| 1 |
<?php |
| 2 |
include_once("inc/settings.php"); |
| 3 |
|
| 4 |
function get_output_url($job_name) { |
| 5 |
return "results/".$job_name."/"; |
| 6 |
} |
| 7 |
|
| 8 |
function get_blast_img($job_name) { |
| 9 |
return get_output_url($job_name).$job_name.".blast.png"; |
| 10 |
} |
| 11 |
|
| 12 |
function get_psiblast_img($job_name) { |
| 13 |
return get_output_url($job_name).$job_name.".psiblast.png"; |
| 14 |
} |
| 15 |
|
| 16 |
function get_blast_img_all($job_name) { |
| 17 |
return get_output_url($job_name).$job_name.".blast.all.png"; |
| 18 |
} |
| 19 |
|
| 20 |
function get_psiblast_img_all($job_name) { |
| 21 |
return get_output_url($job_name).$job_name.".psiblast.all.png"; |
| 22 |
} |
| 23 |
|
| 24 |
function get_report_file($job_name) { |
| 25 |
return get_result_file($job_name,".report"); |
| 26 |
} |
| 27 |
|
| 28 |
function get_blast_file($job_name) { |
| 29 |
return get_result_file($job_name,".pdb-blast.classic.out"); |
| 30 |
} |
| 31 |
|
| 32 |
function get_psiblast_file($job_name) { |
| 33 |
return get_result_file($job_name,".pdb-psiblast.classic.out"); |
| 34 |
} |
| 35 |
|
| 36 |
function get_template_file($job_name) { |
| 37 |
return get_result_file($job_name, ".man.templates"); |
| 38 |
} |
| 39 |
|
| 40 |
// takes an array of template ids and writes a template file for modelling |
| 41 |
function write_template_file($job_name, $templates) { |
| 42 |
$t_file = get_template_file($job_name); |
| 43 |
$fh = fopen($t_file, 'w') or error('Unable to write template file '.$t_file); |
| 44 |
foreach($templates as $num => $pdb) { |
| 45 |
fwrite($fh, $pdb."\n"); |
| 46 |
} |
| 47 |
fclose($fh); |
| 48 |
} |
| 49 |
|
| 50 |
function read_templates($job_name) { |
| 51 |
$result = array(); |
| 52 |
if(file_exists(get_template_file($job_name))) { |
| 53 |
$result = file(get_template_file($job_name), FILE_SKIP_EMPTY_LINES | FILE_IGNORE_NEW_LINES); |
| 54 |
} |
| 55 |
return $result; |
| 56 |
} |
| 57 |
|
| 58 |
// creates the graphical output from the blast and psiblast output files |
| 59 |
function render_blast($job_name) { |
| 60 |
global $num_blast_hits_collapsed; |
| 61 |
global $num_blast_hits_expanded; |
| 62 |
global $eval_cutoff_template_selection; |
| 63 |
$j = escapeshellcmd($job_name); |
| 64 |
$n = $num_blast_hits_collapsed; |
| 65 |
$m = $num_blast_hits_expanded; |
| 66 |
$e = $eval_cutoff_template_selection; |
| 67 |
$w = 900; |
| 68 |
$sc_dir = $GLOBALS['script_dir']; |
| 69 |
$cmd=$sc_dir.'render_blast.pl '.get_blast_file($job_name).' '.$e.' '.$n.' '.$w.' > '.get_blast_img($job_name); |
| 70 |
exec($cmd); |
| 71 |
$cmd=$sc_dir.'render_blast.pl '.get_psiblast_file($job_name).' '.$e.' '.$n.' '.$w.' > '.get_psiblast_img($job_name); |
| 72 |
exec($cmd); |
| 73 |
$cmd=$sc_dir.'render_blast.pl '.get_blast_file($job_name).' '.$e.' '.$m.' '.$w.' > '.get_blast_img_all($job_name); |
| 74 |
exec($cmd); |
| 75 |
$cmd=$sc_dir.'render_blast.pl '.get_psiblast_file($job_name).' '.$e.' '.$m.' '.$w.' > '.get_psiblast_img_all($job_name); |
| 76 |
exec($cmd); |
| 77 |
} |
| 78 |
|
| 79 |
if(isset($_GET['job_name'])) { |
| 80 |
$job_name = $_GET['job_name']; |
| 81 |
} |
| 82 |
|
| 83 |
if(!isset($job_name)) { |
| 84 |
error("No job name specified"); |
| 85 |
} |
| 86 |
|
| 87 |
if(isset($_GET['_submit_check'])) { |
| 88 |
// parse templates |
| 89 |
foreach($_GET as $key => $val) { |
| 90 |
if(substr($key,0,4) == "temp" && !empty($val)) { |
| 91 |
$templates[$key] = $val; |
| 92 |
} |
| 93 |
} |
| 94 |
$custom_templates = trim($_GET['custom_templates']); |
| 95 |
if(isset($custom_templates) && !strlen($custom_templates)==0) { |
| 96 |
$cols = split(",",$custom_templates); |
| 97 |
foreach($cols as $col) { |
| 98 |
$temp = trim($col); |
| 99 |
if(!preg_match("/^[0-9][0-9a-z]{3}[A-Z]$/",$temp)) { |
| 100 |
$form_errors['invalid_custom_template'] = strip_tags($temp); |
| 101 |
} else { |
| 102 |
$templates[] = $temp; # no need to escape shell args because of regexp match above |
| 103 |
} |
| 104 |
} |
| 105 |
} |
| 106 |
if(!isset($templates) || count($templates) == 0) { |
| 107 |
$form_errors['no_templates'] = 1; |
| 108 |
} |
| 109 |
|
| 110 |
// redirect to run_modeling |
| 111 |
if(!isset($form_errors) && isset($templates) && count($templates) > 0) { |
| 112 |
// write to template file |
| 113 |
write_template_file($job_name, $templates); |
| 114 |
// redirect |
| 115 |
header("Location: run_modeling.php?job_name=".$job_name); |
| 116 |
} |
| 117 |
} |
| 118 |
|
| 119 |
render_blast($job_name); |
| 120 |
|
| 121 |
?> |
| 122 |
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> |
| 123 |
<html xmlns="http://www.w3.org/1999/xhtml"> |
| 124 |
|
| 125 |
<head> |
| 126 |
<title>Structure prediction server</title> |
| 127 |
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" /> |
| 128 |
<link rel="stylesheet" type="text/css" href="css/default.css" /> |
| 129 |
|
| 130 |
<script type="text/javascript"> |
| 131 |
// preload images |
| 132 |
|
| 133 |
blast_img = new Image(); |
| 134 |
blast_img.src = "<? echo get_blast_img($job_name); ?>"; |
| 135 |
|
| 136 |
blast_img_all = new Image(); |
| 137 |
blast_img_all.src = "<? echo get_blast_img_all($job_name); ?>"; |
| 138 |
|
| 139 |
psiblast_img = new Image(); |
| 140 |
psiblast_img.src = "<? echo get_psiblast_img($job_name); ?>"; |
| 141 |
|
| 142 |
psiblast_img_all = new Image(); |
| 143 |
psiblast_img_all.src = "<? echo get_psiblast_img_all($job_name); ?>"; |
| 144 |
|
| 145 |
// set up image toggling |
| 146 |
|
| 147 |
var blast_status = true; |
| 148 |
var psiblast_status = true; |
| 149 |
|
| 150 |
function toggle_blast() { |
| 151 |
blast_status = !blast_status; |
| 152 |
if(blast_status) { |
| 153 |
document.getElementById("btn_blast").src = 'images/control_blue_up.png'; |
| 154 |
document.getElementById('img_blast').src = '<? echo get_blast_img_all($job_name); ?>'; |
| 155 |
} else { |
| 156 |
document.getElementById("btn_blast").src= 'images/control_blue_down.png'; |
| 157 |
document.getElementById('img_blast').src = '<? echo get_blast_img($job_name); ?>'; |
| 158 |
} |
| 159 |
} |
| 160 |
|
| 161 |
function toggle_psiblast() { |
| 162 |
psiblast_status = !psiblast_status; |
| 163 |
if(!psiblast_status) { |
| 164 |
document.getElementById("btn_psiblast").src='images/control_blue_up.png' |
| 165 |
document.getElementById('img_psiblast').src = '<? echo get_psiblast_img_all($job_name); ?>'; |
| 166 |
} else { |
| 167 |
document.getElementById("btn_psiblast").src='images/control_blue_down.png' |
| 168 |
document.getElementById('img_psiblast').src = '<? echo get_psiblast_img($job_name); ?>'; |
| 169 |
} |
| 170 |
} |
| 171 |
|
| 172 |
// show/hide parts of template table |
| 173 |
|
| 174 |
var show_min = <? echo $num_rows_visible_in_template_table; ?>; |
| 175 |
var table_status = true; |
| 176 |
|
| 177 |
function toggle_table() { |
| 178 |
|
| 179 |
tbl = document.getElementById("template_table"); |
| 180 |
var len = tbl.rows.length; |
| 181 |
|
| 182 |
if(table_status) { |
| 183 |
document.getElementById("btn_table").src='images/control_blue_up.png' |
| 184 |
for(i=1 ; i< len; i++){ |
| 185 |
tbl.rows[i].style.display = ""; |
| 186 |
} |
| 187 |
} else { |
| 188 |
document.getElementById("btn_table").src='images/control_blue_down.png' |
| 189 |
for(i=show_min+1 ; i< len; i++){ |
| 190 |
tbl.rows[i].style.display = "none"; |
| 191 |
} |
| 192 |
} |
| 193 |
table_status = !table_status; |
| 194 |
} |
| 195 |
|
| 196 |
</script> |
| 197 |
|
| 198 |
</head> |
| 199 |
<body> |
| 200 |
<?php include_once("inc/owl_header.inc.php") ?> |
| 201 |
<div class="main-content"> |
| 202 |
<?php |
| 203 |
echo 'Job name='.$job_name.' [<a href="'.get_output_url($job_name).'">see raw output</a>] '; |
| 204 |
echo '[<a href="'.get_output_url($job_name).$job_name.'.out.log">output log</a>]<br/>'; |
| 205 |
?> |
| 206 |
|
| 207 |
<h3>Blast result</h3> |
| 208 |
<img id="img_blast" src="<? echo get_blast_img($job_name); ?>" border="0" align="left" /> |
| 209 |
<a href="Javascript:toggle_blast();"><img id="btn_blast" title="show/hide more hits" src="images/control_blue_down.png" border="0" style="margin-top:10px;" /></a> |
| 210 |
<div style="clear:both;"></div> |
| 211 |
|
| 212 |
<h3>Psiblast result</h3> |
| 213 |
<img id="img_psiblast" src="<? echo get_psiblast_img($job_name); ?>" border="0" align="left" /> |
| 214 |
<a href="Javascript:toggle_psiblast()"><img id="btn_psiblast" title="show/hide more hits" src="images/control_blue_down.png" border="0" style="margin-top:10px;" /></a> |
| 215 |
<div style="clear:both;"></div> |
| 216 |
|
| 217 |
<h3>Select templates</h3> |
| 218 |
<form action="<?php $_SERVER['PHP_SELF'] ?>" method="GET" enctype="multipart/form-data"> |
| 219 |
<input type="hidden" name="job_name" value="<? echo $job_name; ?>"> |
| 220 |
<input type="hidden" name="_submit_check" value="1"> |
| 221 |
<table border=1 id="template_table" align="left" class="template_table"> |
| 222 |
<tbody> |
| 223 |
|
| 224 |
<?php |
| 225 |
$lines = file(get_report_file($job_name)); |
| 226 |
|
| 227 |
if(file_exists(get_template_file($job_name))) { |
| 228 |
# modeling had already been submitted, show templates being used |
| 229 |
$temps = read_templates($job_name); |
| 230 |
|
| 231 |
if(sizeof($lines) <= 2) { |
| 232 |
echo 'No templates found!<br/><br/>'; |
| 233 |
// echo "<p>Templates used for modeling: "; |
| 234 |
// if(count($temps) == 0) { |
| 235 |
// echo "?"; |
| 236 |
// } else { |
| 237 |
// foreach($temps as $temp) { |
| 238 |
// echo $temp.' '; |
| 239 |
// } |
| 240 |
// echo "<br/>"; |
| 241 |
// } |
| 242 |
// echo '</p>'; |
| 243 |
$no_temps = 1; |
| 244 |
} else { |
| 245 |
for($l = 1; $l < count($lines); $l++) { |
| 246 |
$line = $lines[$l]; |
| 247 |
$fields = explode("\t", $line); |
| 248 |
$pdb = $fields[0]; |
| 249 |
echo "<tr"; |
| 250 |
if($l-1 > $num_rows_visible_in_template_table) echo ' style="display:none" '; |
| 251 |
echo ">"; |
| 252 |
if($l != 1) { |
| 253 |
echo '<td>'; |
| 254 |
if(in_array($pdb,$temps)) { |
| 255 |
$key = array_search($pdb, $temps); |
| 256 |
unset($temps[$key]); |
| 257 |
echo '<img src="images/tick.png" alt="yes" />'; |
| 258 |
} |
| 259 |
echo '</td>'; |
| 260 |
} else { |
| 261 |
echo '<th></th>'; |
| 262 |
} |
| 263 |
for($i = 0; $i < count($fields); $i++){ |
| 264 |
if($i < 5 || $i > 6) { # skip GTG fields |
| 265 |
if($l == 1) { |
| 266 |
echo "<th>"; |
| 267 |
$field = $fields[$i]; |
| 268 |
if(strpos($field, "scop id") !== false) $field = "scop"; |
| 269 |
if(strpos($field, "title") !== false) $field = "description"; |
| 270 |
echo $field; |
| 271 |
echo "</th>"; |
| 272 |
} else { |
| 273 |
echo "<td>"; |
| 274 |
$field = trim($fields[$i]); |
| 275 |
if($i == 0) $field = '<a href="http://pdbwiki.org/index.php/'.substr($pdb,0,4).'">'.$field.'</a>'; |
| 276 |
if($i == 7) $field = '<a href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sccs='.$field.'">'.$field.'</a>'; |
| 277 |
echo $field; |
| 278 |
echo "</td>"; |
| 279 |
} |
| 280 |
} |
| 281 |
} |
| 282 |
echo "</tr>\n"; |
| 283 |
} |
| 284 |
} |
| 285 |
# link to wait for results page |
| 286 |
} else { |
| 287 |
|
| 288 |
# do template selection |
| 289 |
|
| 290 |
if(sizeof($lines) <= 2) { |
| 291 |
echo 'No templates found!<br/><br/>'; |
| 292 |
//echo '<tr><td>Enter a template to use: <input type="text" name="temp1"> e.g. 1tdrA</td></tr>'; |
| 293 |
$no_temps = 1; |
| 294 |
} else { |
| 295 |
|
| 296 |
for($l = 1; $l < count($lines); $l++) { |
| 297 |
$line = $lines[$l]; |
| 298 |
$fields = explode("\t", $line); |
| 299 |
$pdb = $fields[0]; |
| 300 |
echo "<tr"; |
| 301 |
if($l-1 > $num_rows_visible_in_template_table) echo ' style="display:none" '; |
| 302 |
echo ">"; |
| 303 |
if($l != 1) { |
| 304 |
echo '<td><INPUT type="checkbox" name="temp'.$l.'" value="'.$pdb.'"></td>'; |
| 305 |
} else { |
| 306 |
echo '<th></th>'; |
| 307 |
} |
| 308 |
for($i = 0; $i < count($fields); $i++){ |
| 309 |
if($i < 5 || $i > 6) { # skip GTG fields |
| 310 |
if($l == 1) { |
| 311 |
echo "<th>"; |
| 312 |
$field = $fields[$i]; |
| 313 |
if(strpos($field, "scop id") !== false) $field = "scop"; |
| 314 |
if(strpos($field, "title") !== false) $field = "description"; |
| 315 |
echo $field; |
| 316 |
echo "</th>"; |
| 317 |
} else { |
| 318 |
echo "<td>"; |
| 319 |
$field = trim($fields[$i]); |
| 320 |
if($i == 0) $field = '<a href="http://pdbwiki.org/index.php/'.substr($pdb,0,4).'">'.$field.'</a>'; |
| 321 |
if($i == 7) $field = '<a href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sccs='.$field.'">'.$field.'</a>'; |
| 322 |
echo $field; |
| 323 |
echo "</td>"; |
| 324 |
} |
| 325 |
} |
| 326 |
} |
| 327 |
echo "</tr>\n"; |
| 328 |
} |
| 329 |
} |
| 330 |
|
| 331 |
} |
| 332 |
?> |
| 333 |
</tbody> |
| 334 |
</table><? |
| 335 |
if(!isset($no_temps)) { |
| 336 |
echo '<a href="Javascript:toggle_table();"><img id="btn_table" title="show/hide more templates" src="images/control_blue_down.png" border="0"/></a>'; |
| 337 |
echo '<div style="clear:both;"></div>'; |
| 338 |
} |
| 339 |
?> |
| 340 |
<?php if(!file_exists(get_template_file($job_name))) { |
| 341 |
# input user templates |
| 342 |
echo '<table class="template_table"><tbody><tr><td>'; |
| 343 |
echo 'Additional templates to use: <input type="text" name="custom_templates"> e.g. 1tdrA, 7dfrA<br/>'; |
| 344 |
echo '</td></tr></tbody></table>'; |
| 345 |
|
| 346 |
# error messages |
| 347 |
if(isset($form_errors['invalid_custom_template'])) { |
| 348 |
echo '<span class="error_msg">Invalid template string. Please enter a comma separated list of pdb codes including chain identifier, e.g. 1tdrA </span><br/>'; |
| 349 |
} |
| 350 |
if(isset($form_errors['no_templates'])) { |
| 351 |
echo '<span class="error_msg">Please specify at least one template</span><br/>'; |
| 352 |
} |
| 353 |
|
| 354 |
# submit button |
| 355 |
echo '<p><input type="submit" value="Start prediction"></p>'; |
| 356 |
} else { |
| 357 |
# output user templates |
| 358 |
echo '<table class="template_table"><tbody><tr><td>'; |
| 359 |
echo 'Additional templates used: '; |
| 360 |
if(isset($temps) && count($temps) > 0) { |
| 361 |
foreach($temps as $temp) { |
| 362 |
echo "$temp "; |
| 363 |
} |
| 364 |
} else { |
| 365 |
echo 'none'; |
| 366 |
} |
| 367 |
echo '<br/>'; |
| 368 |
echo '</td></tr></tbody></table><br/>'; |
| 369 |
|
| 370 |
echo 'Modeling job has been previously submitted with the templates marked above.'; |
| 371 |
echo '<div class="buttons">'; |
| 372 |
echo '<a href="wait_for_modeling_result.php?job_name='.$job_name.'"><img src="images/eye.png" alt="" /> Check results</a>'; |
| 373 |
} |
| 374 |
?> |
| 375 |
</form> |
| 376 |
<p> |
| 377 |
<div class="buttons"> |
| 378 |
<a href="index.php"><img src="images/new.png" alt="" /> Start new job</a> |
| 379 |
</div> |
| 380 |
<div style="clear:both;"></div> |
| 381 |
</div> |
| 382 |
</body> |
| 383 |
</html> |
