	   
-	   // Allow selection of "Load GO term to the database" only when the submitting job to parse
-	   // html output is enabled
-	   isSubmittingJob ();
-   });
-   
-   // Disable parse GO checkbox if no interpro job is submitted
-   function isSubmittingJob () {
-	   if ($('#edit-interprojob').is(":checked")) {
-		   var fontcolor = $("#edit-parsego").parent().parent().prev().children().css('color');
-		   $("#edit-parsego").attr('disabled', false);
-		   $("#edit-parsego-wrapper").css("color", fontcolor);
-		   
-	   } else {
-		   $("#edit-parsego").attr('checked', false);
-		   $("#edit-parsego").attr('disabled', true);
-		   $("#edit-parsego-wrapper").css("color", "grey");
-	   }
-   }
-}

theme/tripal_subthemes/tripal_analysis_interpro_theme/node-chado_analysis_interpro.tpl.php

@@ -1,100 +0,0 @@
-<?php
-// Purpose: This template provides the layout of the organism node (page)
-//   using the same templates used for the various feature content blocks.
-//
-// To Customize the Featture Node Page:
-//   - This Template: customize basic layout and which elements are included
-//   - Using Panels: Override the node page using Panels3 and place the blocks
-//       of content as you please. This method requires no programming. See
-//       the Tripal User Guide for more details
-//   - Block Templates: customize the content/layout of each block of stock 
-//       content. These templates are found in the tripal_stock subdirectory
-//
-// Variables Available:
-//   - $node: a standard object which contains all the fields associated with
-//       nodes including nid, type, title, taxonomy. It also includes stock
-//       specific fields such as stock_name, uniquename, stock_type, synonyms,
-//       properties, db_references, object_relationships, subject_relationships,
-//       organism, etc.
-//   NOTE: For a full listing of fields available in the node object the
-//       print_r $node line below or install the Drupal Devel module which 
-//       provides an extra tab at the top of the node page labelled Devel
-?>
-
-<?php
- //uncomment this line to see a full listing of the fields avail. to $node
- //print '<pre>'.print_r($variables,TRUE).'</pre>';
-drupal_add_css('./tripal-node-templates.css');
-
-$node = $variables['node'];
-$organism = $variables['node']->organism;
-?>
-
-<?php if ($teaser) { 
-  include('tripal_analysis_interpro/tripal_analysis_interpro_teaser.tpl.php'); 
-} else { ?>
-
-<script type="text/javascript">
-if (Drupal.jsEnabled) {
-   $(document).ready(function() {
-      // hide all tripal info boxes at the start
-      $(".tripal-info-box").hide();
- 
-      // iterate through all of the info boxes and add their titles
-      // to the table of contents
-      $(".tripal-info-box-title").each(function(){
-        var parent = $(this).parent();
-        var id = $(parent).attr('id');
-        var title = $(this).text();
-        $('#tripal_analysis_interpro_toc_list').append('<li><a href="#'+id+'" class="tripal_analysis_interpro_toc_item">'+title+'</a></li>');
-      });
-
-      // when a title in the table of contents is clicked, then
-      // show the corresponding item in the details box
-      $(".tripal_analysis_interpro_toc_item").click(function(){
-         $(".tripal-info-box").hide();
-         href = $(this).attr('href');
-         $(href).fadeIn('slow');
-         // we want to make sure our table of contents and the details
-         // box stay the same height
-         $("#tripal_analysis_interpro_toc").height($(href).parent().height());
-         return false;
-      }); 
-
-      // we want the base details to show up when the page is first shown 
-      // unless the user specified a specific block
-      var block = window.location.href.match(/[\?|\&]block=(.+?)\&/)
-      if(block == null){
-         block = window.location.href.match(/[\?|\&]block=(.+)/)
-      }
-      if(block != null){
-         $("#tripal_analysis_interpro-"+block[1]+"-box").show();
-      } else {
-         $("#tripal_analysis_interpro-base-box").show();
-      }
-
-      $("#tripal_analysis_interpro_toc").height($("#tripal_analysis_interpro-base-box").parent().height());
-      
-   });
-}
-</script>
-
-
-<div id="tripal_analysis_interpro_details" class="tripal_details">
-
-   <!-- Basic Details Theme -->
-   <?php include('tripal_analysis_interpro/tripal_analysis_interpro_base.tpl.php'); ?>
-
-   <?php print $content ?>
-</div>
-
-<!-- Table of contents -->
-<div id="tripal_analysis_interpro_toc" class="tripal_toc">
-   <div id="tripal_analysis_interpro_toc_title" class="tripal_toc_title">Resources</i></div>
-   <span id="tripal_analysis_interpro_toc_desc" class="tripal_toc_desc"></span>
-   <ul id="tripal_analysis_interpro_toc_list" class="tripal_toc_list">
-
-   </ul>
-</div>
-
-<?php } ?>

theme/tripal_subthemes/tripal_analysis_interpro_theme/tripal_analysis_interpro/tripal_analysis_interpro_base.tpl.php

@@ -1,56 +0,0 @@
-<?php
-$node = $variables['node'];
-$analysis = $variables['node']->analysis;
-$interpro = $node->analysis->tripal_analysis_interpro;
-
-// the description is a text field so we want to expand that
-$analysis = tripal_core_expand_chado_vars($analysis,'field','analysis.description');
-?>
-<div id="tripal_analysis_interpro-base-box" class="tripal_analysis_interpro-info-box tripal-info-box">
-  <div class="tripal_analysis_interpro-info-box-title tripal-info-box-title">Details</div>
-   <table id="tripal_analysis_interpro-table-base" class="tripal_analysis_interpro-table tripal-table tripal-table-vert">
-      <tr class="tripal_analysis_interpro-table-even-row tripal-table-even-row">
-        <th>Analysis Name</th>
-        <td><?php print $analysis->name; ?></td>
-      </tr>
-      <tr class="tripal_analysis_interpro-table-odd-row tripal-table-odd-row">
-        <th nowrap>Software</th>
-        <td><?php 
-          print $analysis->program; 
-          if($analysis->programversion){
-             print " (" . $analysis->programversion . ")"; 
-          }
-          if($analysis->algorithm){
-             print ". " . $analysis->algorithm; 
-          }
-          ?>
-        </td>
-      </tr>
-      <tr class="tripal_analysis_interpro-table-even-row tripal-table-even-row">
-        <th nowrap>Source</th>
-        <td><?php 
-          if($analysis->sourceuri){
-             print "<a href=\"$analysis->sourceuri\">$analysis->sourcename</a>"; 
-          } else {
-             print $analysis->sourcename; 
-          }
-          if($analysis->sourceversion){
-             print " (" . $analysis->sourceversion . ")"; 
-          }
-          ?>
-          </td>
-      </tr>
-      <tr class="tripal_analysis_interpro-table-odd-row tripal-table-odd-row">
-        <th nowrap>Date performed</th>
-        <td><?php print preg_replace("/^(\d+-\d+-\d+) .*/","$1",$analysis->timeexecuted); ?></td>
-      </tr>
-      <tr class="tripal_analysis_interpro-table-even-row tripal-table-even-row">
-        <th nowrap>Description</th>
-        <td><?php print $analysis->description; ?></td>
-      </tr>      
-      <tr class="tripal_analysis_interpro-table-odd-row tripal-table-odd-row">
-        <th nowrap>InterProScan Arguments</th>
-        <td><?php print $interpro->interproparameters ?></td>
-      </tr>        	                                
-   </table>   
-</div>

theme/tripal_subthemes/tripal_analysis_interpro_theme/tripal_analysis_interpro/tripal_analysis_interpro_teaser.tpl.php

@@ -1,53 +0,0 @@
-<?php
-$node = $variables['node'];
-$analysis = $variables['node']->analysis;
-
-// the description is a text field so we want to expand that
-$analysis = tripal_core_expand_chado_vars($analysis,'field','analysis.description');
-
-
-?>
-<div id="tripal_analysis-base-box" class="tripal_analysis-info-box tripal-info-box">
-  <div class="tripal_analysis-info-box-title tripal-info-box-title">Details</div>
-   <table id="tripal_analysis-table-base" class="tripal_analysis-table tripal-table tripal-table-vert">
-      <tr class="tripal_analysis-table-odd-row tripal-table-even-row">
-        <th>Analysis Name</th>
-        <td><?php print $analysis->name; ?></td>
-      </tr>
-      <tr class="tripal_analysis-table-odd-row tripal-table-odd-row">
-        <th nowrap>Software</th>
-        <td><?php 
-          print $analysis->program; 
-          if($analysis->programversion){
-             print " (" . $analysis->programversion . ")"; 
-          }
-          if($analysis->algorithm){
-             print ". " . $analysis->algorithm; 
-          }
-          ?>
-        </td>
-      </tr>
-      <tr class="tripal_analysis-table-odd-row tripal-table-even-row">
-        <th nowrap>Source</th>
-        <td><?php 
-          if($analysis->sourceuri){
-             print "<a href=\"$analysis->sourceuri\">$analysis->sourcename</a>"; 
-          } else {
-             print $analysis->sourcename; 
-          }
-          if($analysis->sourceversion){
-             print " (" . $analysis->sourceversion . ")"; 
-          }
-          ?>
-          </td>
-      </tr>
-      <tr class="tripal_analysis-table-odd-row tripal-table-odd-row">
-        <th nowrap>Date performed</th>
-        <td><?php print preg_replace("/^(\d+-\d+-\d+) .*/","$1",$analysis->timeexecuted); ?></td>
-      </tr>
-      <tr class="tripal_analysis-table-odd-row tripal-table-even-row">
-        <th nowrap>Description</th>
-        <td><?php print $analysis->description; ?></td>
-      </tr>             	                                
-   </table>   
-</div>

theme/tripal_subthemes/tripal_analysis_interpro_theme/tripal_analysis_interpro_theme.info

@@ -1,10 +0,0 @@
-name = Tripal Subtheme: Interpro Analysis
-description = A tripal subtheme for tripal analysis interpro module
-version = 6.x-0.3.1b
-core = 6.x
-engine = phptemplate
-base theme = tripal
-
-stylesheets[all][] = css/tripal_analysis_interpro.css
-
-scripts[] = js/tripal_analysis_interpro.js

theme/tripal_subthemes/tripal_analysis_interpro_theme/tripal_feature/tripal_feature_interpro_results.tpl.php

@@ -1,121 +0,0 @@
-<?php
-$feature  = $variables['node']->feature;
-$results = $feature->tripal_analysis_interpro->results->xml;
-$resultsHTML = $feature->tripal_analysis_interpro->results->html;
-
-if(count($results) > 0){ 
-   $i = 0;
-   foreach($results as $analysis_id => $analysisprops){ 
-     $analysis = $analysisprops['analysis'];
-     $protein_ORFs = $analysisprops['protein_ORFs']; 
-     $terms = $analysisprops['allterms']; 
-     ?>
-     <div id="tripal_feature-interpro_results_<?php print $i?>-box" class="tripal_analysis_interpro-box tripal-info-box">
-        <div class="tripal_feature-info-box-title tripal-info-box-title">InterPro Report <?php print preg_replace("/^(\d+-\d+-\d+) .*/","$1",$analysis->timeexecuted); ?></div>
-        <div class="tripal_feature-info-box-desc tripal-info-box-desc"><?php 
-            if($analysis->nid){ ?>
-               Analysis name: <a href="<?php print url('node/'.$analysis->nid) ?>"><?php print $analysis->name?></a><?php
-            } else { ?>
-               Analysis name: <?php print $analysis->name;
-            } ?><br>
-            Date Performed: <?php print preg_replace("/^(\d+-\d+-\d+) .*/","$1",$analysis->timeexecuted); ?>
-        </div>
-
-     <div class="tripal_feature-interpro_results_subtitle">Summary of Annotated IPR terms</div>
-     <table id="tripal_feature-interpro_summary-<?php $i ?>-table" class="tripal_analysis_interpro-summary-table tripal-table tripal-table-horz">
-      <tr>
-        <th>Term</td>
-        <th>Name</td>
-      </tr>
-     <?php 
-     $j=0;
-     foreach($terms as $term){ 
-       $ipr_id = $term[0];
-       $ipr_name = $term[1];
-       $class = 'tripal_feature-table-odd-row tripal-table-odd-row';
-       if($j % 2 == 0 ){
-         $class = 'tripal_feature-table-even-row tripal-table-even-row';
-       }?>
-       <tr class="<?php print $class ?>">
-         <td><?php print $ipr_id ?></td>
-         <td><?php print $ipr_name ?></td>         
-       </tr>
-       <?php
-       $j++;
-     } ?>
-     </table>
-     <br><br>
-     <div class="tripal_feature-interpro_results_subtitle">Analysis Details</div>
-     <table id="tripal_feature-interpro_results-<?php $i ?>-table" class="tripal-table tripal_feature_interpro-results-table tripal-table-horz" style="border-top: 0px; border-bottom: 0px">
-     <?php
-     foreach($protein_ORFs as $orf){  
-        $terms = $orf['terms'];
-        $orf = $orf['orf'];  
-        ?>
-        <?php foreach($terms as $term){ 
-          $matches = $term['matches'];
-          $ipr_id = $term['ipr_id'];
-          $ipr_name = $term['ipr_name'];
-          $ipr_type = $term['ipr_type']; ?>          
-            <tr>
-              <td colspan="4" style="padding-left: 0px">ORF: <?php print $orf['orf_id'] ?>, Length: <?php print $orf['orf_length'] ?> <br>
-                              IPR Term: <?php print "$ipr_id $ipr_name ($ipr_type)"; ?></th>
-            </tr>
-            <tr style="border-top: solid 1px;">
-              <th>Method</th>
-              <th>Identifier</th>
-              <th>Description</th>
-              <th>Matches<sup>*</sup></th>
-            </tr>
-            <?php $j = 0; 
-            foreach ($matches as $match){
-               $match_id = $match['match_id'];
-               $match_name = $match['match_name'];
-               $match_dbname = $match['match_dbname'];
-
-
-               $class = 'tripal_feature-table-odd-row tripal-table-odd-row';
-               if($j % 2 == 0 ){
-                  $class = 'tripal_feature-table-even-row tripal-table-even-row';
-               }?>
-               <tr class="<?php print $class ?>">
-                 <td><?php print $match_dbname ?></td>
-                 <td><?php print $match_id ?></td>
-                 <td><?php print $match_name ?></td>
-                 <td nowrap><?php
-                    $locations = $match['locations'];
-                    foreach($locations as $location){
-                      print $location['match_score']." [".$location['match_start']."-".$location['match_end']."] " . $location['match_status'] ."<br>";
-                      #$match_evidence =  $location['match_evidence'];
-                    } ?>
-                 </td>
-               </tr>
-               <?php
-               $j++;  
-            } // end foreach matches ?>
-            <tr><td colspan="4"><sup>* score [start-end] status</sup></td></tr> <?php
-        } // end foreach terms
-        $i++;
-     } // end foreach orfs ?>
-     </table>
-     </div> <?php
-   } // end for each analysis 
-} // end if
-if($resultsHTML){  ?>
-   <div id="tripal_feature-interpro_results_<?php print $i?>-box" class="tripal_analysis_interpro-box tripal-info-box">
-     <div class="tripal_feature-info-box-title tripal-info-box-title">InterPro Report <?php print preg_replace("/^(\d+-\d+-\d+) .*/","$1",$analysis->timeexecuted); ?></div>
-     <div class="tripal_feature-info-box-desc tripal-info-box-desc"><?php 
-         if($analysis->nid){ ?>
-            Analysis name: <a href="<?php print url('node/'.$analysis->nid) ?>"><?php print $analysis->name?></a><?php
-         } else { ?>
-            Analysis name: <?php print $analysis->name;
-         } ?><br>
-         Date Performed: <?php print preg_replace("/^(\d+-\d+-\d+) .*/","$1",$analysis->timeexecuted); ?>
-     </div>
-
-   <div class="tripal_feature-interpro_results_subtitle">Summary of Annotated IPR terms</div> <?php 
-   print $resultsHTML;?>
-   </div> <?php
-}
-?>
-

theme/tripal_subthemes/tripal_analysis_kegg_theme/css/tripal_analysis_kegg.css

@@ -1,46 +0,0 @@
-/*
- Copyright 2009 Clemson University
-*/
-
-.tripal_kegg-info-box, .tripal_kegg_summary-info-box {
-   margin-top: 10px;
-   margin-left: 0px;
-   margin-right: 0px;
-   margin-bottom: 0px;
-   padding-top: 0px;
-   padding-left: 0px;
-   padding-bottom: 0px;
-   padding-right: 0px;
-   border-collapse: collapse;
-   z-index: 10;
-}
-
-.tripal_kegg_brite_terms {
-   line-height: 170%;
-   text-align: left;
-}
-
-#tripal_kegg_brite_hierarchy {
-   border-collapse: separate;
-}
-
-#tripal_kegg_brite_links {
-   background-image:url("../images/kegg.gif");
-   background-repeat: no-repeat;
-   padding-left:20px;
-}
-
-#tripal_kegg_feature_links {
-   background-image:none;
-   background-repeat: no-repeat;
-   padding:0px 0px 0px 0px;
-}
-
-.tripal_kegg_results_table #tripal_kegg_brite_links {
-   padding: 0px 0px 0px 22px;
-}
-
-#tripal_kegg_brite_results {
-   height: 600px;
-   overflow: auto;   
-}

theme/tripal_subthemes/tripal_analysis_kegg_theme/js/tripal_analysis_kegg.js

@@ -1,162 +0,0 @@
-
-
-if (Drupal.jsEnabled) {
-   $(document).ready(function() {
-
-       // Select default KEGG analysis when available
-       var selectbox = $('#edit-tripal-analysis-kegg-select');
-       if(selectbox.length > 0){ 
-    	   var option = document.getElementById("analysis_id_for_kegg_report");
-    	   if (option) {
-    		   var options = document.getElementsByTagName('option');
-    		   var index = 0;
-    		   for (index = 0; index < options.length; index ++) {
-    			   if (options[index].value == option.value) {
-    				   break;
-    			   }
-    		   }
-    		   selectbox[0].selectedIndex = index;
-    		   var baseurl = tripal_get_base_url();
-    		   tripal_analysis_kegg_org_report(option.value, baseurl);
-    		// Otherwise, show the first option by default
-    	   } else {
-    		   selectbox[0].selectedIndex = 1;
-    		   selectbox.change();
-    	   }
-       }
-
-   });
-
-   //------------------------------------------------------------
-   function tripal_analysis_kegg_org_report(item,baseurl,themedir){
-      if(!item){
-         $("#tripal_analysis_kegg_org_report").html('');
-         return false;
-      }
-      // Form the link for the following ajax call  
-      var link = baseurl + "/";
-      if(!isClean){
-         link += "?q=";
-      }
-      link += 'tripal_analysis_kegg_org_report/' + item;
-
-      tripal_startAjax();
-      $.ajax({
-           url: link,
-           dataType: 'json',
-           type: 'POST',
-           success: function(data){
-             $("#tripal_analysis_kegg_org_report").html(data[0]);
-             $(".tripal_kegg_brite_tree").attr("id", function(){
-                init_kegg_tree($(this).attr("id"));    
-             });
-             tripal_stopAjax();
-           }
-      });
-      return false;
-   }
-   
-   //------------------------------------------------------------
-   // Update the BRITE hierarchy based on the user selection
-   function tripal_update_brite(link,type_id){
-      tripal_startAjax();
-      $.ajax({
-         url: link.href,
-         dataType: 'json',
-         type: 'POST',
-         success: function(data){
-            $("#tripal_kegg_brite_hierarchy").html(data.update);
-            $("#tripal_kegg_brite_header").html(data.brite_term);
-            tripal_stopAjax();
-            init_kegg_tree(data.id);
-         }
-      });
-      return false;
-   }
-
-   //------------------------------------------------------------
-   // This function initializes a KEGG term tree
-   function init_kegg_tree(id){
-
-      // Form the link for the following ajax call
-      var theme_path = baseurl + '/' + themedir + "/js/jsTree/source/themes/";
-	   
-      $("#" + id).tree ({
-	    data    : {
-	        type    : "predefined", // ENUM [json, xml_flat, xml_nested, predefined]
-	        method  : "GET",        // HOW TO REQUEST FILES
-	        async   : false,        // BOOL - async loading onopen
-	        async_data : function (NODE) { return { id : $(NODE).attr("id") || 0 } }, // PARAMETERS PASSED TO SERVER
-	        url     : false,        // FALSE or STRING - url to document to be used (async or not)
-	        json    : false,        // FALSE or OBJECT if type is JSON and async is false - the tree dump as json
-	        xml     : false         // FALSE or STRING
-	    },
-        ui      : {
-           dots        : true,     // BOOL - dots or no dots
-           rtl         : false,    // BOOL - is the tree right-to-left
-           animation   : 0,        // INT - duration of open/close animations in miliseconds
-           hover_mode  : true,     // SHOULD get_* functions chage focus or change hovered item
-           scroll_spd  : 4,
-           theme_path  : theme_path,    // Path to themes
-           theme_name  : "classic",// Name of theme
-        },
-
-        rules   : {
-           multiple    : false,    // FALSE | CTRL | ON - multiple selection off/ with or without holding Ctrl
-           metadata    : false,    // FALSE or STRING - attribute name (use metadata plugin)
-           type_attr   : "rel",    // STRING attribute name (where is the type stored if no metadata)
-           multitree   : false,    // BOOL - is drag n drop between trees allowed
-           createat    : "bottom", // STRING (top or bottom) new nodes get inserted at top or bottom
-           use_inline  : false,    // CHECK FOR INLINE RULES - REQUIRES METADATA
-           clickable   : "all",    // which node types can the user select | default - all
-           renameable  : false,    // which node types can the user select | default - all
-           deletable   : false,    // which node types can the user delete | default - all
-           creatable   : false,    // which node types can the user create in | default - all
-           draggable   : "none",   // which node types can the user move | default - none | "all"
-           dragrules   : "all",    // what move operations between nodes are allowed | default - none | "all"
-           drag_copy   : false,    // FALSE | CTRL | ON - drag to copy off/ with or without holding Ctrl
-           droppable   : [],
-           drag_button : "left"
-        },
-
-        callback    : {             // various callbacks to attach custom logic to
-           // before focus  - should return true | false
-           beforechange: function(NODE,TREE_OBJ) { return true },
-           beforeopen  : function(NODE,TREE_OBJ) { return true },
-           beforeclose : function(NODE,TREE_OBJ) { return true },
-           // before move   - should return true | false
-           beforemove  : function(NODE,REF_NODE,TYPE,TREE_OBJ) { return true }, 
-           // before create - should return true | false
-           beforecreate: function(NODE,REF_NODE,TYPE,TREE_OBJ) { return true }, 
-           // before rename - should return true | false
-           beforerename: function(NODE,LANG,TREE_OBJ) { return true }, 
-           // before delete - should return true | false
-           beforedelete: function(NODE,TREE_OBJ) { return true }, 
-
-           onJSONdata  : function(DATA,TREE_OBJ) { return DATA; },
-           onselect    : function(NODE,TREE_OBJ) {        	   
-               window.onerror = function(){return true;};
-        	   throw 'exit';
-        	},                  // node selected
-           ondeselect  : function(NODE,TREE_OBJ) { },                  // node deselected
-           onchange    : function(NODE,TREE_OBJ) { },                  // focus changed
-           onrename    : function(NODE,LANG,TREE_OBJ,RB) { },              // node renamed ISNEW - TRUE|FALSE, current language
-           onmove      : function(NODE,REF_NODE,TYPE,TREE_OBJ,RB) { }, // move completed (TYPE is BELOW|ABOVE|INSIDE)
-           oncopy      : function(NODE,REF_NODE,TYPE,TREE_OBJ,RB) { }, // copy completed (TYPE is BELOW|ABOVE|INSIDE)
-           oncreate    : function(NODE,REF_NODE,TYPE,TREE_OBJ,RB) { }, // node created, parent node (TYPE is createat)
-           ondelete    : function(NODE, TREE_OBJ,RB) { },                  // node deleted
-           onopen      : function(NODE, TREE_OBJ) { },                 // node opened
-           onopen_all  : function(TREE_OBJ) { },                       // all nodes opened
-           onclose     : function(NODE, TREE_OBJ) { },                 // node closed
-           error       : function(TEXT, TREE_OBJ) { },                 // error occured
-           // double click on node - defaults to open/close & select
-           ondblclk    : function(NODE, TREE_OBJ) { TREE_OBJ.toggle_branch.call(TREE_OBJ, NODE); TREE_OBJ.select_branch.call(TREE_OBJ, NODE); },
-           // right click - to prevent use: EV.preventDefault(); EV.stopPropagation(); return false
-           onrgtclk    : function(NODE, TREE_OBJ, EV) { },
-           onload      : function(TREE_OBJ) { },
-           onfocus     : function(TREE_OBJ) { },
-           ondrop      : function(NODE,REF_NODE,TYPE,TREE_OBJ) {}
-        }
-      });
-   }
-}

theme/tripal_subthemes/tripal_analysis_kegg_theme/node-chado_analysis_kegg.tpl.php

@@ -1,101 +0,0 @@
-<?php
-// Purpose: This template provides the layout of the organism node (page)
-//   using the same templates used for the various feature content blocks.
-//
-// To Customize the Featture Node Page:
-//   - This Template: customize basic layout and which elements are included
-//   - Using Panels: Override the node page using Panels3 and place the blocks
-//       of content as you please. This method requires no programming. See
-//       the Tripal User Guide for more details
-//   - Block Templates: customize the content/layout of each block of stock 
-//       content. These templates are found in the tripal_stock subdirectory
-//
-// Variables Available:
-//   - $node: a standard object which contains all the fields associated with
-//       nodes including nid, type, title, taxonomy. It also includes stock
-//       specific fields such as stock_name, uniquename, stock_type, synonyms,
-//       properties, db_references, object_relationships, subject_relationships,
-//       organism, etc.
-//   NOTE: For a full listing of fields available in the node object the
-//       print_r $node line below or install the Drupal Devel module which 
-//       provides an extra tab at the top of the node page labelled Devel
-?>
-
-<?php
- //uncomment this line to see a full listing of the fields avail. to $node
- //print '<pre>'.print_r($variables,TRUE).'</pre>';
-drupal_add_css('./tripal-node-templates.css');
-$node = $variables['node'];
-$organism = $variables['node']->organism;
-?>
-
-<?php if ($teaser) { 
-  include('tripal_analysis_kegg/tripal_analysis_kegg_teaser.tpl.php'); 
-} else { ?>
-
-<script type="text/javascript">
-if (Drupal.jsEnabled) {
-   $(document).ready(function() {
-      // hide all tripal info boxes at the start
-      $(".tripal-info-box").hide();
- 
-      // iterate through all of the info boxes and add their titles
-      // to the table of contents
-      $(".tripal-info-box-title").each(function(){
-        var parent = $(this).parent();
-        var id = $(parent).attr('id');
-        var title = $(this).text();
-        $('#tripal_analysis_kegg_toc_list').append('<li><a href="#'+id+'" class="tripal_analysis_kegg_toc_item">'+title+'</a></li>');
-      });
-
-      // when a title in the table of contents is clicked, then
-      // show the corresponding item in the details box
-      $(".tripal_analysis_kegg_toc_item").click(function(){
-         $(".tripal-info-box").hide();
-         href = $(this).attr('href');
-         $(href).fadeIn('slow');
-         // we want to make sure our table of contents and the details
-         // box stay the same height
-         $("#tripal_analysis_kegg_toc").height($(href).parent().height());
-         return false;
-      }); 
-
-      // we want the base details to show up when the page is first shown 
-      // unless the user specified a specific block
-      var block = window.location.href.match(/[\?|\&]block=(.+?)\&/)
-      if(block == null){
-         block = window.location.href.match(/[\?|\&]block=(.+)/)
-      }
-      if(block != null){
-         $("#tripal_analysis_kegg-"+block[1]+"-box").show();
-      } else {
-         $("#tripal_analysis_kegg-base-box").show();
-      }
-      
-      // make the height of the table of contents match the height of the details box
-      $("#tripal_analysis_kegg_toc").height($("#tripal_analysis_kegg-base-box").parent().height());
-      
-   });
-}
-</script>
-
-
-<div id="tripal_analysis_kegg_details" class="tripal_details">
-
-   <!-- Basic Details Theme -->
-   <?php include('tripal_analysis_kegg/tripal_analysis_kegg_base.tpl.php'); ?>
-   <?php include('tripal_analysis_kegg/tripal_analysis_kegg_report.tpl.php'); ?>
-
-   <?php print $content ?>
-</div>
-
-<!-- Table of contents -->
-<div id="tripal_analysis_kegg_toc" class="tripal_toc">
-   <div id="tripal_analysis_kegg_toc_title" class="tripal_toc_title">Resources</i></div>
-   <span id="tripal_analysis_kegg_toc_desc" class="tripal_toc_desc"></span>
-   <ul id="tripal_analysis_kegg_toc_list" class="tripal_toc_list">
-
-   </ul>
-</div>
-
-<?php } ?>

theme/tripal_subthemes/tripal_analysis_kegg_theme/tripal_analysis_kegg/tripal_analysis_kegg_base.tpl.php

@@ -1,53 +0,0 @@
-<?php
-$node = $variables['node'];
-$analysis = $variables['node']->analysis;
-
-// the description is a text field so we want to expand that
-$analysis = tripal_core_expand_chado_vars($analysis,'field','analysis.description');
-
-
-?>
-<div id="tripal_analysis_kegg-base-box" class="tripal_analysis_kegg-info-box tripal-info-box">
-  <div class="tripal_analysis_kegg-info-box-title tripal-info-box-title">KEGG Analysis Details</div>
-   <table id="tripal_analysis_kegg-table-base" class="tripal_analysis_kegg-table tripal-table tripal-table-vert">
-      <tr class="tripal_analysis_kegg-table-odd-row tripal-table-even-row">
-        <th>Analysis Name</th>
-        <td><?php print $analysis->name; ?></td>
-      </tr>
-      <tr class="tripal_analysis_kegg-table-odd-row tripal-table-odd-row">
-        <th nowrap>Software</th>
-        <td><?php 
-          print $analysis->program; 
-          if($analysis->programversion){
-             print " (" . $analysis->programversion . ")"; 
-          }
-          if($analysis->algorithm){
-             print ". " . $analysis->algorithm; 
-          }
-          ?>
-        </td>
-      </tr>
-      <tr class="tripal_analysis_kegg-table-odd-row tripal-table-even-row">
-        <th nowrap>Source</th>
-        <td><?php 
-          if($analysis->sourceuri){
-             print "<a href=\"$analysis->sourceuri\">$analysis->sourcename</a>"; 
-          } else {
-             print $analysis->sourcename; 
-          }
-          if($analysis->sourceversion){
-             print " (" . $analysis->sourceversion . ")"; 
-          }
-          ?>
-          </td>
-      </tr>
-      <tr class="tripal_analysis_kegg-table-odd-row tripal-table-odd-row">
-        <th nowrap>Date performed</th>
-        <td><?php print preg_replace("/^(\d+-\d+-\d+) .*/","$1",$analysis->timeexecuted); ?></td>
-      </tr>
-      <tr class="tripal_analysis_kegg-table-odd-row tripal-table-even-row">
-        <th nowrap>Description</th>
-        <td><?php print $analysis->description; ?></td>
-      </tr>             	                                
-   </table>   
-</div>

theme/tripal_subthemes/tripal_analysis_kegg_theme/tripal_analysis_kegg/tripal_analysis_kegg_report.tpl.php

@@ -1,11 +0,0 @@
-<?php
-$analysis = $node->analysis;
-$report = $analysis->tripal_analysis_kegg->kegg_report;
-//dpm($analysis);
-?>
-
-<div id="tripal_analysis_kegg-report-box" class="tripal_analysis_kegg-box tripal-info-box">
-  <div class="tripal_analysis_kegg-info-box-title tripal-info-box-title">KEGG Report</div>
-  <div class="tripal_analysis_kegg-info-box-desc tripal-info-box-desc"><?php print $analysis->name ?></div>
-  <?php print $report ?>
-</div>

theme/tripal_subthemes/tripal_analysis_kegg_theme/tripal_analysis_kegg/tripal_analysis_kegg_teaser.tpl.php

@@ -1,53 +0,0 @@
-<?php
-$node = $variables['node'];
-$analysis = $variables['node']->analysis;
-
-// the description is a text field so we want to expand that
-$analysis = tripal_core_expand_chado_vars($analysis,'field','analysis.description');
-
-
-?>
-<div id="tripal_analysis-base-box" class="tripal_analysis-info-box tripal-info-box">
-  <div class="tripal_analysis-info-box-title tripal-info-box-title">Details</div>
-   <table id="tripal_analysis-table-base" class="tripal_analysis-table tripal-table tripal-table-vert">
-      <tr class="tripal_analysis-table-odd-row tripal-table-even-row">
-        <th>Analysis Name</th>
-        <td><?php print $analysis->name; ?></td>
-      </tr>
-      <tr class="tripal_analysis-table-odd-row tripal-table-odd-row">
-        <th nowrap>Software</th>
-        <td><?php 
-          print $analysis->program; 
-          if($analysis->programversion){
-             print " (" . $analysis->programversion . ")"; 
-          }
-          if($analysis->algorithm){
-             print ". " . $analysis->algorithm; 
-          }
-          ?>
-        </td>
-      </tr>
-      <tr class="tripal_analysis-table-odd-row tripal-table-even-row">
-        <th nowrap>Source</th>
-        <td><?php 
-          if($analysis->sourceuri){
-             print "<a href=\"$analysis->sourceuri\">$analysis->sourcename</a>"; 
-          } else {
-             print $analysis->sourcename; 
-          }
-          if($analysis->sourceversion){
-             print " (" . $analysis->sourceversion . ")"; 
-          }
-          ?>
-          </td>
-      </tr>
-      <tr class="tripal_analysis-table-odd-row tripal-table-odd-row">
-        <th nowrap>Date performed</th>
-        <td><?php print preg_replace("/^(\d+-\d+-\d+) .*/","$1",$analysis->timeexecuted); ?></td>
-      </tr>
-      <tr class="tripal_analysis-table-odd-row tripal-table-even-row">
-        <th nowrap>Description</th>
-        <td><?php print $analysis->description; ?></td>
-      </tr>             	                                
-   </table>   
-</div>

theme/tripal_subthemes/tripal_analysis_kegg_theme/tripal_analysis_kegg_theme.info

@@ -1,10 +0,0 @@
-name = Tripal Subtheme: Kegg Analysis
-description = A tripal subtheme for tripal analysis kegg module
-version = 6.x-0.3.1b
-core = 6.x
-engine = phptemplate
-base theme = tripal
-
-stylesheets[all][] = css/tripal_analysis_kegg.css
-
-scripts[] = js/tripal_analysis_kegg.js

theme/tripal_subthemes/tripal_analysis_kegg_theme/tripal_feature/tripal_feature_kegg_terms.tpl.php

@@ -1,46 +0,0 @@
-<?php
-
-$feature  = $variables['node']->feature;
-$results = $feature->tripal_analysis_kegg->results;
-
-if($feature->cvname != 'gene' and count($results) > 0){ 
-   $i = 0;
-   foreach($results as $analysis_id => $analysisprops){ 
-     $analysis = $analysisprops['analysis'];
-     $terms = $analysisprops['terms']; 
-     ?>
-     <div id="tripal_feature-kegg_results_<?php print $i?>-box" class="tripal_analysis_kegg-box tripal-info-box">
-        <div class="tripal_feature-info-box-title tripal-info-box-title">KEGG Report <?php print preg_replace("/^(\d+-\d+-\d+) .*/","$1",$analysis->timeexecuted); ?></div>
-        <div class="tripal_feature-info-box-desc tripal-info-box-desc"><?php 
-            if($analysis->nid){ ?>
-               Analysis name: <a href="<?php print url('node/'.$analysis->nid) ?>"><?php print $analysis->name?></a><?php
-            } else { ?>
-               Analysis name: <?php print $analysis->name;
-            } ?><br>
-            Date Performed: <?php print preg_replace("/^(\d+-\d+-\d+) .*/","$1",$analysis->timeexecuted); ?>
-        </div>
-
-     <div class="tripal_feature-kegg_results_subtitle">Annotated Terms</div>
-     <table id="tripal_feature-kegg_summary-<?php $i ?>-table" class="tripal_analysis_kegg-summary-table tripal-table tripal-table-horz">
-     <?php 
-     $j=0;
-     foreach($terms as $term){ 
-       $ipr_id = $term[0];
-       $ipr_name = $term[1];
-       $class = 'tripal_feature-table-odd-row tripal-table-odd-row';
-       if($j % 2 == 0 ){
-         $class = 'tripal_feature-table-even-row tripal-table-even-row';
-       }?>
-       <tr class="<?php print $class ?>">
-         <td><?php print $term ?></td>
-       </tr>
-       <?php
-       $j++;
-     } ?>
-     </table>     
-     </div> <?php
-     $i++;
-   } // end for each analysis 
-} // end if
-?>
-

theme/tripal_subthemes/tripal_analysis_kegg_theme/tripal_organism/tripal_organism_kegg_summary.tpl.php

@@ -1,22 +0,0 @@
-<?php
-  $organism = $node->organism;
-  $form = $organism->tripal_analysis_kegg->select_form['form'];
-  $has_results = $organism->tripal_analysis_kegg->select_form['has_results'];
-?>
-<div id="tripal_organism-kegg_summary-box" class="tripal_organism-info-box tripal-info-box">
-  <div  class="tripal_organism-info-box-title tripal-info-box-title">KEGG Analysis Reports</div>
-  <?php 
-     if($has_results){
-        print $form;
-     } else {
-       ?><div class="tripal-no-results">There are no KEGG reports available</div><?php
-     }
-  ?>
-   <div id="tripal_analysis_kegg_org_report"></div>
-   <div id="tripal_ajaxLoading" style="display:none">
-     <div id="loadingText">Loading...</div>
-   </div>   
-</div>
-
-
-

theme/tripal_subthemes/tripal_analysis_unigene_theme/css/tripal_analysis_unigene.css

@@ -1,16 +0,0 @@
-/*
- Copyright 2009 Clemson University
-*/
-
-.tripal_unigene-info-box {
-   margin-top: 10px;
-   margin-left: 0px;
-   margin-right: 0px;
-   margin-bottom: 0px;
-   padding-top: 0px;
-   padding-left: 0px;
-   padding-bottom: 0px;
-   padding-right: 0px;
-   border-collapse: collapse;
-   z-index: 10;
-}

theme/tripal_subthemes/tripal_analysis_unigene_theme/node-chado_analysis_unigene.tpl.php

@@ -1,103 +0,0 @@
-<?php
-// Purpose: This template provides the layout of the organism node (page)
-//   using the same templates used for the various feature content blocks.
-//
-// To Customize the Featture Node Page:
-//   - This Template: customize basic layout and which elements are included
-//   - Using Panels: Override the node page using Panels3 and place the blocks
-//       of content as you please. This method requires no programming. See
-//       the Tripal User Guide for more details
-//   - Block Templates: customize the content/layout of each block of stock 
-//       content. These templates are found in the tripal_stock subdirectory
-//
-// Variables Available:
-//   - $node: a standard object which contains all the fields associated with
-//       nodes including nid, type, title, taxonomy. It also includes stock
-//       specific fields such as stock_name, uniquename, stock_type, synonyms,
-//       properties, db_references, object_relationships, subject_relationships,
-//       organism, etc.
-//   NOTE: For a full listing of fields available in the node object the
-//       print_r $node line below or install the Drupal Devel module which 
-//       provides an extra tab at the top of the node page labelled Devel
-?>
-
-<?php
- //uncomment this line to see a full listing of the fields avail. to $node
-// print '<pre>'.print_r($node,TRUE).'</pre>';
-drupal_add_css('./tripal-node-templates.css');
-$node = $variables['node'];
-$analysis = $variables['node']->analysis;
-$unigene_name = $analysis->tripal_analysis_unigene->unigene_name;
-
-//dpm($analysis);
-
-// get the unigene name from the properties list
-
-
-?>
-
-<?php if ($teaser) { 
-  include('tripal_analysis_unigene/tripal_analysis_unigene_teaser.tpl.php'); 
-} else { ?>
-
-<script type="text/javascript">
-if (Drupal.jsEnabled) {
-   $(document).ready(function() {
-      // hide all tripal info boxes at the start
-      $(".tripal-info-box").hide();
- 
-      // iterate through all of the info boxes and add their titles
-      // to the table of contents
-      $(".tripal-info-box-title").each(function(){
-        var parent = $(this).parent();
-        var id = $(parent).attr('id');
-        var title = $(this).text();
-        $('#tripal_analysis_unigene_toc_list').append('<li><a href="#'+id+'" class="tripal_analysis_unigene_toc_item">'+title+'</a></li>');
-      });
-
-      // when a title in the table of contents is clicked, then
-      // show the corresponding item in the details box
-      $(".tripal_analysis_unigene_toc_item").click(function(){
-         $(".tripal-info-box").hide();
-         href = $(this).attr('href');
-         $(href).fadeIn('slow');
-         // we want to make sure our table of contents and the details
-         // box stay the same height
-         $("#tripal_analysis_unigene_toc").height($(href).parent().height());
-         return false;
-      }); 
-
-      // we want the base details to show up when the page is first shown 
-      // unless the user specified a specific block
-      var block = window.location.href.match(/[\?|\&]block=(.+?)\&/)
-      if(block == null){
-         block = window.location.href.match(/[\?|\&]block=(.+)/)
-      }
-      if(block != null){
-         $("#tripal_analysis_unigene-"+block[1]+"-box").show();
-      } else {
-         $("#tripal_analysis_unigene-base-box").show();
-      }
-      $("#tripal_analysis_unigene_toc").height($("#tripal_analysis_unigene-base-box").parent().height());
-   });
-}
-</script>
-
-<div id="tripal_analysis_unigene_details" class="tripal_details">
-
-   <!-- Basic Details Theme -->
-   <?php include('tripal_analysis_unigene/tripal_analysis_unigene_base.tpl.php'); ?>
-
-   <?php print $content ?>
-</div>
-
-<!-- Table of contents -->
-<div id="tripal_analysis_unigene_toc" class="tripal_toc">
-   <div id="tripal_analysis_unigene_toc_title" class="tripal_toc_title">Resources</div>
-   <span id="tripal_analysis_unigene_toc_desc" class="tripal_toc_desc"></span>
-   <ul id="tripal_analysis_unigene_toc_list" class="tripal_toc_list">
-
-   </ul>
-</div>
-
-<?php } ?>

theme/tripal_subthemes/tripal_analysis_unigene_theme/tripal_analysis_unigene/tripal_analysis_unigene_base.tpl.php

@@ -1,86 +0,0 @@
-<?php
-$node = $variables['node'];
-$analysis = $variables['node']->analysis;
-
-// the description is a text field so we want to expand that
-$analysis = tripal_core_expand_chado_vars($analysis,'field','analysis.description');
-
-$unigene = $node->analysis->tripal_analysis_unigene;
-//dpm($node);
-
-?>
-<div id="tripal_analysis_unigene-base-box" class="tripal_analysis_unigene-info-box tripal-info-box">
-  <div class="tripal_analysis_unigene-info-box-title tripal-info-box-title">Unigene Details</div>
-  <div class="tripal_analysis_unigene-info-box-desc tripal-info-box-desc"></div>
-   <table id="tripal_analysis_unigene-table-base" class="tripal_analysis_unigene-table tripal-table tripal-table-vert">
-      <tr class="tripal_analysis_unigene-table-even-row tripal-table-even-row">
-        <th>Analysis Name</th>
-        <td><?php print $analysis->name; ?></td>
-      </tr>
-      <tr class="tripal_analysis_unigene-table-odd-row tripal-table-odd-row">
-        <th>Unigene Name</th>
-        <td><?php print $unigene->unigene_name; ?></td>
-      </tr>
-      <tr class="tripal_analysis_unigene-table-even-row tripal-table-even-row">
-        <th nowrap>Software</th>
-        <td><?php 
-          print $analysis->program; 
-          if($analysis->programversion){
-             print " (" . $analysis->programversion . ")"; 
-          }
-          if($analysis->algorithm){
-             print ". " . $analysis->algorithm; 
-          }
-          ?>
-        </td>
-      </tr>
-      <tr class="tripal_analysis_unigene-table-odd-row tripal-table-odd-row">
-        <th nowrap>Source</th>
-        <td><?php 
-          if($analysis->sourceuri){
-             print "<a href=\"$analysis->sourceuri\">$analysis->sourcename</a>"; 
-          } else {
-             print $analysis->sourcename; 
-          }
-          if($analysis->sourceversion){
-             print " (" . $analysis->sourceversion . ")"; 
-          }
-          ?>
-          </td>
-      </tr>
-      <tr class="tripal_analysis_unigene-table-even-row tripal-table-even-row">
-        <th nowrap>Date constructed</th>
-        <td><?php print preg_replace("/^(\d+-\d+-\d+) .*/","$1",$analysis->timeexecuted); ?></td>
-      </tr>
-      <tr class="tripal_analysis_unigene-table-odd-row tripal-table-odd-row">
-        <th nowrap>Description</th>
-        <td><?php print $analysis->description; ?></td>
-      </tr> 
-      <tr class="tripal_analysis_unigene-table-even-row tripal-table-even-row">
-        <th nowrap>Stats</th>
-        <td>
-             <?php if($unigene->num_reads){print "Number of reads: $unigene->num_reads<br>";} ?>
-             <?php if($unigene->num_clusters){print "Number of clusters: $unigene->num_clusters<br>";} ?>
-             <?php if($unigene->num_contigs){print "Number of contigs: $unigene->num_contigs<br>";} ?>
-             <?php if($unigene->num_singlets){print "Number of singlets: $unigene->num_singlets<br>";} ?>
-        </td>
-      </tr>  
-      <tr class="tripal_analysis_unigene-table-odd-row tripal-table-odd-row">
-        <th>Organisms</th>
-        <td><?php 
-            if($unigene->organisms and is_array($unigene->organisms)){
-               foreach($unigene->organisms as $organism){
-                  if($organism->nid){
-                     print "<i><a href=\"".url("node/$organism->nid")."\">$organism->genus $organism->species</i></a><br>";
-                  } else {
-                     print "<i>$organism->genus $organism->species</i><br>";
-                  }
-               }
-            } else {
-                // add message here with instructions for administrators to make this work.
-            }
-            ?>
-        </td>
-      </tr>       	                                
-   </table>   
-</div>

theme/tripal_subthemes/tripal_analysis_unigene_theme/tripal_analysis_unigene/tripal_analysis_unigene_teaser.tpl.php

@@ -1,53 +0,0 @@
-<?php
-$node = $variables['node'];
-$analysis = $variables['node']->analysis;
-
-// the description is a text field so we want to expand that
-$analysis = tripal_core_expand_chado_vars($analysis,'field','analysis.description');
-
-
-?>
-<div id="tripal_analysis-base-box" class="tripal_analysis-info-box tripal-info-box">
-  <div class="tripal_analysis-info-box-title tripal-info-box-title">Details</div>
-   <table id="tripal_analysis-table-base" class="tripal_analysis-table tripal-table tripal-table-vert">
-      <tr class="tripal_analysis-table-odd-row tripal-table-even-row">
-        <th>Analysis Name</th>
-        <td><?php print $analysis->name; ?></td>
-      </tr>
-      <tr class="tripal_analysis-table-odd-row tripal-table-odd-row">
-        <th nowrap>Software</th>
-        <td><?php 
-          print $analysis->program; 
-          if($analysis->programversion){
-             print " (" . $analysis->programversion . ")"; 
-          }
-          if($analysis->algorithm){
-             print ". " . $analysis->algorithm; 
-          }
-          ?>
-        </td>
-      </tr>
-      <tr class="tripal_analysis-table-odd-row tripal-table-even-row">
-        <th nowrap>Source</th>
-        <td><?php 
-          if($analysis->sourceuri){
-             print "<a href=\"$analysis->sourceuri\">$analysis->sourcename</a>"; 
-          } else {
-             print $analysis->sourcename; 
-          }
-          if($analysis->sourceversion){
-             print " (" . $analysis->sourceversion . ")"; 
-          }
-          ?>
-          </td>
-      </tr>
-      <tr class="tripal_analysis-table-odd-row tripal-table-odd-row">
-        <th nowrap>Date performed</th>
-        <td><?php print preg_replace("/^(\d+-\d+-\d+) .*/","$1",$analysis->timeexecuted); ?></td>
-      </tr>
-      <tr class="tripal_analysis-table-odd-row tripal-table-even-row">
-        <th nowrap>Description</th>
-        <td><?php print $analysis->description; ?></td>
-      </tr>             	                                
-   </table>   
-</div>

theme/tripal_subthemes/tripal_analysis_unigene_theme/tripal_analysis_unigene_theme.info

@@ -1,10 +0,0 @@
-name = Tripal Subtheme: Unigene Analysis
-description = A tripal subtheme for tripal analysis unigene module
-version = 6.x-0.3.1b
-core = 6.x
-engine = phptemplate
-base theme = tripal
-
-stylesheets[all][] = css/tripal_analysis_unigene.css
-
-scripts[] = js/tripal_analysis_unigene.js

theme/tripal_subthemes/tripal_analysis_unigene_theme/tripal_feature/tripal_feature_unigenes.tpl.php

@@ -1,61 +0,0 @@
-<?php
-$node = $variables['node'];
-$feature = $node->feature;
-$unigenes = $feature->tripal_analysis_unigene->unigenes;
-
-// if this feature has a unigene then we want to show the box
-if($unigenes){
-  //dpm($unigenes);
-?>
-<div id="tripal_feature-unigenes-box" class="tripal_feature-info-box tripal-info-box">
-  <div class="tripal_feature-info-box-title tripal-info-box-title">Unigenes</div>
-  <div class="tripal_feature-info-box-desc tripal-info-box-desc">This <?php print $feature->type_id->name ?> is part of the following unigenes:</div>
-  <?php if(count($unigenes) > 0){ ?>
-  <table id="tripal_feature-unigenes-table" class="tripal_feature-table tripal-table tripal-table-horz">
-    <tr>
-      <th>Unigene Name</th>
-      <th>Analysis Name</th>
-      <th>Sequence type in Unigene</th>
-    </tr>
-    <?php
-    $i = 0; 
-    foreach ($unigenes as $unigene){
-      $class = 'tripal-table-odd-row';
-      if($i % 2 == 0 ){
-         $class = 'tripal-table-even-row';
-      }
-      ?>
-      <tr class="<?php print $class ?>">
-        <td><?php 
-           if($unigene->nid){
-              print "<a href=\"".url("node/$unigene->nid")."\">$unigene->unigene_name</a>";
-           } else {
-              print $unigene->unigene_name;
-           }?>
-        </td>
-        <td><?php 
-           if($analysis->nid){
-              print "<a href=\"".url("node/$analysis->nid")."\">$analysis->name</a>";
-           } else {
-              print $analysis->name;
-           }?>
-        </td>
-        <td nowrap><?php 
-           if($unigene->singlet){
-              print "Singlet";
-           } else {
-              print $feature->type_id->name;
-           }?>
-        </td>
-      </tr>
-      <?php
-      $i++;  
-    } ?>
-  </table>
-  <?php } else { ?>
-    <div class="tripal-no-results">There are no unigenes for this feature</div> 
-  <?php }?>
-</div>
-<?php 
-}
-?>

theme/tripal_subthemes/tripal_analysis_unigene_theme/tripal_organism/tripal_organism_unigenes.tpl.php

@@ -1,52 +0,0 @@
-<?php
-$node = $variables['node'];
-$organism = $node->organism;
-$unigenes = $organism->tripal_analysis_unigene->unigenes;
-
-//dpm($unigenes);
-?>
-<div id="tripal_organism-unigenes-box" class="tripal_feature-info-box tripal-info-box">
-  <div class="tripal_feature-info-box-title tripal-info-box-title">Unigenes</div>
-  <div class="tripal_feature-info-box-desc tripal-info-box-desc">Below is a list of unigenes available for <i><?php print $organism->genus ?> <?php print $organism->species ?></i>. Click the unigene name for further details.</div>
-  <?php if(count($unigenes) > 0){ ?>
-  <table id="tripal_organism-unigenes-table" class="tripal_feature-table tripal-table tripal-table-horz">
-    <tr>
-      <th>Unigene Name</th>
-      <th>Analysis Name</th>
-      <th>Date Constructed</th>
-      <th>Stats</th>
-    </tr>
-    <?php
-    $i = 0; 
-    foreach ($unigenes as $unigene){
-      $class = 'tripal-table-odd-row';
-      if($i % 2 == 0 ){
-         $class = 'tripal-table-even-row';
-      }
-      ?>
-      <tr class="<?php print $class ?>">
-        <td>
-           <?php 
-           if($unigene->nid){
-              print "<a href=\"".url("node/$unigene->nid")."\">$unigene->unigene_name</a>";
-           } else {
-              print $unigene->unigene_name;
-           }?>
-        </td>
-        <td><?php print $unigene->name; ?></td>
-        <td><?php print preg_replace("/^(\d+-\d+-\d+) .*/","$1",$unigene->timeexecuted); ?></td>
-        <td nowrap>
-             <?php if($unigene->num_reads){print "Reads: $unigene->num_reads<br>";} ?>
-             <?php if($unigene->num_clusters){print "Clusters: $unigene->num_clusters<br>";} ?>
-             <?php if($unigene->num_contigs){print "Contigs: $unigene->num_contigs<br>";} ?>
-             <?php if($unigene->num_singlets){print "Singlets: $unigene->num_singlets<br>";} ?>
-        </td>
-      </tr>
-      <?php
-      $i++;  
-    } ?>
-  </table>
-  <?php } else { ?>
-    <div class="tripal-no-results">There are no unigenes for this organism</div> 
-  <?php }?>
-</div>

theme/tripal_subthemes/tripal_bulk_loader_theme/node-tripal_bulk_loader.tpl.php

@@ -1,60 +0,0 @@
-
-<div id="tripal_bulk_loader-base-box" class="tripal_bulk_loader-info-box tripal-info-box">
-  <div class="tripal_bulk_loader-info-box-title tripal-info-box-title">
-  	<?php if ($teaser) { print l($node->title, 'node/'.$node->nid); } ?>
-  </div>
-  <div class="tripal_bulk_loader-info-box-desc tripal-info-box-desc"></div>
-  
-	<table id="tripal_bulk_loader-base-table" class="tripal_bulk_loader-table tripal-table tripal-table-vert">
-		<tr class="tripal_bulk_loader-table-odd-row tripal-table-odd-row">
-			<th>Job Name</th>
-			<td><?php print $node->loader_name;?></td>
-		</tr>
-		<tr class="tripal_bulk_loader-table-even-row tripal-table-even-row">
-			<th>Submitted By</th>
-			<td><span class="author"><?php print theme('username', $node); ?></span></td>
-		</tr>
-		<tr class="tripal_bulk_loader-table-odd-row tripal-table-odd-row">
-			<th>Job Creation Date</th>
-			<td><?php print format_date($node->created, 'custom', "F j, Y, g:i a"); ?></td>
-		</tr>		
-		<tr class="tripal_bulk_loader-table-even-row tripal-table-even-row">
-			<th>Last Updated</th>
-			<td><?php print format_date($node->changed, 'custom', "F j, Y, g:i a"); ?></td>
-		</tr>	
-		<tr class="tripal_bulk_loader-table-odd-row tripal-table-odd-row">
-			<th>Template Name</th>
-			<td><?php print $node->template->name; ?></td>
-		</tr>
-		<tr class="tripal_bulk_loader-table-even-row tripal-table-even-row">
-			<th>Data File</th>
-			<td><?php print $node->file;?></td>
-		</tr>
-		<tr class="tripal_bulk_loader-table-odd-row tripal-table-odd-row">
-			<th>Job Status</th>
-			<td><?php print $node->job_status;?></td>
-		</tr>
-	</table>  
-</div>
-
-<?php if (!$teaser) { ?>
-	<?php print drupal_get_form('tripal_bulk_loader_add_loader_job_form', $node); ?>
-
-  <?php if ($node->inserted_records) { 
-    print '<h3>Loading Summary</h3>';
-    $rows = array();
-    $total = 0;
-    foreach ($node->inserted_records as $r) {
-      $row = array();
-      $row[] = $r->table_inserted_into;
-      $row[] = $r->num_inserted;
-      $rows[] = $row;
-      $total = $total + $r->num_inserted;
-    }
-    $rows[] = array('<b>TOTAL</b>','<b>'.$total.'</b>');
-    print theme_table(array('Chado Table', 'Number of Records Inserted'), $rows);
-  } ?>
-  <br>
-  
-	<?php print theme('tripal_bulk_loader_template', $node->template->template_id); ?>
-<?php } ?>

theme/tripal_subthemes/tripal_bulk_loader_theme/tripal_bulk_loader/tripal_bulk_loader_add_template_field_form.tpl.php

@@ -1,83 +0,0 @@
-
-<?php print $form['add_fields']['#prefix']; ?>
-<fieldset><legend> <?php print $form['add_fields']['#title']; ?> </legend>
-<?php
-  print drupal_render($form['template_name']);
-
-  // Foreach element in the form fieldset 'add_fields'
-  foreach ($form['add_fields'] as $key => $form_array) {
-    if (preg_match('/^#/',$key)) { continue; }
-    
-    // We only care about the additional fieldset
-    if (preg_match('/additional/', $key)) {
-      //print fieldset
-      if ($form_array['#collapsible']) { $class[] = 'collapsible'; }
-      if ($form_array['#collapsed']) { $class[] = 'collapsed'; }
-      if (sizeof($class)) { $class = ' class="'.implode(' ',$class).'"'; }
-      print '<fieldset'.$class.'><legend>'.$form_array['#title'].'</legend>';
-      
-      // Foreach element in the 'additional' fieldset
-      foreach ($form_array as $key => $sub_form_array) {
-        if (preg_match('/^#/',$key)) { continue; }
-        
-        // We only care about the 'regex_transform' fieldset
-        if (preg_match('/regex_transform/', $key)) {
-          
-          // print fieldset
-          if ($sub_form_array['#collapsible']) { $class[] = 'collapsible'; }
-          if ($sub_form_array['#collapsed']) { $class[] = 'collapsed'; }
-          if (sizeof($class)) { $class = ' class="'.implode(' ',$class).'"'; }
-          print '<fieldset'.$class.'><legend>'.$sub_form_array['#title'].'</legend>';
-          
-          // print description
-          print drupal_render($sub_form_array['regex_description']);
-          
-          // Render Draggable Table
-          drupal_add_tabledrag('draggable-table', 'order', 'sibling', 'transform-reorder');
-          $header = array('Match Pattern', 'Replacement Pattern', 'Order', '');
-          $rows = array();
-          foreach ($sub_form_array['regex-data'] as $key => $element) {
-            if (preg_match('/^#/',$key)) { continue; }
-            $element['new_index']['#attributes']['class'] = 'transform-reorder';
-            
-            $row = array();
-            $row[] = drupal_render($element['pattern']);
-            $row[] = drupal_render($element['replace']);
-            $row[] = drupal_render($element['new_index']) . drupal_render($element['id']);
-            $row[] = drupal_render($element['submit-delete']);
-            $rows[] = array('data' => $row, 'class' => 'draggable');
-          }
-          
-          print theme('table', $header, $rows, array('id' => 'draggable-table'));          
-          
-          // render remaining elements
-          foreach ($sub_form_array as $key => $s2_form_array) {
-            if (preg_match('/^#/',$key)) { continue; }
-            if (!preg_match('/regex-data/', $key)) {
-              print drupal_render($s2_form_array);
-            }
-          }
-          
-          print '</fieldset>';
-          
-        } else {
-          // render other elements  in additional fieldset
-          print drupal_render($sub_form_array);
-        }
-      }
-      print '</fieldset>';
-    } else {
-      // render other elements in add_fields fieldset
-      print drupal_render($form_array);
-    }
-  }
-  unset($form['add_fields']);
-?>
-
-</fieldset>
-</div>
-
-<?php
-  //Render remaining -Needed to submit
-  print drupal_render($form);
-?>

theme/tripal_subthemes/tripal_bulk_loader_theme/tripal_bulk_loader/tripal_bulk_loader_edit_template_field_form.tpl.php

@@ -1,83 +0,0 @@
-
-<?php print $form['edit_fields']['#prefix']; ?>
-<fieldset><legend> <?php print $form['edit_fields']['#title']; ?> </legend>
-<?php
-  print drupal_render($form['template_name']);
-
-  // Foreach element in the form fieldset 'edit_fields'
-  foreach ($form['edit_fields'] as $key => $form_array) {
-    if (preg_match('/^#/',$key)) { continue; }
-    
-    // We only care about the additional fieldset
-    if (preg_match('/additional/', $key)) {
-      //print fieldset
-      if ($form_array['#collapsible']) { $class[] = 'collapsible'; }
-      if ($form_array['#collapsed']) { $class[] = 'collapsed'; }
-      if (sizeof($class)) { $class = ' class="'.implode(' ',$class).'"'; }
-      print '<fieldset'.$class.'><legend>'.$form_array['#title'].'</legend>';
-      
-      // Foreach element in the 'additional' fieldset
-      foreach ($form_array as $key => $sub_form_array) {
-        if (preg_match('/^#/',$key)) { continue; }
-        
-        // We only care about the 'regex_transform' fieldset
-        if (preg_match('/regex_transform/', $key)) {
-          
-          // print fieldset
-          if ($sub_form_array['#collapsible']) { $class[] = 'collapsible'; }
-          if ($sub_form_array['#collapsed']) { $class[] = 'collapsed'; }
-          if (sizeof($class)) { $class = ' class="'.implode(' ',$class).'"'; }
-          print '<fieldset'.$class.'><legend>'.$sub_form_array['#title'].'</legend>';
-          
-          // print description
-          print drupal_render($sub_form_array['regex_description']);
-          
-          // Render Draggable Table
-          drupal_add_tabledrag('draggable-table', 'order', 'sibling', 'transform-reorder');
-          $header = array('Match Pattern', 'Replacement Pattern', 'Order', '');
-          $rows = array();
-          foreach ($sub_form_array['regex-data'] as $key => $element) {
-            if (preg_match('/^#/',$key)) { continue; }
-            $element['new_index']['#attributes']['class'] = 'transform-reorder';
-            
-            $row = array();
-            $row[] = drupal_render($element['pattern']);
-            $row[] = drupal_render($element['replace']);
-            $row[] = drupal_render($element['new_index']) . drupal_render($element['id']);
-            $row[] = drupal_render($element['submit-delete']);
-            $rows[] = array('data' => $row, 'class' => 'draggable');
-          }
-          
-          print theme('table', $header, $rows, array('id' => 'draggable-table'));          
-          
-          // render remaining elements
-          foreach ($sub_form_array as $key => $s2_form_array) {
-            if (preg_match('/^#/',$key)) { continue; }
-            if (!preg_match('/regex-data/', $key)) {
-              print drupal_render($s2_form_array);
-            }
-          }
-          
-          print '</fieldset>';
-          
-        } else {
-          // render other elements  in additional fieldset
-          print drupal_render($sub_form_array);
-        }
-      }
-      print '</fieldset>';
-    } else {
-      // render other elements in edit_fields fieldset
-      print drupal_render($form_array);
-    }
-  }
-  unset($form['edit_fields']);
-?>
-
-</fieldset>
-</div>
-
-<?php
-  //Render remaining -Needed to submit
-  print drupal_render($form);
-?>

theme/tripal_subthemes/tripal_bulk_loader_theme/tripal_bulk_loader/tripal_bulk_loader_modify_template_base_form.tpl.php

@@ -1,73 +0,0 @@
-
-<div id="tripal-bulk-loader-fields">
-<?php print drupal_render($form['template_name']); ?>
-
-<!-- For each table display details in a draggable table -->
-<?php if (!$form['records']['no_records']['#value']) { ?>
-  <fieldset><legend><?php print $form['records']['#title']; ?></legend>
-  <?php 
-    print drupal_render($form['records']['description']);
-    
-    // generate table
-    drupal_add_tabledrag('draggable-table', 'order', 'sibling', 'records-reorder');
-    $header = array('Record Name', 'Chado Table', 'Action', 'Order', '');
-    $rows = array();
-    foreach (element_children($form['records']['records-data']) as $key) {
-      $element = &$form['records']['records-data'][$key];
-      $element['new_priority']['#attributes']['class'] = 'records-reorder';
-      
-      $row = array();
-      $row[] = drupal_render($element['title']);
-      $row[] = drupal_render($element['chado_table']);
-      $row[] = drupal_render($element['mode']);
-      $row[] = drupal_render($element['new_priority']) . drupal_render($element['id']);
-      $row[] = drupal_render($element['submit-edit_record']) . '<br>' . drupal_render($element['submit-duplicate_record']) . '<br>' . drupal_render($element['submit-add_field']);
-      $rows[] = array('data' => $row, 'class' => 'draggable');
-    }
-    
-print theme('table', $header, $rows, array('id' => 'draggable-table', 'width' => '100%'));
-    
-    // Render submit
-    print drupal_render($form['records']['submit-new_record']);
-    print drupal_render($form['records']['submit-reorder']);
-    unset($form['records']);
-  ?>
-  </fieldset>
-<?php } ?>
-
-<!-- For each field display details plus edit/delete buttons-->
-<?php if ($form['fields']['total_fields']['#value'] > 0) { ?>
-  <fieldset><legend><?php print $form['fields']['#title']; ?></legend>
-
-  <?php 
-    // generate table
-  $header = array('','Record Name', 'Field Name', 'Chado Table', 'Chado Field', 'Worksheet', 'Column', 'Constant Value', 'Foreign Record');
-    $rows = array();
-    foreach ($form['fields']['fields-data'] as $key => $element) {
-      if (preg_match('/^#/', $key)) { continue; }
-      
-      $row = array();
-      $row[] = drupal_render($element['edit_submit']) . '<br>' . drupal_render($element['delete_submit']);
-      $row[] = drupal_render($element['record_id']);
-      $row[] = drupal_render($element['field_name']);
-      $row[] = drupal_render($element['chado_table_name']);
-      $row[] = drupal_render($element['chado_field_name']);
-      $row[] = drupal_render($element['sheet_name']);
-      $row[] = drupal_render($element['column_num']);
-      $row[] = drupal_render($element['constant_value']);
-      $row[] = drupal_render($element['foreign_record_id']);
-      
-      $rows[] = $row;
-    }
-print theme('table', $header, $rows, array('style'=>'table-layout: fixed; width: 100%'));
-    
-    // Render other elements
-    print drupal_render($form['fields']['add_field']);
-    unset($form['fields']);
-  ?>
-  </fieldset>
-<?php } ?>
-
-<!-- Display Rest of form -->
-<?php print drupal_render($form); ?>
-</div>

theme/tripal_subthemes/tripal_bulk_loader_theme/tripal_bulk_loader/tripal_bulk_loader_template.tpl.php

@@ -1,69 +0,0 @@
-<?php
-	$fields = array();
-	$constants = array();
-	foreach ($template->template_array as $priority => $table_array) {
-		if (!is_array($table_array)) {
-			continue;
-		}
-		
-		$table = $table_array['table'];
-		$record = $table_array['record_id'];
-		foreach ($table_array['fields'] as $field) {
-			if (preg_match('/table field/', $field['type'])) {
-				$field['table'] = $table;
-				$field['record'] = $record;
-				$sheet = $field['spreadsheet sheet'];
-				$column = $field['spreadsheet column'];
-				$fields[$sheet.'-'.$column][] = $field;
-			} elseif ($field['type'] == 'constant') {
-				$field['table'] = $table;
-				$field['record'] = $record;
-				$constants[] = $field;
-			}
-		}
-	}
-?>
-
-<div id="tripal_bulk_loader-base-box" class="tripal_bulk_loader-info-box tripal-info-box">
-  <div class="tripal_bulk_loader-info-box-title tripal-info-box-title">Template Description</div>
-  <div class="tripal_bulk_loader-info-box-desc tripal-info-box-desc"></div>
-
-<?php if (sizeof($constants)) { ?>  
-  <table id="tripal_bulk_loader-template_constant-table" class="tripal_bulk_loader-table tripal-table tripal-table-vert">
-  <caption><b>Constants</b> -These values are applied to all records in the Spreadsheet</caption>
-    <tr><th rowspan="2">Record Name</th><th rowspan="2">Field Name</th><th rowspan="2">Value</th><th colspan="2">Chado Database</th></tr>
-    <tr><th>Table</th><th>Field</th></tr>
-    <?php $row = 'even' ?>
-    <?php foreach ($constants as $field) {?>
-      <tr class="tripal_bulk_loader-table-<?php print $row; ?>-row tripal-table-<?php print $row; ?>-row">
-				<td><?php print $field['record'];?></td>
-        <td><?php print $field['title'];?></td>
-        <td><?php print $field['constant value']; ?></td>
-        <td><?php print $field['table'];?></td>
-        <td><?php print $field['field'];?></td>	
-      </tr>
-      <?php $row = ($row == 'odd') ? 'even':'odd' ; ?>
-    <?php } ?>
-  </table>
-  
-<?php } if (sizeof($fields)) { ?>  
-  <table id="tripal_bulk_loader-template_fields-table" class="tripal_bulk_loader-table tripal-table tripal-table-vert">
-  <caption><b>Fields</b> -Below is a mapping between Spreadsheet columns and the Chado Database</caption>
-  <tr><th rowspan="2">Record Name</th><th rowspan="2">Field Name</th><th colspan="2">Spreadsheet</th><th colspan="2">Chado Datbase</th></tr>
-  <tr><th>Worksheet</th><th>Column</th><th>Table</th><th>Field</th></tr>
-  <?php $row = 'even' ?>
-  <?php foreach ($fields as $column) {?>
-    <?php foreach ($column as $field) {?>
-    <tr class="tripal_bulk_loader-table-<?php print $row; ?>-row tripal-table-<?php print $row; ?>-row">
-    	<td><?php print $field['record'];?></td>
-      <td><?php print $field['title'];?></td>
-      <td><?php print $field['spreadsheet sheet']; ?></td>
-      <td><?php print $field['spreadsheet column'];?></td>
-      <td><?php print $field['table'];?></td>
-      <td><?php print $field['field'];?></td>
-    <tr>
-    <?php $row = ($row == 'odd') ? 'even':'odd' ; ?>
-  <?php }} ?>
-  </table>
-<?php } ?>
-</div>

theme/tripal_subthemes/tripal_bulk_loader_theme/tripal_bulk_loader_theme.info

@@ -1,7 +0,0 @@
-name = Tripal Subtheme: Bulk Loader
-description = A tripal subtheme for tripal bulk loader
-version = 6.x-0.3.1b
-core = 6.x
-engine = phptemplate
-base theme = tripal
-

theme/tripal_subthemes/tripal_gbrowse_theme/node-tripal_gbrowse.tpl.php

@@ -1,177 +0,0 @@
-<?php
-// Developed by: Chad N.A Krilow at The University of Saskatchewan
-//
-// Purpose: This template provides the layout of the Tripal GBrowse Instances node (page)
-//   using the same templates used for the various Tripal GBrowse blocks. An I-Frame is 
-//	 included to show the representation of the GBrowse instance(including tracks). Along with 
-//	 the I-Frame, a link to open a external I-Frame in a new window is supplied
-//
-// To Customize the Stock Node Page:
-//   - This Template: customize basic layout and which elements are included
-//   - Using Panels: Override the node page using Panels3 and place the blocks
-//       of content as you please. This method requires no programming. See
-//       the Tripal User Guide for more details
-//
-// Variables Available:
-//   - $node: a standard object which contains all the fields associated with
-//       nodes and it also includes Tripal GBrowse specific fields.
-//
-//   NOTE: For a full listing of fields available in the node object the
-//       print_r $node line below or install the Drupal Devel module which 
-//       provides an extra tab at the top of the node page labelled Devel
-?>
-
-
-<?php
- //uncomment this line to see a full listing of the fields avail. to $node
- //print '<pre>'.print_r($node,TRUE).'</pre>';
- drupal_add_css('./tripal-node-templates.css');
-?>
-
-<?php if ($teaser) { 
-  
-  include('tripal_gbrowse/tripal_gbrowse_teaser.tpl.php');
-} else { ?>
-	  
-<script type="text/javascript">
- if (Drupal.jsEnabled) {
-   $(document).ready(function() {
-      // hide all tripal info boxes at the start
-      $(".tripal-info-box").hide();
- 
-      // iterate through all of the info boxes and add their titles
-      // to the table of contents
-      $(".tripal-info-box-title").each(function(){
-        var parent = $(this).parent();
-        var id = $(parent).attr('id');
-        var title = $(this).text();
-        $('#tripal_gbrowse_toc_list').append('<li><a href="#'+id+'" class="tripal_gbrowse_toc_item">'+title+'</a></li>');
-      });
-
-      // when a title in the table of contents is clicked, then
-      // show corresponding item in details box
-      $(".tripal_gbrowse_toc_item").click(function(){
-         $(".tripal-info-box").hide();
-         href = $(this).attr('href');
-         $(href).fadeIn('slow');
-         // make sure table of contents and the details
-         // box stay the same height
-         $("#tripal_gbrowse_toc").height($(href).parent().height());
-         return false;
-      }); 
-
-      // base details show up when the page is first shown 
-      // unless the user specified a specific block
-      var block = window.location.href.match(/\?block=.*/);
-      if(block != null){
-         block_title = block.toString().replace(/\?block=/g,'');
-         $("#tripal_gbrowse-"+block_title+"-box").show();
-      } else {
-         $("#tripal_gbrowse-base-box").show();
-      }
-
-      $("#tripal_gbrowse_toc").height($("#tripal_gbrowse-base-box").parent().height());
-   });
-}
-</script>
-
-<style type="text/css">
-  /* these styles are specific for this template and is not included 
-     in the main CSS files for the theme as it is anticipated that the
-     elements on this page may not be used for other customizations */
-  #tripal_gbrowse_toc {
-     float: left;
-     width: 20%;
-     background-color: #EEEEEE;
-     -moz-border-radius: 15px;
-     border-radius: 15px;
-     -moz-box-shadow: 3px 3px 4px #888888;
-	  -webkit-box-shadow: 3px 3px 4px #888888;
-	  box-shadow: 3px 3px 4px #888888;
-     padding: 20px;
-     min-height: 200px;
-     border-style:solid;
-     border-width:1px;
-  }
-  #tripal_gbrowse_toc ul {
-    margin-left: 0px;
-    margin-top: 5px;
-    padding-left: 15px;
-  }
-  #tripal_gbrowse_toc_title {
-     font-size: 1.5em;
-  }
-  #tripal_gbrowse_toc_desc {
-    font-style: italic;
-  }
-  #tripal_gbrowse_details {
-     float: left;
-     width: 70%;
-     background-color: #FFFFFF;
-     -moz-border-radius: 15px;
-     border-radius: 15px;
-     -moz-box-shadow: 3px 3px 4px #888888;
-	  -webkit-box-shadow: 3px 3px 4px #888888;
-	  box-shadow: 3px 3px 4px #888888;
-     padding: 20px;
-     min-height: 200px;
-     margin-right: 10px;
-     border-style:solid;
-     border-width:1px;
-  }
-  #tripal_gbrowse-base-box img {
-    float: left;
-    margin-bottom: 10px;
-  }
-  #tripal_gbrowse-table-base {
-    float: left;
-    width: 400px;
-    margin-left: 10px;
-    margin-bottom: 10px;
-  }
-  #tripal_gbrowse_addtional_content {
-		clear:both;
-  	width: 100%;
-  }
-</style>
-
-<div id ="tripal_gbrowse_content">
-<div id="tripal_gbrowse_details" class="tripal_details"><h2>
-
-   <!-- Basic Details Theme -->
-   <?php include('tripal_gbrowse/tripal_gbrowse_details.tpl.php'); ?>
-
-   <!-- GBrowse Details -->
-   <?php 
-   global $account;
-   if(user_access('access database-related details',$account)){
-     include('tripal_gbrowse/tripal_gbrowse_database_details.tpl.php'); 
-	 }?>
-   <?php print $content ?>
-   
-    <!-- GBrowse Loaded Sources -->
-   <?php 
-     include('tripal_gbrowse/tripal_gbrowse_loaded_sources.tpl.php');
-     ?>
-   <?php print $content ?>
- 
-</div>
-
-<!-- Table of contents -->
-<div id="tripal_gbrowse_toc" class="tripal_toc">
-   <div id="tripal_gbrowse_toc_title" class="tripal_toc_title">Resources</div>
-   <span id="tripal_gbrowse_toc_desc" class="tripal_toc_desc"></span>
-   <ul id="tripal_gbrowse_toc_list" class="tripal_toc_list">
-
-   </ul>
-</div>
-</div>
-
-<!--- I-Frame Code Section --->
-<div id="tripal_gbrowse_addtional_content">
-
-	<!--- Include for file that makes the I-Frame and external window possible --->
- <?php include('tripal_gbrowse/tripal_gbrowse_gbrowse_instance.tpl.php'); ?>
-
-</div>
-<?php } ?>

theme/tripal_subthemes/tripal_gbrowse_theme/tripal_gbrowse/tripal_gbrowse_database_details.tpl.php

@@ -1,48 +0,0 @@
-<?php
-// Developed by: Chad N.A Krilow at The University of Saskatchewan
-//
-// Purpose: Provide layout and content for the GBrowse database details. This
-//   includes database related fields in the tripal_gbrowse_instances table.
-//
-// Note: This template controls the layout/content for the default tripal_gbrowse node
-//   template (node-tripal_grbowse.tpl.php) and the Database Details Block
-//
-// Variables Available:
-//   - $node: a standard object which contains includes GBrowse Databse specific fields such as  
-//			 database_name, database_user, user_password, etc.
-?>
-
-<?php
- //uncomment this line to see a full listing of the fields avail. to $node
- //print '<pre>'.print_r($node,TRUE).'</pre>';
-?>  
-
-<?php
-
-$gbrowse = $node->gbrowse;
-
-?>
-<div id="tripal_gbrowse-database-box" class="tripal_gbrowse-info-box tripal-info-box">
-  <div class="tripal_gbrowse-info-box-title tripal-info-box-title"> Data Base Details</div>
-  <div class="tripal_gbrowse-info-box-desc tripal-info-box-desc"></div>
-
-   <?php //if the gbrowse is deleted/removed issue a warning
-   if(strcmp($gbrowse->is_obsolete,'t')==0){ 
-   ?>
-      <div class="tripal_gbrowse-obsolete">This GBrowse Instance is obsolete or has been deleted/removed</div>
-   <?php }?>
-   <table id="tripal_gbrowse-base-table" class="tripal_gbrowse-table tripal-table tripal-table-vert">
-      <tr class="tripal_gbrowse-table-even-row tripal-table-even-row">
-        <th>Data Base Name</th>
-        <td><?php print $node->gbrowse->database_name; ?></td>
-      </tr>
-      <tr class="tripal_gbrowse-table-odd-row tripal-table-odd-row">
-        <th nowrap>Database User Name</th>
-        <td><?php print $node->gbrowse->database_user; ?></td>
-      </tr>
-      <tr class="tripal_gbrowse-table-even-row tripal-table-even-row">
-        <th>User Password</th>
-        <td><?php print $node->gbrowse->user_password; ?></td>
-      </tr>     	                                
-   </table>
-</div>

theme/tripal_subthemes/tripal_gbrowse_theme/tripal_gbrowse/tripal_gbrowse_details.tpl.php

@@ -1,45 +0,0 @@
-<?php
-// Developed by: Chad N.A Krilow at The University of Saskatchewan 
-//
-// Purpose: Provide layout and content for the GBrowse database details. This
-//   includes databse user specific fields in the tripal_gbrowse_instances table.
-//
-// Note: This template controls the layout/content for the default tripal_gbrowse node
-//   template (node-tripal_grbowse.tpl.php) and the Database Details Block
-//
-// Variables Available:
-//   - $node: a standard object which contains all the fields associated with
-//       nodes. It also includes GBrowse specific fields such as gbrowse_name, 
-//			 database_link, config_file.
-?>
-
-<?php
- //uncomment this line to see a full listing of the fields avail. to $node
- //print '<pre>'.print_r($node,TRUE).'</pre>';
-?> 
-
-
-<?php $gbrowse = $node->gbrowse; ?>
-
-<div id="tripal_gbrowse-base-box" class="tripal_gbrowse-info-box tripal-info-box">
-  <div class="tripal_gbrowse-info-box-title tripal-info-box-title"> GBrowse Details</div>
-  <div class="tripal_gbrowse-info-box-desc tripal-info-box-desc"></div>
-
-   <?php if(strcmp($gbrowse->is_obsolete,'t')==0){ ?>
-      <div class="tripal_gbrowse-obsolete">This GBrowse Instance is obsolete or has been deleted/removed</div>
-   <?php }?>
-   <table id="tripal_gbrowse-base-table" class="tripal_gbrowse-table tripal-table tripal-table-vert">
-      <tr class="tripal_gbrowse-table-even-row tripal-table-even-row">
-        <th>GBrowse Instance</th>
-        <td><?php print $node->gbrowse->gbrowse_name; ?></td>
-      </tr>
-      <tr class="tripal_gbrowse-table-odd-row tripal-table-odd-row">
-        <th nowrap>GBrowse Instance Link</th>
-        <td><?php print $node->gbrowse->gbrowse_link; ?></td>
-      </tr>
-      <tr class="tripal_gbrowse-table-even-row tripal-table-even-row">
-        <th>Configuration File</th>
-        <td><?php print $node->gbrowse->config_file; ?></td>
-      </tr>     	                                
-   </table>
-</div>

theme/tripal_subthemes/tripal_gbrowse_theme/tripal_gbrowse/tripal_gbrowse_gbrowse_instance.tpl.php

@@ -1,28 +0,0 @@
-<?php
-// Developed by: Chad N.A Krilow at The University of Saskatchewan
-//
-// Purpose: Provide a in window I-Frame that displays the GBrowse instance. As well,
-// a link to open the GBrowse instance in a external window is provided. If the window can not be
-// opened a warning is issued
-//   
-// Variables Available:
-//   - $node: a standard object which contains all the fields associated with
-//       nodes. Here it is utilized for accessing the link to a specific GBrowse instance.
-//
-//   NOTE: For a full listing of fields available in the node object the
-//       print_r $node line below or install the Drupal Devel module which 
-//       provides an extra tab at the top of the node page labelled Devel
-?>
-
-<?php
- //uncomment this line to see a full listing of the fields avail. to $node
- //print '<pre>'.print_r($node,TRUE).'</pre>';
-?>
-
-<br />
-<h3><a href="<?php print $node->gbrowse->gbrowse_link; ?>" target="_blank">Open GBrowse Instance in new Window</a></h3>
-<br />
-
-<iframe src="<?php print $node->gbrowse->gbrowse_link; ?>" width="100%" height="800">
-  <p>Your browser does not support iframes.</p>
-</iframe>

theme/tripal_subthemes/tripal_gbrowse_theme/tripal_gbrowse/tripal_gbrowse_loaded_sources.tpl.php

@@ -1,42 +0,0 @@
-<?php
-// Developed by: Chad N.A Krilow at The University of Saskatchewan
-//
-// Variables Available:
-//   - $node: a standard object which contains includes GBrowse Databse specific fields such as  
-//			 database_name, database_user, user_password, etc.
-?>
-
-<?php
- //uncomment this line to see a full listing of the fields avail. to $node
- //print '<pre>'.print_r($node,TRUE).'</pre>';
-?>  
-
-<?php
-
-$gbrowse = $node->gbrowse;
-$node->sources = tripal_gbrowse_getloaded_sources($node->gbrowse);
-
-?>
-<div id="tripal_gbrowse-source-box" class="tripal_gbrowse-info-box tripal-info-box">
-  <div class="tripal_gbrowse-info-box-title tripal-info-box-title"> Loaded Sources</div>
-  <div class="tripal_gbrowse-info-box-desc tripal-info-box-desc">A source can be either a library or analysis or any other grouping of features.</div>
-
-   <?php //if the gbrowse is deleted/removed issue a warning
-   if(strcmp($gbrowse->is_obsolete,'t')==0){ 
-   ?>
-      <div class="tripal_gbrowse-obsolete">This GBrowse Library is obsolete or has been deleted/removed</div>
-   <?php }?>
-   <table id="tripal_gbrowse-base-table" class="tripal_gbrowse-table tripal-table tripal-table-vert">
-   <tr><th>Name</th></tr>
-   
-   
-   <?php 
-   if(!empty($node->sources)){
-   	foreach($node->sources as $key => $source){
-   ?>
-      <tr class="tripal_gbrowse-table-even-row tripal-table-even-row">
-        <td><?php print $source; ?></td>
-      </tr>
-		<?php }} //end of foreach library & end of if statement ?>  	                                
-   </table>
-</div>

theme/tripal_subthemes/tripal_gbrowse_theme/tripal_gbrowse/tripal_gbrowse_teaser.tpl.php

@@ -1,34 +0,0 @@
-<?php
-// Developed by: Chad N.A Krilow at The University of Saskatchewan
-//
-// Purpose: Provide layout and content for the Tripal Gbrowse details.Represents
-// what the user will see if the there is no information in the node
-//
-// Variables Available:
-//   - $node: a standard object which contains all the fields associated with
-//       nodes including nid, gbrowse_id.
-//   NOTE: For a full listing of fields available in the node object the
-//       print_r $node line below or install the Drupal Devel module which 
-//       provides an extra tab at the top of the node page labelled Devel
-?>
-
-<?php
- //uncomment this line to see a full listing of the fields avail. to $node
- //print '<pre>'.print_r($node,TRUE).'</pre>';
-?>
-
-<div id="tripal_gbrowse-base-box" class="tripal_gbrowse-info-box tripal-info-box">
-  <div class="tripal_gbrowse-info-box-title tripal-info-box-title">
-  
-  	<!-- Title -->  	
-    <?php print l($node->gbrowse->gbrowse_name, 'node/'.$node->nid); ?>
-
-		
-  </div>
-  <div class="tripal_gbrowse-info-box-desc tripal-info-box-desc"></div>
-
-<p>This is a representation of a created GBrowse instance.<p>
-<?php print l('See More Details', 'node/'.$node->nid); ?>
-
- 
-</div>

theme/tripal_subthemes/tripal_gbrowse_theme/tripal_gbrowse_theme.info

@@ -1,7 +0,0 @@
-name = Tripal Subtheme: Gbrowse
-description = A tripal subtheme for tripal gbrowse module
-version = 6.x-0.3.1b
-core = 6.x
-engine = phptemplate
-base theme = tripal
-

theme/tripal_subthemes/tripal_genetic_theme/tripal_feature_genotypes.tpl.php

@@ -1,22 +0,0 @@
-
-<?php
-$feature = $variables['node']->feature;
-$genotypes = $variables['tripal_feature']['genotypes'];
-?>
-
-<?php if(count($genotypes) > 0){ ?>
-<div id="tripal_feature-genotypes-box" class="tripal_feature-info-box tripal-info-box">
-  <div class="tripal_feature-info-box-title tripal-info-box-title">Genotypes</div>
-  <div class="tripal_feature-info-box-desc tripal-info-box-desc">
-    Genotypes of this <?php print $feature->type_id->name; ?> in various germplasm
-  </div>
-  <ul>
-    <?php foreach ($genotypes as $g) { 
-        $genotype = $g->description;
-        if (preg_match('/insufficient sequence/',$genotype)) { $genotype = "<font colour='grey'>".$genotype.'</font>'; }
-    ?>
-      <li><?php print $genotype; ?></li>
-    <?php } ?>
-  </ul>
-</div>
-<?php } ?>

theme/tripal_subthemes/tripal_genetic_theme/tripal_genetic_theme.info

@@ -1,7 +0,0 @@
-name = Tripal Subtheme: Genetic Theme
-description = A tripal subtheme for tripal genetic theme
-version = 6.x-0.3.1b
-core = 6.x
-engine = phptemplate
-base theme = tripal
-

theme/tripal_subthemes/tripal_natural_diversity_theme/tripal_feature-genotype_experiments.tpl.php

@@ -1,73 +0,0 @@
-
-<?php
-  $num_results_per_page = 25;
-  $feature = $variables['node']->feature;
-  
-  // get all genotypes associatated with the current feature
-  $query = "SELECT * FROM genotype WHERE genotype_id IN (SELECT genotype_id FROM feature_genotype WHERE feature_id=%d)";
-  $resource = db_query($query, $feature->feature_id);
-  $genotypes = array();
-  while( $r = db_fetch_array($resource)) {
-    $genotypes[$r['genotype_id']] = $r;
-  }
-  
-  if (!empty($genotypes)) {
-    // SELECT all nd_experiments where type=genotype and experiment is connected to the current feature
-    $query = "SELECT nd_experiment_id, genotype_id FROM nd_experiment_genotype "
-      ."WHERE genotype_id IN (%s) "
-      ."ORDER BY nd_experiment_id";
-    $resource = pager_query($query, $num_results_per_page, 0, NULL, implode(',',array_keys($genotypes)));
-    $results = array();
-    while ($r = db_fetch_object($resource)) {
-    
-      // Get the stock associated with each experiment
-      $query2 = "SELECT s.* FROM stock s "
-        ."WHERE s.stock_id IN (SELECT stock_id FROM nd_experiment_stock WHERE nd_experiment_id=%d)";
-      $stock = db_fetch_array(db_query($query2, $r->nd_experiment_id));
-      
-      $item = array(
-        'nd_experiment' => array(
-          'nd_experiment_id' => $r->nd_experiment_id
-        ),
-        'genotype' =>  $genotypes[$r->genotype_id],
-        'stock' => $stock,
-      );
-      
-      // Get the nid associated with the feature (used for linking)
-      $query3 = "SELECT nid FROM chado_stock WHERE stock_id=%d";
-      $nid = db_fetch_object(db_query($query3,$stock['stock_id']));
-      $item['stock']['nid'] = $nid->nid;
-      
-      $results[$r->nd_experiment_id] = $item;
-    }
-  }
-?>
-
-<?php if(count($results) > 0){ ?>
-<div id="tripal_feature-genotype_experiments-box" class="tripal_feature-info-box tripal-info-box">
-  <div class="tripal_feature-info-box-title tripal-info-box-title">Genotype Experiments</div>
-  <div class="tripal_feature-info-box-desc tripal-info-box-desc">
-    Genotypes of this <?php print $feature->type_id->name; ?> in various germplasm
-  </div>
-  <table>
-    <tr><th>Germplasm Assayed</th><th>Genotype Observed</th></tr>
-    <?php foreach ($results as $r) { 
-        $genotype = $r['genotype']['description'];
-        if (preg_match('/insufficient/',$genotype)) { $genotype = "<font color='grey'>".$genotype.'</font>'; }
-        $stock_name = $r['stock']['name'];
-        if ($r['stock']['nid']) {
-          $stock_link = 'node/'.$r['stock']['nid'];
-          $stock = l($stock_name, $stock_link);
-        } else {
-          $stock = $stock_name;
-        }
-    ?>
-      <tr><td><?php print $stock; ?></td><td><?php print $genotype; ?></td></tr>
-    <?php } ?>
-  </table>
-  <?php 
-   print theme('pager', array(), $num_results_per_page, 0, array('block'=>'genotype_experiments'), 5); 
-  ?>
-</div>
-<?php } ?>
-

theme/tripal_subthemes/tripal_natural_diversity_theme/tripal_natural_diversity_theme.info

@@ -1,7 +0,0 @@
-name = Tripal Subtheme: Natural Diversity Theme
-description = A tripal subtheme for tripal natural diversity module
-version = 6.x-0.3.1b
-core = 6.x
-engine = phptemplate
-base theme = tripal
-

theme/tripal_subthemes/tripal_natural_diversity_theme/tripal_stock-genotype_experiments.tpl.php

@@ -1,80 +0,0 @@
-
-<?php
-  $num_results_per_page = 25;
-  
-  // SELECT all nd_experiments where type=genotype and experiment is connected to the current stock
-  $query = "SELECT nd_experiment_id FROM nd_experiment "
-    ."WHERE nd_experiment_id IN (SELECT nd_experiment_id FROM nd_experiment_stock WHERE stock_id=%d) "
-      ."AND type_id IN (SELECT cvterm_id FROM cvterm WHERE name='genotype') "
-    ."ORDER BY nd_experiment_id";
-  $resource = pager_query($query, $num_results_per_page, 0, NULL, $node->stock->stock_id);
-  $results = array();
-  while ($r = db_fetch_object($resource)) {
-
-    // Get the genotype & feature associated with each experiment
-    $query2 = "SELECT g.*, f.uniquename as feature_uniquename, f.name as feature_name, f.feature_id FROM genotype g "
-      ."LEFT JOIN feature_genotype fg ON fg.genotype_id=g.genotype_id "
-      ."LEFT JOIN feature f ON fg.feature_id=f.feature_id "
-      ."WHERE g.genotype_id IN (SELECT genotype_id FROM nd_experiment_genotype WHERE nd_experiment_id=%d)";
-    $genotype_feature = db_fetch_object(db_query($query2, $r->nd_experiment_id));
-
-    $item = array(
-      'nd_experiment' => array(
-        'nd_experiment_id' => $r->nd_experiment_id
-      ),
-      'genotype' => array(
-        'genotype_id' => $genotype_feature->genotype_id,
-        'uniquename' => $genotype_feature->uniquename,
-        'description' => $genotype_feature->description,
-      ),
-      'feature' => array(
-        'feature_id' => $genotype_feature->feature_id,
-        'uniquename' => $genotype_feature->feature_uniquename,
-        'name' => $genotype_feature->feature_name,
-      ),
-    );
-    
-    // Get the nid associated with the feature (used for linking)
-    $query3 = "SELECT nid FROM chado_feature WHERE feature_id=%d";
-    $nid = db_fetch_object(db_query($query3,$genotype_feature->feature_id));
-    $item['feature']['nid'] = $nid->nid;
-    
-    $results[$r->nd_experiment_id] = $item;
-  }
-?>
-
-<?php if (!empty($results)) { ?>
-  <div id="tripal_stock-genotype_experiments-box" class="tripal_stock-info-box tripal-info-box">
-    <div class="tripal_stock-info-box-title tripal-info-box-title">Genotype Experiments</div>
-    <div class="tripal_stock-info-box-desc tripal-info-box-desc"></div>
-    <table>
-      <tr><th>Marker Assayed</th><th>Genotype Observed</th></tr>
-      <?php
-        foreach ($results as $r) {
-          // genotype
-          $genotype = $r['genotype']['description'];
-          if (preg_match('/insufficient/',$genotype)) { 
-            $genotype = "<font color='grey'>".$genotype.'</font>'; 
-          }
-          
-          // feature name
-          if ($r['feature']['name']) {
-            $marker_name = $r['feature']['name'];
-          } else {
-            $marker_name = $r['feature']['uniquename'];
-          }
-          
-          // add link if feature sync'd
-          if ($r['feature']['nid']) {
-            $marker_link = 'node/'.$r['feature']['nid'];
-            $marker = l($marker_name, $marker_link);
-          } else {
-            $marker = $marker_name;
-          }
-      ?>
-      <tr><td><?php print $marker; ?></td><td><?php print $genotype; ?></td></tr>
-      <?php } ?>
-    </table>
-    <?php print theme('pager', array(), $num_results_per_page, 0, array('block'=>'genotype_experiments'), 5); ?>
-  </div>
-<?php } ?>

theme/tripal_subthemes/tripal_pub_theme/node-tripal_pub.tpl.php

@@ -1,13 +0,0 @@
-<?php
-// Developed by: Chad N.A Krilow at The University of Saskatchewan
-//
-// Purpose: This template provides the layout of the Tripal Pub node (page)
-//   using the same templates used for the various Tripal blocks. 
-?> 
-
-<?php
- //uncomment this line to see a full listing of the fields avail. to $node
- //print '<pre>'.print_r($node,TRUE).'</pre>';
-?>
-
-

theme/tripal_subthemes/tripal_pub_theme/tripal_pub_theme.info

@@ -1,7 +0,0 @@
-name = Tripal Subtheme: Pub Theme
-description = A tripal subtheme for tripal pub module
-version = 6.x-0.3.1b
-core = 6.x
-engine = phptemplate
-base theme = tripal
-

theme/tripal_subthemes/tripal_search_unigene_theme/css/tripal_search_unigene.css

@@ -1,40 +0,0 @@
-.tripal_search_unigene-views-exposed-form {
-	margin: 10px;
-	padding:10px;
-	background: #FFFFFF;
-	border: 1px solid #CCCCCC;
-}
-
-.tripal-search-unigene-exposed-widget {
-	clear:both;
-	padding: 5px;
-}
-
-.tripal-search-unigene-form-labels {
-	float:left;
-}
-
-.tripal_search_unigene-views-operator {
-	float:left;
-	clear:none;
-	margin-left: 5px;
-}
-
-.tripal_search_unigene-views-widget {
-	float:left;
-	clear:none;
-	margin-left: 5px;
-}
-
-.tripal_search_unigene-table {
-	margin-left: 10px;
-}
- 
- .tripal-search-unigene-exposed-widgets-fields legend{
-   color:green;
- }
- 
- #tripal_search_unigene-result-top:hover {
-   text-decoration: none;
-   color:#292929;
- }

theme/tripal_subthemes/tripal_search_unigene_theme/js/tripal_search_unigene.js

@@ -1,20 +0,0 @@
-//
-// Copyright 2009 Clemson University
-//
-
-if (Drupal.jsEnabled) {
-
-   $(document).ready(function(){
-
-		// Move to the result top
-		var result_top = document.getElementById('tripal_search_unigene-result-top');
-		if (result_top) {	
-			 var target_offset = $("#tripal_search_unigene-result-top").offset();
-			 var target_top = target_offset.top;
-			 if (navigator.userAgent.indexOf('MSIE 8.0') !=-1) 	{
-				target_top -= 60;	
-			}
-			$('html, body').animate({scrollTop: target_top}, 1000);
-		}
-   });
-}

theme/tripal_subthemes/tripal_search_unigene_theme/tripal_search_unigene_theme.info

@@ -1,10 +0,0 @@
-name = Tripal Subtheme: Unigene Search Theme
-description = A tripal subtheme for tripal search unigene module
-version = 6.x-0.3.1b
-core = 6.x
-engine = phptemplate
-base theme = tripal
-
-stylesheets[all][] = css/tripal_search_unigene.css
-
-scripts[] = js/tripal_analysis_search_unigene.js

theme/tripal_subthemes/tripal_search_unigene_theme/views-exposed-form--unigene_search.tpl.php

@@ -1,195 +0,0 @@
-<?php
-// $Id: views-exposed-form.tpl.php,v 1.4.4.1 2009/11/18 20:37:58 merlinofchaos Exp $
-/**
- * @file views-exposed-form.tpl.php
- *
- * This template handles the layout of the views exposed filter form.
- *
- * Variables available:
- * - $widgets: An array of exposed form widgets. Each widget contains:
- * - $widget->label: The visible label to print. May be optional.
- * - $widget->operator: The operator for the widget. May be optional.
- * - $widget->widget: The widget itself.
- * - $button: The submit button for the form.
- *
- * @ingroup views_templates
- */
-?>
-<?php if (!empty($q)): ?>
-  <?php
-    // This ensures that, if clean URLs are off, the 'q' is added first so that
-    // it shows up first in the URL.
-    print $q;
-
-  ?>
-<?php endif;     //dsm($widgets);?>
-<div class="tripal_search_unigene-views-exposed-form views-exposed-form">
-  <div class="views-exposed-widgets clear-block">
-    
-    <?php 
-    	$feature_type_id =  $widgets['filter-feature_type']; 
-    	$orgnism_common_name =  $widgets['filter-organism_common_name'];
-    	$analysis_name =  $widgets['filter-unigene'];
-    	$feature_name =  $widgets['filter-feature_name'];
-    	$feature_seqlen =  $widgets['filter-feature_seqlen'];
-    	$cvterm_name =  $widgets['filter-go_term'];
-    	$blast_value =  $widgets['filter-blast_value'];
-    	$interpro_value =  $widgets['filter-interpro_value'];
-    	$kegg_value =  $widgets['filter-kegg_value'];
-    ?>
-    
-    <div id="tripal-search-unigene-exposed-widgets">
-    <div> Search ESTs or unigene contigs by name, assembly, sequence type, length, or their putative function. <br><br></div>
-			<fieldset class="tripal-search-unigene-exposed-widgets-fields">
-				<legend>Search by Name</legend>
-				<div class="tripal-search-unigene-exposed-widget">
-					<div class="tripal-search-unigene-form-labels">
-						<label for="<?php print $orgnism_common_name->id; ?>"><?php print $orgnism_common_name->label; ?>
-						</label>
-					</div>
-					<?php if (!empty($orgnism_common_name->operator)): ?>
-					<div class="tripal_search_unigene-views-operator">
-					<?php print $orgnism_common_name->operator; ?>
-					</div>
-					<?php endif; ?>
-					<div class="tripal_search_unigene-views-widget">
-					<?php print $orgnism_common_name->widget; ?>
-					</div>
-				</div>
-				<div class="tripal-search-unigene-exposed-widget">
-					<div class="tripal-search-unigene-form-labels">
-						<label for="<?php print $feature_name->id; ?>"><?php print $feature_name->label; ?>
-						</label>
-					</div>
-					<?php if (!empty($feature_name->operator)): ?>
-					<div class="tripal_search_unigene-views-operator">
-					<?php print $feature_name->operator; ?>
-					</div>
-					<?php endif; ?>
-					<div class="tripal_search_unigene-views-widget">
-						<?php print $feature_name->widget; ?>
-					</div>
-				</div>
-			</fieldset>
-
-			<fieldset class="tripal-search-unigene-exposed-widgets-fields">
-				<legend>Search by Assembly</legend>
-				<div class="tripal-search-unigene-exposed-widget">
-					<div class="tripal-search-unigene-form-labels">
-						<label for="<?php print $feature_type_id->id; ?>"><?php print $feature_type_id->label; ?>
-						</label>
-					</div>
-					<?php if (!empty($feature_type_id->operator)): ?>
-					<div class="tripal_search_unigene-views-operator">
-					<?php print $feature_type_id->operator; ?>
-					</div>
-					<?php endif; ?>
-					<div class="tripal_search_unigene-views-widget">
-					<?php print $feature_type_id->widget; ?>
-					</div>
-				</div>
-				<div class="tripal-search-unigene-exposed-widget">
-					<div class="tripal-search-unigene-form-labels">
-						<label for="<?php print $analysis_name->id; ?>"><?php print $analysis_name->label; ?>
-						</label>
-					</div>
-					<?php if (!empty($analysis_name->operator)): ?>
-					<div class="tripal_search_unigene-views-operator">
-					<?php print $analysis_name->operator; ?>
-					</div>
-					<?php endif; ?>
-					<div class="tripal_search_unigene-views-widget">
-						<?php print $analysis_name->widget; ?>
-					</div>
-				</div>
-			</fieldset>
-
-			<fieldset class="tripal-search-unigene-exposed-widgets-fields">
-				<legend>Search by Sequence</legend>
-				<div class="tripal-search-unigene-exposed-widget">
-					<div class="tripal-search-unigene-form-labels">
-						<label for="<?php print $feature_seqlen->id; ?>"><?php print $feature_seqlen->label; ?>
-						</label>
-					</div>
-					<?php if (!empty($feature_seqlen->operator)): ?>
-					<div class="tripal_search_unigene-views-operator">
-					<?php print $feature_seqlen->operator; ?>
-					</div>
-					<?php endif; ?>
-					<div class="tripal_search_unigene-views-widget">
-					<?php print $feature_seqlen->widget; ?>
-					</div>
-				</div>
-			</fieldset>
-
-			<fieldset class="tripal-search-unigene-exposed-widgets-fields">
-				<legend>Search by Putative Function</legend>
-				<div class="tripal-search-unigene-exposed-widget">
-					<div class="tripal-search-unigene-form-labels">
-						<label for="<?php print $cvterm_name->id; ?>"><?php print $cvterm_name->label; ?>
-						</label>
-					</div>
-					<?php if (!empty($cvterm_name->operator)): ?>
-					<div class="tripal_search_unigene-views-operator">
-					<?php print $cvterm_name->operator; ?>
-					</div>
-					<?php endif; ?>
-					<div class="tripal_search_unigene-views-widget">
-					<?php print $cvterm_name->widget; ?>
-					</div>
-				</div>
-
-				<div class="tripal-search-unigene-exposed-widget">
-					<div class="tripal-search-unigene-form-labels">
-						<label for="<?php print $blast_value->id; ?>"><?php print $blast_value->label; ?>
-						</label>
-					</div>
-					<?php if (!empty($blast_value->operator)): ?>
-					<div class="tripal_search_unigene-views-operator">
-					<?php print $blast_value->operator; ?>
-					</div>
-					<?php endif; ?>
-					<div class="tripal_search_unigene-views-widget">
-						<?php print $blast_value->widget; ?>
-					</div>
-				</div>
-				
-				<div class="tripal-search-unigene-exposed-widget">
-					<div class="tripal-search-unigene-form-labels">
-						<label for="<?php print $kegg_value->id; ?>"><?php print $kegg_value->label; ?>
-						</label>
-					</div>
-					<?php if (!empty($kegg_value->operator)): ?>
-					<div class="tripal_search_unigene-views-operator">
-					<?php print $kegg_value->operator; ?>
-					</div>
-					<?php endif; ?>
-					<div class="tripal_search_unigene-views-widget">
-						<?php print $kegg_value->widget; ?>
-					</div>
-				</div>
-				
-				<div class="tripal-search-unigene-exposed-widget">
-					<div class="tripal-search-unigene-form-labels">
-						<label for="<?php print $interpro_value->id; ?>"><?php print $interpro_value->label; ?>
-						</label>
-					</div>
-					<?php if (!empty($interpro_value->operator)): ?>
-					<div class="tripal_search_unigene-views-operator">
-					<?php print $interpro_value->operator; ?>
-					</div>
-					<?php endif; ?>
-					<div class="tripal_search_unigene-views-widget">
-						<?php print $interpro_value->widget; ?>
-					</div>
-				</div>
-			</fieldset>
-
-		</div>
-    
-    <div class="tripal-search-unigene-exposed-widget">
-    	<input TYPE="Button" value="Reset" onClick="window.location = '<?php global $base_url; print "$base_url/est_search"?>';">
-      <?php $button = preg_replace("'Apply'", "Search", $button); print $button ?>
-    </div>
-  </div>
-</div>

theme/tripal_subthemes/tripal_search_unigene_theme/views-view-table--unigene_search.tpl.php

@@ -1,221 +0,0 @@
-<?php
-// $Id: views-view-table.tpl.php,v 1.8 2009/01/28 00:43:43 merlinofchaos Exp $
-/**
- * @file views-view-table.tpl.php
- * Template to display a view as a table.
- *
- * - $title : The title of this group of rows.  May be empty.
- * - $header: An array of header labels keyed by field id.
- * - $fields: An array of CSS IDs to use for each field id.
- * - $class: A class or classes to apply to the table, based on settings.
- * - $row_classes: An array of classes to apply to each row, indexed by row
- *   number. This matches the index in $rows.
- * - $rows: An array of row items. Each row is an array of content.
- *   $rows are keyed by row number, fields within rows are keyed by field ID.
- * @ingroup views_templates
- */
-?>
-
-<?php
-$total = $view->total_rows;
-$query = $view->build_info['query'];
-$pager = $view->pager;
-$limit = $pager ['items_per_page'];
-$offset = $pager ['current_page'] * $limit;
-$args = $view->build_info['query_args'];
-global $base_url;
-?>
-
-<a id="tripal_search_unigene-result-top" name="search_results">
-&nbsp;&nbsp;&nbsp;Your search produced <b><?php print $total ?></b> results<br>
-<i>&nbsp;&nbsp;&nbsp;Note: To get complete annotation for a sequence, click on the sequence name.</i>
-</a>
-<table class="tripal_search_unigene-table <?php print $class; ?> tripal-table-horz">
-  <?php if (!empty($title)) : ?>
-    <caption><?php print $title; ?></caption>
-  <?php endif; ?>
-  <thead>
-    <tr class="tripal_search_unigene-table-header tripal-table-header">
-      <?php foreach ($header as $field => $label): ?>
-        <th class="views-field views-field-<?php print $fields[$field]; ?>">
-          <?php print $label; ?>
-        </th>
-      <?php endforeach; ?>
-    </tr>
-  </thead>
-  <tbody>
-    <?php foreach ($rows as $count => $row): 
-    			$rowclass = "";
-    			if ($count % 2 != 0) {
-    				$rowclass = "tripal_search_unigene-table-even-row tripal-table-even-row";
-    			} else {
-    				$rowclass = "tripal_search_unigene-table-odd-row tripal-table-odd-row";
-    			}
-    ?>
-      <tr class="<?php print $rowclass?> <?php print implode(' ', $row_classes[$count]); ?>">
-        <?php foreach ($row as $field => $content): ?>
-          <td class="views-field views-field-<?php print $fields[$field]; ?>">
-            <?php print $content; ?>
-          </td>
-        <?php endforeach; ?>
-      </tr>
-    <?php endforeach; ?>
-  </tbody>
-</table>
-
-<?php /* if ($count != 0) {
-	// Generate Excel files
-	// set parameters for excel file
-	$param_excel= array();
-	global $user;
-	$dir = file_directory_path().'/tripal/tripal_search_unigene/'.session_id();
-	if (!file_exists($dir)) {
-		mkdir ($dir, 0777);
-	}
-	$file =session_id().'/unigene_search_result.xls';
-	
-	$param_excel['sheet_name']		= 'unigene_search';
-	$path = "/tripal/tripal_search_unigene/$file";
-	$param_excel['filename']		= file_directory_path().$path;
-	$path_url =url("sites/default/files/tripal/tripal_search_unigene/$file");
-	# set SQL
-	$sql = "$query LIMIT $limit OFFSET $offset";
-	# create heades
-	$col_chr = 'A';
-	$headers = array();
-	$headers[$col_chr++] = array('align' => 'left', 'width' => 20, 'type' => 'hyperlink', 'field' => 'unigene_for_search_feature_name', 'heading' => 'Feature name');
-	$headers[$col_chr++] = array('align' => 'left', 'width' => 10, 'type' => 'text', 'field' => 'unigene_for_search_organism_common_name', 'heading' => 'Organism');
-	$headers[$col_chr++] = array('align' => 'left', 'width' => 10, 'type' => 'text', 'field' => 'unigene_for_search_feature_seqlen', 'heading' => 'Length');
-	$headers[$col_chr++] = array('align' => 'left', 'width' => 10, 'type' => 'text', 'field' => 'unigene_for_search_feature_type', 'heading' => 'Type');
-	$headers[$col_chr++] = array('align' => 'left', 'width' => 20, 'type' => 'text', 'field' => 'unigene_for_search_go_term', 'heading' => 'GO term');
-	$headers[$col_chr++] = array('align' => 'left', 'width' => 20, 'type' => 'text', 'field' => 'unigene_for_search_blast_value', 'heading' => 'Blast');
-	$headers[$col_chr++] = array('align' => 'left', 'width' => 20, 'type' => 'text', 'field' => 'unigene_for_search_kegg_value', 'heading' => 'KEGG');
-	$headers[$col_chr++] = array('align' => 'left', 'width' => 20, 'type' => 'text', 'field' => 'unigene_for_search_interpro_value', 'heading' => 'Interpro');
-	
-	# populate data
-	$result = chado_query($sql, $args);
-	$data = array();
-	while ($row = db_fetch_array($result)) {
-		$data[] = array ('unigene_for_search_feature_name' => $row['unigene_for_search_feature_name'],
-									 'hyperlink_unigene_for_search_feature_name' => "$base_url/ID".$row['unigene_for_search_feature_id'],
-									 'unigene_for_search_organism_common_name' => $row['unigene_for_search_organism_common_name'],
-									 'unigene_for_search_feature_seqlen' => $row['unigene_for_search_feature_seqlen'],
-									 'unigene_for_search_feature_type' => $row['unigene_for_search_feature_type'],
-									 'unigene_for_search_go_term' => $row['unigene_for_search_go_term'],
-									 'unigene_for_search_blast_value' => $row['unigene_for_search_blast_value'],
-									 'unigene_for_search_kegg_value' => $row['unigene_for_search_kegg_value'],
-									 'unigene_for_search_interpro_value' => $row['unigene_for_search_interpro_value']
-									 );
-	}
-	# add headers and data
-	$param_excel['contents']['sheet']['headers']= $headers;
-	$param_excel['contents']['sheet']['data']= $data;
-	# generate excel
-	ml_generate_excel($param_excel);
-	print "&nbsp;&nbsp;&nbsp;<a href=\"$path_url\">Download as Excel file</a>";
-	
-}
-*/?>
-
-<?php 
-# ----------------------------------------- #
-# [UD] ml_generate_excel
-# ----------------------------------------- #
-function ml_generate_excel ($param_excel) {
-	# get and update parameters
-	$writer		= ($param_excel['version'] == '2007') ? 'Excel2007' : 'Excel5';
-	$link_clr	= (empty($param_excel['link_clr'])) ? '0000FF' : $param_excel['link_clr'];
-	$filename	= $param_excel['filename'];
-	if (!preg_match("/(xls|xlsx)$/", $filename)) {
-		$filename = ($param_excel['version'] == '2007') ? $filename.'.xlsx' : $filename.'.xls';
-	}
-	/*********************************************/
-	# create an excel file
-	/*********************************************/
-	# create new PHPExcel object
-	$excel = new PHPExcel();
-	# Set properties
-	$excel->getProperties()->setCreator("Main Lab");
-	$excel->getProperties()->setLastModifiedBy("Main Lab");
-	$excel->getProperties()->setTitle("Office 2007 XLSX Document");
-	$excel->getProperties()->setSubject("");
-	$excel->getProperties()->setKeywords("");
-	$excel->getProperties()->setCategory("");
-	$excel->getProperties()->setDescription("");
-	# set default styles
-	$excel->getDefaultStyle()->getFont()->setName('Times New Roman');
-	$excel->getDefaultStyle()->getFont()->setSize(11);
-	# create worksheets
-	$sheet_no= 0;
-	foreach ($param_excel['contents'] as $sheet_name => $sheet) {
-		if ($sheet_no != 0) {
-			# add a new worksheet
-			$excel->createSheet();
-		}	
-		# set active sheet
-		$excel->setActiveSheetIndex($sheet_no);		
-		# get current worksheet
-		$worksheet = $excel->getActiveSheet();	
-		# set title for this sheet
-		$worksheet->setTitle($sheet_name);
-		# get headers
-		$headers= $param_excel['contents'][$sheet_name]['headers'];
-		# set style and headings for headers
-		foreach ($headers as $col_chr => $prop) {
-			# set alignment for column
-			$align= PHPExcel_Style_Alignment::HORIZONTAL_LEFT;
-			if ($prop['align'] == 'right') {
-				$align= PHPExcel_Style_Alignment::HORIZONTAL_RIGHT;
-			}
-			else if ($prop['align'] == 'center') {
-				$align= PHPExcel_Style_Alignment::HORIZONTAL_CENTER;
-			}
-			$worksheet->getStyle($col_chr.'1')->getAlignment()->setHorizontal($align);		
-			# set width
-			$worksheet->getColumnDimension($col_chr)->setWidth($prop['width']);
-			$worksheet->getStyle($col_chr.'1')->getFont()->setBold(true);
-			$worksheet->getStyle($col_chr.'1')->getFill()->setFillType(PHPExcel_Style_Fill::FILL_SOLID);
-			$worksheet->getStyle($col_chr.'1')->getFill()->getStartColor()->setARGB('FFCDCDCD');
-			$worksheet->setCellValue($col_chr.'1', $prop['heading']);
-		}		
-		# add data to current worksheet
-		foreach ($param_excel['contents'][$sheet_name]['data'] as $idx => $row) {
-			foreach ($headers as $col_chr => $prop) {
-				$loc= $col_chr.($idx+2);
-				# set alignment for cell
-				$align= PHPExcel_Style_Alignment::HORIZONTAL_LEFT;
-				if ($prop['align'] == 'right') {
-					$align= PHPExcel_Style_Alignment::HORIZONTAL_RIGHT;
-				}
-				else if ($prop['align'] == 'center') {
-					$align= PHPExcel_Style_Alignment::HORIZONTAL_CENTER;
-				}
-				$worksheet->getStyle($loc)->getAlignment()->setHorizontal($align);
-				
-				if (!empty($row[$prop['field']])) {
-					# set cell value
-					if ($prop['type'] == 'text') {
-						$worksheet->setCellValue($loc, $row[$prop['field']]);
-					}
-					else if ($prop['type'] == 'hyperlink') {
-						$worksheet->setCellValue($loc, $row[$prop['field']]);
-						if ($row['hyperlink_'.$prop['field']]) {
-							# add underline
-							$worksheet->getStyle($loc)->getFont()->setUnderline(PHPExcel_Style_Font::UNDERLINE_SINGLE);
-							# set link color
-							$worksheet->getStyle($loc)->getFont()->getColor()->setRGB($link_clr);		
-							# set URL
-							$worksheet->getCell($loc)->getHyperlink()->setUrl($row['hyperlink_'.$prop['field']]);
-						}
-					}
-				}
-			}
-		}
-		$sheet_no++;
-	}	
-		# create excel file
- 		$excel->setActiveSheetIndex(0);
- 		$objWriter = PHPExcel_IOFactory::createWriter($excel, $writer);
- 		$objWriter->save($filename);
-}
-?>

theme/tripal_theme_core/css/tripal.css

@@ -1,165 +0,0 @@
-.tripal-info-box {
-   width: 100%;
-   padding-bottom: 10px;
-}
-.tripal-table {
-   width: 100%; 
-}
-.tripal-table th, 
-.tripal-table td {
-   vertical-align:text-top;
-   padding-left: 10px;
-   padding-right: 10px;
-   padding-top: 5px;
-   padding-bottom: 5px;
-}
-.tripal-table-horz {
-   border-top: 2px solid #999999;
-   border-bottom: 2px solid #999999; 
-}
-
-/* settings for vertical tables (headers across left-side) */
-table.tripal-table-vert .tripal-table-even-row th {
-   background-color: #EEEEEE;
-   font-weight: none;
-   text-align: right;
-}
-table.tripal-table-vert .tripal-table-odd-row th {
-   background-color: #FFFFFF;
-   text-align: right;
-}
-table.tripal-table-vert .tripal-table-even-row {
-   background-color: #EEEEEE;
-   border-top: 1px solid #CCCCCC;
-   border-bottom: 1px solid #CCCCCC;
-}
-table.tripal-table-vert .tripal-table-odd-row {
-   background-color: #FFFFFF;
-   border-top: 1px solid #CCCCCC;
-   border-bottom: 1px solid #CCCCCC;
-}
-/* settings for horizontal tables (headers across top) */
-table.tripal-table-horz th {
-   background-color: #EEEEFF;
-   font-weight: none;
-   text-align: left;
-}
-table.tripal-table-horz .tripal-table-even-row {
-   background-color: #FFFFFF;
-   font-weight: none;
-   text-align: left;
-   border-top: 1px solid #CCCCCC;
-   border-bottom: 1px solid #CCCCCC;
-}
-table.tripal-table-horz .tripal-table-odd-row {
-   background-color: #EEEEEE;
-   text-align: left;
-   border-top: 1px solid #CCCCCC;
-   border-bottom: 1px solid #CCCCCC;
-}
-
-.tripal-info-box-title {
-  font-size: 1.5em;
-  padding-bottom: 15px;
-
-}
-.tripal-info-box-desc {
-  padding-bottom: 15px;
-}
-/* hide the title when inside of a block on a panel */
-.pane-block .tripal-info-box-title {
-   visibility: hidden;
-   padding: 0;
-   margin: 0;
-   height: 0px;
-}
-
-/* Ajax loader */
-#tripal_ajaxLoading {
-   position: fixed;
-   top: 40%;
-   left: 40%;
-   padding: 15px;
-   border: 1px solid #000000;
-   background-color: #EEEEEE;
-   opacity: 0.75;
-   -moz-opacity: 0.75;
-   z-index: 10;
-}
-
-#tripal_ajaxLoading #loadingText {
-   font-weight: bold;
-   font-size: 1.5em;
-   color: #000000;
-}
-
-/* Restrict the list of checkboxes in a 300px window */
-.form-checkboxes {
-   height: auto;
-   max-height: 300px;
-   overflow: auto;
-}
-
-/* no results message */
-.tripal-no-results {
-   font-style: italic;
-   padding: 10px;
-   background-color: #FFEEEE;
-}
-
-.tripal_toc {
-  float: left;
-  width: 20%;
-  background-color: #EEEEEE;
-
-  -moz-border-radius: 15px;
-  -webkit-border-radius: 15px;
-  -khtml-border-radius: 15px;
-  border-radius: 15px;
-
-  -moz-box-shadow: 3px 3px 4px #888888;
-  -webkit-box-shadow: 3px 3px 4px #888888;
-  box-shadow: 3px 3px 4px #888888;
-
-
-
-  padding: 20px;
-  min-height: 500px;
-  border-style:solid;
-  border-width:1px;
-}
-.tripal_toc ul {
- margin-left: 0px;
- margin-top: 5px;
- padding-left: 15px;
-}
-.tripal_toc_title {
-  font-size: 1.5em;
-  line-height: 110%;
-  padding-bottom: 10px;
-}
-.tripal_toc_desc {
- /*font-style: italic; */
-}
-.tripal_details {
-  float: left;
-  width: 69%;
-  background-color: #FFFFFF;
-
-  -moz-border-radius: 15px;
-  -webkit-border-radius: 15px;
-  -khtml-border-radius: 15px;
-  border-radius: 15px;
-
-  -moz-box-shadow: 3px 3px 4px #888888;
-  -webkit-box-shadow: 3px 3px 4px #888888;
-  box-shadow: 3px 3px 4px #888888;
-  padding: 20px;
-  min-height: 500px;
-  margin-right: 10px;
-  margin-bottom: 10px;
-  border-style:solid;
-  border-width:1px;
-  
-  overflow:auto;
-}

theme/tripal_theme_core/css/tripal_bulk_loader.css

@@ -1,3 +0,0 @@
-.tripal_bulk_loader_template_col {
-	width:100px;
-}

theme/tripal_theme_core/css/tripal_cv.css

@@ -1,35 +0,0 @@
-/*
- Copyright 2009 Clemson University
-*/
-
-.treeview .placeholder {
-	background: url(images/ajax-loader.gif) 0 0 no-repeat;
-	height: 16px;
-	width: 16px;
-	display: block;
-}
-
-#tripal_cv_cvterm_info_box {
-   position: absolute;
-   top: 0%; left: 30%;
-   padding:10px;
-   width:650px;
-   display: none;
-   border: 1px solid #000000;
-   background-color: #EFEFEF;
-   opacity: 0.90;
-   -moz-opacity: 0.90;
-   z-index: 10;
-   -webkit-border-radius: 5px;
-   -moz-border-radius: 5px;
-   border-radius: 5px;
-   color: #000000;
-}
-
-#tripal_cv_cvterm_info_box h3 {
-   border-bottom: 1px solid #AAAAAA;
-}
-
-#tripal_cv_cvterm_info {
-   color: #000000;
-}

theme/tripal_theme_core/css/tripal_feature.css

@@ -1,76 +0,0 @@
-#tripal_feature-featureloc_sequence,
-#tripal_feature-sequence-residues {
-  /*height: 500px;*/
-  /*overflow: scroll;*/
-  background-color: #FFFFFF;
-  font-family: monospace;
-}
-
-div#tripal_feature-featureloc_sequence-legend {
-   padding: 10px;
-   margin: 10px;
-}
-/* styles for cvterm types in sequences */
-div#tripal_feature-featureloc_sequence-legend span {
-   margin: 5px;
-   padding: 10px;
-}
-span.tripal_feature-featureloc_sequence-five_prime_UTR {
-   background-color: #99FF99;
-}
-
-span.tripal_feature-featureloc_sequence-three_prime_UTR {
-   background-color: #FF9999;
-}
-
-span.tripal_feature-featureloc_sequence-CDS {
-   background-color: #FFFF99;
-}
-
-span.tripal_feature-featureloc_sequence-mRNA {
-   background-color: #FFFF99;
-}
-
-span.tripal_feature-featureloc_sequence-exon {
-   background-color: #9999FF;
-}
-
-span.tripal_feature-featureloc_sequence-intron {
-   background-color: #FFFFFF;
-}
-/* information tables on the feature pages */
-table.tripal_feature-relationships-subject-table th {
-   background-color: #EEEEEE;
-   text-align: left;
-}
-table.tripal_feature-relationships-object-table th {
-   background-color: #EEEEEE;
-   text-align: left;
-}
-table.tripal_feature-locations-table th {
-   background-color: #EEEEEE;
-   text-align: left;
-}
-table.tripal_feature-references-table th {
-   background-color: #EEEEEE;
-   text-align: left;
-
-}
-/* feature relationship edit form */
-#tripal-feature-edit-ALL-relationships-form .form-item,
-#tripal-feature-edit-ALL-db-references-form .form-item {
-   float: left;
-   margin: 0 10px 0 0;
-   
-}
-#tripal-feature-edit-ALL-db-references-form .form-submit {
-   float: none;
-   display: block;
-}
-.tripal_feature-obsolete {
-   color: red;
-   font-weight: bold;
-   font-style: italic;
-   padding-bottom: 15px; 
-   text-align: center;
-}

theme/tripal_theme_core/css/tripal_organism.css

@@ -1,31 +0,0 @@
-
-#tripal_organism-image-box {
-   float: left;
-   margin-left: 10px;
-   margin-bottom: 10px;
-   margin-right: 10px;
-   width: auto;
-}
-#tripal_organism-image-box img {
-   max-height: 200px;
-}
-
-#tripal_organism-base-box {
-   float: left;
-}
-#tripal_organism-description-box {
-   clear: left;
-   width: auto;
-}
-
-#tripal_organism-base-box img {
- float: left;
- margin-bottom: 10px;
-}
-#tripal_organism-table-base {
- float: left;
- width: 330px;
- margin-left: 10px;
- margin-bottom: 10px;
-}
-

theme/tripal_theme_core/js/jgcharts/.project

@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<projectDescription>
-	<name>jgcharts</name>
-	<comment></comment>
-	<projects>
-	</projects>
-	<buildSpec>
-		<buildCommand>
-			<name>net.sourceforge.phpeclipse.parserbuilder</name>
-			<arguments>
-			</arguments>
-		</buildCommand>
-	</buildSpec>
-	<natures>
-		<nature>net.sourceforge.phpeclipse.phpnature</nature>
-	</natures>
-</projectDescription>

theme/tripal_theme_core/js/jgcharts/.settings/org.eclipse.core.resources.prefs

@@ -1,3 +0,0 @@
-#Thu Feb 19 13:56:42 CET 2009
-eclipse.preferences.version=1
-encoding/<project>=UTF-8

theme/tripal_theme_core/js/jgcharts/doc/custom.html

@@ -1,413 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
-    <meta http-equiv="refresh" content="0; url=../include/demo/">
-    <meta http-equiv="Content-type" content="text/html; charset=UTF-8" />
-    <title>jgcharts - jQuery Google Charts</title>
-    <meta http-equiv="Content-Language" content="en-us" />
-    <meta name="author" content="Massimiliano Balestrieri" />
-    <script type="text/javascript" src="../lib/jquery/jquery-1.2.6.min.js"></script>
-    <script type="text/javascript" src="../lib/farbtastic/farbtastic.js"></script>
-    <link rel="stylesheet" href="../lib/farbtastic/farbtastic.css" type="text/css" />
-    <script type="text/javascript" src="../lib/metadata/jquery.metadata.pack.js"></script>
-    <script type="text/javascript" src="../lib/sugar-arrays.js"></script>
-    <script type="text/javascript" src="../lib/iterators.js"></script>
-    <script type="text/javascript" src="../lib/jquery.tablelib.js"></script>
-    <script type="text/javascript" src="../jgcharts.js"></script>
-    <script type="text/javascript" src="../plugins/table/jgtable.js"></script>
-    <script type="text/javascript"><!--
-        jQuery(document).ready(function(){
-            var json = jQuery.getJSON(
-                "json/delpiero.json",
-	            //wait json data
-	            function(json){
-	                var data_custom = [];
-	                for(var x= 0;x< jQuery("#table-9").find("tbody > tr").size();x++){
-		                data_custom.push(jQuery.map( jQuery("#table-9").find("tbody > tr:eq(" + x + ") > td"),
-	                               function(td,index){
-                                        if(index % 11 == 1 || index % 11 == 2){
-                                            if(parseInt(jQuery(td).text()))
-                                                return parseInt(jQuery(td).text());
-                                            else
-                                                return 0;
-                                        } 
-                                   }
-	                    ));
-	                    
-	                }
-	                var axis_custom = jQuery.map( jQuery("#table-9").find("tbody > tr > th.custom"),
-                               function(th) { return jQuery(th).text(); }
-                    );
-                    var legend_custom = ["presenze", "gol"];
-                    
-                    json.axis_labels = axis_custom;
-                    json.data = data_custom;
-                    json.legend = legend_custom;
-                    
-                    
-		            jQuery(".jgtable-json").jgtable(json);
-		            
-		            var data_custom = [];
-                    for(var x= 0;x< jQuery("#table-9").find("tbody > tr").size();x++){
-                        data_custom.push(jQuery.map( jQuery("#table-9").find("tbody > tr:eq(" + x + ") > td"),
-                                   function(td,index){
-                                        if(index % 11 == 9 || index % 11 == 10){
-                                            if(parseInt(jQuery(td).text()))
-                                                return parseInt(jQuery(td).text());
-                                            else
-                                                return 0;
-                                        } 
-                                   }
-                        ));
-                        
-                    }
-                    json.data = data_custom;
-                    json.title = 'Gol e presenze totali';
-                    
-		            jQuery(".jgtable-json").jgtable(json);
-		            jQuery(".example h1").click(function(){
-		                jQuery(this).parent().find("div, table").toggle();
-		            });
-		            //.trigger("click");
-	        });
-            
-        });
-    --></script>
-    <style type="text/css">
-        body{font-family:Trebuchet MS,Arial,FreeSans,sans-serif;}
-        .example h1{border:1px dashed #000;padding:3px;}
-        table {width:100%}
-        table tbody tr td,table tbody tr th,table thead tr th,table tfoot tr th
-        {text-align:left;font-weight:normal;font-size:80%;border:1px dashed #000; padding:3px; margin:1px}
-    </style>
-</head>
-<body>
-<h1>JQuery Google Charts 0.91 - Examples (<a href="dashboard.html">try dashboard for write metadata</a>)</h1>
-<div class="example">
-<h1>Example Custom - Alessandro Del Piero</h1>
-<table id="table-9" class="jgtable-json">
-  <thead>
-    <tr>
-    <th colspan="2">Cronologia</th>
-    <th colspan="2">Campionato</th>
-    <th colspan="2">Coppe di Lega<small><sup>*</sup></small></th>
-    <th colspan="2">Coppe Europee<small><sup>**</sup></small></th>
-    <th colspan="2">Coppe Internazionali<small><sup>***</sup></small></th>
-    <th colspan="2">Totale</th>
-  </tr>
-  <tr>
-    <th>Stagione - Squadra</th>
-    <th>Serie</th>
-    <th>Presenze</th>
-    <th>Gol</th>
-    <th>Presenze</th>
-    <th>Gol</th>
-    <th>Presenze</th>
-    
-    <th>Gol</th>
-    <th>Presenze</th>
-    <th>Gol</th>
-    <th>Presenze</th>
-    <th>Gol</th>
-  </tr>
-  </thead>
-  <tfoot>
-    <tr>
-        <th colspan="2">Totale</th>
-        <th>417</th>
-        <th>176</th>
-        <th>51</th>
-        <th>22</th>
-        <th>105</th>
-        <th>43</th>
-        <th>1</th>
-        
-        <th>1</th>
-        <th>574</th>
-        <th>242</th>
-    </tr>
-    </tfoot>
-  <tbody>
-  
-  <tr>
-	<th class="custom">1991-92 - Padova</th>
-	
-	<td>B</td>
-	<td>4</td>
-	<td>-</td>
-	<td>-</td>
-	<td>-</td>
-	<td>-</td>
-	<td>-</td>
-	<td>-</td>
-	<td>-</td>
-	
-	<td>4</td>
-	<td>-</td>
-	</tr>
-	<tr>
-	<th class="custom">1992-93 - Juventus</th>
-	<td>B</td>
-	<td>10</td>
-	<td>1</td>
-	
-	<td>-</td>
-	<td>-</td>
-	<td>-</td>
-	<td>-</td>
-	<td>-</td>
-	<td>-</td>
-	<td>10</td>
-	<td>1</td>
-	</tr>
-	
-	<tr>
-	<th class="custom">1993-94 - Juventus</th>
-	<td>A</td>
-	<td>11</td>
-	<td>5</td>
-	<td>1</td>
-	<td>-</td>
-	<td>2</td>
-	
-	<td>-</td>
-	<td>-</td>
-	<td>-</td>
-	<td>14</td>
-	<td>5</td>
-	</tr>
-	<tr>
-	<th class="custom">1994-95 - Juventus</th>
-	
-	<td>A</td>
-	<td>29</td>
-	<td>8</td>
-	<td>10</td>
-	<td>1</td>
-	<td>11</td>
-	<td>1</td>
-	<td>-</td>
-	<td>-</td>
-	
-	<td>50</td>
-	<td>10</td>
-	</tr>
-	<tr>
-	<th class="custom">1995-96 - Juventus</th>
-	<td>A</td>
-	<td>29</td>
-	<td>6</td>
-	
-	<td>3</td>
-	<td>1</td>
-	<td>11</td>
-	<td>6</td>
-	<td>-</td>
-	<td>-</td>
-	<td>43</td>
-	<td>13</td>
-	</tr>
-	
-	<tr>
-	<th class="custom">1996-97 - Juventus</th>
-	<td>A</td>
-	<td>22</td>
-	<td>8</td>
-	<td>4</td>
-	<td>-</td>
-	<td>8</td>
-	
-	<td>6</td>
-	<td>1</td>
-	<td>1</td>
-	<td>35</td>
-	<td>15</td>
-	</tr>
-	<tr>
-	<th class="custom">1997-98 - Juventus</th>
-	
-	<td>A</td>
-	<td>32</td>
-	<td>21</td>
-	<td>5</td>
-	<td>1</td>
-	<td>10</td>
-	<td>10</td>
-	<td>-</td>
-	<td>-</td>
-	
-	<td>47</td>
-	<td>32</td>
-	</tr>
-	<tr>
-	<th class="custom">1998-99 - Juventus</th>
-	<td>A</td>
-	<td>8</td>
-	<td>2</td>
-	
-	<td>2</td>
-	<td>1</td>
-	<td>4</td>
-	<td>-</td>
-	<td>-</td>
-	<td>-</td>
-	<td>14</td>
-	<td>3</td>
-	</tr>
-	
-	<tr>
-	<th class="custom">1999-00 - Juventus</th>
-	<td>A</td>
-	<td>34</td>
-	<td>9</td>
-	<td>2</td>
-	<td>1</td>
-	<td>9</td>
-	
-	<td>2</td>
-	<td>-</td>
-	<td>-</td>
-	<td>45</td>
-	<td>12</td>
-	</tr>
-	<tr>
-	<th class="custom">2000-01 - Juventus</th>
-	
-	<td>A</td>
-	<td>25</td>
-	<td>9</td>
-	<td>2</td>
-	<td>-</td>
-	<td>6</td>
-	<td>-</td>
-	<td>-</td>
-	<td>-</td>
-	
-	<td>33</td>
-	<td>9</td>
-	</tr>
-	<tr>
-	<th class="custom">2001-02 - Juventus</th>
-	<td>A</td>
-	<td>32</td>
-	<td>16</td>
-	
-	<td>4</td>
-	<td>1</td>
-	<td>10</td>
-	<td>4</td>
-	<td>-</td>
-	<td>-</td>
-	<td>46</td>
-	<td>21</td>
-	</tr>
-	
-	<tr>
-	<th class="custom">2002-03 - Juventus</th>
-	<td>A</td>
-	<td>24</td>
-	<td>16</td>
-	<td>1</td>
-	<td>2</td>
-	<td>13</td>
-	
-	<td>5</td>
-	<td>-</td>
-	<td>-</td>
-	<td>38</td>
-	<td>23</td>
-	</tr>
-	<tr>
-	<th class="custom">2003-04 - Juventus</th>
-	
-	<td>A</td>
-	<td>22</td>
-	<td>8</td>
-	<td>5</td>
-	<td>3</td>
-	<td>4</td>
-	<td>3</td>
-	<td>-</td>
-	<td>-</td>
-	
-	<td>31</td>
-	<td>14</td>
-	</tr>
-	<tr>
-	<th class="custom">2004-05 - Juventus</th>
-	<td>A</td>
-	<td>30</td>
-	<td>14</td>
-	
-	<td>1</td>
-	<td>-</td>
-	<td>10</td>
-	<td>3</td>
-	<td>-</td>
-	<td>-</td>
-	<td>41</td>
-	<td>17</td>
-	</tr>
-	
-	<tr>
-	<th class="custom">2005-06 - Juventus</th>
-    <td>A</td>
-	<td>33</td>
-	<td>12</td>
-	<td>5</td>
-	<td>5</td>
-	<td>7</td>
-	
-	<td>3</td>
-	<td>-</td>
-	<td>-</td>
-	<td>45</td>
-	<td>20</td>
-	</tr>
-	<tr>
-	<th class="custom">2006-07 - Juventus</th>
-    
-	<td>B</td>
-	<td>35</td>
-	<td>20</td>
-	<td>2</td>
-	<td>3</td>
-	<td>-</td>
-	<td>-</td>
-	<td>-</td>
-	<td>-</td>
-	
-	<td>37</td>
-	<td>23</td>
-	</tr>
-	
-	<tr>
-	<th class="custom">2007-08 - Juventus</th>
-    <td>A</td>
-	<td>37</td>
-	<td>21</td>
-	
-	<td>4</td>
-	<td>3</td>
-	<td>-</td>
-	<td>-</td>
-	<td>-</td>
-	<td>-</td>
-	<td>41</td>
-	<td>24</td>
-	</tr>
-	
-	
-	</tbody>
-	
-</table>
-</div>
-
-<script src="http://www.google-analytics.com/urchin.js" type="text/javascript"></script>
-<script type="text/javascript">
-_uacct = "UA-258871-1";
-urchinTracker();
-</script>
-
-</body>
-</html>    

theme/tripal_theme_core/js/jgcharts/doc/dashboard.html

@@ -1,495 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
-  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en-us">
-<head>
-    <title>jgcharts - jQuery Google Charts</title>
-    <meta http-equiv="refresh" content="0; url=../include/demo/">
-    <meta http-equiv="Content-type" content="text/html; charset=UTF-8" />
-    <meta http-equiv="Content-Language" content="en-us" />
-    <meta name="author" content="Massimiliano Balestrieri" />
-    <script type="text/javascript" src="../lib/jquery-1.2.5.pack.js"></script>
-    <script type="text/javascript" src="../lib/farbtastic/farbtastic.js"></script>
-    <link rel="stylesheet" href="../lib/farbtastic/farbtastic.css" type="text/css" />
-    <script type="text/javascript" src="../lib/sugar-arrays.js"></script>
-    <script type="text/javascript" src="../lib/iterators.js"></script>
-    <script type="text/javascript" src="../lib/jquery.tablelib.js"></script>
-    <script type="text/javascript" src="../jgcharts.js"></script>
-    <script type="text/javascript" src="../plugins/dashboard/jgdash.js"></script>
-    <script type="text/javascript"><!--
-        jQuery(document).ready(function(){
-            jQuery("#dash").jgdash({
-                    target  : "#target", 
-                    debug   : "#debug",
-                    url     : "../plugins/dashboard/",
-                    sources : ["table-0","table-1","table-2","table-3","table-4"] 
-            });
-        });
-    --></script>
-    <style type="text/css">
-        table tbody tr td,table tbody tr th,table thead tr th
-        {font-size:80%;border:1px dashed #000; padding:3px; margin:1px}
-    </style>
-</head>
-<body>
-<div id="test"></div>
-<div id="target"></div>
-<div id="debug"></div>
-<div id="dash"></div>
-
-<div>
-http://www.istat.it/dati/dataset/20080429_00/
-
-Tavola 1        
-Indici dei prezzi alla produzione dei prodotti industriali venduti sul mercato interno.
-Raggruppamento Principale di Industrie: Energia - Serie storica 2003-2008
-</div>
-<table id="table-0">
-<thead>
-<tr>
-    <th></th>
-    <th class="serie">CA</th>
-    <th class="serie">DF</th>
-</tr>
-</thead>
-<tbody>
-   <tr>
-    <th class="serie">01-03</th>
-    <td>105.7</td>
-    <td>97.9</td>
-  </tr>
-  <tr>
-    <th class="serie">02-03</th>
-    <td>108.1</td>
-    <td>101.6</td>
-  </tr>
-  <tr>
-    <th class="serie">03-03</th>
-    <td>110.7</td>
-    <td>102.9</td>
-  </tr>
-  
-  <tr>
-    <th class="serie">04-03</th>
-    <td>111.0</td>
-    <td>93.7</td>
-  </tr>
-  <tr>
-    <th class="serie">05-03</th>
-    <td>110.0</td>
-    <td>89.8</td>
-  </tr>
-  <tr>
-    <th class="serie">06-03</th>
-    <td>109.0</td>
-    <td>90.7</td>
-  </tr>
-  <tr>
-    <th class="serie">07-03</th>
-    <td>107.5</td>
-    <td>93.0</td>
-  </tr>
-  <tr>
-    <th class="serie">08-03</th>
-    <td>106.1</td>
-    <td>94.5</td>
-  </tr>
-  <tr>
-    <th class="serie">09-03</th>
-    <td>104.3</td>
-    <td>91.9</td>
-  </tr>
-  <tr>
-    <th class="serie">10-03</th>
-    <td>102.0</td>
-    <td>93.9</td>
-  </tr>
-  <tr>
-    <th class="serie">11-03</th>
-    <td>102.8</td>
-    <td>93.6</td>
-  </tr>
-  <tr>
-    <th class="serie">12-03</th>
-    <td>103.8</td>
-    <td>92.6</td>
-  </tr>
-  
-  <tr>
-    <th class="serie">01-04</th>
-    <td>102.9</td>
-    <td>94.0</td>
-  </tr>
-  <tr>
-    <th class="serie">02-04</th>
-    <td>102.1</td>
-    <td>92.7</td>
-  </tr>
-  <tr>
-    <th class="serie">03-04</th>
-    <td>100.6</td>
-    <td>96.0</td>
-  </tr>
-  
- <tr>
-    <th class="serie">04-04</th>
-    <td>101.7</td>
-    <td>97.9</td>
-  </tr>
-  <tr>
-    <th class="serie">05-04</th>
-    <td>101.8</td>
-    <td>105.0</td>
-  </tr>
-  <tr>
-    <th class="serie">06-04</th>
-    <td>103.3</td>
-    <td>104.1</td>
-  </tr>
-  <tr>
-    <th class="serie">07-04</th>
-    <td>104.0</td>
-    <td>105.1</td>
-  </tr>
-  <tr>
-    <th class="serie">08-04</th>
-    <td>103.7</td>
-    <td>108.1</td>
-  </tr>
-  <tr>
-    <th class="serie">09-04</th>
-    <td>108.4</td>
-    <td>108.4</td>
-  </tr>
-  <tr>
-    <th class="serie">10-04</th>
-    <td>109.4</td>
-    <td>113.8</td>
-  </tr>
-  <tr>
-    <th class="serie">11-04</th>
-    <td>112.0</td>
-    <td>109.1</td>
-  </tr>
-  <tr>
-    <th class="serie">12-04</th>
-    <td>112.6</td>
-    <td>106.3</td>
-  </tr>
-  <tr>
-    <th class="serie">01-05</th>
-    <td>115.5</td>
-    <td>106.7</td>
-  </tr>
-  <tr>
-    <th class="serie">02-05</th>
-    <td>115.7</td>
-    <td>108.8</td>
-  </tr>
-  <tr>
-    <th class="serie">03-05</th>
-    <td>114.7</td>
-    <td>118.8</td>
-  </tr>
-  <tr>
-    <th class="serie">04-05</th>
-    <td>115.9</td>
-    <td>120.4</td>
-  </tr>
-  <tr>
-    <th class="serie">05-05</th>
-    <td>116.2</td>
-    <td>115.9</td>
-  </tr>
-  <tr>
-    <th class="serie">06-05</th>
-    <td>118.0</td>
-    <td>124.7</td>
-  </tr>
-  <tr>
-    <th class="serie">07-05</th>
-    <td>123.3</td>
-    <td>126.5</td>
-  </tr>
-  <tr>
-    <th class="serie">08-05</th>
-    <td>127.6</td>
-    <td>131.6</td>
-  </tr>
-  <tr>
-    <th class="serie">09-05</th>
-    <td>130.3</td>
-    <td>134.0</td>
-  </tr>
-  <tr>
-    <th class="serie">10-05</th>
-    <td>135.5</td>
-    <td>135.7</td>
-  </tr>
-  <tr>
-    <th class="serie">11-05</th>
-    <td>138.2</td>
-    <td>126.4</td>
-  </tr>
-  <tr>
-    <th class="serie">12-05</th>
-    <td>139.6</td>
-    <td>127.4</td>
-  </tr>
-  <tr>
-    <th class="serie">01-06</th>
-    <td>145.1</td>
-    <td>131.0</td>
-  </tr>
-  <tr>
-    <th class="serie">02-06</th>
-    <td>146.4</td>
-    <td>129.9</td>
-  </tr>
-  <tr>
-    <th class="serie">03-06</th>
-    <td>147.1</td>
-    <td>133.7</td>
-  </tr>
-  <tr>
-    <th class="serie">04-06</th>
-    <td>149.0</td>
-    <td>138.4</td>
-  </tr>
-  <tr>
-    <th class="serie">05-06</th>
-    <td>150.3</td>
-    <td>141.0</td>
-  </tr>
-  <tr>
-    <th class="serie">06-06</th>
-    <td>151.3</td>
-    <td>139.3</td>
-  </tr>
-  <tr>
-    <th class="serie">07-06</th>
-    <td>153.4</td>
-    <td>145.3</td>
-  </tr>
-  <tr>
-    <th class="serie">08-06</th>
-    <td>152.7</td>
-    <td>142.9</td>
-  </tr>
-  <tr>
-    <th class="serie">09-06</th>
-    <td>152.9</td>
-    <td>129.2</td>
-  </tr>
-  <tr>
-    <th class="serie">10-06</th>
-    <td>152.2</td>
-    <td>126.0</td>
-  </tr>
-  <tr>
-    <th class="serie">11-06</th>
-    <td>151.9</td>
-    <td>124.8</td>
-  </tr>
-  <tr>
-    <th class="serie">12-06</th>
-    <td>150.1</td>
-    <td>125.9</td>
-  </tr>
-  <tr>
-    <th class="serie">01-07</th>
-    <td>148.2</td>
-    <td>118.9</td>
-  </tr>
-  <tr>
-    <th class="serie">02-07</th>
-    <td>145.3</td>
-    <td>122.9</td>
-  </tr>
-  <tr>
-    <th class="serie">03-07</th>
-    <td>142.9</td>
-    <td>127.7</td>
-  </tr>
-  <tr>
-    <th class="serie">04-07</th>
-    <td>142.6</td>
-    <td>134.4</td>
-  </tr>
-  <tr>
-    <th class="serie">05-07</th>
-    <td>144.0</td>
-    <td>138.5</td>
-  </tr>
-  <tr>
-    <th class="serie">06-07</th>
-    <td>145.5</td>
-    <td>138.7</td>
-  </tr>
-  <tr>
-    <th class="serie">07-07</th>
-    <td>147.2</td>
-    <td>141.8</td>
-  </tr>
-  <tr>
-    <th class="serie">08-07</th>
-    <td>150.0</td>
-    <td>139.2</td>
-  </tr>
-  <tr>
-    <th class="serie">09-07</th>
-    <td>153.8</td>
-    <td>145.6</td>
-  </tr>
-  <tr>
-    <th class="serie">10-07</th>
-    <td>155.4</td>
-    <td>147.6</td>
-  </tr>
-  <tr>
-    <th class="serie">11-07</th>
-    <td>157.0</td>
-    <td>157.9</td>
-  </tr>
-  <tr>
-    <th class="serie">12-07</th>
-    <td>158.4</td>
-    <td>156.2</td>
-  </tr>
-  <tr>
-    <th class="serie">01-08</th>
-    <td>162.8</td>
-    <td>153.9</td>
-  </tr>
-  <tr>
-    <th class="serie">02-08</th>
-    <td>162.8</td>
-    <td>158.6</td>
-  </tr>
-  <tr>
-    <th class="serie">03-08</th>
-    <td>164.7</td>
-    <td>166.3</td>
-  </tr>
-  <tr>
-    <th class="serie">04-08</th>
-    <td>168.5</td>
-    <td>165.8</td>
-  </tr>
-</tbody>
-</table>
-<table id="table-1">
-  <thead>
-    <tr>
-        <th>Anno</th>
-        <th class="serie">Data 1</th>
-        <th class="serie">Data 2</th>
-        <th class="serie">Data 3</th>
-    </tr>
-  </thead>
-  <tbody>
-    <tr>
-        <th class="serie">2001</th>
-        <td>153</td>
-        <td>60</td>
-        <td>52</td>
-    </tr>
-    <tr>
-        <th class="serie">2002</th>
-        <td>113</td>
-        <td>70</td>
-        <td>60</td>
-    </tr>
-    <tr>
-        <th class="serie">2003</th>
-        <td>120</td>
-        <td>80</td>
-        <td>40</td>
-    </tr>
-  </tbody>
-</table>
-<table id="table-2">
-  <thead>
-    <tr>
-        <th>Anno</th>
-        <th class="serie">Data 1</th>
-        <th class="serie">Data 2</th>
-        <th class="serie">Data 3</th>
-    </tr>
-  </thead>
-  <tbody>
-    <tr>
-        <th class="serie">2001</th>
-        <td>73</td>
-        <td>40</td>
-        <td>423</td>
-    </tr>
-    <tr>
-        <th class="serie">2002</th>
-        <td>63</td>
-        <td>30</td>
-        <td>-40</td>
-    </tr>
-    <tr>
-        <th class="serie">2003</th>
-        <td>2</td>
-        <td>4</td>
-        <td>0</td>
-    </tr>
-  </tbody>
-</table>
-
-<table id="table-3">
-  <thead>
-    <tr>
-        <th>Anno</th>
-        <th class="serie">Data 4</th>
-        <th class="serie">Data 5</th>
-    </tr>
-  </thead>
-  <tbody>
-    <tr>
-        <th class="serie">2001</th>
-        <td>40</td>
-        <td>30</td>
-    </tr>
-    <tr>
-        <th class="serie">2000</th>
-        <td>30</td>
-        <td>40</td>
-    </tr>
-  </tbody>
-</table>
-
-<table id="table-4">
-  <thead>
-    <tr>
-        <th>Anno</th>
-        <th class="serie">Data 4</th>
-        <th class="serie">Data 5</th>
-        <th class="serie">Data 6</th>
-    </tr>
-  </thead>
-  <tbody>
-    <tr>
-        <th class="serie">2001</th>
-        <td>40</td>
-        <td>30</td>
-        <td>20</td>
-    </tr>
-    <tr>
-        <th class="serie">2000</th>
-        <td>30</td>
-        <td>40</td>
-        <td>30</td>
-    </tr>
-  </tbody>
-</table>
-
-<script src="http://www.google-analytics.com/urchin.js" type="text/javascript"></script>
-<script type="text/javascript">
-_uacct = "UA-258871-1";
-urchinTracker();
-</script>
-
-</body>
-</html>    

theme/tripal_theme_core/js/jgcharts/doc/index.html

@@ -1,591 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
-    <meta http-equiv="Content-type" content="text/html; charset=UTF-8" />
-    <title>jgcharts - jQuery Google Charts</title>
-    <meta http-equiv="refresh" content="0; url=../include/demo/">
-    <meta http-equiv="Content-Language" content="en-us" />
-    <meta name="author" content="Massimiliano Balestrieri" />
-    <script type="text/javascript" src="../lib/jquery/jquery-1.3.1.min.js"></script>
-    <script type="text/javascript" src="../lib/farbtastic/farbtastic.js"></script>
-    <link rel="stylesheet" href="../lib/farbtastic/farbtastic.css" type="text/css" />
-    <script type="text/javascript" src="../lib/metadata/jquery.metadata.pack.js"></script>
-    <script type="text/javascript" src="../lib/sugar-arrays.js"></script>
-    <script type="text/javascript" src="../lib/iterators.js"></script>
-    <script type="text/javascript" src="../lib/jquery.tablelib.js"></script>
-    <script type="text/javascript" src="../jgcharts.pack.js"></script>
-    <script type="text/javascript" src="../plugins/table/jgtable.pack.js"></script>
-    <script type="text/javascript"><!--
-        jQuery(document).ready(function(){
-            jQuery(".jgtable").jgtable();
-            jQuery(".example h1").click(function(){
-                jQuery(this).parent().find("div, table").toggle();
-            })
-            .trigger("click");
-            
-            
-        });
-    --></script>
-    <style type="text/css">
-        body{font-family:Trebuchet MS,Arial,FreeSans,sans-serif;}
-        .example h1{border:1px dashed #000;padding:3px;}
-        table {width:100%}
-        table tbody tr td,table tbody tr th,table thead tr th
-        {text-align:left;font-weight:normal;font-size:80%;border:1px dashed #000; padding:3px; margin:1px}
-    </style>
-</head>
-<body>
-<h1>JQuery Google Charts 0.91 - Examples (<a href="dashboard.html">try dashboard for write metadata</a>)</h1>
-<div class="example">
-<h1>Example 1</h1>
-<table id="table-0" class="jgtable {size:'650x450',type:'lc',axis_step:10,title:false,title_color:'000000',title_size:10,bar_width:30,bar_spacing:1,fillarea:true,fillbottom:true,filltop:true,colors:['FFFF00','FFCC00','99CC00'],lines:[[1,1,0],[1,1,0],[1,1,0]],bg:false,bg_type:'solid',bg_angle:90,bg_offset:false,bg_width:20,bg_trasparency:false,chbg:false,chbg_type:'solid',chbg_angle:90,chbg_offset:false,chbg_width:20,chbg_trasparency:false,grid:false,grid_x:10,grid_y:10,grid_line:10,grid_blank:10}">
-<thead>
-<tr>
-    <th></th>
-    <th class="serie">CA</th>
-    <th class="serie">DF</th>
-</tr>
-</thead>
-<tbody>
-   <tr>
-    <th class="serie">01-03</th>
-    <td>105.7</td>
-    <td>97.9</td>
-  </tr>
-  <tr>
-    <th class="serie">02-03</th>
-    <td>108.1</td>
-    <td>101.6</td>
-  </tr>
-  <tr>
-    <th class="serie">03-03</th>
-    <td>110.7</td>
-    <td>102.9</td>
-  </tr>
-  
-  <tr>
-    <th class="serie">04-03</th>
-    <td>111.0</td>
-    <td>93.7</td>
-  </tr>
-  <tr>
-    <th class="serie">05-03</th>
-    <td>110.0</td>
-    <td>89.8</td>
-  </tr>
-  <tr>
-    <th class="serie">06-03</th>
-    <td>109.0</td>
-    <td>90.7</td>
-  </tr>
-  <tr>
-    <th class="serie">07-03</th>
-    <td>107.5</td>
-    <td>93.0</td>
-  </tr>
-  <tr>
-    <th class="serie">08-03</th>
-    <td>106.1</td>
-    <td>94.5</td>
-  </tr>
-  <tr>
-    <th class="serie">09-03</th>
-    <td>104.3</td>
-    <td>91.9</td>
-  </tr>
-  <tr>
-    <th class="serie">10-03</th>
-    <td>102.0</td>
-    <td>93.9</td>
-  </tr>
-  <tr>
-    <th class="serie">11-03</th>
-    <td>102.8</td>
-    <td>93.6</td>
-  </tr>
-  <tr>
-    <th class="serie">12-03</th>
-    <td>103.8</td>
-    <td>92.6</td>
-  </tr>
-  
-  <tr>
-    <th class="serie">01-04</th>
-    <td>102.9</td>
-    <td>94.0</td>
-  </tr>
-  <tr>
-    <th class="serie">02-04</th>
-    <td>102.1</td>
-    <td>92.7</td>
-  </tr>
-  <tr>
-    <th class="serie">03-04</th>
-    <td>100.6</td>
-    <td>96.0</td>
-  </tr>
-  
- <tr>
-    <th class="serie">04-04</th>
-    <td>101.7</td>
-    <td>97.9</td>
-  </tr>
-  <tr>
-    <th class="serie">05-04</th>
-    <td>101.8</td>
-    <td>105.0</td>
-  </tr>
-  <tr>
-    <th class="serie">06-04</th>
-    <td>103.3</td>
-    <td>104.1</td>
-  </tr>
-  <tr>
-    <th class="serie">07-04</th>
-    <td>104.0</td>
-    <td>105.1</td>
-  </tr>
-  <tr>
-    <th class="serie">08-04</th>
-    <td>103.7</td>
-    <td>108.1</td>
-  </tr>
-  <tr>
-    <th class="serie">09-04</th>
-    <td>108.4</td>
-    <td>108.4</td>
-  </tr>
-  <tr>
-    <th class="serie">10-04</th>
-    <td>109.4</td>
-    <td>113.8</td>
-  </tr>
-  <tr>
-    <th class="serie">11-04</th>
-    <td>112.0</td>
-    <td>109.1</td>
-  </tr>
-  <tr>
-    <th class="serie">12-04</th>
-    <td>112.6</td>
-    <td>106.3</td>
-  </tr>
-  <tr>
-    <th class="serie">01-05</th>
-    <td>115.5</td>
-    <td>106.7</td>
-  </tr>
-  <tr>
-    <th class="serie">02-05</th>
-    <td>115.7</td>
-    <td>108.8</td>
-  </tr>
-  <tr>
-    <th class="serie">03-05</th>
-    <td>114.7</td>
-    <td>118.8</td>
-  </tr>
-  <tr>
-    <th class="serie">04-05</th>
-    <td>115.9</td>
-    <td>120.4</td>
-  </tr>
-  <tr>
-    <th class="serie">05-05</th>
-    <td>116.2</td>
-    <td>115.9</td>
-  </tr>
-  <tr>
-    <th class="serie">06-05</th>
-    <td>118.0</td>
-    <td>124.7</td>
-  </tr>
-  <tr>
-    <th class="serie">07-05</th>
-    <td>123.3</td>
-    <td>126.5</td>
-  </tr>
-  <tr>
-    <th class="serie">08-05</th>
-    <td>127.6</td>
-    <td>131.6</td>
-  </tr>
-  <tr>
-    <th class="serie">09-05</th>
-    <td>130.3</td>
-    <td>134.0</td>
-  </tr>
-  <tr>
-    <th class="serie">10-05</th>
-    <td>135.5</td>
-    <td>135.7</td>
-  </tr>
-  <tr>
-    <th class="serie">11-05</th>
-    <td>138.2</td>
-    <td>126.4</td>
-  </tr>
-  <tr>
-    <th class="serie">12-05</th>
-    <td>139.6</td>
-    <td>127.4</td>
-  </tr>
-  <tr>
-    <th class="serie">01-06</th>
-    <td>145.1</td>
-    <td>131.0</td>
-  </tr>
-  <tr>
-    <th class="serie">02-06</th>
-    <td>146.4</td>
-    <td>129.9</td>
-  </tr>
-  <tr>
-    <th class="serie">03-06</th>
-    <td>147.1</td>
-    <td>133.7</td>
-  </tr>
-  <tr>
-    <th class="serie">04-06</th>
-    <td>149.0</td>
-    <td>138.4</td>
-  </tr>
-  <tr>
-    <th class="serie">05-06</th>
-    <td>150.3</td>
-    <td>141.0</td>
-  </tr>
-  <tr>
-    <th class="serie">06-06</th>
-    <td>151.3</td>
-    <td>139.3</td>
-  </tr>
-  <tr>
-    <th class="serie">07-06</th>
-    <td>153.4</td>
-    <td>145.3</td>
-  </tr>
-  <tr>
-    <th class="serie">08-06</th>
-    <td>152.7</td>
-    <td>142.9</td>
-  </tr>
-  <tr>
-    <th class="serie">09-06</th>
-    <td>152.9</td>
-    <td>129.2</td>
-  </tr>
-  <tr>
-    <th class="serie">10-06</th>
-    <td>152.2</td>
-    <td>126.0</td>
-  </tr>
-  <tr>
-    <th class="serie">11-06</th>
-    <td>151.9</td>
-    <td>124.8</td>
-  </tr>
-  <tr>
-    <th class="serie">12-06</th>
-    <td>150.1</td>
-    <td>125.9</td>
-  </tr>
-  <tr>
-    <th class="serie">01-07</th>
-    <td>148.2</td>
-    <td>118.9</td>
-  </tr>
-  <tr>
-    <th class="serie">02-07</th>
-    <td>145.3</td>
-    <td>122.9</td>
-  </tr>
-  <tr>
-    <th class="serie">03-07</th>
-    <td>142.9</td>
-    <td>127.7</td>
-  </tr>
-  <tr>
-    <th class="serie">04-07</th>
-    <td>142.6</td>
-    <td>134.4</td>
-  </tr>
-  <tr>
-    <th class="serie">05-07</th>
-    <td>144.0</td>
-    <td>138.5</td>
-  </tr>
-  <tr>
-    <th class="serie">06-07</th>
-    <td>145.5</td>
-    <td>138.7</td>
-  </tr>
-  <tr>
-    <th class="serie">07-07</th>
-    <td>147.2</td>
-    <td>141.8</td>
-  </tr>
-  <tr>
-    <th class="serie">08-07</th>
-    <td>150.0</td>
-    <td>139.2</td>
-  </tr>
-  <tr>
-    <th class="serie">09-07</th>
-    <td>153.8</td>
-    <td>145.6</td>
-  </tr>
-  <tr>
-    <th class="serie">10-07</th>
-    <td>155.4</td>
-    <td>147.6</td>
-  </tr>
-  <tr>
-    <th class="serie">11-07</th>
-    <td>157.0</td>
-    <td>157.9</td>
-  </tr>
-  <tr>
-    <th class="serie">12-07</th>
-    <td>158.4</td>
-    <td>156.2</td>
-  </tr>
-  <tr>
-    <th class="serie">01-08</th>
-    <td>162.8</td>
-    <td>153.9</td>
-  </tr>
-  <tr>
-    <th class="serie">02-08</th>
-    <td>162.8</td>
-    <td>158.6</td>
-  </tr>
-  <tr>
-    <th class="serie">03-08</th>
-    <td>164.7</td>
-    <td>166.3</td>
-  </tr>
-  <tr>
-    <th class="serie">04-08</th>
-    <td>168.5</td>
-    <td>165.8</td>
-  </tr>
-</tbody>
-</table>
-</div>
-<div class="example">
-<h1>Example 2</h1>
-<table id="table-1" class="jgtable {size:'650x350',type:'bhg',axis_step:1,title:'Example 2',title_color:'000000',title_size:16,bar_width:30,bar_spacing:2,fillarea:true,fillbottom:true,filltop:false,colors:['5131c9','FFCC00','da1b1b'],lines:[[1,1,0],[1,1,0],[1,1,0]],bg:'FFFFFF',bg_type:'gradient',bg_angle:90,bg_offset:'6d6969',bg_width:20,bg_trasparency:false,chbg:'FFFFFF',chbg_type:'solid',chbg_angle:90,chbg_offset:'f8fdbf',chbg_width:10,chbg_trasparency:false,grid:true,grid_x:7,grid_y:10,grid_line:0,grid_blank:0}">
-  <thead>
-    <tr>
-        <th>Anno</th>
-        <th class="serie">Data 1</th>
-        <th class="serie">Data 2</th>
-        <th class="serie">Data 3</th>
-    </tr>
-  </thead>
-  <tbody>
-    <tr>
-        <th class="serie">2001</th>
-        <td>153</td>
-        <td>60</td>
-        <td>52</td>
-    </tr>
-    <tr>
-        <th class="serie">2002</th>
-        <td>113</td>
-        <td>70</td>
-        <td>60</td>
-    </tr>
-    <tr>
-        <th class="serie">2003</th>
-        <td>120</td>
-        <td>80</td>
-        <td>40</td>
-    </tr>
-  </tbody>
-</table>
-</div>
-<div class="example">
-<h1>Example 3</h1>
-<table id="table-2" class="jgtable {size:'400x500',type:'bvg',axis_step:1,title:'Example 3',title_color:'c81e3d',title_size:16,bar_width:30,bar_spacing:2,fillarea:true,fillbottom:true,filltop:false,colors:['1aa22f','FFCC00','da1b1b'],lines:[[1,1,0],[1,1,0],[1,1,0]],bg:'FFFFFF',bg_type:'stripes',bg_angle:90,bg_offset:'b7b4b4',bg_width:10,bg_trasparency:false,chbg:'000000',chbg_type:'solid',chbg_angle:90,chbg_offset:'f8fdbf',chbg_width:10,chbg_trasparency:false,grid:false,grid_x:7,grid_y:10,grid_line:0,grid_blank:0}">
-  <thead>
-    <tr>
-        <th>Anno</th>
-        <th class="serie">Data 1</th>
-        <th class="serie">Data 2</th>
-        <th class="serie">Data 3</th>
-    </tr>
-  </thead>
-  <tbody>
-    <tr>
-        <th class="serie">2001</th>
-        <td>153</td>
-        <td>60</td>
-        <td>52</td>
-    </tr>
-    <tr>
-        <th class="serie">2002</th>
-        <td>113</td>
-        <td>70</td>
-        <td>60</td>
-    </tr>
-    <tr>
-        <th class="serie">2003</th>
-        <td>120</td>
-        <td>80</td>
-        <td>40</td>
-    </tr>
-  </tbody>
-</table>
-</div>
-<div class="example">
-<h1>Example 4</h1>
-<table id="table-3" class="jgtable {size:'700x350',type:'p3',axis_step:1,title:'Example 4',title_color:'28179b',title_size:16,bar_width:30,bar_spacing:2,fillarea:true,fillbottom:true,filltop:false,colors:['a21a9c','FFCC00','da1b1b'],lines:[[1,1,0],[1,1,0],[1,1,0]],bg:'FFFFFF',bg_type:'gradient',bg_angle:90,bg_offset:'b7b4b4',bg_width:10,bg_trasparency:false,chbg:'f7f7f7',chbg_type:'gradient',chbg_angle:90,chbg_offset:'e81711',chbg_width:10,chbg_trasparency:false,grid:false,grid_x:7,grid_y:10,grid_line:0,grid_blank:0}">
-  <thead>
-    <tr>
-        <th>Anno</th>
-        <th class="serie">Data 4</th>
-        <th class="serie">Data 5</th>
-    </tr>
-  </thead>
-  <tbody>
-    <tr>
-        <th class="serie">2001</th>
-        <td>40</td>
-        <td>30</td>
-    </tr>
-    <tr>
-        <th class="serie">2000</th>
-        <td>30</td>
-        <td>40</td>
-    </tr>
-  </tbody>
-</table>
-</div>
-<div class="example">
-<h1>Example 5</h1>
-<table id="table-4" class="jgtable {size:'450x350',type:'p',axis_step:1,title:'Example 5',title_color:'28179b',title_size:16,bar_width:30,bar_spacing:2,fillarea:true,fillbottom:true,filltop:false,colors:['a21a9c','FFCC00','da1b1b'],lines:[[1,1,0],[1,1,0],[1,1,0]],bg:'FFFFFF',bg_type:'gradient',bg_angle:90,bg_offset:'b7b4b4',bg_width:10,bg_trasparency:false,chbg:'f7f7f7',chbg_type:'gradient',chbg_angle:90,chbg_offset:'e81711',chbg_width:10,chbg_trasparency:false,grid:false,grid_x:7,grid_y:10,grid_line:0,grid_blank:0}">
-  <thead>
-    <tr>
-        <th>Anno</th>
-        <th class="serie">Data 4</th>
-        <th class="serie">Data 5</th>
-    </tr>
-  </thead>
-  <tbody>
-    <tr>
-        <th class="serie">2001</th>
-        <td>40</td>
-        <td>30</td>
-    </tr>
-    <tr>
-        <th class="serie">2000</th>
-        <td>30</td>
-        <td>40</td>
-    </tr>
-  </tbody>
-</table>
-</div>
-<div class="example">
-<h1>Example 6</h1>
-<table id="table-5" class="jgtable {size:'650x450',type:'lc',axis_step:1,title:false,title_color:'FFFFFF',title_size:10,bar_width:30,bar_spacing:1,fillarea:false,fillbottom:true,filltop:true,colors:['f04242','FFCC00','99CC00'],lines:[[12,9,7],[14,9,7],[13,9,7]],bg:'dca0ee',bg_type:'solid',bg_angle:90,bg_offset:'FFFFFF',bg_width:20,bg_trasparency:false,chbg:'FFFFFF',chbg_type:'solid',chbg_angle:90,chbg_offset:'FFFFFF',chbg_width:20,chbg_trasparency:false,grid:true,grid_x:3,grid_y:3,grid_line:0,grid_blank:0}">
-  <thead>
-    <tr>
-        <th>Anno</th>
-        <th class="serie">Data 1</th>
-        <th class="serie">Data 2</th>
-        <th class="serie">Data 3</th>
-    </tr>
-  </thead>
-  <tbody>
-    <tr>
-        <th class="serie">2001</th>
-        <td>153</td>
-        <td>60</td>
-        <td>52</td>
-    </tr>
-    <tr>
-        <th class="serie">2002</th>
-        <td>113</td>
-        <td>70</td>
-        <td>60</td>
-    </tr>
-    <tr>
-        <th class="serie">2003</th>
-        <td>120</td>
-        <td>80</td>
-        <td>40</td>
-    </tr>
-  </tbody>
-</table>
-</div>
-<div class="example">
-<h1>Example 7</h1>
-<table id="table-6" class="jgtable {size:'650x450',type:'bhs',axis_step:1,title:false,title_color:'FFFFFF',title_size:10,bar_width:90,bar_spacing:11,fillarea:false,fillbottom:true,filltop:true,colors:['f04242','FFCC00','99CC00'],lines:[[12,9,7],[14,9,7],[13,9,7]],bg:'dca0ee',bg_type:'gradient',bg_angle:40,bg_offset:'FFFFFF',bg_width:20,bg_trasparency:false,chbg:'bfbfbf',chbg_type:'stripes',chbg_angle:0,chbg_offset:'f5f5f5',chbg_width:10,chbg_trasparency:false,grid:false,grid_x:3,grid_y:3,grid_line:0,grid_blank:0}">
-  <thead>
-    <tr>
-        <th>Anno</th>
-        <th class="serie">Data 1</th>
-        <th class="serie">Data 2</th>
-        <th class="serie">Data 3</th>
-    </tr>
-  </thead>
-  <tbody>
-    <tr>
-        <th class="serie">2001</th>
-        <td>153</td>
-        <td>60</td>
-        <td>52</td>
-    </tr>
-    <tr>
-        <th class="serie">2002</th>
-        <td>113</td>
-        <td>70</td>
-        <td>60</td>
-    </tr>
-    <tr>
-        <th class="serie">2003</th>
-        <td>120</td>
-        <td>80</td>
-        <td>40</td>
-    </tr>
-  </tbody>
-</table>
-</div>
-<div class="example">
-<h1>Example 8</h1>
-<table id="table-7" class="jgtable {size:'650x450',type:'bvs',axis_step:1,title:false,title_color:'FFFFFF',title_size:10,bar_width:90,bar_spacing:11,fillarea:false,fillbottom:true,filltop:true,colors:['f04242','FFCC00','99CC00'],lines:[[12,9,7],[14,9,7],[13,9,7]],bg:'dca0ee',bg_type:'gradient',bg_angle:40,bg_offset:'FFFFFF',bg_width:20,bg_trasparency:false,chbg:'bfbfbf',chbg_type:'stripes',chbg_angle:0,chbg_offset:'f5f5f5',chbg_width:10,chbg_trasparency:false,grid:false,grid_x:3,grid_y:3,grid_line:0,grid_blank:0}">
-  <thead>
-    <tr>
-        <th>Anno</th>
-        <th class="serie">Data 1</th>
-        <th class="serie">Data 2</th>
-        <th class="serie">Data 3</th>
-    </tr>
-  </thead>
-  <tbody>
-    <tr>
-        <th class="serie">2001</th>
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-        <td>60</td>
-        <td>52</td>
-    </tr>
-    <tr>
-        <th class="serie">2002</th>
-        <td>113</td>
-        <td>70</td>
-        <td>60</td>
-    </tr>
-    <tr>
-        <th class="serie">2003</th>
-        <td>120</td>
-        <td>80</td>
-        <td>40</td>
-    </tr>
-  </tbody>
-</table>
-</div>
-
-</body>
-</html>    

theme/tripal_theme_core/js/jgcharts/doc/json/delpiero.json

@@ -1,30 +0,0 @@
-{size:'450x600',
-type:'bhg',
-axis_step:1,
-title:'Gol e presenze in campionato',
-title_color:'000000',
-title_size:16,
-bar_width:10,
-bar_spacing:0,
-fillarea:true,
-fillbottom:true,
-filltop:true,
-colors:['5131c9','da1b1b'],
-lines:[[1,1,0],[1,1,0],[1,1,0]],
-bg:false,
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-grid:false,
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-grid_blank:10}

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theme/tripal_theme_core/js/jgcharts/include/css/_top.css

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-#multidesktop{position:absolute;right:0px;top:0px;border:1px solid #aa9c8f;margin-top:1px;}
-.seldesktop{height:25px;width:35px;background:#efebe7;float:left;margin-left:1px;border-left:1px solid #e1dbd5;border-right:1px solid #cec6bd;position:relative;}
-.seldesktop-on{background:#dea040;border-right:1px solid #e2b167;border-left:1px solid #dea040;}
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theme/tripal_theme_core/js/jgcharts/include/css/demo.css

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-img{border:0px;}
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-
-.start_hide{display:none;}
-
-
-.icone_dx{display:block;margin:auto;}
-.text_icone_dx{color:white;margin-bottom:10px;display:block;}
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-      
-.icone_sx{display:block;margin:auto;}
-.text_icone_sx{color:white;margin-bottom:10px;display:block;}
-#icone_sinistra{position:absolute;left:20px;top:30px;text-align:center;width:60px;} 
-

theme/tripal_theme_core/js/jgcharts/include/css/reset.css

@@ -1,8 +0,0 @@
-/*
-Copyright (c) 2008, Yahoo! Inc. All rights reserved.
-Code licensed under the BSD License:
-http://developer.yahoo.net/yui/license.txt
-version: 2.5.1
-*/
-h1{font-size:138.5%;}h2{font-size:123.1%;}h3{font-size:108%;}h1,h2,h3{margin:1em 0;}h1,h2,h3,h4,h5,h6,strong{font-weight:bold;}abbr,acronym{border-bottom:1px dotted #000;cursor:help;} em{font-style:italic;}blockquote,ul,ol,dl{margin:1em;}ol,ul,dl{margin-left:2em;}ol li{list-style:decimal outside;}ul li{list-style:disc outside;}dl dd{margin-left:1em;}th,td{border:1px solid #000;padding:.5em;}th{font-weight:bold;text-align:center;}caption{margin-bottom:.5em;text-align:center;}p,fieldset,table,pre{margin-bottom:1em;}input[type=text],input[type=password],textarea{width:12.25em;*width:11.9em;}
-

theme/tripal_theme_core/js/jgcharts/include/demo/index.html

@@ -1,2004 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
-    <meta http-equiv="Content-type" content="text/html; charset=UTF-8" />
-    <title>jQuery Google Charts 1.0 - Demo Site</title>
-    <meta http-equiv="Content-Language" content="en-us" />
-    <meta name="author" content="Massimiliano Balestrieri" />
-    <link rel="stylesheet" type="text/css" href="../../include/css/reset.css" />
-    <link rel="stylesheet" type="text/css" href="../../include/css/demo.css" />
-    <script src="../../lib/jquery/jquery-1.3.2.min.js" type="text/javascript"></script>
-    <!--script src="../../include/js/lib/ycodaslider-2.0.rc2/lib/jquery-easing-1.3.pack.js" type="text/javascript"></script>
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-    <script src="../../include/js/lib/ycodaslider-2.0.rc2/lib/chili/jquery.chili-2.2.js" type="text/javascript"></script>
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-    <script src="../../include/js/lib/ycodaslider-2.0.rc2/plugins/code-ycodaslider-2.0.pack.js" type="text/javascript"></script-->
-    <script src="../../include/js/lib/ycodaslider-3.0/ycodaslider-3.0.min.js" type="text/javascript"></script>
-    
-    
-    <script src="../../lib/chili/jquery.chili-2.2.js" type="text/javascript"></script>
-    
-    <script src="../../lib/metadata/jquery.metadata.min.js" type="text/javascript"></script>
-    <script src="../../lib/janalytics/janalytics.js" type="text/javascript"></script>
-    <!--todo pack -->
-    <script src="../../jgcharts.pack.js" type="text/javascript"></script>
-    <script src="../../plugins/jgtable/jgtable.pack.js" type="text/javascript"></script>
-    <script src="../../include/js/start-1.0.js" type="text/javascript"></script>
-</head>    
-<body>
-<div id="icone_sinistra">
-    <!-- home -->
-    <a href="#" class="handle h-docs tracking {label : '/jgcharts/home'}"><img class="icone_sx" alt="docs" src="../../include/icons/home.png" /></a>
-    <a href="#" class="handle h-docs text_icone_sx tracking {label : '/jgcharts/home'}">Home</a>
-    <!-- table -->
-    <a href="#" class="handle h-table tracking {label : '/jgcharts/table'}"><img class="icone_sx" alt="table" src="../../include/icons/frame.png" /></a>
-    <a href="#" class="handle h-table text_icone_sx tracking {label : '/jgcharts/table'}">Table</a>
-    <!-- gui -->
-    <a href="../gui/" class="blank tracking {label : '/jgcharts/jggui'}"><img class="icone_sx" alt="gui" src="../../include/icons/important.png" /></a>
-    <a href="../gui/" class="blank text_icone_sx tracking {label : '/jgcharts/jggui'}">Gui *ALPHA</a>
-</div>
-<div id="icone_destra">
-    <!-- docs -->
-    <a href="#" class="handle h-docs tracking {label : '/jgcharts/docs'}"><img class="icone_sx" alt="docs" src="../../include/icons/abc.png" /></a>
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-    <a href="#" class="handle h-code text_icone_sx tracking {label : '/jgcharts/code'}">Code</a>
-    <!-- download -->
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-</div>
-
-<div id="yslider-docs" class="ycodaslider">
-    <div class="yslider-panelwrapper" title="jGCharts 1.0">
-        <h3>jQuery Google Charts 1.0</h3>
-        <p>
-        Copyright (c) 2008 Massimiliano Balestrieri<br />
-        Examples and docs at: http://maxb.net/blog/<br />
-        Licensed GPL licenses:<br />
-        http://www.gnu.org/licenses/gpl.html<br />
-        </p>
-        <blockquote>
-        <p>
-        
-        </p>
-        </blockquote>
-        <p>
-        </p>
-        <h4>Basic usage:</h4>
-        <div class="code javascript"><!--var api = new jGCharts.Api();
-jQuery('<img>')
-.attr('src', api.make({data : [[153, 60, 52], [113, 70, 60], [120, 80, 40]]}))
-.appendTo("#bar1");--></div>
-        <h4>Html:</h4>
-        <div class="code html"><!--<div id="bar1"></div>--></div>
-        <h4>Basic scripts (use packed version in production):</h4>
-        <div class="code html"><!--<script src="jquery-1.3.1.min.js" type="text/javascript"></script>
-<script src="jgcharts.js" type="text/javascript"></script>--></div>
-    </div>
-
-    <!-- panel -->
-    <div class="yslider-panelwrapper" title="Bar">
-        
-        <h4>Basic Bar</h4>
-        <div class="code javascript"><!--//1 ) api
-var api = new jGCharts.Api();        
-
-//2) options
-var opt = {
-    data : [[153, 60, 52], [113, 70, 60], [120, 80, 40]]//mandatory 
-};//set options 
-
-//3) append Img (with jQuery)
-jQuery('<img>')
-.attr('src', api.make(opt))//options 
-.appendTo("#bar1");--></div>
-        
-        <div id="bar1"></div>
-        
-    </div>
-
-    
-    <!-- bar options -->
-
-
-    <div class="yslider-panelwrapper" title="Bar Options">
-        
-        <h4>Schema</h4>
-        <div class="code javascript"><!--//1 ) api
-var api = new jGCharts.Api();        
-//2) options
-var opt = {};//set options 
-//3) append img
-jQuery('<img>')
-.attr('src', api.make(opt))//options 
-.appendTo("#chart_container");
---></div>
-        <h3>Options</h3>
-        <h4>Chart Dimension</h4>
-        <div class="code javascript"><!--{
-data : [[153, 60, 52], [113, 70, 60], [120, 80, 40]],//mandatory 
-size : '400x400'//default 300x200 (width x height) - maximum size 300,000 pixels
-}--></div>
-        <div id="bar2"></div>
-                
-        <h4>Direction</h4>
-        <div class="code javascript"><!--{
-data : [[153, 60, 52], [113, 70, 60], [120, 80, 40]],//mandatory 
-type : 'bhg'//default bvg
-}--></div>
-        <div id="bar3"></div>
-        
-        <h4>Legend and axis labels</h4>
-        <div class="code javascript"><!--{
-data : [[153, 60, 52], [113, 70, 60], [120, 80, 40]],//mandatory 
-axis_labels : ['2008','2007','2006'], //default 0,1,2 etc...
-legend : ['serie1', 'serie2', 'serie3'] //default none
-}--></div>
-        <div id="bar4"></div>
-        
-        <h4>Dimensions and spacing</h4>
-        <div class="code javascript"><!--{
-data : [[153, 60, 52], [113, 70, 60], [120, 80, 40]],//mandatory 
-bar_width : 10, //default 20
-bar_spacing : 10 //default 1
-}--></div>
-        <div id="bar5"></div>
-        
-        <h4>Colors</h4>
-        <div class="code javascript"><!--{
-data : [[153, 60, 52], [113, 70, 60], [120, 80, 40]],//mandatory 
-colors : ['4b9b41','81419b','41599b']
-}--></div>
-        <div id="bar6"></div>
-        
-        <h4>Background - solid</h4>
-        <div class="code javascript"><!--{
-data : [[153, 60, 52], [113, 70, 60], [120, 80, 40]],//mandatory 
-bg   : 'e0e0e0'//default false
-//bg_trasparency : 50 - default false - also chbg_trasparency
-}--></div>
-        <div id="bar7"></div>
-
-        <h4>Background - gradient</h4>
-        <div class="code javascript"><!--{
-data : [[153, 60, 52], [113, 70, 60], [120, 80, 40]],//mandatory 
-bg        : 'FFFFFF',//default false
-bg_offset : '000000',
-bg_angle  : '45',//default 90   
-bg_type   : 'gradient' //default solid
-}--></div>
-        <div id="bar8"></div>
-        
-        <h4>Background - stripes</h4>
-        <div class="code javascript"><!--{
-data : [[153, 60, 52], [113, 70, 60], [120, 80, 40]],//mandatory 
-bg        : 'FFFFFF',//default false
-bg_offset : 'e0e0e0',
-bg_angle  : '0',//default 90   
-bg_type   : 'stripes', //default solid
-bg_width  : '10'//default 10 - min 10
-}--></div>
-        <div id="bar9"></div>
-        
-        <h4>Chart Area Background (like bg)</h4>
-        <div class="code javascript"><!--{
-data : [[153, 60, 52], [113, 70, 60], [120, 80, 40]],//mandatory 
-chbg        : 'FFFFFF',//default false
-chbg_offset : '4b9b41',
-chbg_angle  : '45',//default 90   
-chbg_type   : 'gradient' //default solid
-}--></div>
-        <div id="bar10"></div>
-        
-        
-        
-        <h4>Title</h4>
-        <div class="code javascript"><!--{
-data : [[153, 60, 52], [113, 70, 60], [120, 80, 40]],//mandatory 
-title       : 'Bar Chart', //default false
-title_color : 'a98147',
-title_size  : 20 //default 10
-}--></div>
-        <div id="bar11"></div>
-        
-        <h4>Grid</h4>
-        <div class="code javascript"><!--{
-data : [[153, 60, 52], [113, 70, 60], [120, 80, 40]],//mandatory 
-grid        : true, //default false
-grid_x      : 5,    //default 10
-grid_y      : 5,    //default 10
-grid_line   : 5,   //default 10
-grid_blank  : 0    //default 0
-}--></div>
-        <div id="bar12"></div>
-        
-    </div>
-    
-    <!-- stacked -->
-    
-
-    <div class="yslider-panelwrapper" title="Stacked Bar">
-                    
-        <h4>Horizontal Dataset Stacked</h4>
-        <div class="code javascript"><!--{
-data : [[153, 60, 52], [113, 70, 60], [120, 80, 40]],//mandatory 
-type : 'bhs'//default bvg
-}--></div>
-        <div id="stacked1"></div>
-        
-        <h4>Vertical Dataset Stacked</h4>
-        <div class="code javascript"><!--{
-data : [[153, 60, 52], [113, 70, 60], [120, 80, 40]],//mandatory 
-type : 'bvs'//default bvg
-}--></div>
-        <div id="stacked2"></div>
-
-    </div>    
-
-
-    <!-- line -->
-
-
-    <div class="yslider-panelwrapper" title="Line">
-        <div id="line1"></div>
-        <h4>Js</h4>
-        <div class="code javascript"><!--var api = new jGCharts.Api();
-jQuery('<img>')
-.attr('src', api.make({
-data : [[105.7,97.9],[108.1,101.6],[110.7,102.9],[111.0,93.7],[110.0,89.8],[109.0,90.7],
-[107.5,93.0],[106.1,94.5],[104.3,91.9],[102.0,93.9],[102.8,93.6],[103.8,92.6],
-[102.9,94.0],[102.1,92.7],[100.6,96.0],[101.7,97.9],[101.8,105.0],
-[103.3,104.1],[104.0,105.1],[103.7,108.1],[108.4,108.4],[109.4,113.8],
-[112.0,109.1],[112.6,106.3],[115.5,106.7],[115.7,108.8],[114.7,118.8],
-[115.9,120.4],[116.2,115.9],[118.0,124.7],[123.3,126.5],[127.6,131.6],
-[130.3,134.0],[135.5,135.7],[138.2,126.4],[139.6,127.4],[145.1,131.0],
-[146.4,129.9],[147.1,133.7],[149.0,138.4],[150.3,141.0],[151.3,139.3],
-[153.4,145.3],[152.7,142.9],[152.9,129.2],[152.2,126.0],[151.9,124.8],
-[150.1,125.9],[148.2,118.9],[145.3,122.9],[142.9,127.7],[142.6,134.4],
-[144.0,138.5],[145.5,138.7],[147.2,141.8],[150.0,139.2],[153.8,145.6],
-[155.4,147.6],[157.0,157.9],[158.4,156.2],[162.8,153.9],[162.8,158.6],
-[164.7,166.3],[168.5,165.8]] //MANDATORY
-type : lc 
-}))
-.appendTo("#line1");--></div>
-    </div>
-    
-    <!-- line options -->
-    <div class="yslider-panelwrapper" title="Line Options">
-
-        <h4>Other options</h4>
-        <p>See bar options for legend, axis, grid, background, colors etc....</p>
-                
-        <h4>Schema</h4>
-        <div class="code javascript"><!--//1 ) api
-var api = new jGCharts.Api();    
-//2) options
-var opt = {};//set options 
-//3) append img
-jQuery('<img>')
-.attr('src', api.make(opt))//options 
-.appendTo("#chart_container");--></div>
-
-        <h4>Fillarea</h4>
-        <div class="code javascript"><!--{
-data : [[105.7,97.9] //...[etc] 
-type : 'lc',
-fillarea : true //default false
-}--></div>
-        <div id="line2"></div>
-
-        <h4>FillBottom</h4>
-        <div class="code javascript"><!--{
-data : [[105.7,97.9] //...[etc] 
-type : 'lc',
-fillarea : true, //default false
-fillbottom : true //default false
-}--></div>
-        <div id="line3"></div>
-
-        <h4>FillTop</h4>
-        <div class="code javascript"><!--{
-data : [[105.7,97.9] //...[etc] 
-type : 'lc',
-fillarea : true, //default false
-fillbottom : true, //default false
-filltop : true //default false
-}--></div>
-        <div id="line4"></div>
-
-        <h4>Line options</h4>
-        <div class="code javascript"><!--{
-data : [[105.7,97.9] //...[etc] 
-type : 'lc',
-lines: [[4,2,2],[6,3,3]] 
-//[line width, solid width, blank width], [serie2N,serie2N,serie2N] - default false 
-}--></div>
-        <div id="line5"></div>
-
-        <h4>Axis step</h4>
-        <div class="code javascript"><!--{
-data : [[105.7,97.9] //...[etc] 
-axis_labels : ['01-03','02-03','03-03'// ... [etc]
-axis_step : 10, 
-type : 'lc'
-}--></div>
-        <div id="line6"></div>    
-        
-        <h4>Sparklines</h4>
-        <p>A sparkline chart has exactly the same parameters as a line chart. The only difference is that the axes lines are not drawn for sparklines by default. You can add axes labels if you wish. (Google Api)</p>
-        <div class="code javascript"><!--{data : [[105.7,97.9] //...[etc] 
-type : 'ls'
-}--></div>
-        <div id="line7"></div>        
-    </div>
-    
-    
-    <!-- pie -->
-    
-    <div class="yslider-panelwrapper" title="Pie">
-        
-        <h4>Pie</h4>
-        <div class="code javascript"><!--{
-data : [[153, 60, 52], [113, 70, 60], [120, 80, 40]],//mandatory 
-type : 'p'//default bvg
-}--></div>
-        <div id="pie1"></div>
-        
-    </div>
-    
-    <div class="yslider-panelwrapper" title="Pie 3d">
-        
-        <h4>Pie</h4>
-        <div class="code javascript"><!--{
-data : [[153, 60, 52], [113, 70, 60], [120, 80, 40]],//mandatory 
-type : 'p3',//default bvg
-size : '400x200'
-}--></div>
-        <div id="p3d1"></div>
-        
-    </div>
-    
-    <!--gallery -->
-    
-    <div class="yslider-panelwrapper" title="Charts gallery">
-        <h4>Horizontal Stacked Bar</h4>
-        <div class="code javascript"><!--{
-data : [[153, 60, 52], [113, 70, 60], [120, 80, 40]], 
-//source
-legend      : ['Data 1','Data 2','Data 3'],
-axis_labels : ['2001','2002','2003'],
-                        
-//options 
-size        : '400x250',
-type        : 'bhs',
-colors      : ['2c50f2','FFCC00','99CC00'],
-
-//bar
-bar_width   : 50,
-bar_spacing : 5,
-
-//bg
-bg          : 'FFFFFF',
-bg_type     : 'gradient',
-bg_angle    : 90,
-bg_offset   : '8c8c8c',
-
-//grid
-grid        : true,
-grid_x      : 5,
-grid_y      : 5,
-grid_line   : 5,
-grid_blank  : 5
-}--></div>
-        <div id="gallery1"></div>
-        <h4>Vertical Stacked Bar</h4>
-        <div class="code javascript"><!--{
-data : [[153, 60, 52], [113, 70, 60], [120, 80, 40]], 
-
-//source
-legend      : ['Data 1','Data 2','Data 3'],
-axis_labels : ['2001','2002','2003'],
-                        
-//options 
-size        : '250x400',
-type        : 'bvs',
-
-//bar
-bar_width   : 50,
-bar_spacing : 5,
-
-//bg
-chbg          : 'FFFFFF',
-chbg_type     : 'gradient',
-chbg_angle    : 90,
-chbg_offset   : '8c8c8c',
-
-//grid
-grid        : true,
-grid_x      : 5,
-grid_y      : 5,
-grid_line   : 5,
-grid_blank  : 0
-
-}--></div>
-        <div id="gallery2"></div>
-        <h4>Horizontal Bar</h4>
-        <div class="code javascript"><!--{
-data : [[153, 60, 52], [113, 70, 60], [120, 80, 40]], 
-
-//source
-legend      : ['Data 1','Data 2','Data 3'],
-axis_labels : ['2001','2002','2003'],
-                        
-//options 
-size        : '250x400',
-type        : 'bhg',
-
-//bar
-bar_width   : 50,
-bar_spacing : 5,
-
-//bg
-chbg          : '000000',
-chbg_trasparency: 20
-
-}--></div>
-        <div id="gallery3"></div>
-        <h4>Vertical Bar</h4>
-        <div class="code javascript"><!--{
-data : [[153, 60, 52], [113, 70, 60], [120, 80, 40]], 
-
-//source
-legend      : ['Data 1','Data 2','Data 3'],
-axis_labels : ['2001','2002','2003'],
-                        
-//options 
-size        : '400x250',
-type        : 'bvg',
-colors      : ['4b9b41','81419b','41599b'],
-//bar
-bar_width   : 20,
-bar_spacing : 5,
-
-//style
-bg          : 'ffffff',
-bg_type     : 'stripes',
-bg_angle    : 90,
-bg_offset   : '999999',
-bg_width    : 20,
-}--></div>
-        <div id="gallery4"></div>
-        <h4>Vertical Bar</h4>
-        <div class="code javascript"><!--{
-data : [[153, 60, 52], [113, 70, 60], [120, 80, 40]], 
-
-//source
-legend      : ['Data 1','Data 2','Data 3'],
-axis_labels : ['2001','2002','2003'],
-                        
-//options 
-size        : '400x250',
-type        : 'bvg',
-
-//bar
-bar_width   : 10,
-bar_spacing : 10,
-
-//style
-chbg          : 'ffffff',
-chbg_type     : 'stripes',
-chbg_angle    : 90,
-chbg_offset   : '999999',
-chbg_width    : 20,
-}--></div>
-        <div id="gallery5"></div>
-        <h4>Line chart</h4>
-        <div class="code javascript"><!--{
-data : [[153, 60, 52], [113, 70, 60], [120, 80, 40]], 
-
-//source
-legend      : ['Data 1','Data 2','Data 3'],
-axis_labels : ['2001','2002','2003'],
-                        
-//options 
-size        : '400x250',
-type        : 'lc',
-
-//style
-chbg          : 'ffffff',
-chbg_type     : 'stripes',
-chbg_angle    : 90,
-chbg_offset   : '999999',
-chbg_width    : 20,
-
-bg            : 'ffffff',
-bg_type       : 'gradient',
-bg_angle      : 45,
-bg_offset     : '4b9b41',
-bg_width      : 20
-
-}--></div>
-        <div id="gallery6"></div>
-        <h4>Line chart</h4>
-        <div class="code javascript"><!--{
-data : [[153, 60, 52], [113, 70, 60], [120, 80, 40]], 
-          
-//source
-//legend      : ['Data 1','Data 2','Data 3'],
-axis_labels : ['2001','2002','2003'],
-                        
-//options 
-size        : '400x250',
-type        : 'lc',
-
-//style
-fillarea    : true,
-fillbottom  : true,
-filltop     : true,
- 
-//series line 
-lines       : [[3,3,3],[4,4,4],[5,5,5]],
-
-bg            : 'ffffff',
-bg_type       : 'gradient',
-bg_angle      : 45,
-bg_offset     : '81419b',
-bg_width      : 20
-
-}--></div>
-        <div id="gallery7"></div>
-        <h4>Pie</h4>
-        <div class="code javascript"><!--{
-data : [[153, 60, 52], [113, 70, 60], [120, 80, 40]], 
-//source
-legend      : ['Data 1','Data 2','Data 3'],
-axis_labels : ['2001','2002','2003'],
-                        
-//options 
-size        : '400x250',
-type        : 'p',
-
-bg            : '999999',
-bg_type       : 'gradient',
-bg_angle      : 45,
-bg_offset     : 'ffffff',
-bg_width      : 20
-}--></div>
-        <div id="gallery8"></div>
-        <h4>Pie 3d</h4>
-        <div class="code javascript"><!--{
-   data : [[153, 60, 52], [113, 70, 60], [120, 80, 40]], 
-   //source
-   legend      : ['Data 1','Data 2','Data 3'],
-   axis_labels : ['2001','2002','2003'],
-
-   //options 
-   size        : '400x200',
-   type        : 'p3',
-   
-   bg            : 'ffffff',
-   bg_type       : 'gradient',
-   bg_angle      : 45,
-   bg_offset     : '999999',
-   bg_width      : 20
-}--></div>
-        <div id="gallery9"></div>
-        
-    </div>
-    <!--credits -->
-    
-    <div class="yslider-panelwrapper" title="Credits">
-        <h4>Credits</h4>
-        <p>
-        Google Chart Api - <a href="http://code.google.com/apis/chart/" class="blank">http://code.google.com/apis/chart/</a>
-        </p>     
-        <h4>Libraries</h4>
-        <p>
-        jquery v1.3.1 of John Resig <a href="http://jquery.com" class="blank">jquery.com</a><br />
-        </p>
-        <h4>Demo Libraries (YCodaSlider 2.0)</h4>
-        <p>
-        jquery history_remote v1.0.3 of Klaus Hartl <a href="http://stilbuero.de" class="blank">stilbuero.de</a><br />
-        jquery easing v1.3 of George McGinley Smith<br />
-        jquery.chili-1.9.js of <a href="http://noteslog.com/chili/" class="blank">Andrea Ercolino</a><br />
-        Icons <a class="blank tracking" href="http://www.icon-king.com/?p=15">Nuvola</a><br />
-        Yahoo Css Reset version: 2.5.1
-        GreyBox <a href="http://jquery.com/demo/grey/" class="blank tracking">Css</a>
-        </p>
-    </div>
-</div>    
-
-<div id="yslider-table" class="ycodaslider">
-
-    <div class="yslider-panelwrapper" title="jGTable 1.0">
-    
-        <h3>jQuery Google Charts Table 1.0</h3>
-        <p>
-        Copyright (c) 2008 Massimiliano Balestrieri<br />
-        Examples and docs at: http://maxb.net/blog/<br />
-        Licensed GPL licenses:<br />
-        http://www.gnu.org/licenses/gpl.html<br />
-        </p>
-        <blockquote>
-        <p>
-        
-        </p>
-        </blockquote>
-        <p>
-        </p>
-        <h4>Basic usage:</h4>
-        <div class="code javascript"><!--jQuery(".jgtable").jgtable();--></div>
-        <h4>Html (see class="serie"):</h4>
-        <div class="code html"><!--<div class="jgtable">
-  <table>
-  <thead>
-    <tr>
-        <th>Anno</th>
-        <th class="serie">Data 1</th>
-        <th class="serie">Data 2</th>
-        <th class="serie">Data 3</th>
-    </tr>
-  </thead>
-  <tbody>
-    <tr>
-        <th class="serie">2001</th>
-        <td>153</td>
-        <td>60</td>
-        <td>52</td>
-    </tr>
-    <tr>
-        <th class="serie">2002</th>
-        <td>113</td>
-        <td>70</td>
-        <td>60</td>
-    </tr>
-    <tr>
-        <th class="serie">2003</th>
-        <td>120</td>
-        <td>80</td>
-        <td>40</td>
-    </tr>
-  </tbody>
-  </table>
-</div>--></div>
-        <h4>Basic scripts (use packed version in production):</h4>
-        <div class="code html"><!--<script src="jquery-1.3.1.min.js" type="text/javascript"></script>
-<script src="jquery.metadata.min.js" type="text/javascript"></script>
-<script src="jgcharts.js" type="text/javascript"></script>
-<script src="plugins/jgtable/jgtable.js" type="text/javascript"></script>--></div>
-
-    </div>
-    
-    <div class="yslider-panelwrapper" title="Basic">
-    
-    	<div class="jgtable">
-        <table>
-          <thead>
-            <tr>
-                <th>Anno</th>
-                <th class="serie">Data 1</th>
-                <th class="serie">Data 2</th>
-                <th class="serie">Data 3</th>
-            </tr>
-          </thead>
-          <tbody>
-            <tr>
-                <th class="serie">2001</th>
-                <td>153</td>
-                <td>60</td>
-                <td>52</td>
-            </tr>
-            <tr>
-                <th class="serie">2002</th>
-                <td>113</td>
-                <td>70</td>
-                <td>60</td>
-            </tr>
-            <tr>
-                <th class="serie">2003</th>
-                <td>120</td>
-                <td>80</td>
-                <td>40</td>
-            </tr>
-          </tbody>
-        </table>
-        </div>
-        
-        <div class="code javascript"><!--jQuery(".jgtable").jgtable();--></div>
-        <div class="code html"><!-- <div class="jgtable">
-  <table>
-  <thead>
-    <tr>
-        <th>Anno</th>
-        <th class="serie">Data 1</th>
-        <th class="serie">Data 2</th>
-        <th class="serie">Data 3</th>
-    </tr>
-  </thead>
-  <tbody>
-    <tr>
-        <th class="serie">2001</th>
-        <td>153</td>
-        <td>60</td>
-        <td>52</td>
-    </tr>
-    <tr>
-        <th class="serie">2002</th>
-        <td>113</td>
-        <td>70</td>
-        <td>60</td>
-    </tr>
-    <tr>
-        <th class="serie">2003</th>
-        <td>120</td>
-        <td>80</td>
-        <td>40</td>
-    </tr>
-  </tbody>
-  </table>
-</div>--></div>
-    </div>
-    
-    <div class="yslider-panelwrapper" title="Metadata">
-    
-        
-            <div class="example">
-            <h3>Example 1</h3>
-            <div class="code javascript"><!--jQuery(".jgtable").jgtable();--></div>
-            <div class="code html"><!--<div class="jgtable {size:'550x400',
-type:'bhg',
-title:'Example 1',
-title_color:'000000',
-title_size:16,
-bar_width:30,
-bar_spacing:2,
-colors:['5131c9','FFCC00','da1b1b'],
-bg:'FFFFFF',
-bg_type:'gradient',
-bg_angle:90,
-bg_offset:'6d6969',
-grid:true,
-grid_x:7,
-grid_y:10,
-grid_line:0,
-grid_blank:0}">
-	<table>
-	[etc...]
-	</table>
-</div>--></div>
-            <div class="jgtable {size:'550x400',
-                                                type:'bhg',
-                                                title:'Example 1',
-                                                title_color:'000000',
-                                                title_size:16,
-                                                bar_width:30,
-                                                bar_spacing:2,
-                                                colors:['5131c9','FFCC00','da1b1b'],
-                                                bg:'FFFFFF',
-                                                bg_type:'gradient',
-                                                bg_angle:90,
-                                                bg_offset:'6d6969',
-                                                grid:true,
-                                                grid_x:7,
-                                                grid_y:10,
-                                                grid_line:0,
-                                                grid_blank:0}">
-              <table>
-              <thead>
-                <tr>
-                    <th>Anno</th>
-                    <th class="serie">Data 1</th>
-                    <th class="serie">Data 2</th>
-                    <th class="serie">Data 3</th>
-                </tr>
-              </thead>
-              <tbody>
-                <tr>
-                    <th class="serie">2001</th>
-                    <td>153</td>
-                    <td>60</td>
-                    <td>52</td>
-                </tr>
-                <tr>
-                    <th class="serie">2002</th>
-                    <td>113</td>
-                    <td>70</td>
-                    <td>60</td>
-                </tr>
-                <tr>
-                    <th class="serie">2003</th>
-                    <td>120</td>
-                    <td>80</td>
-                    <td>40</td>
-                </tr>
-              </tbody>
-            </table>
-            </div>
-            </div>
-            <div class="example">
-            <h3>Example 2</h3>
-            <div class="code javascript"><!--jQuery(".jgtable").jgtable();--></div>
-            <div class="code html"><!--<div class="jgtable {size:'400x500',
-type:'bvg',
-title:'Example 2',
-title_color:'c81e3d',
-title_size:16,
-bar_width:30,
-bar_spacing:2,
-colors:['1aa22f','FFCC00','da1b1b'],
-bg:'FFFFFF',
-bg_type:'stripes',
-bg_angle:90,
-bg_offset:'b7b4b4',
-bg_width:10,
-chbg:'000000',
-chbg_type:'solid'}">
-	<table>
-	[etc...]
-	</table>
-</div>--></div>
-            <div class="jgtable {size:'400x500',
-                                type:'bvg',
-                                title:'Example 2',
-                                title_color:'c81e3d',
-                                title_size:16,
-                                bar_width:30,
-                                bar_spacing:2,
-                                colors:['1aa22f','FFCC00','da1b1b'],
-                                bg:'FFFFFF',
-                                bg_type:'stripes',
-                                bg_angle:90,
-                                bg_offset:'b7b4b4',
-                                bg_width:10,
-                                chbg:'000000',
-                                chbg_type:'solid'}">
-              <table>                           
-              <thead>
-                <tr>
-                    <th>Anno</th>
-                    <th class="serie">Data 1</th>
-                    <th class="serie">Data 2</th>
-                    <th class="serie">Data 3</th>
-                </tr>
-              </thead>
-              <tbody>
-                <tr>
-                    <th class="serie">2001</th>
-                    <td>153</td>
-                    <td>60</td>
-                    <td>52</td>
-                </tr>
-                <tr>
-                    <th class="serie">2002</th>
-                    <td>113</td>
-                    <td>70</td>
-                    <td>60</td>
-                </tr>
-                <tr>
-                    <th class="serie">2003</th>
-                    <td>120</td>
-                    <td>80</td>
-                    <td>40</td>
-                </tr>
-              </tbody>
-            </table>
-            </div>
-            </div>
-            <div class="example">
-            <h3>Example 3</h3>
-            <div class="code javascript"><!--jQuery(".jgtable").jgtable();--></div>
-            <div class="code html"><!--<div class="jgtable {size:'500x250',
-type:'p3',
-title:'Example 4',
-title_color:'28179b',
-title_size:16,
-colors:['a21a9c','FFCC00'],
-bg:'FFFFFF',
-bg_type:'gradient',
-bg_angle:90,
-bg_offset:'b7b4b4'}">
-	<table>
-	[etc...]
-	</table>
-</div>--></div>
-             <div class="jgtable {size:'500x250',
-                                                type:'p3',
-                                                title:'Example 4',
-                                                title_color:'28179b',
-                                                title_size:16,
-                                                colors:['a21a9c','FFCC00'],
-                                                bg:'FFFFFF',
-                                                bg_type:'gradient',
-                                                bg_angle:90,
-                                                bg_offset:'b7b4b4'}">
-             <table>
-             <thead>
-                <tr>
-                    <th>Anno</th>
-                    <th class="serie">Data 4</th>
-                    <th class="serie">Data 5</th>
-                </tr>
-              </thead>
-              <tbody>
-                <tr>
-                    <th class="serie">2001</th>
-                    <td>40</td>
-                    <td>30</td>
-                </tr>
-                <tr>
-                    <th class="serie">2000</th>
-                    <td>30</td>
-                    <td>40</td>
-                </tr>
-              </tbody>
-            </table>
-            </div>
-            </div>
-            <div class="example">
-            <h3>Example 4</h3>
-            <div class="code javascript"><!--jQuery(".jgtable").jgtable();--></div>
-            <div class="code html"><!--<div class="jgtable {size:'450x350',
-type:'p',
-title:'Example 5',
-title_color:'28179b',
-title_size:16,
-colors:['a21a9c','FFCC00'],
-bg:'FFFFFF',
-bg_type:'gradient',
-bg_angle:90,
-bg_offset:'b7b4b4'}">
-	<table>
-	[etc...]
-	</table>
-</div>--></div>
-             <div class="jgtable {size:'450x350',
-                                                type:'p',
-                                                title:'Example 5',
-                                                title_color:'28179b',
-                                                title_size:16,
-                                                colors:['a21a9c','FFCC00'],
-                                                bg:'FFFFFF',
-                                                bg_type:'gradient',
-                                                bg_angle:90,
-                                                bg_offset:'b7b4b4'}">
-             <table>
-             <thead>
-                <tr>
-                    <th>Anno</th>
-                    <th class="serie">Data 4</th>
-                    <th class="serie">Data 5</th>
-                </tr>
-              </thead>
-              <tbody>
-                <tr>
-                    <th class="serie">2001</th>
-                    <td>40</td>
-                    <td>30</td>
-                </tr>
-                <tr>
-                    <th class="serie">2000</th>
-                    <td>30</td>
-                    <td>40</td>
-                </tr>
-              </tbody>
-            </table>
-            </div>
-            </div>
-            <div class="example">
-            <h3>Example 5</h3>
-            <div class="code javascript"><!--jQuery(".jgtable").jgtable();--></div>
-            <div class="code html"><!--<div class="jgtable {size:'550x450',
-type:'lc',
-colors:['f04242','FFCC00','99CC00'],
-lines:[[12,9,7],[14,9,7],[13,9,7]],
-bg:'dca0ee',
-bg_type:'solid',
-grid:true,
-grid_x:3,
-grid_y:3,
-grid_line:0,
-grid_blank:0}">
-	<table>
-	[etc...]
-	</table>
-</div>--></div>
-            <div class="jgtable {size:'550x450',
-                                                type:'lc',
-                                                colors:['f04242','FFCC00','99CC00'],
-                                                lines:[[12,9,7],[14,9,7],[13,9,7]],
-                                                bg:'dca0ee',
-                                                bg_type:'solid',
-                                                grid:true,
-                                                grid_x:3,
-                                                grid_y:3,
-                                                grid_line:0,
-                                                grid_blank:0}">
-              <table>
-              <thead>
-                <tr>
-                    <th>Anno</th>
-                    <th class="serie">Data 1</th>
-                    <th class="serie">Data 2</th>
-                    <th class="serie">Data 3</th>
-                </tr>
-              </thead>
-              <tbody>
-                <tr>
-                    <th class="serie">2001</th>
-                    <td>153</td>
-                    <td>60</td>
-                    <td>52</td>
-                </tr>
-                <tr>
-                    <th class="serie">2002</th>
-                    <td>113</td>
-                    <td>70</td>
-                    <td>60</td>
-                </tr>
-                <tr>
-                    <th class="serie">2003</th>
-                    <td>120</td>
-                    <td>80</td>
-                    <td>40</td>
-                </tr>
-              </tbody>
-            </table>
-            </div>
-            </div>
-            <div class="example">
-            <h3>Example 7</h3>
-            <div class="code javascript"><!--jQuery(".jgtable").jgtable();--></div>
-            <div class="code html"><!--<div class="jgtable {size:'550x450',
-type:'bhs',
-bar_width:90,
-bar_spacing:11,
-colors:['f04242','FFCC00','99CC00'],
-bg:'dca0ee',
-bg_type:'gradient',
-bg_angle:40,
-bg_offset:'FFFFFF',
-chbg:'bfbfbf',
-chbg_type:'stripes',
-chbg_angle:0,
-chbg_offset:'f5f5f5',
-chbg_width:10}">
-	<table>
-	[etc...]
-	</table>
-</div>--></div>
-            <div class="jgtable {size:'550x450',
-                                                type:'bhs',
-                                                bar_width:90,
-                                                bar_spacing:11,
-                                                colors:['f04242','FFCC00','99CC00'],
-                                                bg:'dca0ee',
-                                                bg_type:'gradient',
-                                                bg_angle:40,
-                                                bg_offset:'FFFFFF',
-                                                chbg:'bfbfbf',
-                                                chbg_type:'stripes',
-                                                chbg_angle:0,
-                                                chbg_offset:'f5f5f5',
-                                                chbg_width:10}">
-              <table>
-              <thead>
-                <tr>
-                    <th>Anno</th>
-                    <th class="serie">Data 1</th>
-                    <th class="serie">Data 2</th>
-                    <th class="serie">Data 3</th>
-                </tr>
-              </thead>
-              <tbody>
-                <tr>
-                    <th class="serie">2001</th>
-                    <td>153</td>
-                    <td>60</td>
-                    <td>52</td>
-                </tr>
-                <tr>
-                    <th class="serie">2002</th>
-                    <td>113</td>
-                    <td>70</td>
-                    <td>60</td>
-                </tr>
-                <tr>
-                    <th class="serie">2003</th>
-                    <td>120</td>
-                    <td>80</td>
-                    <td>40</td>
-                </tr>
-              </tbody>
-            </table>
-            </div>
-            </div>
-            <div class="example">
-            <h3>Example 8</h3>
-            <div class="code javascript"><!--jQuery(".jgtable").jgtable();--></div>
-            <div class="code html"><!--<div class="jgtable {size:'450x450',
-type:'bvs',
-bar_width:90,
-bar_spacing:11,
-colors:['f04242','FFCC00','99CC00'],
-bg:'dca0ee',
-bg_type:'gradient',
-bg_angle:40,
-bg_offset:'FFFFFF',
-chbg:'bfbfbf',
-chbg_type:'stripes',
-chbg_angle:0,
-chbg_offset:'f5f5f5',
-chbg_width:10}">
-	<table>
-	[etc...]
-	</table>
-</div>--></div>
-             <div class="jgtable {size:'450x450',
-                                                type:'bvs',
-                                                bar_width:90,
-                                                bar_spacing:11,
-                                                colors:['f04242','FFCC00','99CC00'],
-                                                bg:'dca0ee',
-                                                bg_type:'gradient',
-                                                bg_angle:40,
-                                                bg_offset:'FFFFFF',
-                                                chbg:'bfbfbf',
-                                                chbg_type:'stripes',
-                                                chbg_angle:0,
-                                                chbg_offset:'f5f5f5',
-                                                chbg_width:10}">
-             <table>
-             <thead>
-                <tr>
-                    <th>Anno</th>
-                    <th class="serie">Data 1</th>
-                    <th class="serie">Data 2</th>
-                    <th class="serie">Data 3</th>
-                </tr>
-              </thead>
-              <tbody>
-                <tr>
-                    <th class="serie">2001</th>
-                    <td>153</td>
-                    <td>60</td>
-                    <td>52</td>
-                </tr>
-                <tr>
-                    <th class="serie">2002</th>
-                    <td>113</td>
-                    <td>70</td>
-                    <td>60</td>
-                </tr>
-                <tr>
-                    <th class="serie">2003</th>
-                    <td>120</td>
-                    <td>80</td>
-                    <td>40</td>
-                </tr>
-              </tbody>
-            </table>
-            </div>
-    		</div>
-    </div>
-    
-    <div class="yslider-panelwrapper" title="Json">
-        
-        <h3>JS</h3>
-        <div class="code javascript"><!--jQuery.getJSON(
-    "../json/example.json",
-    //wait json data
-    function(json){
-        jQuery("#jgjson").jgtable(json);
-    }
-);--></div>
-        
-        <h3>Options in external json file (../json/example.json)</h3>
-        <div class="code javascript"><!--{
-size:'550x400',
-type:'bhg',
-title:'Example 1',
-title_color:'000000',
-title_size:16,
-bar_width:30,
-bar_spacing:2,
-colors:['5131c9','FFCC00','da1b1b'],
-bg:'FFFFFF',
-bg_type:'gradient',
-bg_angle:90,
-bg_offset:'6d6969',
-grid:true,
-grid_x:7,
-grid_y:10,
-grid_line:0,
-grid_blank:0
-}--></div>
-        
-        <h3>Html Table</h3>
-        <div class="code html"><!--<div id="jgjson">
-  <table>      
-  <thead>
-    <tr>
-        <th>Anno</th>
-        <th class="serie">Data 1</th>
-        <th class="serie">Data 2</th>
-        <th class="serie">Data 3</th>
-    </tr>
-  </thead>
-  <tbody>
-    <tr>
-        <th class="serie">2001</th>
-        <td>153</td>
-        <td>60</td>
-        <td>52</td>
-    </tr>
-    <tr>
-        <th class="serie">2002</th>
-        <td>113</td>
-        <td>70</td>
-        <td>60</td>
-    </tr>
-    <tr>
-        <th class="serie">2003</th>
-        <td>120</td>
-        <td>80</td>
-        <td>40</td>
-    </tr>
-  </tbody>
-  </table>
-</div>--></div>
-              <div id="jgjson">                                  
-              <table>
-              <thead>
-                <tr>
-                    <th>Anno</th>
-                    <th class="serie">Data 1</th>
-                    <th class="serie">Data 2</th>
-                    <th class="serie">Data 3</th>
-                </tr>
-              </thead>
-              <tbody>
-                <tr>
-                    <th class="serie">2001</th>
-                    <td>153</td>
-                    <td>60</td>
-                    <td>52</td>
-                </tr>
-                <tr>
-                    <th class="serie">2002</th>
-                    <td>113</td>
-                    <td>70</td>
-                    <td>60</td>
-                </tr>
-                <tr>
-                    <th class="serie">2003</th>
-                    <td>120</td>
-                    <td>80</td>
-                    <td>40</td>
-                </tr>
-              </tbody>
-            </table>
-    		</div>        
-    </div>
-    
-    <div class="yslider-panelwrapper" title="Custom data">
-        
-        <h3>Alessandro Del Piero</h3>
-        <div id="jgcustomdata">
-        <table>
-          <thead>
-            <tr>
-            <th colspan="2">Cronologia</th>
-            <th colspan="2">Campionato</th>
-            <th colspan="2">Coppe di Lega<small><sup>*</sup></small></th>
-            <th colspan="2">Coppe Europee<small><sup>**</sup></small></th>
-            <th colspan="2">Coppe Internazionali<small><sup>***</sup></small></th>
-            <th colspan="2">Totale</th>
-          </tr>
-          <tr>
-            <th>Stagione - Squadra</th>
-            <th>Serie</th>
-            <th>Presenze</th>
-            <th>Gol</th>
-            <th>Presenze</th>
-            <th>Gol</th>
-            <th>Presenze</th>
-            
-            <th>Gol</th>
-            <th>Presenze</th>
-            <th>Gol</th>
-            <th>Presenze</th>
-            <th>Gol</th>
-          </tr>
-          </thead>
-          <tfoot>
-            <tr>
-                <th colspan="2">Totale</th>
-                <th>417</th>
-                <th>176</th>
-                <th>51</th>
-                <th>22</th>
-                <th>105</th>
-                <th>43</th>
-                <th>1</th>
-                
-                <th>1</th>
-                <th>574</th>
-                <th>242</th>
-            </tr>
-            </tfoot>
-          <tbody>
-          
-          <tr>
-            <th class="custom">1991-92 - Padova</th>
-            
-            <td>B</td>
-            <td>4</td>
-            <td>-</td>
-            <td>-</td>
-            <td>-</td>
-            <td>-</td>
-            <td>-</td>
-            <td>-</td>
-            <td>-</td>
-            
-            <td>4</td>
-            <td>-</td>
-            </tr>
-            <tr>
-            <th class="custom">1992-93 - Juventus</th>
-            <td>B</td>
-            <td>10</td>
-            <td>1</td>
-            
-            <td>-</td>
-            <td>-</td>
-            <td>-</td>
-            <td>-</td>
-            <td>-</td>
-            <td>-</td>
-            <td>10</td>
-            <td>1</td>
-            </tr>
-            
-            <tr>
-            <th class="custom">1993-94 - Juventus</th>
-            <td>A</td>
-            <td>11</td>
-            <td>5</td>
-            <td>1</td>
-            <td>-</td>
-            <td>2</td>
-            
-            <td>-</td>
-            <td>-</td>
-            <td>-</td>
-            <td>14</td>
-            <td>5</td>
-            </tr>
-            <tr>
-            <th class="custom">1994-95 - Juventus</th>
-            
-            <td>A</td>
-            <td>29</td>
-            <td>8</td>
-            <td>10</td>
-            <td>1</td>
-            <td>11</td>
-            <td>1</td>
-            <td>-</td>
-            <td>-</td>
-            
-            <td>50</td>
-            <td>10</td>
-            </tr>
-            <tr>
-            <th class="custom">1995-96 - Juventus</th>
-            <td>A</td>
-            <td>29</td>
-            <td>6</td>
-            
-            <td>3</td>
-            <td>1</td>
-            <td>11</td>
-            <td>6</td>
-            <td>-</td>
-            <td>-</td>
-            <td>43</td>
-            <td>13</td>
-            </tr>
-            
-            <tr>
-            <th class="custom">1996-97 - Juventus</th>
-            <td>A</td>
-            <td>22</td>
-            <td>8</td>
-            <td>4</td>
-            <td>-</td>
-            <td>8</td>
-            
-            <td>6</td>
-            <td>1</td>
-            <td>1</td>
-            <td>35</td>
-            <td>15</td>
-            </tr>
-            <tr>
-            <th class="custom">1997-98 - Juventus</th>
-            
-            <td>A</td>
-            <td>32</td>
-            <td>21</td>
-            <td>5</td>
-            <td>1</td>
-            <td>10</td>
-            <td>10</td>
-            <td>-</td>
-            <td>-</td>
-            
-            <td>47</td>
-            <td>32</td>
-            </tr>
-            <tr>
-            <th class="custom">1998-99 - Juventus</th>
-            <td>A</td>
-            <td>8</td>
-            <td>2</td>
-            
-            <td>2</td>
-            <td>1</td>
-            <td>4</td>
-            <td>-</td>
-            <td>-</td>
-            <td>-</td>
-            <td>14</td>
-            <td>3</td>
-            </tr>
-            
-            <tr>
-            <th class="custom">1999-00 - Juventus</th>
-            <td>A</td>
-            <td>34</td>
-            <td>9</td>
-            <td>2</td>
-            <td>1</td>
-            <td>9</td>
-            
-            <td>2</td>
-            <td>-</td>
-            <td>-</td>
-            <td>45</td>
-            <td>12</td>
-            </tr>
-            <tr>
-            <th class="custom">2000-01 - Juventus</th>
-            
-            <td>A</td>
-            <td>25</td>
-            <td>9</td>
-            <td>2</td>
-            <td>-</td>
-            <td>6</td>
-            <td>-</td>
-            <td>-</td>
-            <td>-</td>
-            
-            <td>33</td>
-            <td>9</td>
-            </tr>
-            <tr>
-            <th class="custom">2001-02 - Juventus</th>
-            <td>A</td>
-            <td>32</td>
-            <td>16</td>
-            
-            <td>4</td>
-            <td>1</td>
-            <td>10</td>
-            <td>4</td>
-            <td>-</td>
-            <td>-</td>
-            <td>46</td>
-            <td>21</td>
-            </tr>
-            
-            <tr>
-            <th class="custom">2002-03 - Juventus</th>
-            <td>A</td>
-            <td>24</td>
-            <td>16</td>
-            <td>1</td>
-            <td>2</td>
-            <td>13</td>
-            
-            <td>5</td>
-            <td>-</td>
-            <td>-</td>
-            <td>38</td>
-            <td>23</td>
-            </tr>
-            <tr>
-            <th class="custom">2003-04 - Juventus</th>
-            
-            <td>A</td>
-            <td>22</td>
-            <td>8</td>
-            <td>5</td>
-            <td>3</td>
-            <td>4</td>
-            <td>3</td>
-            <td>-</td>
-            <td>-</td>
-            
-            <td>31</td>
-            <td>14</td>
-            </tr>
-            <tr>
-            <th class="custom">2004-05 - Juventus</th>
-            <td>A</td>
-            <td>30</td>
-            <td>14</td>
-            
-            <td>1</td>
-            <td>-</td>
-            <td>10</td>
-            <td>3</td>
-            <td>-</td>
-            <td>-</td>
-            <td>41</td>
-            <td>17</td>
-            </tr>
-            
-            <tr>
-            <th class="custom">2005-06 - Juventus</th>
-            <td>A</td>
-            <td>33</td>
-            <td>12</td>
-            <td>5</td>
-            <td>5</td>
-            <td>7</td>
-            
-            <td>3</td>
-            <td>-</td>
-            <td>-</td>
-            <td>45</td>
-            <td>20</td>
-            </tr>
-            <tr>
-            <th class="custom">2006-07 - Juventus</th>
-            
-            <td>B</td>
-            <td>35</td>
-            <td>20</td>
-            <td>2</td>
-            <td>3</td>
-            <td>-</td>
-            <td>-</td>
-            <td>-</td>
-            <td>-</td>
-            
-            <td>37</td>
-            <td>23</td>
-            </tr>
-            
-            <tr>
-            <th class="custom">2007-08 - Juventus</th>
-            <td>A</td>
-            <td>37</td>
-            <td>21</td>
-            
-            <td>4</td>
-            <td>3</td>
-            <td>-</td>
-            <td>-</td>
-            <td>-</td>
-            <td>-</td>
-            <td>41</td>
-            <td>24</td>
-            </tr>
-            
-            
-            </tbody>
-            
-        </table>
-        </div>
-        <h3>JS</h3>
-        <div class="code javascript"><!--jQuery.getJSON(
-"../json/delpiero.json",
-//wait json data
-function(json){
-    var data_custom = [];
-    for(var x= 0;x< jQuery("#jgcustomdata").find("tbody > tr").size();x++){
-        data_custom.push(jQuery.map( jQuery("#jgcustomdata").find("tbody > tr:eq(" + x + ") > td"),
-           function(td,index){
-                if(index % 11 == 1 || index % 11 == 2){
-                    if(parseInt(jQuery(td).text()))
-                        return parseInt(jQuery(td).text());
-                    else
-                        return 0;
-                } 
-           }
-        ));
-        
-    }
-    var axis_custom = jQuery.map( jQuery("#jgcustomdata").find("tbody > tr > th.custom"),
-               function(th) { return jQuery(th).text(); }
-    );
-    var legend_custom = ["presenze", "gol"];
-    
-    json.axis_labels = axis_custom;
-    json.data = data_custom;
-    json.legend = legend_custom;
-    jQuery("#jgcustomdata").jgtable(json);
-    
-    var data_custom = [];
-    for(var x= 0;x< jQuery("#jgcustomdata").find("tbody > tr").size();x++){
-        data_custom.push(jQuery.map( jQuery("#jgcustomdata").find("tbody > tr:eq(" + x + ") > td"),
-           function(td,index){
-                if(index % 11 == 9 || index % 11 == 10){
-                    if(parseInt(jQuery(td).text()))
-                        return parseInt(jQuery(td).text());
-                    else
-                        return 0;
-                } 
-           }
-        ));
-        
-    }
-    json.data = data_custom;
-    json.title = 'Gol e presenze totali';
-    
-    jQuery("#jgcustomdata").jgtable(json);
-    
-});--></div>
-        
-        <h3>Options in json file</h3>
-        <div class="code javascript"><!--{
-size:'450x600',
-type:'bhg',
-axis_step:1,
-title:'Gol e presenze in campionato',
-title_color:'000000',
-title_size:16,
-bar_width:10,
-bar_spacing:0,
-colors:['5131c9','da1b1b'],
-grid:true,
-grid_x:5,
-grid_y:5,
-grid_line:5,
-grid_blank:5
-}--></div>
-        
-        <h3>Html Table</h3>
-        <div class="code html"><!--<div id="jgcustomdata">
-  <table>
-  <thead>
-    <tr>
-    <th colspan="2">Cronologia</th>
-    <th colspan="2">Campionato</th>
-    <th colspan="2">Coppe di Lega<small><sup>*</sup></small></th>
-    <th colspan="2">Coppe Europee<small><sup>**</sup></small></th>
-    <th colspan="2">Coppe Internazionali<small><sup>***</sup></small></th>
-    <th colspan="2">Totale</th>
-  </tr>
-  <tr>
-    <th>Stagione - Squadra</th>
-    <th>Serie</th>
-    <th>Presenze</th>
-    <th>Gol</th>
-    <th>Presenze</th>
-    <th>Gol</th>
-    <th>Presenze</th>
-    
-    <th>Gol</th>
-    <th>Presenze</th>
-    <th>Gol</th>
-    <th>Presenze</th>
-    <th>Gol</th>
-  </tr>
-  </thead>
-  <tfoot>
-    <tr>
-        <th colspan="2">Totale</th>
-        <th>417</th>
-        <th>176</th>
-        <th>51</th>
-        <th>22</th>
-        <th>105</th>
-        <th>43</th>
-        <th>1</th>
-        
-        <th>1</th>
-        <th>574</th>
-        <th>242</th>
-    </tr>
-    </tfoot>
-  <tbody>
-  
-  <tr>
-    <th class="custom">1991-92 - Padova</th>
-    
-    <td>B</td>
-    <td>4</td>
-    <td>-</td>
-    <td>-</td>
-    <td>-</td>
-    <td>-</td>
-    <td>-</td>
-    <td>-</td>
-    <td>-</td>
-    
-    <td>4</td>
-    <td>-</td>
-    </tr>
-    <tr>
-    <th class="custom">1992-93 - Juventus</th>
-    <td>B</td>
-    <td>10</td>
-    <td>1</td>
-    
-    <td>-</td>
-    <td>-</td>
-    <td>-</td>
-    <td>-</td>
-    <td>-</td>
-    <td>-</td>
-    <td>10</td>
-    <td>1</td>
-    </tr>
-    
-    <tr>
-    <th class="custom">1993-94 - Juventus</th>
-    <td>A</td>
-    <td>11</td>
-    <td>5</td>
-    <td>1</td>
-    <td>-</td>
-    <td>2</td>
-    
-    <td>-</td>
-    <td>-</td>
-    <td>-</td>
-    <td>14</td>
-    <td>5</td>
-    </tr>
-    <tr>
-    <th class="custom">1994-95 - Juventus</th>
-    
-    <td>A</td>
-    <td>29</td>
-    <td>8</td>
-    <td>10</td>
-    <td>1</td>
-    <td>11</td>
-    <td>1</td>
-    <td>-</td>
-    <td>-</td>
-    
-    <td>50</td>
-    <td>10</td>
-    </tr>
-    <tr>
-    <th class="custom">1995-96 - Juventus</th>
-    <td>A</td>
-    <td>29</td>
-    <td>6</td>
-    
-    <td>3</td>
-    <td>1</td>
-    <td>11</td>
-    <td>6</td>
-    <td>-</td>
-    <td>-</td>
-    <td>43</td>
-    <td>13</td>
-    </tr>
-    
-    <tr>
-    <th class="custom">1996-97 - Juventus</th>
-    <td>A</td>
-    <td>22</td>
-    <td>8</td>
-    <td>4</td>
-    <td>-</td>
-    <td>8</td>
-    
-    <td>6</td>
-    <td>1</td>
-    <td>1</td>
-    <td>35</td>
-    <td>15</td>
-    </tr>
-    <tr>
-    <th class="custom">1997-98 - Juventus</th>
-    
-    <td>A</td>
-    <td>32</td>
-    <td>21</td>
-    <td>5</td>
-    <td>1</td>
-    <td>10</td>
-    <td>10</td>
-    <td>-</td>
-    <td>-</td>
-    
-    <td>47</td>
-    <td>32</td>
-    </tr>
-    <tr>
-    <th class="custom">1998-99 - Juventus</th>
-    <td>A</td>
-    <td>8</td>
-    <td>2</td>
-    
-    <td>2</td>
-    <td>1</td>
-    <td>4</td>
-    <td>-</td>
-    <td>-</td>
-    <td>-</td>
-    <td>14</td>
-    <td>3</td>
-    </tr>
-    
-    <tr>
-    <th class="custom">1999-00 - Juventus</th>
-    <td>A</td>
-    <td>34</td>
-    <td>9</td>
-    <td>2</td>
-    <td>1</td>
-    <td>9</td>
-    
-    <td>2</td>
-    <td>-</td>
-    <td>-</td>
-    <td>45</td>
-    <td>12</td>
-    </tr>
-    <tr>
-    <th class="custom">2000-01 - Juventus</th>
-    
-    <td>A</td>
-    <td>25</td>
-    <td>9</td>
-    <td>2</td>
-    <td>-</td>
-    <td>6</td>
-    <td>-</td>
-    <td>-</td>
-    <td>-</td>
-    
-    <td>33</td>
-    <td>9</td>
-    </tr>
-    <tr>
-    <th class="custom">2001-02 - Juventus</th>
-    <td>A</td>
-    <td>32</td>
-    <td>16</td>
-    
-    <td>4</td>
-    <td>1</td>
-    <td>10</td>
-    <td>4</td>
-    <td>-</td>
-    <td>-</td>
-    <td>46</td>
-    <td>21</td>
-    </tr>
-    
-    <tr>
-    <th class="custom">2002-03 - Juventus</th>
-    <td>A</td>
-    <td>24</td>
-    <td>16</td>
-    <td>1</td>
-    <td>2</td>
-    <td>13</td>
-    
-    <td>5</td>
-    <td>-</td>
-    <td>-</td>
-    <td>38</td>
-    <td>23</td>
-    </tr>
-    <tr>
-    <th class="custom">2003-04 - Juventus</th>
-    
-    <td>A</td>
-    <td>22</td>
-    <td>8</td>
-    <td>5</td>
-    <td>3</td>
-    <td>4</td>
-    <td>3</td>
-    <td>-</td>
-    <td>-</td>
-    
-    <td>31</td>
-    <td>14</td>
-    </tr>
-    <tr>
-    <th class="custom">2004-05 - Juventus</th>
-    <td>A</td>
-    <td>30</td>
-    <td>14</td>
-    
-    <td>1</td>
-    <td>-</td>
-    <td>10</td>
-    <td>3</td>
-    <td>-</td>
-    <td>-</td>
-    <td>41</td>
-    <td>17</td>
-    </tr>
-    
-    <tr>
-    <th class="custom">2005-06 - Juventus</th>
-    <td>A</td>
-    <td>33</td>
-    <td>12</td>
-    <td>5</td>
-    <td>5</td>
-    <td>7</td>
-    
-    <td>3</td>
-    <td>-</td>
-    <td>-</td>
-    <td>45</td>
-    <td>20</td>
-    </tr>
-    <tr>
-    <th class="custom">2006-07 - Juventus</th>
-    
-    <td>B</td>
-    <td>35</td>
-    <td>20</td>
-    <td>2</td>
-    <td>3</td>
-    <td>-</td>
-    <td>-</td>
-    <td>-</td>
-    <td>-</td>
-    
-    <td>37</td>
-    <td>23</td>
-    </tr>
-    
-    <tr>
-    <th class="custom">2007-08 - Juventus</th>
-    <td>A</td>
-    <td>37</td>
-    <td>21</td>
-    
-    <td>4</td>
-    <td>3</td>
-    <td>-</td>
-    <td>-</td>
-    <td>-</td>
-    <td>-</td>
-    <td>41</td>
-    <td>24</td>
-    </tr>
-    
-    
-    </tbody>
-    
-   </table>
-</div>--></div>
-                                                
-              
-        
-    </div>
-</div>
-<!--todo: copy events -->
-<div id="yslider-code" class="ycodaslider">
-    <a class="javascript" href="../../jgcharts.js" class="tracking {label : '/jgcharts/code/jgcharts'}">jGCharts 1.0</a>
-    <a class="javascript" href="../../plugins/jgtable/jgtable.js" class="tracking {label : '/jgcharts/code/jgtable'}">jGTable 1.0</a>
-</div>
-<div id="analytics" class="UA-258871-1 {host: 'maxb.net'}"></div><!--debug:true-->
-</body>
-</html>    

theme/tripal_theme_core/js/jgcharts/include/gui/index.html

@@ -1,588 +0,0 @@
-<!DOCTYPE html 
-    PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-           "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
-    <title>jQuery Google Charts Gui 1.0 - Demo</title>
-    <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
-    <script src="lib/jquery-1.2.6.min.js" type="text/javascript"></script>
-	<script src="lib/jquery.metadata.js" type="text/javascript"></script>
-	<script src="lib/jquery-ui-personalized-1.6rc2.min.js" type="text/javascript"></script>
-    <script src="lib/farbtastic/farbtastic.js" type="text/javascript"></script>
-	<link href="lib/farbtastic/farbtastic.css" type="text/css" rel="stylesheet" />
-		
-	<script src="../../jgcharts.js" type="text/javascript"></script>
-	<script src="../../plugins/jgtable/jgtable.js" type="text/javascript"></script>
-	<script src="plugins/jggui/jggui.js" type="text/javascript"></script>
-	<link href="plugins/jggui/jggui.css" type="text/css" rel="stylesheet" />
-	<link href="plugins/jggui/theme/jquery-ui-themeroller.css" type="text/css" rel="stylesheet" />
-	<script type="text/javascript">
-		var STATIC = 0;
-		jQuery(document).bind("jggui", function(){
-			var _callback = function(){
-				STATIC++;
-				jQuery(".jgchart").remove();
-				jQuery(".jgtable")
-				.jgtable({
-					single : STATIC,
-					gui    : true
-				});
-			};
-			_callback();
-			
-			jQuery("img.jggui").jggui({
-				url : "plugins/jggui/",
-				height : 400,
-				width : 600,
-				callback : _callback
-			});
-		});
-		jQuery(document).ready(function(){
-			jQuery(document).trigger("jggui");
-		});
-	</script>
-</head>
-<body>
-<h1>Click on chart</h1>
-<div class="jgtable {type : 'p',colors : ['5131C9'],size : '300x200'}">
-<table class="demo">
-  <thead>
-    <tr>
-        <th>Anno</th>
-
-        <th class="serie">Data 1</th>
-        <th class="serie">Data 2</th>
-        <th class="serie">Data 3</th>
-    </tr>
-  </thead>
-  <tbody>
-    <tr>
-
-        <th class="serie">2001</th>
-        <td>153</td>
-        <td>60</td>
-        <td>52</td>
-    </tr>
-    <tr>
-        <th class="serie">2002</th>
-
-        <td>113</td>
-        <td>70</td>
-        <td>60</td>
-    </tr>
-    <tr>
-        <th class="serie">2003</th>
-        <td>120</td>
-
-        <td>80</td>
-        <td>40</td>
-    </tr>
-  </tbody>
-</table>
-</div>
-<div class="jgtable {type : 'bhg',bar_width : 15,grid : true,colors : ['5131C9'],size : '390x490'}">
-<table class="demo">
-  <thead>
-    <tr>
-        <th>Squadra</th>
-
-        <th class="serie">Punti</th>
-    </tr>
-  </thead>
-  <tbody>
-    <tr><th class="serie">Inter</th><td>27</td></tr>
-    <tr><th class="serie">Juventus</th><td>24</td></tr>
-    <tr><th class="serie">Milan</th><td>23</td></tr>
-    <tr><th class="serie">Napoli</th><td>23</td></tr>
-    <tr><th class="serie">Lazio</th><td>22</td></tr>
-    <tr><th class="serie">Udinese</th><td>21</td></tr>
-    <tr><th class="serie">Genoa</th><td>20</td></tr>
-    <tr><th class="serie">Fiorentina</th><td>20</td></tr>
-    <tr><th class="serie">Catania</th><td>18</td></tr>
-    <tr><th class="serie">Palermo</th><td>16</td></tr>
-    <tr><th class="serie">Atalanta</th><td>14</td></tr>
-    <tr><th class="serie">Lecce</th><td>12</td></tr>
-    <tr><th class="serie">Siena</th><td>12</td></tr>
-    <tr><th class="serie">Torino</th><td>11</td></tr>
-    <tr><th class="serie">Cagliari</th><td>10</td></tr>
-    <tr><th class="serie">Sampdoria</th><td>10</td></tr>
-    <tr><th class="serie">Roma</th><td>8</td></tr>
-    <tr><th class="serie">Bologna</th><td>7</td></tr>
-    <tr><th class="serie">Chievo</th><td>6</td></tr>
-    <tr><th class="serie">Reggina</th><td>5</td></tr>
-  </tbody>
-</table>
-</div>
-<div class="jgtable {
-	type : 'bhg',
-	bar_width : 19,
-	bg : 'FFFFFF',
-	bg_type : 'stripes',
-	bg_offset : '7a7a7a',
-	bg_angle : 45,
-	bg_trasparency : 90,
-	chbg : 'FFFFFF',
-	chbg_type : 'gradient',
-	chbg_offset : 'cb7e01',
-	grid : true,
-	grid_x : 3,
-	grid_y : 3,
-	grid_line : 2,
-	grid_blank : 2,
-	colors : ['5131C9','FFCC00','DA1B1B','FF9900','FF6600','CCFFFF','CCFF00','CCCCCC','FF99CC','999900','999999','66FF00','66CC00','669900','660099','33CC00','333399','000000','000000','000000'],
-	size : '300x460'
-}">
-<table class="demo">
-  <thead>
-    <tr>
-        <th>Squadra</th>
-		<th class="serie">Inter</th>
-	    <th class="serie">Juventus</th>
-	    <th class="serie">Milan</th>
-	    <th class="serie">Napoli</th>
-	    <th class="serie">Lazio</th>
-	    <th class="serie">Udinese</th>
-	    <th class="serie">Genoa</th>
-	    <th class="serie">Fiorentina</th>
-	    <th class="serie">Catania</th>
-	    <th class="serie">Palermo</th>
-	    <th class="serie">Atalanta</th>
-	    <th class="serie">Lecce</th>
-	    <th class="serie">Siena</th>
-	    <th class="serie">Torino</th>
-	    <th class="serie">Cagliari</th>
-	    <th class="serie">Sampdoria</th>
-	    <th class="serie">Roma</th>
-	    <th class="serie">Bologna</th>
-	    <th class="serie">Chievo</th>
-	    <th class="serie">Reggina</th>
-    </tr>
-  </thead>
-  <tbody>
-    <tr>
-    <th class="serie">Punti</th>
-    <td>27</td>
-    <td>24</td>
-    <td>23</td>
-    <td>23</td>
-    <td>22</td>
-    <td>21</td>
-    <td>20</td>
-    <td>20</td>
-    <td>18</td>
-    <td>16</td>
-    <td>14</td>
-    <td>12</td>
-    <td>12</td>
-    <td>11</td>
-    <td>10</td>
-    <td>10</td>
-    <td>8</td>
-    <td>7</td>
-    <td>6</td>
-    <td>5</td>
-    </tr>
-  </tbody>
-</table>
-</div>
-<div class="jgtable {
-	type : 'lc',
-	size : '520x370',
-	lines : [['1','0','0'],['1','0','0']],
-	axis_step : 10,
-	bg : '000000',
-	bg_type : 'gradient',
-	bg_offset : 'FFFFFF',
-	bg_trasparency : 90,
-	grid : true,
-	grid_x : 4,
-	grid_y : 4,
-	grid_line : 2,
-	grid_blank : 2,
-	colors : ['5131C9','FFCC00'],
-	filltop : ''
-}">
-<table>
-<thead>
-<tr>
-    <th></th>
-    <th class="serie">CA</th>
-    <th class="serie">DF</th>
-</tr>
-</thead>
-<tbody>
-   <tr>
-    <th class="serie">01-03</th>
-
-    <td>105.7</td>
-    <td>97.9</td>
-  </tr>
-  <tr>
-    <th class="serie">02-03</th>
-    <td>108.1</td>
-    <td>101.6</td>
-
-  </tr>
-  <tr>
-    <th class="serie">03-03</th>
-    <td>110.7</td>
-    <td>102.9</td>
-  </tr>
-  
-  <tr>
-
-    <th class="serie">04-03</th>
-    <td>111.0</td>
-    <td>93.7</td>
-  </tr>
-  <tr>
-    <th class="serie">05-03</th>
-    <td>110.0</td>
-
-    <td>89.8</td>
-  </tr>
-  <tr>
-    <th class="serie">06-03</th>
-    <td>109.0</td>
-    <td>90.7</td>
-  </tr>
-
-  <tr>
-    <th class="serie">07-03</th>
-    <td>107.5</td>
-    <td>93.0</td>
-  </tr>
-  <tr>
-    <th class="serie">08-03</th>
-
-    <td>106.1</td>
-    <td>94.5</td>
-  </tr>
-  <tr>
-    <th class="serie">09-03</th>
-    <td>104.3</td>
-    <td>91.9</td>
-
-  </tr>
-  <tr>
-    <th class="serie">10-03</th>
-    <td>102.0</td>
-    <td>93.9</td>
-  </tr>
-  <tr>
-
-    <th class="serie">11-03</th>
-    <td>102.8</td>
-    <td>93.6</td>
-  </tr>
-  <tr>
-    <th class="serie">12-03</th>
-    <td>103.8</td>
-
-    <td>92.6</td>
-  </tr>
-  
-  <tr>
-    <th class="serie">01-04</th>
-    <td>102.9</td>
-    <td>94.0</td>
-  </tr>
-
-  <tr>
-    <th class="serie">02-04</th>
-    <td>102.1</td>
-    <td>92.7</td>
-  </tr>
-  <tr>
-    <th class="serie">03-04</th>
-
-    <td>100.6</td>
-    <td>96.0</td>
-  </tr>
-  
- <tr>
-    <th class="serie">04-04</th>
-    <td>101.7</td>
-    <td>97.9</td>
-
-  </tr>
-  <tr>
-    <th class="serie">05-04</th>
-    <td>101.8</td>
-    <td>105.0</td>
-  </tr>
-  <tr>
-
-    <th class="serie">06-04</th>
-    <td>103.3</td>
-    <td>104.1</td>
-  </tr>
-  <tr>
-    <th class="serie">07-04</th>
-    <td>104.0</td>
-
-    <td>105.1</td>
-  </tr>
-  <tr>
-    <th class="serie">08-04</th>
-    <td>103.7</td>
-    <td>108.1</td>
-  </tr>
-
-  <tr>
-    <th class="serie">09-04</th>
-    <td>108.4</td>
-    <td>108.4</td>
-  </tr>
-  <tr>
-    <th class="serie">10-04</th>
-
-    <td>109.4</td>
-    <td>113.8</td>
-  </tr>
-  <tr>
-    <th class="serie">11-04</th>
-    <td>112.0</td>
-    <td>109.1</td>
-
-  </tr>
-  <tr>
-    <th class="serie">12-04</th>
-    <td>112.6</td>
-    <td>106.3</td>
-  </tr>
-  <tr>
-
-    <th class="serie">01-05</th>
-    <td>115.5</td>
-    <td>106.7</td>
-  </tr>
-  <tr>
-    <th class="serie">02-05</th>
-    <td>115.7</td>
-
-    <td>108.8</td>
-  </tr>
-  <tr>
-    <th class="serie">03-05</th>
-    <td>114.7</td>
-    <td>118.8</td>
-  </tr>
-
-  <tr>
-    <th class="serie">04-05</th>
-    <td>115.9</td>
-    <td>120.4</td>
-  </tr>
-  <tr>
-    <th class="serie">05-05</th>
-
-    <td>116.2</td>
-    <td>115.9</td>
-  </tr>
-  <tr>
-    <th class="serie">06-05</th>
-    <td>118.0</td>
-    <td>124.7</td>
-
-  </tr>
-  <tr>
-    <th class="serie">07-05</th>
-    <td>123.3</td>
-    <td>126.5</td>
-  </tr>
-  <tr>
-
-    <th class="serie">08-05</th>
-    <td>127.6</td>
-    <td>131.6</td>
-  </tr>
-  <tr>
-    <th class="serie">09-05</th>
-    <td>130.3</td>
-
-    <td>134.0</td>
-  </tr>
-  <tr>
-    <th class="serie">10-05</th>
-    <td>135.5</td>
-    <td>135.7</td>
-  </tr>
-
-  <tr>
-    <th class="serie">11-05</th>
-    <td>138.2</td>
-    <td>126.4</td>
-  </tr>
-  <tr>
-    <th class="serie">12-05</th>
-
-    <td>139.6</td>
-    <td>127.4</td>
-  </tr>
-  <tr>
-    <th class="serie">01-06</th>
-    <td>145.1</td>
-    <td>131.0</td>
-
-  </tr>
-  <tr>
-    <th class="serie">02-06</th>
-    <td>146.4</td>
-    <td>129.9</td>
-  </tr>
-  <tr>
-
-    <th class="serie">03-06</th>
-    <td>147.1</td>
-    <td>133.7</td>
-  </tr>
-  <tr>
-    <th class="serie">04-06</th>
-    <td>149.0</td>
-
-    <td>138.4</td>
-  </tr>
-  <tr>
-    <th class="serie">05-06</th>
-    <td>150.3</td>
-    <td>141.0</td>
-  </tr>
-
-  <tr>
-    <th class="serie">06-06</th>
-    <td>151.3</td>
-    <td>139.3</td>
-  </tr>
-  <tr>
-    <th class="serie">07-06</th>
-
-    <td>153.4</td>
-    <td>145.3</td>
-  </tr>
-  <tr>
-    <th class="serie">08-06</th>
-    <td>152.7</td>
-    <td>142.9</td>
-
-  </tr>
-  <tr>
-    <th class="serie">09-06</th>
-    <td>152.9</td>
-    <td>129.2</td>
-  </tr>
-  <tr>
-
-    <th class="serie">10-06</th>
-    <td>152.2</td>
-    <td>126.0</td>
-  </tr>
-  <tr>
-    <th class="serie">11-06</th>
-    <td>151.9</td>
-
-    <td>124.8</td>
-  </tr>
-  <tr>
-    <th class="serie">12-06</th>
-    <td>150.1</td>
-    <td>125.9</td>
-  </tr>
-
-  <tr>
-    <th class="serie">01-07</th>
-    <td>148.2</td>
-    <td>118.9</td>
-  </tr>
-  <tr>
-    <th class="serie">02-07</th>
-
-    <td>145.3</td>
-    <td>122.9</td>
-  </tr>
-  <tr>
-    <th class="serie">03-07</th>
-    <td>142.9</td>
-    <td>127.7</td>
-
-  </tr>
-  <tr>
-    <th class="serie">04-07</th>
-    <td>142.6</td>
-    <td>134.4</td>
-  </tr>
-  <tr>
-
-    <th class="serie">05-07</th>
-    <td>144.0</td>
-    <td>138.5</td>
-  </tr>
-  <tr>
-    <th class="serie">06-07</th>
-    <td>145.5</td>
-
-    <td>138.7</td>
-  </tr>
-  <tr>
-    <th class="serie">07-07</th>
-    <td>147.2</td>
-    <td>141.8</td>
-  </tr>
-
-  <tr>
-    <th class="serie">08-07</th>
-    <td>150.0</td>
-    <td>139.2</td>
-  </tr>
-  <tr>
-    <th class="serie">09-07</th>
-
-    <td>153.8</td>
-    <td>145.6</td>
-  </tr>
-  <tr>
-    <th class="serie">10-07</th>
-    <td>155.4</td>
-    <td>147.6</td>
-
-  </tr>
-  <tr>
-    <th class="serie">11-07</th>
-    <td>157.0</td>
-    <td>157.9</td>
-  </tr>
-  <tr>
-
-    <th class="serie">12-07</th>
-    <td>158.4</td>
-    <td>156.2</td>
-  </tr>
-  <tr>
-    <th class="serie">01-08</th>
-    <td>162.8</td>
-
-    <td>153.9</td>
-  </tr>
-  <tr>
-    <th class="serie">02-08</th>
-    <td>162.8</td>
-    <td>158.6</td>
-  </tr>
-
-  <tr>
-    <th class="serie">03-08</th>
-    <td>164.7</td>
-    <td>166.3</td>
-  </tr>
-  <tr>
-    <th class="serie">04-08</th>
-
-    <td>168.5</td>
-    <td>165.8</td>
-  </tr>
-</tbody>
-</table>
-</div>
-</body>
-</html>  

theme/tripal_theme_core/js/jgcharts/include/gui/lib/farbtastic/farbtastic.css

@@ -1,43 +0,0 @@
-#picker{
-  z-index: 99999999;
-}
-
-.farbtastic {
-  position: absolute;
-  background: #222;
-  border: 1px solid #444;
-  border-top: 0;
-  top: 1.6em;
-  right: 0;
-  z-index: 99999999;
-}
-.farbtastic * {
-  position: absolute;
-  cursor: crosshair;
-}
-.farbtastic, .farbtastic .wheel {
-  width: 195px;
-  height: 195px;
-}
-.farbtastic .color, .farbtastic .overlay {
-  top: 47px;
-  left: 47px;
-  width: 101px;
-  height: 101px;
-}
-.farbtastic .wheel {
-  background: url(wheel.png) no-repeat;
-  width: 195px;
-  height: 195px;
-}
-.farbtastic .overlay {
-  background: url(mask.png) no-repeat;
-}
-.farbtastic .marker {
-  width: 17px;
-  height: 17px;
-  margin: -8px 0 0 -8px;
-  overflow: hidden; 
-  background: url(colorpicker_select.gif) no-repeat;
-}
-

theme/tripal_theme_core/js/jgcharts/include/gui/lib/farbtastic/farbtastic.js

@@ -1,329 +0,0 @@
-// $Id: farbtastic.js,v 1.1 2009/10/01 18:28:22 ccheng Exp $
-// Farbtastic 1.2
-
-jQuery.fn.farbtastic = function (callback) {
-  $.farbtastic(this, callback);
-  return this;
-};
-
-jQuery.farbtastic = function (container, callback) {
-  var container = $(container).get(0);
-  return container.farbtastic || (container.farbtastic = new jQuery._farbtastic(container, callback));
-}
-
-jQuery._farbtastic = function (container, callback) {
-  // Store farbtastic object
-  var fb = this;
-
-  // Insert markup
-  $(container).html('<div class="farbtastic"><div class="color"></div><div class="wheel"></div><div class="overlay"></div><div class="h-marker marker"></div><div class="sl-marker marker"></div></div>');
-  var e = $('.farbtastic', container);
-  fb.wheel = $('.wheel', container).get(0);
-  // Dimensions
-  fb.radius = 84;
-  fb.square = 100;
-  fb.width = 194;
-
-  // Fix background PNGs in IE6
-  if (navigator.appVersion.match(/MSIE [0-6]\./)) {
-    $('*', e).each(function () {
-      if (this.currentStyle.backgroundImage != 'none') {
-        var image = this.currentStyle.backgroundImage;
-        image = this.currentStyle.backgroundImage.substring(5, image.length - 2);
-        $(this).css({
-          'backgroundImage': 'none',
-          'filter': "progid:DXImageTransform.Microsoft.AlphaImageLoader(enabled=true, sizingMethod=crop, src='" + image + "')"
-        });
-      }
-    });
-  }
-
-  /**
-   * Link to the given element(s) or callback.
-   */
-  fb.linkTo = function (callback) {
-    // Unbind previous nodes
-    if (typeof fb.callback == 'object') {
-      $(fb.callback).unbind('keyup', fb.updateValue);
-    }
-
-    // Reset color
-    fb.color = null;
-
-    // Bind callback or elements
-    if (typeof callback == 'function') {
-      fb.callback = callback;
-    }
-    else if (typeof callback == 'object' || typeof callback == 'string') {
-      fb.callback = $(callback);
-      fb.callback.bind('keyup', fb.updateValue);
-      if (fb.callback.get(0).value) {
-        fb.setColor(fb.callback.get(0).value);
-      }
-    }
-    return this;
-  }
-  fb.updateValue = function (event) {
-    if (this.value && this.value != fb.color) {
-      fb.setColor(this.value);
-    }
-  }
-
-  /**
-   * Change color with HTML syntax #123456
-   */
-  fb.setColor = function (color) {
-    var unpack = fb.unpack(color);
-    if (fb.color != color && unpack) {
-      fb.color = color;
-      fb.rgb = unpack;
-      fb.hsl = fb.RGBToHSL(fb.rgb);
-      fb.updateDisplay();
-    }
-    return this;
-  }
-
-  /**
-   * Change color with HSL triplet [0..1, 0..1, 0..1]
-   */
-  fb.setHSL = function (hsl) {
-    fb.hsl = hsl;
-    fb.rgb = fb.HSLToRGB(hsl);
-    fb.color = fb.pack(fb.rgb);
-    fb.updateDisplay();
-    return this;
-  }
-
-  /////////////////////////////////////////////////////
-
-  /**
-   * Retrieve the coordinates of the given event relative to the center
-   * of the widget.
-   */
-  fb.widgetCoords = function (event) {
-    var x, y;
-    var el = event.target || event.srcElement;
-    var reference = fb.wheel;
-
-    if (typeof event.offsetX != 'undefined') {
-      // Use offset coordinates and find common offsetParent
-      var pos = { x: event.offsetX, y: event.offsetY };
-
-      // Send the coordinates upwards through the offsetParent chain.
-      var e = el;
-      while (e) {
-        e.mouseX = pos.x;
-        e.mouseY = pos.y;
-        pos.x += e.offsetLeft;
-        pos.y += e.offsetTop;
-        e = e.offsetParent;
-      }
-
-      // Look for the coordinates starting from the wheel widget.
-      var e = reference;
-      var offset = { x: 0, y: 0 }
-      while (e) {
-        if (typeof e.mouseX != 'undefined') {
-          x = e.mouseX - offset.x;
-          y = e.mouseY - offset.y;
-          break;
-        }
-        offset.x += e.offsetLeft;
-        offset.y += e.offsetTop;
-        e = e.offsetParent;
-      }
-
-      // Reset stored coordinates
-      e = el;
-      while (e) {
-        e.mouseX = undefined;
-        e.mouseY = undefined;
-        e = e.offsetParent;
-      }
-    }
-    else {
-      // Use absolute coordinates
-      var pos = fb.absolutePosition(reference);
-      x = (event.pageX || 0*(event.clientX + $('html').get(0).scrollLeft)) - pos.x;
-      y = (event.pageY || 0*(event.clientY + $('html').get(0).scrollTop)) - pos.y;
-    }
-    // Subtract distance to middle
-    return { x: x - fb.width / 2, y: y - fb.width / 2 };
-  }
-
-  /**
-   * Mousedown handler
-   */
-  fb.mousedown = function (event) {
-    // Capture mouse
-    if (!document.dragging) {
-      $(document).bind('mousemove', fb.mousemove).bind('mouseup', fb.mouseup);
-      document.dragging = true;
-    }
-
-    // Check which area is being dragged
-    var pos = fb.widgetCoords(event);
-    fb.circleDrag = Math.max(Math.abs(pos.x), Math.abs(pos.y)) * 2 > fb.square;
-
-    // Process
-    fb.mousemove(event);
-    return false;
-  }
-
-  /**
-   * Mousemove handler
-   */
-  fb.mousemove = function (event) {
-    // Get coordinates relative to color picker center
-    var pos = fb.widgetCoords(event);
-
-    // Set new HSL parameters
-    if (fb.circleDrag) {
-      var hue = Math.atan2(pos.x, -pos.y) / 6.28;
-      if (hue < 0) hue += 1;
-      fb.setHSL([hue, fb.hsl[1], fb.hsl[2]]);
-    }
-    else {
-      var sat = Math.max(0, Math.min(1, -(pos.x / fb.square) + .5));
-      var lum = Math.max(0, Math.min(1, -(pos.y / fb.square) + .5));
-      fb.setHSL([fb.hsl[0], sat, lum]);
-    }
-    return false;
-  }
-
-  /**
-   * Mouseup handler
-   */
-  fb.mouseup = function () {
-    // Uncapture mouse
-    $(document).unbind('mousemove', fb.mousemove);
-    $(document).unbind('mouseup', fb.mouseup);
-    document.dragging = false;
-  }
-
-  /**
-   * Update the markers and styles
-   */
-  fb.updateDisplay = function () {
-    // Markers
-    var angle = fb.hsl[0] * 6.28;
-    $('.h-marker', e).css({
-      left: Math.round(Math.sin(angle) * fb.radius + fb.width / 2) + 'px',
-      top: Math.round(-Math.cos(angle) * fb.radius + fb.width / 2) + 'px'
-    });
-
-    $('.sl-marker', e).css({
-      left: Math.round(fb.square * (.5 - fb.hsl[1]) + fb.width / 2) + 'px',
-      top: Math.round(fb.square * (.5 - fb.hsl[2]) + fb.width / 2) + 'px'
-    });
-
-    // Saturation/Luminance gradient
-    $('.color', e).css('backgroundColor', fb.pack(fb.HSLToRGB([fb.hsl[0], 1, 0.5])));
-
-    // Linked elements or callback
-    if (typeof fb.callback == 'object') {
-      // Set background/foreground color
-      $(fb.callback).css({
-        backgroundColor: fb.color,
-        color: fb.hsl[2] > 0.5 ? '#000' : '#fff'
-      });
-
-      // Change linked value
-      $(fb.callback).each(function() {
-        if (this.value && this.value != fb.color) {
-          this.value = fb.color;
-        }
-      });
-    }
-    else if (typeof fb.callback == 'function') {
-      fb.callback.call(fb, fb.color);
-    }
-  }
-
-  /**
-   * Get absolute position of element
-   */
-  fb.absolutePosition = function (el) {
-    var r = { x: el.offsetLeft, y: el.offsetTop };
-    // Resolve relative to offsetParent
-    if (el.offsetParent) {
-      var tmp = fb.absolutePosition(el.offsetParent);
-      r.x += tmp.x;
-      r.y += tmp.y;
-    }
-    return r;
-  };
-
-  /* Various color utility functions */
-  fb.pack = function (rgb) {
-    var r = Math.round(rgb[0] * 255);
-    var g = Math.round(rgb[1] * 255);
-    var b = Math.round(rgb[2] * 255);
-    return '#' + (r < 16 ? '0' : '') + r.toString(16) +
-           (g < 16 ? '0' : '') + g.toString(16) +
-           (b < 16 ? '0' : '') + b.toString(16);
-  }
-
-  fb.unpack = function (color) {
-    if (color.length == 7) {
-      return [parseInt('0x' + color.substring(1, 3)) / 255,
-        parseInt('0x' + color.substring(3, 5)) / 255,
-        parseInt('0x' + color.substring(5, 7)) / 255];
-    }
-    else if (color.length == 4) {
-      return [parseInt('0x' + color.substring(1, 2)) / 15,
-        parseInt('0x' + color.substring(2, 3)) / 15,
-        parseInt('0x' + color.substring(3, 4)) / 15];
-    }
-  }
-
-  fb.HSLToRGB = function (hsl) {
-    var m1, m2, r, g, b;
-    var h = hsl[0], s = hsl[1], l = hsl[2];
-    m2 = (l <= 0.5) ? l * (s + 1) : l + s - l*s;
-    m1 = l * 2 - m2;
-    return [this.hueToRGB(m1, m2, h+0.33333),
-        this.hueToRGB(m1, m2, h),
-        this.hueToRGB(m1, m2, h-0.33333)];
-  }
-
-  fb.hueToRGB = function (m1, m2, h) {
-    h = (h < 0) ? h + 1 : ((h > 1) ? h - 1 : h);
-    if (h * 6 < 1) return m1 + (m2 - m1) * h * 6;
-    if (h * 2 < 1) return m2;
-    if (h * 3 < 2) return m1 + (m2 - m1) * (0.66666 - h) * 6;
-    return m1;
-  }
-
-  fb.RGBToHSL = function (rgb) {
-    var min, max, delta, h, s, l;
-    var r = rgb[0], g = rgb[1], b = rgb[2];
-    min = Math.min(r, Math.min(g, b));
-    max = Math.max(r, Math.max(g, b));
-    delta = max - min;
-    l = (min + max) / 2;
-    s = 0;
-    if (l > 0 && l < 1) {
-      s = delta / (l < 0.5 ? (2 * l) : (2 - 2 * l));
-    }
-    h = 0;
-    if (delta > 0) {
-      if (max == r && max != g) h += (g - b) / delta;
-      if (max == g && max != b) h += (2 + (b - r) / delta);
-      if (max == b && max != r) h += (4 + (r - g) / delta);
-      h /= 6;
-    }
-    return [h, s, l];
-  }
-
-  // Install mousedown handler (the others are set on the document on-demand)
-  $('*', e).mousedown(fb.mousedown);
-
-    // Init color
-  fb.setColor('#000000');
-
-  // Set linked elements/callback
-  if (callback) {
-    fb.linkTo(callback);
-  }
-}

theme/tripal_theme_core/js/jgcharts/include/gui/lib/jquery.metadata.js

@@ -1,129 +0,0 @@
- 
-////////////////////////////////////////////////////////////////////////////////
-//*********** JQUERY METADATA **************************************************
-////////////////////////////////////////////////////////////////////////////////
-
-/*
- * Metadata - jQuery plugin for parsing metadata from elements
- *
- * Copyright (c) 2006 John Resig, Yehuda Katz, J�örn Zaefferer, Paul McLanahan
- *
- * Dual licensed under the MIT and GPL licenses:
- *   http://www.opensource.org/licenses/mit-license.php
- *   http://www.gnu.org/licenses/gpl.html
- *
- * Revision: $Id: jquery.metadata.js,v 1.1 2009/10/01 18:28:20 ccheng Exp $
- *
- */
-
-/**
- * Sets the type of metadata to use. Metadata is encoded in JSON, and each property
- * in the JSON will become a property of the element itself.
- *
- * There are three supported types of metadata storage:
- *
- *   attr:  Inside an attribute. The name parameter indicates *which* attribute.
- *          
- *   class: Inside the class attribute, wrapped in curly braces: { }
- *   
- *   elem:  Inside a child element (e.g. a script tag). The
- *          name parameter indicates *which* element.
- *          
- * The metadata for an element is loaded the first time the element is accessed via jQuery.
- *
- * As a result, you can define the metadata type, use $(expr) to load the metadata into the elements
- * matched by expr, then redefine the metadata type and run another $(expr) for other elements.
- * 
- * @name $.metadata.setType
- *
- * @example <p id="one" class="some_class {item_id: 1, item_label: 'Label'}">This is a p</p>
- * @before $.metadata.setType("class")
- * @after $("#one").metadata().item_id == 1; $("#one").metadata().item_label == "Label"
- * @desc Reads metadata from the class attribute
- * 
- * @example <p id="one" class="some_class" data="{item_id: 1, item_label: 'Label'}">This is a p</p>
- * @before $.metadata.setType("attr", "data")
- * @after $("#one").metadata().item_id == 1; $("#one").metadata().item_label == "Label"
- * @desc Reads metadata from a "data" attribute
- * 
- * @example <p id="one" class="some_class"><script>{item_id: 1, item_label: 'Label'}</script>This is a p</p>
- * @before $.metadata.setType("elem", "script")
- * @after $("#one").metadata().item_id == 1; $("#one").metadata().item_label == "Label"
- * @desc Reads metadata from a nested script element
- * 
- * @param String type The encoding type
- * @param String name The name of the attribute to be used to get metadata (optional)
- * @cat Plugins/Metadata
- * @descr Sets the type of encoding to be used when loading metadata for the first time
- * @type undefined
- * @see metadata()
- */
-
-(function($) {
-
-$.extend({
-	metadata : {
-		defaults : {
-			type: 'class',
-			name: 'metadata',
-			//cre: /({.*})/,
-			cre: /({[\s\S]*})/,
-			single: 'metadata'
-		},
-		setType: function( type, name ){
-			this.defaults.type = type;
-			this.defaults.name = name;
-		},
-		get: function( elem, opts ){
-			var settings = $.extend({},this.defaults,opts);
-			// check for empty string in single property
-			if ( !settings.single.length ) settings.single = 'metadata';
-			
-			var data = $.data(elem, settings.single);
-			// returned cached data if it already exists
-			if ( data ) return data;
-			
-			data = "{}";
-			
-			if ( settings.type == "class" ) {
-				var m = settings.cre.exec( elem.className );
-				if ( m )
-					data = m[1];
-			} else if ( settings.type == "elem" ) {
-				if( !elem.getElementsByTagName )
-					return undefined;
-				var e = elem.getElementsByTagName(settings.name);
-				if ( e.length )
-					data = $.trim(e[0].innerHTML);
-			} else if ( elem.getAttribute != undefined ) {
-				var attr = elem.getAttribute( settings.name );
-				if ( attr )
-					data = attr;
-			}
-			
-			if ( data.indexOf( '{' ) <0 )
-			data = "{" + data + "}";
-			
-			data = eval("(" + data + ")");
-			
-			$.data( elem, settings.single, data );
-			return data;
-		}
-	}
-});
-
-/**
- * Returns the metadata object for the first member of the jQuery object.
- *
- * @name metadata
- * @descr Returns element's metadata object
- * @param Object opts An object contianing settings to override the defaults
- * @type jQuery
- * @cat Plugins/Metadata
- */
-$.fn.metadata = function( opts ){
-	return $.metadata.get( this[0], opts );
-};
-
-})(jQuery);
-