tripal_feature_alignments.tpl.php

<?php
/*
* Typically in a Tripal template, the data needed is retrieved using a call to
* chado_expand_var function.  For example, to retrieve all
* of the feature alignments for this node, the following function call would be made:
*
*   $feature = chado_expand_var($feature,'table','featureloc');
*
* However, this will return all records from the featureloc table without any context.
* To help provide context, a special variable is provided to this template named
* 'all_featurelocs'.
*
*   $feature->all_featurelocs
*
* The records in the 'all_featurelocs' array are all properly arranged for easy iteration.
*
* However, access to the original alignment records is possible through the
* $feature->featureloc object.  In the following ways:
*
* Alignment context #1:
* --------------------
* If the feature for this node is the parent in the alignment relationships,
* then those alignments are available in this variable:
*
*    $feature->featureloc->srcfeature_id;
*
*
* Alignment context #2:
* ---------------------
* If the feature for this node is the child in the alignment relationsips,
* then those alignments are available in this variable:
*
*   $feature->featureloc->feature_id;
*
*
* Alignment context #3:
* --------------------
* If the feature is aligned to another through an intermediary feature (e.g.
* a feature of type 'match', 'EST_match', 'primer_match', etc) then those
* alignments are stored in this variable:
*   feature->matched_featurelocs
*
* Below is an example of a feature that may be aligned to another through
* an intermediary:
*
*    Feature 1: Contig      ---------------   (left feature)
*    Feature 2: EST_match           -------
*    Feature 3: EST                 --------- (right feature)
*
* The feature for this node is always "Feature 1".  The purpose of this type
* alignment is to indicate cases where there is the potential for overhang
* in the alignments, or, the ends of the features are not part of the alignment
* prehaps due to poor quality of the ends.  Blast results and ESTs mapped to
* contigs in Unigenes would fall under this category.
*
*/
$feature = $variables['node']->feature;
$alignments = $feature->all_featurelocs;

if(count($alignments) > 0){ ?>
  <div class="tripal_feature-data-block-desc tripal-data-block-desc">The following features are aligned</div><?php

  // the $headers array is an array of fields to use as the colum headers.
  // additional documentation can be found here
  // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
  $headers = array('Aligned Feature' ,'Feature Type', 'Alignment Location');

  // the $rows array contains an array of rows where each row is an array
  // of values for each column of the table in that row.  Additional documentation
  // can be found here: