to fix themes/subtheme issue: Revert ""branching out" to tripal module only repo"

This reverts commit c88fde163bb7be18cc80a06d03b9c23e7e415535.

theme/tripal_subthemes/tripal_analysis_blast_theme/css/tripal_analysis_blast.css

@@ -0,0 +1,33 @@
+#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

@@ -0,0 +1,183 @@
+
+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

@@ -0,0 +1,100 @@
+<?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

@@ -0,0 +1,78 @@
+<?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

@@ -0,0 +1,123 @@
+<?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

@@ -0,0 +1,53 @@
+<?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

@@ -0,0 +1,10 @@
+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

@@ -0,0 +1,111 @@
+<?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

@@ -0,0 +1,17 @@
+
+.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

@@ -0,0 +1,52 @@
+
+
+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

@@ -0,0 +1,10 @@
+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

@@ -0,0 +1,35 @@
+<?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

@@ -0,0 +1,35 @@
+<?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

@@ -0,0 +1,44 @@
+
+.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

@@ -0,0 +1,29 @@
+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

@@ -0,0 +1,100 @@
+<?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

@@ -0,0 +1,56 @@
+<?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

@@ -0,0 +1,53 @@
+<?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

@@ -0,0 +1,10 @@
+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

@@ -0,0 +1,121 @@
+<?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

@@ -0,0 +1,46 @@
+/*
+ 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

@@ -0,0 +1,162 @@
+
+
+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

@@ -0,0 +1,101 @@
+<?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

@@ -0,0 +1,53 @@
+<?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

@@ -0,0 +1,11 @@
+<?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

@@ -0,0 +1,53 @@
+<?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

@@ -0,0 +1,10 @@
+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

@@ -0,0 +1,46 @@
+<?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

@@ -0,0 +1,22 @@
+<?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

@@ -0,0 +1,16 @@
+/*
+ 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

@@ -0,0 +1,103 @@
+<?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

@@ -0,0 +1,86 @@
+<?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

@@ -0,0 +1,53 @@
+<?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

@@ -0,0 +1,10 @@
+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

@@ -0,0 +1,61 @@
+<?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

@@ -0,0 +1,52 @@
+<?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

@@ -0,0 +1,60 @@
+
+<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

@@ -0,0 +1,83 @@
+
+<?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

@@ -0,0 +1,83 @@
+
+<?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

@@ -0,0 +1,73 @@
+
+<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

@@ -0,0 +1,69 @@
+<?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

@@ -0,0 +1,7 @@
+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

@@ -0,0 +1,177 @@
+<?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

@@ -0,0 +1,48 @@
+<?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

@@ -0,0 +1,45 @@
+<?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

@@ -0,0 +1,28 @@
+<?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

@@ -0,0 +1,42 @@
+<?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

@@ -0,0 +1,34 @@
+<?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

@@ -0,0 +1,7 @@
+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

@@ -0,0 +1,22 @@
+
+<?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

@@ -0,0 +1,7 @@
+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

@@ -0,0 +1,73 @@
+
+<?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

@@ -0,0 +1,7 @@
+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

@@ -0,0 +1,80 @@
+
+<?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

@@ -0,0 +1,13 @@
+<?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

@@ -0,0 +1,7 @@
+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

@@ -0,0 +1,40 @@
+.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

@@ -0,0 +1,20 @@
+//
+// 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

@@ -0,0 +1,10 @@
+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

@@ -0,0 +1,195 @@
+<?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

@@ -0,0 +1,221 @@
+<?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

@@ -0,0 +1,165 @@
+.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

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

theme/tripal_theme_core/css/tripal_cv.css

@@ -0,0 +1,35 @@
+/*
+ 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

@@ -0,0 +1,76 @@
+#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

@@ -0,0 +1,31 @@
+
+#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

@@ -0,0 +1,17 @@
+<?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

@@ -0,0 +1,3 @@
+#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

@@ -0,0 +1,413 @@
+<!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

@@ -0,0 +1,495 @@
+<!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

@@ -0,0 +1,591 @@
+<!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>
+        <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>
+
+</body>
+</html>    

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

@@ -0,0 +1,30 @@
+{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,
+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}

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

@@ -0,0 +1 @@
+#yslider-code div.yslider-viewer {overflow-y:auto;}

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

@@ -0,0 +1,20 @@
+html, body{
+    margin:0px;
+    font-family:'Lucida Grande',Verdana,Arial,Sans-Serif;
+    font-size:1.1em;
+    font-size-adjust:none;
+    font-style:normal;
+    font-variant:normal;
+    font-weight:normal;
+    line-height:1.5em;
+    font-size:12px;
+    background:#000;
+}
+#top *{padding:0px;margin:0px;text-align:left;}
+#top{width:100%;min-height:29px;background-color:#efebe7;border-bottom:1px solid white;position:relative;padding-top:1px;}
+#logo{margin-left:20px;margin-top:5px;font-weight:bold;}
+#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;}
+.seldesktop a{display:block;height:100%;width:100%;}
+a{text-decoration:none;}

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

@@ -0,0 +1,28 @@
+html, body{
+    margin:0px;
+    font-family:'Lucida Grande',Verdana,Arial,Sans-Serif;
+    font-size:1.1em;
+    font-size-adjust:none;
+    font-style:normal;
+    font-variant:normal;
+    font-weight:normal;
+    line-height:1.5em;
+    font-size:12px;
+    background:#000;
+    width:100%;
+}
+a{text-decoration:none;}
+img{border:0px;}
+h3{}
+
+.start_hide{display:none;}
+
+
+.icone_dx{display:block;margin:auto;}
+.text_icone_dx{color:white;margin-bottom:10px;display:block;}
+#icone_destra{position:absolute;right:30px;top:30px;text-align:center;width:60px;}
+      
+.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

@@ -0,0 +1,8 @@
+/*
+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

@@ -0,0 +1,2004 @@
+<!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>
+    <script src="../../include/js/lib/ycodaslider-2.0.rc2/lib/jquery.history_remote.fixed.pack.js" type="text/javascript"></script>
+    <script src="../../include/js/lib/ycodaslider-2.0.rc2/lib/chili/jquery.chili-2.2.js" type="text/javascript"></script>
+    <script src="../../include/js/lib/ycodaslider-2.0.rc2/ycodaslider-2.0.pack.js" type="text/javascript"></script>
+    <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>
+    <a href="#" class="handle h-docs text_icone_sx tracking {label : '/jgcharts/docs'}">Docs</a>
+    <!-- code -->
+    <a href="#" class="handle h-code tracking {label : '/jgcharts/code'}"><img class="icone_sx" alt="docs" src="../../include/icons/code.png" /></a>
+    <a href="#" class="handle h-code text_icone_sx tracking {label : '/jgcharts/code'}">Code</a>
+    <!-- download -->
+    <a href="../../jgcharts-0.96.zip" class="tracking {label : '/jgcharts/download'}"><img class="icone_sx" alt="Download" src="../../include/icons/download.png" /></a>
+    <a href="../../jgcharts-0.96.zip" class="text_icone_sx tracking {label : '/jgcharts/download'}">Download</a>
+</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

@@ -0,0 +1,588 @@
+<!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

@@ -0,0 +1,43 @@
+#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

@@ -0,0 +1,329 @@
+// $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

@@ -0,0 +1,129 @@
+ 
+////////////////////////////////////////////////////////////////////////////////
+//*********** 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);
+