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@@ -15,9 +15,99 @@ function tripal_cv_show_browser() {
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/**
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-*
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-* @ingroup tripal_cv
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-*/
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+ * Generates JSON used for generating an exapandable tree of terms from
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+ * a controlled vocabulary that has associated counts.
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+ *
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+ * The progammer must first create a materialized view that
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+ * will generate count data for a given controlled vocabulary. For example, the Tripal
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+ * Analysis GO creates a materialized view for counting Gene Ontology assignments
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+ * to features. This view is created on install of the module and is named
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+ * 'go_count_analysis'.
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+ *
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+ * Second, the progammer must add an HTML 'div' box to the desired page
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+ * with a class name of 'tripal_cv_tree', and an id of the following format:
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+ *
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+ * tripal_[module_name]_cv_tree_[unique id]
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+ *
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+ * where [module_name] is the name of the tripal module (e.g. tripal_analyisis_go)
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+ * and [unique id] is some unique identifier that the contolling module
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+ * recognizes. This string is the $tree_id variable passed as the first argument
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+ * to the function. For example, the Tripal GO Analysis module generates
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+ * tree ids of the form:
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+ *
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+ * tripal_analysis_go_cv_tree_10_2_bp
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+ *
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+ * In this case the module that will manage this tree is identified as 'tripal_analysis_go' and within
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+ * the [unique id] portion contains the
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+ * organism_id (e.g. 10), analysis_id (e.g. 2) and tree type (bp = biological process).
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+ *
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+ * Second, the programmer must then define a hook in the controlling module for setting
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+ * some options used to build the chart. The hook has the form: hook_cv_tree($tree_id).
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+ * This hook should accept the full $tree_id as the single parameter. For the Tripal
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+ * Analysis GO module the hook is named: tripal_analysis_go_cv_tree.
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+ *
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+ * The array returned by this hook must have the following fields:
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+ * - cv_id
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+ * the cv_id for the controlled vocabulary
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+ * - count_mview
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+ * the name of the materialized view that contains the count data
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+ * this materialized view must have at least two columns, one with the cvterm_id
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+ * for each term and a second column containing the counts. The tree will only
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+ * be expanded to include child terms that have counts.
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+ * - cvterm_id_column
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+ * the column name in the materialized view that contains
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+ * the cvterm_ids
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+ * - count_column
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+ * the column name in the materialized view that contains the
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+ * counts
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+ * - filter
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+ * an SQL compatible WHERE clause string (whithout the word 'WHERE')
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+ * that can be used for filtering the records in the materialized view.
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+ * - label
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+ * the title for the tree
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+ *
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+ * Example from the tripal_analysis_go module:
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+ * @code
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+ * function tripal_analysis_go_cv_tree($tree_id){
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+ *
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+ * $organism_id = preg_replace("/^tripal_analysis_go_cv_tree_(\d+)-(\d+)_(bp|cc|mf)$/","$1",$tree_id);
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+ * $analysis_id = preg_replace("/^tripal_analysis_go_cv_tree_(\d+)-(\d+)_(bp|cc|mf)$/","$2",$tree_id);
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+ * $type = preg_replace("/^tripal_analysis_go_cv_tree_(\d+)-(\d+)_(bp|cc|mf)$/","$3",$tree_id);
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+ *
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+ * if(strcmp($type,'mf')==0){
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+ * $class = 'molecular_function';
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+ * }
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+ * if(strcmp($type,'cc')==0){
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+ * $class = 'cellular_component';
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+ * }
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+ * if(strcmp($type,'bp')==0){
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+ * $class = 'biological_process';
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+ * }
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+ *
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+ * $options = array(
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+ * cv_id => tripal_cv_get_cv_id($class),
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+ * count_mview => 'go_count_analysis',
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+ * cvterm_id_column => 'cvterm_id',
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+ * count_column => 'feature_count',
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+ * filter => "CNT.organism_id = $organism_id AND CNT.analysis_id = $analysis_id",
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+ * label => 'Features',
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+ * );
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+ * return $options;
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+ * }
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+ *
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+ * @endcode
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+ *
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+ * @param $tree_id
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+ * The unique identifier for the tree
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+ *
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+ * @return
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+ * JSON array needed for the jsTree package for generating expandable trees.
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+ *
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+ * With these three components (materialized view, a 'div' box with proper CSS class and ID, and a hook_cv_tree)
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+ * a tree will be created on the page. There is no need to call this function directly.
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+ *
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+ * @ingroup tripal_cv
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+ */
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function tripal_cv_tree($tree_id){
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// parse out the tripal module name from the chart_id to find out
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// which Tripal "hook" to call:
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spficklin