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revision 1.6, Sun Mar 21 02:20:55 2004 UTC revision 1.121, Thu Mar 13 20:10:57 2008 UTC
# Line 1  Line 1 
1    #
2    # Copyright (c) 2003-2006 University of Chicago and Fellowship
3    # for Interpretations of Genomes. All Rights Reserved.
4    #
5    # This file is part of the SEED Toolkit.
6    #
7    # The SEED Toolkit is free software. You can redistribute
8    # it and/or modify it under the terms of the SEED Toolkit
9    # Public License.
10    #
11    # You should have received a copy of the SEED Toolkit Public License
12    # along with this program; if not write to the University of Chicago
13    # at info@ci.uchicago.edu or the Fellowship for Interpretation of
14    # Genomes at veronika@thefig.info or download a copy from
15    # http://www.theseed.org/LICENSE.TXT.
16    #
17    
18  package HTML;  package HTML;
19    
20    use strict;
21    use Tracer;
22    use FIG;
23  use Carp;  use Carp;
24  use Data::Dumper;  use Data::Dumper;
25  use LWP::UserAgent;  use LWP::UserAgent;
26  use LWP::Simple;  use LWP::Simple;
27    use URI::Escape;  # uri_escape()
28  use URI::URL;  use URI::URL;
29  use HTTP::Request::Common;  use HTTP::Request::Common;
30    use POSIX;
31    use CGI;
32    
33  sub show_page {  #use raelib; # now used for the excel function, that should eventually end up in here. Way too experimental!
34      my($cgi,$html,$no_home) = @_;  my $raelib;
35      my $i;  
36    
37    my $top_link_cache;
38    
39    
40    sub new
41    {
42        my($class) = @_;
43    
44        my $self = {};
45    
46        return bless $self, $class;
47    }
48    
49    sub top_link
50    {
51    
52      #      #
53      # Find the HTML header      # Determine if this is a toplevel cgi or one in one of the subdirs (currently
54        # just /p2p).
55      #      #
56    
57      my $html_hdr_file = "./Html/html.hdr";      return $top_link_cache if ($top_link_cache);
58    
59        my @parts = split(/\//, $ENV{SCRIPT_NAME});
60        my $top;
61        if (defined $parts[-2] && $parts[-2] eq 'FIG')
62        {
63            $top = '.';
64    #       warn "toplevel @parts\n";
65        }
66        elsif (defined $parts[-3] && $parts[-3] eq 'FIG')
67        {
68            $top = '..';
69    #       warn "subdir @parts\n";
70        }
71        else
72        {
73            $top = $FIG_Config::cgi_base;
74    #       warn "other @parts\n";
75        }
76    
77        $top_link_cache = $top;
78        return $top;
79    }
80    
81    sub compute_html_header
82    {
83        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
84        my($additional_insert, $user, %options ) = @_;
85    
86        local $/ = "\n";
87    
88        my $header_name = $options{header_name} ? $options{header_name} : "html.hdr";
89        my $tail_name = $options{tail_name} ? $options{tail_name} : "html.tail";
90    
91        my $html_hdr_file = "./Html/$header_name";
92      if (! -f $html_hdr_file)      if (! -f $html_hdr_file)
93      {      {
94          $html_hdr_file = "$FIG_Config::fig/CGI/Html/html.hdr";          $html_hdr_file = "$FIG_Config::fig/CGI/Html/$header_name";
95      }      }
96        my @html_hdr = &FIG::file_read($html_hdr_file);
97    
98      my $html_tail_file = "./Html/html.tail";      # for my $k (sort keys %ENV) { warn "$k = $ENV{$k}\n"; }
99      if (! -f $html_tail_file)  
100        #
101        # Determine if this is a toplevel cgi or one in one of the subdirs (currently
102        # just /p2p).
103        #
104    
105        my @parts = split(/\//, $ENV{SCRIPT_NAME});
106        my $top;
107        if ($parts[-2] eq 'FIG')
108        {
109            $top = '.';
110    #       warn "toplevel @parts\n";
111        }
112        elsif ($parts[-3] eq 'FIG')
113        {
114            $top = '..';
115    #       warn "subdir @parts\n";
116        }
117        else
118        {
119            $top = $FIG_Config::cgi_base;
120    #       warn "other @parts\n";
121        }
122    
123        $options{no_fig_search} or push( @html_hdr, "<br><a href=\"$top/index.cgi?user=$user\">FIG search</a>\n" );
124    
125        if (@html_hdr)
126      {      {
127          $html_tail_file = "$FIG_Config::fig/CGI/Html/html.tail";          my $insert_stuff;
128    
129            if (not $options{no_release_info})
130            {
131                my @ver = &FIG::file_head("$FIG_Config::fig_disk/CURRENT_RELEASE", 1);
132                my $ver = $ver[0];
133                chomp $ver;
134                if ($ver =~ /^cvs\.(\d+)$/)
135                {
136                    my $d = asctime(localtime($1));
137                    chomp($d);
138                    $ver .=  " ($d)";
139                }
140                my $host = &FIG::get_local_hostname();
141                $insert_stuff = "SEED version <b>$ver</b> on $host";
142            }
143    
144            if ($additional_insert)
145            {
146                $insert_stuff .= "<br>" . $additional_insert;
147            }
148    
149            for $_ (@html_hdr)
150            {
151                s,(href|img\s+src)="/FIG/,$1="$top/,g;
152                    s,(\?user\=)\",$1$user",;
153                if ($_ eq "<!-- HEADER_INSERT -->\n")
154                {
155                    $_ = $insert_stuff;
156                }
157      }      }
158        }
159    
160        return @html_hdr;
161    }
162    
163    sub show_page {
164        #warn "SHOWPAGE: cgi=", Dumper(@_);
165        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
166        my($cgi,$html,$no_home, $alt_header, $css, $javasrc, $cookie, $options) = @_;
167        my $i;
168        Trace("Setting top link.") if T(3);
169        my $top = top_link();
170    
171        # ARGUMENTS:
172        #     $cgi is the CGI method
173        #     $html is an array with all the html in it. It is just joined by "\n" (and not <br> or <p>
174        #     $no_home eliminates ONLY the bottom FIG search link in a page
175        #     $alt_header is a reference to an array for an alternate header banner that you can replace the standard one with
176        #     $css is a reference to a hash. The key is the name of the CSS sheet and the value is the URL of that sheet. Note the usual rules about relative css urls
177        #               the sheet named "Default" is considered to be the default style sheet, and if this is not set it points at $FIG_Config::HTML/css/default.css
178        #               the sheet named "Sans Serif" is considered to the the first alternate, and if this is not set it points at $FIG_Config::HTML/css/sanserif.css
179        #     $javasrc is a reference to an array of URLs to javascripts to be included (e.g. "FIG/Html/css/styleswitcher.js")
180        #     $cookie is the name and value of the cookie to set. Note that you should probably use raelib->cookie to get/set your cookies
181        #     $options is a reference to a hash of options that you can pass around the pages
182        #
183        # Find the HTML header
184        #
185        Trace("Reading tail.") if T(3);
186        my $tail_name = $options->{tail_name} ? $options->{tail_name} : "html.tail";
187        my $html_tail_file = "./Html/$tail_name";
188        if (! -f $html_tail_file)
189        {
190            $html_tail_file = "$FIG_Config::fig/CGI/Html/$tail_name";
191        }
192        Trace("Extracting user name and header data.") if T(3);
193        my $user = $cgi->param('user') || "";
194        my @html_hdr;
195        if ($alt_header && ref($alt_header) eq "ARRAY")
196        {
197           @html_hdr = @$alt_header;
198        }
199        else
200        {
201            @html_hdr = compute_html_header(undef,$user,%$options);
202        }
203    
204      print $cgi->header;      # RAE: I am offloading the handling of cookies to CGI.pm since I don't know how they are set up.
205        # This modification adds the cookies if necessary
206    
207        # Note: 3/10/05 commented this line out pending the discussion of adding cookies into the seed that we are waiting to see about
208        # to add cookies back in replace these two header lines with each other
209        #my $hdr_thing = $cgi->header(-cookie=>$cookie);
210        my $hdr_thing = $cgi->header();
211        Trace("Printing HTML header: $hdr_thing.") if T(3);
212        print $hdr_thing;
213        Trace("Header printed.") if T(3);
214      #      #
215      #  The SEED header file goes immediately after <BODY>.  Figure out      #  The SEED header file goes immediately after <BODY>.  Figure out
216      #  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 46  Line 227 
227                       meta     => 1,                       meta     => 1,
228                       nextid   => 1,                       nextid   => 1,
229                       style    => 1,                       style    => 1,
230                       title    => 1                       title    => 1,
231                     );                     );
232    
233      #      #
# Line 74  Line 255 
255      my $body_line = -1;      my $body_line = -1;
256      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.
257      my $done = 0;      my $done = 0;
258        Trace("Processing special cases.") if T(3);
259      for ( $i = 0; $i < @$html; $i++ )      for ( $i = 0; $i < @$html; $i++ )
260      {      {
261          #  Some special cases:          #  Some special cases:
# Line 89  Line 270 
270          if ( $html->[$i] =~ /\<body[^0-9a-z]/i )          if ( $html->[$i] =~ /\<body[^0-9a-z]/i )
271          {          {
272              $body_line = $i;              $body_line = $i;
273              $last;              last;
274          }          }
275    
276          #  Now the general case.          #  Now the general case.
# Line 120  Line 301 
301    
302      if ( 1 )      if ( 1 )
303      {      {
304            Trace("Sanity checks in progress.") if T(3);
305          if ( $html_line >= 0 )          if ( $html_line >= 0 )
306          {          {
307              if ( ( $head_line >= 0 ) && ( $html_line > $head_line ) )              if ( ( $head_line >= 0 ) && ( $html_line > $head_line ) )
308              {              {
309                  print STDERR "<HTML> tag follows <HEAD> tag\n";                  Trace("<HTML> tag follows <HEAD> tag.") if T(1);
310              }              }
311              if ( ( $head_end_line >= 0 ) && ( $html_line > $head_end_line ) )              if ( ( $head_end_line >= 0 ) && ( $html_line > $head_end_line ) )
312              {              {
313                  print STDERR "<HTML> tag follows </HEAD> tag\n";                  Trace("<HTML> tag follows </HEAD> tag.") if T(1);
314              }              }
315          }          }
316          if ( $head_line >= 0 )          if ( $head_line >= 0 )
317          {          {
318              if ( ( $head_end_line >= 0 ) && ( $head_line > $head_end_line ) )              if ( ( $head_end_line >= 0 ) && ( $head_line > $head_end_line ) )
319              {              {
320                  print STDERR "<HEAD> tag follows </HEAD> tag\n";                  Trace("<HEAD> tag follows </HEAD> tag.") if T(1);
321              }              }
322          }          }
323      }      }
324        Trace("Sanity checks complete.") if T(3);
325      #      #
326      #  Okay.  Let's put in the html header file, and missing tags:      #  Okay.  Let's put in the html header file, and missing tags:
327      #      #
328      #  <BODY> goes after last head line      #  <BODY> goes after last head line
329      #      #
330        #  RAE:
331        #  Added the javascript for the buttons immediately after body.
332        #  Note if no buttons are added we still (at the moment) add the script,
333        #  but it only adds a little text (495 characters) to the html and noone will notice!
334        #  RAE: This is now deprecated because everything is in an external file, FIG.js, included later
335      if ( $body_line < 0 )      if ( $body_line < 0 )
336      {      {
337          $body_line = $last_head_line + 1;          $body_line = $last_head_line + 1;
338            Trace("Splicing body line at $body_line.") if T(3);
339          splice( @$html, $body_line, 0, "<BODY>\n" );          splice( @$html, $body_line, 0, "<BODY>\n" );
340      }      }
341    
# Line 156  Line 343 
343      #  Seed page header (if it exists) goes after <BODY>      #  Seed page header (if it exists) goes after <BODY>
344      #      #
345    
346      if ( -f $html_hdr_file )      if (@html_hdr)
347      {      {
348          splice( @$html, $body_line + 1, 0, `cat $html_hdr_file` );          Trace("Splicing SEED page header after $body_line.") if T(3);
349            splice( @$html, $body_line + 1, 0, @html_hdr );
350      }      }
351    
352      #      #
# Line 168  Line 356 
356      if ( $head_end_line < 0 )      if ( $head_end_line < 0 )
357      {      {
358          $head_end_line = $body_line;          $head_end_line = $body_line;
359            Trace("Splicing header terminater at $body_line.") if T(3);
360          splice( @$html, $body_line, 0, "</HEAD>\n" );          splice( @$html, $body_line, 0, "</HEAD>\n" );
361      }      }
362    
363        # RAE:
364        # Add css here
365        # Note that at the moment I define these two sheets here. I think this should
366        # be moved out, but I want to try it and see what happens.  css has the format:
367        #
368        # <link rel='stylesheet' title='default' href='/css/default.css' type='text/css'>
369        Trace("Formatting CSS.") if T(3);
370        # convert the default key to the right case. and eliminate dups
371        foreach my $k (keys %$css) {if (lc($k) eq "default") {$css->{'Default'}=$css->{$k}}}
372    
373        if (!$css || !$css->{'Default'})
374        {
375           $css->{'Default'} = "Html/css/default.css";
376        }
377        if (!$css->{"Sans Serif"})
378        {
379           $css->{'Sans Serif'} = "Html/css/sanserif.css";
380        }
381    
382        my $csstext = "<link rel='stylesheet' title='default' href='".$css->{'Default'}."' type='text/css'>\n";
383        $csstext   .= "<link rel='alternate stylesheet' title='Sans Serif' href='".$css->{'Sans Serif'}."' type='text/css'>\n";
384    
385        foreach my $k (keys %$css)
386        {
387           next if (lc($k) eq "default" || lc($k) eq "sans serif");
388           $csstext .= "<link rel='alternate stylesheet' title='$k' href='".$css->{$k}."' type='text/css'>\n";
389        }
390    
391        $csstext   .= "<link rel='alternate'  title='SEED RSS feeds' href='Html/rss/SEED.rss' type='application/rss+xml'>\n";
392    
393        # RAE: also added support for external javascripts here.
394        # we are cluttering the HTML code with all the javascripts when they could easily be in external files
395        # this solution allows us to source other files
396    
397        # the file FIG.js contains most of the java script we use routinely. Every browser will just cache this and so
398        # it will reduce our overhead.
399        Trace("Formatting javascript.") if T(3);
400        # $javasrc must be a ref to an array with urls (absolute or relative) to the javascripts
401        push @$javasrc, "Html/css/FIG.js";
402        foreach my $script (@$javasrc) {
403            $csstext .= "<script src=\"$script\" type=\"text/javascript\"></script>\n";
404        }
405    
406        Trace("Re-splicing the header terminator at $head_end_line.") if T(3);
407        splice( @$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.
408    
409      #      #
410      #  <BASE ...> goes before </HEAD>      #  <BASE ...> goes before </HEAD>
411      #      #
# Line 183  Line 418 
418          #  only, or every update?), I provide an alternative derivation          #  only, or every update?), I provide an alternative derivation
419          #  from $cgi_url. -- GJO          #  from $cgi_url. -- GJO
420          #          #
421            # BASE href needs to be absolute. RDO.
422          my $base_url = $FIG_Config::cgi_base;          #
423          if ( ! $base_url )                      # if cgi_base was not defined          #
424          {  #        $base_url = &FIG::cgi_url;
425              $base_url = $FIG_Config::cgi_url;   # get the full cgi url  #       my $base_url = $FIG_Config::cgi_base;
426              $base_url =~ s~^http://[^/]*~~;     # remove protocol and host  #       if ( ! $base_url )                      # if cgi_base was not defined
427              $base_url =~ m~/$~ || $base_url =~ s~$~/~; # check trailing slash  #       {
428          }  #           $base_url = $FIG_Config::cgi_url;   # get the full cgi url
429    #           $base_url =~ s~^http://[^/]*~~;     # remove protocol and host
430    #           $base_url =~ m~/$~ || $base_url =~ s~$~/~; # check trailing slash
431    #       }
432    
433          $base_line = $head_end_line;          $base_line = $head_end_line;
434          splice( @$html, $base_line, 0, "<BASE href=\"$base_url\">\n" );          #
435            # RDO 2005-1006. Remove this so proxying works better.
436            #
437    #        splice( @$html, $base_line, 0, "<BASE href=\"$base_url/\">\n" );
438      }      }
439    
440      #      #
# Line 203  Line 444 
444      if ( $html_line < 0 )      if ( $html_line < 0 )
445      {      {
446          $html_line = 0;          $html_line = 0;
447            Trace("Splicing the HTML tag at $html_line.") if T(3);
448          splice( @$html, $html_line, 0, "<HTML>\n" );          splice( @$html, $html_line, 0, "<HTML>\n" );
449      }      }
450    
# Line 213  Line 455 
455      if ( $head_line < 0 )      if ( $head_line < 0 )
456      {      {
457          $head_line = $html_line + 1;          $head_line = $html_line + 1;
458            Trace("Splicing the HEAD tag at $head_line.") if T(3);
459          splice( @$html, $head_line, 0, "<HEAD>\n" );          splice( @$html, $head_line, 0, "<HEAD>\n" );
460      }      }
461    
462      #      #
463      #  Place FIG search link at bottom of page      #  Place FIG search link at bottom of page
464      #      #
465        Trace("Placing FIG search link.") if T(3);
466      my @tail = -f $html_tail_file ? `cat $html_tail_file` : ();      my @tail = -f $html_tail_file ? `cat $html_tail_file` : ();
467      if (! $no_home)      if (! $no_home)
468      {      {
# Line 228  Line 471 
471      }      }
472    
473      #      #
474        # See if we have a site-specific tail (for disclaimers, etc).
475        #
476        Trace("Placing site tail.") if T(3);
477        my $site_tail = "$FIG_Config::fig_disk/config/site_tail.html";
478        my $site_fh;
479        if (open($site_fh, "<$site_tail"))
480        {
481            push(@tail, <$site_fh>);
482            close($site_fh);
483        }
484    
485        #
486      #  Figure out where to insert The SEED tail.  Before </body>,      #  Figure out where to insert The SEED tail.  Before </body>,
487      #  or before </html>, or at end of page.      #  or before </html>, or at end of page.
488      #      #
   
489      my @tags = ();      my @tags = ();
490        Trace("Processing closing tags.") if T(3);
491      for ($i=0; ($i < @$html) && ($html->[$i] !~ /\<\/body\>/i); $i++) {}      for ($i=0; ($i < @$html) && ($html->[$i] !~ /\<\/body\>/i); $i++) {}
492      if ($i >= @$html)        # </body> not found; look for </html>      if ($i >= @$html)        # </body> not found; look for </html>
493      {      {
# Line 248  Line 502 
502    
503      if ( @tail )      if ( @tail )
504      {      {
505            Trace("Splicing tail.") if T(3);
506          splice( @$html, $i, 0, @tail, @tags );          splice( @$html, $i, 0, @tail, @tags );
507      }      }
508      elsif ( @tags )      elsif ( @tags )
509      {      {
510            Trace("Splicing tags.") if T(3);
511          splice( @$html, $i, 0, @tags );          splice( @$html, $i, 0, @tags );
512      }      }
513    
514      print @$html;      Trace("Printing the HTML array.") if T(3);
515        # RAE the chomp will return any new lines at the ends of elements in the array,
516        # and then we can join  with a "\n". This is because somethings put newlines in,
517        # and others don't. This should make nicer looking html
518        #
519        # chomp(@$html);
520        # print join "\n", @$html;
521        #
522        # Apparently the above still breaks things. This is the correct code:
523        foreach $_ (@$html)
524        {
525            my $line = $_;
526            if (T(4)) {
527                my $escapedLine = CGI::escapeHTML($line);
528                Trace("Printing:\n$escapedLine") if T(4);
529            }
530            print $line;
531        }
532    
533  }  }
534    
535    
536    =head1 make_table
537    
538    The main method to convert an array into a table.
539    
540    The col_hdrs are set to the <th> headers, the $tab is an array of arrays. The first is the rows, and the second is the columns. The title is the title of the table.
541    
542    The options define the settings for the table such as border, width, and class for css formatting. If the option "excelfile" is set to a filename that will be created in FIG_Config::temp, and the link included that allows the user to download the file as an excel file.
543    
544    =cut
545    
546  sub make_table {  sub make_table {
547      my($col_hdrs,$tab,$title,$instr) = @_;      my($col_hdrs,$tab,$title, %options ) = @_;
548      my(@tab);      my(@tab);
549    
550      push( @tab, "\n<table border>\n",      my $border = defined $options{border} ? "border=\"$options{border}\"" : "border";
551        my $width = defined $options{width} ? "width=\"$options{width}\"" : "";
552        my $class = defined $options{class} ? "class=\"$options{class}\"" : "";
553        push( @tab, "\n<table $border $width $class>\n",
554                  "\t<caption><b>$title</b></caption>\n",                  "\t<caption><b>$title</b></caption>\n",
555                  "\t<tr>\n\t\t<th>"                  "\t<tr>\n\t\t"
556                . join( "</th>\n\t\t<th>", @$col_hdrs )                . join( "\n", map { &expand($_, "th") } @$col_hdrs )
557                . "</th>\n\t</tr>\n"                . "\n\t</tr>\n"
558          );          );
559      my($i,$nowrap);      my($i);
   
     for ($i=0; ($i < @$instr) && ($instr->[$i] !~ /nowrap/); $i++) {}  
     $nowrap = ($i == @$instr) ? "" : " nowrap";  
560    
561      my $row;      my $row;
562      foreach $row (@$tab)      foreach $row (@$tab)
563      {      {
564          push( @tab, "\t<tr>\n"          push( @tab, "\t<tr>\n"
565                    . join( "\n", map { &expand($_,$nowrap) } @$row )                    . join( "\n", map { &expand($_) } @$row )
566                    . "\n\t</tr>\n"                    . "\n\t</tr>\n"
567              );              );
568      }      }
569      push(@tab,"</table>\n");      push(@tab,"</table>\n");
570    
571        # excelfile should be appropriate for a filename (no spaces/special characters)
572        if (defined $options{"excelfile"}) {
573            if (! defined($raelib)) {
574                require raelib;
575                $raelib = new raelib;
576            }
577            push @tab, $raelib->tab2excel($col_hdrs,$tab,$title,\%options,$options{"excelfile"})}
578    
579      return join("",@tab);      return join("",@tab);
580  }  }
581    
582    sub abstract_coupling_table {
583        my($cgi,$prot,$coupling) = @_;
584        my %fc;
585    
586        my $col_hdrs = ["coupled to","Score","Type of Coupling", "Type-specific Data"];
587        my $tab = [];
588        my %by_peg;
589        foreach my $x (@$coupling)
590        {
591            my($peg2,$psc,$type,$extra) = @$x;
592            if (($type !~ /^[ID]FC$/) || (! $fc{$peg2}))
593            {
594                if ($type =~  /^[ID]FC$/)
595                {
596                    $fc{$peg2} = 1;
597                }
598    
599                $by_peg{$peg2} += $psc;
600            }
601        }
602    
603        foreach my $x (sort { ($by_peg{$b->[0]} <=> $by_peg{$a->[0]})
604                              or ($a->[0] cmp $b->[0])
605                              or ($b->[1] <=> $a->[1])
606                              or ($a->[2] cmp $b->[2]) } @$coupling)
607        {
608            my($peg2,$psc,$type,$extra) = @$x;
609            push(@$tab,[&fid_link($cgi,$peg2,1),$psc,$type,&set_prot_links($cgi,join(", ",@$extra))]);
610        }
611    
612    
613         my $help = "<a href=\"Html/abstract_coupling.html\" target=\"SEED_or_SPROUT_help\">for help</a>";
614    #    my @html = &make_table($col_hdrs,$tab,"Abstract Coupling Data for $prot");
615    #    push(@html,"<hr>\n",$cgi->h3($help),"<br>");
616    #    return @html;
617    
618        return &make_table($col_hdrs,$tab,"Abstract Coupling Data for $prot [$help]");
619    }
620    
621  sub expand {  sub expand {
622      my($x,$nowrap) = @_;      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
623        my( $x, $tag ) = @_;
624    
625        $tag = "td" unless $tag;
626        my $endtag = $tag;
627    
628        # RAE modified this so that you can pass in a reference to an array where
629        # the first element is the data to display and the second element is optional
630        # things like colspan and align. Note that in this case you need to include the td
631        # use something like ["some data to appear", "td colspan=4 bgcolor=gray"]
632    
633      if ($x =~ /^\@([^:]+)\:([^:]+)\:(.*)$/)      # per GJO's request modified this line so it can take any tag.
634        if ( ref($x) eq "ARRAY" ) { ($x, $tag) = @$x; $tag =~ /^(\S+)/; $endtag = $1 }
635    
636        if ( $x =~ /^\@([^:]+)\:(.*)$/ )
637      {      {
638          return "\t\t<td$nowrap $1=\"$2\">$3</td>";          return "\t\t<$tag $1>$2</$endtag>";
639      }      }
640      else      else
641      {      {
642          return "\t\t<td$nowrap>$x</td>";          return "\t\t<$tag>$x</$endtag>";
643        }
644    }
645    
646    
647    =head2 merge_table_rows()
648    
649    Merge table rows together. This will merge a table so that adjacent cells with the same content will only be shown once.
650    
651    Something like this:
652    
653        -----------------------
654        |    1     |    a     |
655        -----------------------
656        |    1     |    b     |
657        -----------------------
658        |    2     |    c     |
659        -----------------------
660        |    3     |    d     |
661        -----------------------
662        |    4     |    d     |
663        -----------------------
664        |    5     |    d     |
665        -----------------------
666    
667    Will become:
668    
669        -----------------------
670        |          |    a     |
671        |    1     |-----------
672        |          |    b     |
673        -----------------------
674        |    2     |    c     |
675        -----------------------
676        |    3     |          |
677        ------------          |
678        |    4     |    5     |
679        ------------          |
680        |    5     |          |
681        -----------------------
682    
683    
684    The method takes two arguments. The reference to the array that is the table ($tab). This is the standard table that is created for HTML.pm to draw, and a reference to a hash of columns that you don't want to merge together. The reference to the hash is optional, and if not included, everything will be merged.
685    
686     $tab=&HTML::merge_table_rows($tab);
687    
688     or
689    
690     $skip=(1=>1, 3=>1, 5=>1);
691     $tab=&HTML::merge_table_rows($tab, $skip);  # will merge all columns except 1, 3 and 5. Note the first column in the table is #0
692    
693    
694    =cut
695    
696    
697    
698    
699    sub merge_table_rows {
700     # RAE:
701     # Experimental piece of code. We often want to have rows or columns were cells are merged. It just looks so much nicer
702     # this block should merge adjacent rows that have the same text in them.
703     # use like this:
704     #      $tab=&HTML::merge_table_rows($tab);
705     # before you do a make_table call
706    
707     my $self=shift if UNIVERSAL::isa($_[0],__PACKAGE__);
708     my ($tab, $skip)=@_;
709    
710     my $newtable;
711     my $lastrow;
712     my $rowspan;
713     my $refs;
714    
715     for (my $y=0; $y <= $#$tab; $y++) {
716     #$y is the row in the table;
717      for (my $x=0; $x <= $#{$tab->[$y]}; $x++) {
718       # this is the user definable columns not to merge
719       if ($skip->{$x})
720       {
721        $newtable->[$y]->[$x] = $tab->[$y]->[$x];
722        next;
723       }
724    
725       #$x is the column in the table
726       # if the column in the row we are looking at is the same as the column in the previous row, we don't add
727       # this cell to $newtable. Instead we increment the rowspan of the previous row by one
728    
729       # handle cells that are references to arrays
730       if (ref($tab->[$y]->[$x]) eq "ARRAY") {$refs->[$y]->[$x]=$tab->[$y]->[$x]->[1]; $tab->[$y]->[$x]=$tab->[$y]->[$x]->[0]}
731    
732       # now we go back through the table looking where to draw the merge line:
733       my $lasty=$y;
734       while ($lasty >= 0 && $tab->[$y]->[$x] eq $tab->[$lasty]->[$x]) {$lasty--}
735       $lasty++; # this is the last identical cell. If lasty==y it is the current cell, so we just save the data. Otherwise we increment the rowspan
736       if ($lasty == $y) {
737        # we always want to have something in rows that may otherwise be empty but should be there (see below)
738        unless ($tab->[$y]->[$x]) {$tab->[$y]->[$x]=" &nbsp; "}
739        $newtable->[$y]->[$x] = $tab->[$y]->[$x];
740       }
741       else {$rowspan->[$lasty]->[$x]++}
742      }
743     }
744    
745     # now just join everything back together
746     for (my $y=0; $y <= $#$tab; $y++) {
747      for (my $x=0; $x <= $#{$tab->[$y]}; $x++) {
748       if ($rowspan->[$y]->[$x]) {
749        if ($refs->[$y]->[$x]) {$refs->[$y]->[$x] .= " rowspan=". ($rowspan->[$y]->[$x]+1)}
750        else {$refs->[$y]->[$x] = "td rowspan=". ($rowspan->[$y]->[$x]+1)}
751        $newtable->[$y]->[$x]=[$newtable->[$y]->[$x], $refs->[$y]->[$x]];
752       }
753       elsif ($newtable->[$y]->[$x] && $refs->[$y]->[$x]) {
754        $newtable->[$y]->[$x]=[$newtable->[$y]->[$x], $refs->[$y]->[$x]];
755       }
756      }
757     }
758    
759    
760     # finally we have to remove any completely empty cells that have been added by the array mechanism
761     # (e.g. if you define $a->[2] then $a->[0] and $a->[1] are now undef).
762     # that is why in the loop above I replace empty cells with nbsp. They are now not undef!
763     # I am sure that Gary can do this in one line, but I am hacking.
764     my @trimmed;
765     foreach my $a (@$newtable) {
766      my @row;
767      foreach my $b (@$a) {
768       push @row, $b if ($b);
769      }
770      push @trimmed, \@row;
771     }
772    
773     return \@trimmed;
774    }
775    
776    
777    
778    
779    sub set_ec_links {
780        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
781        my($cgi,$x) = @_;
782        my($before,$match,$after);
783    
784        if ($x =~ /^(.*)(EC \d+\.\d+\.\d+\.\d+)(.*)/s)
785        {
786            $before = $1;
787            $match = $2;
788            $after = $3;
789            return &set_ec_links($cgi,$before) . &HTML::ec_link($match) . &set_ec_links($cgi,$after);
790      }      }
791        return $x;
792  }  }
793    
794  sub ec_link {  sub ec_link {
795        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
796      my($role) = @_;      my($role) = @_;
797    
798      if ($role =~ /(\d+\.\d+\.\d+\.\d+)/)      if ($role =~ /(\d+\.\d+\.\d+\.\d+)/)
# Line 312  Line 806 
806  }  }
807    
808  sub role_link {  sub role_link {
809        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
810      my($cgi,$role) = @_;      my($cgi,$role) = @_;
811    
812      my $roleR = ($role =~ /^(\d+\.\d+\.\d+\.\d+)\s+-\s+/) ? $1 : $role;      my $roleR = ($role =~ /^(\d+\.\d+\.\d+\.\d+)\s+-\s+/) ? $1 : $role;
# Line 322  Line 817 
817      return "<a href=$link>$role</a>";      return "<a href=$link>$role</a>";
818  }  }
819    
820    =head2 fid_link
821    
822    Get a link to a fid.
823    
824    use: my $html=&HTML::fid_link($cgi, $fid, Local, Just_URL, Full_Path);
825    
826    Local is a boolean means to eliminate the fig|org.peg from the text of the link.
827    
828    Just_URL will only return the URL and not the HTML code. The default is to return the full code.
829    
830    Full_Path is a boolean that will get the full path to the URL not just a relative path. This is required in pages where the base href changes (e.g. if an image is imported like on the metabolic pages).
831    
832    =cut
833    
834    
835  sub fid_link {  sub fid_link {
836      my($cgi,$fid,$local,$just_url) = @_;      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
837        my($cgi,$fid,$local,$just_url,$fullpath) = @_;
838        Trace("Creating link for feature $fid.") if T(4);
839        my $err=join(" ", $cgi,$fid,$local,$just_url,$fullpath);
840    
841      my($n);      my($n);
842    
843      if ($fid =~ /^fig\|\d+\.\d+\.([a-z]+)\.(\d+)/)      my $top = top_link();
844        if ($fullpath) {$top=$FIG_Config::cgi_url}
845    
846        if ($fid =~ /^fig\|\d+\.\d+\.([a-zA-Z]+)\.(\d+)/)
847      {      {
848          if ($local)          if ($local)
849          {          {
# Line 343  Line 860 
860          {          {
861              $n = $fid;              $n = $fid;
862          }          }
863          if ($1 ne "peg") { return $n }  
864            my $link;
865            my $new_framework = $cgi->param('new_framework') ? 1 : 0;
866            #added to format prophage and path island links to feature.cgi
867            my $sprout = $cgi->param('SPROUT') ? "&SPROUT=1" : "";
868            my $virt = "&48hr_job=" . $cgi->param("48hr_job");
869            Trace("Sprout mode is \"$sprout\".") if T(4);
870            if ($1 ne "peg" && ! $sprout)
871            {
872               Trace("Creating feature link for $fid.") if T(4);
873               my $user = $cgi->param('user');
874               if (! $user) { $user = "" }
875               $link = "$top/feature.cgi?feature=$fid&user=$user$sprout$virt";
876               $link =~ s/[a-z_A-Z0-9]+\.cgi\?/feature.cgi?/;
877            }
878            else
879            {
880                Trace("Creating protein link for $fid.") if T(4);
881          my $user = $cgi->param('user');          my $user = $cgi->param('user');
882          if (! $user) { $user = "" }          if (! $user) { $user = "" }
883          my $trans = $cgi->param('translate') ? "&translate=1" : "";          my $trans = $cgi->param('translate') ? "&translate=1" : "";
884          my $link = $cgi->url() . "?prot=$fid&user=$user$trans";              my $sprout = $cgi->param('SPROUT') ? "&SPROUT=1" : "";
885          $link =~ s/[a-z_A-Z]+\.cgi\?/protein.cgi?/;  ###a
886    
887    ### This used to be
888    ###     my $link = &FIG::cgi_url . "/protein.cgi?prot=$fid&user=$user$trans$sprout";
889    ###
890    ### The cost became prohibitive in the subsystem spreadsheets.  Hence, we cache the value
891    ###
892    ### RAO
893    
894                #if (! $cgi_url) { $cgi_url = &FIG::cgi_url }
895                #$link = $cgi_url . "/protein.cgi?prot=$fid&user=$user$trans$sprout";
896                $link = "$top/protein.cgi?prot=$fid&user=$user$trans$sprout$virt\&new_framework=$new_framework";
897                $link =~ s/[a-z_A-Z0-9]+\.cgi\?/protein.cgi?/;
898            }
899          if ($just_url)          if ($just_url)
900          {          {
901              return $link;              return $link;
902          }          }
903          else          else
904          {          {
905              return "<a href=$link>$n</a>";              return "<a href='$link'>$n</a>";
906          }          }
907      }      }
908      return $fid;      return $fid;
909  }  }
910    
911  sub family_link {  sub family_link {
912        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
913      my($family,$user) = @_;      my($family,$user) = @_;
914    
915      return $family;      return $family;
916  }  }
917    
918  use URI::Escape;  =head2 evidence_codes_explain
919    
920    Given an evidence code, returns a string that explains this eveidence code.
921    
922    =cut
923    
924    sub evidence_codes_explain {
925     my($ec)=@_;
926     return unless ($ec);
927    
928     $ec=uc($ec);
929     return "IDA: Inferred from Direct Assay" if ($ec =~ /IDA/);
930     return "IGI: Inferred from Genetic Interaction" if ($ec =~ /IGI/);
931     return "TAS: Traceable Author Statement" if ($ec =~ /TAS/);
932     return "ISU: in subsystem unique" if ($ec =~ /ISU/);
933     return "$ec: in subsystem duplicates" if ($ec =~ /IDU/);
934     return "$ec: in cluster with" if ($ec =~ /ICW/);
935     return "FF: in FIGfam" if ($ec =~ /FF/);
936     return "CWN: clustered with nonhypothetical" if ($ec =~ /CWN/);
937     return "CWH: clustered, but only with hypotheticals" if ($ec =~ /CWH/);
938     return "DLIT: literature references to this gene exist" if ($ec =~ /DLIT/);
939     return "ILIT: no references to this gene exist, but they do to other genes with the same functional role" if ($ec =~ /ILIT/);
940     return "$ec: unknown!";
941    }
942    
943  sub get_html {  sub get_html {
944        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
945      my( $url, $type, $kv_pairs) = @_;      my( $url, $type, $kv_pairs) = @_;
946      my( $encoded, $ua, $args, @args, $out, @output, $x );      my( $encoded, $ua, $args, @args, $out, @output, $x );
947    
948      $ua = new LWP::UserAgent;      $ua = new LWP::UserAgent;
949      $ua->timeout( 900 );      $ua->timeout( 900 );
   
950      if ($type =~/post/i)      if ($type =~/post/i)
951      {      {
952          $args = [];          $args = [];
# Line 387  Line 958 
958          my $response = $ua->request($request);          my $response = $ua->request($request);
959          $out = $response->content;          $out = $response->content;
960      }      }
961      else  
962        if ($type =~/get/i)
963      {      {
964          @args = ();          @args = ();
965          foreach $x (@$kv_pairs)          foreach $x (@$kv_pairs)
# Line 399  Line 971 
971          {          {
972              $url .= "?" . join("&",@args);              $url .= "?" . join("&",@args);
973          }          }
974          $request = new HTTP::Request('GET', $url);          my $request = new HTTP::Request('GET', $url);
975          my $response = $ua->request($request);          my $response = $ua->request($request);
976    
977          if ($response->is_success)          if ($response->is_success)
# Line 417  Line 989 
989    
990  #   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
991  #   properly.  Remove the header.  #   properly.  Remove the header.
992        my $i;
993      for ($i=0; ($i < @output) && ($output[$i] !~ /^\s*\</); $i++) {}      for ($i=0; ($i < @output) && ($output[$i] !~ /^\s*\</); $i++) {}
994      if ($i < @output)      if ($i < @output) {
     {  
   
995          splice(@output,0,$i);          splice(@output,0,$i);
996      }      }
997    
# Line 435  Line 1005 
1005  }  }
1006    
1007  sub trim_output {  sub trim_output {
1008        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1009      my($out) = @_;      my($out) = @_;
1010      my $i;      my ($i, $j);
1011    
1012      for ($i=0; ($i < @$out) && ($out->[$i] !~ /^\</); $i++) {}      for ($i=0; ($i < @$out) && ($out->[$i] !~ /^\</); $i++) {}
1013      splice(@$out,0,$i);      splice(@$out,0,$i);
# Line 465  Line 1036 
1036      for ($j=$i-1; ($j > 0) && ($out->[$j] !~ /FIG search/); $j--) {}      for ($j=$i-1; ($j > 0) && ($out->[$j] !~ /FIG search/); $j--) {}
1037      if ($j > 0)      if ($j > 0)
1038      {      {
1039            #
1040            # Hm. We would have tried using the options here:
1041            # my $tail_name = $options{tail_name} ? $options{tail_name} : "html.tail";
1042            # but they're not passed in. So use the default html.tail.
1043            #
1044            my $html_tail_file = "./Html/html.tail";
1045          my @tmp = `cat $html_tail_file`;          my @tmp = `cat $html_tail_file`;
1046          my $n = @tmp;          my $n = @tmp;
1047          splice(@$out,$j-$n,$n+1);          splice(@$out,$j-$n,$n+1);
1048      }      }
1049  }  }
1050    
1051  sub set_prot_links {  =head2 alias_url
     my($cgi,$x) = @_;  
     my($before,$match,$after);  
1052    
1053      if ($x =~ /^(.*)(fig\|\d+\.\d+\.peg\.\d+)(.*)$/)  Returns the url that links to an external page showing information about the given alias.
1054      {  The type of the alias will be determined by the prefix (i.e. 'tr|' for Trembl) If the type
1055          $before = $1;  cannot be determined, the function will return undef.
1056          $match = $2;  
1057          $after = $3;  use: my $html=&HTML::alias_url($alias, $type);
1058          return &set_prot_links($cgi,$before) . &HTML::fid_link($cgi,$match) . &set_prot_links($cgi,$after) . "\n";  
1059    =cut
1060    
1061    sub alias_url {
1062      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1063    
1064      my ($id, $type) = @_;
1065    
1066      if ($type eq "SEED") { # 1
1067        return "http://seed-viewer.theseed.org/linkin.cgi?id=$id";
1068      }      }
1069      elsif ($x =~ /^(.*)(gi\|\d+)(.*)$/)    elsif ($type eq "UniProt") {
1070      {      return "http://www.uniprot.org/entry/$id";
         $before = $1;  
         $match = $2;  
         $after = $3;  
         return &set_prot_links($cgi,$before) . &HTML::gi_link($cgi,$match) . &set_prot_links($cgi,$after) . "\n";  
1071      }      }
1072      elsif ($x =~ /^(.*)(sp\|[A-Z0-9]{6})(.*)$/)    elsif ($type eq "UniProt_ac") { # 2
1073      {      return "http://www.uniprot.org/entry/$id";
1074          $before = $1;    }
1075          $match = $2;    elsif ($type eq "UniProt_id") { # 3
1076        return "http://www.uniprot.org/entry/$id";
1077      }
1078      elsif ($type eq "EntrezGene") { # 4
1079        return "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&id=$id";
1080      }
1081      elsif ($type eq "RefSeq") { # 5
1082        return "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&id=$id";
1083      }
1084      elsif ($type eq "GIID") { # 6
1085        return "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&id=$id";
1086      }
1087      elsif ($type eq "NCBI") {
1088        return "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&id=$id";
1089      }
1090      elsif ($type eq "PDB") { # 7
1091        $id =~ s/\:\w//;
1092        return "http://www.rcsb.org/pdb/explore/explore.do?structureId=$id";
1093      }
1094      elsif ($type eq "PFAM") { # 8
1095        return "http://pfam.janelia.org/family?acc=$id";
1096      }
1097      elsif ($type eq "GO") { # 9
1098        return "http://amigo.geneontology.org/cgi-bin/amigo/go.cgi?view=details&search_constraint=terms&depth=0&query=$id";
1099      }
1100      elsif ($type eq "PIRSF") { # 10
1101        return "http://pir.georgetown.edu/cgi-bin/ipcSF?id=$id";
1102      }
1103      elsif ($type eq "IPI") { # 11
1104        return "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+[IPI-AllText:".$id."*]+-lv+30+-view+SeqSimpleView+-page+qResult";
1105      }
1106      elsif ($type eq "UniRef_100") { # 12
1107        return "http://www.uniprot.org/entry/$id";
1108      }
1109      elsif ($type eq "UniRef_90") { # 13
1110        return "http://www.uniprot.org/entry/$id";
1111      }
1112      elsif ($type eq "UniRef_50") { # 14
1113        return "http://www.uniprot.org/entry/$id";
1114      }
1115      elsif ($type eq "UniParc") { # 15
1116        return "http://www.uniprot.org/entry/$id";
1117      }
1118      elsif ($type eq "PIR-PSD") { # 16
1119        return "http://pir.georgetown.edu/cgi-bin/pir_psd_get.pl?id=$id";
1120      }
1121      elsif ($type eq "Taxon_ID") { # 17
1122        return "http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=$id";
1123      }
1124      elsif ($type eq "OMIM") { # 18
1125        return "http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=$id";
1126      }
1127      elsif ($type eq "UniGene") { # 19
1128        return "http://www.ncbi.nlm.nih.gov/sites/entrez?db=unigene&cmd=search&term=$id";
1129      }
1130      elsif ($type eq "Ensemble_ID") { # 20
1131        #return "$id";
1132      }
1133      elsif ($type eq "PMID") { # 21
1134        return "http://www.ncbi.nlm.nih.gov/pubmed/$id";
1135      }
1136      elsif ($type eq "EMBL_DNA_AC") { # 22
1137        return "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBL:".$id."]+-newId";
1138      }
1139      elsif ($type eq "EMBL_Protein_AC") { # 23
1140        $id =~ s/\.\d//;
1141        return "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[{EMBL}-ProteinID:".$id."]";
1142      }
1143      elsif ($type eq "CMR") { # 24
1144        if ($id =~ s/^\d+$//) {
1145          return "http://cmr.jcvi.org/cgi-bin/CMR/shared/GenePage.cgi?type=PID&acc=".$id;
1146        } else {
1147          return "http://cmr.jcvi.org/tigr-scripts/CMR/shared/GenePage.cgi?locus=".$id;
1148        }
1149      }
1150    
1151      return undef;
1152    }
1153    
1154    sub set_prot_links {
1155        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1156        my($cgi,$x) = @_;
1157        my($before,$match,$after);
1158    
1159        if ($x =~ /^(.*)(fig\|\d+\.\d+\.peg\.\d+)(.*)/s)
1160        {
1161            $before = $1;
1162            $match = $2;
1163            $after = $3;
1164            return &set_prot_links($cgi,$before) . &HTML::fid_link($cgi,$match) . &set_prot_links($cgi,$after);
1165        }
1166        elsif ($x =~ /^(.*)\b([NXYZA][PM]_[0-9\.]+)\b(.*)/s)
1167        {
1168            $before = $1;
1169            $match = $2;
1170            $after = $3;
1171            return &set_prot_links($cgi,$before) . &HTML::refseq_link($cgi,$match) . &set_prot_links($cgi,$after);
1172        }
1173        elsif ($x =~ /^(.*)(gi\|\d+)(.*)/s)
1174        {
1175            $before = $1;
1176            $match = $2;
1177            $after = $3;
1178            return &set_prot_links($cgi,$before) . &HTML::gi_link($cgi,$match) . &set_prot_links($cgi,$after);
1179        }
1180        elsif ($x =~ /^(.*)(img\|\d+)(.*)/s)
1181        {
1182            $before = $1;
1183            $match = $2;
1184            $after = $3;
1185            return &set_prot_links($cgi,$before) . &HTML::img_link($cgi,$match) . &set_prot_links($cgi,$after);
1186        }
1187        elsif ($x =~ /^(.*)(tigr\|\w+)(.*)/s)
1188        {
1189            $before = $1;
1190            $match = $2;
1191            $after = $3;
1192            return &set_prot_links($cgi,$before) . &HTML::tigr_link($cgi,$match) . &set_prot_links($cgi,$after);
1193        }
1194        elsif ($x =~ /^(.*)(tigrcmr\|\w+)(.*)/s)
1195        {
1196            $before = $1;
1197            $match = $2;
1198            $after = $3;
1199            return &set_prot_links($cgi,$before) . &HTML::tigr_link($cgi,$match) . &set_prot_links($cgi,$after);
1200        }
1201        elsif ($x =~ /^(.*)\b(eric\|\S+)\b(.*)/s)
1202        {
1203            $before = $1;
1204            $match = $2;
1205            $after = $3;
1206            return &set_prot_links($cgi,$before) . &HTML::eric_link($cgi,$match) . &set_prot_links($cgi,$after);
1207        }
1208    
1209        elsif ($x =~ /^(.*)\b(bhb\|.*?)\b(.*)/s)
1210        {
1211            $before = $1;
1212            $match = $2;
1213            $after = $3;
1214            return &set_prot_links($cgi,$before) . &HTML::bhb_link($cgi,$match) . &set_prot_links($cgi,$after);
1215        }
1216    
1217        elsif ($x =~ /^(.*)\b(apidb\|[0-9\.a-z_]+)\b(.*)/s)
1218        {
1219            $before = $1;
1220            $match = $2;
1221            $after = $3;
1222            return &set_prot_links($cgi,$before) . &HTML::apidb_link($cgi,$match) . &set_prot_links($cgi,$after);
1223        }
1224    
1225        elsif ($x =~ /^(.*)\b(patric\|.*?)\b(.*)/s)
1226        {
1227            $before = $1;
1228            $match = $2;
1229            $after = $3;
1230            return &set_prot_links($cgi,$before) . &HTML::patric_link($cgi,$match) . &set_prot_links($cgi,$after);
1231        }
1232    
1233        elsif ($x =~ /^(.*)\b(vbrc\|.*?)\b(.*)/s)
1234        {
1235            $before = $1;
1236            $match = $2;
1237            $after = $3;
1238            return &set_prot_links($cgi,$before) . &HTML::vbrc_link($cgi,$match) . &set_prot_links($cgi,$after);
1239        }
1240    
1241        elsif ($x =~ /^(.*)\b(vectorbase\|.*?)\b(.*)/s)
1242        {
1243            $before = $1;
1244            $match = $2;
1245            $after = $3;
1246            return &set_prot_links($cgi,$before) . &HTML::vectorbase_link($cgi,$match) . &set_prot_links($cgi,$after);
1247        }
1248        elsif ($x =~  /^(.*)(uni\|[A-Z0-9]{6})(.*)/s)
1249        {
1250            $before = $1;
1251            $match = $2;
1252            $after = $3;
1253            return &set_prot_links($cgi,$before) . &HTML::uni_link($cgi,$match) . &set_prot_links($cgi,$after);
1254        }
1255        elsif ($x =~ /^(.*)(sp\|[A-Z0-9]{6})(.*)/s)
1256        {
1257            $before = $1;
1258            $match = $2;
1259            $after = $3;
1260            return &set_prot_links($cgi,$before) . &HTML::sp_link($cgi,$match) . &set_prot_links($cgi,$after);
1261        }
1262        elsif ($x =~ /^(.*)(pirnr\|NF\d+)(.*)/s)
1263        {
1264            $before = $1;
1265            $match = $2;
1266            $after = $3;
1267            return &set_prot_links($cgi,$before) . &HTML::pir_link($cgi,$match) . &set_prot_links($cgi,$after);
1268        }
1269        elsif ($x =~ /^(.*)(kegg\|[a-z]{2,4}:[a-zA-Z_0-9]+)(.*)/s)
1270        {
1271            $before = $1;
1272            $match = $2;
1273            $after = $3;
1274            return &set_prot_links($cgi,$before) . &HTML::kegg_link($cgi,$match) . &set_prot_links($cgi,$after);
1275        }
1276        elsif ($x =~ /^(.*)(Ensembl[a-zA-Z]+:[a-zA-Z_0-9\.]+)(.*)/s)
1277        {
1278            $before = $1;
1279            $match = $2;
1280            $after = $3;
1281            return &set_prot_links($cgi,$before) . &HTML::ensembl_link($cgi,$match) . &set_prot_links($cgi,$after);
1282        }
1283        elsif ($x =~ /^(.*)(EntrezGene:[a-zA-Z_0-9\.]+)(.*)/s)
1284        {
1285            $before = $1;
1286            $match = $2;
1287            $after = $3;
1288            return &set_prot_links($cgi,$before) . &HTML::entrezgene_link($cgi,$match) . &set_prot_links($cgi,$after);
1289        }
1290        elsif ($x =~ /^(.*)(MIM:[a-zA-Z_0-9\.]+)(.*)/s)
1291        {
1292            $before = $1;
1293            $match = $2;
1294            $after = $3;
1295            return &set_prot_links($cgi,$before) . &HTML::mim_link($cgi,$match) . &set_prot_links($cgi,$after);
1296        }
1297        elsif ($x =~ /^(.*)(HGNC:[a-zA-Z_0-9\.]+)(.*)/s)
1298        {
1299            $before = $1;
1300            $match = $2;
1301            $after = $3;
1302            return &set_prot_links($cgi,$before) . &HTML::hgnc_link($cgi,$match) . &set_prot_links($cgi,$after);
1303        }
1304        elsif ($x =~ /^(.*)(UniGene:[a-zA-Z_0-9\.]+)(.*)/s)
1305        {
1306            $before = $1;
1307            $match = $2;
1308            $after = $3;
1309            return &set_prot_links($cgi,$before) . &HTML::unigene_link($cgi,$match) . &set_prot_links($cgi,$after);
1310        }
1311    # IPI stopped working. turn off for now.
1312    #    elsif ($x =~ /^(.*)(IPI:[a-zA-Z_0-9\.]+)(.*)/s)
1313    #    {
1314    #        $before = $1;
1315    #        $match = $2;
1316    #        $after = $3;
1317    #        return &set_prot_links($cgi,$before) . &HTML::ipi_link($cgi,$match) . &set_prot_links($cgi,$after);
1318    #    }
1319        elsif ($x =~ /^(.*)(WP:[a-zA-Z_0-9\.]+)(.*)/s)
1320        {
1321            #wormbase
1322    
1323            $before = $1;
1324            $match = $2;
1325            $after = $3;
1326            return &set_prot_links($cgi,$before) . &HTML::wp_link($cgi,$match) . &set_prot_links($cgi,$after);
1327        }
1328        elsif ($x =~ /^(.*)(FB:[a-zA-Z_0-9\.]+)(.*)/s)
1329        {
1330            #flybase
1331    
1332            $before = $1;
1333            $match = $2;
1334            $after = $3;
1335            return &set_prot_links($cgi,$before) . &HTML::fb_link($cgi,$match) . &set_prot_links($cgi,$after);
1336        }
1337        elsif ($x =~ /^(.*)(FlyBaseORFNames:[a-zA-Z_0-9\.]+)(.*)/s)
1338        {
1339            #flybase
1340    
1341            $before = $1;
1342            $match = $2;
1343          $after = $3;          $after = $3;
1344          return &set_prot_links($cgi,$before) . &HTML::sp_link($cgi,$match) . &set_prot_links($cgi,$after) . "\n";          return &set_prot_links($cgi,$before) . &HTML::fborf_link($cgi,$match) . &set_prot_links($cgi,$after);
1345      }      }
1346      elsif ($x =~ /^(.*)(pirnr\|NF\d+)(.*)$/)      elsif ($x =~ /^(.*)(SGD_LOCUS:[a-zA-Z_0-9\.]+)(.*)/s)
1347      {      {
1348            #flybase
1349    
1350          $before = $1;          $before = $1;
1351          $match = $2;          $match = $2;
1352          $after = $3;          $after = $3;
1353          return &set_prot_links($cgi,$before) . &HTML::pir_link($cgi,$match) . &set_prot_links($cgi,$after) . "\n";          return &set_prot_links($cgi,$before) . &HTML::sgd_link($cgi,$match) . &set_prot_links($cgi,$after);
1354        }
1355        elsif ($x =~ /^(.*)(tr\|[a-zA-Z0-9]+)(.*)/s)
1356        {
1357    
1358          $before = $1;
1359          $match = $2;
1360          $after = $3;
1361    
1362          return &set_prot_links($cgi,$before) .  &HTML::trembl_link($cgi,$match) . &set_prot_links($cgi,$after);
1363      }      }
1364      return $x;      return $x;
1365  }  }
1366    
1367    sub trembl_link {
1368        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1369        my($cgi,$id) = @_;
1370    
1371        if ($id =~ /^tr\|(.*)/) {
1372          return "<a href='http://ca.expasy.org/uniprot/$1' target=_blank>$id</a>";
1373        } else {
1374          return "invalid call to trembl link";
1375        }
1376    }
1377    
1378    sub refseq_link {
1379        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1380        my($cgi,$id) = @_;
1381    
1382        if ($id =~ /^[NXYZA]P_/)
1383        {
1384            return "<a href='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=protein&cmd=search&term=$id' target=_blank>$id</a>";
1385        }
1386        elsif ($id =~ /^[NXYZA]M_/)
1387        {
1388            return "<a href='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=nuccore&cmd=search&term=$id' target=_blank>$id</a>";
1389        }
1390    }
1391    
1392  sub gi_link {  sub gi_link {
1393        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1394      my($cgi,$gi) = @_;      my($cgi,$gi) = @_;
1395    
1396      if ($gi =~ /^gi\|(\d+)$/)      if ($gi =~ /^gi\|(\d+)$/)
1397      {      {
1398          return "<a href=http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=Protein&list_uids=$1&dopt=GenPept>$gi</a>";          return "<a href='http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=Protein&list_uids=$1&dopt=GenPept' target=_blank>$gi</a>";
1399      }      }
1400      return $gi;      return $gi;
1401  }  }
1402    
1403    sub tigr_link {
1404        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1405        my($cgi,$tigr) = @_;
1406    
1407        if ($tigr =~ /^tigr\|(NT|ntbp|ntbpA|BA|BMAA|BXB|GBA)(\w+)$/)
1408        {
1409            my $id=$1.$2;
1410            return "<a href=\"http://pathema.tigr.org/tigr-scripts/pathema/shared/GenePage.cgi?locus=$id\" target=_blank>$tigr</a> (Pathema)";
1411        }
1412        elsif ($tigr =~ /^tigr(cmr)?\|(\S+)$/)
1413        {
1414            return "<a href=\"http://www.tigr.org/tigr-scripts/CMR2/GenePage.spl?locus=$2\" target=_blank>$tigr</a>";
1415        }
1416        return $tigr;
1417    }
1418    
1419    sub eric_link {
1420        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1421        my($cgi,$eric) = @_;
1422    
1423        if ($eric =~ /^eric\|(\S+)/)
1424        {
1425            return "<a href=\"https://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=$1\" target=_blank>$eric</a>";
1426        }
1427        return $eric;
1428    }
1429    
1430    sub bhb_link {
1431        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1432        my($cgi,$bhb) = @_;
1433    
1434        return "<a href=\"http://www.biohealthbase.org\" target=_blank>$bhb</a>";
1435    }
1436    
1437    sub apidb_link {
1438        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1439        my($cgi,$api) = @_;
1440    
1441        if ($api =~ /apidb\|(.*?)\.(.*)$/)
1442        {
1443            return "<a href=\"http://www.apidb.org/cgi-bin/redirect.cgi?taxon_id=$1&source_id=$2\" target=_blank>$api</a>";
1444        }
1445        return $api;
1446    }
1447    
1448    sub patric_link {
1449        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1450        my($cgi,$patric) = @_;
1451    
1452        if ($patric =~ /patric\|(.*)/)
1453        {
1454            return "<a href=\"https://patric.vbi.vt.edu/software/curationTool/gep/pgiCuration.php?locus_name=$1\" target=_blank>$patric</a>";
1455        }
1456        return $patric;
1457    }
1458    
1459    sub vbrc_link {
1460        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1461        my($cgi,$vbrc) = @_;
1462    
1463        if ($vbrc =~ /vbrc\|(.*)/)
1464        {
1465            return "<a href=\"http://www.biovirus.org/gene_detail.asp?name=$1\" target=_blank>$vbrc</a>";
1466        }
1467        return $vbrc;
1468    }
1469    
1470    sub vectorbase_link {
1471        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1472        my($cgi,$vec) = @_;
1473        return "<a href=\"http://www.vectorbase.org\" target=_blank>$vec</a>";
1474    }
1475    
1476    
1477    sub uni_link {
1478        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1479        my($cgi,$uni) = @_;
1480    
1481        if ($uni =~ /^uni\|(\S+)$/)
1482        {
1483            #return "<a href=http://www.pir.uniprot.org/cgi-bin/upEntry?id=$1>$uni</a>";
1484            return "<a href='http://www.ebi.uniprot.org/uniprot-srv/uniProtView.do?proteinAc=$1' target=_blank>$uni</a>";
1485        }
1486        return $uni;
1487    }
1488    
1489  sub sp_link {  sub sp_link {
1490        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1491      my($cgi,$sp) = @_;      my($cgi,$sp) = @_;
1492    
1493      if ($sp =~ /^sp\|(\S+)$/)      if ($sp =~ /^sp\|(\S+)$/)
1494      {      {
1495          return "<a href=http://us.expasy.org/cgi-bin/get-sprot-entry?$1>$sp</a>";          return "<a href='http://us.expasy.org/cgi-bin/get-sprot-entry?$1' target=_blank>$sp</a>";
1496      }      }
1497      return $sp;      return $sp;
1498  }  }
1499    
1500  sub pir_link {  sub pir_link {
1501        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1502      my($cgi,$pir) = @_;      my($cgi,$pir) = @_;
1503    
1504      if ($pir =~ /^pirnr\|(NF\d+)$/)      if ($pir =~ /^pirnr\|(NF\d+)$/)
1505      {      {
1506          return "<a href=http://pir.georgetown.edu/cgi-bin/nfEntry.pl?id=$1>$pir</a>";          return "<a href='http://pir.georgetown.edu/cgi-bin/nfEntry.pl?id=$1' target=_blank>$pir</a>";
1507      }      }
1508      return $pir;      return $pir;
1509  }  }
1510    
1511    sub kegg_link {
1512        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1513        my($cgi,$kegg) = @_;
1514    
1515        if ($kegg =~ /^kegg\|([^:]+):(\S+)$/)
1516        {
1517            return "<a href='http://www.genome.ad.jp/dbget-bin/www_bget?$1+$2' target=_blank>$kegg</a>";
1518        }
1519        return $kegg;
1520    }
1521    
1522    sub img_link {
1523        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1524        my($cgi,$img) = @_;
1525    
1526        if ($img =~ /^img\|(\S+)$/)
1527        {
1528            return "<a href='http://img.jgi.doe.gov/cgi-bin/pub/main.cgi?page=geneDetail&gene_oid=$1' target=_blank>$img</a>";
1529        }
1530        return $img;
1531    }
1532    
1533    sub ensembl_link {
1534        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1535        my($cgi,$ensembl) = @_;
1536    
1537        if ($ensembl =~ /^(\S+):(\S+)$/)
1538        {
1539            my $what=$1;
1540            my $key=$2;
1541            my $idx="All";
1542            if ($what eq "EnsemblGene") { $idx = "Gene" }
1543            if ($what eq "EnsemblTranscript") { $idx = "All" }
1544            if ($what eq "EnsemblProtein") { $idx = "All" }
1545    
1546            #I really want to get right to the transcript and peptide pages, but
1547            #can't see how to do that without knowing the org name too, which
1548            #I don't know at this point. (ensembl org name, not real org name)
1549    
1550            return "<a href='http://www.ensembl.org/Homo_sapiens/searchview?species=all&idx=$idx&q=$key' target=_blank>$ensembl</a>";
1551        }
1552        return $ensembl;
1553    }
1554    
1555    sub entrezgene_link {
1556        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1557        my($cgi,$entrezgene) = @_;
1558    
1559        if ($entrezgene =~ /^EntrezGene:(\S+)$/)
1560        {
1561            return "<a href='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=full_report&list_uids=$1' target=_blank>$entrezgene</a>";
1562        }
1563        return $entrezgene;
1564    }
1565    
1566    sub mim_link {
1567        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1568        my($cgi,$mim) = @_;
1569    
1570        if ($mim =~ /^MIM:(\S+)$/)
1571        {
1572            return "<a href='http://www3.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=$1' target=_blank>$mim</a>";
1573        }
1574        return $mim;
1575    }
1576    
1577    sub hgnc_link {
1578        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1579        my($cgi,$hgnc) = @_;
1580    
1581        if ($hgnc =~ /^HGNC:(\S+)$/)
1582        {
1583            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>";
1584        }
1585    
1586        return $hgnc;
1587    }
1588    
1589    sub unigene_link {
1590        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1591        my($cgi,$unigene) = @_;
1592    
1593        if ($unigene =~ /^UniGene:(\S+)$/)
1594        {
1595            return "<a href='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unigene&cmd=search&term=$1' target=_blank>$unigene</a>";
1596        }
1597        return $unigene;
1598    }
1599    
1600    sub ipi_link {
1601        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1602        my($cgi,$ipi) = @_;
1603    
1604        if ($ipi =~ /^IPI:(\S+)$/)
1605        {
1606            return "<a href='http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-id+AEoS1R8Jnn+-e+[IPI:\'$1\']+-qnum+1+-enum+1' target=_blank>$ipi</a>";
1607        }
1608        return $ipi;
1609    }
1610    
1611    sub wp_link {
1612        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1613        my($cgi,$wp) = @_;
1614    
1615        #wormbase
1616    
1617        if ($wp =~ /^WP:(\S+)$/)
1618        {
1619            return "<a href='http://www.wormbase.org/db/searches/basic?class=Any&query=$1&Search=Search' target=_blank>$wp</a>";
1620        }
1621        return $wp;
1622    }
1623    
1624    sub fb_link {
1625        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1626        my($cgi,$fb) = @_;
1627    
1628        #flybase
1629    
1630        if ($fb =~ /^FB:(\S+)$/)
1631        {
1632            return "<a href='http://flybase.bio.indiana.edu/.bin/fbidq.html?$1' target=_blank>$fb</a>";
1633        }
1634        return $fb;
1635    }
1636    
1637    sub fborf_link {
1638        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1639        my($cgi,$fb) = @_;
1640    
1641        #flybase
1642    
1643        if ($fb =~ /^FlyBaseORFNames:(\S+)$/)
1644        {
1645            return "<a href='http://flybase.bio.indiana.edu/.bin/fbidq.html?$1' target=_blank>$fb</a>";
1646        }
1647        return $fb;
1648    }
1649    
1650    sub sgd_link {
1651        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1652        my($cgi,$sgd) = @_;
1653    
1654        #yeast
1655    
1656        if ($sgd =~ /^SGD_LOCUS:(\S+)$/)
1657        {
1658            return "<a href='http://db.yeastgenome.org/cgi-bin/locus.pl?locus=$1' target=_blank>$sgd</a>";
1659        }
1660        return $sgd;
1661    }
1662    
1663    
1664    
1665    
1666    sub set_map_links {
1667        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1668        my($cgi,$x) = @_;
1669        my($before,$match,$after);
1670    
1671        my $org = ($cgi->param('org') || $cgi->param('genome') || "");
1672    
1673        if ($x =~ /^(.*)(MAP\d+)(.*)/s)
1674        {
1675            $before = $1;
1676            $match = $2;
1677            $after = $3;
1678            return &set_map_links($cgi,$before) . &map_link($cgi,$match,$org) . &set_map_links($cgi,$after);
1679        }
1680        return $x;
1681    }
1682    
1683    
1684    
1685    sub map_link {
1686        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1687        my($cgi,$map,$org) = @_;
1688    
1689        my $user = $cgi->param('user');
1690        $user = $user ? $user : "";
1691        $org = $org ? $org : "";
1692    
1693        my $url = "show_kegg_map.cgi?user=$user&map=$map&org=$org";
1694    #rel    my $url = &FIG::cgi_url() . "/show_kegg_map.cgi?user=$user&map=$map&org=$org";
1695        my $link = "<a href=\"$url\">$map</a>";
1696        return $link;
1697    }
1698    
1699    sub java_buttons {
1700        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1701      ## ADDED BY RAE
1702      # Provides code to include check all/first half/second half/none for javascrspt
1703      # this takes two variables - the form name provided in start_form with the
1704      # -name => field and the checkbox name
1705      my ($form, $button)=@_;
1706    
1707      my $java_script="<input type=\"button\" name=\"CheckAll\" value=\"Check All\"\nonClick=\"checkAll(document.$form.$button)\">\n";
1708      $java_script.="<input type=\"button\" name=\"CheckFirst\" value=\"Check First Half\"\nonClick=\"checkFirst(document.$form.$button)\">\n";
1709      $java_script.="<input type=\"button\" name=\"CheckSecond\" value=\"Check Second Half\"\nonClick=\"checkSecond(document.$form.$button)\">\n";
1710      $java_script.="<input type=\"button\" name=\"UnCheckAll\" value=\"Uncheck All\"\nonClick=\"uncheckAll(document.$form.$button)\">\n";
1711    
1712      return $java_script;
1713    }
1714    
1715    =head3 sub_link
1716    
1717        my $htmlText = HTML::sub_link($cgi, $sub, gid);
1718    
1719    Create a subsystem link. The link will be to the display page if there is no
1720    user or we are in SPROUT mode; otherwise it will be to the edit page.
1721    
1722    =over 4
1723    
1724    =item cgi
1725    
1726    CGI query object for the current web session. The parameters of special interest
1727    are C<SPROUT> and C<user>. If the user is non-blank and SPROUT mode is 0, then
1728    the subsystem's edit page will be shown rather than its display page.
1729    
1730    =item sub
1731    
1732    Name of the desired subsystem. It will be cleaned of underscores before the
1733    hyperlink is applied.
1734    
1735    =item gid
1736    
1737    Genome ID to be specified as the focus.
1738    
1739    =back
1740    
1741    =cut
1742    
1743    sub sub_link {
1744        # Allow call as an instance in addition to the authorized method.
1745        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1746        # Get the parameters.
1747        my ($cgi, $sub, $gid) = @_;
1748        # Declare the return variable.
1749        my $retVal;
1750        # Clean the subsystem name for display purposes. This is a very
1751        # different thing from URL-escaping.
1752        my $cleaned = CGI::escapeHTML($sub);
1753        $cleaned =~ s/_/ /g;
1754        # URL-escape the subsystem name for use in the link.
1755        my $linkable = uri_escape($sub);
1756        # Determine the mode. Note we use the little OR trick to insure that
1757        # we have the correct value for plugging into the output link.
1758        my $user = $cgi->param('user') || "";
1759        my $sproutMode = $cgi->param('SPROUT') || 0;
1760        if ($user && ! $sproutMode) {
1761            # A SEED user is calling, so we go to the edit page.
1762            $retVal = "<a href=\"subsys.cgi?ssa_name=$linkable&request=show_ssa&user=$user\">$cleaned</a>";
1763        } else {
1764            # A visitor or SPROUT user is calling, so we go to the display page.
1765            $retVal = "<a href=\"display_subsys.cgi?ssa_name=$linkable;request=show_ssa;sort=by_phylo;focus=$gid;SPROUT=$sproutMode\">$cleaned</a>";
1766        }
1767        # Return the result.
1768        return $retVal;
1769    }
1770    
1771    sub reaction_map_link {
1772        my($mapID, @reaction_list) = @_;
1773        if($mapID =~ /\d+/)
1774        {
1775            my $reactions = join "+", @reaction_list;
1776            if ($reactions ne "")
1777            {
1778                $reactions = "+".$reactions;
1779            }
1780    
1781            return "<a href=http://www.genome.jp/dbget-bin/show_pathway?rn$mapID$reactions>$mapID</a>";
1782        }
1783        else
1784        {
1785            return $mapID;
1786        }
1787    }
1788    
1789    sub compound_link {
1790        my($compound) = @_;
1791        if($compound =~ /^C\d+/)
1792        {
1793            return "<a href=\"javascript:void(0)\"onclick=\"window.open('http://www.genome.jp/dbget-bin/www_bget?compound+$compound','$&','height=640,width=800,scrollbars=yes,toolbar=yes,status=yes,resizable=yes')\">$compound</a>";
1794        }
1795        else
1796        {
1797            return $compound;
1798        }
1799    }
1800    
1801    
1802    sub reaction_link {
1803        my($reaction) = @_;
1804        if ($reaction =~ /^(\*)?(R\d+)/)
1805        {
1806            # return "<a href=\"http://www.genome.ad.jp/dbget-bin/www_bget?rn+$2\" target=reaction$$>$reaction</a>";
1807            return "<a href=\"javascript:void(0)\"onclick=\"window.open('http://www.genome.ad.jp/dbget-bin/www_bget?rn+$reaction','$&','height=640,width=800,scrollbars=yes,toolbar=yes,status=yes,resizable=yes')\">$reaction</a>";
1808        }
1809        return $reaction;
1810    }
1811    
1812    
1813    sub html_for_assignments {
1814        my($fig,$user,$peg_sets) = @_;
1815        my $i;
1816    
1817        my @vals = ();
1818        my $set = 1;
1819        foreach my $peg_set (@$peg_sets)
1820        {
1821            for ($i=0; ($i < @$peg_set); $i++)
1822            {
1823                my $peg = $peg_set->[$i];
1824                push(@vals,'show=' . join("@",($set,$i+1,$peg,&FIG::abbrev($fig->org_of($peg)),"")));
1825            }
1826            $set++;
1827        }
1828    
1829        $ENV{'REQUEST_METHOD'} = 'GET';
1830        $ENV{'QUERY_STRING'} = join('&',('request=show_commentary',"uni=1","user=$user",@vals));
1831        my $out = join("",`$FIG_Config::fig/CGI/chromosomal_clusters.cgi`);
1832        $out =~ s/^.*?<form/<form/si;
1833        $out =~ s/^(.*)<table.*/$1/si;
1834        return $out;
1835    }
1836    
1837    =head1 rss_feed
1838    
1839    Add something to the RSS feed. The rss feeds are stored in the Html directory, and there are several RSS feeds:
1840            SEED.rss                - everything gets written here
1841            SEEDgenomes.rss                 - whenever a genome is added to the SEED
1842            SEEDsubsystems.rss      - whenever a subsystem is edited (or should this be added?)
1843    
1844    
1845    RSS feeds must contain a title, description, and link. The title is what is seen e.g. from the firefox or safari pull down menu. The description is seen from within an rss aggregator, and may be displayed on web pages and so on.
1846    
1847    The method takes a reference to an array containing the file names for the RSS feeds to add your item to, and a hash of items for the xml. Only title, description, and link are required tags in the XML.
1848    
1849    The file names are the full name of the file, eg SEEDsubsystems.rss, SEEDgenomes.rss. Be aware that this is a file name, though, so don't uses special characters. The path will be added.
1850    
1851    The has can have these keys:
1852    
1853    REQUIRED:
1854    title       : the title. This is usually what is seen by the user in the pull down menu
1855    description : a more complete description that is often seen is rss viewers but not always
1856    link        : link to the item that was added/edited
1857    All other keys are treated as optional RSS arguments and written to the file.
1858    
1859    At most, $max_entries recent entries are stored in the rss file, and this is currently 50.
1860    
1861    RSS files are quite simple, and contain some standard header information, and then individual items surrounded by an <item> </item> tag. Note that there is also an initial title/description/link set that describes the file.
1862    
1863    
1864    =cut
1865    
1866    sub rss_feed {
1867     shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1868     my ($files, $args)=@_;
1869    
1870     # how many entries to store in the file
1871     my $max_entries=50;
1872    
1873     foreach my $a (keys %$args) {if ($a =~ /^-(.*)/) {my $b=$1; $args->{$b}=$args->{$a}; delete $args->{$a}}}
1874    
1875     my $filepath=$FIG_Config::fig."/CGI/Html/rss";
1876     # check for the directory and if not, make it
1877     mkdir $filepath unless (-d $filepath);
1878    
1879     # note that $info is a hash of references to hashes that are written out as headers in the file
1880     my $info=
1881     {
1882      "SEED.rss" =>
1883       {
1884            title           => "The SEED",
1885            description     => "Latest news from the SEED",
1886            link            => "Html/rss/SEED.rss",
1887       },
1888    
1889      "SEEDsubsystems.rss" =>
1890      {
1891            title           => "SEED Subsystems",
1892            description     => "Recently updated SEED subsystems",
1893            link            => "Html/rss/SEEDsubsystems.rss",
1894      },
1895    
1896      "SEEDsubsystems.rss" =>
1897      {
1898            title           => "SEED Genomes",
1899            description     => "Genomes recently added to the SEED",
1900            link            => &FIG::cgi_url()."/Html/rss/SEEDsubsystems.rss",
1901      },
1902    
1903     };
1904    
1905    
1906     # build the new xml
1907     my $xml = "\t<item>\n";
1908     foreach my $qw ("title", "description", "link") {
1909      unless ($args->{$qw}) {
1910       print STDERR "You need to include a $qw tag in your RSS description\n";
1911       return(0);
1912      }
1913      # we need to do something a bit funky with the link. We can't have ampersands in the <link> </link> in valid html
1914      # so we are going to pull out the links and uri_escape just the part after the .cgi
1915      if ($qw eq "link")
1916      {
1917       $args->{$qw} =~ /^(.*?\.cgi.)(.*)$/;
1918       $args->{$qw} = $1.uri_escape($2) if ($1 && $2);
1919      }
1920    
1921      $xml .= "\t\t<$qw>".$args->{$qw}."</$qw>\n";
1922      delete $args->{$qw};
1923     }
1924    
1925     foreach my $tag (grep {!/type/i} keys %$args)
1926     {
1927      $xml .= "\t\t<$tag>".$args->{$tag}."</$tag>\n";
1928     }
1929    
1930     $xml .= "\t</item>\n";
1931    
1932    
1933     my @files=("SEED.rss");
1934     if ($args->{"type"}) {
1935        my $type = $args->{type};
1936        push @files, "SEED.$type.rss"
1937    }
1938    
1939     foreach my $file ("SEED.rss", @$files)
1940     {
1941      if (-e "$filepath/$file")
1942      {
1943       my @out; # the new content of the file
1944       my $itemcount=0; # how many <item> </item>'s are we keeping
1945       my $initem; # are we in an item?
1946       open(IN, "$filepath/$file") || die "Can't open $filepath/$file";
1947       while (<IN>)
1948       {
1949        if (/\<item\>/) {
1950         push @out, $xml, unless ($itemcount);
1951         $itemcount++;
1952         $initem=1;
1953        }
1954        if (/\<\/item\>/) {$initem=0; next if ($itemcount > $max_entries)}
1955        next if ($initem && $itemcount > $max_entries);
1956        push @out, $_;
1957       }
1958       close IN;
1959       open(OUT, ">$filepath/$file") || die "Can't open $filepath/$file for writing";
1960       print OUT @out;
1961      }
1962      else
1963      {
1964       open(OUT, ">$filepath/$file") || die "Can't open $filepath/$file for writing";
1965       print OUT "<?xml version=\"1.0\"?>\n<rss version=\"2.0\">\n<channel>\n";
1966       if ($info->{$file})
1967       {
1968         # we're going to sanity check each of the three options we output, just to be sure
1969         foreach my $qw ("title", "description", "link")
1970         {
1971           if ($info->{$file}->{$qw})
1972           {
1973              print OUT "<$qw>", $info->{$file}->{$qw}, "</$qw>\n";
1974           } else {
1975              print STDERR "Please add a $qw for $file\n"; print OUT "<$qw>$file</$qw>\n";
1976           }
1977         }
1978       }
1979       else {
1980        print STDERR "Please define title, link, and description information for $file\n";
1981        print OUT "<title>$file</title>\n<description>An RSS feed</description>\n<link>", &FIG::cgi_url, "</link>\n";
1982       }
1983       print OUT "\n", $xml;
1984       print OUT "\n", "</channel>\n</rss>\n"
1985      }
1986     }
1987    }
1988    
1989    
1990    
1991    1;
1992    
 1  

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