Adding back in the theme templates for organism and feature nodes

theme_tripal/node-chado_feature.tpl.php

@@ -0,0 +1,156 @@
+<?php
+// Purpose: This template provides the layout of the feature 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>';
+$feature  = $variables['node']->feature;
+?>
+<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_feature_toc_list').append('<li><a href="#'+id+'" class="tripal_feature_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_feature_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
+         $("#tripal_feature_toc").height($(href).parent().height());
+         return false;
+      }); 
+
+      // we want the base details to show up when the page is first shown
+      $("#tripal_feature-base-box").show();
+      $("#tripal_organism_toc").height($("#tripal_feature-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_feature_toc {
+     float: left;
+     width: 350px;
+     background-color: #EEEEEE;
+     -moz-border-radius: 15px;
+     border-radius: 15px;
+     -moz-box-shadow: 3px 3px 4px #000;
+	  -webkit-box-shadow: 3px 3px 4px #000;
+	  box-shadow: 3px 3px 4px #000;
+     padding: 20px;
+     min-height: 500px;
+     border-style:solid;
+     border-width:1px;
+  }
+  #tripal_feature_toc ul {
+    margin-left: 0px;
+    margin-top: 5px;
+    padding-left: 15px;
+  }
+  #tripal_feature_toc_title {
+     font-size: 1.5em;
+  }
+  #tripal_feature_toc_desc {
+    font-style: italic;
+  }
+  #tripal_feature_details {
+     float: left;
+     width: 650px;
+     background-color: #FFFFFF;
+     -moz-border-radius: 15px;
+     border-radius: 15px;
+     -moz-box-shadow: 3px 3px 4px #000;
+	  -webkit-box-shadow: 3px 3px 4px #000;
+	  box-shadow: 3px 3px 4px #000;
+     padding: 20px;
+     min-height: 500px;
+     margin-right: 10px;
+     border-style:solid;
+     border-width:1px;
+  }
+</style>
+
+
+<div id="tripal_feature_details">
+
+   <!-- Basic Details Theme -->
+   <?php include('tripal_feature/tripal_feature_base.tpl.php'); ?>
+
+   <!-- Database References -->
+   <?php include('tripal_feature/tripal_feature_references.tpl.php'); ?>
+
+   <!-- Properties -->
+   <?php include('tripal_feature/tripal_feature_properties.tpl.php'); ?>
+
+   <!-- Synonyms -->
+   <?php include('tripal_feature/tripal_feature_synonyms.tpl.php'); ?>
+
+   <!-- Sequence -->
+   <?php include('tripal_feature/tripal_feature_sequence.tpl.php'); ?>
+
+   <!-- Formatted Sequences -->
+   <?php include('tripal_feature/tripal_feature_featureloc_sequences.tpl.php'); ?>
+
+   <!-- Object Relationships -->
+   <?php include('tripal_feature/tripal_feature_relationships_as_object.tpl.php'); ?>
+
+   <!-- Subject Relationships -->
+   <?php include('tripal_feature/tripal_feature_relationships_as_subject.tpl.php'); ?>
+
+   <!-- Feature locations as Child -->
+   <?php include('tripal_feature/tripal_feature_featurelocs_as_child.tpl.php'); ?>
+
+   <!-- Subject Relationships -->
+   <?php include('tripal_feature/tripal_feature_featurelocs_as_parent.tpl.php'); ?>
+
+   <!-- Blast Results -->
+   <?php include('tripal_analysis_blast/tripal_analysis_blast_results.tpl.php'); ?>
+
+   <!-- InterProScan Results -->
+   <?php include('tripal_analysis_interpro/tripal_analysis_interpro_results.tpl.php'); ?>
+</div>
+
+<!-- Table of contents -->
+<div id="tripal_feature_toc">
+   <div id="tripal_feature_toc_title"><?php print $feature->featurename ?> Resources</div>
+   <span id="tripal_feature_toc_desc">Select a link below for more information</span>
+   <ul id="tripal_feature_toc_list">
+
+   </ul>
+</div>

theme_tripal/node-chado_organism.tpl.php

@@ -0,0 +1,134 @@
+<?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>';
+$organism = $variables['node']->organism;
+?>
+<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_organism_toc_list').append('<li><a href="#'+id+'" class="tripal_organism_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_organism_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
+         $("#tripal_organism_toc").height($(href).parent().height());
+         return false;
+      }); 
+
+      // we want the base details to show up when the page is first shown
+      $("#tripal_organism-base-box").show();
+      $("#tripal_organism_toc").height($("#tripal_organism-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_organism_toc {
+     float: left;
+     width: 350px;
+     background-color: #EEEEEE;
+     -moz-border-radius: 15px;
+     border-radius: 15px;
+     -moz-box-shadow: 3px 3px 4px #000;
+	  -webkit-box-shadow: 3px 3px 4px #000;
+	  box-shadow: 3px 3px 4px #000;
+     padding: 20px;
+     min-height: 500px;
+     border-style:solid;
+     border-width:1px;
+  }
+  #tripal_organism_toc ul {
+    margin-left: 0px;
+    margin-top: 5px;
+    padding-left: 15px;
+  }
+  #tripal_organism_toc_title {
+     font-size: 1.5em;
+  }
+  #tripal_organism_toc_desc {
+    font-style: italic;
+  }
+  #tripal_organism_details {
+     float: left;
+     width: 650px;
+     background-color: #FFFFFF;
+     -moz-border-radius: 15px;
+     border-radius: 15px;
+     -moz-box-shadow: 3px 3px 4px #000;
+	  -webkit-box-shadow: 3px 3px 4px #000;
+	  box-shadow: 3px 3px 4px #000;
+     padding: 20px;
+     min-height: 500px;
+     margin-right: 10px;
+     border-style:solid;
+     border-width:1px;
+  }
+  #tripal_organism-base-box img {
+    float: left;
+    margin-bottom: 10px;
+  }
+  #tripal_organism-table-base {
+    float: left;
+    width: 400px;
+    margin-left: 10px;
+    margin-bottom: 10px;
+  }
+</style>
+
+
+<div id="tripal_organism_details">
+
+   <!-- Basic Details Theme -->
+   <?php include('tripal_organism/tripal_organism_base.tpl.php'); ?>
+
+</div>
+
+<!-- Table of contents -->
+<div id="tripal_organism_toc">
+   <div id="tripal_organism_toc_title"><?php print $organism->genus ?> <?php print $organism->species ?> Resources</div>
+   <span id="tripal_organism_toc_desc">Select a link below for more information</span>
+   <ul id="tripal_organism_toc_list">
+
+   </ul>
+</div>