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revision 1.31, Fri Jun 10 16:43:27 2005 UTC revision 1.32, Thu Aug 4 22:25:12 2005 UTC
# Line 87  Line 87 
87  elsif ($cgi->param('pirsf') && !($cgi->param('submit') eq "Update view")) {  elsif ($cgi->param('pirsf') && !($cgi->param('submit') eq "Update view")) {
88   # we want to display one of the correspondences   # we want to display one of the correspondences
89   my $selfurl=$cgi->url;   my $selfurl=$cgi->url;
90   push @$html, $cgi->p, "<a href=\"/FIG/Html/pir.html#correspondence\" class=\"help\" target=\"pirhelp\">Help on this correspondence table</a>";   push @$html, $cgi->p, "<a href=\"Html/pir.html#correspondence\" class=\"help\" target=\"pirhelp\">Help on this correspondence table</a>";
91   if ($cgi->param('ssonly')) {push @$html, "<a href=\"$selfurl?pirsf=" . $cgi->param("pirsf") . "&user=$user\">Show All Matches</a>\n"}   if ($cgi->param('ssonly')) {push @$html, "<a href=\"$selfurl?pirsf=" . $cgi->param("pirsf") . "&user=$user\">Show All Matches</a>\n"}
92   else {push @$html, "<a href=\"$selfurl?pirsf=" . $cgi->param("pirsf") . "&ssonly='1'&user=$user\">Show only matches with a subsystem</a>\n"}   else {push @$html, "<a href=\"$selfurl?pirsf=" . $cgi->param("pirsf") . "&ssonly='1'&user=$user\">Show only matches with a subsystem</a>\n"}
93    
# Line 201  Line 201 
201   push (@$html, $cgi->start_form(-action => "pir.cgi"),   push (@$html, $cgi->start_form(-action => "pir.cgi"),
202    $cgi->h2("Please choose your super family"),    $cgi->h2("Please choose your super family"),
203    "\nFirst, please enter a username: ", $cgi->textfield(-name=>"user", -value=>$user), $cgi->p,    "\nFirst, please enter a username: ", $cgi->textfield(-name=>"user", -value=>$user), $cgi->p,
204    "\n<a href=\"/FIG/Html/pir.html\" class=\"help\" target=\"pirhelp\">Help on SEED/PIR Correspondence</a>",    "\n<a href=\"Html/pir.html\" class=\"help\" target=\"pirhelp\">Help on SEED/PIR Correspondence</a>",
205    "\nThe list shows the PIR superfamilies. If only one number is shown (default) this is the number of PEGs that map to that superfamily. ",    "\nThe list shows the PIR superfamilies. If only one number is shown (default) this is the number of PEGs that map to that superfamily. ",
206    "\nIf you choose to show subsystem counts in this menu, you will get two numbers. The first of the two numbers in parenthesis is the number ",    "\nIf you choose to show subsystem counts in this menu, you will get two numbers. The first of the two numbers in parenthesis is the number ",
207    "\nof PEGs that map to that superfamily, and the second number in parenthesis is the number of <em>different</em> ",    "\nof PEGs that map to that superfamily, and the second number in parenthesis is the number of <em>different</em> ",
208    "\nsubsystems that those PEGs are in.\n", $cgi->p,"\n",    "\nsubsystems that those PEGs are in.\n", $cgi->p,"\n",
209    $cgi->scrolling_list(-name=>'pirsf', -values=>[keys %$display], -labels=>$display, -size=>$size+1), $cgi->p,"\n",    $cgi->scrolling_list(-name=>'pirsf', -values=>[keys %$display], -labels=>$display, -size=>$size+1), $cgi->p,"\n",
210    "\nNumber of superfamilies shown: ", $numberpirfams, $cgi->p,"\n",    "\nNumber of superfamilies shown: ", $numberpirfams, $cgi->p,"\n",
211    "\n<a href=\"/FIG/Html/pir.html#menu\" class=\"help\" target=\"pirhelp\">Help on the menu contents</a>","\n",    "\n<a href=\"Html/pir.html#menu\" class=\"help\" target=\"pirhelp\">Help on the menu contents</a>","\n",
212    "\nMinimum number of pegs per PIR superfamily shown in list &nbsp; <input type='text' name='min' value='$min' size=3 />","\n",    "\nMinimum number of pegs per PIR superfamily shown in list &nbsp; <input type='text' name='min' value='$min' size=3 />","\n",
213    "\nor show all PIR superfamilies: ", $cgi->checkbox(-name=>"showall", -label=>""), $cgi->p,"\n",    "\nor show all PIR superfamilies: ", $cgi->checkbox(-name=>"showall", -label=>""), $cgi->p,"\n",
214    $cgi->checkbox(-name=>"showsubsys", -label=>"Show subsystem counts in list"), $cgi->p,"\n",    $cgi->checkbox(-name=>"showsubsys", -label=>"Show subsystem counts in list"), $cgi->p,"\n",
# Line 219  Line 219 
219    $cgi->reset,"\n",    $cgi->reset,"\n",
220    $cgi->p, $cgi->hr, $cgi->p,"\n",    $cgi->p, $cgi->hr, $cgi->p,"\n",
221    $cgi->p("<strong>Generate Data Tables</strong>"),    $cgi->p("<strong>Generate Data Tables</strong>"),
222    "<a href=\"/FIG/Html/pir.html#datatables\" class=\"help\" target=\"pirhelp\">Help on Generating Data Tables</a>",    "<a href=\"Html/pir.html#datatables\" class=\"help\" target=\"pirhelp\">Help on Generating Data Tables</a>",
223    $cgi->p("The data tables are an alternative way to view the data in summary form. For the summary of the comparisons between PIR and SEED annotations, please check here:\n"),    $cgi->p("The data tables are an alternative way to view the data in summary form. For the summary of the comparisons between PIR and SEED annotations, please check here:\n"),
224    $cgi->checkbox(-name=>"onlyss", -label=>"Show only those PEGs that are in a subsystem and a superfamily", -checked=>"on"), $cgi->p,"\n",    $cgi->checkbox(-name=>"onlyss", -label=>"Show only those PEGs that are in a subsystem and a superfamily", -checked=>"on"), $cgi->p,"\n",
225    $cgi->checkbox(-name=>"totalsort", -label=>"Sort by the total number of different annotations"), $cgi->p,"\n",    $cgi->checkbox(-name=>"totalsort", -label=>"Sort by the total number of different annotations"), $cgi->p,"\n",
# Line 227  Line 227 
227    $cgi->reset,"\n",    $cgi->reset,"\n",
228    $cgi->p, $cgi->hr, "\n",    $cgi->p, $cgi->hr, "\n",
229    $cgi->p("<strong>Check for Updates</strong>"),"\n",    $cgi->p("<strong>Check for Updates</strong>"),"\n",
230    "<a href=\"/FIG/Html/pir.html#updates\" class=\"help\" target=\"pirhelp\">Help on updates</a>", "\n",    "<a href=\"Html/pir.html#updates\" class=\"help\" target=\"pirhelp\">Help on updates</a>", "\n",
231    $cgi->p("Please click the button to check the PIR site and see whether there is a new version of the PIR superfamily data you should use"),"\n",    $cgi->p("Please click the button to check the PIR site and see whether there is a new version of the PIR superfamily data you should use"),"\n",
232    $cgi->submit('submit', 'Check for updates'),"\n",    $cgi->submit('submit', 'Check for updates'),"\n",
233    
234    $cgi->p, $cgi->hr, $cgi->p,"\n",    $cgi->p, $cgi->hr, $cgi->p,"\n",
235    $cgi->p("<strong>Data for PIR</strong>"),    $cgi->p("<strong>Data for PIR</strong>"),
236    "<a href=\"/FIG/Html/pir.html#ftpdown\" class=\"help\" target=\"pirhelp\">Help on Data for PIR</a>\n",    "<a href=\"Html/pir.html#ftpdown\" class=\"help\" target=\"pirhelp\">Help on Data for PIR</a>\n",
237    $ftpfile,    $ftpfile,
238    $cgi->p("Please click the button to create a new file.\n"),    $cgi->p("Please click the button to create a new file.\n"),
239    $cgi->submit('submit', 'Create Download File'),"\n",    $cgi->submit('submit', 'Create Download File'),"\n",
# Line 339  Line 339 
339    push @$tab, [    push @$tab, [
340     "\n".$countinss->{$sf},     "\n".$countinss->{$sf},
341     $count->{$sf},     $count->{$sf},
342     "<a href=\"/FIG/pir.cgi?pirsf=$sf&ssonly='1'&user='$user'\">$sf</a>",     "<a href=\"pir.cgi?pirsf=$sf&ssonly='1'&user='$user'\">$sf</a>",
343     $pirid->{$sf},     $pirid->{$sf},
344     $subsystems->{$sf},     $subsystems->{$sf},
345    ];    ];
# Line 418  Line 418 
418    
419   push @$html, "<h2>Downloading and installing new data has started</h2>",   push @$html, "<h2>Downloading and installing new data has started</h2>",
420      "<p>The job has started in the background but will likely take some time.<br />\n",      "<p>The job has started in the background but will likely take some time.<br />\n",
421      "The job has an ID of $bkj, and you can check it out from the <A href=\"/FIG/seed_ctl.cgi\">SEED Control Panel</a></p>\n",      "The job has an ID of $bkj, and you can check it out from the <A href=\"seed_ctl.cgi\">SEED Control Panel</a></p>\n",
422      "<p>You should not use the PIR superfamilies while the job is runnning</p>\n";      "<p>You should not use the PIR superfamilies while the job is runnning</p>\n";
423   return $html;   return $html;
424  }  }
# Line 437  Line 437 
437    
438   push @$html, "<h2>Creating your data has started</h2>",   push @$html, "<h2>Creating your data has started</h2>",
439      "<p>The job has started in the background but will likely take some time.<br />\n",      "<p>The job has started in the background but will likely take some time.<br />\n",
440      "The job has an ID of $bkj, and you can check it out from the <A href=\"/FIG/seed_ctl.cgi\">SEED Control Panel</a></p>\n";      "The job has an ID of $bkj, and you can check it out from the <A href=\"seed_ctl.cgi\">SEED Control Panel</a></p>\n";
441   return $html;   return $html;
442  }  }
443    

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