theme_tripal/tripal_feature/tripal_feature_go_terms.tpl.php

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

theme_tripal/tripal_feature/tripal_feature_kegg_terms.tpl.php

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

theme_tripal/tripal_feature/tripal_feature_unigenes.tpl.php

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

theme_tripal/tripal_organism/tripal_organism_go_summary.tpl.php

@@ -1,25 +0,0 @@
-<?php
-  $form = $variables['tripal_analysis_go']['select_form']['form'];
-  $has_results = $variables['tripal_analysis_go']['select_form']['has_results'];
-?>
-<div id="tripal_organism-go_summary-box" class="tripal_organism-info-box tripal-info-box">
-  <div  class="tripal_organism-info-box-title tripal-info-box-title">GO Analysis Reports</div>
-  <?php 
-     if($has_results){
-        print $form;
-     } else {
-       ?><div class="tripal-no-results">There are no GO reports avaialble</div><?php
-     }
-  ?>
-  <div id="tripal_analysis_go_org_charts"></div>    
-  <div id="tripal_cv_cvterm_info_box">
-      <a href="#" onclick="$('#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/tripal_organism/tripal_organism_kegg_summary.tpl.php

@@ -1,20 +0,0 @@
-<?php
-  $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/tripal_organism/tripal_organism_unigenes.tpl.php

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