Unigene and other theming work

theme_tripal/node-chado_analysis_interpro.tpl.php

@@ -1,7 +1,5 @@
 <?php
-//
-// Copyright 2009 Clemson University
-//
+
 ?>
 
    <?php if ($picture) {

theme_tripal/node-chado_organism.tpl.php

@@ -24,6 +24,7 @@
 <?php
  //uncomment this line to see a full listing of the fields avail. to $node
  //print '<pre>'.print_r($variables,TRUE).'</pre>';
+
 $node = $variables['node'];
 $organism = $variables['node']->organism;
 ?>

theme_tripal/tripal_analysis_unigene/tripal_analysis_unigene_base.tpl.php

@@ -0,0 +1,76 @@
+<?php
+$node = $variables['node'];
+$analysis = $variables['node']->analysis;
+$unigene = $node->analysis->tripal_analysis_unigene;
+
+?>
+<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-odd-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 nowrap>Unigene Name</th>
+        <td><?php print $unigene->unigene_name; ?></td>
+      </tr>
+      <tr class="tripal_analysis_unigene-table-odd-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-odd-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 $analysis->description; ?></td>
+      </tr> 
+      <tr class="tripal_analysis_unigene-table-even-row tripal-table-odd-row">
+        <th nowrap>Stats</th>
+        <td>
+             <?php if($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: $unigene->num_singlets<br>";} ?>
+        </td>
+      </tr>  
+      <tr class="tripal_analysis_unigene-table-odd-row tripal-table-odd-row">
+        <th>Organisms</th>
+        <td><?php foreach($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>";
+               }
+            }
+            ?>
+        </td>
+      </tr>       	                                
+   </table>   
+</div>

theme_tripal/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>