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revision 1.100, Sun Sep 24 15:22:58 2006 UTC revision 1.128, Thu Jul 17 19:33:19 2008 UTC
# Line 20  Line 20 
20  use strict;  use strict;
21  use Tracer;  use Tracer;
22  use FIG;  use FIG;
23    use FIGRules;
24  use Carp;  use Carp;
25  use Data::Dumper;  use Data::Dumper;
26  use LWP::UserAgent;  use LWP::UserAgent;
# Line 28  Line 29 
29  use URI::URL;  use URI::URL;
30  use HTTP::Request::Common;  use HTTP::Request::Common;
31  use POSIX;  use POSIX;
32    use CGI;
33    
34  #use raelib; # now used for the excel function, that should eventually end up in here. Way too experimental!  #use raelib; # now used for the excel function, that should eventually end up in here. Way too experimental!
35  my $raelib;  my $raelib;
# Line 57  Line 59 
59    
60      my @parts = split(/\//, $ENV{SCRIPT_NAME});      my @parts = split(/\//, $ENV{SCRIPT_NAME});
61      my $top;      my $top;
62      if ($parts[-2] eq 'FIG')      if (defined $parts[-2] && $parts[-2] eq 'FIG')
63      {      {
64          $top = '.';          $top = '.';
65  #       warn "toplevel @parts\n";  #       warn "toplevel @parts\n";
66      }      }
67      elsif ($parts[-3] eq 'FIG')      elsif (defined $parts[-3] && $parts[-3] eq 'FIG')
68      {      {
69          $top = '..';          $top = '..';
70  #       warn "subdir @parts\n";  #       warn "subdir @parts\n";
# Line 164  Line 166 
166      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
167      my($cgi,$html,$no_home, $alt_header, $css, $javasrc, $cookie, $options) = @_;      my($cgi,$html,$no_home, $alt_header, $css, $javasrc, $cookie, $options) = @_;
168      my $i;      my $i;
169        Trace("Setting top link.") if T(3);
170      my $top = top_link();      my $top = top_link();
171    
172      # ARGUMENTS:      # ARGUMENTS:
# Line 181  Line 183 
183      #      #
184      # Find the HTML header      # Find the HTML header
185      #      #
186        Trace("Reading tail.") if T(3);
187      ### TRS ### "tail_name" has no value here.      my $tail_name = $options->{tail_name} ? $options->{tail_name} : "html.tail";
188      my $html_tail_file = ""; # "./Html/$tail_name";      my $html_tail_file = "./Html/$tail_name";
189  #    if (! -f $html_tail_file)      if (! -f $html_tail_file)
190  #    {      {
191  #        $html_tail_file = "$FIG_Config::fig/CGI/Html/$tail_name";          $html_tail_file = "$FIG_Config::fig/CGI/Html/$tail_name";
192  #    }      }
193        Trace("Extracting user name and header data.") if T(3);
194      my $user = $cgi->param('user') || "";      my $user = $cgi->param('user') || "";
195      my @html_hdr;      my @html_hdr;
196      if ($alt_header && ref($alt_header) eq "ARRAY")      if ($alt_header && ref($alt_header) eq "ARRAY")
# Line 205  Line 207 
207    
208      # Note: 3/10/05 commented this line out pending the discussion of adding cookies into the seed that we are waiting to see about      # Note: 3/10/05 commented this line out pending the discussion of adding cookies into the seed that we are waiting to see about
209      # to add cookies back in replace these two header lines with each other      # to add cookies back in replace these two header lines with each other
210        #my $hdr_thing = $cgi->header(-cookie=>$cookie);
211      #print $cgi->header(-cookie=>$cookie);      my $hdr_thing = $cgi->header();
212      print $cgi->header();      Trace("Printing HTML header: $hdr_thing.") if T(3);
213        print $hdr_thing;
214        Trace("Header printed.") if T(3);
215      #      #
216      #  The SEED header file goes immediately after <BODY>.  Figure out      #  The SEED header file goes immediately after <BODY>.  Figure out
217      #  what parts of the HTML document skeleton are there, and fill in      #  what parts of the HTML document skeleton are there, and fill in
# Line 253  Line 256 
256      my $body_line = -1;      my $body_line = -1;
257      my $last_head_line = -1;  #  If no head tags are found, text goes at top.      my $last_head_line = -1;  #  If no head tags are found, text goes at top.
258      my $done = 0;      my $done = 0;
259        Trace("Processing special cases.") if T(3);
260      for ( $i = 0; $i < @$html; $i++ )      for ( $i = 0; $i < @$html; $i++ )
261      {      {
262          #  Some special cases:          #  Some special cases:
# Line 299  Line 302 
302    
303      if ( 1 )      if ( 1 )
304      {      {
305            Trace("Sanity checks in progress.") if T(3);
306          if ( $html_line >= 0 )          if ( $html_line >= 0 )
307          {          {
308              if ( ( $head_line >= 0 ) && ( $html_line > $head_line ) )              if ( ( $head_line >= 0 ) && ( $html_line > $head_line ) )
309              {              {
310                  print STDERR "<HTML> tag follows <HEAD> tag\n";                  Trace("<HTML> tag follows <HEAD> tag.") if T(1);
311              }              }
312              if ( ( $head_end_line >= 0 ) && ( $html_line > $head_end_line ) )              if ( ( $head_end_line >= 0 ) && ( $html_line > $head_end_line ) )
313              {              {
314                  print STDERR "<HTML> tag follows </HEAD> tag\n";                  Trace("<HTML> tag follows </HEAD> tag.") if T(1);
315              }              }
316          }          }
317          if ( $head_line >= 0 )          if ( $head_line >= 0 )
318          {          {
319              if ( ( $head_end_line >= 0 ) && ( $head_line > $head_end_line ) )              if ( ( $head_end_line >= 0 ) && ( $head_line > $head_end_line ) )
320              {              {
321                  print STDERR "<HEAD> tag follows </HEAD> tag\n";                  Trace("<HEAD> tag follows </HEAD> tag.") if T(1);
322              }              }
323          }          }
324      }      }
325        Trace("Sanity checks complete.") if T(3);
326      #      #
327      #  Okay.  Let's put in the html header file, and missing tags:      #  Okay.  Let's put in the html header file, and missing tags:
328      #      #
# Line 329  Line 333 
333      #  Note if no buttons are added we still (at the moment) add the script,      #  Note if no buttons are added we still (at the moment) add the script,
334      #  but it only adds a little text (495 characters) to the html and noone will notice!      #  but it only adds a little text (495 characters) to the html and noone will notice!
335      #  RAE: This is now deprecated because everything is in an external file, FIG.js, included later      #  RAE: This is now deprecated because everything is in an external file, FIG.js, included later
   
336      if ( $body_line < 0 )      if ( $body_line < 0 )
337      {      {
338          $body_line = $last_head_line + 1;          $body_line = $last_head_line + 1;
339            Trace("Splicing body line at $body_line.") if T(3);
340          splice( @$html, $body_line, 0, "<BODY>\n" );          splice( @$html, $body_line, 0, "<BODY>\n" );
341      }      }
342    
# Line 342  Line 346 
346    
347      if (@html_hdr)      if (@html_hdr)
348      {      {
349            Trace("Splicing SEED page header after $body_line.") if T(3);
350          splice( @$html, $body_line + 1, 0, @html_hdr );          splice( @$html, $body_line + 1, 0, @html_hdr );
351      }      }
352    
# Line 352  Line 357 
357      if ( $head_end_line < 0 )      if ( $head_end_line < 0 )
358      {      {
359          $head_end_line = $body_line;          $head_end_line = $body_line;
360            Trace("Splicing header terminater at $body_line.") if T(3);
361          splice( @$html, $body_line, 0, "</HEAD>\n" );          splice( @$html, $body_line, 0, "</HEAD>\n" );
362      }      }
363    
# Line 361  Line 367 
367      # be moved out, but I want to try it and see what happens.  css has the format:      # be moved out, but I want to try it and see what happens.  css has the format:
368      #      #
369      # <link rel='stylesheet' title='default' href='/css/default.css' type='text/css'>      # <link rel='stylesheet' title='default' href='/css/default.css' type='text/css'>
370        Trace("Formatting CSS.") if T(3);
371      # convert the default key to the right case. and eliminate dups      # convert the default key to the right case. and eliminate dups
372      foreach my $k (keys %$css) {if (lc($k) eq "default") {$css->{'Default'}=$css->{$k}}}      foreach my $k (keys %$css) {if (lc($k) eq "default") {$css->{'Default'}=$css->{$k}}}
373    
# Line 391  Line 397 
397    
398      # the file FIG.js contains most of the java script we use routinely. Every browser will just cache this and so      # the file FIG.js contains most of the java script we use routinely. Every browser will just cache this and so
399      # it will reduce our overhead.      # it will reduce our overhead.
400        Trace("Formatting javascript.") if T(3);
401      # $javasrc must be a ref to an array with urls (absolute or relative) to the javascripts      # $javasrc must be a ref to an array with urls (absolute or relative) to the javascripts
402      push @$javasrc, "Html/css/FIG.js";      push @$javasrc, "Html/css/FIG.js";
403      foreach my $script (@$javasrc) {      foreach my $script (@$javasrc) {
404          $csstext .= "<script src=\"$script\" type=\"text/javascript\"></script>\n";          $csstext .= "<script src=\"$script\" type=\"text/javascript\"></script>\n";
405      }      }
406    
407        Trace("Re-splicing the header terminator at $head_end_line.") if T(3);
   
408      splice( @$html, $head_end_line, 1, "$csstext</HEAD>\n" );  # note here I am replacing the </head> line. Could be bad...? But it doesn't increment everything else.      splice( @$html, $head_end_line, 1, "$csstext</HEAD>\n" );  # note here I am replacing the </head> line. Could be bad...? But it doesn't increment everything else.
409    
410      #      #
# Line 440  Line 445 
445      if ( $html_line < 0 )      if ( $html_line < 0 )
446      {      {
447          $html_line = 0;          $html_line = 0;
448            Trace("Splicing the HTML tag at $html_line.") if T(3);
449          splice( @$html, $html_line, 0, "<HTML>\n" );          splice( @$html, $html_line, 0, "<HTML>\n" );
450      }      }
451    
# Line 450  Line 456 
456      if ( $head_line < 0 )      if ( $head_line < 0 )
457      {      {
458          $head_line = $html_line + 1;          $head_line = $html_line + 1;
459            Trace("Splicing the HEAD tag at $head_line.") if T(3);
460          splice( @$html, $head_line, 0, "<HEAD>\n" );          splice( @$html, $head_line, 0, "<HEAD>\n" );
461      }      }
462    
463      #      #
464      #  Place FIG search link at bottom of page      #  Place FIG search link at bottom of page
465      #      #
466        Trace("Placing FIG search link.") if T(3);
467      my @tail = -f $html_tail_file ? `cat $html_tail_file` : ();      my @tail = -f $html_tail_file ? `cat $html_tail_file` : ();
468      if (! $no_home)      if (! $no_home)
469      {      {
# Line 467  Line 474 
474      #      #
475      # See if we have a site-specific tail (for disclaimers, etc).      # See if we have a site-specific tail (for disclaimers, etc).
476      #      #
477        Trace("Placing site tail.") if T(3);
478      my $site_tail = "$FIG_Config::fig_disk/config/site_tail.html";      my $site_tail = "$FIG_Config::fig_disk/config/site_tail.html";
479      my $site_fh;      my $site_fh;
480      if (open($site_fh, "<$site_tail"))      if (open($site_fh, "<$site_tail"))
# Line 481  Line 488 
488      #  or before </html>, or at end of page.      #  or before </html>, or at end of page.
489      #      #
490      my @tags = ();      my @tags = ();
491      # Check for a tracing queue.      Trace("Processing closing tags.") if T(3);
     my $traceString = QTrace("HTML");  
     if ($traceString) {  
         push @tags, $traceString;  
     }  
492      for ($i=0; ($i < @$html) && ($html->[$i] !~ /\<\/body\>/i); $i++) {}      for ($i=0; ($i < @$html) && ($html->[$i] !~ /\<\/body\>/i); $i++) {}
493      if ($i >= @$html)        # </body> not found; look for </html>      if ($i >= @$html)        # </body> not found; look for </html>
494      {      {
# Line 500  Line 503 
503    
504      if ( @tail )      if ( @tail )
505      {      {
506            Trace("Splicing tail.") if T(3);
507          splice( @$html, $i, 0, @tail, @tags );          splice( @$html, $i, 0, @tail, @tags );
508      }      }
509      elsif ( @tags )      elsif ( @tags )
510      {      {
511            Trace("Splicing tags.") if T(3);
512          splice( @$html, $i, 0, @tags );          splice( @$html, $i, 0, @tags );
513      }      }
514    
515        Trace("Printing the HTML array.") if T(3);
516      # RAE the chomp will return any new lines at the ends of elements in the array,      # RAE the chomp will return any new lines at the ends of elements in the array,
517      # and then we can join  with a "\n". This is because somethings put newlines in,      # and then we can join  with a "\n". This is because somethings put newlines in,
518      # and others don't. This should make nicer looking html      # and others don't. This should make nicer looking html
# Line 515  Line 521 
521      # print join "\n", @$html;      # print join "\n", @$html;
522      #      #
523      # Apparently the above still breaks things. This is the correct code:      # Apparently the above still breaks things. This is the correct code:
   
524      foreach $_ (@$html)      foreach $_ (@$html)
525      {      {
526          print $_;          my $line = $_;
527            if (T(4)) {
528                my $escapedLine = Tracer::Clean($line);
529                Trace("Printing:\n$escapedLine") if T(4);
530            }
531            print $line;
532      }      }
533    
534  }  }
# Line 539  Line 549 
549      my(@tab);      my(@tab);
550    
551      my $border = defined $options{border} ? "border=\"$options{border}\"" : "border";      my $border = defined $options{border} ? "border=\"$options{border}\"" : "border";
552      my $width = defined $options{width} ? "width=\"$options{width}\"" : undef;      my $width = defined $options{width} ? "width=\"$options{width}\"" : "";
553      my $class = defined $options{class} ? "class=\"$options{class}\"" : undef;      my $class = defined $options{class} ? "class=\"$options{class}\"" : "";
554      push( @tab, "\n<table $border $width $class>\n",      push( @tab, "\n<table $border $width $class>\n",
555                  "\t<caption><b>$title</b></caption>\n",                  "\t<caption><b>$title</b></caption>\n",
556                  "\t<tr>\n\t\t"                  "\t<tr>\n\t\t"
# Line 808  Line 818 
818      return "<a href=$link>$role</a>";      return "<a href=$link>$role</a>";
819  }  }
820    
821  #  =head2 fid_link
822  # Local means to eliminate the fig|org.peg from the  
823  # text of the link.  Get a link to a fid.
824  #  
825    use: my $html=&HTML::fid_link($cgi, $fid, Local, Just_URL, Full_Path);
826    
827    Local is a boolean means to eliminate the fig|org.peg from the text of the link.
828    
829    Just_URL will only return the URL and not the HTML code. The default is to return the full code.
830    
831    Full_Path is a boolean that will get the full path to the URL not just a relative path. This is required in pages where the base href changes (e.g. if an image is imported like on the metabolic pages).
832    
833    =cut
834    
835    
836  sub fid_link {  sub fid_link {
837      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
838      my($cgi,$fid,$local,$just_url) = @_;      my($cgi,$fid,$local,$just_url,$fullpath) = @_;
839        Trace("Creating link for feature $fid.") if T(4);
840        my $err=join(" ", $cgi,$fid,$local,$just_url,$fullpath);
841        if (FIGRules::nmpdr_mode($cgi)) {
842            # We're NMPDR. Compute the link to the seed viewer feature page.
843            my $link = "seedviewer.cgi?page=Annotation;feature=$fid";
844            if ($fullpath) {
845                # Full-path mode: add the base URL.
846                $link = "$FIG_Config::cgi_url/$link";
847            }
848            if ($just_url) {
849                # URL-only mode: return the link.
850                return $link;
851            } else {
852                # HTML mode. We need to compute the link text.
853                my $text = $fid;
854                # If we're in local mode, we remove everything but the final number from the fig ID.
855                if ($local) {
856                    $fid =~ s/^.+\.//;
857                }
858                # Return the full HTML for the link.
859                return "<a href=\"$link\">$text</a>";
860            }
861        }
862      my($n);      my($n);
863    
864      my $top = top_link();      my $top = top_link();
865        if ($fullpath) {$top=$FIG_Config::cgi_url}
866    
867      if ($fid =~ /^fig\|\d+\.\d+\.([a-z]+)\.(\d+)/)      if ($fid =~ /^fig\|\d+\.\d+\.([a-zA-Z]+)\.(\d+)/)
868      {      {
869          if ($local)          if ($local)
870          {          {
# Line 841  Line 886 
886          my $new_framework = $cgi->param('new_framework') ? 1 : 0;          my $new_framework = $cgi->param('new_framework') ? 1 : 0;
887          #added to format prophage and path island links to feature.cgi          #added to format prophage and path island links to feature.cgi
888          my $sprout = $cgi->param('SPROUT') ? "&SPROUT=1" : "";          my $sprout = $cgi->param('SPROUT') ? "&SPROUT=1" : "";
889            my $virt = "&48hr_job=" . $cgi->param("48hr_job");
890            Trace("Sprout mode is \"$sprout\".") if T(4);
891          if ($1 ne "peg" && ! $sprout)          if ($1 ne "peg" && ! $sprout)
892          {          {
893               Trace("Creating feature link for $fid.") if T(4);
894             my $user = $cgi->param('user');             my $user = $cgi->param('user');
895             if (! $user) { $user = "" }             if (! $user) { $user = "" }
896             $link = "$top/feature.cgi?feature=$fid&user=$user$sprout";             $link = "$top/feature.cgi?feature=$fid&user=$user$sprout$virt";
897             $link =~ s/[a-z_A-Z0-9]+\.cgi\?/feature.cgi?/;             $link =~ s/[a-z_A-Z0-9]+\.cgi\?/feature.cgi?/;
898          }          }
899          else          else
900          {          {
901                Trace("Creating protein link for $fid.") if T(4);
902              my $user = $cgi->param('user');              my $user = $cgi->param('user');
903              if (! $user) { $user = "" }              if (! $user) { $user = "" }
904              my $trans = $cgi->param('translate') ? "&translate=1" : "";              my $trans = $cgi->param('translate') ? "&translate=1" : "";
# Line 865  Line 914 
914    
915              #if (! $cgi_url) { $cgi_url = &FIG::cgi_url }              #if (! $cgi_url) { $cgi_url = &FIG::cgi_url }
916              #$link = $cgi_url . "/protein.cgi?prot=$fid&user=$user$trans$sprout";              #$link = $cgi_url . "/protein.cgi?prot=$fid&user=$user$trans$sprout";
917              $link = "$top/protein.cgi?prot=$fid&user=$user$trans$sprout\&new_framework=$new_framework";              $link = "$top/protein.cgi?prot=$fid&user=$user$trans$sprout$virt\&new_framework=$new_framework";
918              $link =~ s/[a-z_A-Z0-9]+\.cgi\?/protein.cgi?/;              $link =~ s/[a-z_A-Z0-9]+\.cgi\?/protein.cgi?/;
919          }          }
920          if ($just_url)          if ($just_url)
# Line 874  Line 923 
923          }          }
924          else          else
925          {          {
926              return "<a href='$link'>$n</a>";              return "<a target=_blank href='$link'>$n</a>";
927          }          }
928      }      }
929      return $fid;      return $fid;
# Line 887  Line 936 
936      return $family;      return $family;
937  }  }
938    
939    =head2 evidence_codes_explain
940    
941    Given an evidence code, returns a string that explains this eveidence code.
942    
943    =cut
944    
945    sub evidence_codes_explain {
946     my($ec)=@_;
947     return unless ($ec);
948    
949     $ec=uc($ec);
950     return "IDA: Inferred from Direct Assay" if ($ec =~ /IDA/);
951     return "IGI: Inferred from Genetic Interaction" if ($ec =~ /IGI/);
952     return "TAS: Traceable Author Statement" if ($ec =~ /TAS/);
953     return "ISU: in subsystem unique" if ($ec =~ /ISU/);
954     return "$ec: in subsystem duplicates" if ($ec =~ /IDU/);
955     return "$ec: in cluster with" if ($ec =~ /ICW/);
956     return "FF: in FIGfam" if ($ec =~ /FF/);
957     return "CWN: clustered with nonhypothetical" if ($ec =~ /CWN/);
958     return "CWH: clustered, but only with hypotheticals" if ($ec =~ /CWH/);
959     return "DLIT: literature references to this gene exist" if ($ec =~ /DLIT/);
960     return "ILIT: no references to this gene exist, but they do to other genes with the same functional role" if ($ec =~ /ILIT/);
961     return "$ec: unknown!";
962    }
963    
964  sub get_html {  sub get_html {
965      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
# Line 984  Line 1057 
1057      for ($j=$i-1; ($j > 0) && ($out->[$j] !~ /FIG search/); $j--) {}      for ($j=$i-1; ($j > 0) && ($out->[$j] !~ /FIG search/); $j--) {}
1058      if ($j > 0)      if ($j > 0)
1059      {      {
1060           ### TRS ###          #
1061  #        my @tmp = `cat $html_tail_file`;          # Hm. We would have tried using the options here:
1062  #        my $n = @tmp;          # my $tail_name = $options{tail_name} ? $options{tail_name} : "html.tail";
1063  #        splice(@$out,$j-$n,$n+1);          # but they're not passed in. So use the default html.tail.
1064            #
1065            my $html_tail_file = "./Html/html.tail";
1066            my @tmp = `cat $html_tail_file`;
1067            my $n = @tmp;
1068            splice(@$out,$j-$n,$n+1);
1069        }
1070    }
1071    
1072    =head2 alias_url
1073    
1074    Returns the url that links to an external page showing information about the given alias.
1075    The type of the alias will be determined by the prefix (i.e. 'tr|' for Trembl) If the type
1076    cannot be determined, the function will return undef.
1077    
1078    use: my $html=&HTML::alias_url($alias, $type);
1079    
1080    =cut
1081    
1082    sub alias_url {
1083      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1084    
1085      my ($id, $type) = @_;
1086    
1087      if ($type eq "SEED") { # 1
1088        return "http://seed-viewer.theseed.org/linkin.cgi?id=$id";
1089      }
1090      elsif ($type eq "UniProt") {
1091        return "http://www.uniprot.org/entry/$id";
1092      }
1093      elsif ($type eq "UniProt_ac") { # 2
1094        return "http://www.uniprot.org/entry/$id";
1095      }
1096      elsif ($type eq "UniProt_id") { # 3
1097        return "http://www.uniprot.org/entry/$id";
1098      }
1099      elsif ($type eq "EntrezGene") { # 4
1100        return "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&id=$id";
1101      }
1102      elsif ($type eq "RefSeq") { # 5
1103        return "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&id=$id";
1104      }
1105      elsif ($type eq "GIID") { # 6
1106        return "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&id=$id";
1107      }
1108      elsif ($type eq "NCBI") {
1109        return "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&id=$id";
1110      }
1111      elsif ($type eq "PDB") { # 7
1112        $id =~ s/\:\w//;
1113        return "http://www.rcsb.org/pdb/explore/explore.do?structureId=$id";
1114      }
1115      elsif ($type eq "PFAM") { # 8
1116        return "http://pfam.janelia.org/family?acc=$id";
1117      }
1118      elsif ($type eq "GO") { # 9
1119        return "http://amigo.geneontology.org/cgi-bin/amigo/go.cgi?view=details&search_constraint=terms&depth=0&query=$id";
1120      }
1121      elsif ($type eq "PIRSF") { # 10
1122        return "http://pir.georgetown.edu/cgi-bin/ipcSF?id=$id";
1123      }
1124      elsif ($type eq "IPI") { # 11
1125        return "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+[IPI-AllText:".$id."*]+-lv+30+-view+SeqSimpleView+-page+qResult";
1126      }
1127      elsif ($type eq "UniRef_100") { # 12
1128        return "http://www.uniprot.org/entry/$id";
1129      }
1130      elsif ($type eq "UniRef_90") { # 13
1131        return "http://www.uniprot.org/entry/$id";
1132      }
1133      elsif ($type eq "UniRef_50") { # 14
1134        return "http://www.uniprot.org/entry/$id";
1135      }
1136      elsif ($type eq "UniParc") { # 15
1137        return "http://www.uniprot.org/entry/$id";
1138      }
1139      elsif ($type eq "PIR-PSD") { # 16
1140        return "http://pir.georgetown.edu/cgi-bin/pir_psd_get.pl?id=$id";
1141      }
1142      elsif ($type eq "Taxon_ID") { # 17
1143        return "http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=$id";
1144      }
1145      elsif ($type eq "OMIM") { # 18
1146        return "http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=$id";
1147      }
1148      elsif ($type eq "UniGene") { # 19
1149        return "http://www.ncbi.nlm.nih.gov/sites/entrez?db=unigene&cmd=search&term=$id";
1150      }
1151      elsif ($type eq "Ensemble_ID") { # 20
1152        #return "$id";
1153      }
1154      elsif ($type eq "PMID") { # 21
1155        return "http://www.ncbi.nlm.nih.gov/pubmed/$id";
1156      }
1157      elsif ($type eq "EMBL_DNA_AC") { # 22
1158        return "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBL:".$id."]+-newId";
1159      }      }
1160      elsif ($type eq "EMBL_Protein_AC") { # 23
1161        $id =~ s/\.\d//;
1162        return "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[{EMBL}-ProteinID:".$id."]";
1163      }
1164      elsif ($type eq "CMR") { # 24
1165        if ($id =~ /^\d+$/) {
1166          return "http://cmr.jcvi.org/cgi-bin/CMR/shared/GenePage.cgi?type=PID&acc=".$id;
1167        } else {
1168          return "http://cmr.jcvi.org/tigr-scripts/CMR/shared/GenePage.cgi?locus=".$id;
1169        }
1170      }
1171      elsif ($type eq "SwissProt"){ # 25
1172          return "http://www.uniprot.org/entry/$id";
1173      }
1174      elsif ($type eq "IMG"){ # 26
1175          return "http://img.jgi.doe.gov/cgi-bin/pub/main.cgi?page=geneDetail&gene_oid=$id";
1176      }
1177      elsif ($type eq "KEGG") { # 27
1178          my ($pre,$post) = ($id) =~ /(.*):(.*)/;
1179          return "http://www.genome.ad.jp/dbget-bin/www_bget?" . $pre . "+" . $post;
1180      }
1181      elsif ($type eq "ASAP") { # 28
1182        return "https://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=$id";
1183      }
1184      elsif ($type eq "GenBank") { # 29
1185          return "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&id=$id";
1186      }
1187      elsif ($type eq "DBJ") { # 30
1188          return "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&id=$id";
1189      }
1190      elsif ($type eq "SCOP") { # 31
1191          $id =~ s/\:\w//;
1192          return "http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?pdb=$id";
1193      }
1194      elsif ($type eq "CATH") { # 32
1195          $id =~ s/\:\w//;
1196          return "http://www.cathdb.info/cgi-bin/CATHSrch.pl?type=PDB&query=$id";
1197      }
1198      elsif ($type eq "FSSP") { # 33
1199          $id =~ s/\:\w//;
1200          return "http://ekhidna.biocenter.helsinki.fi/dali/daliquery?find=$id";
1201      }
1202      elsif ($type eq "MMDB") { # 34
1203          $id =~ s/\:\w//;
1204          return "http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?form=6&db=tDopt=s&uid=$id";
1205      }
1206      elsif ($type eq "PDBsum") { # 35
1207          $id =~ s/\:\w//;
1208          return "http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=$id";
1209      }
1210    
1211      return undef;
1212  }  }
1213    
1214  sub set_prot_links {  sub set_prot_links {
# Line 1017  Line 1237 
1237          $after = $3;          $after = $3;
1238          return &set_prot_links($cgi,$before) . &HTML::gi_link($cgi,$match) . &set_prot_links($cgi,$after);          return &set_prot_links($cgi,$before) . &HTML::gi_link($cgi,$match) . &set_prot_links($cgi,$after);
1239      }      }
1240        elsif ($x =~ /^(.*)(img\|\d+)(.*)/s)
1241        {
1242            $before = $1;
1243            $match = $2;
1244            $after = $3;
1245            return &set_prot_links($cgi,$before) . &HTML::img_link($cgi,$match) . &set_prot_links($cgi,$after);
1246        }
1247      elsif ($x =~ /^(.*)(tigr\|\w+)(.*)/s)      elsif ($x =~ /^(.*)(tigr\|\w+)(.*)/s)
1248      {      {
1249          $before = $1;          $before = $1;
# Line 1024  Line 1251 
1251          $after = $3;          $after = $3;
1252          return &set_prot_links($cgi,$before) . &HTML::tigr_link($cgi,$match) . &set_prot_links($cgi,$after);          return &set_prot_links($cgi,$before) . &HTML::tigr_link($cgi,$match) . &set_prot_links($cgi,$after);
1253      }      }
1254        elsif ($x =~ /^(.*)(tigrcmr\|\w+)(.*)/s)
1255        {
1256            $before = $1;
1257            $match = $2;
1258            $after = $3;
1259            return &set_prot_links($cgi,$before) . &HTML::tigr_link($cgi,$match) . &set_prot_links($cgi,$after);
1260        }
1261      elsif ($x =~ /^(.*)\b(eric\|\S+)\b(.*)/s)      elsif ($x =~ /^(.*)\b(eric\|\S+)\b(.*)/s)
1262      {      {
1263          $before = $1;          $before = $1;
# Line 1190  Line 1424 
1424      return $x;      return $x;
1425  }  }
1426    
1427  sub trembl_link {  sub lit_link {
1428      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1429      my($cgi,$id) = @_;      my($id) = @_;
1430    
1431      if ($id =~ /^tr\|(.*)/) {      if ( $id =~ /([di]lit)\((\d+)\)/ )
1432        return "<a href='http://ca.expasy.org/uniprot/$1' target=_blank>$id</a>";      {
1433      } else {          my($pre, $pubmed_id) = ($1, $2);
1434        return "invalid call to trembl link";          my $pubmed_url = &alias_url($pubmed_id, 'PMID');
1435            $id = "$pre(<a href='$pubmed_url' target=_blank>$pubmed_id</a>)";
1436      }      }
1437        return $id;
1438  }  }
1439    
1440  sub refseq_link {  sub refseq_link {
# Line 1235  Line 1471 
1471          my $id=$1.$2;          my $id=$1.$2;
1472          return "<a href=\"http://pathema.tigr.org/tigr-scripts/pathema/shared/GenePage.cgi?locus=$id\" target=_blank>$tigr</a> (Pathema)";          return "<a href=\"http://pathema.tigr.org/tigr-scripts/pathema/shared/GenePage.cgi?locus=$id\" target=_blank>$tigr</a> (Pathema)";
1473      }      }
1474      elsif ($tigr =~ /^tigr\|(\S+)$/)      elsif ($tigr =~ /^tigr(cmr)?\|(\S+)$/)
1475      {      {
1476          return "<a href=\"http://www.tigr.org/tigr-scripts/CMR2/GenePage.spl?locus=$1\" target=_blank>$tigr</a>";          return "<a href=\"http://www.tigr.org/tigr-scripts/CMR2/GenePage.spl?locus=$2\" target=_blank>$tigr</a>";
1477      }      }
1478      return $tigr;      return $tigr;
1479  }  }
# Line 1299  Line 1535 
1535      return "<a href=\"http://www.vectorbase.org\" target=_blank>$vec</a>";      return "<a href=\"http://www.vectorbase.org\" target=_blank>$vec</a>";
1536  }  }
1537    
1538    sub uniprot_link {
1539        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1540        my($cgi,$uni) = @_;
1541    
1542        if ($uni =~ /^(sp|tr|uni)\|(\S+)$/)
1543        {
1544            return "<a href='" . &HTML::alias_url($2, 'UniProt') . "' target=_blank>$uni</a>";
1545        }
1546        return $uni;
1547    }
1548    
1549  sub uni_link {  sub uni_link {
1550      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
# Line 1307  Line 1553 
1553      if ($uni =~ /^uni\|(\S+)$/)      if ($uni =~ /^uni\|(\S+)$/)
1554      {      {
1555          #return "<a href=http://www.pir.uniprot.org/cgi-bin/upEntry?id=$1>$uni</a>";          #return "<a href=http://www.pir.uniprot.org/cgi-bin/upEntry?id=$1>$uni</a>";
1556          return "<a href='http://www.ebi.uniprot.org/uniprot-srv/uniProtView.do?proteinAc=$1' target=_blank>$uni</a>";          #return "<a href='http://www.ebi.uniprot.org/uniprot-srv/uniProtView.do?proteinAc=$1' target=_blank>$uni</a>";
1557            return "<a href='" . &HTML::alias_url($1, 'UniProt') . "' target=_blank>$uni</a>";
1558      }      }
1559      return $uni;      return $uni;
1560  }  }
# Line 1318  Line 1565 
1565    
1566      if ($sp =~ /^sp\|(\S+)$/)      if ($sp =~ /^sp\|(\S+)$/)
1567      {      {
1568          return "<a href='http://us.expasy.org/cgi-bin/get-sprot-entry?$1' target=_blank>$sp</a>";          #return "<a href='http://us.expasy.org/cgi-bin/get-sprot-entry?$1' target=_blank>$sp</a>";
1569            return "<a href='" . &HTML::alias_url($1, 'UniProt') . "' target=_blank>$sp</a>";
1570      }      }
1571      return $sp;      return $sp;
1572  }  }
1573    
1574    sub trembl_link {
1575        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1576        my($cgi,$tr) = @_;
1577    
1578        if ($tr =~ /^tr\|(\S+)$/)
1579        {
1580            #return "<a href='http://us.expasy.org/cgi-bin/get-sprot-entry?$1' target=_blank>$tr</a>";
1581            return "<a href='" . &HTML::alias_url($1, 'UniProt') . "' target=_blank>$tr</a>";
1582        }
1583        return $tr;
1584    }
1585    
1586  sub pir_link {  sub pir_link {
1587      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1588      my($cgi,$pir) = @_;      my($cgi,$pir) = @_;
# Line 1345  Line 1605 
1605      return $kegg;      return $kegg;
1606  }  }
1607    
1608    sub img_link {
1609        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1610        my($cgi,$img) = @_;
1611    
1612        if ($img =~ /^img\|(\S+)$/)
1613        {
1614            return "<a href='http://img.jgi.doe.gov/cgi-bin/pub/main.cgi?page=geneDetail&gene_oid=$1' target=_blank>$img</a>";
1615        }
1616        return $img;
1617    }
1618    
1619  sub ensembl_link {  sub ensembl_link {
1620      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1621      my($cgi,$ensembl) = @_;      my($cgi,$ensembl) = @_;
# Line 1397  Line 1668 
1668      {      {
1669          return "<a href='http://www.gene.ucl.ac.uk/cgi-bin/nomenclature/searchgenes.pl?field=symbol&anchor=equals&match=$1&symbol_search=Search&number=50&format=html&sortby=symbol' target=_blank>$hgnc</a>";          return "<a href='http://www.gene.ucl.ac.uk/cgi-bin/nomenclature/searchgenes.pl?field=symbol&anchor=equals&match=$1&symbol_search=Search&number=50&format=html&sortby=symbol' target=_blank>$hgnc</a>";
1670      }      }
1671      ### TRS ###: was $mim, changed to $hgnc  
1672      return $hgnc;      return $hgnc;
1673  }  }
1674    
# Line 1527  Line 1798 
1798    return $java_script;    return $java_script;
1799  }  }
1800    
1801    =head3 sub_link
1802    
1803        my $htmlText = HTML::sub_link($cgi, $sub, gid);
1804    
1805    Create a subsystem link. The link will be to the display page if there is no
1806    user or we are in SPROUT mode; otherwise it will be to the edit page.
1807    
1808    =over 4
1809    
1810    =item cgi
1811    
1812    CGI query object for the current web session. The parameters of special interest
1813    are C<SPROUT> and C<user>. If the user is non-blank and SPROUT mode is 0, then
1814    the subsystem's edit page will be shown rather than its display page.
1815    
1816    =item sub
1817    
1818    Name of the desired subsystem. It will be cleaned of underscores before the
1819    hyperlink is applied.
1820    
1821    =item gid
1822    
1823    Genome ID to be specified as the focus.
1824    
1825    =back
1826    
1827    =cut
1828    
1829  sub sub_link {  sub sub_link {
1830        # Allow call as an instance in addition to the authorized method.
1831      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1832      my($cgi,$sub) = @_;      # Get the parameters.
1833      my($sub_link);      my ($cgi, $sub, $gid) = @_;
1834        # Declare the return variable.
1835        my $retVal;
1836        # Clean the subsystem name for display purposes. This is a very
1837        # different thing from URL-escaping.
1838        my $cleaned = Tracer::Clean($sub);
1839        $cleaned =~ s/_/ /g;
1840        # URL-escape the subsystem name for use in the link.
1841        my $linkable = uri_escape($sub);
1842        # Determine the mode. Note we use the little OR trick to insure that
1843        # we have the correct value for plugging into the output link.
1844        my $user = $cgi->param('user') || "";
1845        my $sproutMode = $cgi->param('SPROUT') || 0;
1846        if ($user && ! $sproutMode) {
1847            # A SEED user is calling, so we go to the edit page.
1848            $retVal = "<a href=\"subsys.cgi?ssa_name=$linkable&request=show_ssa&user=$user\">$cleaned</a>";
1849        } else {
1850            # A visitor or SPROUT user is calling, so we go to the display page.
1851            $retVal = "<a href=\"display_subsys.cgi?ssa_name=$linkable;request=show_ssa;sort=by_phylo;focus=$gid;SPROUT=$sproutMode\">$cleaned</a>";
1852        }
1853        # Return the result.
1854        return $retVal;
1855    }
1856    
1857      my $user = $cgi->param('user');  sub reaction_map_link {
1858      my $esc_sub = uri_escape( $sub );      my($mapID, @reaction_list) = @_;
1859      $sub =~ s/\_/ /g;      if($mapID =~ /\d+/)
1860      if ($user)      {
1861            my $reactions = join "+", @reaction_list;
1862            if ($reactions ne "")
1863      {      {
1864          $sub_link = "<a href=./subsys.cgi?ssa_name=$esc_sub&request=show_ssa&user=$user>$sub</a>";              $reactions = "+".$reactions;
1865            }
1866    
1867            return "<a href=http://www.genome.jp/dbget-bin/show_pathway?rn$mapID$reactions>$mapID</a>";
1868        }
1869        else
1870        {
1871            return $mapID;
1872        }
1873    }
1874    
1875    sub compound_link {
1876        my($compound) = @_;
1877        if($compound =~ /^C\d+/)
1878        {
1879            return "<a href=\"javascript:void(0)\"onclick=\"window.open('http://www.genome.jp/dbget-bin/www_bget?compound+$compound','$&','height=640,width=800,scrollbars=yes,toolbar=yes,status=yes,resizable=yes')\">$compound</a>";
1880      }      }
1881      else      else
1882      {      {
1883          $sub_link = "<a href=\"display_subsys.cgi?ssa_name=$esc_sub&request=show_ssa&sort=by_phylo\">$sub</a>";          return $compound;
1884      }      }
     return $sub_link;  
1885  }  }
1886    
1887    
1888  sub reaction_link {  sub reaction_link {
1889      my($reaction) = @_;      my($reaction) = @_;
1890      if ($reaction =~ /^(\*)?(R\d+)/)      if ($reaction =~ /^(\*)?(R\d+)/)
1891      {      {
1892          return "<a href=\"http://www.genome.ad.jp/dbget-bin/www_bget?rn+$2\" target=reaction$$>$reaction</a>";          # return "<a href=\"http://www.genome.ad.jp/dbget-bin/www_bget?rn+$2\" target=reaction$$>$reaction</a>";
1893            return "<a href=\"javascript:void(0)\"onclick=\"window.open('http://www.genome.ad.jp/dbget-bin/www_bget?rn+$reaction','$&','height=640,width=800,scrollbars=yes,toolbar=yes,status=yes,resizable=yes')\">$reaction</a>";
1894      }      }
1895      return $reaction;      return $reaction;
1896  }  }
# Line 1678  Line 2018 
2018    
2019   my @files=("SEED.rss");   my @files=("SEED.rss");
2020   if ($args->{"type"}) {   if ($args->{"type"}) {
     ### TRS ### "$type" had no value here, so guessed what it should be.  
2021      my $type = $args->{type};      my $type = $args->{type};
2022      push @files, "SEED.$type.rss"      push @files, "SEED.$type.rss"
2023  }  }

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