readblast.php

<?php
include("template.php");
include("parseBlast.php");
############################## parse BLAST results ##################################
$jobtitle=$_GET['JOBTITLE'];
$infile=$_GET['RESULT'];
$blast=parseBlast($infile);

PHP_VERSION < '4.2.0' && mt_srand((double)microtime() * 1000000);
$jsonfile="temp/blast.json".date("YmdHis").mt_rand(1000,9999);
$jsonfile2="temp/blast.json2".date("YmdHis").mt_rand(1000,9999);
file_put_contents($jsonfile,plotdata($blast,50));
file_put_contents($jsonfile2,plotdata2($blast,250));
######################################################################################


?>

<?php echoHtmlHead("BLAST result"); ?>
<script type="text/javascript" src="js/scrolltop.js"></script>
<link rel="stylesheet" type="text/css" href="css/lrtk.css">
<script type="text/javascript" src="js/blast_results.js"></script>

<link rel="stylesheet" type="text/css" href="css/blast_results.css" media="all" />
<script type="text/javascript" src="js/jquery-ui/jquery-ui.min.js"></script>
<script type="text/javascript" src="js/d3.js"></script>
<script type="text/javascript" src="js/d3.geom.js"></script>
<script type="text/javascript" src="js/d3.layout.js"></script>
<script type="text/javascript" src="js/json_parse.js"></script>
<script type="text/javascript" src="js/blast_plot.js"></script>
<?php echo "<script type=\"text/javascript\">
		var seqlen=".$blast['query_seq_length'].";
		var jfile='".$jsonfile."';
                var jfile2='".$jsonfile2."';
		</script>"; 
?>
<style type="text/css">
@import url("js/jquery-ui/jquery-ui.css");
.ui-widget {
                        font: 14px Helvetica Neue;
                } 

#blast_plot{
	position:relative;
}
.chart{
	font: 10px sans-serif;
	border:1px solid #888;
}

#info{
	display:none;
	position:absolute;
	z-index:100;
	border:1px solid #555;
	background-color:#eee;
	padding:2px 5px;
	font:12px sans-serif;
}

circle.node {
  			stroke: #fff;
  			stroke-width: 1.5px;
  			fill:blue;
  			cursor: pointer;
		}
		line.link {
  			stroke: #999;
  			stroke-opacity: .6;
		}
		.slide{
			width: 900px;
			margin-bottom: 10px;
		}
</style>
<?php echoPageHeader(); ?>

<!-- ================================== main content start ===================================== -->
<div id="main">
	<div id="jobtitle"><?php echo $jobtitle; ?></div>

	<div id="blast_summary">
		<div id="query_summary">
			<dl><dt>Query ID</dt><dd><?php echo $blast['query_seq_name']; ?></dd>
		 		<dt>Query Length</dt><dd><?php echo $blast['query_seq_length']; ?></dd>
			</dl>
		</div>
		<div id="db_summary">
			<dl><dt>Database Name</dt><dd><?php echo $blast['db_name']; ?></dd>
		 		<dt>Description</dt><dd><?php echo $blast['db_desc']; ?></dd>
			</dl>
		</div>
	</div>
	
	<div id="blast_title"><a href="#" onclick="toggle(['blast_plot'])">Graphic Summary</a></div>
	<div id="blast_plot" class="blast_panel expand">
		<script type="text/javascript">showPlot(jfile,document.getElementById("blast_plot"));</script>
	</div>
	<div id="blast_plot2" class="blast_panel expand">
		<div id="ball"></div>
		<script type="text/javascript">
//======================================================
showPlot2(jfile2,"#ball");
//=====================================================
		</script>
		<div id="score-pan" class="slide">Max Score: <span></span><div id="score"></div></div> 
   		<div id="e-pan" class="slide">Min E-value: <span></span><div id="e"></div></div>
    		<div id="coverage-pan" class="slide">Hit Coverage: <span></span><div id="coverage"></div></div>
    		<div id="acc"></div>
		<span class="button" onclick="getSeq()">get selected sequences</span>
	</div>
	<div class="blast_title"><a href="#" onclick="toggle(['blast_brief'])">Descriptions</a></div>
	<div id="blast_brief" class="blast_panel expand">
	<table class="brief">
		<caption>Sequences producing significant alignments:</caption>
		<thead>
			<tr class="first">
				<th>Accession</th>
				<th>Description</th>
				<th>Max Score</th>
				<th>E value</th>
				<th>Identity</th>
				<th>Coverage</th>			
			</tr>		
		</thead>
		<tbody>
		<?php 
			$i=0;
			foreach($blast['hit'] as $hit) {
//print_r($hit);
				echo "<tr>\n";
				echo "<td class=\"l\"><a href=\"detail.php?acc=".$hit['acc']."\" title=\"Show report for ".$hit['acc']."\" onclick='loading()'>".$hit['acc']."</a></td>\n";
				echo "<td class=\"l\">".substr($hit['desc'],0,65)."...</td>\n";
				echo "<td><a href=\"#$i\" title=\"Show alignment for ".$hit['acc']."\">".$hit['hsp'][0]['score']."</a></td>\n";
				echo "<td>".$hit['hsp'][0]['e']."</td>\n";
				echo "<td>".$hit['hsp'][0]['identity']."</td>\n";
				echo "<td>".round(coverage($hit)/$blast['query_seq_length']*100,2)."%</td>\n";

				echo "</tr>\n";
				$i++;	
			}
		?>		
			<tr>
				<td></td>			
			</tr>		
		</tbody>
	</table>
	</div>

	<div class="blast_title"><a href="#" onclick="toggle(['blast_detail'])">Alignments</a></div>
	<div id="blast_detail" class="blast_panel">
	<div id='handle'>
	<input type="checkbox" onclick="selectBox(this,'getSeqAlignment')">select all
	<span class="button" onclick="getSeq()">get selected sequences</span>
	<!--<span class="button">make tree</span>-->
	</div>
	<form name="getSeqAlignment" method="post" action="search2.php">
	
	<?php 
	$i=0;	
	foreach($blast['result'] as $hit) {
		echo "<div class='aln'><a name='".$blast['hit'][$i]['acc']."'><pre>\n";
		echo "&gt;<input name=\"accs[]\" id=\"".$blast['hit'][$i]['acc']."\" value=\"".$blast['hit'][$i]['acc']."\" type=\"checkbox\">";
		echo "<a title=\"Show report for ".$blast['hit'][$i]['acc']."\" href=\"detail.php?acc=".$blast['hit'][$i]['acc']."\" onclick='loading()'>".$blast['hit'][$i]['acc']."</a><a name=\"$i\"></a>";
		echo substr($hit, strpos($hit," "));
		echo "</pre></div>\n";
		$i++;
	}
	?>
		<input type="hidden" name="fromblast" value="fromblast">
	</form>
	
	</div>
	
	<div id="blast_info" class="blast_panel expand">
		<pre>
		<?php
			echo $info;
		?>
		</pre>
	</div>
</div>
<div id="info"></div>
<div style="DISPLAY: none" id='goTopBtn'><img border=0 src="images/lanren_top.jpg"></div>
<script type="text/javascript">goTopEx();</script>
<!-- =================================== main content end ======================================== -->

<?php echoPageFooter(); ?>