modelit/server/show_modeling_result.php

<?php
include_once("inc/settings.php");

if(isset($_GET['job_name'])) {
        $job_name = $_GET['job_name'];
}

if(!isset($job_name)) {
        $errors['no_job_name'] = 1;
}

function get_output_url($job_name) {
        return "results/".$job_name."/";
}

function get_orig_pdb_file($job_name) {
        return get_result_file($job_name, ".reconstructed.pdb");
}

function get_renum_pdb_file($job_name) {
        return get_result_file($job_name, ".renum.pdb");
}

function get_pdb_url($job_name) {
        if(file_exists(get_renum_pdb_file($job_name))) {
                return get_output_url($job_name).$job_name.".renum.pdb";
        } else {
                return get_output_url($job_name).$job_name.".reconstructed.pdb";
        }
}

function get_img_file($job_name) {
        return get_result_file($job_name, ".png");
}

function get_img_url($job_name) {
        return get_output_url($job_name).$job_name.".png";
}

function get_blast_img($job_name) {
        return get_output_url($job_name)."blast.png";   
}

function get_psiblast_img($job_name) {
        return get_output_url($job_name)."psiblast.png";                
}

function get_ss_compare_file($job_name) {
        return get_result_file($job_name, ".ss.compare");
}

function get_ss_compare_img_file($job_name) {
        return get_result_file($job_name, ".ss.compare.png");
}

function get_ss_compare_img_url($job_name) {
        return get_output_url($job_name).$job_name.".ss.compare.png";
}

function get_ss_pred_file($job_name) {
        return get_result_file($job_name, ".horiz");
}

function get_template_file($job_name) {
        return get_result_file($job_name, ".man.templates");
}

function read_templates($job_name) {
        $result = array();
        if(file_exists(get_template_file($job_name))) {
                $result = file(get_template_file($job_name), FILE_SKIP_EMPTY_LINES);
        }
        return $result;
}

function get_seq_file($job_name) {
        return get_result_file($job_name, ".fa");
}

function get_full_seq_file($job_name) {
        return get_result_file($job_name, ".full.fa");
}

function read_sequence($job_name) {
        if(file_exists(get_seq_file($job_name))) {
                $lines = file(get_seq_file($job_name));
                if(count($lines) < 2) {
                        return "";
                } else {
                        $seq = $lines[1];
                        return $seq;
                }
        } else {
                return "";
        }
}

function read_full_sequence($job_name) {
        if(file_exists(get_full_seq_file($job_name))) {
                $lines = file(get_full_seq_file($job_name));
                if(count($lines) < 2) {
                        return "";
                } else {
                        $seq = $lines[1];
                        return $seq;
                }
        } else {
                return "";
        }
}

function read_subseq_interval($job_name) {
        if(file_exists(get_full_seq_file($job_name))) {
                $lines = file(get_full_seq_file($job_name));
                if(count($lines) < 2) {
                        return "";
                } else {
                        $header = $lines[0];
                        return trim(substr($header,1));
                }
        } else {
                return "";
        }
}

function print_seq($seq) {
        echo '<div class="sequence">';
        $upper = 1;
        for($i = 0; $i < strlen($seq); $i++) {
                if($i > 0 && $i % 100 == 0) {
                        echo '<br/>';
                }
                if($upper && strtoupper($seq[$i])!=$seq[$i]) {
                        $upper = 0;
                        echo '<span class="fadeseq">';
                }
                if(!$upper && strtoupper($seq[$i])==$seq[$i]) {
                        $upper = 1;
                        echo '</span>';
                }
                echo $seq[$i];
        }
        echo '</div>';
}

function create_png_preview($job_name) {
        $j = escapeshellcmd($job_name);
        $pdb_file = get_orig_pdb_file($job_name);
        $png_file = get_img_file($job_name);
        
        $width = 480;
        $height = 360;
        $cmd = $GLOBALS['script_dir']."pdb2png.sh ".$pdb_file." ".$width." ".$height." ".$png_file;
        exec($cmd);     
}

function create_ss_compare_img($job_name) {
        $cmp_file = escapeshellcmd(get_ss_compare_file($job_name));
        $img_file = escapeshellcmd(get_ss_compare_img_file($job_name));
        $width = 880;
        $cmd = $GLOBALS['script_dir']."render_ss_compare.pl $cmp_file $width > $img_file";
        $result = exec($cmd);
        //echo $cmd."<br/>";
}

function renum_pdb($job_name, $offset) {
        $offs = $offset + 1; # needed because script works unintuitively, taking new starting residue instead of offset
        $old_file = escapeshellcmd(get_orig_pdb_file($job_name));
        $new_file = escapeshellcmd(get_renum_pdb_file($job_name));
        $chain = 'A';
        $cmd = $GLOBALS['script_dir']."renumpdb.py ".$offs." ".$old_file." ".$new_file." ".$chain;
        $result = exec($cmd);
}

?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">

<head>
  <title>Structure prediction server</title>
  <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
  <link rel="stylesheet" type="text/css" href="css/default.css" />

  <script type="text/javascript">
      
    function toggle_fieldset(infobox_id) {
        var ib_obj = document.getElementById(infobox_id);
        var fs_obj = ib_obj.getElementsByTagName('fieldset')[0];
        var div_obj = fs_obj.getElementsByTagName('div')[0];
        var d = div_obj.style.display;
        if(d == "none") {
                div_obj.style.display = "";
                fs_obj.style.border = ''; //"1px solid #CCCCCC";
                fs_obj.style.margin = ''; //"top:5px bottom:5px"
        } else {
                div_obj.style.display = "none";
                fs_obj.style.borderBottom = "none";
                fs_obj.style.borderLeft = "none";
                fs_obj.style.borderRight = "none";              
                fs_obj.style.marginBottom = "-10px";
        }
    }
  
  </script>

</head>

<body>
<?php include_once("inc/owl_header.inc.php") ?>

<h3>Modeling result</h3>

<? # job name ?>
<div class="infobox" id="ib_name">
<form>
<fieldset>
<legend  onclick="javascript:toggle_fieldset('ib_name')">Jobname</legend>
<div>
<? echo $job_name; ?>
</div>
</fieldset>
</form>
</div>

<? # full sequence ?>
<? $full_seq = read_full_sequence($job_name); 
if(strlen($full_seq) > 0) { ?>
<div class="infobox" id="ib_full_seq">
<form><fieldset>
<legend onclick="javascript:toggle_fieldset('ib_full_seq')" >Full sequence</legend>
<div>
<? print_seq($full_seq); ?>
</div>
</fieldset></form>
</div>
<? } ?>

<? # sequence ?>
<div class="infobox" id="ib_seq">
<form>
<fieldset>
<?  $intv = read_subseq_interval($job_name); if(strlen($intv) > 0) { $intv = '('.$intv.')'; } ?>
<legend onclick="javascript:toggle_fieldset('ib_seq')" >Target sequence <? echo $intv; ?> </legend>
<div>
<? print_seq(read_sequence($job_name)); ?>
</div>
</fieldset>
</form>
</div>

<? # templates ?>
<div class="infobox" id="ib_temps">
<fieldset>
<legend onclick="javascript:toggle_fieldset('ib_temps')">Templates used for modeling</legend>
<div>
<?php
$temps = read_templates($job_name);
if(count($temps) > 0) {
        foreach($temps as $temp) {
                $code = rtrim($temp);
                $pdb = substr($code, 0, 4);
                echo '<a href="http://pdbwiki.org/index.php/'.$pdb.'">'.rtrim($temp).'</a> ';
        }
} else {
        echo 'Template file not found';
}
?>
</div>
</fieldset>
</div>

<? # predicted structure ?>
<?php  
        $intv = read_subseq_interval($job_name);
        if(strlen($intv) > 0) {
                $start_end = split("-",$intv);
                $offset = $start_end[0] - 1;
                if($offset > 0) {
                        renum_pdb($job_name, $offset);
                }
        } 
?>
<div class="infobox" id="ib_pdb">
<form>
<fieldset>
<legend onclick="javascript:toggle_fieldset('ib_pdb')">Predicted structure</legend>
<div>
<?php create_png_preview($job_name); ?>
<A href="<?php echo get_pdb_url($job_name); ?>"><IMG src="<? echo get_img_url($job_name); ?>" border="0"></A>
</div>
</fieldset>
</form>
</div>

<? # secondary structure 
if($GLOBALS['show_ss_on_result_page']) {
?>
<div class="infobox" id="ib_ss">
<form>
<fieldset>
<legend onclick="javascript:toggle_fieldset('ib_ss')">Secondary structure</legend>
<div>
<?
        create_ss_compare_img($job_name);
        if(file_exists(get_ss_compare_file($job_name))) {
                echo '<img src="'.get_ss_compare_img_url($job_name).'" alt="">';
        } else {
//      if(file_exists(get_ss_pred_file($job_name))) {
//              $cont = file_get_contents(get_ss_pred_file($job_name));
//              echo '<pre>'.$cont.'</pre>';                            
//      } else {
                echo "Secondary structure file not found!";
        }
?>
</div>
</fieldset>
</form>
</div>
<? } ?>

<div class="buttons">
<p><a href="<?php echo get_pdb_url($job_name); ?>"><img src="images/pdb.png" alt="" /> Download pdb file</a></p>
<a href="results.php"><img src="images/application_view_list.png" alt="" /> View result list</a>
<p><a href="index.php"><img src="images/new.png" alt="" /> Start new job</A></p>
</div>
<div style="clear:both;"></div>
<p></p>

</body>
</html>
Revision:	1433
Committed:	Tue Aug 16 15:36:21 2011 UTC (10 years, 9 months ago) by jmduarteg
Original Path:	*branches/owl-for-cmview-1.9/modelit/server/show_modeling_result.php*
File size:	8148 byte(s)
Log Message:	Creating owl branch from tag owl-1.9.3 for bug fixes of cmview (release 1.1). To go together with branch cmview-1.9
Line	File contents
1	<?php
2	include_once("inc/settings.php");
3
4	if(isset($_GET['job_name'])) {
5	$job_name = $_GET['job_name'];
6	}
7
8	if(!isset($job_name)) {
9	$errors['no_job_name'] = 1;
10	}
11
12	function get_output_url($job_name) {
13	return "results/".$job_name."/";
14	}
15
16	function get_orig_pdb_file($job_name) {
17	return get_result_file($job_name, ".reconstructed.pdb");
18	}
19
20	function get_renum_pdb_file($job_name) {
21	return get_result_file($job_name, ".renum.pdb");
22	}
23
24	function get_pdb_url($job_name) {
25	if(file_exists(get_renum_pdb_file($job_name))) {
26	return get_output_url($job_name).$job_name.".renum.pdb";
27	} else {
28	return get_output_url($job_name).$job_name.".reconstructed.pdb";
29	}
30	}
31
32	function get_img_file($job_name) {
33	return get_result_file($job_name, ".png");
34	}
35
36	function get_img_url($job_name) {
37	return get_output_url($job_name).$job_name.".png";
38	}
39
40	function get_blast_img($job_name) {
41	return get_output_url($job_name)."blast.png";
42	}
43
44	function get_psiblast_img($job_name) {
45	return get_output_url($job_name)."psiblast.png";
46	}
47
48	function get_ss_compare_file($job_name) {
49	return get_result_file($job_name, ".ss.compare");
50	}
51
52	function get_ss_compare_img_file($job_name) {
53	return get_result_file($job_name, ".ss.compare.png");
54	}
55
56	function get_ss_compare_img_url($job_name) {
57	return get_output_url($job_name).$job_name.".ss.compare.png";
58	}
59
60	function get_ss_pred_file($job_name) {
61	return get_result_file($job_name, ".horiz");
62	}
63
64	function get_template_file($job_name) {
65	return get_result_file($job_name, ".man.templates");
66	}
67
68	function read_templates($job_name) {
69	$result = array();
70	if(file_exists(get_template_file($job_name))) {
71	$result = file(get_template_file($job_name), FILE_SKIP_EMPTY_LINES);
72	}
73	return $result;
74	}
75
76	function get_seq_file($job_name) {
77	return get_result_file($job_name, ".fa");
78	}
79
80	function get_full_seq_file($job_name) {
81	return get_result_file($job_name, ".full.fa");
82	}
83
84	function read_sequence($job_name) {
85	if(file_exists(get_seq_file($job_name))) {
86	$lines = file(get_seq_file($job_name));
87	if(count($lines) < 2) {
88	return "";
89	} else {
90	$seq = $lines[1];
91	return $seq;
92	}
93	} else {
94	return "";
95	}
96	}
97
98	function read_full_sequence($job_name) {
99	if(file_exists(get_full_seq_file($job_name))) {
100	$lines = file(get_full_seq_file($job_name));
101	if(count($lines) < 2) {
102	return "";
103	} else {
104	$seq = $lines[1];
105	return $seq;
106	}
107	} else {
108	return "";
109	}
110	}
111
112	function read_subseq_interval($job_name) {
113	if(file_exists(get_full_seq_file($job_name))) {
114	$lines = file(get_full_seq_file($job_name));
115	if(count($lines) < 2) {
116	return "";
117	} else {
118	$header = $lines[0];
119	return trim(substr($header,1));
120	}
121	} else {
122	return "";
123	}
124	}
125
126	function print_seq($seq) {
127	echo '<div class="sequence">';
128	$upper = 1;
129	for($i = 0; $i < strlen($seq); $i++) {
130	if($i > 0 && $i % 100 == 0) {
131	echo '<br/>';
132	}
133	if($upper && strtoupper($seq[$i])!=$seq[$i]) {
134	$upper = 0;
135	echo '<span class="fadeseq">';
136	}
137	if(!$upper && strtoupper($seq[$i])==$seq[$i]) {
138	$upper = 1;
139	echo '</span>';
140	}
141	echo $seq[$i];
142	}
143	echo '</div>';
144	}
145
146	function create_png_preview($job_name) {
147	$j = escapeshellcmd($job_name);
148	$pdb_file = get_orig_pdb_file($job_name);
149	$png_file = get_img_file($job_name);
150
151	$width = 480;
152	$height = 360;
153	$cmd = $GLOBALS['script_dir']."pdb2png.sh ".$pdb_file." ".$width." ".$height." ".$png_file;
154	exec($cmd);
155	}
156
157	function create_ss_compare_img($job_name) {
158	$cmp_file = escapeshellcmd(get_ss_compare_file($job_name));
159	$img_file = escapeshellcmd(get_ss_compare_img_file($job_name));
160	$width = 880;
161	$cmd = $GLOBALS['script_dir']."render_ss_compare.pl $cmp_file $width > $img_file";
162	$result = exec($cmd);
163	//echo $cmd."<br/>";
164	}
165
166	function renum_pdb($job_name, $offset) {
167	$offs = $offset + 1; # needed because script works unintuitively, taking new starting residue instead of offset
168	$old_file = escapeshellcmd(get_orig_pdb_file($job_name));
169	$new_file = escapeshellcmd(get_renum_pdb_file($job_name));
170	$chain = 'A';
171	$cmd = $GLOBALS['script_dir']."renumpdb.py ".$offs." ".$old_file." ".$new_file." ".$chain;
172	$result = exec($cmd);
173	}
174
175	?>
176	<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
177	<html xmlns="http://www.w3.org/1999/xhtml">
178
179	<head>
180	<title>Structure prediction server</title>
181	<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
182	<link rel="stylesheet" type="text/css" href="css/default.css" />
183
184	<script type="text/javascript">
185
186	function toggle_fieldset(infobox_id) {
187	var ib_obj = document.getElementById(infobox_id);
188	var fs_obj = ib_obj.getElementsByTagName('fieldset')[0];
189	var div_obj = fs_obj.getElementsByTagName('div')[0];
190	var d = div_obj.style.display;
191	if(d == "none") {
192	div_obj.style.display = "";
193	fs_obj.style.border = ''; //"1px solid #CCCCCC";
194	fs_obj.style.margin = ''; //"top:5px bottom:5px"
195	} else {
196	div_obj.style.display = "none";
197	fs_obj.style.borderBottom = "none";
198	fs_obj.style.borderLeft = "none";
199	fs_obj.style.borderRight = "none";
200	fs_obj.style.marginBottom = "-10px";
201	}
202	}
203
204	</script>
205
206	</head>
207
208	<body>
209	<?php include_once("inc/owl_header.inc.php") ?>
210
211	<h3>Modeling result</h3>
212
213	<? # job name ?>
214	<div class="infobox" id="ib_name">
215	<form>
216	<fieldset>
217	<legend onclick="javascript:toggle_fieldset('ib_name')">Jobname</legend>
218	<div>
219	<? echo $job_name; ?>
220	</div>
221	</fieldset>
222	</form>
223	</div>
224
225	<? # full sequence ?>
226	<? $full_seq = read_full_sequence($job_name);
227	if(strlen($full_seq) > 0) { ?>
228	<div class="infobox" id="ib_full_seq">
229	<form><fieldset>
230	<legend onclick="javascript:toggle_fieldset('ib_full_seq')" >Full sequence</legend>
231	<div>
232	<? print_seq($full_seq); ?>
233	</div>
234	</fieldset></form>
235	</div>
236	<? } ?>
237
238	<? # sequence ?>
239	<div class="infobox" id="ib_seq">
240	<form>
241	<fieldset>
242	<? $intv = read_subseq_interval($job_name); if(strlen($intv) > 0) { $intv = '('.$intv.')'; } ?>
243	<legend onclick="javascript:toggle_fieldset('ib_seq')" >Target sequence <? echo $intv; ?> </legend>
244	<div>
245	<? print_seq(read_sequence($job_name)); ?>
246	</div>
247	</fieldset>
248	</form>
249	</div>
250
251	<? # templates ?>
252	<div class="infobox" id="ib_temps">
253	<fieldset>
254	<legend onclick="javascript:toggle_fieldset('ib_temps')">Templates used for modeling</legend>
255	<div>
256	<?php
257	$temps = read_templates($job_name);
258	if(count($temps) > 0) {
259	foreach($temps as $temp) {
260	$code = rtrim($temp);
261	$pdb = substr($code, 0, 4);
262	echo '<a href="http://pdbwiki.org/index.php/'.$pdb.'">'.rtrim($temp).'</a> ';
263	}
264	} else {
265	echo 'Template file not found';
266	}
267	?>
268	</div>
269	</fieldset>
270	</div>
271
272	<? # predicted structure ?>
273	<?php
274	$intv = read_subseq_interval($job_name);
275	if(strlen($intv) > 0) {
276	$start_end = split("-",$intv);
277	$offset = $start_end[0] - 1;
278	if($offset > 0) {
279	renum_pdb($job_name, $offset);
280	}
281	}
282	?>
283	<div class="infobox" id="ib_pdb">
284	<form>
285	<fieldset>
286	<legend onclick="javascript:toggle_fieldset('ib_pdb')">Predicted structure</legend>
287	<div>
288	<?php create_png_preview($job_name); ?>
289	<A href="<?php echo get_pdb_url($job_name); ?>"><IMG src="<? echo get_img_url($job_name); ?>" border="0"></A>
290	</div>
291	</fieldset>
292	</form>
293	</div>
294
295	<? # secondary structure
296	if($GLOBALS['show_ss_on_result_page']) {
297	?>
298	<div class="infobox" id="ib_ss">
299	<form>
300	<fieldset>
301	<legend onclick="javascript:toggle_fieldset('ib_ss')">Secondary structure</legend>
302	<div>
303	<?
304	create_ss_compare_img($job_name);
305	if(file_exists(get_ss_compare_file($job_name))) {
306	echo '<img src="'.get_ss_compare_img_url($job_name).'" alt="">';
307	} else {
308	// if(file_exists(get_ss_pred_file($job_name))) {
309	// $cont = file_get_contents(get_ss_pred_file($job_name));
310	// echo '<pre>'.$cont.'</pre>';
311	// } else {
312	echo "Secondary structure file not found!";
313	}
314	?>
315	</div>
316	</fieldset>
317	</form>
318	</div>
319	<? } ?>
320
321	<div class="buttons">
322	<p><a href="<?php echo get_pdb_url($job_name); ?>"><img src="images/pdb.png" alt="" /> Download pdb file</a></p>
323	<a href="results.php"><img src="images/application_view_list.png" alt="" /> View result list</a>
324	<p><a href="index.php"><img src="images/new.png" alt="" /> Start new job</A></p>
325	</div>
326	<div style="clear:both;"></div>
327	<p></p>
328
329	</body>
330	</html>