Views: Cleaned up doc

tripal_views/api/tripal_views.api.inc

@@ -1,5 +1,4 @@
 <?php
-
 /**
  * @file
  * API functions for Tripal Views Integration
@@ -169,6 +168,8 @@ function tripal_views_is_lightest_priority_setup($setup_id, $table_name) {
  *   The machine-name of the view to be enabled
  * @param $redirect_link
  *   The path to redirect to. FALSE if no redirect needed
+ *
+ * @ingroup tripal_views_api
  */
 function tripal_views_admin_enable_view($view_name, $redirect_link = FALSE) {
 
@@ -193,6 +194,8 @@ function tripal_views_admin_enable_view($view_name, $redirect_link = FALSE) {
  *   The machine-name of the view to be enabled
  * @param $redirect_link
  *   The path to redirect to. FALSE if no redirect needed
+ *
+ * @ingroup tripal_views_api
  */
 function tripal_views_admin_disable_view($view_name, $redirect_link = FALSE) {
 
@@ -212,6 +215,8 @@ function tripal_views_admin_disable_view($view_name, $redirect_link = FALSE) {
 
 /**
  * Purpose: Deletes ALL Tripal Views Integrations.
+ *
+ * @ingroup tripal_views_api
  */
 function tripal_views_delete_all_integrations() {
 
@@ -224,12 +229,13 @@ function tripal_views_delete_all_integrations() {
 
 }
 
-
 /**
  * Rebuilds all the default integrations
  *
  * @param $delete_first
  *   If TRUE then all integrations are first deleted.
+ *
+ * @ingroup tripal_views_api
  */
 function tripal_views_rebuild_views_integrations($delete_first = FALSE) {
 
@@ -645,7 +651,7 @@ function tripal_views_get_integration_array_for_chado_table($table_name, $base_t
   );
   // Add fields
   if (!isset($schema['fields'])) {
-    tripal_report_error('tripal_views', TRIPAL_NOTICE, 
+    tripal_report_error('tripal_views', TRIPAL_NOTICE,
       'There are no fields defined for %table in the Chado Schema API.', array('%table' => $table_name));
     return FALSE;
   }
@@ -1041,4 +1047,4 @@ function tripal_views_remove_join_from_integration($setup_id, $base_table, $base
       ':left-field' => $left_field
     )
   );
-}
+}

tripal_views/includes/tripal_views_integration.inc

@@ -1,5 +1,4 @@
 <?php
-
 /**
  * @file
  * Functions related to the UI for integrating tables with views
@@ -13,7 +12,7 @@
  * @return
  *    a themed HTML table
  *
- * @ingroup tripal_views_integration
+ * @ingroup tripal_views
  */
 function tripal_views_integration_setup_list() {
   $output = '';
@@ -127,7 +126,7 @@ function tripal_views_integration_setup_list() {
  * @param $setup_id
  *    the unique setup id for the integrated table
  *
- * @ingroup tripal_views_integration
+ * @ingroup tripal_views
  */
 function tripal_views_integration_delete($setup_id) {
 
@@ -142,7 +141,7 @@ function tripal_views_integration_delete($setup_id) {
  *   function is meant to be called from a menu item. After completion it
  *   redirects the user to the views intergation page.
  *
- * @ingroup tripal_views_integration
+ * @ingroup tripal_views
  */
 function tripal_views_integration_delete_all_form ($form, $form_state) {
 
@@ -184,7 +183,7 @@ function tripal_views_integration_delete_all_form ($form, $form_state) {
  *   function is meant to be called from a menu item. After completion it
  *   redirects the user to the views intergation page.
  *
- * @ingroup tripal_views_integration
+ * @ingroup tripal_views
  */
 function tripal_views_integration_delete_all_form_submit ($form, &$form_state) {
 
@@ -212,7 +211,7 @@ function tripal_views_integration_delete_all_form_submit ($form, &$form_state) {
  * D7 @todo: Add ability to manage custom fields
  * D7 @todo: Update relationship handler to work with the new tripal_views_join method
  *
- * @ingroup tripal_views_integration
+ * @ingroup tripal_views
  */
 function tripal_views_integration_form($form, $form_state, $arg) {
 
@@ -994,7 +993,6 @@ function tripal_views_integration_form($form, $form_state, $arg) {
   return $form;
 }
 
-
 /**
  * Purpose: validates the tripal_views_integration_form after submission
  *
@@ -1004,7 +1002,7 @@ function tripal_views_integration_form($form, $form_state, $arg) {
  * @param $form_state
  *    The form state pbject which is passed automatically by drupal
  *
- * @ingroup tripal_views_integration
+ * @ingroup tripal_views
  */
 function tripal_views_integration_form_validate($form, &$form_state) {
   $name_array = explode(" ", $form_state['values']['row_name']);
@@ -1039,7 +1037,7 @@ function tripal_views_integration_form_validate($form, &$form_state) {
  * @param $form_state
  *    The form state pbject which is passed automatically by drupal
  *
- * @ingroup tripal_views_integration
+ * @ingroup tripal_views
  */
 function tripal_views_integration_form_submit($form, &$form_state) {
   $name = $form_state['values']['row_name'];
@@ -1196,7 +1194,7 @@ function tripal_views_integration_form_submit($form, &$form_state) {
  * @return
  *   Returns an array of handler names
  *
- * @ingroup tripal_views_integration
+ * @ingroup tripal_views
  */
 function tripal_views_integration_discover_handlers() {
 
@@ -1273,6 +1271,8 @@ function tripal_views_integration_discover_handlers() {
 /*
  * Ajax Callback: Tripal Views Integration Form
  * Replaces the entire fields table when the table or materialized view is set/changed
+ *
+ * @ingroup tripal_views
  */
 function tripal_views_integration_ajax_view_setup_table($form, $form_state) {
   return $form['view_setup_table'];
@@ -1281,6 +1281,8 @@ function tripal_views_integration_ajax_view_setup_table($form, $form_state) {
 /*
  * Ajax Callback: Tripal Views Integration Form
  * Replaces the join db field dropdown when the join table dropdown is changed
+ *
+ * @ingroup tripal_views
  */
 function tripal_views_integration_ajax_join_field($form, $form_state) {
 
@@ -1292,8 +1294,8 @@ function tripal_views_integration_ajax_join_field($form, $form_state) {
     return $form['view_setup_table'][$field]['column-3'][$join_field];
   }
   else {
-    tripal_report_error('tripal_views', TRIPAL_ERROR, 
+    tripal_report_error('tripal_views', TRIPAL_ERROR,
       'Tripal Views Integration Ajax failed due to being unable to determine which row needs updating', array());
     return $form;
   }
-}
+}

tripal_views/includes/tripal_views_integration_port.inc

@@ -1,5 +1,4 @@
 <?php
-
 /**
  * @file
  * This file contains the UI to import/export tripal views integration setups
@@ -7,19 +6,29 @@
  */
 
 /**
- * The form to export a particular tripal views integration
+ * Form: The form to export a particular tripal views integration
+ *
+ * No submit is needed since the setup_id is in the path and the export code is
+ * rendered based on that
+ *
+ * @param $form_state
+ *   The state of the form
+ * @param $setup_id
+ *   The tripal views integration setup id
+ *
+ * @ingroup tripal_views
  */
 function tripal_views_integration_export_form($form_state, $setup_id) {
   $form = array();
 
   $defn_array = tripal_views_integration_export_entry($setup_id);
-  
+
   $t = var_export($defn_array, TRUE);
   $t = preg_replace("/\n\s+array/", "array", $t); // move array( to previous line
   $t = preg_replace("/true/", "TRUE", $t); // upper case true
   $t = preg_replace("/false/", "FALSE", $t); // upper case false
-  $t = preg_replace("/array\(/", "array (", $t); // put a space between array and paren   
-        
+  $t = preg_replace("/array\(/", "array (", $t); // put a space between array and paren
+
   $form['export'] = array(
     '#type' => 'textarea',
     '#title' => 'Export',
@@ -33,7 +42,9 @@ function tripal_views_integration_export_form($form_state, $setup_id) {
 }
 
 /**
- * Imports a tripal views integration
+ * Form: Imports a tripal views integration
+ *
+ * @ingroup tripal_views
  */
 function tripal_views_integration_import_form() {
   $form = array();
@@ -76,7 +87,12 @@ function tripal_views_integration_import_form() {
 }
 
 /**
- * Imports a tripal views integration
+ * Submit: Imports a tripal views integration
+ *
+ * @param $form
+ * @param $form_state
+ *
+ * @ingroup tripal_views
  */
 function tripal_views_integration_import_form_submit($form, &$form_state) {
 

tripal_views/tripal_views.install

@@ -1,14 +1,13 @@
 <?php
-
 /**
  * @file
  * Functions related to installing/uninstalling this module
  */
 
-
 /**
  * Implementation of hook_requirements().
  *
+ * @ingroup tripal_views
  */
 function tripal_views_requirements($phase) {
   $requirements = array();
@@ -74,6 +73,8 @@ function tripal_views_get_schemas() {
  *   - Add priority field to tripal_views
  *   - Add handler field to tripal_views_join
  *   - Add tripal_views_field table to keep track of fields for views integration
+ *
+ * @ingroup tripal_views
  */
 function tripal_views_update_6040() {
 
@@ -131,6 +132,8 @@ function tripal_views_update_6040() {
  * Tripal Views Update for 7.x-2.0
  *   - Add relationship_only field to tripal_views_join
  *   - Add relationship_handler field to tripal_views_join
+ *
+ * @ingroup tripal_views
  */
 function tripal_views_update_7020() {
 

tripal_views/tripal_views.module

@@ -1,4 +1,8 @@
 <?php
+/**
+ * @file
+ * Basic Tripal Views functionality
+ */
 
 /**
  * @defgroup tripal_views Tripal Views Module
@@ -8,14 +12,14 @@
  * @}
  */
 
-require_once "tripal_views.views.inc";
+require_once 'tripal_views.views.inc';
 
-require_once "includes/tripal_views_integration.inc";
-require_once "includes/tripal_views_integration_port.inc";
+require_once 'includes/tripal_views_integration.inc';
+require_once 'includes/tripal_views_integration_port.inc';
 
 /**
- * Implements hook_menu()
- * Purpose: this hook provides details about new menu items added by this module
+ * Implements hook_menu().
+ * This hook provides details about new menu items added by this module
  *
  * @ingroup tripal_views
  */
@@ -136,6 +140,8 @@ function tripal_views_menu() {
 
 /**
  * Implements hook_init().
+ *
+ * @ingroup tripal_views
  */
 function tripal_views_init() {
 
@@ -153,8 +159,10 @@ function tripal_views_init() {
 }
 
 /**
- * Implements hook_help()
- * Purpose: Adds a help page to the module list
+ * Implements hook_help().
+ * Adds a help page to the module list
+ *
+ * @ingroup tripal_views
  */
 function tripal_views_help ($path, $arg) {
   if ($path == 'admin/help#tripal_views') {
@@ -179,7 +187,7 @@ function tripal_views_permission() {
 }
 
 /**
- * Implements hook_views_api()
+ * Implements hook_views_api().
  *
  * Purpose: Essentially this hook tells drupal that there is views support for
  *  for this module which then includes tripal_views.views.inc where all the
@@ -194,9 +202,9 @@ function tripal_views_views_api() {
 }
 
 /**
- * Implements hook_theme()
+ * Implements hook_theme().
  *
- * Purpose: this hook provides details about themable objects added by
+ * This hook provides details about themable objects added by
  *   this module
  *
  * @ingroup tripal_views
@@ -225,6 +233,8 @@ function tripal_views_theme($existing, $type, $theme, $path) {
 /**
  * Implements hook_coder_ignore().
  * Defines the path to the file (tripal_views.coder_ignores.txt) where ignore rules for coder are stored
+ *
+ * @ingroup tripal_views
  */
 function tripal_views_coder_ignore() {
   return array(
@@ -236,6 +246,8 @@ function tripal_views_coder_ignore() {
 /**
  * A landing page for all views of chado content. Simply lists all menu items that
  * are children of it.
+ *
+ * @ingroup tripal_views
  */
 function tripal_views_biological_data_page() {
   $output = '';
@@ -253,25 +265,11 @@ function tripal_views_biological_data_page() {
   return $output;
 }
 
-/*
+/**
+ * Admin launchpad
  *
+ * @ingroup tripal_views
  */
-function tripal_views_form_alter($form, $form_state, $form_id) {
-  if ($form_id == "tripal_views_integration_form") {
-    // updating the form through the ahah callback sets the action of
-    // the form to the ahah callback URL. We need to set it back
-    // to the normal form URL
-    /**
-    if (isset($form_state['input']['setup_id'])) {
-      $form['#action'] = url("admin/tripal/views/integration/edit/" . $form_state['input']['setup_id']);
-    }
-    else {
-      $form['#action'] = url("admin/tripal/views/integration/new");
-    }
-    */
-  }
-}
-
 function tripal_views_admin_integration_view() {
   $output = '';
 
@@ -299,4 +297,4 @@ function tripal_views_admin_integration_view() {
   }
 
   return $output;
-}
+}

tripal_views/tripal_views.views.inc

@@ -1,51 +1,14 @@
 <?php
-
-include('api/tripal_views.api.inc');
-include('views/handlers/tripal_views_handler_area_action_links.inc');
-
 /**
  * @file
  * Tripal Views Integration
  */
 
-/**
- * @defgroup views_handlers Views Integration Handlers
- * @ingroup views
- * @{
- * Provide rules for formatting and composition of fields
- * @}
- */
-/**
- * @defgroup views_field_handlers Views Field Handlers
- * @ingroup views_handlers
- * @{
- * Provide rules for formatting and composition of fields
- * @}
- */
-/**
- * @defgroup views_filter_handlers Views Filter Handlers
- * @ingroup views_handlers
- * @{
- * Provide the ability to filter based on specified data
- * @}
- */
-/**
- * @defgroup views_sort_handlers Views Sort Handlers
- * @ingroup views_handlers
- * @{
- * Provide methods describing how specific data should be sorted
- * @}
- */
-/**
- * @defgroup views_argument_handlers Views Arguement Handlers
- * @ingroup views_handlers
- * @{
- * Provide the ability to filter pased on arguments in the path of the view
- * @}
- */
+include 'api/tripal_views.api.inc';
+include 'views/handlers/tripal_views_handler_area_action_links.inc';
 
 /**
- * Implements hook_views_handlers()
+ * Implements hook_views_handlers().
  *
  * Purpose: Register all custom handlers with views
  *   where a handler describes either "the type of field",
@@ -105,7 +68,7 @@ function tripal_views_views_handlers() {
 }
 
 /**
- * Implements hook_views_pre_render
+ * Implements hook_views_pre_render().
  *
  * Purpose: Intercepts the view after the query has been executed
  *   All the results are stored in $view->result
@@ -131,9 +94,10 @@ function tripal_views_views_pre_render(&$view) {
 }
 
 /**
+ * Implements hook_views_date().
  * Generates a dynamic data array for Views
  *
- * Purpose: This function is a hook used by the Views module. It populates and
+ * This function is a hook used by the Views module. It populates and
  *   returns a data array that specifies for the Views module the base table,
  *   the tables it joins with and handlers.  The data array is populated
  *   using the data stored in the tripal_views tables.
@@ -370,7 +334,9 @@ function tripal_views_views_data() {
 }
 
 /**
+ * Describes the tripal views integration tables to views for the administration views
  *
+ * @ingroup tripal_views
  */
 function tripal_views_views_data_tripal_views_tables($data) {
 
@@ -607,12 +573,14 @@ function tripal_views_views_data_alter(&$data) {
 
 /**
  * Implementation of hook_views_pre_view().
+ *
+ * Merge the $_GET and $_POST into the $_GET. This is because
+ * Views and Views Data Export modules only uses the $_GET variable but
+ * file uploads require $_POST. We need to make sure these two modules
+ * have access to everything needed for this view to work properly.
+ *
+ * @ingroup tripal_views
  */
 function tripal_views_views_pre_view(&$view, &$display_id, &$args) {
-
-  // merge the $_GET and $_POST into the $_GET. This is because
-  // Views and Views Data Export modules only uses the $_GET variable but
-  // file uploads require $_POST. We need to make sure these two modules
-  // have access to everything needed for this view to work properly
   $_GET = array_merge($_GET, $_POST);
 }

tripal_views/tripal_views.views_default.inc

@@ -1,7 +1,10 @@
 <?php
+/**
+ * Describes default views for tripal views integrations
+ */
 
 /**
- *
+ * Implements hook_views_default_views().
  *
  * @ingroup tripal_views
  */
@@ -14,6 +17,11 @@ function tripal_views_views_default_views() {
   return $views;
 }
 
+/**
+ * Default integrations administration view
+ *
+ * @ingroup tripal_views
+ */
 function tripal_views_defaultview_admin_integrations() {
 
   $view = new view();
@@ -312,4 +320,4 @@ function tripal_views_defaultview_admin_integrations() {
   $handler->display->display_options['tab_options']['weight'] = '0';
 
   return $view;
-}
+}

tripal_views/views/handlers/tripal_views_handler_area_action_links.inc

@@ -1,7 +1,19 @@
 <?php
-
+/**
+ * @file
+ * Contains tripal_views_handler_area_action_links Area Handler
+ */
+
+/**
+ * Provides an area for adding action links to a view.
+ *
+ * @ingroup tripal_views
+ */
 class tripal_views_handler_area_action_links extends views_handler_area {
 
+  /**
+   * {@inheritdoc}
+   */
   function option_definition() {
     $options = parent::option_definition();
 
@@ -20,6 +32,9 @@ class tripal_views_handler_area_action_links extends views_handler_area {
     return $options;
   }
 
+  /**
+   * {@inheritdoc}
+   */
   function options_form(&$form, &$form_state) {
     parent::options_form($form, $form_state);
 
@@ -103,6 +118,9 @@ class tripal_views_handler_area_action_links extends views_handler_area {
 
   }
 
+  /**
+   * {@inheritdoc}
+   */
   function options_submit(&$form, &$form_state) {
     parent::options_submit($form, $form_state);
     ddl($form_state, 'form state in submit');
@@ -119,6 +137,9 @@ class tripal_views_handler_area_action_links extends views_handler_area {
     $this->options['link-4']['path-4'] = $form_state['values']['options']['link-4']['path-4'];
   }
 
+  /**
+   * {@inheritdoc}
+   */
   function render($empty = FALSE) {
     if (!$empty || !empty($this->options['empty'])) {
       $output = '<ul class="action-links">';

tripal_views/views/handlers/tripal_views_handler_field_sequence.inc

@@ -1,16 +1,19 @@
 <?php
-
 /**
  * @file
- * A chado wrapper for the views_handler_field.
- *
+ * Contains tripal_views_handler_field_sequence
+ */
+
+/**
  * Handles display of sequence data.  If will aggregate sequences that need
  * to be aggregated (e.g. coding sequences) and provide
+ *
+ * @ingroup tripal_views
  */
 class tripal_views_handler_field_sequence extends views_handler_field {
 
   /**
-   * Defines the options form (form available to admin when they add a field to a view)
+   * {@inheritdoc}
    */
   function options_form(&$form, &$form_state) {
     parent::options_form($form, $form_state);
@@ -69,8 +72,8 @@ class tripal_views_handler_field_sequence extends views_handler_field {
   }
 
   /**
-  * We need to add a few fields to our query
-  */
+   * {@inheritdoc}
+   */
   function query() {
     parent::query();
 
@@ -85,8 +88,10 @@ class tripal_views_handler_field_sequence extends views_handler_field {
   }
 
   /**
-  * Prior to display of results we want to format the sequence
-  */
+   * {@inheritdoc}
+   *
+   * Prior to display of results we want to format the sequence
+   */
   function render($values) {
     $residues = '';
 
@@ -260,5 +265,4 @@ class tripal_views_handler_field_sequence extends views_handler_field {
     return $residues;
   }
 
-
 }

tripal_views/views/handlers/tripal_views_handler_filter_file_upload.inc

@@ -1,17 +1,19 @@
 <?php
-
 /**
  * @file
- * Purpose: This Handler provides a file upload field by extending the
+ * Contains tripal_views_handler_filter_file_upload filter handler
+ */
+
+/**
+ * This Handler provides a file upload field by extending the
  * views_handler_filter object.
  *
- * @ingroup tripal_views_integration
+ * @ingroup tripal_views
  */
 class tripal_views_handler_filter_file_upload extends views_handler_filter {
 
   /**
-   * Defines the value field in both the views filter options form
-   *   and the exposed form
+   * {@inheritdoc}
    */
   function value_form(&$form, &$form_state) {
     parent::value_form($form, $form_state);
@@ -28,8 +30,7 @@ class tripal_views_handler_filter_file_upload extends views_handler_filter {
   }
 
   /**
-   * Ensures the upload field gets rendered when the filter is exposed. It also
-   * changes the form type from a GET to a POST so that file uploads will work.
+   * {@inheritdoc}
    */
   function exposed_form(&$form, &$form_state) {
 
@@ -57,7 +58,7 @@ class tripal_views_handler_filter_file_upload extends views_handler_filter {
   }
 
   /**
-   * Add the where clause
+   * {@inheritdoc}
    */
   function query() {
     $this->ensure_my_table();

tripal_views/views/handlers/tripal_views_handler_filter_no_results.inc

@@ -1,10 +1,15 @@
 <?php
-
 /**
  * @file
+ * Contains tripal_views_handler_filter_no_results
+ */
+
+/**
  * This filter ensures that when a page is first loaded, there are no results (ie: the
  * query is not run). This imitates an advanced search form allowing users to fist
  * enter other filter values and then retrieve results.
+ *
+ * @ingroup tripal_views
  */
 class tripal_views_handler_filter_no_results extends views_handler_filter {
 
@@ -16,7 +21,7 @@ class tripal_views_handler_filter_no_results extends views_handler_filter {
   }
 
   /**
-   * Defines the options form (form available to admin when they add a field to a view)
+   * {@inheritdoc}
    */
   function options_form(&$form, &$form_state) {
 
@@ -46,6 +51,9 @@ class tripal_views_handler_filter_no_results extends views_handler_filter {
 
   }
 
+  /**
+   * {@inheritdoc}
+   */
   function query() {
     global $base_url;
     $jquery_loaded = FALSE;

tripal_views/views/handlers/tripal_views_handler_filter_select_cvterm.inc

@@ -1,14 +1,16 @@
 <?php
-
 /**
  * @file
- * Purpose: This Handler provides a select list for the type field
+ * Contains tripal_views_handler_filter_select_cvterm
+ */
+
+/**
+ * This Handler provides a select list for the type field
  *
  *  NOTE: This handler only works when applied to the type_id field in the base_table of
  *  this view.
  *
- * @ingroup views_filter_handlers
- * @ingroup tripal_core
+ * @ingroup tripal_views
  */
 class tripal_views_handler_filter_select_cvterm extends tripal_views_handler_filter_select_string {
 

tripal_views/views/handlers/tripal_views_handler_filter_select_string.inc

@@ -1,17 +1,19 @@
 <?php
-
 /**
  * @file
- * Purpose: This Handler provides a generic select list for any chado field that is a string
+ * Contains tripal_views_handler_filter_select_string Filter Handler
+ */
+
+/**
+ * This Handler provides a generic select list for any chado field that is a string
  *  The select list includes all distinct values for that field.
  *
- * @ingroup views_filter_handlers
- * @ingroup tripal_core
+ * @ingroup tripal_views
  */
 class tripal_views_handler_filter_select_string extends views_handler_filter_string {
 
   /**
-   * Define our new options (needed for export!)
+   * {@inheritdoc}
    */
   function options_definition() {
     $options = parent::option_definition();
@@ -95,6 +97,9 @@ class tripal_views_handler_filter_select_string extends views_handler_filter_str
     return $options;
   }
 
+  /**
+   * {@inheritdoc}
+   */
   function expose_form(&$form, &$form_state) {
     parent::expose_form($form, $form_state);
 
@@ -141,7 +146,7 @@ class tripal_views_handler_filter_select_string extends views_handler_filter_str
   }
 
   /**
-   * Set values for my options
+   * {@inheritdoc}
    */
   function expose_submit($form, &$form_state) {
     $this->options['expose']['values_form_type'] = $form_state['values']['options']['expose']['values_form_type'];
@@ -151,7 +156,7 @@ class tripal_views_handler_filter_select_string extends views_handler_filter_str
   }
 
   /**
-   * Assign defaults for our new options
+   * {@inheritdoc}
    */
   function expose_options() {
     $this->options['expose']['values_form_type'] = 'textfield';
@@ -160,10 +165,9 @@ class tripal_views_handler_filter_select_string extends views_handler_filter_str
     $this->options['expose']['max_length'] = 40;
   }
 
- /**
-  * Defines the value field in both the views filter options form
-  *   and the exposed form
-  */
+  /**
+   * {@inheritdoc}
+   */
   function value_form(&$form, &$form_state) {
     parent::value_form($form, $form_state);
 
@@ -195,7 +199,7 @@ class tripal_views_handler_filter_select_string extends views_handler_filter_str
   }
 
   /**
-   * Ensure the value form gets exposed correctly
+   * {@inheritdoc}
    */
   function exposed_form(&$form, &$form_state) {
     parent::exposed_form($form, $form_state);
@@ -207,9 +211,9 @@ class tripal_views_handler_filter_select_string extends views_handler_filter_str
     }
   }
 
- /**
-  * Adds this filter to the where clause of the views query
-  */
+  /**
+   * {@inheritdoc}
+   */
   function query() {
 
     // make optional

tripal_views/views/handlers/tripal_views_handler_filter_sequence.inc

@@ -1,17 +1,19 @@
 <?php
-
 /**
  * @file
- * Purpose: This Handler provides a file upload field by extending the
+ * Contains tripal_views_handler_filter_sequence Filter handler
+ */
+
+/**
+ * This Handler provides a file upload field by extending the
  * views_handler_filter object.
  *
- * @ingroup tripal_views_integration
+ * @ingroup tripal_views
  */
 class tripal_views_handler_filter_sequence extends views_handler_filter {
- 
- /**
-   * Defines the value field in both the views filter options form
-   *   and the exposed form
+
+  /**
+   * {@inheritdoc}
    */
   function value_form(&$form, &$form_state) {
     parent::value_form($form, $form_state);
@@ -20,12 +22,13 @@ class tripal_views_handler_filter_sequence extends views_handler_filter {
        '#type' => 'sequence_combo',
        '#title' => t('%label', array('%label' => $this->options['expose']['label'])),
        '#default_value' => $this->value,
-       '#multiple' => FALSE,       
+       '#multiple' => FALSE,
     );
     $form['value'] = &$this->value_form;
   }
 
   /**
+   * {@inheritdoc}
    * Ensures the upload field gets rendered when the filter is exposed. It also
    * changes the form type from a GET to a POST so that file uploads will work.
    */
@@ -49,16 +52,16 @@ class tripal_views_handler_filter_sequence extends views_handler_filter {
     }
   }
 
- 
+
   /**
-   *
+   * {@inheritdoc}
    */
   function query() {
     $this->ensure_my_table();
 
     $upstream = $this->value[0]['upstream'];
-    $downstream = $this->value[0]['downstream'];       
-    
+    $downstream = $this->value[0]['downstream'];
+
     // we need the values provided by the user so that the field
     // handler can generate the results properly.  Saving these as session
     // variables may not be the best way but it works.
@@ -67,6 +70,6 @@ class tripal_views_handler_filter_sequence extends views_handler_filter {
     }
     if ($downstream) {
       $_SESSION['downstream'] = $downstream;
-    }    
+    }
   }
 }

tripal_views/views/handlers/tripal_views_handler_filter_textarea.inc

@@ -1,17 +1,19 @@
 <?php
-
 /**
  * @file
- * Purpose: This Handler provides a file upload field by extending the
+ * Contants tripal_views_handler_filter_textarea Filter Handler
+ */
+
+/**
+ * This Handler provides a file upload field by extending the
  * views_handler_filter object.
  *
- * @ingroup tripal_views_integration
+ * @ingroup tripal_views
  */
 class tripal_views_handler_filter_textarea extends views_handler_filter {
 
   /**
-   * Defines the value field in both the views filter options form
-   *   and the exposed form
+   * {@inheritdoc}
    */
   function value_form(&$form, &$form_state) {
     parent::value_form($form, $form_state);
@@ -28,7 +30,7 @@ class tripal_views_handler_filter_textarea extends views_handler_filter {
   }
 
   /**
-   * Ensures the textarea field gets rendered when the filter is exposed.
+   * {@inheritdoc}
    */
   function exposed_form(&$form, &$form_state) {
 
@@ -53,7 +55,7 @@ class tripal_views_handler_filter_textarea extends views_handler_filter {
   }
 
   /**
-   *
+   * {@inheritdoc}
    */
   function query() {