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@@ -0,0 +1,582 @@
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+<?php
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+
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+//
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+// Copyright 2009 Clemson University
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+//
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+
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+function tripal_analysis_go_init(){
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+ // Add style sheet
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+ drupal_add_css(drupal_get_path('theme', 'tripal').
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+ '/css/tripal_analysis_go.css');
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+
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+ drupal_add_js(drupal_get_path('theme', 'tripal').
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+ '/js/tripal_analysis_go.js');
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+}
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+
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+/*******************************************************************************
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+ * Menu items are automatically added for the new node types created
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+ * by this module to the 'Create Content' Navigation menu item. This function
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+ * adds more menu items needed for this module.
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+ */
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+function tripal_analysis_go_menu() {
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+ $items = array();
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+
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+ $items['node/%/goterms'] = array(
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+ 'title' => t('GO Analysis'),
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+ 'page callback' => 'tripal_analysis_go_organism_goterms',
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+ 'page arguments' => array(1),
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+ 'access callback' => 'tripal_analysis_go_node_has_menu',
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+ 'access arguments' => array('access chado_analysis_go content',1),
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+ 'type' => MENU_LOCAL_TASK | MENU_NORMAL_ITEM
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+ );
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+ $items['download_goterm_features'] = array(
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+ 'path' => 'download_goterm_features',
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+ 'title' => t('Get GO Term Features'),
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+ 'page callback' => 'tripal_analysis_go_get_goterm_features',
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+ 'page arguments' => array(1,2),
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+ 'access arguments' => array('access chado_analysis_go content'),
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+ 'type' => MENU_CALLBACK
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+ );
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+ $items['tripal_analysis_go_org_charts'] = array(
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+ 'path' => 'tripal_analysis_go_org_charts',
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+ 'title' => t('Analysis GO Charts'),
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+ 'page callback' => 'tripal_analysis_go_org_charts',
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+ 'page arguments' => array(1),
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+ 'access arguments' => array('access chado_analysis_go content'),
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+ 'type' => MENU_CALLBACK
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+ );
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+
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+
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+ return $items;
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+}
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+/*******************************************************************************
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+ * Set the permission types that the chado module uses. Essentially we
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+ * want permissionis that protect creation, editing and deleting of chado
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+ * data objects
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+ */
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+function tripal_analysis_go_perm(){
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+ return array(
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+ 'access chado_analysis_go content',
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+ 'create chado_analysis_go content',
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+ 'delete chado_analysis_go content',
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+ 'edit chado_analysis_go content',
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+ );
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+}
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+/*******************************************************************************
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+ * The following function proves access control for users trying to
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+ * perform actions on data managed by this module
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+ */
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+function chado_analysis_go_access($op, $node, $account){
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+ if ($op == 'create') {
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+ return user_access('create chado_analysis_go content', $account);
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+ }
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+
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+ if ($op == 'update') {
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+ if (user_access('edit chado_analysis_go content', $account)) {
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+ return TRUE;
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+ }
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+ }
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+ if ($op == 'delete') {
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+ if (user_access('delete chado_analysis_go content', $account)) {
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+ return TRUE;
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+ }
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+ }
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+ if ($op == 'view') {
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+ if (user_access('access chado_analysis_go content', $account)) {
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+ return TRUE;
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+ }
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+ }
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+ return FALSE;
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+}
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+/*******************************************************************************
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+ * Dynamic addition/removal of menu item
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+ */
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+function tripal_analysis_go_node_has_menu($type,$vid){
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+
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+ // check to see if this node is an organism node
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+ $sql = 'SELECT organism_id FROM {chado_organism} WHERE vid = %d';
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+ $result = db_query($sql, $vid);
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+
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+ // menu status
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+ $box_status =variable_get("tripal_analysis_go-box-goterms","menu_off");
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+
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+ // if this node is not an organism or a feature node then return false
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+ // we don't want the menu item to be shown, otherwise get the normal perms
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+ if($org_id = db_fetch_object($result)){
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+ if(strcmp($box_status,"menu_on")==0){
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+ return user_access($type);
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+ }
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+ } else {
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+ return FALSE;
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+ }
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+}
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+/*******************************************************************************
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+ * HOOK: Implementation of hook_nodeapi()
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+ * Display library information for associated features or organisms
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+ * This function also provides contents for indexing
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+ */
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+function tripal_analysis_go_nodeapi(&$node, $op, $teaser, $page) {
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+
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+ switch ($op) {
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+ // Note that this function only adds library view to an organism/feature
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+ // node. The view of a library node is controled by the theme *.tpl file
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+ case 'view':
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+
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+ // Set the node types for showing library information
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+ $types_to_show = variable_get('tripal_analysis_go_setting',
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+ array('chado_feature','chado_organism'));
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+
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+ // Abort if this node is not one of the types we should show.
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+ if (!in_array($node->type, $types_to_show, TRUE)) {
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+ // Turn the menu off if it's on
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+ $box_status = variable_get("tripal_analysis_go-box-goterms","menu_off");
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+ if (strcmp($box_status,"menu_on")==0 && $node->type =='chado_organism'){
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+ variable_set("tripal_analysis_go-box-goterms","menu_off");
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+ }
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+ break;
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+ }
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+
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+ // Add library to the content item if it's not a teaser
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+ if (!$teaser) {
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+ // add the library to the organism/feature search indexing
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+ if($node->build_mode == NODE_BUILD_SEARCH_INDEX){
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+ $node->content['tripal_analysis_go_search_index'] = array(
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+ '#value' => theme('tripal_analysis_go_search_index',$node),
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+ '#weight' => 5,
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+ );
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+ } else if ($node->build_mode == NODE_BUILD_SEARCH_RESULT) {
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+ $node->content['tripal_analysis_go_search_result'] = array(
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+ '#value' => theme('tripal_analysis_go_search_result',$node),
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+ '#weight' => 5,
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+ );
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+ } else {
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+ // Show go terms if the organism/feature is not at teaser view
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+ $node->content['tripal_analysis_go_node_add'] = array(
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+ '#value' => theme('tripal_analysis_go_node_add', $node),
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+ '#weight' => 5
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+ );
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+ }
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+ }
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+ }
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+}
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+
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+/************************************************************************
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+ * We need to let drupal know about our theme functions and their arguments.
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+ * We create theme functions to allow users of the module to customize the
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+ * look and feel of the output generated in this module
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+ */
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+function tripal_analysis_go_theme () {
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+ return array(
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+
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+ 'tripal_analysis_go_search_index' => array (
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+ 'arguments' => array('node'),
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+ ),
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+ 'tripal_analysis_go_search_result' => array (
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+ 'arguments' => array('node'),
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+ ),
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+ 'tripal_analysis_go_node_add' => array (
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+ 'arguments' => array('node'),
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+ )
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+ );
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+}
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+/************************************************************************
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+*/
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+function theme_tripal_analysis_go_search_index($node){
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+
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+}
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+
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+/************************************************************************
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+*/
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+function theme_tripal_analysis_go_search_result($node){
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+
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+}
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+/************************************************************************
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+*/
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+function theme_tripal_analysis_go_node_add($node){
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+ $content = '';
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+ if(strcmp($node->type,'chado_feature')==0){
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+ $content = tripal_analysis_go_feature_add($node);
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+ }
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+ if(strcmp($node->type,'chado_organism')==0){
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+ $box_status = variable_get("tripal_analysis_go-box-goterms","menu_off");
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+ if (strcmp($box_status,"menu_off")==0){
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+ $content = tripal_analysis_go_organism_add($node);
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+ }
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+ }
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+ return $content;
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+}
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+/************************************************************************
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+*/
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+function tripal_analysis_go_organism_goterms($node) {
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+ $node = node_load($node);
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+ return tripal_analysis_go_organism_add($node);
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+}
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+/************************************************************************
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+*/
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+function tripal_analysis_go_select_form(&$form_state = NULL,$node){
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+
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+ $form = array();
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+ // find analyses that have GO terms
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+ $sql = "
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+ SELECT DISTINCT A.analysis_id, A.name, GCA.organism_id
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+ FROM {go_count_analysis} GCA
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+ INNER JOIN Analysis A on GCA.analysis_id = A.analysis_id
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+ WHERE organism_id = %d
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+ ORDER BY analysis_id DESC
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+ ";
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+ $previous_db = db_set_active('chado');
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+ $results = db_query($sql,$node->organism_id);
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+ db_set_active($previous_db);
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+
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+ $analyses = array();
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+ $analyses[''] = '';
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+ while($analysis = db_fetch_object($results)){
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+ $analyses[$analysis->analysis_id."-".$analysis->organism_id] = "$analysis->name";
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+ }
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+
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+ # create the select box
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+ $form['analysis_select'] = array(
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+ '#title' => t('Select a GO report to view'),
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+ '#description' => t('Any analysis with GO results related to this organism are available for viewing. For further information, see the analysis information page.'),
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+ '#type' => 'select',
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+ '#options' => $analyses,
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+ '#attributes' => array (
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+ 'onchange' => 'tripal_analysis_go_org_charts(this.options[this.selectedIndex].value)'
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+ ),
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+ );
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+ return $form;
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+}
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+/************************************************************************
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+*/
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+function tripal_analysis_go_org_charts ($element) {
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+ $analysis_id = preg_replace("/^(\d+)-(\d+)$/","$1",$element);
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+ $organism_id = preg_replace("/^(\d+)-(\d+)$/","$2",$element);
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+ $content = '';
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+
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+ if($analysis_id and $organism_id){
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+ $content = "
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+
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+ <b>Biological Process</b>
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+ <br><i>Expand the tree to browse term counts. Click a term to view term details.</i>
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+ <div class=\"tripal_cv_tree\" id=\"tripal_analysis_go_cv_tree_".$organism_id."-".$analysis_id."_bp\"></div>
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+ <br><br><img class=\"tripal_cv_chart\" id=\"tripal_analysis_go_cv_chart_".$organism_id."-".$analysis_id."_bp\" src=\"\" border=\"0\">
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+ <br><br><br><br>
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+
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+ <b>Cellular Component</b>
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+ <br><i>Expand the tree to browse term counts. Click a term to view term details.</i>
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+ <div class=\"tripal_cv_tree\" id=\"tripal_analysis_go_cv_tree_".$organism_id."-".$analysis_id."_cc\"></div>
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+ <br><br><img class=\"tripal_cv_chart\" id=\"tripal_analysis_go_cv_chart_".$organism_id."-".$analysis_id."_cc\" src=\"\" border=\"0\">
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+
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+ <br><br><br><br>
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+ <b>Molecular Function</b>
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+ <br><i>Expand the tree to browse term counts. Click a term to view term details.</i>
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+ <div class=\"tripal_cv_tree\" id=\"tripal_analysis_go_cv_tree_".$organism_id."-".$analysis_id."_mf\"></div>
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+ <br><br><img class=\"tripal_cv_chart\" id=\"tripal_analysis_go_cv_chart_".$organism_id."-".$analysis_id."_mf\" src=\"\" border=\"0\">
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+ ";
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+ }
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+ $opt = array($content);
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+ return drupal_json($opt);
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+}
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+/************************************************************************
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+*/
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+function tripal_analysis_go_organism_add($node) {
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+ // Show GO information in a expandable box for a organism page.
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+ // Make sure we have $node->organism_id. In the case of creating a new
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+ // organism, the organism_id is not created until we save. This will cause
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+ // an error when users preview the creation without a $node->organism_id
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+ $box_status = variable_get("tripal_analysis_go-box-goterms","menu_off");
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+
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+ if(strcmp($box_status,"menu_off")==0){
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+ $content .= "
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+ <div class=\"tripal_go_summary-info-box\">
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+ <div class=\"tripal_expandableBox\">
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+ <h3>Gene Ontology Summary</h3>
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+ </div>
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+ <div class=\"tripal_expandableBoxContent\">
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+ ";
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+ }
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+
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+ // check to see if we have any analyses
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+ $sql = "
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+ SELECT DISTINCT A.analysis_id, A.name, GCA.organism_id
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+ FROM {go_count_analysis} GCA
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+ INNER JOIN Analysis A on GCA.analysis_id = A.analysis_id
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+ WHERE organism_id = %d
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+ ORDER BY analysis_id DESC
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+ ";
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+ $previous_db = db_set_active('chado');
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+ $results = db_fetch_object(db_query($sql,$node->organism_id));
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+ db_set_active($previous_db);
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+
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+ if($results){
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+ $select_analysis = drupal_get_form('tripal_analysis_go_select_form',$node);
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+
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+ $url = url("sites/all/themes/theme_tripal/images/ajax-loader.gif");
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+ $content .= "
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+ $select_analysis
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+ <div id=\"tripal_cv_cvterm_info_box\">
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+ <a href=\"#\" onclick=\"$('#tripal_cv_cvterm_info_box').hide()\" style=\"float: right\">Close [X]</a>
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+ <h3>Term Information</h3>
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+ <div id=\"tripal_cv_cvterm_info\"></div>
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+ </div>
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+ <div id=\"tripal_ajaxLoading\" style=\"display:none\">
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+ <div id=\"loadingText\">Loading...</div>
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+ <img src=\"$url\"></div><div id=\"tripal_analysis_go_org_charts\"></div>
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+ ";
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+ } else {
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+ $content .= "There are currently no Gene Ontology (GO) reports for this organism\n";
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+ }
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+
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+ if(user_access('access administrative pages')){
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+ $link = url("tripal_toggle_box_menu/tripal_analysis_go/goterms/$node->nid");
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+ if(strcmp($box_status,"menu_off")==0){
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+ $content .= "<br><a href=\"$link\">Show on menu</a>";
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+ } else {
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+ $content .= "<br><a href=\"$link\">Remove from menu</a>";
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+ }
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+ }
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+ if(strcmp($box_status,"menu_off")==0){
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+ $content .= "</div></div>";
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+ }
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+
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+ return $content;
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+}
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+/************************************************************************
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+ *
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+ */
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+function tripal_analysis_go_cv_chart($chart_id){
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+
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+ // The CV module will create the JSON array necessary for buillding a
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+ // pie chart using jgChart and Google Charts. We have to pass to it
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+ // a table that contains count information, tell it which column
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+ // contains the cvterm_id and provide a filter for getting the
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+ // results we want from the table.
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+ $organism_id = preg_replace("/^tripal_analysis_go_cv_chart_(\d+)-(\d+)_(bp|cc|mf)$/","$1",$chart_id);
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+ $analysis_id = preg_replace("/^tripal_analysis_go_cv_chart_(\d+)-(\d+)_(bp|cc|mf)$/","$2",$chart_id);
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+ $type = preg_replace("/^tripal_analysis_go_cv_chart_(\d+)-(\d+)_(bp|cc|mf)$/","$3",$chart_id);
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+
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+ $sql = "SELECT * FROM {Analysis} WHERE analysis_id = %d";
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+ $previous_db = db_set_active('chado'); // use chado database
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+ $analysis = db_fetch_object(db_query($sql,$analysis_id));
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+ db_set_active($previous_db); // now use drupal database
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+
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+ if(strcmp($type,'mf')==0){
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+ $class = 'molecular_function';
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+ $title = "Number of Molecular Function Terms From $analysis->name Analysis";
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+ }
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+ if(strcmp($type,'cc')==0){
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+ $class = 'cellular_component';
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+ $title = "Number of Cellular Component Terms From $analysis->name Analysis";
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+ }
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+ if(strcmp($type,'bp')==0){
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+ $class = 'biological_process';
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+ $title = "Number of Biological Process Terms From $analysis->name Analysis";
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+ }
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+ $options = array(
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+ count_mview => 'go_count_analysis',
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+ cvterm_id_column => 'cvterm_id',
|
|
|
+ count_column => 'feature_count',
|
|
|
+ filter => "
|
|
|
+ CNT.organism_id = $organism_id AND
|
|
|
+ CNT.analysis_id = $analysis_id AND
|
|
|
+ CNT.cvterm_id IN (
|
|
|
+ SELECT CVTR.subject_id
|
|
|
+ FROM {CVTerm_relationship} CVTR
|
|
|
+ INNER JOIN CVTerm CVT on CVTR.object_id = CVT.cvterm_id
|
|
|
+ INNER JOIN CV on CVT.cv_id = CV.cv_id
|
|
|
+ WHERE CVT.name = '$class' AND
|
|
|
+ CV.name = '$class'
|
|
|
+ )
|
|
|
+ ",
|
|
|
+ type => 'p',
|
|
|
+ size => '680x230',
|
|
|
+ title => $title,
|
|
|
+ );
|
|
|
+ return $options;
|
|
|
+}
|
|
|
+/************************************************************************
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_analysis_go_cv_tree($tree_id){
|
|
|
+
|
|
|
+ $organism_id = preg_replace("/^tripal_analysis_go_cv_tree_(\d+)-(\d+)_(bp|cc|mf)$/","$1",$tree_id);
|
|
|
+ $analysis_id = preg_replace("/^tripal_analysis_go_cv_tree_(\d+)-(\d+)_(bp|cc|mf)$/","$2",$tree_id);
|
|
|
+ $type = preg_replace("/^tripal_analysis_go_cv_tree_(\d+)-(\d+)_(bp|cc|mf)$/","$3",$tree_id);
|
|
|
+
|
|
|
+ if(strcmp($type,'mf')==0){
|
|
|
+ $class = 'molecular_function';
|
|
|
+ }
|
|
|
+ if(strcmp($type,'cc')==0){
|
|
|
+ $class = 'cellular_component';
|
|
|
+ }
|
|
|
+ if(strcmp($type,'bp')==0){
|
|
|
+ $class = 'biological_process';
|
|
|
+ }
|
|
|
+
|
|
|
+ $options = array(
|
|
|
+ cv_id => tripal_cv_get_cv_id($class),
|
|
|
+ count_mview => 'go_count_analysis',
|
|
|
+ cvterm_id_column => 'cvterm_id',
|
|
|
+ count_column => 'feature_count',
|
|
|
+ filter => "CNT.organism_id = $organism_id AND CNT.analysis_id = $analysis_id",
|
|
|
+ label => 'Features',
|
|
|
+ );
|
|
|
+ return $options;
|
|
|
+}
|
|
|
+/************************************************************************
|
|
|
+*/
|
|
|
+function tripal_analysis_go_cvterm_add($cvterm_id,$tree_id){
|
|
|
+ $organism_id = preg_replace("/^tripal_analysis_go_cv_tree_(\d+)-(\d+)_(bp|cc|mf)$/","$1",$tree_id);
|
|
|
+ $analysis_id = preg_replace("/^tripal_analysis_go_cv_tree_(\d+)-(\d+)_(bp|cc|mf)$/","$2",$tree_id);
|
|
|
+
|
|
|
+ $sql = "
|
|
|
+ SELECT DBX.accession
|
|
|
+ FROM {cvterm} CVT
|
|
|
+ INNER JOIN dbxref DBX on DBX.dbxref_id = CVT.dbxref_id
|
|
|
+ WHERE cvterm_id = %d
|
|
|
+ ";
|
|
|
+ $previous_db = db_set_active('chado');
|
|
|
+ $xref = db_fetch_object(db_query($sql,$cvterm_id));
|
|
|
+ db_set_active($previous_db);
|
|
|
+
|
|
|
+ $link = url("download_goterm_features/$cvterm_id/$tree_id");
|
|
|
+ $options = array(
|
|
|
+ 'Download sequences' => "<a href=\"$link\">GO_".$xref->accession.".fasta</a>",
|
|
|
+ );
|
|
|
+ return $options;
|
|
|
+}
|
|
|
+/************************************************************************
|
|
|
+*/
|
|
|
+function tripal_analysis_go_get_goterm_features($cvterm_id,$tree_id){
|
|
|
+
|
|
|
+ // get hte accession number for this cvterm and use it in naming the download
|
|
|
+ $sql = "
|
|
|
+ SELECT DBX.accession
|
|
|
+ FROM {cvterm} CVT
|
|
|
+ INNER JOIN dbxref DBX on DBX.dbxref_id = CVT.dbxref_id
|
|
|
+ WHERE cvterm_id = %d
|
|
|
+ ";
|
|
|
+ $previous_db = db_set_active('chado');
|
|
|
+ $xref = db_fetch_object(db_query($sql,$cvterm_id));
|
|
|
+ db_set_active($previous_db);
|
|
|
+
|
|
|
+ drupal_set_header('Content-Type: text');
|
|
|
+ drupal_set_header('Content-Disposition: attachment; filename="GO_'.$xref->accession.'.fasta"');
|
|
|
+
|
|
|
+ $organism_id = preg_replace("/^tripal_analysis_go_cv_tree_(\d+)-(\d+)_(bp|cc|mf)$/","$1",$tree_id);
|
|
|
+ $analysis_id = preg_replace("/^tripal_analysis_go_cv_tree_(\d+)-(\d+)_(bp|cc|mf)$/","$2",$tree_id);
|
|
|
+ $sql = "
|
|
|
+ SELECT DISTINCT F.name,F.residues,F.feature_id
|
|
|
+ FROM {cvtermpath} CVTP
|
|
|
+ INNER JOIN CVTerm CVT1 on CVTP.subject_id = CVT1.cvterm_id
|
|
|
+ INNER JOIN CVTerm CVT2 on CVTP.object_id = CVT2.cvterm_id
|
|
|
+ INNER JOIN AnalysisFeatureProp AFP on AFP.type_id = CVTP.subject_id
|
|
|
+ INNER JOIN AnalysisFeature AF on AF.analysisfeature_id = AFP.analysisfeature_id
|
|
|
+ INNER JOIN Feature F on AF.feature_id = F.feature_id
|
|
|
+ WHERE CVTP.object_id = %d and F.organism_id = %d and AF.analysis_id = %d
|
|
|
+ ORDER BY F.name
|
|
|
+ ";
|
|
|
+ $previous_db = db_set_active('chado');
|
|
|
+ $results = db_query($sql,$cvterm_id,$organism_id,$analysis_id);
|
|
|
+ db_set_active($previous_db);
|
|
|
+ while($feature = db_fetch_object($results)){
|
|
|
+ // get the go term information for each sequence
|
|
|
+ $sql = "
|
|
|
+ SELECT CVT.name,DBX.accession
|
|
|
+ FROM {Feature_CVTerm} FCVT
|
|
|
+ INNER JOIN CVTerm CVT on FCVT.cvterm_id = CVT.cvterm_id
|
|
|
+ INNER JOIN DBXref DBX on CVT.dbxref_id = DBX.dbxref_id
|
|
|
+ WHERE FCVT.feature_id = %d
|
|
|
+ ";
|
|
|
+
|
|
|
+ $previous_db = db_set_active('chado');
|
|
|
+ $terms = db_query($sql,$feature->feature_id);
|
|
|
+ db_set_active($previous_db);
|
|
|
+ $desc = '[';
|
|
|
+ while($term = db_fetch_object($terms)){
|
|
|
+ $desc .= "GO:$term->accession $term->name; ";
|
|
|
+ }
|
|
|
+ $desc = chop($desc);
|
|
|
+ $desc = chop($desc,';');
|
|
|
+ $desc .= ']';
|
|
|
+ print tripal_feature_return_fasta($feature, $desc);
|
|
|
+ }
|
|
|
+ return;
|
|
|
+}
|
|
|
+/************************************************************************
|
|
|
+*/
|
|
|
+function tripal_analysis_go_feature_add($node) {
|
|
|
+ $content = "";
|
|
|
+ $sql = "
|
|
|
+ SELECT DISTINCT FCVT.feature_id,DBX.accession,CVT.name as goterm,
|
|
|
+ CVT.cvterm_id as go_id, CV.name as cvname
|
|
|
+ FROM {Feature_Cvterm} FCVT
|
|
|
+ INNER JOIN Cvterm CVT ON CVT.cvterm_ID = FCVT.cvterm_ID
|
|
|
+ INNER JOIN CV ON CV.cv_id = CVT.cv_id
|
|
|
+ INNER JOIN dbxref DBX ON DBX.dbxref_id = CVT.dbxref_id
|
|
|
+ WHERE
|
|
|
+ (CV.name = 'biological_process' OR
|
|
|
+ CV.name = 'cellular_component' OR
|
|
|
+ CV.name = 'molecular_function') AND
|
|
|
+ FCVT.feature_id = %d
|
|
|
+ ORDER BY CV.name, CVT.name
|
|
|
+ ";
|
|
|
+
|
|
|
+ $previous_db = db_set_active('chado');
|
|
|
+ $results = db_query($sql,$node->feature->feature_id);
|
|
|
+ db_set_active($previous_db);
|
|
|
+ $term = db_fetch_object($results); // retrive the first result
|
|
|
+ if ($term) {
|
|
|
+ $content .= "<div id=\"tripal_go_box\" class=\"tripal_go-info-box\">";
|
|
|
+ $content .= "<div class=\"tripal_expandableBox\">".
|
|
|
+ "<h3>GO terms assigned to this feature</h3>".
|
|
|
+ "</div>";
|
|
|
+ $content .= "<div class=\"tripal_expandableBoxContent\">";
|
|
|
+ $content .= "<table class=\"feature-go-terms\">";
|
|
|
+ $content .= " <tr>";
|
|
|
+ $content .= " <th class=\"dbfieldname\">Accession</th>";
|
|
|
+ $content .= " <th class=\"dbfieldname\">Category</th>";
|
|
|
+ $content .= " <th class=\"dbfieldname\">Term</th>";
|
|
|
+ $content .= " </tr>";
|
|
|
+ do {
|
|
|
+ $content .= "<tr>";
|
|
|
+ $content .= " <td>GO:$term->accession</td>";
|
|
|
+ $content .= " <td>$term->cvname</td>";
|
|
|
+ $content .= " <td>$term->goterm</td>";
|
|
|
+ $content .= "</tr>";
|
|
|
+ } while($term = db_fetch_object($results));
|
|
|
+ $content .= "</table>";
|
|
|
+ $content .= "</div></div>";
|
|
|
+ }
|
|
|
+ return $content;
|
|
|
+}
|
|
|
+
|
|
|
+/*******************************************************************************
|
|
|
+ * Tripal GO administrative setting form. This function is called by
|
|
|
+ * tripal_analysis module which asks for an admin form to show on the page
|
|
|
+ */
|
|
|
+function tripal_analysis_go_get_settings() {
|
|
|
+ // Get an array of node types with internal names as keys
|
|
|
+ $options = node_get_types('names');
|
|
|
+ // Add 'chado_feature' to allowed content types for showing unigene results
|
|
|
+ $allowedoptions ['chado_feature'] = "Show GO terms on feature pages";
|
|
|
+ $allowedoptions ['chado_organism'] = "Show GO analysis on organism pages";
|
|
|
+
|
|
|
+ $form['description'] = array(
|
|
|
+ '#type' => 'item',
|
|
|
+ '#value' => t("This option allows user to display the Gene Ontology (GO) ".
|
|
|
+ "information. For features, this would include all GO terms assigned to a feature ".
|
|
|
+ "and for organisms this would be statistical pie charts of GO terms for a organism. Check the box to ".
|
|
|
+ "enable the display of GO information. Uncheck to disable."),
|
|
|
+ '#weight' => 0,
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['tripal_analysis_go_setting'] = array(
|
|
|
+ '#type' => 'checkboxes',
|
|
|
+ '#options' => $allowedoptions,
|
|
|
+ '#default_value'=>variable_get('tripal_analysis_go_setting',array('chado_feature', 'chado_organism')),
|
|
|
+ );
|
|
|
+ $settings->form = $form;
|
|
|
+ $settings->title = "Tripal GO";
|
|
|
+ return $settings;
|
|
|
+}
|
spficklin