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revision 1.29, Tue Jan 25 08:40:10 2005 UTC revision 1.123, Tue Apr 29 05:43:12 2008 UTC
# Line 1  Line 1 
1    #
2    # Copyright (c) 2003-2006 University of Chicago and Fellowship
3    # for Interpretations of Genomes. All Rights Reserved.
4    #
5    # This file is part of the SEED Toolkit.
6    #
7    # The SEED Toolkit is free software. You can redistribute
8    # it and/or modify it under the terms of the SEED Toolkit
9    # Public License.
10    #
11    # You should have received a copy of the SEED Toolkit Public License
12    # along with this program; if not write to the University of Chicago
13    # at info@ci.uchicago.edu or the Fellowship for Interpretation of
14    # Genomes at veronika@thefig.info or download a copy from
15    # http://www.theseed.org/LICENSE.TXT.
16    #
17    
18  package HTML;  package HTML;
19    
20    use strict;
21    use Tracer;
22  use FIG;  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;  use POSIX;
32    use CGI;
33    
34    #use raelib; # now used for the excel function, that should eventually end up in here. Way too experimental!
35    my $raelib;
36    
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        # Determine if this is a toplevel cgi or one in one of the subdirs (currently
55        # just /p2p).
56        #
57    
58        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 $top;
80    }
81    
82  sub compute_html_header  sub compute_html_header
83  {  {
84      my($additional_insert) = @_;      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
85      my $html_hdr_file = "./Html/html.hdr";      my($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);      my @html_hdr = &FIG::file_read($html_hdr_file);
98      push( @html_hdr, "<br><a href=\"index.cgi?user=$user\">FIG search</a>\n" );  
99        # for my $k (sort keys %ENV) { warn "$k = $ENV{$k}\n"; }
100    
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)      if (@html_hdr)
127      {      {
128          my $insert_stuff;          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);          my @ver = &FIG::file_head("$FIG_Config::fig_disk/CURRENT_RELEASE", 1);
133          my $ver = $ver[0];          my $ver = $ver[0];
134          chomp $ver;          chomp $ver;
# Line 34  Line 140 
140          }          }
141          my $host = &FIG::get_local_hostname();          my $host = &FIG::get_local_hostname();
142          $insert_stuff = "SEED version <b>$ver</b> on $host";          $insert_stuff = "SEED version <b>$ver</b> on $host";
143            }
144    
145          if ($additional_insert)          if ($additional_insert)
146          {          {
147              $insert_stuff .= "<br>" . $additional_insert;              $insert_stuff .= "<br>" . $additional_insert;
# Line 41  Line 149 
149    
150          for $_ (@html_hdr)          for $_ (@html_hdr)
151          {          {
152              s,(href|img\s+src)="/FIG/,\1="$FIG_Config::cgi_base,g;              s,(href|img\s+src)="/FIG/,$1="$top/,g;
153                    s,(\?user\=)\",$1$user",;
154              if ($_ eq "<!-- HEADER_INSERT -->\n")              if ($_ eq "<!-- HEADER_INSERT -->\n")
155              {              {
156                  $_ = $insert_stuff;                  $_ = $insert_stuff;
# Line 53  Line 162 
162  }  }
163    
164  sub show_page {  sub show_page {
165      my($cgi,$html,$no_home) = @_;      #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;      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      # Find the HTML header
185      #      #
186        Trace("Reading tail.") if T(3);
187      my $html_tail_file = "./Html/html.tail";      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)      if (! -f $html_tail_file)
190      {      {
191          $html_tail_file = "$FIG_Config::fig/CGI/Html/html.tail";          $html_tail_file = "$FIG_Config::fig/CGI/Html/$tail_name";
192      }      }
193        Trace("Extracting user name and header data.") if T(3);
     my @html_hdr = compute_html_header();  
   
194      my $user = $cgi->param('user') || "";      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 88  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 116  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 131  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 162  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: Added the javascript for the buttons immediately after body.      #  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,      #  Note if no buttons are added we still (at the moment) add the script,
334      #  but it only adds a little text (495 characters) to the html and noone will notice!      #  but it only adds a little text (495 characters) to the html and noone will notice!
335        #  RAE: This is now deprecated because everything is in an external file, FIG.js, included later
336      if ( $body_line < 0 )      if ( $body_line < 0 )
337      {      {
         my $js=&javascript;  
338          $body_line = $last_head_line + 1;          $body_line = $last_head_line + 1;
339          splice( @$html, $body_line, 0, "<BODY>\n$js\n" );          Trace("Splicing body line at $body_line.") if T(3);
340            splice( @$html, $body_line, 0, "<BODY>\n" );
341      }      }
342    
343      #      #
# Line 204  Line 346 
346    
347      if (@html_hdr)      if (@html_hdr)
348      {      {
349            Trace("Splicing SEED page header after $body_line.") if T(3);
350          splice( @$html, $body_line + 1, 0, @html_hdr );          splice( @$html, $body_line + 1, 0, @html_hdr );
351      }      }
352    
# Line 214  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 232  Line 422 
422          # BASE href needs to be absolute. RDO.          # BASE href needs to be absolute. RDO.
423          #          #
424          #          #
425          $base_url = &FIG::cgi_url;  #        $base_url = &FIG::cgi_url;
426  #       my $base_url = $FIG_Config::cgi_base;  #       my $base_url = $FIG_Config::cgi_base;
427  #       if ( ! $base_url )                      # if cgi_base was not defined  #       if ( ! $base_url )                      # if cgi_base was not defined
428  #       {  #       {
# Line 242  Line 432 
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 252  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 262  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 279  Line 474 
474      #      #
475      # See if we have a site-specific tail (for disclaimers, etc).      # See if we have a site-specific tail (for disclaimers, etc).
476      #      #
477        Trace("Placing site tail.") if T(3);
478      my $site_tail = "$FIG_Config::fig_disk/config/site_tail.html";      my $site_tail = "$FIG_Config::fig_disk/config/site_tail.html";
479      my $site_fh;      my $site_fh;
480      if (open($site_fh, "<$site_tail"))      if (open($site_fh, "<$site_tail"))
# Line 292  Line 487 
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 >= @$html)        # </body> not found; look for </html>
494      {      {
# Line 309  Line 503 
503    
504      if ( @tail )      if ( @tail )
505      {      {
506            Trace("Splicing tail.") if T(3);
507          splice( @$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 $escapedLine = CGI::escapeHTML($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, %options ) = @_;      my($col_hdrs,$tab,$title, %options ) = @_;
549      my(@tab);      my(@tab);
550    
551      my $border = defined $options{border} ? "border=\"$options{border}\"" : "border";      my $border = defined $options{border} ? "border=\"$options{border}\"" : "border";
552      push( @tab, "\n<table $border>\n",      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>$title</b></caption>\n",
556                  "\t<tr>\n\t\t"                  "\t<tr>\n\t\t"
557                . join( "\n", map { &expand($_, "th") } @$col_hdrs )                . join( "\n", map { &expand($_, "th") } @$col_hdrs )
# Line 341  Line 568 
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        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
624      my($x, $tag) = @_;      my($x, $tag) = @_;
625    
626      $tag = "td" unless $tag;      $tag = "td" unless $tag;
627      # RAE modified this so that you can pass in a reference to an array where the first element is the data to      my $endtag = $tag;
628      # display and the second element is optional things like colspan and align. Note that in this case you need to include the td  
629      if (ref($x) eq "ARRAY") {($x, $tag)=@$x}      # 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        # 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 =~ /^\@([^:]+)\:(.*)$/)      if ($x =~ /^\@([^:]+)\:(.*)$/)
638      {      {
639          return "\t\t<$tag $1>$2</$tag>";          return "\t\t<$tag $1>$2</$endtag>";
640      }      }
641      else      else
642      {      {
643          return "\t\t<$tag>$x</$tag>";          return "\t\t<$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 {  sub set_ec_links {
781        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
782      my($cgi,$x) = @_;      my($cgi,$x) = @_;
783      my($before,$match,$after);      my($before,$match,$after);
784    
# Line 377  Line 793 
793  }  }
794    
795  sub ec_link {  sub ec_link {
796        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
797      my($role) = @_;      my($role) = @_;
798    
799      if ($role =~ /(\d+\.\d+\.\d+\.\d+)/)      if ($role =~ /(\d+\.\d+\.\d+\.\d+)/)
# Line 390  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 : $role;
# Line 400  Line 818 
818      return "<a href=$link>$role</a>";      return "<a href=$link>$role</a>";
819  }  }
820    
821  #  =head2 fid_link
822  # Local means to eliminate the fig|org.peg from the  
823  # text of the link.  Get a link to a fid.
824  #  
825    use: my $html=&HTML::fid_link($cgi, $fid, Local, Just_URL, Full_Path);
826    
827    Local is a boolean means to eliminate the fig|org.peg from the text of the link.
828    
829    Just_URL will only return the URL and not the HTML code. The default is to return the full code.
830    
831    Full_Path is a boolean that will get the full path to the URL not just a relative path. This is required in pages where the base href changes (e.g. if an image is imported like on the metabolic pages).
832    
833    =cut
834    
835    
836  sub fid_link {  sub fid_link {
837      my($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 425  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 $sprout = $cgi->param('SPROUT') ? "&SPROUT=1" : "";          my $sprout = $cgi->param('SPROUT') ? "&SPROUT=1" : "";
906          my $link = &FIG::cgi_url . "/protein.cgi?prot=$fid&user=$user$trans$sprout";  ###a
         $link =~ s/[a-z_A-Z0-9]+\.cgi\?/protein.cgi?/;  
         #  
         # Elimin the p2p part if we're in that subdir. Ugh.  
         #  
         $link =~ s,p2p/protein.cgi,protein.cgi,;  
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>$n</a>";              return "<a href='$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    
# Line 474  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 486  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 504  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 522  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,$i);
# Line 552  Line 1057 
1057      for ($j=$i-1; ($j > 0) && ($out->[$j] !~ /FIG search/); $j--) {}      for ($j=$i-1; ($j > 0) && ($out->[$j] !~ /FIG search/); $j--) {}
1058      if ($j > 0)      if ($j > 0)
1059      {      {
1060            #
1061            # Hm. We would have tried using the options here:
1062            # my $tail_name = $options{tail_name} ? $options{tail_name} : "html.tail";
1063            # but they're not passed in. So use the default html.tail.
1064            #
1065            my $html_tail_file = "./Html/html.tail";
1066          my @tmp = `cat $html_tail_file`;          my @tmp = `cat $html_tail_file`;
1067          my $n = @tmp;          my $n = @tmp;
1068          splice(@$out,$j-$n,$n+1);          splice(@$out,$j-$n,$n+1);
1069      }      }
1070  }  }
1071    
1072    =head2 alias_url
1073    
1074    Returns the url that links to an external page showing information about the given alias.
1075    The type of the alias will be determined by the prefix (i.e. 'tr|' for Trembl) If the type
1076    cannot be determined, the function will return undef.
1077    
1078    use: my $html=&HTML::alias_url($alias, $type);
1079    
1080    =cut
1081    
1082    sub alias_url {
1083      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1084    
1085      my ($id, $type) = @_;
1086    
1087      if ($type eq "SEED") { # 1
1088        return "http://seed-viewer.theseed.org/linkin.cgi?id=$id";
1089      }
1090      elsif ($type eq "UniProt") {
1091        return "http://www.uniprot.org/entry/$id";
1092      }
1093      elsif ($type eq "UniProt_ac") { # 2
1094        return "http://www.uniprot.org/entry/$id";
1095      }
1096      elsif ($type eq "UniProt_id") { # 3
1097        return "http://www.uniprot.org/entry/$id";
1098      }
1099      elsif ($type eq "EntrezGene") { # 4
1100        return "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&id=$id";
1101      }
1102      elsif ($type eq "RefSeq") { # 5
1103        return "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&id=$id";
1104      }
1105      elsif ($type eq "GIID") { # 6
1106        return "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&id=$id";
1107      }
1108      elsif ($type eq "NCBI") {
1109        return "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&id=$id";
1110      }
1111      elsif ($type eq "PDB") { # 7
1112        $id =~ s/\:\w//;
1113        return "http://www.rcsb.org/pdb/explore/explore.do?structureId=$id";
1114      }
1115      elsif ($type eq "PFAM") { # 8
1116        return "http://pfam.janelia.org/family?acc=$id";
1117      }
1118      elsif ($type eq "GO") { # 9
1119        return "http://amigo.geneontology.org/cgi-bin/amigo/go.cgi?view=details&search_constraint=terms&depth=0&query=$id";
1120      }
1121      elsif ($type eq "PIRSF") { # 10
1122        return "http://pir.georgetown.edu/cgi-bin/ipcSF?id=$id";
1123      }
1124      elsif ($type eq "IPI") { # 11
1125        return "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+[IPI-AllText:".$id."*]+-lv+30+-view+SeqSimpleView+-page+qResult";
1126      }
1127      elsif ($type eq "UniRef_100") { # 12
1128        return "http://www.uniprot.org/entry/$id";
1129      }
1130      elsif ($type eq "UniRef_90") { # 13
1131        return "http://www.uniprot.org/entry/$id";
1132      }
1133      elsif ($type eq "UniRef_50") { # 14
1134        return "http://www.uniprot.org/entry/$id";
1135      }
1136      elsif ($type eq "UniParc") { # 15
1137        return "http://www.uniprot.org/entry/$id";
1138      }
1139      elsif ($type eq "PIR-PSD") { # 16
1140        return "http://pir.georgetown.edu/cgi-bin/pir_psd_get.pl?id=$id";
1141      }
1142      elsif ($type eq "Taxon_ID") { # 17
1143        return "http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=$id";
1144      }
1145      elsif ($type eq "OMIM") { # 18
1146        return "http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=$id";
1147      }
1148      elsif ($type eq "UniGene") { # 19
1149        return "http://www.ncbi.nlm.nih.gov/sites/entrez?db=unigene&cmd=search&term=$id";
1150      }
1151      elsif ($type eq "Ensemble_ID") { # 20
1152        #return "$id";
1153      }
1154      elsif ($type eq "PMID") { # 21
1155        return "http://www.ncbi.nlm.nih.gov/pubmed/$id";
1156      }
1157      elsif ($type eq "EMBL_DNA_AC") { # 22
1158        return "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBL:".$id."]+-newId";
1159      }
1160      elsif ($type eq "EMBL_Protein_AC") { # 23
1161        $id =~ s/\.\d//;
1162        return "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[{EMBL}-ProteinID:".$id."]";
1163      }
1164      elsif ($type eq "CMR") { # 24
1165        if ($id =~ /^\d+$/) {
1166          return "http://cmr.jcvi.org/cgi-bin/CMR/shared/GenePage.cgi?type=PID&acc=".$id;
1167        } else {
1168          return "http://cmr.jcvi.org/tigr-scripts/CMR/shared/GenePage.cgi?locus=".$id;
1169        }
1170      }
1171    
1172      return undef;
1173    }
1174    
1175  sub set_prot_links {  sub set_prot_links {
1176        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1177      my($cgi,$x) = @_;      my($cgi,$x) = @_;
1178      my($before,$match,$after);      my($before,$match,$after);
1179    
# Line 569  Line 1184 
1184          $after = $3;          $after = $3;
1185          return &set_prot_links($cgi,$before) . &HTML::fid_link($cgi,$match) . &set_prot_links($cgi,$after);          return &set_prot_links($cgi,$before) . &HTML::fid_link($cgi,$match) . &set_prot_links($cgi,$after);
1186      }      }
1187      elsif ($x =~ /^(.*)\b([NXYZA]P_[0-9\.]+)\b(.*)/s)      elsif ($x =~ /^(.*)\b([NXYZA][PM]_[0-9\.]+)\b(.*)/s)
1188      {      {
1189          $before = $1;          $before = $1;
1190          $match = $2;          $match = $2;
# Line 583  Line 1198 
1198          $after = $3;          $after = $3;
1199          return &set_prot_links($cgi,$before) . &HTML::gi_link($cgi,$match) . &set_prot_links($cgi,$after);          return &set_prot_links($cgi,$before) . &HTML::gi_link($cgi,$match) . &set_prot_links($cgi,$after);
1200      }      }
1201      elsif ($x =~  /^(.*)(uni\|[A-Z0-9]{6})(.*)/s)      elsif ($x =~ /^(.*)(img\|\d+)(.*)/s)
1202      {      {
1203          $before = $1;          $before = $1;
1204          $match = $2;          $match = $2;
1205          $after = $3;          $after = $3;
1206          return &set_prot_links($cgi,$before) . &HTML::uni_link($cgi,$match) . &set_prot_links($cgi,$after);          return &set_prot_links($cgi,$before) . &HTML::img_link($cgi,$match) . &set_prot_links($cgi,$after);
1207      }      }
1208      elsif ($x =~ /^(.*)(sp\|[A-Z0-9]{6})(.*)/s)      elsif ($x =~ /^(.*)(tigr\|\w+)(.*)/s)
1209      {      {
1210          $before = $1;          $before = $1;
1211          $match = $2;          $match = $2;
1212          $after = $3;          $after = $3;
1213          return &set_prot_links($cgi,$before) . &HTML::sp_link($cgi,$match) . &set_prot_links($cgi,$after);          return &set_prot_links($cgi,$before) . &HTML::tigr_link($cgi,$match) . &set_prot_links($cgi,$after);
1214      }      }
1215      elsif ($x =~ /^(.*)(pirnr\|NF\d+)(.*)/s)      elsif ($x =~ /^(.*)(tigrcmr\|\w+)(.*)/s)
1216      {      {
1217          $before = $1;          $before = $1;
1218          $match = $2;          $match = $2;
1219          $after = $3;          $after = $3;
1220          return &set_prot_links($cgi,$before) . &HTML::pir_link($cgi,$match) . &set_prot_links($cgi,$after);          return &set_prot_links($cgi,$before) . &HTML::tigr_link($cgi,$match) . &set_prot_links($cgi,$after);
1221      }      }
1222      elsif ($x =~ /^(.*)(kegg\|[a-z]{2,4}:[a-zA-Z_0-9]+)(.*)/s)      elsif ($x =~ /^(.*)\b(eric\|\S+)\b(.*)/s)
1223      {      {
1224          $before = $1;          $before = $1;
1225          $match = $2;          $match = $2;
1226          $after = $3;          $after = $3;
1227          return &set_prot_links($cgi,$before) . &HTML::kegg_link($cgi,$match) . &set_prot_links($cgi,$after);          return &set_prot_links($cgi,$before) . &HTML::eric_link($cgi,$match) . &set_prot_links($cgi,$after);
1228      }      }
     return $x;  
 }  
   
 sub refseq_link {  
     my($cgi,$id) = @_;  
1229    
1230      if ($id =~ /^[NXYZA]P_/)      elsif ($x =~ /^(.*)\b(bhb\|.*?)\b(.*)/s)
1231      {      {
1232          return "<a href=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=protein&cmd=search&term=$id>$id</a>";          $before = $1;
1233      }          $match = $2;
1234  }          $after = $3;
1235            return &set_prot_links($cgi,$before) . &HTML::bhb_link($cgi,$match) . &set_prot_links($cgi,$after);
1236        }
1237    
1238        elsif ($x =~ /^(.*)\b(apidb\|[0-9\.a-z_]+)\b(.*)/s)
1239        {
1240            $before = $1;
1241            $match = $2;
1242            $after = $3;
1243            return &set_prot_links($cgi,$before) . &HTML::apidb_link($cgi,$match) . &set_prot_links($cgi,$after);
1244        }
1245    
1246        elsif ($x =~ /^(.*)\b(patric\|.*?)\b(.*)/s)
1247        {
1248            $before = $1;
1249            $match = $2;
1250            $after = $3;
1251            return &set_prot_links($cgi,$before) . &HTML::patric_link($cgi,$match) . &set_prot_links($cgi,$after);
1252        }
1253    
1254        elsif ($x =~ /^(.*)\b(vbrc\|.*?)\b(.*)/s)
1255        {
1256            $before = $1;
1257            $match = $2;
1258            $after = $3;
1259            return &set_prot_links($cgi,$before) . &HTML::vbrc_link($cgi,$match) . &set_prot_links($cgi,$after);
1260        }
1261    
1262        elsif ($x =~ /^(.*)\b(vectorbase\|.*?)\b(.*)/s)
1263        {
1264            $before = $1;
1265            $match = $2;
1266            $after = $3;
1267            return &set_prot_links($cgi,$before) . &HTML::vectorbase_link($cgi,$match) . &set_prot_links($cgi,$after);
1268        }
1269        elsif ($x =~  /^(.*)(uni\|[A-Z0-9]{6})(.*)/s)
1270        {
1271            $before = $1;
1272            $match = $2;
1273            $after = $3;
1274            return &set_prot_links($cgi,$before) . &HTML::uni_link($cgi,$match) . &set_prot_links($cgi,$after);
1275        }
1276        elsif ($x =~ /^(.*)(sp\|[A-Z0-9]{6})(.*)/s)
1277        {
1278            $before = $1;
1279            $match = $2;
1280            $after = $3;
1281            return &set_prot_links($cgi,$before) . &HTML::sp_link($cgi,$match) . &set_prot_links($cgi,$after);
1282        }
1283        elsif ($x =~ /^(.*)(pirnr\|NF\d+)(.*)/s)
1284        {
1285            $before = $1;
1286            $match = $2;
1287            $after = $3;
1288            return &set_prot_links($cgi,$before) . &HTML::pir_link($cgi,$match) . &set_prot_links($cgi,$after);
1289        }
1290        elsif ($x =~ /^(.*)(kegg\|[a-z]{2,4}:[a-zA-Z_0-9]+)(.*)/s)
1291        {
1292            $before = $1;
1293            $match = $2;
1294            $after = $3;
1295            return &set_prot_links($cgi,$before) . &HTML::kegg_link($cgi,$match) . &set_prot_links($cgi,$after);
1296        }
1297        elsif ($x =~ /^(.*)(Ensembl[a-zA-Z]+:[a-zA-Z_0-9\.]+)(.*)/s)
1298        {
1299            $before = $1;
1300            $match = $2;
1301            $after = $3;
1302            return &set_prot_links($cgi,$before) . &HTML::ensembl_link($cgi,$match) . &set_prot_links($cgi,$after);
1303        }
1304        elsif ($x =~ /^(.*)(EntrezGene:[a-zA-Z_0-9\.]+)(.*)/s)
1305        {
1306            $before = $1;
1307            $match = $2;
1308            $after = $3;
1309            return &set_prot_links($cgi,$before) . &HTML::entrezgene_link($cgi,$match) . &set_prot_links($cgi,$after);
1310        }
1311        elsif ($x =~ /^(.*)(MIM:[a-zA-Z_0-9\.]+)(.*)/s)
1312        {
1313            $before = $1;
1314            $match = $2;
1315            $after = $3;
1316            return &set_prot_links($cgi,$before) . &HTML::mim_link($cgi,$match) . &set_prot_links($cgi,$after);
1317        }
1318        elsif ($x =~ /^(.*)(HGNC:[a-zA-Z_0-9\.]+)(.*)/s)
1319        {
1320            $before = $1;
1321            $match = $2;
1322            $after = $3;
1323            return &set_prot_links($cgi,$before) . &HTML::hgnc_link($cgi,$match) . &set_prot_links($cgi,$after);
1324        }
1325        elsif ($x =~ /^(.*)(UniGene:[a-zA-Z_0-9\.]+)(.*)/s)
1326        {
1327            $before = $1;
1328            $match = $2;
1329            $after = $3;
1330            return &set_prot_links($cgi,$before) . &HTML::unigene_link($cgi,$match) . &set_prot_links($cgi,$after);
1331        }
1332    # IPI stopped working. turn off for now.
1333    #    elsif ($x =~ /^(.*)(IPI:[a-zA-Z_0-9\.]+)(.*)/s)
1334    #    {
1335    #        $before = $1;
1336    #        $match = $2;
1337    #        $after = $3;
1338    #        return &set_prot_links($cgi,$before) . &HTML::ipi_link($cgi,$match) . &set_prot_links($cgi,$after);
1339    #    }
1340        elsif ($x =~ /^(.*)(WP:[a-zA-Z_0-9\.]+)(.*)/s)
1341        {
1342            #wormbase
1343    
1344            $before = $1;
1345            $match = $2;
1346            $after = $3;
1347            return &set_prot_links($cgi,$before) . &HTML::wp_link($cgi,$match) . &set_prot_links($cgi,$after);
1348        }
1349        elsif ($x =~ /^(.*)(FB:[a-zA-Z_0-9\.]+)(.*)/s)
1350        {
1351            #flybase
1352    
1353            $before = $1;
1354            $match = $2;
1355            $after = $3;
1356            return &set_prot_links($cgi,$before) . &HTML::fb_link($cgi,$match) . &set_prot_links($cgi,$after);
1357        }
1358        elsif ($x =~ /^(.*)(FlyBaseORFNames:[a-zA-Z_0-9\.]+)(.*)/s)
1359        {
1360            #flybase
1361    
1362            $before = $1;
1363            $match = $2;
1364            $after = $3;
1365            return &set_prot_links($cgi,$before) . &HTML::fborf_link($cgi,$match) . &set_prot_links($cgi,$after);
1366        }
1367        elsif ($x =~ /^(.*)(SGD_LOCUS:[a-zA-Z_0-9\.]+)(.*)/s)
1368        {
1369            #flybase
1370    
1371            $before = $1;
1372            $match = $2;
1373            $after = $3;
1374            return &set_prot_links($cgi,$before) . &HTML::sgd_link($cgi,$match) . &set_prot_links($cgi,$after);
1375        }
1376        elsif ($x =~ /^(.*)(tr\|[a-zA-Z0-9]+)(.*)/s)
1377        {
1378    
1379          $before = $1;
1380          $match = $2;
1381          $after = $3;
1382    
1383          return &set_prot_links($cgi,$before) .  &HTML::trembl_link($cgi,$match) . &set_prot_links($cgi,$after);
1384        }
1385        return $x;
1386    }
1387    
1388    sub trembl_link {
1389        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1390        my($cgi,$id) = @_;
1391    
1392        if ($id =~ /^tr\|(.*)/) {
1393          return "<a href='http://ca.expasy.org/uniprot/$1' target=_blank>$id</a>";
1394        } else {
1395          return "invalid call to trembl link";
1396        }
1397    }
1398    
1399    sub refseq_link {
1400        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1401        my($cgi,$id) = @_;
1402    
1403        if ($id =~ /^[NXYZA]P_/)
1404        {
1405            return "<a href='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=protein&cmd=search&term=$id' target=_blank>$id</a>";
1406        }
1407        elsif ($id =~ /^[NXYZA]M_/)
1408        {
1409            return "<a href='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=nuccore&cmd=search&term=$id' target=_blank>$id</a>";
1410        }
1411    }
1412    
1413  sub gi_link {  sub gi_link {
1414        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1415      my($cgi,$gi) = @_;      my($cgi,$gi) = @_;
1416    
1417      if ($gi =~ /^gi\|(\d+)$/)      if ($gi =~ /^gi\|(\d+)$/)
1418      {      {
1419          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>";
1420      }      }
1421      return $gi;      return $gi;
1422  }  }
1423    
1424    sub tigr_link {
1425        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1426        my($cgi,$tigr) = @_;
1427    
1428        if ($tigr =~ /^tigr\|(NT|ntbp|ntbpA|BA|BMAA|BXB|GBA)(\w+)$/)
1429        {
1430            my $id=$1.$2;
1431            return "<a href=\"http://pathema.tigr.org/tigr-scripts/pathema/shared/GenePage.cgi?locus=$id\" target=_blank>$tigr</a> (Pathema)";
1432        }
1433        elsif ($tigr =~ /^tigr(cmr)?\|(\S+)$/)
1434        {
1435            return "<a href=\"http://www.tigr.org/tigr-scripts/CMR2/GenePage.spl?locus=$2\" target=_blank>$tigr</a>";
1436        }
1437        return $tigr;
1438    }
1439    
1440    sub eric_link {
1441        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1442        my($cgi,$eric) = @_;
1443    
1444        if ($eric =~ /^eric\|(\S+)/)
1445        {
1446            return "<a href=\"https://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=$1\" target=_blank>$eric</a>";
1447        }
1448        return $eric;
1449    }
1450    
1451    sub bhb_link {
1452        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1453        my($cgi,$bhb) = @_;
1454    
1455        return "<a href=\"http://www.biohealthbase.org\" target=_blank>$bhb</a>";
1456    }
1457    
1458    sub apidb_link {
1459        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1460        my($cgi,$api) = @_;
1461    
1462        if ($api =~ /apidb\|(.*?)\.(.*)$/)
1463        {
1464            return "<a href=\"http://www.apidb.org/cgi-bin/redirect.cgi?taxon_id=$1&source_id=$2\" target=_blank>$api</a>";
1465        }
1466        return $api;
1467    }
1468    
1469    sub patric_link {
1470        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1471        my($cgi,$patric) = @_;
1472    
1473        if ($patric =~ /patric\|(.*)/)
1474        {
1475            return "<a href=\"https://patric.vbi.vt.edu/software/curationTool/gep/pgiCuration.php?locus_name=$1\" target=_blank>$patric</a>";
1476        }
1477        return $patric;
1478    }
1479    
1480    sub vbrc_link {
1481        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1482        my($cgi,$vbrc) = @_;
1483    
1484        if ($vbrc =~ /vbrc\|(.*)/)
1485        {
1486            return "<a href=\"http://www.biovirus.org/gene_detail.asp?name=$1\" target=_blank>$vbrc</a>";
1487        }
1488        return $vbrc;
1489    }
1490    
1491    sub vectorbase_link {
1492        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1493        my($cgi,$vec) = @_;
1494        return "<a href=\"http://www.vectorbase.org\" target=_blank>$vec</a>";
1495    }
1496    
1497    
1498  sub uni_link {  sub uni_link {
1499        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1500      my($cgi,$uni) = @_;      my($cgi,$uni) = @_;
1501    
1502      if ($uni =~ /^uni\|(\S+)$/)      if ($uni =~ /^uni\|(\S+)$/)
1503      {      {
1504          return "<a href=http://www.pir.uniprot.org/cgi-bin/upEntry?id=$1>$uni</a>";          #return "<a href=http://www.pir.uniprot.org/cgi-bin/upEntry?id=$1>$uni</a>";
1505            return "<a href='http://www.ebi.uniprot.org/uniprot-srv/uniProtView.do?proteinAc=$1' target=_blank>$uni</a>";
1506      }      }
1507      return $uni;      return $uni;
1508  }  }
1509    
1510  sub sp_link {  sub sp_link {
1511        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1512      my($cgi,$sp) = @_;      my($cgi,$sp) = @_;
1513    
1514      if ($sp =~ /^sp\|(\S+)$/)      if ($sp =~ /^sp\|(\S+)$/)
1515      {      {
1516          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>";
1517      }      }
1518      return $sp;      return $sp;
1519  }  }
1520    
1521  sub pir_link {  sub pir_link {
1522        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1523      my($cgi,$pir) = @_;      my($cgi,$pir) = @_;
1524    
1525      if ($pir =~ /^pirnr\|(NF\d+)$/)      if ($pir =~ /^pirnr\|(NF\d+)$/)
1526      {      {
1527          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>";
1528      }      }
1529      return $pir;      return $pir;
1530  }  }
1531    
1532  sub kegg_link {  sub kegg_link {
1533        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1534      my($cgi,$kegg) = @_;      my($cgi,$kegg) = @_;
1535    
1536      if ($kegg =~ /^kegg\|([^:]+):(\S+)$/)      if ($kegg =~ /^kegg\|([^:]+):(\S+)$/)
1537      {      {
1538          return "<a href=http://www.genome.ad.jp/dbget-bin/www_bget?$1+$2>$kegg</a>";          return "<a href='http://www.genome.ad.jp/dbget-bin/www_bget?$1+$2' target=_blank>$kegg</a>";
1539      }      }
1540      return $kegg;      return $kegg;
1541  }  }
1542    
1543    sub img_link {
1544        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1545        my($cgi,$img) = @_;
1546    
1547        if ($img =~ /^img\|(\S+)$/)
1548        {
1549            return "<a href='http://img.jgi.doe.gov/cgi-bin/pub/main.cgi?page=geneDetail&gene_oid=$1' target=_blank>$img</a>";
1550        }
1551        return $img;
1552    }
1553    
1554    sub ensembl_link {
1555        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1556        my($cgi,$ensembl) = @_;
1557    
1558        if ($ensembl =~ /^(\S+):(\S+)$/)
1559        {
1560            my $what=$1;
1561            my $key=$2;
1562            my $idx="All";
1563            if ($what eq "EnsemblGene") { $idx = "Gene" }
1564            if ($what eq "EnsemblTranscript") { $idx = "All" }
1565            if ($what eq "EnsemblProtein") { $idx = "All" }
1566    
1567            #I really want to get right to the transcript and peptide pages, but
1568            #can't see how to do that without knowing the org name too, which
1569            #I don't know at this point. (ensembl org name, not real org name)
1570    
1571            return "<a href='http://www.ensembl.org/Homo_sapiens/searchview?species=all&idx=$idx&q=$key' target=_blank>$ensembl</a>";
1572        }
1573        return $ensembl;
1574    }
1575    
1576    sub entrezgene_link {
1577        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1578        my($cgi,$entrezgene) = @_;
1579    
1580        if ($entrezgene =~ /^EntrezGene:(\S+)$/)
1581        {
1582            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>";
1583        }
1584        return $entrezgene;
1585    }
1586    
1587    sub mim_link {
1588        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1589        my($cgi,$mim) = @_;
1590    
1591        if ($mim =~ /^MIM:(\S+)$/)
1592        {
1593            return "<a href='http://www3.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=$1' target=_blank>$mim</a>";
1594        }
1595        return $mim;
1596    }
1597    
1598    sub hgnc_link {
1599        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1600        my($cgi,$hgnc) = @_;
1601    
1602        if ($hgnc =~ /^HGNC:(\S+)$/)
1603        {
1604            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>";
1605        }
1606    
1607        return $hgnc;
1608    }
1609    
1610    sub unigene_link {
1611        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1612        my($cgi,$unigene) = @_;
1613    
1614        if ($unigene =~ /^UniGene:(\S+)$/)
1615        {
1616            return "<a href='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unigene&cmd=search&term=$1' target=_blank>$unigene</a>";
1617        }
1618        return $unigene;
1619    }
1620    
1621    sub ipi_link {
1622        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1623        my($cgi,$ipi) = @_;
1624    
1625        if ($ipi =~ /^IPI:(\S+)$/)
1626        {
1627            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>";
1628        }
1629        return $ipi;
1630    }
1631    
1632    sub wp_link {
1633        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1634        my($cgi,$wp) = @_;
1635    
1636        #wormbase
1637    
1638        if ($wp =~ /^WP:(\S+)$/)
1639        {
1640            return "<a href='http://www.wormbase.org/db/searches/basic?class=Any&query=$1&Search=Search' target=_blank>$wp</a>";
1641        }
1642        return $wp;
1643    }
1644    
1645    sub fb_link {
1646        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1647        my($cgi,$fb) = @_;
1648    
1649        #flybase
1650    
1651        if ($fb =~ /^FB:(\S+)$/)
1652        {
1653            return "<a href='http://flybase.bio.indiana.edu/.bin/fbidq.html?$1' target=_blank>$fb</a>";
1654        }
1655        return $fb;
1656    }
1657    
1658    sub fborf_link {
1659        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1660        my($cgi,$fb) = @_;
1661    
1662        #flybase
1663    
1664        if ($fb =~ /^FlyBaseORFNames:(\S+)$/)
1665        {
1666            return "<a href='http://flybase.bio.indiana.edu/.bin/fbidq.html?$1' target=_blank>$fb</a>";
1667        }
1668        return $fb;
1669    }
1670    
1671    sub sgd_link {
1672        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1673        my($cgi,$sgd) = @_;
1674    
1675        #yeast
1676    
1677        if ($sgd =~ /^SGD_LOCUS:(\S+)$/)
1678        {
1679            return "<a href='http://db.yeastgenome.org/cgi-bin/locus.pl?locus=$1' target=_blank>$sgd</a>";
1680        }
1681        return $sgd;
1682    }
1683    
1684    
1685    
1686    
1687  sub set_map_links {  sub set_map_links {
1688        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1689      my($cgi,$x) = @_;      my($cgi,$x) = @_;
1690      my($before,$match,$after);      my($before,$match,$after);
1691    
# Line 689  Line 1701 
1701      return $x;      return $x;
1702  }  }
1703    
1704    
1705    
1706  sub map_link {  sub map_link {
1707        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1708      my($cgi,$map,$org) = @_;      my($cgi,$map,$org) = @_;
1709    
1710      $user = $cgi->param('user');      my $user = $cgi->param('user');
1711      $user = $user ? $user : "";      $user = $user ? $user : "";
1712      $org = $org ? $org : "";      $org = $org ? $org : "";
1713      my $url = "$FIG_Config::cgi_url/show_kegg_map.cgi?user=$user&map=$map&org=$org";  
1714        my $url = "show_kegg_map.cgi?user=$user&map=$map&org=$org";
1715    #rel    my $url = &FIG::cgi_url() . "/show_kegg_map.cgi?user=$user&map=$map&org=$org";
1716      my $link = "<a href=\"$url\">$map</a>";      my $link = "<a href=\"$url\">$map</a>";
1717      return $link;      return $link;
1718  }  }
1719    
1720  sub javascript {  sub java_buttons {
1721          #### MODIFIED BY RAE TO ADD JAVA SUPPORT FOR CHECK ALL/UNCHECK ALL      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1722          # This routine takes three arguments, $html, $form, and $button    ## ADDED BY RAE
1723          # $html is the ref to the array with the html in it    # Provides code to include check all/first half/second half/none for javascrspt
1724          # $form is the name of the form. This must be added whenever start_form is called    # this takes two variables - the form name provided in start_form with the
1725          # by including a -name entry. This is only used for the javascript    # -name => field and the checkbox name
1726          # $button is the name of the button that should be checked/unchecked.    my ($form, $button)=@_;
         #  
         # At the moment this add's four buttons:  
         # Check all, check's all  
         # Check first half will check the first 50% of the entries  
         # Check second half will check the second 50% of the entries  
         # Uncheck all will remove the checks.  
1727    
1728          # Note that the other change is I added a -name=>'fig_checked' to the start_form    my $java_script="<input type=\"button\" name=\"CheckAll\" value=\"Check All\"\nonClick=\"checkAll(document.$form.$button)\">\n";
1729          # field. The name is needed for the java script.    $java_script.="<input type=\"button\" name=\"CheckFirst\" value=\"Check First Half\"\nonClick=\"checkFirst(document.$form.$button)\">\n";
1730          #    $java_script.="<input type=\"button\" name=\"CheckSecond\" value=\"Check Second Half\"\nonClick=\"checkSecond(document.$form.$button)\">\n";
1731      $java_script.="<input type=\"button\" name=\"UnCheckAll\" value=\"Uncheck All\"\nonClick=\"uncheckAll(document.$form.$button)\">\n";
1732    
1733      return $java_script;
1734    }
1735    
1736    =head3 sub_link
1737    
1738        my $htmlText = HTML::sub_link($cgi, $sub, gid);
1739    
1740    Create a subsystem link. The link will be to the display page if there is no
1741    user or we are in SPROUT mode; otherwise it will be to the edit page.
1742    
1743    =over 4
1744    
1745    =item cgi
1746    
1747    CGI query object for the current web session. The parameters of special interest
1748    are C<SPROUT> and C<user>. If the user is non-blank and SPROUT mode is 0, then
1749    the subsystem's edit page will be shown rather than its display page.
1750    
1751    =item sub
1752    
1753    Name of the desired subsystem. It will be cleaned of underscores before the
1754    hyperlink is applied.
1755    
1756    =item gid
1757    
1758    Genome ID to be specified as the focus.
1759    
1760    =back
1761    
1762            $java_script=<<EOF;  =cut
1763    <SCRIPT LANGUAGE="JavaScript">  
1764    <!-- Begin  sub sub_link {
1765    function checkAll(field)      # Allow call as an instance in addition to the authorized method.
1766        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1767        # Get the parameters.
1768        my ($cgi, $sub, $gid) = @_;
1769        # Declare the return variable.
1770        my $retVal;
1771        # Clean the subsystem name for display purposes. This is a very
1772        # different thing from URL-escaping.
1773        my $cleaned = CGI::escapeHTML($sub);
1774        $cleaned =~ s/_/ /g;
1775        # URL-escape the subsystem name for use in the link.
1776        my $linkable = uri_escape($sub);
1777        # Determine the mode. Note we use the little OR trick to insure that
1778        # we have the correct value for plugging into the output link.
1779        my $user = $cgi->param('user') || "";
1780        my $sproutMode = $cgi->param('SPROUT') || 0;
1781        if ($user && ! $sproutMode) {
1782            # A SEED user is calling, so we go to the edit page.
1783            $retVal = "<a href=\"subsys.cgi?ssa_name=$linkable&request=show_ssa&user=$user\">$cleaned</a>";
1784        } else {
1785            # A visitor or SPROUT user is calling, so we go to the display page.
1786            $retVal = "<a href=\"display_subsys.cgi?ssa_name=$linkable;request=show_ssa;sort=by_phylo;focus=$gid;SPROUT=$sproutMode\">$cleaned</a>";
1787        }
1788        # Return the result.
1789        return $retVal;
1790    }
1791    
1792    sub reaction_map_link {
1793        my($mapID, @reaction_list) = @_;
1794        if($mapID =~ /\d+/)
1795    {    {
1796     for (i = 0; i < field.length; i++)          my $reactions = join "+", @reaction_list;
1797     field[i].checked = true ;          if ($reactions ne "")
1798            {
1799                $reactions = "+".$reactions;
1800    }    }
1801    
1802    function checkFirst(field)          return "<a href=http://www.genome.jp/dbget-bin/show_pathway?rn$mapID$reactions>$mapID</a>";
1803        }
1804        else
1805    {    {
1806     for (i = 0; i < field.length/2; i++)          return $mapID;
1807     field[i].checked = true;      }
1808    }    }
1809    
1810    function checkSecond(field)  sub compound_link {
1811        my($compound) = @_;
1812        if($compound =~ /^C\d+/)
1813        {
1814            return "<a href=\"javascript:void(0)\"onclick=\"window.open('http://www.genome.jp/dbget-bin/www_bget?compound+$compound','$&','height=640,width=800,scrollbars=yes,toolbar=yes,status=yes,resizable=yes')\">$compound</a>";
1815        }
1816        else
1817    {    {
1818     for (i=Math.round(field.length/2); i < field.length; i++)          return $compound;
1819     field[i].checked = true ;      }
1820    }    }
1821    
1822    function uncheckAll(field)  
1823    sub reaction_link {
1824        my($reaction) = @_;
1825        if ($reaction =~ /^(\*)?(R\d+)/)
1826    {    {
1827     for (i = 0; i < field.length; i++)          # return "<a href=\"http://www.genome.ad.jp/dbget-bin/www_bget?rn+$2\" target=reaction$$>$reaction</a>";
1828     field[i].checked = false ;          return "<a href=\"javascript:void(0)\"onclick=\"window.open('http://www.genome.ad.jp/dbget-bin/www_bget?rn+$reaction','$&','height=640,width=800,scrollbars=yes,toolbar=yes,status=yes,resizable=yes')\">$reaction</a>";
1829    }    }
1830    //  End -->      return $reaction;
   </script>  
 EOF  
         return $java_script;  
1831  }  }
1832    
 sub java_buttons {  
   ## ADDED BY RAE  
   # Provides code to include check all/first half/second half/none for javascrspt  
   # this takes two variables - the form name provided in start_form with the  
   # -name => field and the checkbox name  
   my ($form, $button)=@_;  
1833    
1834    $java_script="<input type=\"button\" name=\"CheckAll\" value=\"Check All\"\nonClick=\"checkAll(document.$form.$button)\">\n";  sub html_for_assignments {
1835    $java_script.="<input type=\"button\" name=\"CheckFirst\" value=\"Check First Half\"\nonClick=\"checkFirst(document.$form.$button)\">\n";      my($fig,$user,$peg_sets) = @_;
1836    $java_script.="<input type=\"button\" name=\"CheckSecond\" value=\"Check Second Half\"\nonClick=\"checkSecond(document.$form.$button)\">\n";      my $i;
   $java_script.="<input type=\"button\" name=\"UnCheckAll\" value=\"Uncheck All\"\nonClick=\"uncheckAll(document.$form.$button)\">\n";  
1837    
1838    return $java_script;      my @vals = ();
1839        my $set = 1;
1840        foreach my $peg_set (@$peg_sets)
1841        {
1842            for ($i=0; ($i < @$peg_set); $i++)
1843            {
1844                my $peg = $peg_set->[$i];
1845                push(@vals,'show=' . join("@",($set,$i+1,$peg,&FIG::abbrev($fig->org_of($peg)),"")));
1846            }
1847            $set++;
1848  }  }
1849    
1850  sub sub_link {      $ENV{'REQUEST_METHOD'} = 'GET';
1851      my($cgi,$sub) = @_;      $ENV{'QUERY_STRING'} = join('&',('request=show_commentary',"uni=1","user=$user",@vals));
1852      my($sub_link);      my $out = join("",`$FIG_Config::fig/CGI/chromosomal_clusters.cgi`);
1853        $out =~ s/^.*?<form/<form/si;
1854        $out =~ s/^(.*)<table.*/$1/si;
1855        return $out;
1856    }
1857    
1858      my $user = $cgi->param('user');  =head1 rss_feed
1859      if ($user)  
1860    Add something to the RSS feed. The rss feeds are stored in the Html directory, and there are several RSS feeds:
1861            SEED.rss                - everything gets written here
1862            SEEDgenomes.rss                 - whenever a genome is added to the SEED
1863            SEEDsubsystems.rss      - whenever a subsystem is edited (or should this be added?)
1864    
1865    
1866    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.
1867    
1868    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.
1869    
1870    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.
1871    
1872    The has can have these keys:
1873    
1874    REQUIRED:
1875    title       : the title. This is usually what is seen by the user in the pull down menu
1876    description : a more complete description that is often seen is rss viewers but not always
1877    link        : link to the item that was added/edited
1878    All other keys are treated as optional RSS arguments and written to the file.
1879    
1880    At most, $max_entries recent entries are stored in the rss file, and this is currently 50.
1881    
1882    RSS files are quite simple, and contain some standard header information, and then individual items surrounded by an <item> </item> tag. Note that there is also an initial title/description/link set that describes the file.
1883    
1884    
1885    =cut
1886    
1887    sub rss_feed {
1888     shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1889     my ($files, $args)=@_;
1890    
1891     # how many entries to store in the file
1892     my $max_entries=50;
1893    
1894     foreach my $a (keys %$args) {if ($a =~ /^-(.*)/) {my $b=$1; $args->{$b}=$args->{$a}; delete $args->{$a}}}
1895    
1896     my $filepath=$FIG_Config::fig."/CGI/Html/rss";
1897     # check for the directory and if not, make it
1898     mkdir $filepath unless (-d $filepath);
1899    
1900     # note that $info is a hash of references to hashes that are written out as headers in the file
1901     my $info=
1902     {
1903      "SEED.rss" =>
1904       {
1905            title           => "The SEED",
1906            description     => "Latest news from the SEED",
1907            link            => "Html/rss/SEED.rss",
1908       },
1909    
1910      "SEEDsubsystems.rss" =>
1911      {
1912            title           => "SEED Subsystems",
1913            description     => "Recently updated SEED subsystems",
1914            link            => "Html/rss/SEEDsubsystems.rss",
1915      },
1916    
1917      "SEEDsubsystems.rss" =>
1918      {      {
1919          $sub_link = "<a href=./subsys.cgi?ssa_name=$sub&request=show_ssa&user=$user>$sub</a>";          title           => "SEED Genomes",
1920            description     => "Genomes recently added to the SEED",
1921            link            => &FIG::cgi_url()."/Html/rss/SEEDsubsystems.rss",
1922      },
1923    
1924     };
1925    
1926    
1927     # build the new xml
1928     my $xml = "\t<item>\n";
1929     foreach my $qw ("title", "description", "link") {
1930      unless ($args->{$qw}) {
1931       print STDERR "You need to include a $qw tag in your RSS description\n";
1932       return(0);
1933      }
1934      # we need to do something a bit funky with the link. We can't have ampersands in the <link> </link> in valid html
1935      # so we are going to pull out the links and uri_escape just the part after the .cgi
1936      if ($qw eq "link")
1937      {
1938       $args->{$qw} =~ /^(.*?\.cgi.)(.*)$/;
1939       $args->{$qw} = $1.uri_escape($2) if ($1 && $2);
1940      }
1941    
1942      $xml .= "\t\t<$qw>".$args->{$qw}."</$qw>\n";
1943      delete $args->{$qw};
1944     }
1945    
1946     foreach my $tag (grep {!/type/i} keys %$args)
1947     {
1948      $xml .= "\t\t<$tag>".$args->{$tag}."</$tag>\n";
1949     }
1950    
1951     $xml .= "\t</item>\n";
1952    
1953    
1954     my @files=("SEED.rss");
1955     if ($args->{"type"}) {
1956        my $type = $args->{type};
1957        push @files, "SEED.$type.rss"
1958    }
1959    
1960     foreach my $file ("SEED.rss", @$files)
1961     {
1962      if (-e "$filepath/$file")
1963      {
1964       my @out; # the new content of the file
1965       my $itemcount=0; # how many <item> </item>'s are we keeping
1966       my $initem; # are we in an item?
1967       open(IN, "$filepath/$file") || die "Can't open $filepath/$file";
1968       while (<IN>)
1969       {
1970        if (/\<item\>/) {
1971         push @out, $xml, unless ($itemcount);
1972         $itemcount++;
1973         $initem=1;
1974        }
1975        if (/\<\/item\>/) {$initem=0; next if ($itemcount > $max_entries)}
1976        next if ($initem && $itemcount > $max_entries);
1977        push @out, $_;
1978       }
1979       close IN;
1980       open(OUT, ">$filepath/$file") || die "Can't open $filepath/$file for writing";
1981       print OUT @out;
1982      }      }
1983      else      else
1984      {      {
1985          $sub_link = $sub;     open(OUT, ">$filepath/$file") || die "Can't open $filepath/$file for writing";
1986       print OUT "<?xml version=\"1.0\"?>\n<rss version=\"2.0\">\n<channel>\n";
1987       if ($info->{$file})
1988       {
1989         # we're going to sanity check each of the three options we output, just to be sure
1990         foreach my $qw ("title", "description", "link")
1991         {
1992           if ($info->{$file}->{$qw})
1993           {
1994              print OUT "<$qw>", $info->{$file}->{$qw}, "</$qw>\n";
1995           } else {
1996              print STDERR "Please add a $qw for $file\n"; print OUT "<$qw>$file</$qw>\n";
1997           }
1998         }
1999       }
2000       else {
2001        print STDERR "Please define title, link, and description information for $file\n";
2002        print OUT "<title>$file</title>\n<description>An RSS feed</description>\n<link>", &FIG::cgi_url, "</link>\n";
2003      }      }
2004      return $sub_link;     print OUT "\n", $xml;
2005       print OUT "\n", "</channel>\n</rss>\n"
2006  }  }
2007     }
2008    }
2009    
2010    
2011    
2012    1;
2013    
 1  

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