<?php
function tripal_analysis_unigene_init(){
// Add style sheet
drupal_add_css(drupal_get_path('theme', 'tripal').'/css/tripal_analysis_unigene.css');
}
/**
*
*/
function tripal_analysis_unigene_node_info() {
$nodes = array();
$nodes['chado_analysis_unigene'] = array(
'name' => t('Analysis: Unigene'),
'module' => 'chado_analysis_unigene',
'description' => t('A unigene assembly constructed from transcriptomic reads.'),
'has_title' => FALSE,
'title_label' => t('Analysis: Unigene'),
'has_body' => FALSE,
'body_label' => t('Unigene Analysis Description'),
'locked' => TRUE
);
return $nodes;
}
/*******************************************************************************
* Set the permission types that the chado module uses. Essentially we
* want permissionis that protect creation, editing and deleting of chado
* data objects
*/
function tripal_analysis_unigene_perm(){
return array(
'access chado_analysis_unigene content',
'create chado_analysis_unigene content',
'delete chado_analysis_unigene content',
'edit chado_analysis_unigene content',
);
}
/*******************************************************************************
* The following function proves access control for users trying to
* perform actions on data managed by this module
*/
function chado_analysis_unigene_access($op, $node, $account){
if ($op == 'create') {
return user_access('create chado_analysis_unigene content', $account);
}
if ($op == 'update') {
if (user_access('edit chado_analysis_unigene content', $account)) {
return TRUE;
}
}
if ($op == 'delete') {
if (user_access('delete chado_analysis_unigene content', $account)) {
return TRUE;
}
}
if ($op == 'view') {
if (user_access('access chado_analysis_unigene content', $account)) {
return TRUE;
}
}
return FALSE;
}
/**
*
*/
function chado_analysis_unigene_form ($node){
$unigene = $node->analysis->tripal_analysis_unigene;
// set the form defaults
$unigene_name = $node->unigene_name;
if(!$unigene_name){
$unigene_name = $unigene->unigene_name;
}
$num_reads = $node->num_reads;
if(!$num_reads){
$num_reads = $unigene->num_reads;
}
$avg_length = $node->avg_length;
if(!$avg_length){
$avg_length = $unigene->avg_length;
}
$num_clusters = $node->num_clusters;
if(!$num_clusters){
$num_clusters = $unigene->num_clusters;
}
$num_contigs = $node->num_contigs;
if(!$num_contigs){
$num_contigs = $unigene->num_contigs;
}
$num_singlets = $node->num_singlets;
if(!$num_singlets){
$num_singlets = $unigene->num_singlets;
}
// add in the default fields for an analysis
$form = chado_analysis_form($node);
$form['unigene_name'] = array(
'#title' => t('Unigene Name'),
'#type' => 'textfield',
'#required' => TRUE,
'#description' => t('A distinct name used to identify this unigene'),
'#default_value' => $unigene_name,
);
$form['num_reads'] = array(
'#title' => t('Number of Reads'),
'#type' => 'textfield',
'#required' => FALSE,
'#description' => t('Provide the number of reads, after filtering that were used for input into the assembly'),
'#default_value' => $num_reads,
);
$form['avg_length'] = array(
'#title' => t('Average Contig Length'),
'#type' => 'textfield',
'#required' => FALSE,
'#description' => t('Provide the average contig length.'),
'#default_value' => $avg_length,
);
$form['num_clusters'] = array(
'#title' => t('Number of Clusters'),
'#type' => 'textfield',
'#required' => FALSE,
'#description' => t('Provide the number of clusters generated by the asssembly if a clustering mechanism was used for unigene constructions'),
'#default_value' => $num_clusters,
);
$form['num_contigs'] = array(
'#title' => t('Number of Contigs'),
'#type' => 'textfield',
'#required' => FALSE,
'#description' => t('Provide the number of contigs generated by the assembly'),
'#default_value' => $num_contigs,
);
$form['num_singlets'] = array(
'#title' => t('Number of Singlets'),
'#type' => 'textfield',
'#required' => FALSE,
'#description' => t('Provide the number of singlets remaining in the assembly'),
'#default_value' => $num_singlets,
);
return $form;
}
/**
*
*/
function chado_analysis_unigene_insert($node){
// insert the analysis
chado_analysis_insert($node);
// add the unigene name as a property of the anslysis
tripal_analysis_insert_property($node->analysis->analysis_id,'analysis_type','tripal_analysis_unigene');
tripal_analysis_insert_property($node->analysis->analysis_id,'analysis_unigene_name',$node->unigene_name);
tripal_analysis_insert_property($node->analysis->analysis_id,'analysis_unigene_num_contigs',$node->num_contigs);
tripal_analysis_insert_property($node->analysis->analysis_id,'analysis_unigene_num_reads',$node->num_reads);
tripal_analysis_insert_property($node->analysis->analysis_id,'analysis_unigene_avg_length',$node->avg_length);
tripal_analysis_insert_property($node->analysis->analysis_id,'analysis_unigene_num_clusters',$node->num_clusters);
tripal_analysis_insert_property($node->analysis->analysis_id,'analysis_unigene_num_singlets',$node->num_clusters);
}
/**
*
*/
function chado_analysis_unigene_update($node){
chado_analysis_update($node);
tripal_analysis_update_property($node->analysis_id,'analysis_unigene_name',$node->unigene_name,1);
tripal_analysis_update_property($node->analysis_id,'analysis_unigene_num_contigs',$node->num_contigs,1);
tripal_analysis_update_property($node->analysis_id,'analysis_unigene_num_reads',$node->num_reads,1);
tripal_analysis_update_property($node->analysis_id,'analysis_unigene_avg_length',$node->avg_length,1);
tripal_analysis_update_property($node->analysis_id,'analysis_unigene_num_clusters',$node->num_clusters,1);
tripal_analysis_update_property($node->analysis_id,'analysis_unigene_num_singlets',$node->num_singlets,1);
}
/**
*
*/
function chado_analysis_unigene_delete($node){
chado_analysis_delete($node);
}
/**
*
*/
function chado_analysis_unigene_view ($node, $teaser = FALSE, $page = FALSE) {
// use drupal's default node view:
$node = node_prepare($node, $teaser);
return $node;
}
/**
*
*/
function chado_analysis_unigene_load($node){
// load the default set of analysis fields
$additions = chado_analysis_load($node);
// create some variables for easier lookup
$analysis = $additions->analysis;
$analysis_id = $analysis->analysis_id;
// add in the properties
$unigene_name = tripal_analysis_get_property($analysis_id,'analysis_unigene_name');
$num_contigs = tripal_analysis_get_property($analysis_id,'analysis_unigene_num_contigs');
$num_reads = tripal_analysis_get_property($analysis_id,'analysis_unigene_num_reads');
$avg_length = tripal_analysis_get_property($analysis_id,'analysis_unigene_avg_length');
$num_clusters = tripal_analysis_get_property($analysis_id,'analysis_unigene_num_clusters');
$num_singlets = tripal_analysis_get_property($analysis_id,'analysis_unigene_num_singlets');
$analysis->tripal_analysis_unigene->unigene_name = $unigene_name->value;
$analysis->tripal_analysis_unigene->num_contigs = $num_contigs->value;
$analysis->tripal_analysis_unigene->num_reads = $num_reads->value;
$analysis->tripal_analysis_unigene->avg_length = $avg_length->value;
$analysis->tripal_analysis_unigene->num_clusters = $num_clusters->value;
$analysis->tripal_analysis_unigene->num_singlets = $num_singlets->value;
// add in organism information using the materialized view
$sql = "SELECT * FROM {organism_unigene_mview} OUM ".
" INNER JOIN {organism} O on OUM.organism_id = O.organism_id ".
"WHERE OUM.analysis_id = %d ".
"ORDER BY O.genus, O.species";
$previous_db = tripal_db_set_active('chado'); // use chado database
$organisms = db_query($sql,$analysis_id);
tripal_db_set_active($previous_db); // now use drupal database
while($organism = db_fetch_object($organisms)){
$sql = "SELECT nid FROM {chado_organism} WHERE organism_id = %d";
$c_org = db_fetch_object(db_query($sql,$organism->organism_id));
$organism->nid = $c_org->nid;
$analysis->tripal_analysis_unigene->organisms[] = $organism;
}
return $additions;
}
/*******************************************************************************
* tripal_analysis_unigene_nodeapi()
* HOOK: Implementation of hook_nodeapi()
* Display unigene results for allowed node types
*/
function tripal_analysis_unigene_nodeapi(&$node, $op, $teaser, $page) {
switch ($op) {
case 'view':
// Find out which node types for showing the unigene
$types_to_show = variable_get('tripal_analysis_unigene_setting',
array('chado_feature','chado_organism'));
// Abort if this node is not one of the types we should show.
if (in_array($node->type, $types_to_show, TRUE)) {
// Add unigene to the content item if it's not a teaser
if ($teaser) {
return '';
}
// add the alignment to the feature search indexing
if($node->build_mode == NODE_BUILD_SEARCH_INDEX){
$node->content['tripal_analysis_unigene_index_version'] = array(
'#value' => theme('tripal_analysis_unigene_search_index',$node),
'#weight' => 4,
);
} else if ($node->build_mode == NODE_BUILD_SEARCH_RESULT) {
$node->content['tripal_analysis_unigene_index_version'] = array(
'#value' => theme('tripal_analysis_unigene_search_result',$node),
'#weight' => 4,
);
} else {
if(strcmp($node->type,'chado_organism')==0){
$node->content['tripal_organism_unigenes'] = array(
'#value' => theme('tripal_organism_unigenes', $node),
'#weight' => 4
);
}
if(strcmp($node->type,'chado_feature')==0){
$node->content['tripal_feature_unigenes'] = array(
'#value' => theme('tripal_feature_unigenes', $node),
'#weight' => 4
);
}
}
}
break;
}
}
/************************************************************************
* We need to let drupal know about our theme functions and their arguments.
* We create theme functions to allow users of the module to customize the
* look and feel of the output generated in this module
*/
function tripal_analysis_unigene_theme () {
return array(
'tripal_analysis_unigene_search_index' => array (
'arguments' => array('node'),
),
'tripal_analysis_unigene_search_result' => array (
'arguments' => array('node'),
),
'tripal_organism_unigenes' => array (
'arguments' => array('node'=> null),
'template' => 'tripal_organism_unigenes',
),
'tripal_feature_unigenes' => array (
'arguments' => array('node'=> null),
'template' => 'tripal_feature_unigenes',
),
'tripal_analysis_unigene_base' => array (
'arguments' => array('node'=> null),
'template' => 'tripal_analysis_unigene_base',
),
);
}
/*******************************************************************************
*
*/
function tripal_analysis_unigene_preprocess_tripal_organism_unigenes(&$variables){
$node = $variables['node'];
$organism = $node->organism;
$unigenes = tripal_analysis_unigene_load_organism_unigenes($organism);
$node->organism->tripal_analysis_unigene->unigenes = $unigenes;
}
/*******************************************************************************
*
*/
function tripal_analysis_unigene_preprocess_tripal_feature_unigenes(&$variables){
$node = $variables['node'];
$feature = $node->feature;
$unigenes = tripal_analysis_unigene_load_feature_unigenes($feature);
$node->feature->tripal_analysis_unigene->unigenes = $unigenes;
}
/************************************************************************
* This function is an extension of the chado_feature_view by providing
* the markup for the feature object THAT WILL BE INDEXED.
*/
function theme_tripal_analysis_unigene_search_index ($node) {
$feature = $node->feature;
$obj_feature = tripal_analysis_unigene_get_alignments($feature);
$alignments = $obj_feature->alignments;
$content = "<strong>";
if(count($alignments) > 0){
// iterate through each alignment
foreach ($alignments as $result){
// EST alignments in chado use an EST_match type to map ESTs to
// contigs and a rank to indicate the major srcfeature.
// We don't want to show EST_matches on the alignment view
// since that doesn't make much sense to the end user. If this
// is an EST_match and the feature is an EST then we want to show
// the contig in the alignments. The contig name is part of the
// uniquename in the EST_match
if($node->feature->cvname == 'EST' && $result->cvname == 'EST_match'){
$sql = "SELECT srcfeature_id ".
"FROM {featureloc} ".
"WHERE feature_id = $result->feature_id ".
"ORDER BY rank";
$previous_db = tripal_db_set_active ('chado');
$contig_fid = db_result(db_query($sql));
$sql = "SELECT name FROM {feature} WHERE feature_id = $contig_fid";
$contig_name = db_result(db_query($sql));
tripal_db_set_active($previous_db);
$sql = "SELECT nid ".
"FROM {chado_feature} ".
"WHERE feature_id = $contig_fid";
$contig_nid = db_result(db_query($sql));
// Check if the EST exists as a drupal node. If yes, add a link to
// it. If no, just show the name
if ($contig_nid != 0) {
$sql = "SELECT nid FROM {node} WHERE nid=$contig_nid";
$node_exists = db_result(db_query($sql));
}
$content .= "$contig_name " ;
}
elseif($node->feature->cvname == 'contig' && $result->cvname == 'EST_match'){
$sql = "SELECT vid ".
"FROM {node} ".
"WHERE title = '$result->feature_name'".
"ORDER BY vid DESC";
// since the feature name is also the node title we can look it up
$est_node = db_fetch_object(db_query($sql));
$content .= "$result->feature_name ";
}
else {
$content .= "$result->cvname $result->feature_name ";
}
}
}
$content .= "</strong>";
return $content;
}
/************************************************************************
* This function is an extension of the chado_feature_view by providing
* the markup for the feature object to show on a search result page.
*/
function theme_tripal_analysis_unigene_search_result ($node) {
$feature = $node->feature;
$obj_feature = tripal_analysis_unigene_get_alignments($feature);
$alignments = $obj_feature->alignments;
$content = "<strong>";
if(count($alignments) > 0){
// iterate through each alignment
foreach ($alignments as $result){
// EST alignments in chado use an EST_match type to map ESTs to
// contigs and a rank to indicate the major srcfeature.
// We don't want to show EST_matches on the alignment view
// since that doesn't make much sense to the end user. If this
// is an EST_match and the feature is an EST then we want to show
// the contig in the alignments. The contig name is part of the
// uniquename in the EST_match
if($node->feature->cvname == 'EST' && $result->cvname == 'EST_match'){
$sql = "SELECT srcfeature_id ".
"FROM {featureloc} ".
"WHERE feature_id = $result->feature_id ".
"ORDER BY rank";
$previous_db = tripal_db_set_active ('chado');
$contig_fid = db_result(db_query($sql));
$sql = "SELECT name FROM {feature} WHERE feature_id = $contig_fid";
$contig_name = db_result(db_query($sql));
tripal_db_set_active($previous_db);
$sql = "SELECT nid ".
"FROM {chado_feature} ".
"WHERE feature_id = $contig_fid";
$contig_nid = db_result(db_query($sql));
// Check if the EST exists as a drupal node. If yes, add a link to
// it. If no, just show the name
if ($contig_nid != 0) {
$sql = "SELECT nid FROM {node} WHERE nid=$contig_nid";
$node_exists = db_result(db_query($sql));
}
$content .= "Alignment to contig $contig_name. " ;
}
elseif($node->feature->cvname == 'contig' && $result->cvname == 'EST_match'){
$sql = "SELECT vid ".
"FROM {node} ".
"WHERE title = '$result->feature_name'".
"ORDER BY vid DESC";
// since the feature name is also the node title we can look it up
$est_node = db_fetch_object(db_query($sql));
$content .= "Aligned EST: $result->feature_name ";
}
else {
$content .= "Aligned $result->cvname: $result->feature_name ";
}
}
}
$content .= "</strong>";
return $content;
}
/*******************************************************************************
* tripal_analysis_unigene_results ()
* Prepare unigene result for the feature shown on the page
*/
function theme_tripal_analysis_unigene_feature_alignments($node) {
$feature = $node->feature;
$obj_feature = tripal_analysis_unigene_get_alignments($feature);
$alignments = $obj_feature->alignments;
if(count($alignments) > 0){
$content = "<div id=\"tripal_analysis_unigene_box\" class=\"tripal_unigene-info-box\">";
// we're showing contig alignments in GBrowse so create a link here for
// that if this feature is a contig
if($node->feature->cvname == 'contig'){
$content .= "<div class=\"tripal_expandableBox\">".
" <h3>ESTs in this contig</h3>".
"</div>";
$content .= "<div class=\"tripal_expandableBoxContent\">";
} else {
$content .= "<div class=\"tripal_expandableBox\">".
" <h3>Alignments</h3>".
"</div>";
$content .= "<div class=\"tripal_expandableBoxContent\">";
}
$content .= "".
"<table class=\"tripal_table_horz\">".
" <tr>".
" <th>Type</th>".
" <th>Feature</th>".
" <th align=\"right\">Position</th>".
" </tr>";
// iterate through each alignment
foreach ($alignments as $result){
// EST alignments in chado use an EST_match type to map ESTs to
// contigs and a rank to indicate the major srcfeature.
// We don't want to show EST_matches on the alignment view
// since that doesn't make much sense to the end user. If this
// is an EST_match and the feature is an EST then we want to show
// the contig in the alignments. The contig name is part of the
// uniquename in the EST_match
if($node->feature->cvname == 'EST' && $result->cvname == 'EST_match'){
$sql = "SELECT srcfeature_id ".
"FROM {featureloc} ".
"WHERE feature_id = $result->feature_id ".
"ORDER BY rank";
$previous_db = tripal_db_set_active ('chado');
$contig_fid = db_result(db_query($sql));
$sql = "SELECT name FROM {feature} WHERE feature_id = $contig_fid";
$contig_name = db_result(db_query($sql));
tripal_db_set_active($previous_db);
$sql = "SELECT nid ".
"FROM {chado_feature} ".
"WHERE feature_id = $contig_fid";
$contig_nid = db_result(db_query($sql));
// Check if the EST exists as a drupal node. If yes, add a link to
// it. If no, just show the name
if ($contig_nid != 0) {
$sql = "SELECT nid FROM {node} WHERE nid=$contig_nid";
$node_exists = db_result(db_query($sql));
}
$content .=
"<tr>".
" <td>Contig</td>".
" <td>";
if ($node_exists != 0) {
$content .= "<a href=\"".url("node/$contig_nid")."\">".
"$contig_name</a>";
} else {
$content .= $contig_name;
}
$content .=
" </td>".
" <td align=\"right\">".
number_format($result->fmin).
"-".
number_format($result->fmax).
" </td>".
"</tr>";
}
elseif($node->feature->cvname == 'contig' &&
$result->cvname == 'EST_match'){
$sql = "SELECT vid ".
"FROM {node} ".
"WHERE title = '$result->feature_name'".
"ORDER BY vid DESC";
// since the feature name is also the node title we can look it up
$est_node = db_fetch_object(db_query($sql));
$content .=
"<tr>".
" <td>EST</td>".
" <td>";
//Check if the EST exists as a drupal node before adding a hyperlink
if ($est_node->vid != 0) {
$content .=
"<a href=\"".url("node/$est_node->vid")."\">".
$result->feature_name.
"</a>";
} else {
$content .= $result->feature_name;
}
$content .=
" </td>".
" <td align=\"right\">".
number_format($result->fmin).
"-".
number_format($result->fmax).
" </td>".
"</tr>";
}
else {
$content .= "".
"<tr>".
" <td>$result->cvname</td>".
" <td>$result->feature_name</td>".
" <td align=\"right\">$result->fmin</td>".
" <td align=\"right\">$result->fmax</td>".
" <td align=\"right\">$result->strand</td>".
"</tr>";
}
}
$content .= "</table>";
/* if this is a contig then get the alignment
if($node->feature->cvname == 'contig'){
// get the directory prefix
$prefix = preg_replace("/^(\d*)\d{3}$/","$1",$node->feature_id);
if(!$prefix){
$prefix = '0';
}
$data_url = variable_get('chado_feature_data_url','sites/default/files/data');
$fh = fopen("$data_url/misc/$prefix/$node->feature->feature_id/alignment.txt", 'r');
if($fh){
$content .= "<b>Alignment:</b><div class=\"tripal_feature_assembly_alignment\"><pre>";
while(!feof($fh)){
$content .= fgets($fh);
}
$content .="</pre></div>";
}
fclose($fh);
}
*/
$content .= "</div></div>";
}
return $content;
}
/*******************************************************************************
*
*/
function tripal_analysis_unigene_get_alignments($map) {
// get the alignments for this feature
$sql = "SELECT F.name as feature_name, FL.fmin, FL.fmax, FL.strand, ".
" FL.phase, CVT.name as cvname, F.feature_id, F.uniquename, ".
" FL.featureloc_id ".
"FROM {featureloc} FL ".
" INNER JOIN Feature F ON F.feature_id = FL.feature_id ".
" INNER JOIN Cvterm CVT ON CVT.cvterm_id = F.type_id ".
"WHERE srcfeature_id = %d AND ".
" NOT(CVT.name = 'match' or CVT.name = 'match_part') ".
"ORDER BY FL.fmin, FL.fmax";
$previous_db = tripal_db_set_active('chado');
$results = db_query($sql,$map->feature_id);
$alignments = array();
$i=0;
while($subfeature = db_fetch_object($results)){
$alignments[$i++] = $subfeature;
}
$additions->alignments = $alignments;
/* get the GO Terms
$sql = "SELECT DISTINCT * FROM {go_results_mview} ".
"WHERE feature_id = %d";
$results = db_query($sql,$map->feature_id);
$go_terms = array();
$i=0;
while($term = db_fetch_object($results)){
$go_terms[$i++] = $term;
}
$additions->go_terms = $go_terms;
// get the feature properties
$sql = "SELECT FP.value,FP.rank,CVT.name,CVT.definition ".
"FROM {featureprop} FP".
" INNER JOIN Cvterm CVT ".
" ON FP.type_id = CVT.cvterm_id ".
"WHERE feature_id = %d";
$results = db_query($sql,$map->feature_id);
$properties = array();
$i=0;
while($property = db_fetch_object($results)){
$properties[$i++] = $property;
}
$additions->properties = $properties;
*/
tripal_db_set_active($previous_db);
return $additions;
}
/************************************************************************
*
*/
function tripal_analysis_unigene_load_organism_unigenes($organism){
// get information about this assemblies and add it to the items in this node
$sql = "SELECT * FROM {organism_unigene_mview} OUM ".
" INNER JOIN {analysis} A ON A.analysis_id = OUM.analysis_id ".
"WHERE OUM.organism_id = %d ".
"ORDER BY A.timeexecuted DESC";
$previous_db = tripal_db_set_active('chado'); // use chado database
$results = db_query($sql,$organism->organism_id);
tripal_db_set_active($previous_db); // now use drupal database
$unigenes = array();
$i=0;
$sql = "SELECT nid FROM {chado_analysis} WHERE analysis_id = %d";
while($unigene = db_fetch_object($results)){
$analysis_id = $unigene->analysis_id;
$c_node = db_fetch_object(db_query($sql,$analysis_id));
if($c_node){
$unigene->nid = $c_node->nid;
}
// add in the properties
$unigene_name = tripal_analysis_get_property($analysis_id,'analysis_unigene_name');
$num_contigs = tripal_analysis_get_property($analysis_id,'analysis_unigene_num_contigs');
$num_reads = tripal_analysis_get_property($analysis_id,'analysis_unigene_num_reads');
$num_clusters = tripal_analysis_get_property($analysis_id,'analysis_unigene_num_clusters');
$num_singlets = tripal_analysis_get_property($analysis_id,'analysis_unigene_num_singlets');
$unigene->unigene_name = $unigene_name->value;
$unigene->num_reads = $num_reads->value;
$unigene->num_clusters = $num_clusters->value;
$unigene->num_contigs = $num_contigs->value;
$unigene->num_singlets = $num_singlets->value;
$unigenes[$i++] = $unigene;
}
return $unigenes;
}
/************************************************************************
*
*/
function tripal_analysis_unigene_load_feature_unigenes($feature){
// first get all the unigene analyses for this organism
$sql = "SELECT * FROM {organism_unigene_mview} OUM ".
" INNER JOIN {analysis} A ON A.analysis_id = OUM.analysis_id ".
"WHERE OUM.organism_id = %d ".
"ORDER BY A.timeexecuted DESC";
$previous_db = tripal_db_set_active('chado'); // use chado database
$results = db_query($sql,$feature->organism_id->organism_id);
tripal_db_set_active($previous_db); // now use drupal database
// iterate through the unigenes and find those that use this feature
$unigenes = array();
$i=0;
$sql = "SELECT nid FROM {chado_analysis} WHERE analysis_id = %d";
while($unigene = db_fetch_object($results)){
$analysis_id = $unigene->analysis_id;
// check if this feature is present in the unigene
$values = array(
'feature_id' => $feature->feature_id,
'analysis_id' => $analysis_id,
);
$hasFeature = tripal_core_chado_select('analysisfeatureprop',array('*'),$values);
// if the feature is present then get information about it
if(sizeof($hasFeature) > 0){
// see if there is a drupal node for this unigene
$c_node = db_fetch_object(db_query($sql,$analysis_id));
if($c_node){
$unigene->nid = $c_node->nid;
}
// add in the properties
$unigene_name = tripal_analysis_get_property($analysis_id,'analysis_unigene_name');
$singlet = tripal_core_get_property('analysisfeature',$analysis_id,'singlet','tripal');
$unigene->unigene_name = $unigene_name->value;
$unigene->singlet = $num_singlets->value;
$unigenes[$i++] = $unigene;
}
}
return $unigenes;
}
/*******************************************************************************
* Tripal Unigene administrative setting form. This function is called by
* tripal_analysis module which asks for an admin form to show on the page
*/
function tripal_analysis_unigene_get_settings() {
// Get an array of node types with internal names as keys
$options = node_get_types('names');
// Add 'chado_feature' to allowed content types for showing unigene results
$allowedoptions ['chado_feature'] = "Show 'ESTs in this contig' on feature pages";
$allowedoptions ['chado_organism'] = "Show assemblies on organism pages";
$form['description'] = array(
'#type' => 'item',
'#value' => t("This option allows user to display the unigene assembly ".
"information. For contigs, this would include an alignment and for ".
"organisms this would be a list of assemblies. Check the box to ".
"enable the display of unigene information. Uncheck to disable."),
'#weight' => 0,
);
$form['tripal_analysis_unigene_setting'] = array(
'#type' => 'checkboxes',
'#options' => $allowedoptions,
'#default_value'=>variable_get('tripal_analysis_unigene_setting',array()),
);
$settings->form = $form;
$settings->title = "Tripal Unigene";
return $settings;
}