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){ ?>
The following features are aligned
name;
if (property_exists($alignment, 'nid')) {
$feature_name = l($feature_name, "node/" . $alignment->nid);
}
$feature_loc = '';
$strand = '.';
if ($alignment->strand == -1) {
$strand = '-';
}
elseif ($alignment->strand == 1) {
$strand = '+';
}
// if this is a match then make the other location
if(property_exists($alignment, 'right_feature')){
$rstrand = '.';
if ($alignment->right_strand == -1) {
$rstrand = '-';
}
elseif ($alignment->right_strand == 1) {
$rstrand = '+';
}
$feature_loc = $feature->name .":". ($alignment->fmin + 1) . ".." . $alignment->fmax . " " . $strand;
$feature_loc .= "
" . $alignment->name .":". ($alignment->right_fmin + 1) . ".." . $alignment->right_fmax . " " . $rstrand;
}
else {
$feature_loc = $alignment->name .":". ($alignment->fmin + 1) . ".." . $alignment->fmax . " " . $strand;
}
$rows[] = array(
$feature_name,
$alignment->type,
$feature_loc
);
}
// the $table array contains the headers and rows array as well as other
// options for controlling the display of the table. Additional
// documentation can be found here:
// https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
$table = array(
'header' => $headers,
'rows' => $rows,
'attributes' => array(
'id' => 'tripal_feature-table-alignments',
'class' => 'tripal-data-table'
),
'sticky' => FALSE,
'caption' => '',
'colgroups' => array(),
'empty' => '',
);
// once we have our table array structure defined, we call Drupal's theme_table()
// function to generate the table.
print theme_table($table);
}