Blast best hit report updated

tripal_analysis_blast/tripal_analysis_blast.module

@@ -100,6 +100,10 @@ function tripal_analysis_blast_theme () {
 		'tripal_feature_blast_results' => array(
 			'arguments' =>  array('node'=> null),
 		   'template' => 'tripal_feature_blast_results',
+		),
+		'tripal_analysis_blast_report' => array(
+			'arguments' =>  array('report_object'=> null),
+		   'template' => 'tripal_analysis_blast_report',
 		)
 	);
 }
@@ -552,7 +556,24 @@ function chado_analysis_blast_load($node){
    $query_type      = tripal_analysis_get_property($analysis->analysis_id,'analysis_blast_query_type');	
    $query_uniquename= tripal_analysis_get_property($analysis->analysis_id,'analysis_blast_query_uniquename');	
    $blastfile_ext   = tripal_analysis_get_property($analysis->analysis_id,'analysis_blast_blastfile_ext');	
-
+	
+   // check if there exists a best hit report. if yes, reuturn the report url
+   $select = array(
+      'analysisfeature_id' => array(
+         'analysis_id' => $analysis_id,
+      ), 
+      'type_id' => array(
+         'name' => 'analysis_blast_besthit_query',
+         'cv_id' => array(
+            'name' => 'tripal'
+         ),
+      ),         
+   );
+   $blast_report = tripal_core_chado_select('analysisfeatureprop',array('analysisfeatureprop_id'),$select);
+	if ($blast_report) {
+		$report_url = url("tripal_blast_report/".$analysis->analysis_id."/1/0/0/20");
+		$analysis->blast_report = $report_url;
+	}
 
    $analysis->tripal_analysis_blast->blastdb         = $blastdb->value;
    $analysis->tripal_analysis_blast->blastfile       = $blastfile->value;	

tripal_analysis_blast/tripal_analysis_blast_htmlreport.inc

@@ -1,12 +1,9 @@
 <?php
 
 function tripal_get_blast_report ($analysis_id, $currentpage, $sort, $descending, $per_page) {
-	/*
-	if (!tripal_check_permission_by_analysis_id($analysis_id)) {
-		$html_out = "Access denied. You are not authorized to access this report.";
-		return $html_out;
-	}
-   */
+
+	$report_object = new stdClass;
+	
 	$symbol = "&and;";
 	$sort_key = "ASC";
 	if ($descending == 1) {
@@ -38,12 +35,9 @@ function tripal_get_blast_report ($analysis_id, $currentpage, $sort, $descending
                 WHERE A.analysis_id = %d
                 AND type_id= (SELECT cvterm_id 
                                            FROM {cvterm} 
-                                           WHERE name = 'analysis_blast_settings')";
+                                           WHERE name = 'analysis_blast_blastdb')";
 	$analysis = db_fetch_object(db_query($sql, $analysis_id));
-	
-	// Parse the blast settings
-	$blastsettings = explode("|", $analysis->value);
-	$db_id = $blastsettings [0];
+	$db_id = $analysis->value;
 	
 	// Get db 'urlprefix'
 	$sql = "SELECT urlprefix FROM {db} WHERE db_id=%d";
@@ -82,17 +76,15 @@ function tripal_get_blast_report ($analysis_id, $currentpage, $sort, $descending
 		$no_page ++;
 	}
 	$first_item = ($currentpage - 1)* $per_page;
-	$url = url(drupal_get_path('theme', 'tripal')."/images/ajax-loader.gif");
-	$html_out .= "<div id=\"tripal_ajaxLoading\" style=\"display:none\">".
-                   "<div id=\"loadingText\">Loading...</div>".
-                   "<img src=\"$url\"></div>";
-	$html_out .= "<div id=\"blast-hits-report\">
-                             <strong>Analysis Date: </strong>$analysis->time (<a href=$ana_url>$analysis->name</a>)<br>
-                             There are <strong>$counter</strong> records. <div id=tripal_blast_report_current_page>page <strong>$currentpage</strong> of <strong>$no_page</strong></div>
-	                          <table id=\"tripal_analysi_blast-report-table\" class=\"tripal_analysis_blast-table tripal-table tripal-table-horz\">
-	                            <tr class=\"tripal_analysis_blast-table-odd-row tripal-table-odd-row\">";
 
-	$html_out .= "  <th nowrap>";	if ($sort == 0) {$html_out .= $symbol;}
+	$report_object->time = $analysis->time;
+	$report_object->name = $analysis->name;
+	$report_object->url = $ana_url;
+	$report_object->counter = $counter;
+	$report_object->currentpage = $currentpage;
+	$report_object->no_page = $no_page;
+	$report_object->symbol = $symbol;
+	$report_object->sort = $sort;
 
 	// Construct URL path for different sorting column
 	$path =  "tripal_blast_report/$analysis_id/1/0/";
@@ -103,7 +95,7 @@ function tripal_get_blast_report ($analysis_id, $currentpage, $sort, $descending
 	}
 	$path .= "/$per_page";
 	$url_path = url ($path);
-	$html_out.="<a href=$url_path>Query</a></th><th nowrap>";	if ($sort == 1) {$html_out .= $symbol;}
+	$report_object->byQuery = $url_path;
 
 	$path =  "tripal_blast_report/$analysis_id/1/1/";
 	if ($descending == 0 && $sort == 1) {
@@ -113,7 +105,7 @@ function tripal_get_blast_report ($analysis_id, $currentpage, $sort, $descending
 	}
 	$path .= "/$per_page";
 	$url_path = url ($path);
-	$html_out.="<a href=$url_path>Match Name</a></th><th nowrap>";	if ($sort == 2) {$html_out .= $symbol;}
+	$report_object->byMatchName =$url_path;
 
 	$path =  "tripal_blast_report/$analysis_id/1/2/";
 	if ($descending == 0 && $sort == 2) {
@@ -123,7 +115,7 @@ function tripal_get_blast_report ($analysis_id, $currentpage, $sort, $descending
 	}
 	$path .= "/$per_page";
 	$url_path = url ($path);
-	$html_out.="<a href=$url_path>Description</a></th><th nowrap>";	if ($sort == 3) {$html_out .= $symbol;}
+	$report_object->byDescription = $url_path;
 
 	$path =  "tripal_blast_report/$analysis_id/1/3/";
 	if ($descending == 0 && $sort == 3) {
@@ -133,8 +125,8 @@ function tripal_get_blast_report ($analysis_id, $currentpage, $sort, $descending
 	}
 	$path .= "/$per_page";
 	$url_path = url ($path);
-	$html_out.="<a href=$url_path>E-value</a></th><th nowrap>";	if ($sort == 4) {$html_out .= $symbol;}
-
+	$report_object->byEvalue = $url_path;
+	
 	$path =  "tripal_blast_report/$analysis_id/1/4/";
 	if ($descending == 0 && $sort == 4) {
 		$path .= "1";
@@ -143,7 +135,7 @@ function tripal_get_blast_report ($analysis_id, $currentpage, $sort, $descending
 	}
 	$path .= "/$per_page";
 	$url_path = url ($path);
-	$html_out.="<a href=$url_path>%Identity</a></th><th nowrap>";	if ($sort == 5) {$html_out .= $symbol;}
+	$report_object->byIdentity = $url_path;
 
 	$path =  "tripal_blast_report/$analysis_id/1/5/";
 	if ($descending == 0 && $sort == 5) {
@@ -153,9 +145,7 @@ function tripal_get_blast_report ($analysis_id, $currentpage, $sort, $descending
 	}
 	$path .= "/$per_page";
 	$url_path = url ($path);
-	$html_out.="<a href=$url_path>Length</a></th>";
-
-	$html_out .=      "</tr>";
+	$report_object->byLength = $url_path;
 
 	// Get table content
 	$sql = "SELECT value
@@ -163,6 +153,7 @@ function tripal_get_blast_report ($analysis_id, $currentpage, $sort, $descending
 	             WHERE analysisfeature_id = %d 
 	             AND type_id = (SELECT cvterm_id FROM {cvterm} WHERE name = '%s' AND cv_id = (SELECT cv_id FROM {cv} WHERE name = 'tripal'))";
 	$j = 0;
+	$hits = array ();
 	for ($i = $first_item; $i < $first_item +$per_page; $i ++) {
 		$previous_db = tripal_db_set_active('chado');
 		$query = db_result(db_query($sql, $analysisfeatureSet[$i], 'analysis_blast_besthit_query'));
@@ -181,63 +172,34 @@ function tripal_get_blast_report ($analysis_id, $currentpage, $sort, $descending
 	 	if($j % 2 == 0 ){
          $class = 'tripal_analysis_blast-table-even-row tripal-table-even-row';
       }
+      $hit = new stdClass();
 		if ($query) {
-			$html_out .= "<tr class=\"$class\">
-		                           <td nowrap><a href=$q_url>$query</a></td>
-		                           <td nowrap><a href=\"$urlprefix$match\" target=\"_blank\">$match</td>
-		                           <td>$desc</td>
-		                           <td nowrap>$evalue</td>
-		                           <td nowrap>$identity</td>
-		                           <td nowrap>$length</td>
-		                         </tr>";
+			$hit->class = $class;
+			$hit->q_url = $q_url;
+			$hit->query = $query;
+			$hit->urlprefix = $urlprefix;
+			$hit->match = $match;
+			$hit->desc = $desc;
+			$hit->evalue = $evalue;
+			$hit->identity = $identity;
+			$hit->length = $length;
+			$hits [$j] = $hit;
 		}
 		$j ++;
 	}
+	$report_object->hits = $hits;
 	
 	// The number of items to show on the page
 	$path =  "tripal_blast_report/$analysis_id/1/$sort/$descending/";
-	$html_out .= '</table>
-	                           <div id=tripal_blast_report_per_page>Show ';
-	if ($per_page == 10) {
-		$html_out .= "<strong>10</strong> | ";
-	} else {
-		$url_path = url($path."10");
-		$html_out .= "<a href=$url_path>10</a> | ";
-	}
-	if ($per_page == 20) {
-		$html_out .= "<strong>20</strong> | ";
-	} else {
-		$url_path = url($path."20");
-		$html_out .= "<a href=$url_path>20</a> | ";
-	}
-	if ($per_page == 50) {
-		$html_out .= "<strong>50</strong> | ";
-	} else {
-		$url_path = url($path."50");
-		$html_out .= "<a href=$url_path>50</a> | ";
-	}
-	if ($per_page == 100) {
-		$html_out .= "<strong>100</strong> | ";
-	} else {
-		$url_path = url($path."100");
-		$html_out .= "<a href=$url_path>100</a> | ";
-	}
-	if ($per_page == 200) {
-		$html_out .= "<strong>200</strong> | ";
-	} else {
-		$url_path = url($path."200");
-   	$html_out .= "<a href=$url_path>200</a>";
-	}
+	$report_object->path = $path;
+	$report_object->per_page = $per_page;
 
 	// Make AJAX call to update the  page which user selected 
-   $html_out .= ' records per page
-	                           </div>
-	                           <div id=tripal_blast_report_pager>page
-	                             <select id=tripal_blast_report_page_selector onChange="tripal_update_best_hit_report(this,'.$analysis_id.','.$sort.','.$descending.','.$per_page.')">';
-   for ($i = 1; $i <= $no_page; $i ++) {
-   	$html_out .= "<option value=$i>$i</option>";
-   }	                           
-   $html_out .=  '</select></div>
-	                        </div>';
-	return $html_out;
+	$report_object->analysis_id = $analysis_id;
+	$report_object->sort = $sort;
+	$report_object->descending = $descending;
+	$report_object->per_page = $per_page;
+	$report_object->no_page = $no_page;
+
+    return theme('tripal_analysis_blast_report',$report_object);
 }