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revision 1.1, Fri Oct 22 17:05:18 2004 UTC revision 1.4, Thu Nov 11 04:22:48 2004 UTC
# Line 1  Line 1 
1  package FIGGenDB;  package FIGGenDB;
2    
3    use FIG;
4  use strict;  use strict;
5    
6  use Fcntl qw/:flock/;  # import LOCK_* constants  use Fcntl qw/:flock/;  # import LOCK_* constants
7    use CGI;
8  use POSIX;  use POSIX;
9  use IPC::Open2;  use IPC::Open2;
10    
11  use DBrtns;  use DBrtns;
12  use FIG_Config;  use FIG_Config;
13    
14  use constant GENDB_CGI=>"http://localhost/GENDB2.2/gendb-cgi/";  
15  use constant SEED_USER=>"seed";  use constant GENDB_CGI => "/GENDB/cgi-bin/";
 use constant SEED_PASS=>'seed';  
 use constant GENDB_PROJECT=>"GenDB_SEED";  
16    
17    
18  sub linkPEGGenDB {  sub linkPEGGenDB {
19      my ($peg) = @_;      my ($peg) = @_;
20      $peg =~ /fig\|(.+)\.peg/;      $peg =~ /fig\|(.+)\.peg/;
21      my $taxon = $1;      my $taxon = $1;
22      return "<a target=\"_blank\" href=\"".GENDB_CGI."seed_interface.cgi?action=view&login=".SEED_USER."&pass=".SEED_PASS."&project=".GENDB_PROJECT."&region=$peg&taxon_id=$taxon\">To View in GenDB</a>\n";  
23        my $cgi = &FIG::plug_url(GENDB_CGI);
24    
25        return q(<a target="_blank" href=") . $cgi .
26            "seed_interface.cgi?action=view".
27            "&region=$peg&taxon_id=$taxon\">To View in GenDB</a>\n";
28    }
29    
30    sub importOrganismGenDB {
31        my ($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  sub linkClusterGenDB {  sub linkClusterGenDB {
44      my ($peg, $taxon) = @_;      my ($peg, $taxon) = @_;
45      my $html = "<form action=\"".GENDB_CGI."seed_interface.cgi\">\n      my $cgi = &FIG::plug_url(GENDB_CGI);
46                  Action:<input type=\"text\" name=\"action\"/>\n      my $html = "<form target=\"_blank\" action=\"${cgi}seed_interface.cgi\">\n
47                  Organism (taxon ID):<input type=\"text\" name=\"taxon_id\"/>\n                  Bound1<input type=\"text\" id=\"bound1\" name=\"bound1\"/>\n
48                  [Start]:<input type=\"text\" name=\"start\"/>\n                  Bound2<input type=\"text\" id=\"bound2\" name=\"bound2\"/>\n
49                  [Stop]:<input type=\"text\" name=\"stop\"/>\n                  Candidate(s):<input type=\"text\" id=\"candidates\" name=\"candidates\"/>\n
50                  <input type=\"hidden\" name=\"login\"/ value=\"".SEED_USER."\">\n                  Threshold<input type=\"text\" name=\"fmgth\" value=\"1e-20\"/>\n
51                  <input type=\"hidden\" name=\"pass\"/ value=\"".SEED_PASS."\">\n                  <input type=\"hidden\" name=\"action\" value=\"predict\"/>\n
52                  <input type=\"submit\" name=\"GenDB\" value=\"GenDB\">\n                  <input type=\"hidden\" name=\"peg_id\" value=\"$peg\"/>\n
53                    <input type=\"submit\" name=\"GenDB\" value=\"Find uncalled Gene\"/>\n
54                  </form>";                  </form>";
55      return $html;      return $html;
56  }  }

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