NatDiv: cleaned up doc

tripal_natural_diversity/api/tripal_natural_diversity.api.inc

@@ -1,6 +1,6 @@
 <?php
 /**
  * @file
- * @todo Add file header description
+ * API for natural diversity data
  */
 

tripal_natural_diversity/includes/tripal_natural_diversity.admin.inc

@@ -1,7 +1,13 @@
 <?php
+/**
+ * @file
+ * Administration of the natural diversity module
+ */
 
 /**
+ * Admin Launchpad
  *
+ * @ingroup tripal_natural_diversity
  */
 function tripal_natural_diversity_admin_natdiv_view() {
   $output = '';
@@ -31,4 +37,4 @@ function tripal_natural_diversity_admin_natdiv_view() {
   }
 
   return $output;
-}
+}

tripal_natural_diversity/includes/tripal_natural_diversity.schema.inc

@@ -1,12 +1,13 @@
 <?php
 /**
  * @file
- * 
+ * Adds to the tripal schema description.
+ *
  * This file contains hooks for specifying the natural diversity tables
  * when Chado v1.11 is installed.  This is only useful for some specific
  * sites that required the ND tables before they were released.  These
  * files should not be needed for most sites as the ND tables are now part
- * of Chado v1.2. However these hooks remain here for backwards compatibility. 
+ * of Chado v1.2. However these hooks remain here for backwards compatibility.
  */
 
 /**

tripal_natural_diversity/tripal_natural_diversity.install

@@ -5,7 +5,10 @@
  */
 
 /**
+ * Implements hook_disable().
  * Disable default views when module is disabled
+ *
+ * @ingroup tripal_natural_diversity
  */
 function tripal_natural_diversity_disable() {
 
@@ -20,6 +23,8 @@ function tripal_natural_diversity_disable() {
 
 /**
  * Implementation of hook_requirements().
+ *
+ * @ingroup tripal_natural_diversity
  */
 function tripal_natural_diversity_requirements($phase) {
   $requirements = array();
@@ -38,6 +43,8 @@ function tripal_natural_diversity_requirements($phase) {
 
 /**
  * Implementation of hook_install().
+ *
+ * @ingroup tripal_natural_diversity
  */
 function tripal_natural_diversity_install() {
 
@@ -51,13 +58,17 @@ function tripal_natural_diversity_install() {
 
 /**
  * Implementation of hook_uninstall().
+ *
+ * @ingroup tripal_natural_diversity
  */
 function tripal_natural_diversity_uninstall() {
 
 }
 
-/*
+/**
+ * Add cvterms related to natural diversity
  *
+ * @ingroup tripal_natural_diversity
  */
 function tripal_natural_diversity_add_cvterms(){
 

tripal_natural_diversity/tripal_natural_diversity.module

@@ -1,9 +1,16 @@
 <?php
+/**
+ * @file
+ * Basic function for the natural diversity module
+ */
+
+require_once 'api/tripal_natural_diversity.api.inc';
+
+require_once 'theme/tripal_natural_diversity.theme.inc';
+
+require_once 'includes/tripal_natural_diversity.schema.inc';
+require_once 'includes/tripal_natural_diversity.admin.inc';
 
-require_once('api/tripal_natural_diversity.api.inc');
-require_once('theme/tripal_natural_diversity.theme.inc');
-require_once('includes/tripal_natural_diversity.schema.inc');
-require_once('includes/tripal_natural_diversity.admin.inc');
 /**
  * @defgroup tripal_natural_diversity Natural Diversity Module
  * @ingroup tripal_modules
@@ -28,7 +35,10 @@ function tripal_natural_diversity_permission() {
     ),
   );
 }
+
 /**
+ *  Implements hook_menu().
+ *
  *  Menu items are automatically added for the new node types created
  *  by this module to the 'Create Content' Navigation menu item.  This function
  *  adds more menu items needed for this module.
@@ -69,8 +79,9 @@ function tripal_natural_diversity_menu() {
 }
 
 /**
- * Implements hook_views_api()
- * Purpose: Essentially this hook tells drupal that there is views support for
+ * Implements hook_views_api().
+ *
+ * Essentially this hook tells drupal that there is views support for
  *  for this module which then includes tripal_natural_diversity.views.inc where all the
  *  views integration code is
  *
@@ -83,7 +94,7 @@ function tripal_natural_diversity_views_api() {
 }
 
 /**
- * Implements hook_theme
+ * Implements hook_theme().
  *
  * @ingroup tripal_natural_diversity
  */
@@ -118,6 +129,8 @@ function tripal_natural_diversity_theme($existing, $type, $theme, $path) {
 }
 
 /**
+ * Implements hook_block_info().
+ *
  * @ingroup tripal_library
  */
 function tripal_natural_diversity_block_info() {
@@ -133,7 +146,10 @@ function tripal_natural_diversity_block_info() {
 
   return $blocks;
 }
+
 /**
+ * Implements hook_block_view().
+ *
  * @ingroup tripal_library
  */
 function tripal_natural_diversity_block_view($delta = '') {
@@ -161,7 +177,9 @@ function tripal_natural_diversity_block_view($delta = '') {
     return $block;
   }
 }
+
 /**
+ * Implements hook_node_view(). Acts on all content types.
  *
  * @ingroup tripal_natural_diversity
  */

tripal_natural_diversity/tripal_natural_diversity.views_default.inc

@@ -1,6 +1,14 @@
 <?php
+/**
+ * @file
+ * Describes default natural diversity views
+ */
 
-
+/**
+ * Implements hook_views_default_views().
+ *
+ * @ingroup tripal_natural_diversity
+ */
 function tripal_natural_diversity_views_default_views() {
   $views = array();
 
@@ -23,6 +31,11 @@ function tripal_natural_diversity_views_default_views() {
   return $views;
 }
 
+/**
+ * Describes the default experiment administration view
+ *
+ * @ingroup tripal_natural_diversity
+ */
 function tripal_natural_diversity_defaultview_admin_natdiv_exp() {
 
   $view = new view();
@@ -140,6 +153,11 @@ function tripal_natural_diversity_defaultview_admin_natdiv_exp() {
   return $view;
 }
 
+/**
+ * Describes the default geological locations administration view
+ *
+ * @ingroup tripal_natural_diversity
+ */
 function tripal_natural_diversity_defaultview_admin_geolocations() {
 
   $view = new view();
@@ -309,6 +327,11 @@ function tripal_natural_diversity_defaultview_admin_geolocations() {
   return $view;
 }
 
+/**
+ * Describes the default reagents administration view
+ *
+ * @ingroup tripal_natural_diversity
+ */
 function tripal_natural_diversity_defaultview_admin_reagents() {
 
   $view = new view();
@@ -411,6 +434,11 @@ function tripal_natural_diversity_defaultview_admin_reagents() {
   return $view;
 }
 
+/**
+ * Describes the default protocols administration view
+ *
+ * @ingroup tripal_natural_diversity
+ */
 function tripal_natural_diversity_defaultview_admin_protocols() {
 
   $view = new view();
@@ -484,4 +512,4 @@ function tripal_natural_diversity_defaultview_admin_protocols() {
   $handler->display->display_options['menu']['context_only_inline'] = 0;
 
   return $view;
-}
+}