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Annotation of /FigKernelPackages/FIGGenDB.pm

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1 : heiko 1.1 package FIGGenDB;
2 :    
3 : olson 1.2 use FIG;
4 : heiko 1.1 use strict;
5 :    
6 :     use Fcntl qw/:flock/; # import LOCK_* constants
7 : olson 1.4 use CGI;
8 : heiko 1.1 use POSIX;
9 :     use IPC::Open2;
10 :    
11 :     use DBrtns;
12 :     use FIG_Config;
13 :    
14 : olson 1.4
15 :     use constant GENDB_CGI => "/GENDB/cgi-bin/";
16 : heiko 1.1
17 :    
18 :     sub linkPEGGenDB {
19 :     my ($peg) = @_;
20 :     $peg =~ /fig\|(.+)\.peg/;
21 :     my $taxon = $1;
22 : olson 1.2
23 :     my $cgi = &FIG::plug_url(GENDB_CGI);
24 :    
25 :     return q(<a target="_blank" href=") . $cgi .
26 : olson 1.4 "seed_interface.cgi?action=view".
27 : olson 1.2 "&region=$peg&taxon_id=$taxon\">To View in GenDB</a>\n";
28 : heiko 1.1 }
29 :    
30 : olson 1.4 sub importOrganismGenDB {
31 :     my ($peg) = @_;
32 :     $peg =~ /fig\|(.+)\.peg/;
33 :     my $taxon = $1;
34 :    
35 :     my $cgi = &FIG::plug_url(GENDB_CGI);
36 :    
37 :     return q(<a target="_blank" href=") . $cgi .
38 :     "seed_interface.cgi?action=import".
39 :     "&taxon_id=$taxon\">Import Organism into GenDB</a>\n";
40 :    
41 :     }
42 :    
43 : heiko 1.1 sub linkClusterGenDB {
44 :     my ($peg, $taxon) = @_;
45 : redwards 1.5 # RAE: just return undef here so that we don't display the form for the Bounds as people think that this is working
46 :     return undef;
47 :    
48 : olson 1.3 my $cgi = &FIG::plug_url(GENDB_CGI);
49 : olson 1.4 my $html = "<form target=\"_blank\" action=\"${cgi}seed_interface.cgi\">\n
50 :     Bound1<input type=\"text\" id=\"bound1\" name=\"bound1\"/>\n
51 :     Bound2<input type=\"text\" id=\"bound2\" name=\"bound2\"/>\n
52 :     Candidate(s):<input type=\"text\" id=\"candidates\" name=\"candidates\"/>\n
53 :     Threshold<input type=\"text\" name=\"fmgth\" value=\"1e-20\"/>\n
54 :     <input type=\"hidden\" name=\"action\" value=\"predict\"/>\n
55 :     <input type=\"hidden\" name=\"peg_id\" value=\"$peg\"/>\n
56 :     <input type=\"submit\" name=\"GenDB\" value=\"Find uncalled Gene\"/>\n
57 : heiko 1.1 </form>";
58 :     return $html;
59 :     }
60 :    
61 :    
62 :    
63 :     1;

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