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# 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 FIGRules;
24  use Carp;  use Carp;
25  use Data::Dumper;  use Data::Dumper;
26  use LWP::UserAgent;  use LWP::UserAgent;
27  use LWP::Simple;  use LWP::Simple;
28    use URI::Escape;  # uri_escape()
29  use URI::URL;  use URI::URL;
30  use HTTP::Request::Common;  use HTTP::Request::Common;
31    use POSIX;
32    use CGI;
33    
34  sub show_page {  #use raelib; # now used for the excel function, that should eventually end up in here. Way too experimental!
35      my($cgi,$html,$no_home) = @_;  my $raelib;
36      my $i;  
37    
38    my $top_link_cache;
39    
40    
41    sub new
42    {
43        my($class) = @_;
44    
45        my $self = {};
46    
47        return bless $self, $class;
48    }
49    
50    sub top_link
51    {
52    
53      #      #
54      # Find the HTML header      # Determine if this is a toplevel cgi or one in one of the subdirs (currently
55        # just /p2p).
56      #      #
57    
58      my $html_hdr_file = "./Html/html.hdr";      return $top_link_cache if ($top_link_cache);
59    
60        my @parts = split(/\//, $ENV{SCRIPT_NAME});
61        my $top;
62        if (defined $parts[-2] && $parts[-2] eq 'FIG')
63        {
64            $top = '.';
65    #       warn "toplevel @parts\n";
66        }
67        elsif (defined $parts[-3] && $parts[-3] eq 'FIG')
68        {
69            $top = '..';
70    #       warn "subdir @parts\n";
71        }
72        else
73        {
74            $top = $FIG_Config::cgi_base;
75    #       warn "other @parts\n";
76        }
77    
78        $top_link_cache = $top;
79        return $top;
80    }
81    
82    sub compute_html_header
83    {
84        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
85        my($additional_insert, $user, %options ) = @_;
86    
87        local $/ = "\n";
88    
89        my $header_name = $options{header_name} ? $options{header_name} : "html.hdr";
90        my $tail_name = $options{tail_name} ? $options{tail_name} : "html.tail";
91    
92        my $html_hdr_file = "./Html/$header_name";
93      if (! -f $html_hdr_file)      if (! -f $html_hdr_file)
94      {      {
95          $html_hdr_file = "$FIG_Config::fig/CGI/Html/html.hdr";          $html_hdr_file = "$FIG_Config::fig/CGI/Html/$header_name";
96      }      }
97        my @html_hdr = &FIG::file_read($html_hdr_file);
98    
99      my $html_tail_file = "./Html/html.tail";      # for my $k (sort keys %ENV) { warn "$k = $ENV{$k}\n"; }
100      if (! -f $html_tail_file)  
101        #
102        # Determine if this is a toplevel cgi or one in one of the subdirs (currently
103        # just /p2p).
104        #
105    
106        my @parts = split(/\//, $ENV{SCRIPT_NAME});
107        my $top;
108        if ($parts[-2] eq 'FIG')
109        {
110            $top = '.';
111    #       warn "toplevel @parts\n";
112        }
113        elsif ($parts[-3] eq 'FIG')
114        {
115            $top = '..';
116    #       warn "subdir @parts\n";
117        }
118        else
119        {
120            $top = $FIG_Config::cgi_base;
121    #       warn "other @parts\n";
122        }
123    
124        $options{no_fig_search} or push( @html_hdr, "<br><a href=\"$top/index.cgi?user=$user\">FIG search</a>\n" );
125    
126        if (@html_hdr)
127      {      {
128          $html_tail_file = "$FIG_Config::fig/CGI/Html/html.tail";          my $insert_stuff;
129    
130            if (not $options{no_release_info})
131            {
132                my @ver = &FIG::file_head("$FIG_Config::fig_disk/CURRENT_RELEASE", 1);
133                my $ver = $ver[0];
134                chomp $ver;
135                if ($ver =~ /^cvs\.(\d+)$/)
136                {
137                    my $d = asctime(localtime($1));
138                    chomp($d);
139                    $ver .=  " ($d)";
140                }
141                my $host = &FIG::get_local_hostname();
142                $insert_stuff = "SEED version <b>$ver</b> on $host";
143            }
144    
145            if ($additional_insert)
146            {
147                $insert_stuff .= "<br>" . $additional_insert;
148            }
149    
150            for $_ (@html_hdr)
151            {
152                s,(href|img\s+src)="/FIG/,$1="$top/,g;
153                    s,(\?user\=)\",$1$user",;
154                if ($_ eq "<!-- HEADER_INSERT -->\n")
155                {
156                    $_ = $insert_stuff;
157                }
158      }      }
159        }
160    
161        return @html_hdr;
162    }
163    
164    sub show_page {
165        #warn "SHOWPAGE: cgi=", Dumper(@_);
166        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
167        my($cgi,$html,$no_home, $alt_header, $css, $javasrc, $cookie, $options) = @_;
168        my $i;
169        Trace("Setting top link.") if T(3);
170        my $top = top_link();
171    
172        # ARGUMENTS:
173        #     $cgi is the CGI method
174        #     $html is an array with all the html in it. It is just joined by "\n" (and not <br> or <p>
175        #     $no_home eliminates ONLY the bottom FIG search link in a page
176        #     $alt_header is a reference to an array for an alternate header banner that you can replace the standard one with
177        #     $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
178        #               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
179        #               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
180        #     $javasrc is a reference to an array of URLs to javascripts to be included (e.g. "FIG/Html/css/styleswitcher.js")
181        #     $cookie is the name and value of the cookie to set. Note that you should probably use raelib->cookie to get/set your cookies
182        #     $options is a reference to a hash of options that you can pass around the pages
183        #
184        # 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";
189        if (! -f $html_tail_file)
190        {
191            $html_tail_file = "$FIG_Config::fig/CGI/Html/$tail_name";
192        }
193        Trace("Extracting user name and header data.") if T(3);
194        my $user = $cgi->param('user') || "";
195        my @html_hdr;
196        if ($alt_header && ref($alt_header) eq "ARRAY")
197        {
198           @html_hdr = @$alt_header;
199        }
200        else
201        {
202            @html_hdr = compute_html_header(undef,$user,%$options);
203        }
204    
205      print $cgi->header;      # RAE: I am offloading the handling of cookies to CGI.pm since I don't know how they are set up.
206        # This modification adds the cookies if necessary
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
209        # to add cookies back in replace these two header lines with each other
210        #my $hdr_thing = $cgi->header(-cookie=>$cookie);
211        my $hdr_thing = $cgi->header();
212        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 46  Line 228 
228                       meta     => 1,                       meta     => 1,
229                       nextid   => 1,                       nextid   => 1,
230                       style    => 1,                       style    => 1,
231                       title    => 1                       title    => 1,
232                     );                     );
233    
234      #      #
# Line 74  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 89  Line 271 
271          if ( $html->[$i] =~ /\<body[^0-9a-z]/i )          if ( $html->[$i] =~ /\<body[^0-9a-z]/i )
272          {          {
273              $body_line = $i;              $body_line = $i;
274              $last;              last;
275          }          }
276    
277          #  Now the general case.          #  Now the general case.
# Line 120  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      #      #
329      #  <BODY> goes after last head line      #  <BODY> goes after last head line
330      #      #
331        #  RAE:
332        #  Added the javascript for the buttons immediately after body.
333        #  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!
335        #  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 156  Line 344 
344      #  Seed page header (if it exists) goes after <BODY>      #  Seed page header (if it exists) goes after <BODY>
345      #      #
346    
347      if ( -f $html_hdr_file )      if (@html_hdr)
348      {      {
349          splice( @$html, $body_line + 1, 0, `cat $html_hdr_file` );          Trace("Splicing SEED page header after $body_line.") if T(3);
350            splice( @$html, $body_line + 1, 0, @html_hdr );
351      }      }
352    
353      #      #
# Line 168  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    
364        # RAE:
365        # Add css here
366        # Note that at the moment I define these two sheets here. I think this should
367        # 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'>
370        Trace("Formatting CSS.") if T(3);
371        # 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}}}
373    
374        if (!$css || !$css->{'Default'})
375        {
376           $css->{'Default'} = "Html/css/default.css";
377        }
378        if (!$css->{"Sans Serif"})
379        {
380           $css->{'Sans Serif'} = "Html/css/sanserif.css";
381        }
382    
383        my $csstext = "<link rel='stylesheet' title='default' href='".$css->{'Default'}."' type='text/css'>\n";
384        $csstext   .= "<link rel='alternate stylesheet' title='Sans Serif' href='".$css->{'Sans Serif'}."' type='text/css'>\n";
385    
386        foreach my $k (keys %$css)
387        {
388           next if (lc($k) eq "default" || lc($k) eq "sans serif");
389           $csstext .= "<link rel='alternate stylesheet' title='$k' href='".$css->{$k}."' type='text/css'>\n";
390        }
391    
392        $csstext   .= "<link rel='alternate'  title='SEED RSS feeds' href='Html/rss/SEED.rss' type='application/rss+xml'>\n";
393    
394        # RAE: also added support for external javascripts here.
395        # we are cluttering the HTML code with all the javascripts when they could easily be in external files
396        # this solution allows us to source other files
397    
398        # 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.
400        Trace("Formatting javascript.") if T(3);
401        # $javasrc must be a ref to an array with urls (absolute or relative) to the javascripts
402        push @$javasrc, "Html/css/FIG.js";
403        foreach my $script (@$javasrc) {
404            $csstext .= "<script src=\"$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.
409    
410      #      #
411      #  <BASE ...> goes before </HEAD>      #  <BASE ...> goes before </HEAD>
412      #      #
# Line 183  Line 419 
419          #  only, or every update?), I provide an alternative derivation          #  only, or every update?), I provide an alternative derivation
420          #  from $cgi_url. -- GJO          #  from $cgi_url. -- GJO
421          #          #
422            # BASE href needs to be absolute. RDO.
423          my $base_url = $FIG_Config::cgi_base;          #
424          if ( ! $base_url )                      # if cgi_base was not defined          #
425          {  #        $base_url = &FIG::cgi_url;
426              $base_url = $FIG_Config::cgi_url;   # get the full cgi url  #       my $base_url = $FIG_Config::cgi_base;
427              $base_url =~ s~^http://[^/]*~~;     # remove protocol and host  #       if ( ! $base_url )                      # if cgi_base was not defined
428              $base_url =~ m~/$~ || $base_url =~ s~$~/~; # check trailing slash  #       {
429          }  #           $base_url = $FIG_Config::cgi_url;   # get the full cgi url
430    #           $base_url =~ s~^http://[^/]*~~;     # remove protocol and host
431    #           $base_url =~ m~/$~ || $base_url =~ s~$~/~; # check trailing slash
432    #       }
433    
434          $base_line = $head_end_line;          $base_line = $head_end_line;
435          splice( @$html, $base_line, 0, "<BASE href=\"$base_url\">\n" );          #
436            # RDO 2005-1006. Remove this so proxying works better.
437            #
438    #        splice( @$html, $base_line, 0, "<BASE href=\"$base_url/\">\n" );
439      }      }
440    
441      #      #
# Line 203  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 213  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 228  Line 472 
472      }      }
473    
474      #      #
475        # 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";
479        my $site_fh;
480        if (open($site_fh, "<$site_tail"))
481        {
482            push(@tail, <$site_fh>);
483            close($site_fh);
484        }
485    
486        #
487      #  Figure out where to insert The SEED tail.  Before </body>,      #  Figure out where to insert The SEED tail.  Before </body>,
488      #  or before </html>, or at end of page.      #  or before </html>, or at end of page.
489      #      #
   
490      my @tags = ();      my @tags = ();
491        Trace("Processing closing tags.") if T(3);
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 >= @$html)        # </body> not found; look for </html>
494      {      {
# Line 248  Line 503 
503    
504      if ( @tail )      if ( @tail )
505      {      {
506            Trace("Splicing tail.") if T(3);
507          splice( @$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, $i, 0, @tags );
513      }      }
514    
515      print @$html;      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,
517        # 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
519        #
520        # chomp(@$html);
521        # print join "\n", @$html;
522        #
523        # Apparently the above still breaks things. This is the correct code:
524        foreach $_ (@$html)
525        {
526            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  }  }
535    
536    
537    =head1 make_table
538    
539    The main method to convert an array into a table.
540    
541    The col_hdrs are set to the <th> headers, the $tab is an array of arrays. The first is the rows, and the second is the columns. The title is the title of the table.
542    
543    The options define the settings for the table such as border, width, and class for css formatting. If the option "excelfile" is set to a filename that will be created in FIG_Config::temp, and the link included that allows the user to download the file as an excel file.
544    
545    =cut
546    
547  sub make_table {  sub make_table {
548      my($col_hdrs,$tab,$title,$instr) = @_;      my($col_hdrs,$tab,$title, %options ) = @_;
549      my(@tab);      my(@tab);
550    
551      push( @tab, "\n<table border>\n",      my $border = defined $options{border} ? "border=\"$options{border}\"" : "border";
552        my $width = defined $options{width} ? "width=\"$options{width}\"" : "";
553        my $class = defined $options{class} ? "class=\"$options{class}\"" : "";
554        push( @tab, "\n<table $border $width $class>\n",
555                  "\t<caption><b>$title</b></caption>\n",                  "\t<caption><b>$title</b></caption>\n",
556                  "\t<tr>\n\t\t<th>"                  "\t<tr>\n\t\t"
557                . join( "</th>\n\t\t<th>", @$col_hdrs )                . join( "\n", map { &expand($_, "th") } @$col_hdrs )
558                . "</th>\n\t</tr>\n"                . "\n\t</tr>\n"
559          );          );
560      my($i,$nowrap);      my($i);
   
     for ($i=0; ($i < @$instr) && ($instr->[$i] !~ /nowrap/); $i++) {}  
     $nowrap = ($i == @$instr) ? "" : " nowrap";  
561    
562      my $row;      my $row;
563      foreach $row (@$tab)      foreach $row (@$tab)
564      {      {
565          push( @tab, "\t<tr>\n"          push( @tab, "\t<tr>\n"
566                    . join( "\n", map { &expand($_,$nowrap) } @$row )                    . join( "\n", map { &expand($_) } @$row )
567                    . "\n\t</tr>\n"                    . "\n\t</tr>\n"
568              );              );
569      }      }
570      push(@tab,"</table>\n");      push(@tab,"</table>\n");
571    
572        # excelfile should be appropriate for a filename (no spaces/special characters)
573        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,$options{"excelfile"})}
579    
580      return join("",@tab);      return join("",@tab);
581  }  }
582    
583    sub abstract_coupling_table {
584        my($cgi,$prot,$coupling) = @_;
585        my %fc;
586    
587        my $col_hdrs = ["coupled to","Score","Type of Coupling", "Type-specific Data"];
588        my $tab = [];
589        my %by_peg;
590        foreach my $x (@$coupling)
591        {
592            my($peg2,$psc,$type,$extra) = @$x;
593            if (($type !~ /^[ID]FC$/) || (! $fc{$peg2}))
594            {
595                if ($type =~  /^[ID]FC$/)
596                {
597                    $fc{$peg2} = 1;
598                }
599    
600                $by_peg{$peg2} += $psc;
601            }
602        }
603    
604        foreach my $x (sort { ($by_peg{$b->[0]} <=> $by_peg{$a->[0]})
605                              or ($a->[0] cmp $b->[0])
606                              or ($b->[1] <=> $a->[1])
607                              or ($a->[2] cmp $b->[2]) } @$coupling)
608        {
609            my($peg2,$psc,$type,$extra) = @$x;
610            push(@$tab,[&fid_link($cgi,$peg2,1),$psc,$type,&set_prot_links($cgi,join(", ",@$extra))]);
611        }
612    
613    
614         my $help = "<a href=\"Html/abstract_coupling.html\" target=\"SEED_or_SPROUT_help\">for help</a>";
615    #    my @html = &make_table($col_hdrs,$tab,"Abstract Coupling Data for $prot");
616    #    push(@html,"<hr>\n",$cgi->h3($help),"<br>");
617    #    return @html;
618    
619        return &make_table($col_hdrs,$tab,"Abstract Coupling Data for $prot [$help]");
620    }
621    
622  sub expand {  sub expand {
623      my($x,$nowrap) = @_;      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
624        my( $x, $tag ) = @_;
625    
626        $tag = "td" unless $tag;
627        my $endtag = $tag;
628    
629        # RAE modified this so that you can pass in a reference to an array where
630        # the first element is the data to display and the second element is optional
631        # things like colspan and align. Note that in this case you need to include the td
632        # use something like ["some data to appear", "td colspan=4 bgcolor=gray"]
633    
634      if ($x =~ /^\@([^:]+)\:([^:]+)\:(.*)$/)      # per GJO's request modified this line so it can take any tag.
635        if ( ref($x) eq "ARRAY" ) { ($x, $tag) = @$x; $tag =~ /^(\S+)/; $endtag = $1 }
636    
637        if ( $x =~ /^\@([^:]+)\:(.*)$/ )
638      {      {
639          return "\t\t<td$nowrap $1=\"$2\">$3</td>";          return "\t\t<$tag $1>$2</$endtag>";
640      }      }
641      else      else
642      {      {
643          return "\t\t<td$nowrap>$x</td>";          return "\t\t<$tag>$x</$endtag>";
644        }
645    }
646    
647    
648    =head2 merge_table_rows()
649    
650    Merge table rows together. This will merge a table so that adjacent cells with the same content will only be shown once.
651    
652    Something like this:
653    
654        -----------------------
655        |    1     |    a     |
656        -----------------------
657        |    1     |    b     |
658        -----------------------
659        |    2     |    c     |
660        -----------------------
661        |    3     |    d     |
662        -----------------------
663        |    4     |    d     |
664        -----------------------
665        |    5     |    d     |
666        -----------------------
667    
668    Will become:
669    
670        -----------------------
671        |          |    a     |
672        |    1     |-----------
673        |          |    b     |
674        -----------------------
675        |    2     |    c     |
676        -----------------------
677        |    3     |          |
678        ------------          |
679        |    4     |    5     |
680        ------------          |
681        |    5     |          |
682        -----------------------
683    
684    
685    The method takes two arguments. The reference to the array that is the table ($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.
686    
687     $tab=&HTML::merge_table_rows($tab);
688    
689     or
690    
691     $skip=(1=>1, 3=>1, 5=>1);
692     $tab=&HTML::merge_table_rows($tab, $skip);  # will merge all columns except 1, 3 and 5. Note the first column in the table is #0
693    
694    
695    =cut
696    
697    
698    
699    
700    sub merge_table_rows {
701     # RAE:
702     # Experimental piece of code. We often want to have rows or columns were cells are merged. It just looks so much nicer
703     # this block should merge adjacent rows that have the same text in them.
704     # use like this:
705     #      $tab=&HTML::merge_table_rows($tab);
706     # before you do a make_table call
707    
708     my $self=shift if UNIVERSAL::isa($_[0],__PACKAGE__);
709     my ($tab, $skip)=@_;
710    
711     my $newtable;
712     my $lastrow;
713     my $rowspan;
714     my $refs;
715    
716     for (my $y=0; $y <= $#$tab; $y++) {
717     #$y is the row in the table;
718      for (my $x=0; $x <= $#{$tab->[$y]}; $x++) {
719       # this is the user definable columns not to merge
720       if ($skip->{$x})
721       {
722        $newtable->[$y]->[$x] = $tab->[$y]->[$x];
723        next;
724       }
725    
726       #$x is the column in the table
727       # if the column in the row we are looking at is the same as the column in the previous row, we don't add
728       # this cell to $newtable. Instead we increment the rowspan of the previous row by one
729    
730       # handle cells that are references to arrays
731       if (ref($tab->[$y]->[$x]) eq "ARRAY") {$refs->[$y]->[$x]=$tab->[$y]->[$x]->[1]; $tab->[$y]->[$x]=$tab->[$y]->[$x]->[0]}
732    
733       # now we go back through the table looking where to draw the merge line:
734       my $lasty=$y;
735       while ($lasty >= 0 && $tab->[$y]->[$x] eq $tab->[$lasty]->[$x]) {$lasty--}
736       $lasty++; # this is the last identical cell. If lasty==y it is the current cell, so we just save the data. Otherwise we increment the rowspan
737       if ($lasty == $y) {
738        # we always want to have something in rows that may otherwise be empty but should be there (see below)
739        unless ($tab->[$y]->[$x]) {$tab->[$y]->[$x]=" &nbsp; "}
740        $newtable->[$y]->[$x] = $tab->[$y]->[$x];
741       }
742       else {$rowspan->[$lasty]->[$x]++}
743      }
744     }
745    
746     # now just join everything back together
747     for (my $y=0; $y <= $#$tab; $y++) {
748      for (my $x=0; $x <= $#{$tab->[$y]}; $x++) {
749       if ($rowspan->[$y]->[$x]) {
750        if ($refs->[$y]->[$x]) {$refs->[$y]->[$x] .= " rowspan=". ($rowspan->[$y]->[$x]+1)}
751        else {$refs->[$y]->[$x] = "td rowspan=". ($rowspan->[$y]->[$x]+1)}
752        $newtable->[$y]->[$x]=[$newtable->[$y]->[$x], $refs->[$y]->[$x]];
753       }
754       elsif ($newtable->[$y]->[$x] && $refs->[$y]->[$x]) {
755        $newtable->[$y]->[$x]=[$newtable->[$y]->[$x], $refs->[$y]->[$x]];
756       }
757      }
758     }
759    
760    
761     # finally we have to remove any completely empty cells that have been added by the array mechanism
762     # (e.g. if you define $a->[2] then $a->[0] and $a->[1] are now undef).
763     # that is why in the loop above I replace empty cells with nbsp. They are now not undef!
764     # I am sure that Gary can do this in one line, but I am hacking.
765     my @trimmed;
766     foreach my $a (@$newtable) {
767      my @row;
768      foreach my $b (@$a) {
769       push @row, $b if ($b);
770      }
771      push @trimmed, \@row;
772     }
773    
774     return \@trimmed;
775    }
776    
777    
778    
779    
780    sub set_ec_links {
781        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
782        my($cgi,$x) = @_;
783        my($before,$match,$after);
784    
785        if ($x =~ /^(.*)(EC \d+\.\d+\.\d+\.\d+)(.*)/s)
786        {
787            $before = $1;
788            $match = $2;
789            $after = $3;
790            return &set_ec_links($cgi,$before) . &HTML::ec_link($match) . &set_ec_links($cgi,$after);
791      }      }
792        return $x;
793  }  }
794    
795  sub ec_link {  sub ec_link {
796        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
797      my($role) = @_;      my($role) = @_;
798    
799      if ($role =~ /(\d+\.\d+\.\d+\.\d+)/)      if ($role =~ /(\d+\.\d+\.\d+\.\d+)/)
# Line 312  Line 807 
807  }  }
808    
809  sub role_link {  sub role_link {
810        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
811      my($cgi,$role) = @_;      my($cgi,$role) = @_;
812    
813      my $roleR = ($role =~ /^(\d+\.\d+\.\d+\.\d+)\s+-\s+/) ? $1 : $role;      my $roleR = ($role =~ /^(\d+\.\d+\.\d+\.\d+)\s+-\s+/) ? $1 : $role;
# Line 322  Line 818 
818      return "<a href=$link>$role</a>";      return "<a href=$link>$role</a>";
819  }  }
820    
821    =head2 fid_link
822    
823    Get a link to a fid.
824    
825    use: my $html=&HTML::fid_link($cgi, $fid, Local, Just_URL, Full_Path);
826    
827    Local is a boolean means to eliminate the fig|org.peg from the text of the link.
828    
829    Just_URL will only return the URL and not the HTML code. The default is to return the full code.
830    
831    Full_Path is a boolean that will get the full path to the URL not just a relative path. This is required in pages where the base href changes (e.g. if an image is imported like on the metabolic pages).
832    
833    =cut
834    
835    
836  sub fid_link {  sub fid_link {
837      my($cgi,$fid,$local,$just_url) = @_;      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
838        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($n);
863    
864      if ($fid =~ /^fig\|\d+\.\d+\.([a-z]+)\.(\d+)/)      my $top = top_link();
865        if ($fullpath) {$top=$FIG_Config::cgi_url}
866    
867        if ($fid =~ /^fig\|\d+\.\d+\.([a-zA-Z]+)\.(\d+)/)
868      {      {
869          if ($local)          if ($local)
870          {          {
# Line 343  Line 881 
881          {          {
882              $n = $fid;              $n = $fid;
883          }          }
884          if ($1 ne "peg") { return $n }  
885            my $link;
886            my $new_framework = $cgi->param('new_framework') ? 1 : 0;
887            #added to format prophage and path island links to feature.cgi
888            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)
892            {
893               Trace("Creating feature link for $fid.") if T(4);
894               my $user = $cgi->param('user');
895               if (! $user) { $user = "" }
896               $link = "$top/feature.cgi?feature=$fid&user=$user$sprout$virt";
897               $link =~ s/[a-z_A-Z0-9]+\.cgi\?/feature.cgi?/;
898            }
899            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" : "";
905          my $link = $cgi->url() . "?prot=$fid&user=$user$trans";              my $sprout = $cgi->param('SPROUT') ? "&SPROUT=1" : "";
906          $link =~ s/[a-z_A-Z]+\.cgi\?/protein.cgi?/;  ###a
907    
908    ### This used to be
909    ###     my $link = &FIG::cgi_url . "/protein.cgi?prot=$fid&user=$user$trans$sprout";
910    ###
911    ### The cost became prohibitive in the subsystem spreadsheets.  Hence, we cache the value
912    ###
913    ### RAO
914    
915                #if (! $cgi_url) { $cgi_url = &FIG::cgi_url }
916                #$link = $cgi_url . "/protein.cgi?prot=$fid&user=$user$trans$sprout";
917                $link = "$top/protein.cgi?prot=$fid&user=$user$trans$sprout$virt\&new_framework=$new_framework";
918                $link =~ s/[a-z_A-Z0-9]+\.cgi\?/protein.cgi?/;
919            }
920          if ($just_url)          if ($just_url)
921          {          {
922              return $link;              return $link;
923          }          }
924          else          else
925          {          {
926              return "<a href=$link>$n</a>";              return "<a target=_blank href='$link'>$n</a>";
927          }          }
928      }      }
929      return $fid;      return $fid;
930  }  }
931    
932  sub family_link {  sub family_link {
933        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
934      my($family,$user) = @_;      my($family,$user) = @_;
935    
936      return $family;      return $family;
937  }  }
938    
939  use URI::Escape;  =head2 evidence_codes_explain
940    
941    Given an evidence code, returns a string that explains this eveidence code.
942    
943    =cut
944    
945    sub evidence_codes_explain {
946     my($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__);
966      my( $url, $type, $kv_pairs) = @_;      my( $url, $type, $kv_pairs) = @_;
967      my( $encoded, $ua, $args, @args, $out, @output, $x );      my( $encoded, $ua, $args, @args, $out, @output, $x );
968    
969      $ua = new LWP::UserAgent;      $ua = new LWP::UserAgent;
970      $ua->timeout( 900 );      $ua->timeout( 900 );
   
971      if ($type =~/post/i)      if ($type =~/post/i)
972      {      {
973          $args = [];          $args = [];
# Line 387  Line 979 
979          my $response = $ua->request($request);          my $response = $ua->request($request);
980          $out = $response->content;          $out = $response->content;
981      }      }
982      else  
983        if ($type =~/get/i)
984      {      {
985          @args = ();          @args = ();
986          foreach $x (@$kv_pairs)          foreach $x (@$kv_pairs)
# Line 399  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 417  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 435  Line 1026 
1026  }  }
1027    
1028  sub trim_output {  sub trim_output {
1029        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,$i);
# Line 465  Line 1057 
1057      for ($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,$n+1);
1069      }      }
1070  }  }
1071    
1072  sub set_prot_links {  =head2 alias_url
     my($cgi,$x) = @_;  
     my($before,$match,$after);  
1073    
1074      if ($x =~ /^(.*)(fig\|\d+\.\d+\.peg\.\d+)(.*)$/)  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          $before = $1;  cannot be determined, the function will return undef.
1077          $match = $2;  
1078          $after = $3;  use: my $html=&HTML::alias_url($alias, $type);
1079          return &set_prot_links($cgi,$before) . &HTML::fid_link($cgi,$match) . &set_prot_links($cgi,$after) . "\n";  
1080    =cut
1081    
1082    sub alias_url {
1083      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1084    
1085      my ($id, $type) = @_;
1086    
1087      if ($type eq "SEED") { # 1
1088        return "http://seed-viewer.theseed.org/linkin.cgi?id=$id";
1089      }      }
1090      elsif ($x =~ /^(.*)(gi\|\d+)(.*)$/)    elsif ($type eq "UniProt") {
1091      {      return "http://www.uniprot.org/entry/$id";
1092          $before = $1;    }
1093          $match = $2;    elsif ($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 {
1215        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1216        my($cgi,$x) = @_;
1217        my($before,$match,$after);
1218    
1219        if ($x =~ /^(.*)(fig\|\d+\.\d+\.peg\.\d+)(.*)/s)
1220        {
1221            $before = $1;
1222            $match = $2;
1223            $after = $3;
1224            return &set_prot_links($cgi,$before) . &HTML::fid_link($cgi,$match) . &set_prot_links($cgi,$after);
1225        }
1226        elsif ($x =~ /^(.*)\b([NXYZA][PM]_[0-9\.]+)\b(.*)/s)
1227        {
1228            $before = $1;
1229            $match = $2;
1230            $after = $3;
1231            return &set_prot_links($cgi,$before) . &HTML::refseq_link($cgi,$match) . &set_prot_links($cgi,$after);
1232        }
1233        elsif ($x =~ /^(.*)(gi\|\d+)(.*)/s)
1234        {
1235            $before = $1;
1236            $match = $2;
1237            $after = $3;
1238            return &set_prot_links($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)
1248        {
1249            $before = $1;
1250            $match = $2;
1251            $after = $3;
1252            return &set_prot_links($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)
1262        {
1263            $before = $1;
1264            $match = $2;
1265            $after = $3;
1266            return &set_prot_links($cgi,$before) . &HTML::eric_link($cgi,$match) . &set_prot_links($cgi,$after);
1267        }
1268    
1269        elsif ($x =~ /^(.*)\b(bhb\|.*?)\b(.*)/s)
1270        {
1271            $before = $1;
1272            $match = $2;
1273            $after = $3;
1274            return &set_prot_links($cgi,$before) . &HTML::bhb_link($cgi,$match) . &set_prot_links($cgi,$after);
1275        }
1276    
1277        elsif ($x =~ /^(.*)\b(apidb\|[0-9\.a-z_]+)\b(.*)/s)
1278        {
1279            $before = $1;
1280            $match = $2;
1281            $after = $3;
1282            return &set_prot_links($cgi,$before) . &HTML::apidb_link($cgi,$match) . &set_prot_links($cgi,$after);
1283        }
1284    
1285        elsif ($x =~ /^(.*)\b(patric\|.*?)\b(.*)/s)
1286        {
1287            $before = $1;
1288            $match = $2;
1289            $after = $3;
1290            return &set_prot_links($cgi,$before) . &HTML::patric_link($cgi,$match) . &set_prot_links($cgi,$after);
1291        }
1292    
1293        elsif ($x =~ /^(.*)\b(vbrc\|.*?)\b(.*)/s)
1294        {
1295            $before = $1;
1296            $match = $2;
1297            $after = $3;
1298            return &set_prot_links($cgi,$before) . &HTML::vbrc_link($cgi,$match) . &set_prot_links($cgi,$after);
1299        }
1300    
1301        elsif ($x =~ /^(.*)\b(vectorbase\|.*?)\b(.*)/s)
1302        {
1303            $before = $1;
1304            $match = $2;
1305            $after = $3;
1306            return &set_prot_links($cgi,$before) . &HTML::vectorbase_link($cgi,$match) . &set_prot_links($cgi,$after);
1307        }
1308        elsif ($x =~  /^(.*)(uni\|[A-Z0-9]{6})(.*)/s)
1309        {
1310            $before = $1;
1311            $match = $2;
1312            $after = $3;
1313            return &set_prot_links($cgi,$before) . &HTML::uni_link($cgi,$match) . &set_prot_links($cgi,$after);
1314        }
1315        elsif ($x =~ /^(.*)(sp\|[A-Z0-9]{6})(.*)/s)
1316        {
1317            $before = $1;
1318            $match = $2;
1319            $after = $3;
1320            return &set_prot_links($cgi,$before) . &HTML::sp_link($cgi,$match) . &set_prot_links($cgi,$after);
1321        }
1322        elsif ($x =~ /^(.*)(pirnr\|NF\d+)(.*)/s)
1323        {
1324            $before = $1;
1325            $match = $2;
1326            $after = $3;
1327            return &set_prot_links($cgi,$before) . &HTML::pir_link($cgi,$match) . &set_prot_links($cgi,$after);
1328        }
1329        elsif ($x =~ /^(.*)(kegg\|[a-z]{2,4}:[a-zA-Z_0-9]+)(.*)/s)
1330        {
1331            $before = $1;
1332            $match = $2;
1333            $after = $3;
1334            return &set_prot_links($cgi,$before) . &HTML::kegg_link($cgi,$match) . &set_prot_links($cgi,$after);
1335        }
1336        elsif ($x =~ /^(.*)(Ensembl[a-zA-Z]+:[a-zA-Z_0-9\.]+)(.*)/s)
1337        {
1338            $before = $1;
1339            $match = $2;
1340            $after = $3;
1341            return &set_prot_links($cgi,$before) . &HTML::ensembl_link($cgi,$match) . &set_prot_links($cgi,$after);
1342        }
1343        elsif ($x =~ /^(.*)(EntrezGene:[a-zA-Z_0-9\.]+)(.*)/s)
1344        {
1345            $before = $1;
1346            $match = $2;
1347            $after = $3;
1348            return &set_prot_links($cgi,$before) . &HTML::entrezgene_link($cgi,$match) . &set_prot_links($cgi,$after);
1349        }
1350        elsif ($x =~ /^(.*)(MIM:[a-zA-Z_0-9\.]+)(.*)/s)
1351        {
1352            $before = $1;
1353            $match = $2;
1354            $after = $3;
1355            return &set_prot_links($cgi,$before) . &HTML::mim_link($cgi,$match) . &set_prot_links($cgi,$after);
1356        }
1357        elsif ($x =~ /^(.*)(HGNC:[a-zA-Z_0-9\.]+)(.*)/s)
1358        {
1359            $before = $1;
1360            $match = $2;
1361            $after = $3;
1362            return &set_prot_links($cgi,$before) . &HTML::hgnc_link($cgi,$match) . &set_prot_links($cgi,$after);
1363        }
1364        elsif ($x =~ /^(.*)(UniGene:[a-zA-Z_0-9\.]+)(.*)/s)
1365        {
1366            $before = $1;
1367            $match = $2;
1368            $after = $3;
1369            return &set_prot_links($cgi,$before) . &HTML::unigene_link($cgi,$match) . &set_prot_links($cgi,$after);
1370        }
1371    # IPI stopped working. turn off for now.
1372    #    elsif ($x =~ /^(.*)(IPI:[a-zA-Z_0-9\.]+)(.*)/s)
1373    #    {
1374    #        $before = $1;
1375    #        $match = $2;
1376    #        $after = $3;
1377    #        return &set_prot_links($cgi,$before) . &HTML::ipi_link($cgi,$match) . &set_prot_links($cgi,$after);
1378    #    }
1379        elsif ($x =~ /^(.*)(WP:[a-zA-Z_0-9\.]+)(.*)/s)
1380        {
1381            #wormbase
1382    
1383            $before = $1;
1384            $match = $2;
1385            $after = $3;
1386            return &set_prot_links($cgi,$before) . &HTML::wp_link($cgi,$match) . &set_prot_links($cgi,$after);
1387        }
1388        elsif ($x =~ /^(.*)(FB:[a-zA-Z_0-9\.]+)(.*)/s)
1389        {
1390            #flybase
1391    
1392            $before = $1;
1393            $match = $2;
1394            $after = $3;
1395            return &set_prot_links($cgi,$before) . &HTML::fb_link($cgi,$match) . &set_prot_links($cgi,$after);
1396        }
1397        elsif ($x =~ /^(.*)(FlyBaseORFNames:[a-zA-Z_0-9\.]+)(.*)/s)
1398        {
1399            #flybase
1400    
1401            $before = $1;
1402            $match = $2;
1403          $after = $3;          $after = $3;
1404          return &set_prot_links($cgi,$before) . &HTML::gi_link($cgi,$match) . &set_prot_links($cgi,$after) . "\n";          return &set_prot_links($cgi,$before) . &HTML::fborf_link($cgi,$match) . &set_prot_links($cgi,$after);
1405      }      }
1406      elsif ($x =~ /^(.*)(sp\|[A-Z0-9]{6})(.*)$/)      elsif ($x =~ /^(.*)(SGD_LOCUS:[a-zA-Z_0-9\.]+)(.*)/s)
1407      {      {
1408            #flybase
1409    
1410          $before = $1;          $before = $1;
1411          $match = $2;          $match = $2;
1412          $after = $3;          $after = $3;
1413          return &set_prot_links($cgi,$before) . &HTML::sp_link($cgi,$match) . &set_prot_links($cgi,$after) . "\n";          return &set_prot_links($cgi,$before) . &HTML::sgd_link($cgi,$match) . &set_prot_links($cgi,$after);
1414      }      }
1415      elsif ($x =~ /^(.*)(pirnr\|NF\d+)(.*)$/)      elsif ($x =~ /^(.*)(tr\|[a-zA-Z0-9]+)(.*)/s)
1416      {      {
1417    
1418          $before = $1;          $before = $1;
1419          $match = $2;          $match = $2;
1420          $after = $3;          $after = $3;
1421          return &set_prot_links($cgi,$before) . &HTML::pir_link($cgi,$match) . &set_prot_links($cgi,$after) . "\n";  
1422          return &set_prot_links($cgi,$before) .  &HTML::trembl_link($cgi,$match) . &set_prot_links($cgi,$after);
1423      }      }
1424      return $x;      return $x;
1425  }  }
1426    
1427    sub trembl_link {
1428        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1429        my($cgi,$id) = @_;
1430    
1431        if ($id =~ /^tr\|(.*)/) {
1432          return "<a href='http://ca.expasy.org/uniprot/$1' target=_blank>$id</a>";
1433        } else {
1434          return "invalid call to trembl link";
1435        }
1436    }
1437    
1438    sub refseq_link {
1439        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1440        my($cgi,$id) = @_;
1441    
1442        if ($id =~ /^[NXYZA]P_/)
1443        {
1444            return "<a href='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=protein&cmd=search&term=$id' target=_blank>$id</a>";
1445        }
1446        elsif ($id =~ /^[NXYZA]M_/)
1447        {
1448            return "<a href='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=nuccore&cmd=search&term=$id' target=_blank>$id</a>";
1449        }
1450    }
1451    
1452  sub gi_link {  sub gi_link {
1453        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1454      my($cgi,$gi) = @_;      my($cgi,$gi) = @_;
1455    
1456      if ($gi =~ /^gi\|(\d+)$/)      if ($gi =~ /^gi\|(\d+)$/)
1457      {      {
1458          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>";
1459      }      }
1460      return $gi;      return $gi;
1461  }  }
1462    
1463    sub tigr_link {
1464        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1465        my($cgi,$tigr) = @_;
1466    
1467        if ($tigr =~ /^tigr\|(NT|ntbp|ntbpA|BA|BMAA|BXB|GBA)(\w+)$/)
1468        {
1469            my $id=$1.$2;
1470            return "<a href=\"http://pathema.tigr.org/tigr-scripts/pathema/shared/GenePage.cgi?locus=$id\" target=_blank>$tigr</a> (Pathema)";
1471        }
1472        elsif ($tigr =~ /^tigr(cmr)?\|(\S+)$/)
1473        {
1474            return "<a href=\"http://www.tigr.org/tigr-scripts/CMR2/GenePage.spl?locus=$2\" target=_blank>$tigr</a>";
1475        }
1476        return $tigr;
1477    }
1478    
1479    sub eric_link {
1480        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1481        my($cgi,$eric) = @_;
1482    
1483        if ($eric =~ /^eric\|(\S+)/)
1484        {
1485            return "<a href=\"https://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=$1\" target=_blank>$eric</a>";
1486        }
1487        return $eric;
1488    }
1489    
1490    sub bhb_link {
1491        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1492        my($cgi,$bhb) = @_;
1493    
1494        return "<a href=\"http://www.biohealthbase.org\" target=_blank>$bhb</a>";
1495    }
1496    
1497    sub apidb_link {
1498        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1499        my($cgi,$api) = @_;
1500    
1501        if ($api =~ /apidb\|(.*?)\.(.*)$/)
1502        {
1503            return "<a href=\"http://www.apidb.org/cgi-bin/redirect.cgi?taxon_id=$1&source_id=$2\" target=_blank>$api</a>";
1504        }
1505        return $api;
1506    }
1507    
1508    sub patric_link {
1509        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1510        my($cgi,$patric) = @_;
1511    
1512        if ($patric =~ /patric\|(.*)/)
1513        {
1514            return "<a href=\"https://patric.vbi.vt.edu/software/curationTool/gep/pgiCuration.php?locus_name=$1\" target=_blank>$patric</a>";
1515        }
1516        return $patric;
1517    }
1518    
1519    sub vbrc_link {
1520        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1521        my($cgi,$vbrc) = @_;
1522    
1523        if ($vbrc =~ /vbrc\|(.*)/)
1524        {
1525            return "<a href=\"http://www.biovirus.org/gene_detail.asp?name=$1\" target=_blank>$vbrc</a>";
1526        }
1527        return $vbrc;
1528    }
1529    
1530    sub vectorbase_link {
1531        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1532        my($cgi,$vec) = @_;
1533        return "<a href=\"http://www.vectorbase.org\" target=_blank>$vec</a>";
1534    }
1535    
1536    
1537    sub uni_link {
1538        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1539        my($cgi,$uni) = @_;
1540    
1541        if ($uni =~ /^uni\|(\S+)$/)
1542        {
1543            #return "<a href=http://www.pir.uniprot.org/cgi-bin/upEntry?id=$1>$uni</a>";
1544            return "<a href='http://www.ebi.uniprot.org/uniprot-srv/uniProtView.do?proteinAc=$1' target=_blank>$uni</a>";
1545        }
1546        return $uni;
1547    }
1548    
1549  sub sp_link {  sub sp_link {
1550        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1551      my($cgi,$sp) = @_;      my($cgi,$sp) = @_;
1552    
1553      if ($sp =~ /^sp\|(\S+)$/)      if ($sp =~ /^sp\|(\S+)$/)
1554      {      {
1555          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>";
1556      }      }
1557      return $sp;      return $sp;
1558  }  }
1559    
1560  sub pir_link {  sub pir_link {
1561        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1562      my($cgi,$pir) = @_;      my($cgi,$pir) = @_;
1563    
1564      if ($pir =~ /^pirnr\|(NF\d+)$/)      if ($pir =~ /^pirnr\|(NF\d+)$/)
1565      {      {
1566          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>";
1567      }      }
1568      return $pir;      return $pir;
1569  }  }
1570    
1571    sub kegg_link {
1572        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1573        my($cgi,$kegg) = @_;
1574    
1575        if ($kegg =~ /^kegg\|([^:]+):(\S+)$/)
1576        {
1577            return "<a href='http://www.genome.ad.jp/dbget-bin/www_bget?$1+$2' target=_blank>$kegg</a>";
1578        }
1579        return $kegg;
1580    }
1581    
1582    sub img_link {
1583        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1584        my($cgi,$img) = @_;
1585    
1586        if ($img =~ /^img\|(\S+)$/)
1587        {
1588            return "<a href='http://img.jgi.doe.gov/cgi-bin/pub/main.cgi?page=geneDetail&gene_oid=$1' target=_blank>$img</a>";
1589        }
1590        return $img;
1591    }
1592    
1593    sub ensembl_link {
1594        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1595        my($cgi,$ensembl) = @_;
1596    
1597        if ($ensembl =~ /^(\S+):(\S+)$/)
1598        {
1599            my $what=$1;
1600            my $key=$2;
1601            my $idx="All";
1602            if ($what eq "EnsemblGene") { $idx = "Gene" }
1603            if ($what eq "EnsemblTranscript") { $idx = "All" }
1604            if ($what eq "EnsemblProtein") { $idx = "All" }
1605    
1606            #I really want to get right to the transcript and peptide pages, but
1607            #can't see how to do that without knowing the org name too, which
1608            #I don't know at this point. (ensembl org name, not real org name)
1609    
1610            return "<a href='http://www.ensembl.org/Homo_sapiens/searchview?species=all&idx=$idx&q=$key' target=_blank>$ensembl</a>";
1611        }
1612        return $ensembl;
1613    }
1614    
1615    sub entrezgene_link {
1616        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1617        my($cgi,$entrezgene) = @_;
1618    
1619        if ($entrezgene =~ /^EntrezGene:(\S+)$/)
1620        {
1621            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>";
1622        }
1623        return $entrezgene;
1624    }
1625    
1626    sub mim_link {
1627        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1628        my($cgi,$mim) = @_;
1629    
1630        if ($mim =~ /^MIM:(\S+)$/)
1631        {
1632            return "<a href='http://www3.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=$1' target=_blank>$mim</a>";
1633        }
1634        return $mim;
1635    }
1636    
1637    sub hgnc_link {
1638        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1639        my($cgi,$hgnc) = @_;
1640    
1641        if ($hgnc =~ /^HGNC:(\S+)$/)
1642        {
1643            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>";
1644        }
1645    
1646        return $hgnc;
1647    }
1648    
1649    sub unigene_link {
1650        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1651        my($cgi,$unigene) = @_;
1652    
1653        if ($unigene =~ /^UniGene:(\S+)$/)
1654        {
1655            return "<a href='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unigene&cmd=search&term=$1' target=_blank>$unigene</a>";
1656        }
1657        return $unigene;
1658    }
1659    
1660    sub ipi_link {
1661        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1662        my($cgi,$ipi) = @_;
1663    
1664        if ($ipi =~ /^IPI:(\S+)$/)
1665        {
1666            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>";
1667        }
1668        return $ipi;
1669    }
1670    
1671    sub wp_link {
1672        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1673        my($cgi,$wp) = @_;
1674    
1675        #wormbase
1676    
1677        if ($wp =~ /^WP:(\S+)$/)
1678        {
1679            return "<a href='http://www.wormbase.org/db/searches/basic?class=Any&query=$1&Search=Search' target=_blank>$wp</a>";
1680        }
1681        return $wp;
1682    }
1683    
1684    sub fb_link {
1685        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1686        my($cgi,$fb) = @_;
1687    
1688        #flybase
1689    
1690        if ($fb =~ /^FB:(\S+)$/)
1691        {
1692            return "<a href='http://flybase.bio.indiana.edu/.bin/fbidq.html?$1' target=_blank>$fb</a>";
1693        }
1694        return $fb;
1695    }
1696    
1697    sub fborf_link {
1698        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1699        my($cgi,$fb) = @_;
1700    
1701        #flybase
1702    
1703        if ($fb =~ /^FlyBaseORFNames:(\S+)$/)
1704        {
1705            return "<a href='http://flybase.bio.indiana.edu/.bin/fbidq.html?$1' target=_blank>$fb</a>";
1706        }
1707        return $fb;
1708    }
1709    
1710    sub sgd_link {
1711        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1712        my($cgi,$sgd) = @_;
1713    
1714        #yeast
1715    
1716        if ($sgd =~ /^SGD_LOCUS:(\S+)$/)
1717        {
1718            return "<a href='http://db.yeastgenome.org/cgi-bin/locus.pl?locus=$1' target=_blank>$sgd</a>";
1719        }
1720        return $sgd;
1721    }
1722    
1723    
1724    
1725    
1726    sub set_map_links {
1727        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1728        my($cgi,$x) = @_;
1729        my($before,$match,$after);
1730    
1731        my $org = ($cgi->param('org') || $cgi->param('genome') || "");
1732    
1733        if ($x =~ /^(.*)(MAP\d+)(.*)/s)
1734        {
1735            $before = $1;
1736            $match = $2;
1737            $after = $3;
1738            return &set_map_links($cgi,$before) . &map_link($cgi,$match,$org) . &set_map_links($cgi,$after);
1739        }
1740        return $x;
1741    }
1742    
1743    
1744    
1745    sub map_link {
1746        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1747        my($cgi,$map,$org) = @_;
1748    
1749        my $user = $cgi->param('user');
1750        $user = $user ? $user : "";
1751        $org = $org ? $org : "";
1752    
1753        my $url = "show_kegg_map.cgi?user=$user&map=$map&org=$org";
1754    #rel    my $url = &FIG::cgi_url() . "/show_kegg_map.cgi?user=$user&map=$map&org=$org";
1755        my $link = "<a href=\"$url\">$map</a>";
1756        return $link;
1757    }
1758    
1759    sub java_buttons {
1760        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1761      ## ADDED BY RAE
1762      # Provides code to include check all/first half/second half/none for javascrspt
1763      # this takes two variables - the form name provided in start_form with the
1764      # -name => field and the checkbox name
1765      my ($form, $button)=@_;
1766    
1767      my $java_script="<input type=\"button\" name=\"CheckAll\" value=\"Check All\"\nonClick=\"checkAll(document.$form.$button)\">\n";
1768      $java_script.="<input type=\"button\" name=\"CheckFirst\" value=\"Check First Half\"\nonClick=\"checkFirst(document.$form.$button)\">\n";
1769      $java_script.="<input type=\"button\" name=\"CheckSecond\" value=\"Check Second Half\"\nonClick=\"checkSecond(document.$form.$button)\">\n";
1770      $java_script.="<input type=\"button\" name=\"UnCheckAll\" value=\"Uncheck All\"\nonClick=\"uncheckAll(document.$form.$button)\">\n";
1771    
1772      return $java_script;
1773    }
1774    
1775    =head3 sub_link
1776    
1777        my $htmlText = HTML::sub_link($cgi, $sub, gid);
1778    
1779    Create a subsystem link. The link will be to the display page if there is no
1780    user or we are in SPROUT mode; otherwise it will be to the edit page.
1781    
1782    =over 4
1783    
1784    =item cgi
1785    
1786    CGI query object for the current web session. The parameters of special interest
1787    are C<SPROUT> and C<user>. If the user is non-blank and SPROUT mode is 0, then
1788    the subsystem's edit page will be shown rather than its display page.
1789    
1790    =item sub
1791    
1792    Name of the desired subsystem. It will be cleaned of underscores before the
1793    hyperlink is applied.
1794    
1795    =item gid
1796    
1797    Genome ID to be specified as the focus.
1798    
1799    =back
1800    
1801    =cut
1802    
1803    sub sub_link {
1804        # Allow call as an instance in addition to the authorized method.
1805        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1806        # Get the parameters.
1807        my ($cgi, $sub, $gid) = @_;
1808        # Declare the return variable.
1809        my $retVal;
1810        # Clean the subsystem name for display purposes. This is a very
1811        # different thing from URL-escaping.
1812        my $cleaned = Tracer::Clean($sub);
1813        $cleaned =~ s/_/ /g;
1814        # URL-escape the subsystem name for use in the link.
1815        my $linkable = uri_escape($sub);
1816        # Determine the mode. Note we use the little OR trick to insure that
1817        # we have the correct value for plugging into the output link.
1818        my $user = $cgi->param('user') || "";
1819        my $sproutMode = $cgi->param('SPROUT') || 0;
1820        if ($user && ! $sproutMode) {
1821            # A SEED user is calling, so we go to the edit page.
1822            $retVal = "<a href=\"subsys.cgi?ssa_name=$linkable&request=show_ssa&user=$user\">$cleaned</a>";
1823        } else {
1824            # A visitor or SPROUT user is calling, so we go to the display page.
1825            $retVal = "<a href=\"display_subsys.cgi?ssa_name=$linkable;request=show_ssa;sort=by_phylo;focus=$gid;SPROUT=$sproutMode\">$cleaned</a>";
1826        }
1827        # Return the result.
1828        return $retVal;
1829    }
1830    
1831    sub reaction_map_link {
1832        my($mapID, @reaction_list) = @_;
1833        if($mapID =~ /\d+/)
1834        {
1835            my $reactions = join "+", @reaction_list;
1836            if ($reactions ne "")
1837            {
1838                $reactions = "+".$reactions;
1839            }
1840    
1841            return "<a href=http://www.genome.jp/dbget-bin/show_pathway?rn$mapID$reactions>$mapID</a>";
1842        }
1843        else
1844        {
1845            return $mapID;
1846        }
1847    }
1848    
1849    sub compound_link {
1850        my($compound) = @_;
1851        if($compound =~ /^C\d+/)
1852        {
1853            return "<a href=\"javascript:void(0)\"onclick=\"window.open('http://www.genome.jp/dbget-bin/www_bget?compound+$compound','$&','height=640,width=800,scrollbars=yes,toolbar=yes,status=yes,resizable=yes')\">$compound</a>";
1854        }
1855        else
1856        {
1857            return $compound;
1858        }
1859    }
1860    
1861    
1862    sub reaction_link {
1863        my($reaction) = @_;
1864        if ($reaction =~ /^(\*)?(R\d+)/)
1865        {
1866            # return "<a href=\"http://www.genome.ad.jp/dbget-bin/www_bget?rn+$2\" target=reaction$$>$reaction</a>";
1867            return "<a href=\"javascript:void(0)\"onclick=\"window.open('http://www.genome.ad.jp/dbget-bin/www_bget?rn+$reaction','$&','height=640,width=800,scrollbars=yes,toolbar=yes,status=yes,resizable=yes')\">$reaction</a>";
1868        }
1869        return $reaction;
1870    }
1871    
1872    
1873    sub html_for_assignments {
1874        my($fig,$user,$peg_sets) = @_;
1875        my $i;
1876    
1877        my @vals = ();
1878        my $set = 1;
1879        foreach my $peg_set (@$peg_sets)
1880        {
1881            for ($i=0; ($i < @$peg_set); $i++)
1882            {
1883                my $peg = $peg_set->[$i];
1884                push(@vals,'show=' . join("@",($set,$i+1,$peg,&FIG::abbrev($fig->org_of($peg)),"")));
1885            }
1886            $set++;
1887        }
1888    
1889        $ENV{'REQUEST_METHOD'} = 'GET';
1890        $ENV{'QUERY_STRING'} = join('&',('request=show_commentary',"uni=1","user=$user",@vals));
1891        my $out = join("",`$FIG_Config::fig/CGI/chromosomal_clusters.cgi`);
1892        $out =~ s/^.*?<form/<form/si;
1893        $out =~ s/^(.*)<table.*/$1/si;
1894        return $out;
1895    }
1896    
1897    =head1 rss_feed
1898    
1899    Add something to the RSS feed. The rss feeds are stored in the Html directory, and there are several RSS feeds:
1900            SEED.rss                - everything gets written here
1901            SEEDgenomes.rss                 - whenever a genome is added to the SEED
1902            SEEDsubsystems.rss      - whenever a subsystem is edited (or should this be added?)
1903    
1904    
1905    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.
1906    
1907    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.
1908    
1909    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.
1910    
1911    The has can have these keys:
1912    
1913    REQUIRED:
1914    title       : the title. This is usually what is seen by the user in the pull down menu
1915    description : a more complete description that is often seen is rss viewers but not always
1916    link        : link to the item that was added/edited
1917    All other keys are treated as optional RSS arguments and written to the file.
1918    
1919    At most, $max_entries recent entries are stored in the rss file, and this is currently 50.
1920    
1921    RSS files are quite simple, and contain some standard header information, and then individual items surrounded by an <item> </item> tag. Note that there is also an initial title/description/link set that describes the file.
1922    
1923    
1924    =cut
1925    
1926    sub rss_feed {
1927     shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1928     my ($files, $args)=@_;
1929    
1930     # how many entries to store in the file
1931     my $max_entries=50;
1932    
1933     foreach my $a (keys %$args) {if ($a =~ /^-(.*)/) {my $b=$1; $args->{$b}=$args->{$a}; delete $args->{$a}}}
1934    
1935     my $filepath=$FIG_Config::fig."/CGI/Html/rss";
1936     # check for the directory and if not, make it
1937     mkdir $filepath unless (-d $filepath);
1938    
1939     # note that $info is a hash of references to hashes that are written out as headers in the file
1940     my $info=
1941     {
1942      "SEED.rss" =>
1943       {
1944            title           => "The SEED",
1945            description     => "Latest news from the SEED",
1946            link            => "Html/rss/SEED.rss",
1947       },
1948    
1949      "SEEDsubsystems.rss" =>
1950      {
1951            title           => "SEED Subsystems",
1952            description     => "Recently updated SEED subsystems",
1953            link            => "Html/rss/SEEDsubsystems.rss",
1954      },
1955    
1956      "SEEDsubsystems.rss" =>
1957      {
1958            title           => "SEED Genomes",
1959            description     => "Genomes recently added to the SEED",
1960            link            => &FIG::cgi_url()."/Html/rss/SEEDsubsystems.rss",
1961      },
1962    
1963     };
1964    
1965    
1966     # build the new xml
1967     my $xml = "\t<item>\n";
1968     foreach my $qw ("title", "description", "link") {
1969      unless ($args->{$qw}) {
1970       print STDERR "You need to include a $qw tag in your RSS description\n";
1971       return(0);
1972      }
1973      # we need to do something a bit funky with the link. We can't have ampersands in the <link> </link> in valid html
1974      # so we are going to pull out the links and uri_escape just the part after the .cgi
1975      if ($qw eq "link")
1976      {
1977       $args->{$qw} =~ /^(.*?\.cgi.)(.*)$/;
1978       $args->{$qw} = $1.uri_escape($2) if ($1 && $2);
1979      }
1980    
1981      $xml .= "\t\t<$qw>".$args->{$qw}."</$qw>\n";
1982      delete $args->{$qw};
1983     }
1984    
1985     foreach my $tag (grep {!/type/i} keys %$args)
1986     {
1987      $xml .= "\t\t<$tag>".$args->{$tag}."</$tag>\n";
1988     }
1989    
1990     $xml .= "\t</item>\n";
1991    
1992    
1993     my @files=("SEED.rss");
1994     if ($args->{"type"}) {
1995        my $type = $args->{type};
1996        push @files, "SEED.$type.rss"
1997    }
1998    
1999     foreach my $file ("SEED.rss", @$files)
2000     {
2001      if (-e "$filepath/$file")
2002      {
2003       my @out; # the new content of the file
2004       my $itemcount=0; # how many <item> </item>'s are we keeping
2005       my $initem; # are we in an item?
2006       open(IN, "$filepath/$file") || die "Can't open $filepath/$file";
2007       while (<IN>)
2008       {
2009        if (/\<item\>/) {
2010         push @out, $xml, unless ($itemcount);
2011         $itemcount++;
2012         $initem=1;
2013        }
2014        if (/\<\/item\>/) {$initem=0; next if ($itemcount > $max_entries)}
2015        next if ($initem && $itemcount > $max_entries);
2016        push @out, $_;
2017       }
2018       close IN;
2019       open(OUT, ">$filepath/$file") || die "Can't open $filepath/$file for writing";
2020       print OUT @out;
2021      }
2022      else
2023      {
2024       open(OUT, ">$filepath/$file") || die "Can't open $filepath/$file for writing";
2025       print OUT "<?xml version=\"1.0\"?>\n<rss version=\"2.0\">\n<channel>\n";
2026       if ($info->{$file})
2027       {
2028         # we're going to sanity check each of the three options we output, just to be sure
2029         foreach my $qw ("title", "description", "link")
2030         {
2031           if ($info->{$file}->{$qw})
2032           {
2033              print OUT "<$qw>", $info->{$file}->{$qw}, "</$qw>\n";
2034           } else {
2035              print STDERR "Please add a $qw for $file\n"; print OUT "<$qw>$file</$qw>\n";
2036           }
2037         }
2038       }
2039       else {
2040        print STDERR "Please define title, link, and description information for $file\n";
2041        print OUT "<title>$file</title>\n<description>An RSS feed</description>\n<link>", &FIG::cgi_url, "</link>\n";
2042       }
2043       print OUT "\n", $xml;
2044       print OUT "\n", "</channel>\n</rss>\n"
2045      }
2046     }
2047    }
2048    
2049    
2050    
2051    1;
2052    
 1  

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