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revision 1.12, Tue Feb 5 04:44:46 2008 UTC revision 1.23, Wed Sep 3 20:42:27 2008 UTC
# Line 16  Line 16 
16    
17  if ($@)  if ($@)
18  {  {
19      my $cgi = new CGI();      my $error = $@;
20        Warn("Script error: $error") if T(SeedViewer => 0);
21    
22      print $cgi->header();      print CGI::header();
23      print $cgi->start_html();      print CGI::start_html();
24    
25      # print out the error      # print out the error
26      print '<pre>'.$@.'</pre>';      print '<pre>'.$error.'</pre>';
27    
28      print $cgi->end_html();      print CGI::end_html();
29    
30  }  }
31    
# Line 32  Line 33 
33    
34      # initialize cgi      # initialize cgi
35      my $cgi = new CGI();      my $cgi = new CGI();
36      ETracing($cgi);      if ($FIG_Config::linkinSV) {
37            my $parms = $cgi->query_string();
38            if ($parms) {
39                $parms = "?$parms";
40            } else {
41                $parms = "?page=Home";
42            }
43            print CGI::redirect(-uri => "$FIG_Config::cgi_url/wiki/rest.cgi/NmpdrPlugin/SeedViewer$parms",
44                                -status => 301);
45            return;
46        }
47    
48      # initialize layout      # initialize layout
49      # Use the template file for the current mode-- NMPDR or SEED      # Use the template file for the current mode-- NMPDR or SEED
50      my $templateFile = (FIGRules::nmpdr_mode($cgi) ? './Html/NmpdrViewer.tmpl' : './Html/SeedViewer.tmpl');      my $templateFile = (FIGRules::nmpdr_mode($cgi) ? "$FIG_Config::cgi_url/Html/NmpdrViewer.tmpl" : "$FIG_Config::cgi_url/Html/SeedViewer.tmpl");
51      Trace("Template file is $templateFile") if T(3);      Trace("Template file is $templateFile") if T(3);
52      my $layout = WebLayout->new($templateFile);      my $layout = WebLayout->new($templateFile);
     # Start with the normal style.  
     $layout->add_css('./Html/default.css');  
53      # Choose the body/header style sheet according to the mode.      # Choose the body/header style sheet according to the mode.
54      if (FIGRules::nmpdr_mode($cgi)) {      if (FIGRules::nmpdr_mode($cgi)) {
55          # NMPDR mode.          # NMPDR mode.
56          $layout->add_css('./Html/nmpdrviewer.css');          $layout->add_css("$FIG_Config::cgi_url/Html/nmpdrviewer.css");
57          # Show the NMPDR version in the header.          $layout->add_css("$FIG_Config::cgi_url/Html/commonviewer.css");
58          $layout->set_variable(VERSION => "Sprout version $FIG_Config::nmpdr_version on $ENV{HTTP_HOST}.");          # Display the official NMPDR icon for this machine.
59            $layout->add_metatag("<link rel=\"icon\" href=\"${FIG_Config::cgi_base}wiki/pub/logos/nmpdr.ico\" type=\"image/x-icon\" />");
60            $layout->add_metatag("<link rel=\"shortcut icon\" href=\"${FIG_Config::cgi_base}wiki/pub/logos/nmpdr.ico\" type=\"image/x-icon\" />");
61      } else {      } else {
62          # SEED mode.          # SEED mode.
63          $layout->add_css('./Html/seedviewer.css');          $layout->add_css("$FIG_Config::cgi_url/Html/seedviewer.css");
64     }          $layout->add_css("$FIG_Config::cgi_url/Html/commonviewer.css");
65      # Add the common styles.          $layout->add_css("$FIG_Config::cgi_url/Html/default.css");
     $layout->add_css('./Html/commonviewer.css');  
   
     # add site meter  
     my $site_meter = $FIG_Config::site_meter;  
     if ($site_meter) {  
         $layout->add_javascript("http://s20.sitemeter.com/js/counter.js?site=s20nmpdr");  
66      }      }
   
67      # build menu      # build menu
68      my $menu;      my $menu;
69      $menu = WebMenu->new();      $menu = WebMenu->new();
70        if (FIGRules::nmpdr_mode($cgi)) {
71            $menu->add_category('&raquo;Navigate', '?page=Home');
72            $menu->add_entry('&raquo;Navigate', 'NMPDR home', "$FIG_Config::nmpdr_site_url/index.php");
73            $menu->add_entry('&raquo;Navigate', 'Organisms', "$FIG_Config::nmpdr_site_url/content/organisms.php");
74            $menu->add_entry('&raquo;Navigate', 'Subsystems', "$FIG_Config::nmpdr_site_url/content/subsystems.php");
75            $menu->add_entry('&raquo;Navigate', 'FigFams', '?page=FigFamViewer');
76        } else {
77      $menu->add_category('&raquo;Navigate', '?page=Home');      $menu->add_category('&raquo;Navigate', '?page=Home');
78      $menu->add_entry('&raquo;Navigate', 'Startpage', '?page=Home');      $menu->add_entry('&raquo;Navigate', 'Startpage', '?page=Home');
79      $menu->add_entry('&raquo;Navigate', 'Organisms', '?page=OrganismSelect');      $menu->add_entry('&raquo;Navigate', 'Organisms', '?page=OrganismSelect');
80      $menu->add_entry('&raquo;Navigate', 'Subsystems', '?page=SubsystemSelect');      $menu->add_entry('&raquo;Navigate', 'Subsystems', '?page=SubsystemSelect');
81      $menu->add_entry('&raquo;Navigate', '<a>Jump to Feature by</a>');          $menu->add_entry('&raquo;Navigate', 'FigFams', '?page=FigFamViewer');
82      $menu->add_entry('&raquo;Navigate', '&nbsp;&nbsp;BLAST Search', '?page=BlastRun');          $menu->add_entry('&raquo;Navigate', 'BLAST Search', '?page=BlastRun');
83      $menu->add_entry('&raquo;Navigate', "<form style='margin: 0px 0px 0px 6px;'>&nbsp;&nbsp;ID&nbsp;&nbsp;<input type='text' name='pattern' style='border: 1px solid #5da668; width: 100px; height: 17px; margin-top: 2px; font-size: 11px;'><input type='hidden' name='page' value='SearchResult'><input type='hidden' name='action' value='check_search'><input type='submit' style='display:none;'></form>");      }
   
84      if (defined($FIG_Config::teacher_db)) {      if (defined($FIG_Config::teacher_db)) {
85          $menu->add_category('&raquo;Teacher', '?page=Teach', undef, ['edit', 'problem_list'], 96);          $menu->add_category('&raquo;Teacher', '?page=Teach', undef, ['edit', 'problem_list'], 96);
86          $menu->add_entry('&raquo;Teacher', 'Class Performance', '?page=Teach');          $menu->add_entry('&raquo;Teacher', 'Class Performance', '?page=Teach');
# Line 78  Line 88 
88          $menu->add_entry('&raquo;Teacher', 'Problem Sets', '?page=ManageProblemSets');          $menu->add_entry('&raquo;Teacher', 'Problem Sets', '?page=ManageProblemSets');
89          $menu->add_entry('&raquo;Teacher', 'Annotation Resolve', '?page=ClassAnnotationResolve');          $menu->add_entry('&raquo;Teacher', 'Annotation Resolve', '?page=ClassAnnotationResolve');
90      }      }
     #$menu->add_category('&raquo;Admin', '?page=Admin', undef, ['edit', 'scope', '*'], 99);  
91      if (FIGRules::nmpdr_mode($cgi)) {      if (FIGRules::nmpdr_mode($cgi)) {
92          $menu->add_category('&raquo;Help', "$FIG_Config::nmpdr_site_url/content/help.php", 'help', undef, 98);          $menu->add_category('Help', "$FIG_Config::nmpdr_site_url/content/help.php", 'help', undef, 98);
93          $menu->add_entry('&raquo;Help', 'Searching NMPDR', "$FIG_Config::nmpdr_site_url/content/find.php");          $menu->add_entry('Help', 'Searching NMPDR', "$FIG_Config::nmpdr_site_url/content/find.php");
94          $menu->add_entry('&raquo;Help', 'SEED Viewer Tutorial', 'http://www.theseed.org/wiki/SEED_Viewer_Tutorial');          $menu->add_entry('Help', 'Contact', "$FIG_Config::nmpdr_site_url/content/contactus.php");
         $menu->add_entry('&raquo;Help', 'Contact', "$FIG_Config::nmpdr_site_url/content/contact.php");  
95      } else {      } else {
96          $menu->add_category('&raquo;Help', 'http://www.theseed.org', 'help', undef, 98);          $menu->add_category('&raquo;Help', 'http://www.theseed.org', 'help', undef, 98);
97          $menu->add_entry('&raquo;Help', 'What is the SEED', 'http://www.theseed.org/wiki/Home_of_the_SEED');          $menu->add_entry('&raquo;Help', 'What is the SEED', 'http://www.theseed.org/wiki/Home_of_the_SEED');
# Line 99  Line 107 
107                                          layout   => $layout,                                          layout   => $layout,
108                                          default  => 'Home',                                          default  => 'Home',
109                                        } );                                        } );
110      $WebApp->page_title_prefix('SEED Viewer - ');      my $prefix = (FIGRules::nmpdr_mode($cgi) ? "NMPDR " : "") . "Seed Viewer - ";
111        $WebApp->page_title_prefix($prefix);
112      $WebApp->show_login_user_info(1);      $WebApp->show_login_user_info(1);
113    
114      # run application      # run application

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