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revision 1.20, Sat Feb 12 23:36:21 2005 UTC revision 1.21, Sat Mar 26 13:30:57 2005 UTC
# Line 59  Line 59 
59   push @$html, $cgi->p({class=>"diagnostic"}, ("<small>Generating this table took approximately " . (time-$^T) . " seconds\n</small>"));   push @$html, $cgi->p({class=>"diagnostic"}, ("<small>Generating this table took approximately " . (time-$^T) . " seconds\n</small>"));
60  }  }
61  elsif ($cgi->param('pirsf') && !($cgi->param('submit') eq "Update view")) {  elsif ($cgi->param('pirsf') && !($cgi->param('submit') eq "Update view")) {
62   # we want to display one of the correspondances   # we want to display one of the correspondences
63   my $selfurl=$cgi->url;   my $selfurl=$cgi->url;
64   push @$html, $cgi->p;   push @$html, $cgi->p;
65   if ($cgi->param('ssonly')) {push @$html, "<a href=\"$selfurl?pirsf=" . $cgi->param("pirsf") . "&user=" . $cgi->param('user') . "\">Show All Matches</a>\n"}   if ($cgi->param('ssonly')) {push @$html, "<a href=\"$selfurl?pirsf=" . $cgi->param("pirsf") . "&user=" . $cgi->param('user') . "\">Show All Matches</a>\n"}
66   else {push @$html, "<a href=\"$selfurl?pirsf=" . $cgi->param("pirsf") . "&ssonly='1'&user=" . $cgi->param('user') . "\">Show only matches with a subsystem</a>\n"}   else {push @$html, "<a href=\"$selfurl?pirsf=" . $cgi->param("pirsf") . "&ssonly='1'&user=" . $cgi->param('user') . "\">Show only matches with a subsystem</a>\n"}
67    
68   my $col_hdrs = ["PIR Superfamily<br><small>Link goes to PIR<small>", "Genome", "PEG", "FIG Function", "FIG Subsystem"];   my $col_hdrs = ["PIR Superfamily<br><small>Link goes to PIR<small>", "Genome", "UniProt","PEG", "FIG Function", "FIG Subsystem"];
69   my $tab = [];   my $tab = [];
70   foreach my $peg (@{$pegbypir->{$cgi->param('pirsf')}}) {   foreach my $peg (@{$pegbypir->{$cgi->param('pirsf')}}) {
71    my @sslinks;    my @sslinks;
# Line 77  Line 77 
77    $pirlink =~ /^PIR(SF\d+)/;    $pirlink =~ /^PIR(SF\d+)/;
78    $pirlink="<a href='http://pir.georgetown.edu/sfcs-cgi/new/pirclassif.pl?id=$1'>PIR$1</a>" . $pirid->{$cgi->param('pirsf')};    $pirlink="<a href='http://pir.georgetown.edu/sfcs-cgi/new/pirclassif.pl?id=$1'>PIR$1</a>" . $pirid->{$cgi->param('pirsf')};
79    next if ($cgi->param("ssonly") && !(scalar @sslinks));    next if ($cgi->param("ssonly") && !(scalar @sslinks));
80    push (@$tab, [$pirlink, $fig->genus_species($fig->genome_of($peg)), &HTML::fid_link($cgi, $peg, 1), (scalar $fig->function_of($peg)), (join ", ", @sslinks)]);    push (@$tab, [$pirlink, $fig->genus_species($fig->genome_of($peg)), &HTML::uni_link($cgi,$fig->to_alias($peg,"uni")),&HTML::fid_link($cgi, $peg, 1), (scalar $fig->function_of($peg)), (join ", ", @sslinks)]);
81   }   }
82   push(@$html,&HTML::make_table($col_hdrs,$tab,"Correspondance between SEED and PIR"));   push(@$html,&HTML::make_table($col_hdrs,$tab,"Correspondence between SEED and PIR"));
83  }  }
84  else {  else {
85   unshift @$html, "<TITLE>The SEED - PIR comparison page</TITLE>\n";   unshift @$html, "<TITLE>The SEED - PIR comparison page</TITLE>\n";
# Line 143  Line 143 
143    $cgi->checkbox(-name=>"showsubsys", -label=>"Show subsystem counts in pull down menu (this will slow things down!)"), $cgi->p,    $cgi->checkbox(-name=>"showsubsys", -label=>"Show subsystem counts in pull down menu (this will slow things down!)"), $cgi->p,
144    $cgi->checkbox(-name=>"preliminary", -label=>"Show only preliminary PIR superfamilies"), $cgi->p,    $cgi->checkbox(-name=>"preliminary", -label=>"Show only preliminary PIR superfamilies"), $cgi->p,
145    $cgi->submit('submit', 'Update view'),    $cgi->submit('submit', 'Update view'),
146    $cgi->submit('submit', 'Show Correspondance'),    $cgi->submit('submit', 'Show Correspondence'),
147    $cgi->reset,    $cgi->reset,
148    $cgi->p, $cgi->hr, $cgi->p,    $cgi->p, $cgi->hr, $cgi->p,
149    "To view a summary of the comparisons between PIR and SEED annotations, please check here:", $cgi->p,    "To view a summary of the comparisons between PIR and SEED annotations, please check here:", $cgi->p,
# Line 175  Line 175 
175    
176  # just read the file, convert it to an HTML table and return it  # just read the file, convert it to an HTML table and return it
177   unless (-e "$FIG_Config::data/Global/pirsfcorrespondance.txt") {   unless (-e "$FIG_Config::data/Global/pirsfcorrespondance.txt") {
178    print STDERR "Can't find the correspondance file pirsfcorrespondance.txt so we are going to make it\n";    print STDERR "Can't find the correspondence file pirsfcorrespondance.txt so we are going to make it\n";
179    raelib->pirsfcorrespondance("$FIG_Config::data/Global/pirsfinfo.dat", "$FIG_Config::data/Global/pirsfcorrespondance.txt");    raelib->pirsfcorrespondance("$FIG_Config::data/Global/pirsfinfo.dat", "$FIG_Config::data/Global/pirsfcorrespondance.txt");
180   }   }
181   open (IN, "$FIG_Config::data/Global/pirsfcorrespondance.txt") || die "Can't open $FIG_Config::data/Global/pirsfcorrespondance.txt";   open (IN, "$FIG_Config::data/Global/pirsfcorrespondance.txt") || die "Can't open $FIG_Config::data/Global/pirsfcorrespondance.txt";

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