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revision 1.99, Tue Sep 19 21:19:14 2006 UTC revision 1.127, Wed Jul 16 22:12:00 2008 UTC
# Line 17  Line 17 
17    
18  package HTML;  package HTML;
19    
20    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 27  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=new raelib;  my $raelib;
36    
37    
38  my $top_link_cache;  my $top_link_cache;
# Line 56  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 = '..';          $top = '..';
70  #       warn "subdir @parts\n";  #       warn "subdir @parts\n";
# Line 163  Line 166 
166      shift if UNIVERSAL::isa($_[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 180  Line 183 
183      #      #
184      # Find the HTML header      # Find the HTML header
185      #      #
186        Trace("Reading tail.") if T(3);
187        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 203  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 251  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 297  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 327  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 340  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 350  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 359  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 389  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 415  Line 422 
422          # BASE href needs to be absolute. RDO.          # BASE href needs to be absolute. RDO.
423          #          #
424          #          #
425          $base_url = &FIG::cgi_url;  #        $base_url = &FIG::cgi_url;
426  #       my $base_url = $FIG_Config::cgi_base;  #       my $base_url = $FIG_Config::cgi_base;
427  #       if ( ! $base_url )                      # if cgi_base was not defined  #       if ( ! $base_url )                      # if cgi_base was not defined
428  #       {  #       {
# Line 438  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 448  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 465  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 479  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 >= @$html)        # </body> not found; look for </html>
494      {      {
# Line 498  Line 503 
503    
504      if ( @tail )      if ( @tail )
505      {      {
506            Trace("Splicing tail.") if T(3);
507          splice( @$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, $i, 0, @tags );
513      }      }
514    
515        Trace("Printing the HTML array.") if T(3);
516      # RAE the chomp will return any new lines at the ends of elements in the array,      # RAE the chomp will return any new lines at the ends of elements in the array,
517      # and then we can join  with a "\n". This is because somethings put newlines in,      # and then we can join  with a "\n". This is because somethings put newlines in,
518      # and others don't. This should make nicer looking html      # and others don't. This should make nicer looking html
# Line 513  Line 521 
521      # print join "\n", @$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 537  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 558  Line 570 
570      push(@tab,"</table>\n");      push(@tab,"</table>\n");
571    
572      # excelfile should be appropriate for a filename (no spaces/special characters)      # excelfile should be appropriate for a filename (no spaces/special characters)
573      if (defined $options{"excelfile"}) {push @tab, $raelib->tab2excel($col_hdrs,$tab,$title,\%options,$options{"excelfile"})}      if (defined $options{"excelfile"}) {
574            if (! defined($raelib)) {
575                require raelib;
576                $raelib = new raelib;
577            }
578            push @tab, $raelib->tab2excel($col_hdrs,$tab,$title,\%options,$options{"excelfile"})}
579    
580      return join("",@tab);      return join("",@tab);
581  }  }
# Line 801  Line 818 
818      return "<a href=$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 834  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 858  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 ($just_url)
# Line 867  Line 923 
923          }          }
924          else          else
925          {          {
926              return "<a href='$link'>$n</a>";              return "<a target=_blank href='$link'>$n</a>";
927          }          }
928      }      }
929      return $fid;      return $fid;
# Line 880  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 912  Line 992 
992          {          {
993              $url .= "?" . join("&",@args);              $url .= "?" . join("&",@args);
994          }          }
995          $request = new HTTP::Request('GET', $url);          my $request = new HTTP::Request('GET', $url);
996          my $response = $ua->request($request);          my $response = $ua->request($request);
997    
998          if ($response->is_success)          if ($response->is_success)
# Line 930  Line 1010 
1010    
1011  #   Now splice in a line of the form <base href=URL> to cause all relative links to work  #   Now splice in a line of the form <base href=URL> to cause all relative links to work
1012  #   properly.  Remove the header.  #   properly.  Remove the header.
1013        my $i;
1014      for ($i=0; ($i < @output) && ($output[$i] !~ /^\s*\</); $i++) {}      for ($i=0; ($i < @output) && ($output[$i] !~ /^\s*\</); $i++) {}
1015      if ($i < @output)      if ($i < @output) {
     {  
   
1016          splice(@output,0,$i);          splice(@output,0,$i);
1017      }      }
1018    
# Line 950  Line 1028 
1028  sub trim_output {  sub trim_output {
1029      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1030      my($out) = @_;      my($out) = @_;
1031      my $i;      my ($i, $j);
1032    
1033      for ($i=0; ($i < @$out) && ($out->[$i] !~ /^\</); $i++) {}      for ($i=0; ($i < @$out) && ($out->[$i] !~ /^\</); $i++) {}
1034      splice(@$out,0,$i);      splice(@$out,0,$i);
# Line 979  Line 1057 
1057      for ($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            #
1061            # Hm. We would have tried using the options here:
1062            # my $tail_name = $options{tail_name} ? $options{tail_name} : "html.tail";
1063            # 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`;          my @tmp = `cat $html_tail_file`;
1067          my $n = @tmp;          my $n = @tmp;
1068          splice(@$out,$j-$n,$n+1);          splice(@$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 {
1215      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1216      my($cgi,$x) = @_;      my($cgi,$x) = @_;
# Line 1011  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 1018  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 1184  Line 1424 
1424      return $x;      return $x;
1425  }  }
1426    
1427    sub lit_link {
1428        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1429        my($id) = @_;
1430    
1431        if ( $id =~ /([di]lit)\((\d+)\)/ )
1432        {
1433            my($pre, $pubmed_id) = ($1, $2);
1434            my $pubmed_url = &alias_url($pubmed_id, 'PMID');
1435            $id = "$pre(<a href='$pubmed_url' target=_blank>$pubmed_id</a>)";
1436        }
1437        return $id;
1438    }
1439    
1440  sub trembl_link {  sub trembl_link {
1441      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1442      my($cgi,$id) = @_;      my($cgi,$id) = @_;
# Line 1229  Line 1482 
1482          my $id=$1.$2;          my $id=$1.$2;
1483          return "<a href=\"http://pathema.tigr.org/tigr-scripts/pathema/shared/GenePage.cgi?locus=$id\" target=_blank>$tigr</a> (Pathema)";          return "<a href=\"http://pathema.tigr.org/tigr-scripts/pathema/shared/GenePage.cgi?locus=$id\" target=_blank>$tigr</a> (Pathema)";
1484      }      }
1485      elsif ($tigr =~ /^tigr\|(\S+)$/)      elsif ($tigr =~ /^tigr(cmr)?\|(\S+)$/)
1486      {      {
1487          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>";
1488      }      }
1489      return $tigr;      return $tigr;
1490  }  }
# Line 1339  Line 1592 
1592      return $kegg;      return $kegg;
1593  }  }
1594    
1595    sub img_link {
1596        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1597        my($cgi,$img) = @_;
1598    
1599        if ($img =~ /^img\|(\S+)$/)
1600        {
1601            return "<a href='http://img.jgi.doe.gov/cgi-bin/pub/main.cgi?page=geneDetail&gene_oid=$1' target=_blank>$img</a>";
1602        }
1603        return $img;
1604    }
1605    
1606  sub ensembl_link {  sub ensembl_link {
1607      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1608      my($cgi,$ensembl) = @_;      my($cgi,$ensembl) = @_;
# Line 1391  Line 1655 
1655      {      {
1656          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>";
1657      }      }
1658      return $mim;  
1659        return $hgnc;
1660  }  }
1661    
1662  sub unigene_link {  sub unigene_link {
# Line 1494  Line 1759 
1759      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1760      my($cgi,$map,$org) = @_;      my($cgi,$map,$org) = @_;
1761    
1762      $user = $cgi->param('user');      my $user = $cgi->param('user');
1763      $user = $user ? $user : "";      $user = $user ? $user : "";
1764      $org = $org ? $org : "";      $org = $org ? $org : "";
1765    
# Line 1512  Line 1777 
1777    # -name => field and the checkbox name    # -name => field and the checkbox name
1778    my ($form, $button)=@_;    my ($form, $button)=@_;
1779    
1780    $java_script="<input type=\"button\" name=\"CheckAll\" value=\"Check All\"\nonClick=\"checkAll(document.$form.$button)\">\n";    my $java_script="<input type=\"button\" name=\"CheckAll\" value=\"Check All\"\nonClick=\"checkAll(document.$form.$button)\">\n";
1781    $java_script.="<input type=\"button\" name=\"CheckFirst\" value=\"Check First Half\"\nonClick=\"checkFirst(document.$form.$button)\">\n";    $java_script.="<input type=\"button\" name=\"CheckFirst\" value=\"Check First Half\"\nonClick=\"checkFirst(document.$form.$button)\">\n";
1782    $java_script.="<input type=\"button\" name=\"CheckSecond\" value=\"Check Second Half\"\nonClick=\"checkSecond(document.$form.$button)\">\n";    $java_script.="<input type=\"button\" name=\"CheckSecond\" value=\"Check Second Half\"\nonClick=\"checkSecond(document.$form.$button)\">\n";
1783    $java_script.="<input type=\"button\" name=\"UnCheckAll\" value=\"Uncheck All\"\nonClick=\"uncheckAll(document.$form.$button)\">\n";    $java_script.="<input type=\"button\" name=\"UnCheckAll\" value=\"Uncheck All\"\nonClick=\"uncheckAll(document.$form.$button)\">\n";
# Line 1520  Line 1785 
1785    return $java_script;    return $java_script;
1786  }  }
1787    
1788    =head3 sub_link
1789    
1790        my $htmlText = HTML::sub_link($cgi, $sub, gid);
1791    
1792    Create a subsystem link. The link will be to the display page if there is no
1793    user or we are in SPROUT mode; otherwise it will be to the edit page.
1794    
1795    =over 4
1796    
1797    =item cgi
1798    
1799    CGI query object for the current web session. The parameters of special interest
1800    are C<SPROUT> and C<user>. If the user is non-blank and SPROUT mode is 0, then
1801    the subsystem's edit page will be shown rather than its display page.
1802    
1803    =item sub
1804    
1805    Name of the desired subsystem. It will be cleaned of underscores before the
1806    hyperlink is applied.
1807    
1808    =item gid
1809    
1810    Genome ID to be specified as the focus.
1811    
1812    =back
1813    
1814    =cut
1815    
1816  sub sub_link {  sub sub_link {
1817        # Allow call as an instance in addition to the authorized method.
1818      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1819      my($cgi,$sub) = @_;      # Get the parameters.
1820      my($sub_link);      my ($cgi, $sub, $gid) = @_;
1821        # Declare the return variable.
1822        my $retVal;
1823        # Clean the subsystem name for display purposes. This is a very
1824        # different thing from URL-escaping.
1825        my $cleaned = Tracer::Clean($sub);
1826        $cleaned =~ s/_/ /g;
1827        # URL-escape the subsystem name for use in the link.
1828        my $linkable = uri_escape($sub);
1829        # Determine the mode. Note we use the little OR trick to insure that
1830        # we have the correct value for plugging into the output link.
1831        my $user = $cgi->param('user') || "";
1832        my $sproutMode = $cgi->param('SPROUT') || 0;
1833        if ($user && ! $sproutMode) {
1834            # A SEED user is calling, so we go to the edit page.
1835            $retVal = "<a href=\"subsys.cgi?ssa_name=$linkable&request=show_ssa&user=$user\">$cleaned</a>";
1836        } else {
1837            # A visitor or SPROUT user is calling, so we go to the display page.
1838            $retVal = "<a href=\"display_subsys.cgi?ssa_name=$linkable;request=show_ssa;sort=by_phylo;focus=$gid;SPROUT=$sproutMode\">$cleaned</a>";
1839        }
1840        # Return the result.
1841        return $retVal;
1842    }
1843    
1844      my $user = $cgi->param('user');  sub reaction_map_link {
1845      my $esc_sub = uri_escape( $sub );      my($mapID, @reaction_list) = @_;
1846      $sub =~ s/\_/ /g;      if($mapID =~ /\d+/)
1847      if ($user)      {
1848            my $reactions = join "+", @reaction_list;
1849            if ($reactions ne "")
1850      {      {
1851          $sub_link = "<a href=./subsys.cgi?ssa_name=$esc_sub&request=show_ssa&user=$user>$sub</a>";              $reactions = "+".$reactions;
1852            }
1853    
1854            return "<a href=http://www.genome.jp/dbget-bin/show_pathway?rn$mapID$reactions>$mapID</a>";
1855      }      }
1856      else      else
1857      {      {
1858          $sub_link = "<a href=\"display_subsys.cgi?ssa_name=$esc_sub&request=show_ssa&sort=by_phylo\">$sub</a>";          return $mapID;
1859      }      }
     return $sub_link;  
1860  }  }
1861    
1862    sub compound_link {
1863        my($compound) = @_;
1864        if($compound =~ /^C\d+/)
1865        {
1866            return "<a href=\"javascript:void(0)\"onclick=\"window.open('http://www.genome.jp/dbget-bin/www_bget?compound+$compound','$&','height=640,width=800,scrollbars=yes,toolbar=yes,status=yes,resizable=yes')\">$compound</a>";
1867        }
1868        else
1869        {
1870            return $compound;
1871        }
1872    }
1873    
1874    
1875  sub reaction_link {  sub reaction_link {
1876      my($reaction) = @_;      my($reaction) = @_;
1877      if ($reaction =~ /^(\*)?(R\d+)/)      if ($reaction =~ /^(\*)?(R\d+)/)
1878      {      {
1879          return "<a href=\"http://www.genome.ad.jp/dbget-bin/www_bget?rn+$2\" target=reaction$$>$reaction</a>";          # return "<a href=\"http://www.genome.ad.jp/dbget-bin/www_bget?rn+$2\" target=reaction$$>$reaction</a>";
1880            return "<a href=\"javascript:void(0)\"onclick=\"window.open('http://www.genome.ad.jp/dbget-bin/www_bget?rn+$reaction','$&','height=640,width=800,scrollbars=yes,toolbar=yes,status=yes,resizable=yes')\">$reaction</a>";
1881      }      }
1882      return $reaction;      return $reaction;
1883  }  }
# Line 1555  Line 1889 
1889    
1890      my @vals = ();      my @vals = ();
1891      my $set = 1;      my $set = 1;
1892      foreach $peg_set (@$peg_sets)      foreach my $peg_set (@$peg_sets)
1893      {      {
1894          for ($i=0; ($i < @$peg_set); $i++)          for ($i=0; ($i < @$peg_set); $i++)
1895          {          {
1896              $peg = $peg_set->[$i];              my $peg = $peg_set->[$i];
1897              push(@vals,'show=' . join("@",($set,$i+1,$peg,&FIG::abbrev($fig->org_of($peg)),"")));              push(@vals,'show=' . join("@",($set,$i+1,$peg,&FIG::abbrev($fig->org_of($peg)),"")));
1898          }          }
1899          $set++;          $set++;
# Line 1670  Line 2004 
2004    
2005    
2006   my @files=("SEED.rss");   my @files=("SEED.rss");
2007   if ($args->{"type"}) {push @files, "SEED.$type.rss"}   if ($args->{"type"}) {
2008        my $type = $args->{type};
2009        push @files, "SEED.$type.rss"
2010    }
2011    
2012   foreach my $file ("SEED.rss", @$files)   foreach my $file ("SEED.rss", @$files)
2013   {   {

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