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revision 1.6, Sun Mar 21 02:20:55 2004 UTC revision 1.130, Mon Mar 23 13:28:14 2009 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 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, "$FIG_Config::cgi_url/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,$n+1);
1069      }      }
1070  }  }
1071    
1072  sub set_prot_links {  =head2 alias_rl
     my($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;          $after = $3;
1231          return &set_prot_links($cgi,$before) . &HTML::gi_link($cgi,$match) . &set_prot_links($cgi,$after) . "\n";          return &set_prot_links($cgi,$before) . &HTML::refseq_link($cgi,$match) . &set_prot_links($cgi,$after);
1232      }      }
1233      elsif ($x =~ /^(.*)(sp\|[A-Z0-9]{6})(.*)$/)      elsif ($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 =~ /^(.*)(gb\|\S+)(.*)/s)
1241        {
1242            $before = $1;
1243            $match = $2;
1244            $after = $3;
1245            return &set_prot_links($cgi,$before) . &HTML::gb_link($cgi,$match) . &set_prot_links($cgi,$after);
1246        }
1247        elsif ($x =~ /^(.*)(img\|\d+)(.*)/s)
1248        {
1249            $before = $1;
1250            $match = $2;
1251            $after = $3;
1252            return &set_prot_links($cgi,$before) . &HTML::img_link($cgi,$match) . &set_prot_links($cgi,$after);
1253        }
1254        elsif ($x =~ /^(.*)(tigr\|\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 =~ /^(.*)(tigrcmr\|\w+)(.*)/s)
1262        {
1263            $before = $1;
1264            $match = $2;
1265            $after = $3;
1266            return &set_prot_links($cgi,$before) . &HTML::tigr_link($cgi,$match) . &set_prot_links($cgi,$after);
1267        }
1268        elsif ($x =~ /^(.*)(cmr\|\w+)(.*)/s)
1269        {
1270            $before = $1;
1271            $match = $2;
1272            $after = $3;
1273            return &set_prot_links($cgi,$before) . &HTML::cmr_link($cgi,$match) . &set_prot_links($cgi,$after);
1274        }
1275        elsif ($x =~ /^(.*)(dbj\|\S+)(.*)/s)
1276        {
1277            $before = $1;
1278            $match = $2;
1279            $after = $3;
1280            return &set_prot_links($cgi,$before) . &HTML::dbj_link($cgi,$match) . &set_prot_links($cgi,$after);
1281        }
1282        elsif ($x =~ /^(.*)\b(eric\|\S+)\b(.*)/s)
1283        {
1284            $before = $1;
1285            $match = $2;
1286            $after = $3;
1287            return &set_prot_links($cgi,$before) . &HTML::eric_link($cgi,$match) . &set_prot_links($cgi,$after);
1288        }
1289    
1290        elsif ($x =~ /^(.*)\b(bhb\|.*?)\b(.*)/s)
1291        {
1292            $before = $1;
1293            $match = $2;
1294            $after = $3;
1295            return &set_prot_links($cgi,$before) . &HTML::bhb_link($cgi,$match) . &set_prot_links($cgi,$after);
1296        }
1297    
1298        elsif ($x =~ /^(.*)\b(apidb\|[0-9\.a-z_]+)\b(.*)/s)
1299        {
1300            $before = $1;
1301            $match = $2;
1302            $after = $3;
1303            return &set_prot_links($cgi,$before) . &HTML::apidb_link($cgi,$match) . &set_prot_links($cgi,$after);
1304        }
1305    
1306        elsif ($x =~ /^(.*)\b(patric\|.*?)\b(.*)/s)
1307        {
1308            $before = $1;
1309            $match = $2;
1310            $after = $3;
1311            return &set_prot_links($cgi,$before) . &HTML::patric_link($cgi,$match) . &set_prot_links($cgi,$after);
1312        }
1313    
1314        elsif ($x =~ /^(.*)\b(vbrc\|.*?)\b(.*)/s)
1315        {
1316            $before = $1;
1317            $match = $2;
1318            $after = $3;
1319            return &set_prot_links($cgi,$before) . &HTML::vbrc_link($cgi,$match) . &set_prot_links($cgi,$after);
1320        }
1321    
1322        elsif ($x =~ /^(.*)\b(vectorbase\|.*?)\b(.*)/s)
1323      {      {
1324          $before = $1;          $before = $1;
1325          $match = $2;          $match = $2;
1326          $after = $3;          $after = $3;
1327          return &set_prot_links($cgi,$before) . &HTML::sp_link($cgi,$match) . &set_prot_links($cgi,$after) . "\n";          return &set_prot_links($cgi,$before) . &HTML::vectorbase_link($cgi,$match) . &set_prot_links($cgi,$after);
1328      }      }
1329      elsif ($x =~ /^(.*)(pirnr\|NF\d+)(.*)$/)      elsif ($x =~  /^(.*)(uni\|[A-Z0-9]{6})(.*)/s)
1330      {      {
1331          $before = $1;          $before = $1;
1332          $match = $2;          $match = $2;
1333          $after = $3;          $after = $3;
1334          return &set_prot_links($cgi,$before) . &HTML::pir_link($cgi,$match) . &set_prot_links($cgi,$after) . "\n";          return &set_prot_links($cgi,$before) . &HTML::uni_link($cgi,$match) . &set_prot_links($cgi,$after);
1335        }
1336        elsif ($x =~ /^(.*)(sp\|[A-Z0-9]{6})(.*)/s)
1337        {
1338            $before = $1;
1339            $match = $2;
1340            $after = $3;
1341            return &set_prot_links($cgi,$before) . &HTML::sp_link($cgi,$match) . &set_prot_links($cgi,$after);
1342        }
1343        elsif ($x =~ /^(.*)(pirnr\|NF\d+)(.*)/s)
1344        {
1345            $before = $1;
1346            $match = $2;
1347            $after = $3;
1348            return &set_prot_links($cgi,$before) . &HTML::pir_link($cgi,$match) . &set_prot_links($cgi,$after);
1349        }
1350        elsif ($x =~ /^(.*)(kegg\|[a-z]{2,4}:[a-zA-Z_0-9]+)(.*)/s)
1351        {
1352            $before = $1;
1353            $match = $2;
1354            $after = $3;
1355            return &set_prot_links($cgi,$before) . &HTML::kegg_link($cgi,$match) . &set_prot_links($cgi,$after);
1356        }
1357        elsif ($x =~ /^(.*)(Ensembl[a-zA-Z]+:[a-zA-Z_0-9\.]+)(.*)/s)
1358        {
1359            $before = $1;
1360            $match = $2;
1361            $after = $3;
1362            return &set_prot_links($cgi,$before) . &HTML::ensembl_link($cgi,$match) . &set_prot_links($cgi,$after);
1363        }
1364        elsif ($x =~ /^(.*)(EntrezGene:[a-zA-Z_0-9\.]+)(.*)/s)
1365        {
1366            $before = $1;
1367            $match = $2;
1368            $after = $3;
1369            return &set_prot_links($cgi,$before) . &HTML::entrezgene_link($cgi,$match) . &set_prot_links($cgi,$after);
1370        }
1371        elsif ($x =~ /^(.*)(MIM:[a-zA-Z_0-9\.]+)(.*)/s)
1372        {
1373            $before = $1;
1374            $match = $2;
1375            $after = $3;
1376            return &set_prot_links($cgi,$before) . &HTML::mim_link($cgi,$match) . &set_prot_links($cgi,$after);
1377        }
1378        elsif ($x =~ /^(.*)(HGNC:[a-zA-Z_0-9\.]+)(.*)/s)
1379        {
1380            $before = $1;
1381            $match = $2;
1382            $after = $3;
1383            return &set_prot_links($cgi,$before) . &HTML::hgnc_link($cgi,$match) . &set_prot_links($cgi,$after);
1384        }
1385        elsif ($x =~ /^(.*)(UniGene:[a-zA-Z_0-9\.]+)(.*)/s)
1386        {
1387            $before = $1;
1388            $match = $2;
1389            $after = $3;
1390            return &set_prot_links($cgi,$before) . &HTML::unigene_link($cgi,$match) . &set_prot_links($cgi,$after);
1391        }
1392    # IPI stopped working. turn off for now.
1393    #    elsif ($x =~ /^(.*)(IPI:[a-zA-Z_0-9\.]+)(.*)/s)
1394    #    {
1395    #        $before = $1;
1396    #        $match = $2;
1397    #        $after = $3;
1398    #        return &set_prot_links($cgi,$before) . &HTML::ipi_link($cgi,$match) . &set_prot_links($cgi,$after);
1399    #    }
1400        elsif ($x =~ /^(.*)(WP:[a-zA-Z_0-9\.]+)(.*)/s)
1401        {
1402            #wormbase
1403    
1404            $before = $1;
1405            $match = $2;
1406            $after = $3;
1407            return &set_prot_links($cgi,$before) . &HTML::wp_link($cgi,$match) . &set_prot_links($cgi,$after);
1408        }
1409        elsif ($x =~ /^(.*)(FB:[a-zA-Z_0-9\.]+)(.*)/s)
1410        {
1411            #flybase
1412    
1413            $before = $1;
1414            $match = $2;
1415            $after = $3;
1416            return &set_prot_links($cgi,$before) . &HTML::fb_link($cgi,$match) . &set_prot_links($cgi,$after);
1417        }
1418        elsif ($x =~ /^(.*)(FlyBaseORFNames:[a-zA-Z_0-9\.]+)(.*)/s)
1419        {
1420            #flybase
1421    
1422            $before = $1;
1423            $match = $2;
1424            $after = $3;
1425            return &set_prot_links($cgi,$before) . &HTML::fborf_link($cgi,$match) . &set_prot_links($cgi,$after);
1426        }
1427        elsif ($x =~ /^(.*)(SGD_LOCUS:[a-zA-Z_0-9\.]+)(.*)/s)
1428        {
1429            #flybase
1430    
1431            $before = $1;
1432            $match = $2;
1433            $after = $3;
1434            return &set_prot_links($cgi,$before) . &HTML::sgd_link($cgi,$match) . &set_prot_links($cgi,$after);
1435        }
1436        elsif ($x =~ /^(.*)(tr\|[a-zA-Z0-9]+)(.*)/s)
1437        {
1438    
1439          $before = $1;
1440          $match = $2;
1441          $after = $3;
1442    
1443          return &set_prot_links($cgi,$before) .  &HTML::trembl_link($cgi,$match) . &set_prot_links($cgi,$after);
1444      }      }
1445      return $x;      return $x;
1446  }  }
1447    
1448    sub lit_link {
1449        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1450        my($id) = @_;
1451    
1452        if ( $id =~ /([di]lit)\((\d+)\)/ )
1453        {
1454            my($pre, $pubmed_id) = ($1, $2);
1455            my $pubmed_url = &alias_url($pubmed_id, 'PMID');
1456            $id = "$pre(<a href='$pubmed_url' target=_blank>$pubmed_id</a>)";
1457        }
1458        return $id;
1459    }
1460    
1461    sub refseq_link {
1462        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1463        my($cgi,$id) = @_;
1464    
1465        if ($id =~ /^[NXYZA]P_/)
1466        {
1467            return "<a href='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=protein&cmd=search&term=$id' target=_blank>$id</a>";
1468        }
1469        elsif ($id =~ /^[NXYZA]M_/)
1470        {
1471            return "<a href='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=nuccore&cmd=search&term=$id' target=_blank>$id</a>";
1472        }
1473    }
1474    
1475  sub gi_link {  sub gi_link {
1476        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1477      my($cgi,$gi) = @_;      my($cgi,$gi) = @_;
1478    
1479      if ($gi =~ /^gi\|(\d+)$/)      if ($gi =~ /^gi\|(\d+)$/)
1480      {      {
1481          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>";
1482      }      }
1483      return $gi;      return $gi;
1484  }  }
1485    
1486    sub gb_link {
1487        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1488        my($cgi,$gb) = @_;
1489    
1490        if ($gb =~ /^gb\|(\S+)$/)
1491        {
1492            return "<a href='http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&id=$1' target=_blank>$gb</a>";
1493        }
1494        return $gb;
1495    }
1496    
1497    sub tigr_link {
1498        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1499        my($cgi,$tigr) = @_;
1500    
1501        if ($tigr =~ /^tigr\|(NT|ntbp|ntbpA|BA|BMAA|BXB|GBA)(\w+)$/)
1502        {
1503            my $id=$1.$2;
1504            return "<a href=\"http://pathema.tigr.org/tigr-scripts/pathema/shared/GenePage.cgi?locus=$id\" target=_blank>$tigr</a> (Pathema)";
1505        }
1506        elsif ($tigr =~ /^tigr(cmr)?\|(\S+)$/)
1507        {
1508            return "<a href=\"http://www.tigr.org/tigr-scripts/CMR2/GenePage.spl?locus=$2\" target=_blank>$tigr</a>";
1509        }
1510        return $tigr;
1511    }
1512    
1513    sub cmr_link {
1514        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1515        my($cgi,$cmr) = @_;
1516    
1517        if ($cmr =~ /^cmr\|(\d+)$/)
1518        {
1519            my $id=$1;
1520            return "<a href=\"http://cmr.jcvi.org/cgi-bin/CMR/shared/GenePage.cgi?type=PID&acc=".$id."\" target=_blank>$cmr</a>";
1521        }
1522        elsif ($cmr =~ /^cmr\|(\S+)$/)
1523        {
1524            my $id = $1;
1525            return "<a href=\"http://cmr.jcvi.org/tigr-scripts/CMR/shared/GenePage.cgi?locus=".$id."\" target=_blank>$cmr</a>";
1526        }
1527        return $cmr;
1528    }
1529    
1530    sub eric_link {
1531        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1532        my($cgi,$eric) = @_;
1533    
1534        if ($eric =~ /^eric\|(\S+)/)
1535        {
1536            return "<a href=\"https://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=$1\" target=_blank>$eric</a>";
1537        }
1538        return $eric;
1539    }
1540    
1541    sub dbj_link {
1542        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1543        my($cgi,$dbj) = @_;
1544    
1545        if ($dbj =~ /^dbj\|(\S+)/)
1546        {
1547            return "<a href=\"http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&id=$1\" target=_blank>$dbj</a>";
1548        }
1549        return $dbj;
1550    }
1551    
1552    sub bhb_link {
1553        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1554        my($cgi,$bhb) = @_;
1555    
1556        return "<a href=\"http://www.biohealthbase.org\" target=_blank>$bhb</a>";
1557    }
1558    
1559    sub apidb_link {
1560        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1561        my($cgi,$api) = @_;
1562    
1563        if ($api =~ /apidb\|(.*?)\.(.*)$/)
1564        {
1565            return "<a href=\"http://www.apidb.org/cgi-bin/redirect.cgi?taxon_id=$1&source_id=$2\" target=_blank>$api</a>";
1566        }
1567        return $api;
1568    }
1569    
1570    sub patric_link {
1571        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1572        my($cgi,$patric) = @_;
1573    
1574        if ($patric =~ /patric\|(.*)/)
1575        {
1576            return "<a href=\"https://patric.vbi.vt.edu/software/curationTool/gep/pgiCuration.php?locus_name=$1\" target=_blank>$patric</a>";
1577        }
1578        return $patric;
1579    }
1580    
1581    sub vbrc_link {
1582        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1583        my($cgi,$vbrc) = @_;
1584    
1585        if ($vbrc =~ /vbrc\|(.*)/)
1586        {
1587            return "<a href=\"http://www.biovirus.org/gene_detail.asp?name=$1\" target=_blank>$vbrc</a>";
1588        }
1589        return $vbrc;
1590    }
1591    
1592    sub vectorbase_link {
1593        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1594        my($cgi,$vec) = @_;
1595        return "<a href=\"http://www.vectorbase.org\" target=_blank>$vec</a>";
1596    }
1597    
1598    sub uniprot_link {
1599        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1600        my($cgi,$uni) = @_;
1601    
1602        if ($uni =~ /^(sp|tr|uni)\|(\S+)$/)
1603        {
1604            return "<a href='" . &HTML::alias_url($2, 'UniProt') . "' target=_blank>$uni</a>";
1605        }
1606        return $uni;
1607    }
1608    
1609    sub uni_link {
1610        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1611        my($cgi,$uni) = @_;
1612    
1613        if ($uni =~ /^uni\|(\S+)$/)
1614        {
1615            #return "<a href=http://www.pir.uniprot.org/cgi-bin/upEntry?id=$1>$uni</a>";
1616            #return "<a href='http://www.ebi.uniprot.org/uniprot-srv/uniProtView.do?proteinAc=$1' target=_blank>$uni</a>";
1617            return "<a href='" . &HTML::alias_url($1, 'UniProt') . "' target=_blank>$uni</a>";
1618        }
1619        return $uni;
1620    }
1621    
1622  sub sp_link {  sub sp_link {
1623        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1624      my($cgi,$sp) = @_;      my($cgi,$sp) = @_;
1625    
1626      if ($sp =~ /^sp\|(\S+)$/)      if ($sp =~ /^sp\|(\S+)$/)
1627      {      {
1628          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>";
1629            return "<a href='" . &HTML::alias_url($1, 'UniProt') . "' target=_blank>$sp</a>";
1630      }      }
1631      return $sp;      return $sp;
1632  }  }
1633    
1634    sub trembl_link {
1635        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1636        my($cgi,$tr) = @_;
1637    
1638        if ($tr =~ /^tr\|(\S+)$/)
1639        {
1640            #return "<a href='http://us.expasy.org/cgi-bin/get-sprot-entry?$1' target=_blank>$tr</a>";
1641            return "<a href='" . &HTML::alias_url($1, 'UniProt') . "' target=_blank>$tr</a>";
1642        }
1643        return $tr;
1644    }
1645    
1646  sub pir_link {  sub pir_link {
1647        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1648      my($cgi,$pir) = @_;      my($cgi,$pir) = @_;
1649    
1650      if ($pir =~ /^pirnr\|(NF\d+)$/)      if ($pir =~ /^pirnr\|(NF\d+)$/)
1651      {      {
1652          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>";
1653      }      }
1654      return $pir;      return $pir;
1655  }  }
1656    
1657    sub kegg_link {
1658        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1659        my($cgi,$kegg) = @_;
1660    
1661        if ($kegg =~ /^kegg\|([^:]+):(\S+)$/)
1662        {
1663            return "<a href='http://www.genome.ad.jp/dbget-bin/www_bget?$1+$2' target=_blank>$kegg</a>";
1664        }
1665        return $kegg;
1666    }
1667    
1668    sub img_link {
1669        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1670        my($cgi,$img) = @_;
1671    
1672        if ($img =~ /^img\|(\S+)$/)
1673        {
1674            return "<a href='http://img.jgi.doe.gov/cgi-bin/pub/main.cgi?page=geneDetail&gene_oid=$1' target=_blank>$img</a>";
1675        }
1676        return $img;
1677    }
1678    
1679    sub ensembl_link {
1680        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1681        my($cgi,$ensembl) = @_;
1682    
1683        if ($ensembl =~ /^(\S+):(\S+)$/)
1684        {
1685            my $what=$1;
1686            my $key=$2;
1687            my $idx="All";
1688            if ($what eq "EnsemblGene") { $idx = "Gene" }
1689            if ($what eq "EnsemblTranscript") { $idx = "All" }
1690            if ($what eq "EnsemblProtein") { $idx = "All" }
1691    
1692            #I really want to get right to the transcript and peptide pages, but
1693            #can't see how to do that without knowing the org name too, which
1694            #I don't know at this point. (ensembl org name, not real org name)
1695    
1696            return "<a href='http://www.ensembl.org/Homo_sapiens/searchview?species=all&idx=$idx&q=$key' target=_blank>$ensembl</a>";
1697        }
1698        return $ensembl;
1699    }
1700    
1701    sub entrezgene_link {
1702        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1703        my($cgi,$entrezgene) = @_;
1704    
1705        if ($entrezgene =~ /^EntrezGene:(\S+)$/)
1706        {
1707            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>";
1708        }
1709        return $entrezgene;
1710    }
1711    
1712    sub mim_link {
1713        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1714        my($cgi,$mim) = @_;
1715    
1716        if ($mim =~ /^MIM:(\S+)$/)
1717        {
1718            return "<a href='http://www3.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=$1' target=_blank>$mim</a>";
1719        }
1720        return $mim;
1721    }
1722    
1723    sub hgnc_link {
1724        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1725        my($cgi,$hgnc) = @_;
1726    
1727        if ($hgnc =~ /^HGNC:(\S+)$/)
1728        {
1729            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>";
1730        }
1731    
1732        return $hgnc;
1733    }
1734    
1735    sub unigene_link {
1736        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1737        my($cgi,$unigene) = @_;
1738    
1739        if ($unigene =~ /^UniGene:(\S+)$/)
1740        {
1741            return "<a href='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unigene&cmd=search&term=$1' target=_blank>$unigene</a>";
1742        }
1743        return $unigene;
1744    }
1745    
1746    sub ipi_link {
1747        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1748        my($cgi,$ipi) = @_;
1749    
1750        if ($ipi =~ /^IPI:(\S+)$/)
1751        {
1752            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>";
1753        }
1754        return $ipi;
1755    }
1756    
1757    sub wp_link {
1758        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1759        my($cgi,$wp) = @_;
1760    
1761        #wormbase
1762    
1763        if ($wp =~ /^WP:(\S+)$/)
1764        {
1765            return "<a href='http://www.wormbase.org/db/searches/basic?class=Any&query=$1&Search=Search' target=_blank>$wp</a>";
1766        }
1767        return $wp;
1768    }
1769    
1770    sub fb_link {
1771        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1772        my($cgi,$fb) = @_;
1773    
1774        #flybase
1775    
1776        if ($fb =~ /^FB:(\S+)$/)
1777        {
1778            return "<a href='http://flybase.bio.indiana.edu/.bin/fbidq.html?$1' target=_blank>$fb</a>";
1779        }
1780        return $fb;
1781    }
1782    
1783    sub fborf_link {
1784        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1785        my($cgi,$fb) = @_;
1786    
1787        #flybase
1788    
1789        if ($fb =~ /^FlyBaseORFNames:(\S+)$/)
1790        {
1791            return "<a href='http://flybase.bio.indiana.edu/.bin/fbidq.html?$1' target=_blank>$fb</a>";
1792        }
1793        return $fb;
1794    }
1795    
1796    sub sgd_link {
1797        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1798        my($cgi,$sgd) = @_;
1799    
1800        #yeast
1801    
1802        if ($sgd =~ /^SGD_LOCUS:(\S+)$/)
1803        {
1804            return "<a href='http://db.yeastgenome.org/cgi-bin/locus.pl?locus=$1' target=_blank>$sgd</a>";
1805        }
1806        return $sgd;
1807    }
1808    
1809    
1810    
1811    
1812    sub set_map_links {
1813        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1814        my($cgi,$x) = @_;
1815        my($before,$match,$after);
1816    
1817        my $org = ($cgi->param('org') || $cgi->param('genome') || "");
1818    
1819        if ($x =~ /^(.*)(MAP\d+)(.*)/s)
1820        {
1821            $before = $1;
1822            $match = $2;
1823            $after = $3;
1824            return &set_map_links($cgi,$before) . &map_link($cgi,$match,$org) . &set_map_links($cgi,$after);
1825        }
1826        return $x;
1827    }
1828    
1829    
1830    
1831    sub map_link {
1832        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1833        my($cgi,$map,$org) = @_;
1834    
1835        my $user = $cgi->param('user');
1836        $user = $user ? $user : "";
1837        $org = $org ? $org : "";
1838    
1839        my $url = "show_kegg_map.cgi?user=$user&map=$map&org=$org";
1840    #rel    my $url = &FIG::cgi_url() . "/show_kegg_map.cgi?user=$user&map=$map&org=$org";
1841        my $link = "<a href=\"$url\">$map</a>";
1842        return $link;
1843    }
1844    
1845    sub java_buttons {
1846        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1847      ## ADDED BY RAE
1848      # Provides code to include check all/first half/second half/none for javascrspt
1849      # this takes two variables - the form name provided in start_form with the
1850      # -name => field and the checkbox name
1851      my ($form, $button)=@_;
1852    
1853      my $java_script="<input type=\"button\" name=\"CheckAll\" value=\"Check All\"\nonClick=\"checkAll(document.$form.$button)\">\n";
1854      $java_script.="<input type=\"button\" name=\"CheckFirst\" value=\"Check First Half\"\nonClick=\"checkFirst(document.$form.$button)\">\n";
1855      $java_script.="<input type=\"button\" name=\"CheckSecond\" value=\"Check Second Half\"\nonClick=\"checkSecond(document.$form.$button)\">\n";
1856      $java_script.="<input type=\"button\" name=\"UnCheckAll\" value=\"Uncheck All\"\nonClick=\"uncheckAll(document.$form.$button)\">\n";
1857    
1858      return $java_script;
1859    }
1860    
1861    =head3 sub_link
1862    
1863        my $htmlText = HTML::sub_link($cgi, $sub, gid);
1864    
1865    Create a subsystem link. The link will be to the display page if there is no
1866    user or we are in SPROUT mode; otherwise it will be to the edit page.
1867    
1868    =over 4
1869    
1870    =item cgi
1871    
1872    CGI query object for the current web session. The parameters of special interest
1873    are C<SPROUT> and C<user>. If the user is non-blank and SPROUT mode is 0, then
1874    the subsystem's edit page will be shown rather than its display page.
1875    
1876    =item sub
1877    
1878    Name of the desired subsystem. It will be cleaned of underscores before the
1879    hyperlink is applied.
1880    
1881    =item gid
1882    
1883    Genome ID to be specified as the focus.
1884    
1885    =back
1886    
1887    =cut
1888    
1889    sub sub_link {
1890        # Allow call as an instance in addition to the authorized method.
1891        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1892        # Get the parameters.
1893        my ($cgi, $sub, $gid) = @_;
1894        # Declare the return variable.
1895        my $retVal;
1896        # Clean the subsystem name for display purposes. This is a very
1897        # different thing from URL-escaping.
1898        my $cleaned = Tracer::Clean($sub);
1899        $cleaned =~ s/_/ /g;
1900        # URL-escape the subsystem name for use in the link.
1901        my $linkable = uri_escape($sub);
1902        # Determine the mode. Note we use the little OR trick to insure that
1903        # we have the correct value for plugging into the output link.
1904        my $user = $cgi->param('user') || "";
1905        my $sproutMode = $cgi->param('SPROUT') || 0;
1906        if ($user && ! $sproutMode) {
1907            # A SEED user is calling, so we go to the edit page.
1908            $retVal = "<a href=\"subsys.cgi?ssa_name=$linkable&request=show_ssa&user=$user\">$cleaned</a>";
1909        } else {
1910            # A visitor or SPROUT user is calling, so we go to the display page.
1911            $retVal = "<a href=\"$FIG_Config::cgi_url/seedviewer.cgi?page=Subsystems;subsystem=$linkable\">$cleaned</a>";
1912        }
1913        # Return the result.
1914        return $retVal;
1915    }
1916    
1917    sub reaction_map_link {
1918        my($mapID, @reaction_list) = @_;
1919        if($mapID =~ /\d+/)
1920        {
1921            my $reactions = join "+", @reaction_list;
1922            if ($reactions ne "")
1923            {
1924                $reactions = "+".$reactions;
1925            }
1926    
1927            return "<a href=http://www.genome.jp/dbget-bin/show_pathway?rn$mapID$reactions>$mapID</a>";
1928        }
1929        else
1930        {
1931            return $mapID;
1932        }
1933    }
1934    
1935    sub compound_link {
1936        my($compound) = @_;
1937        if($compound =~ /^C\d+/)
1938        {
1939            return "<a href=\"javascript:void(0)\"onclick=\"window.open('http://www.genome.jp/dbget-bin/www_bget?compound+$compound','$&','height=640,width=800,scrollbars=yes,toolbar=yes,status=yes,resizable=yes')\">$compound</a>";
1940        }
1941        else
1942        {
1943            return $compound;
1944        }
1945    }
1946    
1947    
1948    sub reaction_link {
1949        my($reaction) = @_;
1950        if ($reaction =~ /^(\*)?(R\d+)/)
1951        {
1952            # return "<a href=\"http://www.genome.ad.jp/dbget-bin/www_bget?rn+$2\" target=reaction$$>$reaction</a>";
1953            return "<a href=\"javascript:void(0)\"onclick=\"window.open('http://www.genome.ad.jp/dbget-bin/www_bget?rn+$reaction','$&','height=640,width=800,scrollbars=yes,toolbar=yes,status=yes,resizable=yes')\">$reaction</a>";
1954        }
1955        return $reaction;
1956    }
1957    
1958    
1959    sub html_for_assignments {
1960        my($fig,$user,$peg_sets) = @_;
1961        my $i;
1962    
1963        my @vals = ();
1964        my $set = 1;
1965        foreach my $peg_set (@$peg_sets)
1966        {
1967            for ($i=0; ($i < @$peg_set); $i++)
1968            {
1969                my $peg = $peg_set->[$i];
1970                push(@vals,'show=' . join("@",($set,$i+1,$peg,&FIG::abbrev($fig->org_of($peg)),"")));
1971            }
1972            $set++;
1973        }
1974    
1975        $ENV{'REQUEST_METHOD'} = 'GET';
1976        $ENV{'QUERY_STRING'} = join('&',('request=show_commentary',"uni=1","user=$user",@vals));
1977        my $out = join("",`$FIG_Config::fig/CGI/chromosomal_clusters.cgi`);
1978        $out =~ s/^.*?<form/<form/si;
1979        $out =~ s/^(.*)<table.*/$1/si;
1980        return $out;
1981    }
1982    
1983    =head1 rss_feed
1984    
1985    Add something to the RSS feed. The rss feeds are stored in the Html directory, and there are several RSS feeds:
1986            SEED.rss                - everything gets written here
1987            SEEDgenomes.rss                 - whenever a genome is added to the SEED
1988            SEEDsubsystems.rss      - whenever a subsystem is edited (or should this be added?)
1989    
1990    
1991    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.
1992    
1993    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.
1994    
1995    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.
1996    
1997    The has can have these keys:
1998    
1999    REQUIRED:
2000    title       : the title. This is usually what is seen by the user in the pull down menu
2001    description : a more complete description that is often seen is rss viewers but not always
2002    link        : link to the item that was added/edited
2003    All other keys are treated as optional RSS arguments and written to the file.
2004    
2005    At most, $max_entries recent entries are stored in the rss file, and this is currently 50.
2006    
2007    RSS files are quite simple, and contain some standard header information, and then individual items surrounded by an <item> </item> tag. Note that there is also an initial title/description/link set that describes the file.
2008    
2009    
2010    =cut
2011    
2012    sub rss_feed {
2013     shift if UNIVERSAL::isa($_[0],__PACKAGE__);
2014     my ($files, $args)=@_;
2015    
2016     # how many entries to store in the file
2017     my $max_entries=50;
2018    
2019     foreach my $a (keys %$args) {if ($a =~ /^-(.*)/) {my $b=$1; $args->{$b}=$args->{$a}; delete $args->{$a}}}
2020    
2021     my $filepath=$FIG_Config::fig."/CGI/Html/rss";
2022     # check for the directory and if not, make it
2023     mkdir $filepath unless (-d $filepath);
2024    
2025     # note that $info is a hash of references to hashes that are written out as headers in the file
2026     my $info=
2027     {
2028      "SEED.rss" =>
2029       {
2030            title           => "The SEED",
2031            description     => "Latest news from the SEED",
2032            link            => "Html/rss/SEED.rss",
2033       },
2034    
2035      "SEEDsubsystems.rss" =>
2036      {
2037            title           => "SEED Subsystems",
2038            description     => "Recently updated SEED subsystems",
2039            link            => "Html/rss/SEEDsubsystems.rss",
2040      },
2041    
2042      "SEEDsubsystems.rss" =>
2043      {
2044            title           => "SEED Genomes",
2045            description     => "Genomes recently added to the SEED",
2046            link            => &FIG::cgi_url()."/Html/rss/SEEDsubsystems.rss",
2047      },
2048    
2049     };
2050    
2051    
2052     # build the new xml
2053     my $xml = "\t<item>\n";
2054     foreach my $qw ("title", "description", "link") {
2055      unless ($args->{$qw}) {
2056       print STDERR "You need to include a $qw tag in your RSS description\n";
2057       return(0);
2058      }
2059      # we need to do something a bit funky with the link. We can't have ampersands in the <link> </link> in valid html
2060      # so we are going to pull out the links and uri_escape just the part after the .cgi
2061      if ($qw eq "link")
2062      {
2063       $args->{$qw} =~ /^(.*?\.cgi.)(.*)$/;
2064       $args->{$qw} = $1.uri_escape($2) if ($1 && $2);
2065      }
2066    
2067      $xml .= "\t\t<$qw>".$args->{$qw}."</$qw>\n";
2068      delete $args->{$qw};
2069     }
2070    
2071     foreach my $tag (grep {!/type/i} keys %$args)
2072     {
2073      $xml .= "\t\t<$tag>".$args->{$tag}."</$tag>\n";
2074     }
2075    
2076     $xml .= "\t</item>\n";
2077    
2078    
2079     my @files=("SEED.rss");
2080     if ($args->{"type"}) {
2081        my $type = $args->{type};
2082        push @files, "SEED.$type.rss"
2083    }
2084    
2085     foreach my $file ("SEED.rss", @$files)
2086     {
2087      if (-e "$filepath/$file")
2088      {
2089       my @out; # the new content of the file
2090       my $itemcount=0; # how many <item> </item>'s are we keeping
2091       my $initem; # are we in an item?
2092       open(IN, "$filepath/$file") || die "Can't open $filepath/$file";
2093       while (<IN>)
2094       {
2095        if (/\<item\>/) {
2096         push @out, $xml, unless ($itemcount);
2097         $itemcount++;
2098         $initem=1;
2099        }
2100        if (/\<\/item\>/) {$initem=0; next if ($itemcount > $max_entries)}
2101        next if ($initem && $itemcount > $max_entries);
2102        push @out, $_;
2103       }
2104       close IN;
2105       open(OUT, ">$filepath/$file") || die "Can't open $filepath/$file for writing";
2106       print OUT @out;
2107      }
2108      else
2109      {
2110       open(OUT, ">$filepath/$file") || die "Can't open $filepath/$file for writing";
2111       print OUT "<?xml version=\"1.0\"?>\n<rss version=\"2.0\">\n<channel>\n";
2112       if ($info->{$file})
2113       {
2114         # we're going to sanity check each of the three options we output, just to be sure
2115         foreach my $qw ("title", "description", "link")
2116         {
2117           if ($info->{$file}->{$qw})
2118           {
2119              print OUT "<$qw>", $info->{$file}->{$qw}, "</$qw>\n";
2120           } else {
2121              print STDERR "Please add a $qw for $file\n"; print OUT "<$qw>$file</$qw>\n";
2122           }
2123         }
2124       }
2125       else {
2126        print STDERR "Please define title, link, and description information for $file\n";
2127        print OUT "<title>$file</title>\n<description>An RSS feed</description>\n<link>", &FIG::cgi_url, "</link>\n";
2128       }
2129       print OUT "\n", $xml;
2130       print OUT "\n", "</channel>\n</rss>\n"
2131      }
2132     }
2133    }
2134    
2135    
2136    
2137    1;
2138    
 1  

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