Changed theming of Analysis modules so that they are not part of the core Tripal release. They will be released as extensions and users will need to copy the themes for these modules

theme_tripal/css/tripal_analysis_blast.css

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

theme_tripal/css/tripal_analysis_interpro.css

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

theme_tripal/js/tripal_analysis_blast.js

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

theme_tripal/js/tripal_analysis_interpro.js

@@ -1,33 +0,0 @@
-//
-// Copyright 2009 Clemson University
-//
-
-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/node-chado_analysis_blast.tpl.php

@@ -1,98 +0,0 @@
-<?php
-// Purpose: This template provides the layout of the organism node (page)
-//   using the same templates used for the various feature content blocks.
-//
-// To Customize the Featture Node Page:
-//   - This Template: customize basic layout and which elements are included
-//   - Using Panels: Override the node page using Panels3 and place the blocks
-//       of content as you please. This method requires no programming. See
-//       the Tripal User Guide for more details
-//   - Block Templates: customize the content/layout of each block of stock 
-//       content. These templates are found in the tripal_stock subdirectory
-//
-// Variables Available:
-//   - $node: a standard object which contains all the fields associated with
-//       nodes including nid, type, title, taxonomy. It also includes stock
-//       specific fields such as stock_name, uniquename, stock_type, synonyms,
-//       properties, db_references, object_relationships, subject_relationships,
-//       organism, etc.
-//   NOTE: For a full listing of fields available in the node object the
-//       print_r $node line below or install the Drupal Devel module which 
-//       provides an extra tab at the top of the node page labelled Devel
-?>
-
-<?php
- //uncomment this line to see a full listing of the fields avail. to $node
- //print '<pre>'.print_r($variables,TRUE).'</pre>';
-drupal_add_css('./tripal-node-templates.css');
-
-$node = $variables['node'];
-$organism = $variables['node']->organism;
-?>
-
-<?php if ($teaser) { 
-  include('tripal_analysis_blast/tripal_analysis_blast_teaser.tpl.php'); 
-} else { ?>
-
-<script type="text/javascript">
-if (Drupal.jsEnabled) {
-   $(document).ready(function() {
-      // hide all tripal info boxes at the start
-      $(".tripal-info-box").hide();
- 
-      // iterate through all of the info boxes and add their titles
-      // to the table of contents
-      $(".tripal-info-box-title").each(function(){
-        var parent = $(this).parent();
-        var id = $(parent).attr('id');
-        var title = $(this).text();
-        $('#tripal_analysis_blast_toc_list').append('<li><a href="#'+id+'" class="tripal_analysis_blast_toc_item">'+title+'</a></li>');
-      });
-
-      // when a title in the table of contents is clicked, then
-      // show the corresponding item in the details box
-      $(".tripal_analysis_blast_toc_item").click(function(){
-         $(".tripal-info-box").hide();
-         href = $(this).attr('href');
-         $(href).fadeIn('slow');
-         // we want to make sure our table of contents and the details
-         // box stay the same height
-         $("#tripal_analysis_blast_toc").height($(href).parent().height());
-         return false;
-      }); 
-
-      // we want the base details to show up when the page is first shown 
-      // unless the user specified a specific block
-      var block = window.location.href.match(/\?block=.*/);
-      if(block != null){
-         block_title = block.toString().replace(/\?block=/g,'');
-         $("#tripal_analysis_blast-"+block_title+"-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/node-chado_analysis_interpro.tpl.php

@@ -1,98 +0,0 @@
-<?php
-// Purpose: This template provides the layout of the organism node (page)
-//   using the same templates used for the various feature content blocks.
-//
-// To Customize the Featture Node Page:
-//   - This Template: customize basic layout and which elements are included
-//   - Using Panels: Override the node page using Panels3 and place the blocks
-//       of content as you please. This method requires no programming. See
-//       the Tripal User Guide for more details
-//   - Block Templates: customize the content/layout of each block of stock 
-//       content. These templates are found in the tripal_stock subdirectory
-//
-// Variables Available:
-//   - $node: a standard object which contains all the fields associated with
-//       nodes including nid, type, title, taxonomy. It also includes stock
-//       specific fields such as stock_name, uniquename, stock_type, synonyms,
-//       properties, db_references, object_relationships, subject_relationships,
-//       organism, etc.
-//   NOTE: For a full listing of fields available in the node object the
-//       print_r $node line below or install the Drupal Devel module which 
-//       provides an extra tab at the top of the node page labelled Devel
-?>
-
-<?php
- //uncomment this line to see a full listing of the fields avail. to $node
- //print '<pre>'.print_r($variables,TRUE).'</pre>';
-drupal_add_css('./tripal-node-templates.css');
-
-$node = $variables['node'];
-$organism = $variables['node']->organism;
-?>
-
-<?php if ($teaser) { 
-  include('tripal_analysis_interpro/tripal_analysis_interpro_teaser.tpl.php'); 
-} else { ?>
-
-<script type="text/javascript">
-if (Drupal.jsEnabled) {
-   $(document).ready(function() {
-      // hide all tripal info boxes at the start
-      $(".tripal-info-box").hide();
- 
-      // iterate through all of the info boxes and add their titles
-      // to the table of contents
-      $(".tripal-info-box-title").each(function(){
-        var parent = $(this).parent();
-        var id = $(parent).attr('id');
-        var title = $(this).text();
-        $('#tripal_analysis_interpro_toc_list').append('<li><a href="#'+id+'" class="tripal_analysis_interpro_toc_item">'+title+'</a></li>');
-      });
-
-      // when a title in the table of contents is clicked, then
-      // show the corresponding item in the details box
-      $(".tripal_analysis_interpro_toc_item").click(function(){
-         $(".tripal-info-box").hide();
-         href = $(this).attr('href');
-         $(href).fadeIn('slow');
-         // we want to make sure our table of contents and the details
-         // box stay the same height
-         $("#tripal_analysis_interpro_toc").height($(href).parent().height());
-         return false;
-      }); 
-
-      // we want the base details to show up when the page is first shown 
-      // unless the user specified a specific block
-      var block = window.location.href.match(/\?block=.*/);
-      if(block != null){
-         block_title = block.toString().replace(/\?block=/g,'');
-         $("#tripal_analysis_interpro-"+block_title+"-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/node-chado_analysis_unigene.tpl.php

@@ -1,101 +0,0 @@
-<?php
-// Purpose: This template provides the layout of the organism node (page)
-//   using the same templates used for the various feature content blocks.
-//
-// To Customize the Featture Node Page:
-//   - This Template: customize basic layout and which elements are included
-//   - Using Panels: Override the node page using Panels3 and place the blocks
-//       of content as you please. This method requires no programming. See
-//       the Tripal User Guide for more details
-//   - Block Templates: customize the content/layout of each block of stock 
-//       content. These templates are found in the tripal_stock subdirectory
-//
-// Variables Available:
-//   - $node: a standard object which contains all the fields associated with
-//       nodes including nid, type, title, taxonomy. It also includes stock
-//       specific fields such as stock_name, uniquename, stock_type, synonyms,
-//       properties, db_references, object_relationships, subject_relationships,
-//       organism, etc.
-//   NOTE: For a full listing of fields available in the node object the
-//       print_r $node line below or install the Drupal Devel module which 
-//       provides an extra tab at the top of the node page labelled Devel
-?>
-
-<?php
- //uncomment this line to see a full listing of the fields avail. to $node
-// print '<pre>'.print_r($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_title = block.toString().replace(/\?block=/g,'');
-         $("#tripal_analysis_unigene-"+block_title+"-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/tripal_analysis_blast/tripal_analysis_blast_base.tpl.php

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

theme_tripal/tripal_analysis_blast/tripal_analysis_blast_report.tpl.php

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

theme_tripal/tripal_analysis_interpro/tripal_analysis_interpro_base.tpl.php

@@ -1,58 +0,0 @@
-<?php
-$node = $variables['node'];
-$analysis = $variables['node']->analysis;
-
-// the description is a text field so we want to expand that
-$analysis = tripal_core_expand_chado_vars($analysis,'field','analysis.description');
-
-$interpro = $node->analysis->tripal_analysis_interpro;
-
-?>
-<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/tripal_analysis_kegg/tripal_analysis_kegg_base.tpl.php

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

theme_tripal/tripal_analysis_kegg/tripal_analysis_kegg_report.tpl.php

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

theme_tripal/tripal_analysis_unigene/tripal_analysis_unigene_base.tpl.php

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

theme_tripal/tripal_feature/tripal_feature_blast_results.tpl.php

@@ -1,111 +0,0 @@
-<?php
-$feature  = $variables['node']->feature;
-$blast_results_list = $feature->tripal_analysis_blast->blast_results_list;
-
-?>
-<div id="tripal_ajaxLoading" style="display:none">
-	<div id="loadingText">Loading...</div>
-	<img src="sites/all/themes/theme_tripal/images/ajax-loader.gif">
-</div>
-
-<?php 
-if(count($blast_results_list) > 0){
-   foreach ($blast_results_list as $blast_result) {
-	  $hits_array = $blast_result->hits_array;
-	  $db = $blast_result->db;
-     $analysis = $blast_result->analysis;
-?>
-<div id="blast_db_<?php print $db->db_id ?>">
-<div id="tripal_analysis_blast-results-<?php print "$db->db_id" ?>-box" class="tripal_analysis_blast-box tripal-info-box">
-	<div class="tripal-info-box-title tripal_analysis_blast-info-box-title"><?php 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/tripal_feature/tripal_feature_interpro_results.tpl.php

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