<?php require_once "seq2png.php"; $GLOBAL_DEFAULTSEQ = "gccgggagcagacaagcccgtcagggcgcgtcagcgcgtgttggcgggtgtcggggctggcttaactatgcggcatcagagcagattgtactgagagtgcaccataaattcccgttttaagagcttggtgagcgctaggagtcactgccaggtatcgtttgaacacggcattagtcagggaagtcataacacagtcctttcccgcaattttctttttctattactcttggcctcctctagtacactctatatttttttatgcctcggtaatgattttcatttttttttttcccctagcggatgactctttttttttcttagcgattggcattatcacataatgaattatacattatataaagtaatgtgatttcttcgaagaatatactaaaaaatgagcaggcaagataaacgaaggcaaagatgacagagcagaaagccctagtaaagcgtattacaaatgaaaccaagattcagattgcgatctctttaaagggtggtcccctagcgatagagcactcgatcttcccagaaaaagaggcagaagcagtagcagaacaggccacacaatcgcaagtgattaacgtccacacaggtatagggtttctggaccatatgatacatgctctggccaagcattccggctggtcgctaatcgttgagtgcattggtgacttacacatagacgaccatcacaccactgaagactgcgggattgctctcggtcaagcttttaaagaggccctactggcgcgtggagtaaaaaggtttggatcaggatttgcgcctttggatgaggcactttccagagcggtggtagatctttcgaacaggccgtacgcagttgtcgaacttggtttgcaaagggagaaagtaggagatctctcttgcgagatgatcccgcattttcttgaaagctttgcagaggctagcagaattaccctccacgttgattgtctgcgaggcaagaatgatcatcaccgtagtgagagtgcgttcaaggctcttgcggttgccataagagaagccacctcgcccaatggtaccaacgatgttccctccaccaaaggtgttcttatgtagtgacaccgattatttaaagctgcagcatacgatatatatacatgtgtatatatgtatacctatgaatgtcagtaagtatgtatacgaacagtatgatactgaagatgacaaggtaatgcatcattctatacgtgtcattctgaacgaggcgcgctttccttttttctttttgctttttctttttttttctcttgaactcgacggatctatgcggtgtgaaataccgcacagatgcgtaaggagaaaataccgcatcaggaaattgtaaacgttaatattttgttaaaattcgcgttaaatttttgttaaatcagctcattttttaaccaataggccgaaatcggcaaaatcccttataaatcaaaagaatagaccgagatagggttgagtgttgttccagtttggaacaagagtccactattaaagaacgtggactccaacgtcaaagggcgaaaaaccgtctatcagggcgatggcccactacgtgaaccatcaccctaatcaagttttttggggtcgaggtgccgtaaagcactaaatcggaaccctaaagggagcccccgatttagagcttgacggggaaagccggcgaacgtggcgagaaaggaagggaagaaagcgaaaggagcgggcgctagggcgctggcaagtgtagcggtcacgctgcgcgtaaccaccacacccgccgcgcttaatgcgccgctacagggcgcgtcgcgccattcgccattcaggctgcgcaactgttgggaagggcgatcggtgcgggcctcttcgctattacgccagctggcgaaagggggatgtgctgcaaggcgattaagttgggtaacgccagggttttcccagtcacgacgttgtaaaacgacggccagtgagcgcgcgtaatacgactcactatagggcgaattgggtaccggccgcaaattaaagccttcgagcgtcccaaaaccttctcaagcaaggttttcagtataatgttacatgcgtacacgcgtctgtacagaaaaaaaagaaaaatttgaaatataaataacgttcttaatactaacataactataaaaaaataaatagggacctagacttcaggttgtctaactccttccttttcggttagagcggatgtggggggagggcgtgaatgtaagcgtgacataactaattacatgactcgaccagttatttgtacaattcatccataccatgggtaataccagcagcagtaacaaattctaacaagaccatgtggtctctcttttcgtttggatctttggataaggcagattgagtggataagtaatggttgtctggtaacaagactggaccatcaccaattggagtattttgttgataatggtcagctaattgaacagaaccatcttcaatgttgtgtctaattttgaagttaactttgataccattcttttgtttgtcagccatgatgtaaacattgtgagagttatagttgtattccaatttgtgacctaaaatgttaccatcttctttaaaatcaataccttttaattcgattctattaactaaggtatcaccttcaaacttgacttcagctctggtcttgtagttaccgtcatctttgaaaaaaatagttctttcttgaacataaccttctggcatggcagacttgaaaaagtcatgttgtttcatatgatctgggtatctagcaaaacattgaacaccataaccgaaagtagtgactaaggttggccatggaactggcaatttaccagtagtacaaataaattttaaggtcaatttaccgtaagtagcatcaccttcaccttcaccggagacagaaaatttgtgaccattaacatcaccatctaattcaaccaaaattgggacaacaccagtgaataattcttcacctttagacatgtcgaggtcgacggtatcgataagcttgatatcgaattcctgcagcccgggggatccactagttctagagtatggatgggggtaatagaattgtatctatgtatctgacgaccctgtattacacgaaggaaatagtagatgaaaagacaagagagcaagaaaaaggaaaaacttcctttctaacagacgctttacttaaccttatatatatcttatttttttcatcgagcgtgttcaattggacaaggtgccaccttttcgacacttcggttattatgttacacagttttcatgaggatggcgccttgactaacttaattagtcatttgccaaccaccacagttccccaatatcgacagcttcacgtgccatttgccattttgcgatcatgtgacctcaagagaaaaagcaaaaaataatgagagctaagggattcgaacccttgcatccggagctccagcttttgttccctttagtgagggttaattgcgcgcttggcgtaatcatggtcatagctgtttcctgtgtgaaattgttatccgctcacaattccacacaacataggagccggaagcataaagtgtaaagcctggggtgcctaatgagtgaggtaactcacattaattgcgttgcgctcactgcccgctttccagtcgggaaacctgtcgtgccagctgcattaatgaatcggccaacgcgcggggagaggcggtttgcgtattgggcgctcttccgcttcctcgctcactgactcgctgcgctcggtcgttcggctgcggcgagcggtatcagctcactcaaaggcggtaatacggttatccacagaatcaggggataacgcaggaaagaacatgtgagcaaaaggccagcaaaaggccaggaaccgtaaaaaggccgcgttgctggcgtttttccataggctccgcccccctgacgagcatcacaaaaatcgacgctcaagtcagaggtggcgaaacccgacaggactataaagataccaggcgtttccccctggaagctccctcgtgcgctctcctgttccgaccctgccgcttaccggatacctgtccgcctttctcccttcgggaagcgtggcgctttctcatagctcacgctgtaggtatctcagttcggtgtaggtcgttcgctccaagctgggctgtgtgcacgaaccccccgttcagcccgaccgctgcgccttatccggtaactatcgtcttgagtccaacccggtaagacacgacttatcgccactggcagcagccactggtaacaggattagcagagcgaggtatgtaggcggtgctacagagttcttgaagtggtggcctaactacggctacactagaaggacagtatttggtatctgcgctctgctgaagccagttaccttcggaaaaagagttggtagctcttgatccggcaaacaaaccaccgctggtagcggtggtttttttgtttgcaagcagcagattacgcgcagaaaaaaaggatctcaagaagatcctttgatcttttctacggggtctgacgctcagtggaacgaaaactcacgttaagggattttggtcatgagattatcaaaaaggatcttcacctagatccttttaaattaaaaatgaagttttaaatcaatctaaagtatatatgagtaaacttggtctgacagttaccaatgcttaatcagtgaggcacctatctcagcgatctgtctatttcgttcatccatagttgcctgactccccgtcgtgtagataactacgatacgggagggcttaccatctggccccagtgctgcaatgataccgcgagacccacgctcaccggctccagatttatcagcaataaaccagccagccggaagggccgagcgcagaagtggtcctgcaactttatccgcctccatccagtctattaattgttgccgggaagctagagtaagtagttcgccagttaatagtttgcgcaacgttgttgccattgctacaggcatcgtggtgtcacgctcgtcgtttggtatggcttcattcagctccggttcccaacgatcaaggcgagttacatgatcccccatgttgtgcaaaaaagcggttagctccttcggtcctccgatcgttgtcagaagtaagttggccgcagtgttatcactcatggttatggcagcactgcataattctcttactgtcatgccatccgtaagatgcttttctgtgactggtgagtactcaaccaagtcattctgagaatagtgtatgcggcgaccgagttgctcttgcccggcgtcaatacgggataataccgcgccacatagcagaactttaaaagtgctcatcattggaaaacgttcttcggggcgaaaactctcaaggatcttaccgctgttgagatccagttcgatgtaacccactcgtgcacccaactgatcttcagcatcttttactttcaccagcgtttctgggtgagcaaaaacaggaaggcaaaatgccgcaaaaaagggaataagggcgacacggaaatgttgaatactcatactcttcctttttcaatattattgaagcatttatcagggttattgtctcatgagcggatacatatttgaatgtatttagaaaaataaacaaataggggttccgcgcacatttccccgaaaagtgccacctgacgtctaagaaaccattattatcatgacattaacctataaaaataggcgtatcacgaggccctttcgtctcgcgcgtttcggtgatgacggtgaaaacctctgacacatgcagctcccggagacggtcacagcttgtctgtaagcggatgccgggagcagacaagcccgtcagggcgcgtcagcgggtgttggcgggtgtcggggctggcttaactatgcggcatcagagcagattgtactgagagtgcaccatacataatcatcgatgaattcgagctcgttttcgacactggatggcggcgttagtatcgaatcgacagcagtatagcgaccagcattcacatacgattgacgcatgatattactttctgcgcacttaacttcgcatctgggcagatgatgtcgaggcgaaaaaaaatataaatcacgctaacatttgattaaaatagaacaactacaatataaaaaaactatacaaatgacaagttcttgaaaacaagaatctttttattgtcagtactcggagacaatcatatgggagaagcaattggaagatagaaaaaaggtactcggtacataaatatatgtgattctgggtagaagatcggtctgcattggatggtggtaacgcatttttttacacacattacttgcctcgagcatcaaatggtggttattcgtggatctatatcacgtgatttgcttaagaattgtcgttcatggtgacacttttagctttgacatgattaagctcatctcaattgatgttatctaaagtcatttcaactatctaagatgtggttgtgattgggccattttgtgaaagccagtacgccagcgtcaatacactcccgtcaattagttgcaccatgtccacaaaatcatataccagtagagctgagactcatgcaagtccggttgcatcgaaacttttacgtttaatggatgaaaagaagaccaatttgtgtgcttctcttgacgttcgttcgactgatgagctattgaaacttgttgaaacgttgggtccatacatttgccttttgaaaacacacgttgatatcttggatgatttcagttatgagggtactgtcgttccattgaaagcattggcagagaaatacaagttcttgatatttgaggacagaaaattcgccgatatcggtaacacagtcaaattacaatatacatcgggcgtttaccgtatcgcagaatggtctgatatcaccaacgcccacggggttactggtgctggtattgttgctggcttgaaacaaggtgcgcaagaggtcaccaaagaaccaaggggattattgatgcttgctgaattgtcttccaagggttctctagcacacggtgaatatactaagggtaccgttgatattgcaaagagtgataaagatttcgttattgggttcattgctcagaacgatatgggaggaagagaagaagggtttgattggctaatcatgaccccaggtgtaggtttagacgacaaaggcgatgcattgggtcagcagtacagaaccgtcgacgaagttgtaagtggtggatcagatatcatcattgttggcagaggacttttcgccaagggtagagatcctaaggttgaaggtgaaagatacagaaatgctggatgggaagcgtaccaaaagagaatcagcgctccccattaattatacaggaaacttaatagaacaaatcacatatttaatctaatagccacctgcattggcacggtgcaacactcacttcaacttcatcttacaaaagatcacgtgatctgttgtattgaactgaaaattttttgtttgcttctctctctctctttcattatgtgagagtttaaaaaccagaaactacatcatcgaaaaagagtttaaaccattacaaccattgcgataagccctctcaaacttcctccagactgtttgtcatccaattggtaagattaattatcatataccccggataagaaaagaagcaagcacacaatggatcaacttaatggtaaggaacaacaagccgcggagacggtcacagcttgtctgtaagcggat"; echo "open -a safari " . seq2png($GLOBAL_DEFAULTSEQ);
* VIEW
*/
$in_edit_mode = $_REQUEST["PME_sys_operation"] == "Change" || $_REQUEST["PME_sys_operation"] == "PME_op_Change";
if ($plasmid->sequence) {
if ($in_edit_mode) {
$remove_gbgz_form = <<<EOD
<form action='' method='post'>
Remove file, filename and sequence for this plasmid:
<input type='hidden' name='PME_sys_operation' value='PME_op_Change'/>
<input type='hidden' name='PME_sys_rec' value='{$this->rec}'/>
<input type='hidden' name='action' value='REMOVE_FILE_SEQ'/>
<input type='button' name='send' value='Remove' onclick='if(confirm("Are you sure that you want to remove file, filename and sequence for this plasmid?")){this.form.submit()}else{return false;}'/>
</form>
EOD;
}
$imgurl = seq2png($plasmid->sequence, PLASMAPPER_SERVER);
$plasmapper_output = <<<EOD
<center>
<img src="{$imgurl}">
<br/>
<textarea readonly rows="10" cols="100">{$plasmid->sequence}</textarea></center>
</center>
EOD;
$wwwblast_url = WWWBLAST_SERVER . "blast.cgi";
$resp = post_vars($wwwblast_url, array("DATALIB" => "plfeatstock_db", "PROGRAM" => "blastn", "EXPECT" => 10, "OOF_ALIGN" => 0, "OVERVIEW" => "on", "ALIGNMENT_VIEW" => 0, "DESCRIPTIONS" => 100, "ALIGNMENTS" => 50, "COLOR_SCHEMA" => 0, "SEQUENCE" => $plasmid->sequence));
$blast_output = preg_replace("/nph-viewgif.cgi/", WWWBLAST_SERVER . "nph-viewgif.cgi", $resp);
} else {
if ($in_edit_mode) {
$add_gbgz_form = <<<EOD
<div class="centered_form">
<i>Add a <b>.gb</b> or a <b>.gb.gz</b> file to this plasmid</i>
