'blast_report',
'path' => "$path/theme",
);
$items['blast_report_alignment_row'] = array(
'template' => 'blast_report_alignment_row',
'variables' => array('hsps' => NULL),
'path' => "$path/theme",
);
return $items;
}
/**
*
* Implements hook_menu()
*
*/
function blast_ui_menu() {
$items['blast'] = array(
'title' => 'BLAST',
'page callback' => 'drupal_get_form',
'page arguments' => array('blast_nucleotide_form'),
'access arguments' => array('access content'),
'type' => MENU_NORMAL_ITEM,
'expanded' => TRUE,
);
$items['blast/report/%'] = array(
'title' => 'BLAST result:',
'page callback' => 'show_blast_output',
'page arguments' => array(2),
'access arguments' => array('access content'),
'type' => MENU_CALLBACK,
);
$items['blast/blastn'] = array(
'title' => 'Nucleotide BLAST',
'page callback' => 'drupal_get_form',
'page arguments' => array('blast_nucleotide_form'),
'access arguments' => array('access content'),
'type' => MENU_NORMAL_ITEM
);
$items['blast/blastp'] = array(
'title' => 'Protein BLAST',
'page callback' => 'drupal_get_form',
'page arguments' => array('blast_protein_form'),
'access arguments' => array('access content'),
'type' => MENU_NORMAL_ITEM
);
return $items;
}
/**
* Facilitate presenting the result of the blast search
*
* @param $args
* A string containing name of the blast output file.
*
* @return $result
* Return a string containing the blast search output. A link is also provided to let users download the output file.
*
*/
function show_blast_output($args = 'all') {
if (preg_match('/^[^\/]*/',$args)) {
// Since the blast results are in the files directory we can use public:// to get around hard-coding the full path
$full_path_filename = 'public://'.$args;
if (file_exists($full_path_filename)) {
// $result = t('
BLAST Results: HTML
', array('@url' => url('sites/default/files/' . $args)));
// $result .= check_markup(file_get_contents($full_path_filename), 'full_html');
// $result = str_replace('','',$result);
$result = theme('show_blast_report');
}
else {
tripal_report_error(
'blast_ui',
TRIPAL_ERROR,
'Unable to open blast results file (%file)',
array('%file' => $full_path_filename)
);
$result = 'An error was encountered while trying to process your blast results
';
}
}
else {
$result = 'An error was encountered while trying to process your blast results
';
}
return $result;
}