organism;
// get the list of available sequence ontology terms for which
// we will build drupal pages from features in chado. If a feature
// is not one of the specified typse we won't build a node for it.
$allowed_types = variable_get('chado_browser_feature_types', 'gene mRNA');
$allowed_types = preg_replace("/[\s\n\r]+/", " ", $allowed_types);
$so_terms = explode(' ', $allowed_types);
// get the feature_id's of the feature that belong to this organism. But we only
// want 25 and we want a pager to let the user cycle between pages of features.
// so we, use the tripal_core_chado_select API function to get the results and
// generate the pager. The function is smart enough to know which page the user is
// on and retrieves the proper set of features
$element = 0; // an index to specify the pager if more than one is on the page
$num_per_page = 25; // the number of features to show per page
$values = array(
'organism_id' => $organism->organism_id,
'type_id' => array(
'name' => $so_terms
),
);
$columns = array('feature_id');
$options = array(
'pager' => array(
'limit' => $num_per_page,
'element' => $element
),
'order_by' => array('name' => 'ASC'),
);
$results = tripal_core_chado_select('feature', $columns, $values, $options);
// now that we have all of the feature IDs, we want to expand each one so that we
// have all of the neccessary values, including the node ID, if one exists, and the
// cvterm type name.
$features = array();
foreach ($results as $result) {
$values = array('feature_id' => $result->feature_id);
$options = array(
'include_fk' => array(
'type_id' => 1
)
);
$features[] = tripal_core_generate_chado_var('feature', $values, $options);
}
if (count($features) > 0) { ?>
The following browser provides a quick view for new visitors. Use the searching mechanism to find specific features.
array('target' => '_blank'))),
TRIPAL_INFO,
array('return_html' => 1)
);
foreach ($features as $feature){
$fname = $feature->name;
if (property_exists($feature, 'nid')) {
$fname = l($fname, "node/$feature->nid", array('attributes' => array('target' => '_blank')));
}
$rows[] = array(
$fname,
$feature->uniquename,
$feature->type_id->name
);
}
// 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' => $rows,
'attributes' => array(
'id' => 'tripal_organism-table-features',
'class' => 'tripal-data-table'
),
'sticky' => FALSE,
'caption' => '',
'colgroups' => array(),
'empty' => '',
);
// once we have our table array structure defined, we call Drupal's theme_table()
// function to generate the table.
print theme_table($table);
// the $pager array values that control the behavior of the pager. For
// documentation on the values allows in this array see:
// https://api.drupal.org/api/drupal/includes!pager.inc/function/theme_pager/7
// here we add the paramter 'block' => 'feature_browser'. This is because
// the pager is not on the default block that appears. When the user clicks a
// page number we want the browser to re-appear with the page is loaded.
$pager = array(
'tags' => array(),
'element' => $element,
'parameters' => array(
'block' => 'feature_browser'
),
'quantity' => $num_per_page,
);
print theme_pager($pager);
}
else { ?>
There are no results.
Load features for this organism using the " .
l("FASTA loader", 'admin/tripal/loaders/fasta_loader') . ", ".
l("GFF Loader", 'admin/tripal/loaders/gff3_load') . " or ".
l("Bulk Loader", 'admin/tripal/loaders/bulk'). "
Sync the features that should have pages using the ".
l("Sync features page", 'admin/tripal/chado/tripal_feature/sync'). "
Return to this page to browse features.
Ensure the user " .
l("has permission", 'admin/people/permissions') . " to view the feature content
You can specify the feature types
that should appear in this browser or remove it from the list of resources by navigating to the " .
l("Tripal feature settings page", "admin/tripal/chado/tripal_feature/configuration", array('attributes' => array('target' => '_blank'))) . "
The feature browser will not appear to site visitors unless features are present. ",
TRIPAL_INFO,
array('return_html' => 1));
}