Added to documentation of tripal_feature using doxygen standards

tripal_feature/fasta_loader.php

@@ -1,5 +1,18 @@
 <?php
 
+/**
+ * @defgroup fasta_loader FASTA Feature Loader
+ * @{
+ * Provides fasta loading functionality. Creates features based on their specification in a fasta file.
+ * @}
+ */
+ 
+/**
+ *
+ *
+ * @ingroup tripal_feature
+ * @ingroup fasta_loader
+ */
 function tripal_feature_fasta_load_form (){
 
    $form['fasta_file']= array(
@@ -183,9 +196,13 @@ function tripal_feature_fasta_load_form (){
    );
    return $form;   
 }
-/*************************************************************************
-*
-*/
+
+/**
+ *
+ *
+ * @ingroup tripal_feature
+ * @ingroup fasta_loader
+ */
 function tripal_feature_fasta_load_form_validate($form, &$form_state){
    $fasta_file = trim($form_state['values']['fasta_file']);
    $organism_id  = $form_state['values']['organism_id'];
@@ -251,9 +268,13 @@ function tripal_feature_fasta_load_form_validate($form, &$form_state){
    // check to make sure the 'relationship' and 'sequence' ontologies are loaded
    $form_state['storage']['dfile'] = $dfile;
 }
-/*************************************************************************
-*
-*/
+
+/**
+ *
+ *
+ * @ingroup tripal_feature
+ * @ingroup fasta_loader
+ */
 function tripal_feature_fasta_load_form_submit ($form, &$form_state){
    global $user;
 
@@ -276,9 +297,13 @@ function tripal_feature_fasta_load_form_submit ($form, &$form_state){
    tripal_add_job("Import FASTA file: $dfile",'tripal_core',
       'tripal_feature_load_fasta',$args,$user->uid);
 }
-/*************************************************************************
-*
-*/
+
+/**
+ *
+ *
+ * @ingroup tripal_feature
+ * @ingroup fasta_loader
+ */
 function tripal_feature_load_fasta($dfile, $organism_id, $type,
    $library_id, $re_name, $re_uname, $re_accession, $db_id, $rel_type,
    $re_subject, $parent_type, $update,$uid, $job = NULL)
@@ -352,9 +377,13 @@ function tripal_feature_load_fasta($dfile, $organism_id, $type,
       $source,$residues,$update,$re_name);
    return '';
 }
-/*************************************************************************
-*
-*/
+
+/**
+ *
+ *
+ * @ingroup tripal_feature
+ * @ingroup fasta_loader
+ */
 function tripal_feature_fasta_loader_insert_feature($name,$uname,$db_id,$accession,
               $parent,$rel_type,$parent_type,$library_id,$organism_id,$type, 
               $source,$residues,$update,$re_name) 

tripal_feature/gff_loader.php

@@ -1,14 +1,22 @@
 <?php
 
-
+/**
+ * @defgroup gff3_loader GFF3 Feature Loader
+ * @{
+ * Provides gff3 loading functionality. Creates features based on their specification in a GFF3 file.
+ * @}
+ */
 // TODO: The rank column on the feature_relationship table needs to be used to
 //       make sure the ordering of CDS (exons) is correct.
 
 // The entries in the GFF file are not in order so the order of the relationships
 // is not put in correctly.
-/*************************************************************************
-*
-*/
+/**
+ *
+ *
+ * @ingroup tripal_feature
+ * @ingroup gff3_loader
+ */
 function tripal_core_gff3_load_form (){
 
    $form['gff_file']= array(
@@ -124,9 +132,13 @@ function tripal_core_gff3_load_form (){
 
    return $form;
 }
-/*************************************************************************
-*
-*/
+
+/**
+ *
+ *
+ * @ingroup tripal_feature
+ * @ingroup gff3_loader
+ */
 function tripal_core_gff3_load_form_validate ($form, &$form_state){
 
    $gff_file = $form_state['values']['gff_file'];
@@ -154,9 +166,12 @@ function tripal_core_gff3_load_form_validate ($form, &$form_state){
        form_set_error('add_only',t("Please select only one checkbox from the import options section"));
    }
 }
-/*************************************************************************
-*
-*/
+
+/**
+ *
+ * @ingroup tripal_feature
+ * @ingroup gff3_loader
+ */
 function tripal_core_gff3_load_form_submit ($form, &$form_state){
    global $user;
 
@@ -187,9 +202,13 @@ function tripal_core_gff3_load_form_submit ($form, &$form_state){
 
    return '';
 }
-/*************************************************************************
-*
-*/
+
+/**
+ *
+ *
+ * @ingroup tripal_feature
+ * @ingroup gff3_loader
+ */
 function tripal_core_load_gff3($gff_file, $organism_id,$analysis_id,$add_only =0, 
    $update = 0, $refresh = 0, $remove = 0, $job = NULL)
 {
@@ -442,9 +461,13 @@ function tripal_core_load_gff3($gff_file, $organism_id,$analysis_id,$add_only =0
    tripal_db_set_active($previous_db);
    return '';
 }
-/*************************************************************************
-*
-*/
+
+/**
+ *
+ *
+ * @ingroup tripal_feature
+ * @ingroup gff3_loader
+ */
 function tripal_core_load_gff3_parents($feature,$cvterm,$parents,$gff_features,$organism_id){
 
    $uname = $feature->uniquename;
@@ -493,9 +516,13 @@ function tripal_core_load_gff3_parents($feature,$cvterm,$parents,$gff_features,$
       }
    }
 }
-/*************************************************************************
-*
-*/
+
+/**
+ *
+ *
+ * @ingroup tripal_feature
+ * @ingroup gff3_loader
+ */
 function tripal_core_load_gff3_dbxref($feature,$dbxrefs){
 
    // iterate through each of the dbxrefs
@@ -563,9 +590,12 @@ function tripal_core_load_gff3_dbxref($feature,$dbxrefs){
    return 1;
 }
 
-/*************************************************************************
-*
-*/
+/**
+ *
+ *
+ * @ingroup tripal_feature
+ * @ingroup gff3_loader
+ */
 function tripal_core_load_gff3_alias($feature,$aliases){
 
    // make sure we have a 'synonym_type' vocabulary
@@ -660,9 +690,13 @@ function tripal_core_load_gff3_alias($feature,$aliases){
    }
    return 1;
 }
-/*************************************************************************
-*
-*/
+
+/**
+ *
+ *
+ * @ingroup tripal_feature
+ * @ingroup gff3_loader
+ */
 function tripal_core_load_gff3_feature($organism,$analysis_id,$cvterm,$uniquename,$name,
    $residues,$is_analysis='f',$is_obsolete='f',$add_only,$generate_name)  {
 
@@ -747,9 +781,13 @@ function tripal_core_load_gff3_feature($organism,$analysis_id,$cvterm,$uniquenam
 
    return $feature;
 }
-/*************************************************************************
-*
-*/
+
+/**
+ *
+ *
+ * @ingroup tripal_feature
+ * @ingroup gff3_loader
+ */
 function tripal_core_load_gff3_featureloc($feature,$organism,$landmark,$fmin,
    $fmax,$strand,$phase,$is_fmin_partial,$is_fmax_partial,$residue_info,$locgroup)
 {
@@ -827,7 +865,5 @@ exit;
    }
    return 1;
 }
-/*************************************************************************
-*
-*/
+
 

tripal_feature/indexFeatures.php

@@ -48,8 +48,10 @@ if(isset($arguments['i'])){
 
 }
 
-/************************************************************************
+/**
  *
+ *
+ * @ingroup tripal_feature
  */
 function tripal_features_reindex ($max_sync,$job_id = NULL){
    $i = 0;
@@ -120,8 +122,10 @@ function tripal_features_reindex ($max_sync,$job_id = NULL){
    return '';
 }
 
-/************************************************************************
+/**
+ *
  *
+ * @ingroup tripal_feature
  */
 function tripal_feature_index_feature ($feature_id,$nid){
    #print "\tfeature $feature_id nid $nid\n";

tripal_feature/syncFeatures.php

@@ -30,8 +30,10 @@ if(isset($arguments['f'])){
 }
    
 
-/************************************************************************
+/**
  *
+ *
+ * @ingroup tripal_feature
  */
 function tripal_feature_sync_features ($max_sync = 0, $job_id = NULL){
    //print "Syncing features (max of $max_sync)\n";
@@ -115,6 +117,11 @@ function tripal_feature_sync_features ($max_sync = 0, $job_id = NULL){
    return '';
 }
 
+/**
+ *
+ *
+ * @ingroup tripal_feature
+ */
 function tripal_feature_sync_feature ($feature_id){
 //   print "\tfeature $feature_id\n";
 
@@ -264,8 +271,10 @@ function tripal_feature_sync_feature ($feature_id){
 
 
 
-/*******************************************************************************
+/**
  *  Returns a list of organisms that are currently synced with Drupal
+ *
+ * @ingroup tripal_feature
  */
 function organism_get_synced() {
 

tripal_feature/tripal_feature-db_references.inc

@@ -1,10 +1,10 @@
 <?php
 
-/*************************************************************************************************************
- * @section 
- * Deals with Adding DB references
+/**
+ * 
+ *
+ * @ingroup tripal_feature
  */
-
 function tripal_feature_add_ALL_dbreferences_page($node) {
   $output = '';
 
@@ -19,9 +19,11 @@ function tripal_feature_add_ALL_dbreferences_page($node) {
   return $output;
 }
 
-/*******************************************************************************
+/**
  * Implements Hook_form()
  * Handles adding of Database References to features
+ *
+ * @ingroup tripal_feature
  */
 function tripal_feature_add_ONE_dbreference_form($form_state, $node) {
 
@@ -69,9 +71,12 @@ function tripal_feature_add_ONE_dbreference_form($form_state, $node) {
 
   return $form;
 }
-/*******************************************************************************
-*
-*/
+
+/**
+ *
+ *
+ * @ingroup tripal_feature
+ */
 function tripal_feature_add_ONE_dbreference_form_validate($form, &$form_state) {
 
    $db_id = $form_state['values']['db_id'];
@@ -99,9 +104,12 @@ function tripal_feature_add_ONE_dbreference_form_validate($form, &$form_state) {
    }
 
 } 
-/*******************************************************************************
-*
-*/
+
+/**
+ *
+ *
+ * @ingroup tripal_feature
+ */
 function tripal_feature_add_ONE_dbreference_form_submit($form, &$form_state) {
 
    $db_id = $form_state['values']['db_id'];
@@ -133,11 +141,12 @@ function tripal_feature_add_ONE_dbreference_form_submit($form, &$form_state) {
 
 }
 
-/************************************************************************************************************* 
- * @section                                    
- * Deals with Editing and Deleting Properties  
- */                                            
 
+/**
+ *
+ *
+ * @ingroup tripal_feature
+ */
 function tripal_feature_edit_ALL_dbreferences_page($node) {
   $output = '';
 
@@ -149,9 +158,12 @@ function tripal_feature_edit_ALL_dbreferences_page($node) {
 
   return $output;
 }
-/*******************************************************************************                                           
+
+/**                                           
  * Implements Hook_form()                      
- * Handles adding of Properties & Synonyms to Features
+ * Handles adding of DB References to Features
+ *
+ * @ingroup tripal_feature
  */                                        
 function tripal_feature_edit_ALL_db_references_form($form_state, $node) {
   $form = array();
@@ -221,9 +233,12 @@ function tripal_feature_edit_ALL_db_references_form($form_state, $node) {
   } //end of foreach db ref
   return $form;
 }
-/*******************************************************************************
-*
-*/
+
+/**
+ *
+ *
+ * @ingroup tripal_feature
+ */
 function tripal_feature_edit_ALL_db_references_form_submit($form, &$form_state) {
 
   $num_refs = $form_state['values']['num_db_references'];
@@ -257,9 +272,12 @@ function tripal_feature_edit_ALL_db_references_form_submit($form, &$form_state)
   }
 
 }
-/*******************************************************************************
-*
-*/
+
+/**
+ *
+ *
+ * @ingroup tripal_feature
+ */
 function tripal_feature_update_db_reference($dbxref_id, $db_id, $accession) {
 
   $previous_db = tripal_db_set_active('chado');
@@ -268,9 +286,12 @@ function tripal_feature_update_db_reference($dbxref_id, $db_id, $accession) {
   tripal_db_set_active($previous_db);
 
 }
-/*******************************************************************************
-*
-*/
+
+/**
+ *
+ *
+ * @ingroup tripal_feature
+ */
 function tripal_feature_delete_db_reference($dbxref_id) {
 
   $previous_db = tripal_db_set_active('chado');
@@ -286,9 +307,12 @@ function tripal_feature_delete_db_reference($dbxref_id) {
   tripal_db_set_active($previous_db);
 
 }
-/*******************************************************************************
-*
-*/
+
+/**
+ *
+ *
+ * @ingroup tripal_feature
+ */
 function theme_tripal_feature_edit_ALL_db_references_form ($form) {
   $output = '';
 
@@ -313,13 +337,10 @@ function theme_tripal_feature_edit_ALL_db_references_form ($form) {
   return $output;
 }
 
-/*************************************************************************************************************
- * @section
- * Supplimentary functions
- */
-
 /**
  * 
+ *
+ * @ingroup tripal_feature
  */
 function list_dbreferences_for_node($db_references) {
 

tripal_feature/tripal_feature-properties.inc

@@ -1,13 +1,10 @@
 <?php
 
-/*************************************************************************************************************
- * @section
- * Deals with Adding Properties
- */
-
 /**
  * Implements Hook_form()
  * Handles adding of Properties for features
+ *
+ * @ingroup tripal_feature
  */
 function tripal_getfeature_add_ALL_property_page($node) {
   $output = '';
@@ -21,9 +18,12 @@ function tripal_getfeature_add_ALL_property_page($node) {
   $output .= drupal_get_form('tripal_feature_implement_add_chado_properties_navigate', 'properties', $node->nid);
   return $output;
 }
+
 /**
-* 
-*/
+ * 
+ *
+ * @ingroup tripal_feature
+ */
 function tripal_feature_add_ONE_property_form($form_state, $node) {
   $form = array();
   $feature_id = $node->feature->feature_id;
@@ -65,10 +65,12 @@ function tripal_feature_add_ONE_property_form($form_state, $node) {
 
   return $form;
 }
-/**
-* 
-*/
 
+/**
+ * 
+ *
+ * @ingroup tripal_feature
+ */
 function tripal_feature_add_ONE_property_form_validate($form, &$form_state) {
 
   // Only Require if Adding Property
@@ -97,10 +99,12 @@ function tripal_feature_add_ONE_property_form_validate($form, &$form_state) {
   } // if add Property
 
 }
-/**
-* 
-*/
 
+/**
+ * 
+ *
+ * @ingroup tripal_feature
+ */
 function tripal_feature_add_ONE_property_form_submit($form, &$form_state) {
 	
   // if there is a property add it (only won't be a property if clicked next step w/ no property)
@@ -127,11 +131,11 @@ function tripal_feature_add_ONE_property_form_submit($form, &$form_state) {
   } //end of if property to add
 }
 
-/*************************************************************************************************************
- * @section
- * Deals with Editing and Deleting Properties
+/**
+ *
+ *
+ * @ingroup tripal_feature
  */
-
 function tripal_feature_edit_ALL_properties_page($node) {
   $output = '';
 
@@ -147,6 +151,8 @@ function tripal_feature_edit_ALL_properties_page($node) {
 /**
  * Implements Hook_form()
  * Handles adding of Properties for features
+ *
+ * @ingroup tripal_feature
  */
 function tripal_feature_edit_ALL_properties_form($form_state, $node) {
   $form = array();
@@ -211,10 +217,12 @@ function tripal_feature_edit_ALL_properties_form($form_state, $node) {
 
   return $form;
 }
-/**
-* 
-*/
 
+/**
+ * 
+ *
+ * @ingroup tripal_feature
+ */
 function tripal_feature_edit_ALL_properties_form_submit($form, &$form_state) {
 
   if ($form_state['clicked_button']['#value'] == t('Update All Properties') ) {
@@ -234,10 +242,12 @@ function tripal_feature_edit_ALL_properties_form_submit($form, &$form_state) {
 
   
 }
-/**
-* 
-*/
 
+/**
+ * 
+ *
+ * @ingroup tripal_feature
+ */
 function tripal_feature_update_property($featureprop_id, $cvterm_id, $value, $preferred, $nid) {
 
 	$previous_db = tripal_db_set_active('chado');
@@ -277,10 +287,12 @@ function tripal_feature_update_property($featureprop_id, $cvterm_id, $value, $pr
     drupal_execute('chado_feature_node_form', $node_form_state, $node);  
 
 }
-/**
-* 
-*/
 
+/**
+ * 
+ *
+ * @ingroup tripal_feature
+ */
 function tripal_feature_delete_property($featureprop_id) {
 
   $previous_db = tripal_db_set_active('chado');
@@ -291,10 +303,12 @@ function tripal_feature_delete_property($featureprop_id) {
   tripal_db_set_active($previous_db);
 
 }
-/**
-* 
-*/
 
+/**
+ * 
+ *
+ * @ingroup tripal_feature
+ */
 function theme_tripal_feature_edit_ALL_properties_form ($form) {
   $output = '';
 
@@ -316,13 +330,10 @@ function theme_tripal_feature_edit_ALL_properties_form ($form) {
   return $output;
 }
 
-/*************************************************************************************************************
- * @section
- * Supplimentary functions
- */
-
 /**
  * 
+ *
+ * @ingroup tripal_feature
  */
 function list_properties_for_node($properties) {
 

tripal_feature/tripal_feature-relationships.inc

@@ -1,10 +1,11 @@
 <?php
 
-/*************************************************************************************************************
- * @section
- * Deals with Adding Relationships
- */
 
+/**
+ *
+ *
+ * @ingroup tripal_feature
+ */
 function tripal_feature_add_ALL_relationships_page($node) {
   $output = '';
 
@@ -18,9 +19,12 @@ function tripal_feature_add_ALL_relationships_page($node) {
   $output .= drupal_get_form('tripal_feature_implement_add_chado_properties_navigate', 'relationships', $node->nid);
   return $output;
 }
-/*************************************************************************
+
+/**
  * Implements Hook_form()
  * Handles adding of Relationships to Features
+ *
+ * @ingroup tripal_feature
  */
 function tripal_feature_add_ONE_relationship_form($form_state, $node) {
 
@@ -93,9 +97,12 @@ function tripal_feature_add_ONE_relationship_form($form_state, $node) {
   return $form;
 
 }
-/*************************************************************************
-*
-*/
+
+/**
+ *
+ *
+ * @ingroup tripal_feature
+ */
 function tripal_feature_add_ONE_relationship_form_validate($form, &$form_state) {
 
   //Require Validation if adding
@@ -158,9 +165,12 @@ function tripal_feature_add_ONE_relationship_form_validate($form, &$form_state)
     }
   } //end of require validation if adding relationship
 }
-/*************************************************************************
-*
-*/
+
+/**
+ *
+ *
+ * @ingroup tripal_feature
+ */
 function tripal_feature_add_ONE_relationship_form_submit($form, &$form_state) {
 
   if ($form_state['values']['subject_id'] > 0) {
@@ -179,11 +189,11 @@ function tripal_feature_add_ONE_relationship_form_submit($form, &$form_state) {
 
 }
 
-/************************************************************************************************************* 
- * @section                                           
- * Deals with Editing and Deleting Properties         
+/** 
+ *
+ *
+ * @ingroup tripal_feature
  */
-
 function tripal_feature_edit_ALL_relationships_page($node) {
   $output = '';
 	
@@ -196,9 +206,11 @@ function tripal_feature_edit_ALL_relationships_page($node) {
   return $output;
 }
                                                       
-/*************************************************************************                                                 
+/**                                                 
  * Implements Hook_form()                             
  * Handles adding of Properties & Synonyms to Stocks  
+ *
+ * @ingroup tripal_feature
  */                                                   
 function tripal_feature_edit_ALL_relationships_form($form_state, $node) {
   $form = array();
@@ -307,9 +319,12 @@ function tripal_feature_edit_ALL_relationships_form($form_state, $node) {
 
   return $form;
 }
-/*************************************************************************
-*
-*/
+
+/**
+ *
+ *
+ * @ingroup tripal_feature
+ */
 function tripal_feature_edit_ALL_relationships_form_validate($form, &$form_state) {
 
   // Only Require if Updating Relationships
@@ -377,9 +392,12 @@ function tripal_feature_edit_ALL_relationships_form_validate($form, &$form_state
   } //end of if updating relationships
 
 }
-/*************************************************************************
-*
-*/
+
+/**
+ *
+ *
+ * @ingroup tripal_feature
+ */
 function tripal_feature_edit_ALL_relationships_form_submit($form, &$form_state) {
 
   if ($form_state['clicked_button']['#value'] == t('Update Relationships') ) {
@@ -410,9 +428,12 @@ function tripal_feature_edit_ALL_relationships_form_submit($form, &$form_state)
   }
 
 }
-/*************************************************************************
-*
-*/
+
+/**
+ *
+ *
+ * @ingroup tripal_feature
+ */
 function tripal_feature_update_relationship ($stock_relationship_id, $subject_id, $cvterm_id, $object_id) {
 
   $previous_db = db_set_active('chado');
@@ -426,9 +447,12 @@ function tripal_feature_update_relationship ($stock_relationship_id, $subject_id
   db_set_active($previous_db);
 
 }
-/*************************************************************************
-*
-*/
+
+/**
+ *
+ *
+ * @ingroup tripal_feature
+ */
 function tripal_feature_delete_relationship ($stock_relationship_id) {
 
   $previous_db = db_set_active('chado');
@@ -439,9 +463,12 @@ function tripal_feature_delete_relationship ($stock_relationship_id) {
   db_set_active($previous_db);
 
 }
-/*************************************************************************
-*
-*/
+
+/**
+ *
+ *
+ * @ingroup tripal_feature
+ */
 function theme_tripal_feature_edit_ALL_relationships_form ($form) {
   $output = '';
   
@@ -468,13 +495,10 @@ function theme_tripal_feature_edit_ALL_relationships_form ($form) {
   return $output;
 }
 
-/*************************************************************************************************************
- * @section
- * Supplementary Functions
- */
-
 /**
  *
+ *
+ * @ingroup tripal_feature
  */
 function tripal_feature_list_relationships_for_node($feature_name, $subject_relationships, $object_relationships) {
 

tripal_feature/tripal_feature-secondary_tables.inc

@@ -1,6 +1,11 @@
 <?php
 // $Id$
 
+/**
+ *
+ *
+ * @ingroup tripal_feature
+ */
 function tripal_feature_implement_back_to_feature_button($form_state, $nid) {
   $form = array();
 
@@ -16,15 +21,21 @@ function tripal_feature_implement_back_to_feature_button($form_state, $nid) {
 
   return $form;
 }
-/*******************************************************************************
-*
-*/
+
+/**
+ *
+ *
+ * @ingroup tripal_feature
+ */
 function tripal_feature_implement_back_to_feature_button_submit($form, $form_state) {
   drupal_goto('node/'.$form_state['values']['nid']);
 }
-/*******************************************************************************
-*
-*/
+
+/**
+ *
+ *
+ * @ingroup tripal_feature
+ */
 function tripal_feature_implement_add_chado_properties_progress($current) {
 
     $value = '<div class="form_progress"><div class="form_progress-text">'; 
@@ -52,9 +63,12 @@ function tripal_feature_implement_add_chado_properties_progress($current) {
     return $value;
 
 }
-/*******************************************************************************
-*
-*/
+
+/**
+ *
+ *
+ * @ingroup tripal_feature
+ */
 function tripal_feature_implement_add_chado_properties_navigate($form_state, $step, $nid) {
   $form = array();
 
@@ -115,9 +129,12 @@ function tripal_feature_implement_add_chado_properties_navigate($form_state, $st
 
   return $form;
 }
-/*******************************************************************************
-*
-*/
+
+/**
+ *
+ *
+ * @ingroup tripal_feature
+ */
 function tripal_feature_implement_add_chado_properties_navigate_submit($form, $form_state) {
 
   $raw_steps = preg_split('/::/', $form_state['values']['steps']); 
@@ -165,9 +182,11 @@ function tripal_feature_implement_add_chado_properties_navigate_submit($form, $f
 
 }
 
-/*************************************************************************************************************
+/**
  * Implements Hook_form()
  * Handles setting the is_obsolete property of stocks
+ *
+ * @ingroup tripal_feature
  */
 function tripal_feature_is_obsolete_form($node, $stock_id) {
 
@@ -184,9 +203,12 @@ function tripal_feature_is_obsolete_form($node, $stock_id) {
 
   return $form;
 }
-/*******************************************************************************
-*
-*/
+
+/**
+ *
+ *
+ * @ingroup tripal_feature
+ */
 function tripal_feature_is_obsolete_form_submit($form, &$form_state) {
 
   $previous_db = db_set_active('chado');

tripal_feature/tripal_feature.admin.inc

@@ -1,9 +1,12 @@
 <?php
 
-/*************************************************************************
+/**
  * Purpose: Provide Guidance to new Tripal Admin
  *
- * @return HTML Formatted text
+ * @return 
+ *   HTML Formatted text
+ *
+ * @ingroup tripal_feature
  */
 function tripal_feature_module_description_page() {
 
@@ -29,8 +32,10 @@ function tripal_feature_module_description_page() {
   return $text;
 }
 
-/************************************************************************
+/**
+ *
  *
+ * @ingroup tripal_feature
  */
 function tripal_feature_admin () {
 
@@ -134,8 +139,10 @@ function tripal_feature_admin () {
    return system_settings_form($form);
 }
 
-/************************************************************************
+/**
  *
+ *
+ * @ingroup tripal_feature
  */
 function tripal_feature_admin_validate($form, &$form_state) {
    global $user;  // we need access to the user info
@@ -171,8 +178,10 @@ function tripal_feature_admin_validate($form, &$form_state) {
       variable_set('tripal_feature_summary_setting',$form_state['values']['feature_summary']);
    }
 }
-/************************************************************************
+/**
+ *
  *
+ * @ingroup tripal_feature
  */
 function get_tripal_feature_admin_form_cleanup_set(&$form) {
    $form['cleanup'] = array(
@@ -198,8 +207,11 @@ function get_tripal_feature_admin_form_cleanup_set(&$form) {
       '#weight' => 2,
    );
 }
-/************************************************************************
+
+/**
+ *
  *
+ * @ingroup tripal_feature
  */
 function get_tripal_feature_admin_form_reindex_set(&$form) {
    $form['reindex'] = array(
@@ -222,8 +234,11 @@ function get_tripal_feature_admin_form_reindex_set(&$form) {
       '#weight' => 2,
    );
 }
-/************************************************************************
+
+/**
+ *
  *
+ * @ingroup tripal_feature
  */
 function get_tripal_feature_admin_form_taxonomy_set (&$form) {
 
@@ -265,8 +280,11 @@ function get_tripal_feature_admin_form_taxonomy_set (&$form) {
    );
 
 }
-/************************************************************************
+
+/**
+ *
  *
+ * @ingroup tripal_feature
  */
 function get_tripal_feature_admin_form_sync_set (&$form) {
 
@@ -313,9 +331,11 @@ function get_tripal_feature_admin_form_sync_set (&$form) {
 
 }
 
-/*************************************************************************
-*
-*/
+/**
+ *
+ *
+ * @ingroup tripal_feature
+ */
 function tripal_feature_aggregator_page(){
    $add_url = url("admin/tripal/tripal_feature/aggregate/new");
    $output = "<a href=\"$add_url\">Add a new aggregator</a>"; 
@@ -323,9 +343,12 @@ function tripal_feature_aggregator_page(){
    $output .= '<div id="db-edit-div">Please select an aggregator base type to view or edit</div>';
    return $output;
 }
-/*************************************************************************
-*
-*/
+
+/**
+ *
+ *
+ * @ingroup tripal_feature
+ */
 function tripal_feature_aggregator_select_form(){
 
 	// get a list of base terms from chado for user to choose
@@ -357,9 +380,12 @@ function tripal_feature_aggregator_select_form(){
 
    return $form;
 }
-/*************************************************************************
-*
-*/
+
+/**
+ *
+ *
+ * @ingroup tripal_feature
+ */
 function tripal_feature_aggregator_form(&$form_state = NULL,$type_id = NULL){
 
    // get this requested database
@@ -429,9 +455,11 @@ function tripal_feature_aggregator_form(&$form_state = NULL,$type_id = NULL){
    return $form;
 }
 
-/************************************************************************
-*
-*/
+/**
+ *
+ *
+ * @ingroup tripal_feature
+ */
 function tripal_feature_aggregator_form_validate($form, &$form_state){
    $type_id  = $form_state['values']['type_id'];
    $base     = $form_state['values']['base'];
@@ -476,9 +504,12 @@ function tripal_feature_aggregator_form_validate($form, &$form_state){
       }
    }   
 }
-/************************************************************************
-*
-*/
+
+/**
+ *
+ *
+ * @ingroup tripal_feature
+ */
 function tripal_feature_aggregator_form_submit($form, &$form_state){
 
    $type_id  = $form_state['values']['type_id'];
@@ -543,9 +574,12 @@ function tripal_feature_aggregator_form_submit($form, &$form_state){
    } 
    return '';
 }
-/*************************************************************************
-*
-*/
+
+/**
+ *
+ *
+ * @ingroup tripal_feature
+ */
 function tripal_feature_aggregator_ajax_edit (){ 
    // get the database id, build the form and then return the JSON object
    $type_id = $_POST['type_id'];

tripal_feature/tripal_feature.api.inc

@@ -1,16 +1,14 @@
 <?php
-
-/****************************************************************************
- * @section Chado Table Descriptions
- ****************************************************************************/
  
-/****************************************************************************
+/**
  * Implements hook_chado_feature_schema()
  * Purpose: To add descriptions and foreign keys to default table description
  * Note: This array will be merged with the array from all other implementations
  *
  * @return
  *    Array describing the feature table
+ *
+ * @ingroup tripal_feature
  */
 function tripal_stock_chado_feature_schema() {
   $description = array();

tripal_feature/tripal_feature.module

@@ -1,5 +1,11 @@
 <?php
 
+/**
+ * @defgroup tripal_feature Feature Module
+ * @{
+ * Provides functions for managing chado features including creating details pages for each feature
+ */
+ 
 require_once "tripal_feature.admin.inc";
 require_once "syncFeatures.php";
 require_once "indexFeatures.php";
@@ -14,9 +20,10 @@ require_once "tripal_feature-relationships.inc";
 require_once "tripal_feature-db_references.inc";
 
 
-/*************************************************************************
-*
-*/
+/**
+ *
+ * @ingroup tripal_feature
+ */
 function tripal_feature_init(){
 
    // add the jGCharts JS and CSS
@@ -27,11 +34,14 @@ function tripal_feature_init(){
                                   '/css/tripal_feature.css');
 }
 
-/*************************************************************************
+/**
  * Implements hook_views_api()
+ *
  * Purpose: Essentially this hook tells drupal that there is views support for
  *  for this module which then includes tripal_db.views.inc where all the
  *  views integration code is
+ *
+ * @ingroup tripal_feature
  */ 
 function tripal_feature_views_api() {
    return array(
@@ -39,11 +49,18 @@ function tripal_feature_views_api() {
    );
 }
 
-/************************************************************************
+/**
  * Display help and module information
- * @param path which path of the site we're displaying help
- * @param arg array that holds the current path as would be returned from arg() function
- * @return help text for the path
+ *
+ * @param 
+ *   path which path of the site we're displaying help
+ * @param 
+ *   arg array that holds the current path as would be returned from arg() function
+ *
+ * @return 
+ *   help text for the path
+ *
+ * @ingroup tripal_feature
  */
 function tripal_feature_help($path, $arg) {
    $output = '';
@@ -55,9 +72,11 @@ function tripal_feature_help($path, $arg) {
    return $output;
 }
 
-/************************************************************************
+/**
  *  Provide information to drupal about the node types that we're creating
  *  in this module
+ *
+ * @ingroup tripal_feature
  */
 function tripal_feature_node_info() {
    $nodes = array();
@@ -75,10 +94,12 @@ function tripal_feature_node_info() {
    return $nodes;
 }
 
-/************************************************************************
+/**
  *  Set the permission types that the chado module uses.  Essentially we
  *  want permissionis that protect creation, editing and deleting of chado
  *  data objects
+ *
+ * @ingroup tripal_feature
  */
 function tripal_feature_perm(){
    return array(
@@ -90,8 +111,10 @@ function tripal_feature_perm(){
    );
 }
 
-/************************************************************************
+/**
  *  Set the permission types that the module uses.
+ *
+ * @ingroup tripal_feature
  */
 function chado_feature_access($op, $node, $account) {
    if ($op == 'create') {
@@ -115,10 +138,12 @@ function chado_feature_access($op, $node, $account) {
    }
    return FALSE;
 }
-/************************************************************************
+/**
  *  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.
+ *
+ * @ingroup tripal_feature
  */
 function tripal_feature_menu() {
    $items = array();
@@ -186,7 +211,7 @@ function tripal_feature_menu() {
     'type' => MENU_CALLBACK
   );
   //Edit/Deleting Secondary Properties-------------
-/*
+/**
   $items['node/%tf_node/tf_edit_properties'] = array(
     'title' => t('Edit Properties'),
     'description' => t('Settings for Features'),
@@ -243,11 +268,13 @@ function tripal_feature_menu() {
    return $items;
 }
 
-/*************************************************************************
+/**
  * Implements Menu wildcard_load hook
  * Purpose: Allows the node ID of a chado feature to be dynamically 
  *   pulled from the path. The node is loaded from this node ID
  *   and supplied to the page as an arguement
+ *
+ * @ingroup tripal_feature
  */
 function tf_node_load($nid) {
   if (is_numeric($nid)) {
@@ -258,9 +285,11 @@ function tf_node_load($nid) {
   }
   return FALSE;
 }
-/*************************************************************************
-*
-*/
+/**
+ *
+ *
+ * @ingroup tripal_feature
+ */
 function tripal_feature_block($op = 'list', $delta = 0, $edit=array()){
    switch($op) {
       case 'list':
@@ -364,10 +393,12 @@ function tripal_feature_block($op = 'list', $delta = 0, $edit=array()){
 
    }
 }
-/************************************************************************
+/**
  *  When a new chado_feature node is created we also need to add information
  *  to our chado_feature table.  This function is called on insert of a new node
  *  of type 'chado_feature' and inserts the necessary information.
+ *
+ * @ingroup tripal_feature
  */
 function chado_feature_insert($node){
    // remove spaces, newlines from residues
@@ -425,7 +456,10 @@ function chado_feature_insert($node){
       db_query($sql,$node->nid,$node->vid,$feature->feature_id);
    }
 }
-/************************************************************************
+/**
+ *
+ *
+ * @ingroup tripal_feature
  */
 function chado_feature_delete($node){
    // get feature_id so we can remove it from chado database
@@ -460,7 +494,10 @@ function chado_feature_delete($node){
       "chado");
 
 }
-/************************************************************************
+/**
+ *
+ *
+ * @ingroup tripal_feature
  */
 function chado_feature_update($node){
    if($node->revision){
@@ -500,8 +537,10 @@ function chado_feature_update($node){
       chado_feature_add_synonyms($node->synonyms,$feature->feature_id);
    }
 }
-/************************************************************************
+/**
+ *
  *
+ * @ingroup tripal_feature
  */
 function chado_feature_add_synonyms($synonyms,$feature_id){
 
@@ -567,8 +606,10 @@ drupal_set_message($synonyms);
    return $error;
 
 }
-/************************************************************************
+/**
+ *
  *
+ * @ingroup tripal_feature
  */
 function chado_feature_add_gbaccession($accession,$feature_id){
 
@@ -627,8 +668,10 @@ function chado_feature_add_gbaccession($accession,$feature_id){
    return $error;
 }
 
-/************************************************************************
+/**
  *
+ *
+ * @ingroup tripal_feature
  */
 function chado_feature_form ($node,$param){
    $type = node_get_types('type', $node);
@@ -778,8 +821,10 @@ function chado_feature_form ($node,$param){
    );
    return $form;
 }
-/************************************************************************
+/**
+ *
  *
+ * @ingroup tripal_feature
  */
 function chado_feature_validate($node){
    $result = 0;
@@ -833,9 +878,11 @@ function chado_feature_validate($node){
    }
 
 }
-/************************************************************************
+/**
  *  When a node is requested by the user this function is called to allow us
  *  to add auxiliary data to the node object.
+ *
+ * @ingroup tripal_feature
  */
 function chado_feature_load($node){
    // add the feature_id for this node:
@@ -871,8 +918,10 @@ function chado_feature_load($node){
 
    return $additions;
 }
-/************************************************************************
+/**
  *  
+ *
+ * @ingroup tripal_feature
  */
 function tripal_feature_load_organism ($organism_id){
    // add organism details
@@ -882,8 +931,10 @@ function tripal_feature_load_organism ($organism_id){
    tripal_db_set_active($previous_db);  // now use drupal database
    return $organism;
 }
-/************************************************************************
+/**
  *  
+ *
+ * @ingroup tripal_feature
  */
 function tripal_feature_load_synonyms ($feature_id){
 
@@ -903,8 +954,10 @@ function tripal_feature_load_synonyms ($feature_id){
    }
    return $synonyms;
 }
-/************************************************************************
- *  
+/**
+ * 
+ *
+ * @ingroup tripal_feature
  */
 function tripal_feature_load_properties ($feature_id){
 
@@ -928,8 +981,10 @@ function tripal_feature_load_properties ($feature_id){
    }
    return $properties;
 }
-/************************************************************************
+/**
  *  
+ *
+ * @ingroup tripal_feature
  */
 function tripal_feature_load_references ($feature_id){
 
@@ -951,8 +1006,10 @@ function tripal_feature_load_references ($feature_id){
    }
    return $references;
 }
-/************************************************************************
+/**
  *  
+ *
+ * @ingroup tripal_feature
  */
 function tripal_feature_load_featurelocs ($feature_id,$side = 'as_parent',$aggregate = 1){
 
@@ -1016,14 +1073,18 @@ function tripal_feature_load_featurelocs ($feature_id,$side = 'as_parent',$aggre
    usort($featurelocs,'tripal_feature_sort_locations');
    return $featurelocs;
 }
-/************************************************************************
+/**
  *  used to sort the feature locs by start position
+ *
+ * @ingroup tripal_feature
  */
 function tripal_feature_sort_locations($a,$b){
    return strnatcmp($a->fmin, $b->fmin); 
 }
-/************************************************************************
+/**
  *  
+ *
+ * @ingroup tripal_feature
  */
 function tripal_feature_load_relationships ($feature_id,$side = 'as_subject'){
    // get the relationships for this feature.  The query below is used for both
@@ -1081,8 +1142,10 @@ function tripal_feature_load_relationships ($feature_id,$side = 'as_subject'){
    }
    return $relationships;
 }
-/************************************************************************
+/**
  *  
+ *
+ * @ingroup tripal_feature
  */
 function tripal_feature_get_aggregate_types($feature_id){
    // get the feature details
@@ -1101,8 +1164,10 @@ function tripal_feature_get_aggregate_types($feature_id){
    
    return $types;
 }
-/************************************************************************
+/**
  *  
+ *
+ * @ingroup tripal_feature
  */
 function tripal_feature_get_aggregate_relationships($feature_id, $substitute=1,
   $levels=0, $base_type_id=NULL, $depth=0)
@@ -1158,8 +1223,10 @@ function tripal_feature_get_aggregate_relationships($feature_id, $substitute=1,
    } 
    return $new_relationships;
 }
-/************************************************************************
+/**
  *  
+ *
+ * @ingroup tripal_feature
  */
 function tripal_feature_load_featureloc_sequences($feature_id,$featurelocs){
 
@@ -1226,8 +1293,10 @@ function tripal_feature_load_featureloc_sequences($feature_id,$featurelocs){
    }
    return $floc_sequences;
 }
-/*******************************************************************************
+/**
  *  
+ *
+ * @ingroup tripal_feature
  */
 function tripal_feature_load_organism_feature_counts($organism){
 
@@ -1258,8 +1327,10 @@ function tripal_feature_load_organism_feature_counts($organism){
    }
    return array ( 'types' => $types, 'enabled' => true );
 }
-/************************************************************************
+/**
  * 
+ *
+ * @ingroup tripal_feature
  */
 function tripal_feature_load_organism_feature_browser($organism){
 
@@ -1314,20 +1385,29 @@ function tripal_feature_load_organism_feature_browser($organism){
 
    return array ( 'features' => $features, 'pager' => $pager, 'enabled' => true );
 }
-/************************************************************************
+
+/**
  *  used to sort the list of relationship objects by start position
+ *
+ * @ingroup tripal_feature
  */
 function tripal_feature_sort_rel_objects($a,$b){
    return strnatcmp($a->fmin, $b->fmin);
 }
-/************************************************************************
+
+/**
  *  used to sort the list of relationship parts by start position
+ *
+ * @ingroup tripal_feature
  */
 function tripal_feature_sort_rel_parts($a,$b){
    return strnatcmp($a['start'], $b['start']); 
 }
-/************************************************************************
- *  
+
+/**
+ * 
+ *
+ * @ingroup tripal_feature
  */
 function tripal_feature_color_sequence ($sequence,$parts){
 
@@ -1384,9 +1464,12 @@ function tripal_feature_color_sequence ($sequence,$parts){
    $newseq .= "</pre>";
    return $newseq;
 }
-/************************************************************************
+
+/**
  *  This function customizes the view of the chado_feature node.  It allows
  *  us to generate the markup.
+ *
+ * @ingroup tripal_feature
  */
 function chado_feature_view ($node, $teaser = FALSE, $page = FALSE) {
 
@@ -1418,9 +1501,11 @@ function chado_feature_view ($node, $teaser = FALSE, $page = FALSE) {
    return $node;
 }
 
-/*******************************************************************************
+/**
  * Display feature information for associated organisms. This function also
  * provides contents for indexing
+ *
+ * @ingroup tripal_feature
  */
 function tripal_feature_nodeapi(&$node, $op, $teaser, $page) {
 
@@ -1448,10 +1533,13 @@ function tripal_feature_nodeapi(&$node, $op, $teaser, $page) {
          break;
    }
 }
-/************************************************************************
+
+/**
  *  We need to let drupal know about our theme functions and their arguments.
  *  We create theme functions to allow users of the module to customize the
  *  look and feel of the output generated in this module
+ *
+ * @ingroup tripal_feature
  */
 function tripal_feature_theme () {
    return array(
@@ -1511,8 +1599,11 @@ function tripal_feature_theme () {
       ),
    );
 }
-/*******************************************************************************
+
+/**
  *  
+ *
+ * @ingroup tripal_feature
  */
 function tripal_feature_preprocess(&$variables){
 
@@ -1529,76 +1620,112 @@ function tripal_feature_preprocess(&$variables){
       $variables['tripal_feature']['featureloc_sequences'] = tripal_feature_load_featureloc_sequences ($feature->feature_id,$featurelocs);   
    }
 }
+
+/**
+ *
+ *
+ * @ingroup tripal_feature
+ */
 function tripal_feature_preprocess_tripal_organism_feature_counts(&$variables){
    $organism = $variables['node']->organism;
    $variables['tripal_feature']['feature_counts'] = tripal_feature_load_organism_feature_counts($organism);
 }
-/*******************************************************************************
+
+/**
  *  
+ *
+ * @ingroup tripal_feature
  */
 function tripal_feature_preprocess_tripal_organism_feature_browser(&$variables){
    $organism = $variables['node']->organism;
    $variables['tripal_feature']['browser'] = tripal_feature_load_organism_feature_browser($organism);
 }
-/*******************************************************************************
+
+/**
  *  
+ *
+ * @ingroup tripal_feature
  */
 function tripal_feature_preprocess_tripal_feature_properties(&$variables){
    $feature = $variables['node']->feature;
    $variables['tripal_feature']['properties'] = tripal_feature_load_properties($feature->feature_id);
 }
-/*******************************************************************************
+
+/**
  *  
+ *
+ * @ingroup tripal_feature
  */
 function tripal_feature_preprocess_tripal_feature_synonyms(&$variables){
    $feature = $variables['node']->feature;
    $variables['tripal_feature']['synonyms'] = tripal_feature_load_synonyms($feature->feature_id);
 }
-/*******************************************************************************
+
+/**
  *  
+ *
+ * @ingroup tripal_feature
  */
 function tripal_feature_preprocess_tripal_feature_relationships_as_object(&$variables){
    $feature = $variables['node']->feature;
    $variables['tripal_feature']['object_relationships'] = tripal_feature_get_aggregate_relationships($feature->feature_id,0);
 }
-/*******************************************************************************
+
+/**
  *  
+ *
+ * @ingroup tripal_feature
  */
 function tripal_feature_preprocess_tripal_feature_relationships_as_subject(&$variables){
    $feature = $variables['node']->feature;
    $variables['tripal_feature']['subject_relationships'] = tripal_feature_load_relationships($feature->feature_id,'as_subject');
 }
-/*******************************************************************************
-*
-*/
+
+/**
+ *
+ *
+ * @ingroup tripal_feature
+ */
 function tripal_feature_preprocess_tripal_feature_featurelocs_as_child(&$variables){
    $feature = $variables['node']->feature;
    $variables['tripal_feature']['featurelocs_as_child'] = tripal_feature_load_featurelocs($feature->feature_id,'as_child',0);
 }
-/*******************************************************************************
+
+/**
  *  
+ *
+ * @ingroup tripal_feature
  */
 function tripal_feature_preprocess_tripal_feature_featurelocs_as_parent(&$variables){
    $feature = $variables['node']->feature;
    $variables['tripal_feature']['featurelocs_as_parent'] = tripal_feature_load_featurelocs($feature->feature_id,'as_parent');
 }
-/*******************************************************************************
+
+/**
  *  
+ *
+ * @ingroup tripal_feature
  */
 function tripal_feature_preprocess_tripal_feature_references(&$variables){
    $feature = $variables['node']->feature;
    $variables['tripal_feature']['references'] = tripal_feature_load_references($feature->feature_id);
 }
-/*******************************************************************************
+
+/**
  *  
+ *
+ * @ingroup tripal_feature
  */
 function tripal_feature_preprocess_tripal_feature_featureloc_sequences(&$variables){
    $feature = $variables['node']->feature;
    $featurelocs = tripal_feature_load_featurelocs($feature->feature_id,'as_child',0);
    $variables['tripal_feature']['featureloc_sequences'] = tripal_feature_load_featureloc_sequences ($feature->feature_id,$featurelocs);   
 }
-/************************************************************************
+
+/**
  *
+ *
+ * @ingroup tripal_feature
  */
 function tripal_feature_cv_chart($chart_id){
 
@@ -1617,8 +1744,11 @@ function tripal_feature_cv_chart($chart_id){
   );
   return $options;
 }
-/************************************************************************
+
+/**
+ *
  *
+ * @ingroup tripal_feature
  */
 function tripal_feature_cv_tree($tree_id){
 
@@ -1639,9 +1769,11 @@ function tripal_feature_cv_tree($tree_id){
   return $options;
 }
 
-/************************************************************************
+/**
  *  This function is an extension of the chado_feature_view by providing
  *  the markup for the feature object THAT WILL BE INDEXED.
+ *
+ * @ingroup tripal_feature
  */
 function theme_tripal_feature_search_index ($node) {
    $feature = $node->feature;
@@ -1665,9 +1797,12 @@ function theme_tripal_feature_search_index ($node) {
 
    return $content;
 }
-/************************************************************************
+
+/**
  *  This function is an extension of the chado_feature_view by providing
  *  the markup for the feature object THAT WILL BE INDEXED.
+ *
+ * @ingroup tripal_feature
  */
 function theme_tripal_feature_search_results ($node) {
    $feature = $node->feature;
@@ -1692,8 +1827,11 @@ function theme_tripal_feature_search_results ($node) {
 
    return $content;
 }
-/************************************************************************
+
+/**
+ *
  *
+ * @ingroup tripal_feature
  */
 function tripal_feature_set_vocabulary (){
 
@@ -1800,8 +1938,11 @@ function tripal_feature_set_vocabulary (){
       drupal_execute('taxonomy_form_vocabulary', $form_state);
    }
 }
-/************************************************************************
+
+/**
  *
+ *
+ * @ingroup tripal_feature
  */
 function tripal_feature_del_vocabulary(){
    //include the file containing the required functions for adding taxonomy vocabs
@@ -1831,8 +1972,11 @@ function tripal_feature_del_vocabulary(){
    }
 
 }
-/************************************************************************
+
+/**
+ *
  *
+ * @ingroup tripal_feature
  */
 function tripal_features_set_taxonomy($max_sync = 0,$job_id = NULL){
 
@@ -1868,8 +2012,11 @@ function tripal_features_set_taxonomy($max_sync = 0,$job_id = NULL){
       $i++;
    }
 }
-/************************************************************************
+
+/**
+ *
  *
+ * @ingroup tripal_feature
  */
 function tripal_feature_set_taxonomy ($node,$feature_id){
 
@@ -1972,8 +2119,11 @@ function tripal_feature_set_taxonomy ($node,$feature_id){
    }
 
 }
-/************************************************************************
+
+/**
  *
+ *
+ * @ingroup tripal_feature
  */
 function tripal_features_cleanup($dummy = NULL, $job_id = NULL) {
 
@@ -2061,8 +2211,11 @@ function tripal_features_cleanup($dummy = NULL, $job_id = NULL) {
    }
    return '';
 }
-/************************************************************************
+
+/**
+ *
  *
+ * @ingroup tripal_feature
  */
 function tripal_feature_return_fasta($feature,$desc){   
    $fasta  = ">" . variable_get('chado_feature_accession_prefix','ID') . "$feature->feature_id|$feature->name";

tripal_feature/tripal_feature.views.inc

@@ -10,8 +10,9 @@
  *  http://views2.logrus.com/doc/html/index.html.
  */
  
-/*************************************************************************
+/**
  * Implements hook_views_data()
+ *
  * Purpose: Describe chado/tripal tables & fields to views
  *
  * @return: a data array which follows the structure outlined in the
@@ -19,6 +20,8 @@
  *   definitions keyed by chado/tripal table name. Each table definition 
  *   includes basic details about the table, fields in that table and
  *   relationships between that table and others (joins)
+ *
+ * @ingroup tripal_feature
  */
 require_once('views/feature.views.inc');
 require_once('views/chado_feature.views.inc');
@@ -33,13 +36,16 @@ function tripal_feature_views_data()  {
   return $data;
 }
 
-/*************************************************************************
+/**
  * Implements hook_views_handlers()
+ *
  * Purpose: Register all custom handlers with views
  *   where a handler describes either "the type of field", 
  *   "how a field should be filtered", "how a field should be sorted"
  *
  * @return: An array of handler definitions
+ *
+ * @ingroup tripal_feature
  */
 function tripal_feature_views_handlers() {
  return array(

tripal_feature/views/chado_feature.views.inc

@@ -7,6 +7,7 @@
  *
  * The main need for description of this table to views is to join chado data with drupal nodes
  *
+ * @ingroup tripal_feature
  */
 function retrieve_chado_feature_views_data () {
 	global $db_url;

tripal_feature/views/feature.views.inc

@@ -32,6 +32,8 @@
  *        constraint feature_c1 unique (organism_id,uniquename,type_id)
  *   );
  * @endcode
+ *
+ * @ingroup tripal_feature
  */
  function retrieve_feature_views_data() {
 	global $db_url;

tripal_feature/views/handlers/views_handler_field_computed_feature_nid.inc

@@ -1,5 +1,11 @@
 <?php
 
+/**
+ *
+ *
+ * @ingroup tripal_feature
+ * @ingroup views_field_handlers
+ */
 class views_handler_field_computed_feature_nid extends views_handler_field_numeric {
 	function construct() {
 		parent::construct();

tripal_feature/views/handlers/views_handler_field_residues.inc

@@ -2,6 +2,7 @@
 /**
  * A handler to provide proper displays for sequence residues.
  *
+ * @ingroup tripal_feature
  * @ingroup views_field_handlers
  */
 class views_handler_field_residues extends views_handler_field {

tripal_feature/views/misc_tables.views.inc

@@ -15,6 +15,8 @@
         ),
       ); 
  *   @endcode
+ *
+ * @ingroup tripal_feature
  */
 function retrieve_feature_misc_tables_views_data() {
   $data = array();