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revision 1.37, Tue Mar 15 22:29:27 2005 UTC revision 1.95, Tue Jun 27 22:40:49 2006 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 Tracer;
21  use FIG;  use FIG;
22  use Carp;  use Carp;
23  use Data::Dumper;  use Data::Dumper;
24  use LWP::UserAgent;  use LWP::UserAgent;
25  use LWP::Simple;  use LWP::Simple;
26    use URI::Escape;  # uri_escape()
27  use URI::URL;  use URI::URL;
28  use HTTP::Request::Common;  use HTTP::Request::Common;
29  use POSIX;  use POSIX;
30    
31    use raelib; # now used for the excel function, that should eventually end up in here. Way too experimental!
32    my $raelib=new raelib;
33    
34    
35    my $top_link_cache;
36    
37    
38  sub new  sub new
39  {  {
40      my($class) = @_;      my($class) = @_;
# Line 18  Line 44 
44      return bless $self, $class;      return bless $self, $class;
45  }  }
46    
47    sub top_link
48    {
49    
50        #
51        # Determine if this is a toplevel cgi or one in one of the subdirs (currently
52        # just /p2p).
53        #
54    
55        return $top_link_cache if ($top_link_cache);
56    
57        my @parts = split(/\//, $ENV{SCRIPT_NAME});
58        my $top;
59        if ($parts[-2] eq 'FIG')
60        {
61            $top = '.';
62    #       warn "toplevel @parts\n";
63        }
64        elsif ($parts[-3] eq 'FIG')
65        {
66            $top = '..';
67    #       warn "subdir @parts\n";
68        }
69        else
70        {
71            $top = $FIG_Config::cgi_base;
72    #       warn "other @parts\n";
73        }
74    
75        $top_link_cache = $top;
76        return $top;
77    }
78    
79  sub compute_html_header  sub compute_html_header
80  {  {
81      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
82      my($additional_insert,$user) = @_;      my($additional_insert, $user, %options ) = @_;
83      my $html_hdr_file = "./Html/html.hdr";  
84        local $/ = "\n";
85    
86        my $header_name = $options{header_name} ? $options{header_name} : "html.hdr";
87        my $tail_name = $options{tail_name} ? $options{tail_name} : "html.tail";
88    
89        my $html_hdr_file = "./Html/$header_name";
90      if (! -f $html_hdr_file)      if (! -f $html_hdr_file)
91      {      {
92          $html_hdr_file = "$FIG_Config::fig/CGI/Html/html.hdr";          $html_hdr_file = "$FIG_Config::fig/CGI/Html/$header_name";
93      }      }
94      my @html_hdr = &FIG::file_read($html_hdr_file);      my @html_hdr = &FIG::file_read($html_hdr_file);
95      push( @html_hdr, "<br><a href=\"index.cgi?user=$user\">FIG search</a>\n" );  
96        # for my $k (sort keys %ENV) { warn "$k = $ENV{$k}\n"; }
97    
98        #
99        # Determine if this is a toplevel cgi or one in one of the subdirs (currently
100        # just /p2p).
101        #
102    
103        my @parts = split(/\//, $ENV{SCRIPT_NAME});
104        my $top;
105        if ($parts[-2] eq 'FIG')
106        {
107            $top = '.';
108    #       warn "toplevel @parts\n";
109        }
110        elsif ($parts[-3] eq 'FIG')
111        {
112            $top = '..';
113    #       warn "subdir @parts\n";
114        }
115        else
116        {
117            $top = $FIG_Config::cgi_base;
118    #       warn "other @parts\n";
119        }
120    
121        $options{no_fig_search} or push( @html_hdr, "<br><a href=\"$top/index.cgi?user=$user\">FIG search</a>\n" );
122    
123      if (@html_hdr)      if (@html_hdr)
124      {      {
125          my $insert_stuff;          my $insert_stuff;
126    
127            if (not $options{no_release_info})
128            {
129          my @ver = &FIG::file_head("$FIG_Config::fig_disk/CURRENT_RELEASE", 1);          my @ver = &FIG::file_head("$FIG_Config::fig_disk/CURRENT_RELEASE", 1);
130          my $ver = $ver[0];          my $ver = $ver[0];
131          chomp $ver;          chomp $ver;
# Line 44  Line 137 
137          }          }
138          my $host = &FIG::get_local_hostname();          my $host = &FIG::get_local_hostname();
139          $insert_stuff = "SEED version <b>$ver</b> on $host";          $insert_stuff = "SEED version <b>$ver</b> on $host";
140            }
141    
142          if ($additional_insert)          if ($additional_insert)
143          {          {
144              $insert_stuff .= "<br>" . $additional_insert;              $insert_stuff .= "<br>" . $additional_insert;
# Line 51  Line 146 
146    
147          for $_ (@html_hdr)          for $_ (@html_hdr)
148          {          {
149              s,(href|img\s+src)="/FIG/,\1="$FIG_Config::cgi_base,g;              s,(href|img\s+src)="/FIG/,$1="$top/,g;
150                    s,(\?user\=)\",$1$user",;
151              if ($_ eq "<!-- HEADER_INSERT -->\n")              if ($_ eq "<!-- HEADER_INSERT -->\n")
152              {              {
153                  $_ = $insert_stuff;                  $_ = $insert_stuff;
# Line 65  Line 161 
161  sub show_page {  sub show_page {
162      #warn "SHOWPAGE: cgi=", Dumper(@_);      #warn "SHOWPAGE: cgi=", Dumper(@_);
163      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
164      my($cgi,$html,$no_home, $alt_header, $css) = @_;      my($cgi,$html,$no_home, $alt_header, $css, $javasrc, $cookie, $options) = @_;
165      my $i;      my $i;
166    
167        my $top = top_link();
168    
169      # ARGUMENTS:      # ARGUMENTS:
170      #     $cgi is the CGI method      #     $cgi is the CGI method
# Line 77  Line 174 
174      #     $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      #     $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
175      #               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      #               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
176      #               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      #               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
177        #     $javasrc is a reference to an array of URLs to javascripts to be included (e.g. "FIG/Html/css/styleswitcher.js")
178        #     $cookie is the name and value of the cookie to set. Note that you should probably use raelib->cookie to get/set your cookies
179        #     $options is a reference to a hash of options that you can pass around the pages
180      #      #
181      # Find the HTML header      # Find the HTML header
182      #      #
183    
184      my $html_tail_file = "./Html/html.tail";      my $html_tail_file = "./Html/$tail_name";
185      if (! -f $html_tail_file)      if (! -f $html_tail_file)
186      {      {
187          $html_tail_file = "$FIG_Config::fig/CGI/Html/html.tail";          $html_tail_file = "$FIG_Config::fig/CGI/Html/$tail_name";
188      }      }
189    
190      my $user = $cgi->param('user') || "";      my $user = $cgi->param('user') || "";
191      my @html_hdr;      my @html_hdr;
192      if ($alt_header)      if ($alt_header && ref($alt_header) eq "ARRAY")
193      {      {
194         @html_hdr = @$alt_header;         @html_hdr = @$alt_header;
195      }      }
196      else      else
197      {      {
198          @html_hdr = compute_html_header(undef,$user);          @html_hdr = compute_html_header(undef,$user,%$options);
199      }      }
200    
201        # RAE: I am offloading the handling of cookies to CGI.pm since I don't know how they are set up.
202        # This modification adds the cookies if necessary
203    
204        # Note: 3/10/05 commented this line out pending the discussion of adding cookies into the seed that we are waiting to see about
205        # to add cookies back in replace these two header lines with each other
206    
207      print $cgi->header;      #print $cgi->header(-cookie=>$cookie);
208        print $cgi->header();
209    
210      #      #
211      #  The SEED header file goes immediately after <BODY>.  Figure out      #  The SEED header file goes immediately after <BODY>.  Figure out
# Line 118  Line 223 
223                       meta     => 1,                       meta     => 1,
224                       nextid   => 1,                       nextid   => 1,
225                       style    => 1,                       style    => 1,
226                       title    => 1                       title    => 1,
227                     );                     );
228    
229      #      #
# Line 161  Line 266 
266          if ( $html->[$i] =~ /\<body[^0-9a-z]/i )          if ( $html->[$i] =~ /\<body[^0-9a-z]/i )
267          {          {
268              $body_line = $i;              $body_line = $i;
269              $last;              last;
270          }          }
271    
272          #  Now the general case.          #  Now the general case.
# Line 221  Line 326 
326      #  Added the javascript for the buttons immediately after body.      #  Added the javascript for the buttons immediately after body.
327      #  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,
328      #  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!
329        #  RAE: This is now deprecated because everything is in an external file, FIG.js, included later
330    
331      if ( $body_line < 0 )      if ( $body_line < 0 )
332      {      {
         my $js=&javascript;  
333          $body_line = $last_head_line + 1;          $body_line = $last_head_line + 1;
334          splice( @$html, $body_line, 0, "<BODY>\n$js\n" );          splice( @$html, $body_line, 0, "<BODY>\n" );
335      }      }
336    
337      #      #
# Line 250  Line 355 
355    
356      # RAE:      # RAE:
357      # Add css here      # Add css here
358      # Note that at the moment I define these two sheets here. I think this should be moved out, but I want to try it and see what happens      # Note that at the moment I define these two sheets here. I think this should
359      # css has the format      # be moved out, but I want to try it and see what happens.  css has the format:
360        #
361      # <link rel='stylesheet' title='default' href='/css/default.css' type='text/css'>      # <link rel='stylesheet' title='default' href='/css/default.css' type='text/css'>
362    
363      # convert the default key to the right case. and eliminate dups      # convert the default key to the right case. and eliminate dups
# Line 259  Line 365 
365    
366      if (!$css || !$css->{'Default'})      if (!$css || !$css->{'Default'})
367      {      {
368         $css->{'Default'}="/FIG/Html/css/default.css";         $css->{'Default'} = "Html/css/default.css";
369      }      }
370      if (!$css->{"Sans Serif"})      if (!$css->{"Sans Serif"})
371      {      {
372         $css->{'Sans Serif'}="/FIG/Html/css/sanserif.css";         $css->{'Sans Serif'} = "Html/css/sanserif.css";
373      }      }
374    
375      my $csstext = "<link rel='stylesheet' title='default' href='".$css->{'Default'}."' type='text/css'>\n";      my $csstext = "<link rel='stylesheet' title='default' href='".$css->{'Default'}."' type='text/css'>\n";
376      $csstext   .= "<link rel='alternate stylesheet' title='Sans Serif' href='".$css->{'Sans Serif'}."' type='text/css'>\n";      $csstext   .= "<link rel='alternate stylesheet' title='Sans Serif' href='".$css->{'Sans Serif'}."' type='text/css'>\n";
377    
378      foreach my $k (keys %$css)      foreach my $k (keys %$css)
379      {      {
380         next if (lc($k) eq "default" || lc($k) eq "sans serif");         next if (lc($k) eq "default" || lc($k) eq "sans serif");
381         $csstext .= "<link rel='stylesheet' title='$k' href='".$css->{$k}."' type='text/css'>\n";         $csstext .= "<link rel='alternate stylesheet' title='$k' href='".$css->{$k}."' type='text/css'>\n";
382      }      }
383    
384        $csstext   .= "<link rel='alternate'  title='SEED RSS feeds' href='Html/rss/SEED.rss' type='application/rss+xml'>\n";
385    
386        # RAE: also added support for external javascripts here.
387        # we are cluttering the HTML code with all the javascripts when they could easily be in external files
388        # this solution allows us to source other files
389    
390        # the file FIG.js contains most of the java script we use routinely. Every browser will just cache this and so
391        # it will reduce our overhead.
392    
393        # $javasrc must be a ref to an array with urls (absolute or relative) to the javascripts
394        push @$javasrc, "Html/css/FIG.js";
395        foreach my $script (@$javasrc) {
396            $csstext .= "<script src=\"$script\" type=\"text/javascript\"></script>\n";
397        }
398    
399    
400    
401      splice( @$html, $head_end_line, 1, "$csstext</HEAD>\n" );  # note here I am replacing the </head> line. Could be bad...? But it doesn't increment everything else.      splice( @$html, $head_end_line, 1, "$csstext</HEAD>\n" );  # note here I am replacing the </head> line. Could be bad...? But it doesn't increment everything else.
402    
403      #      #
# Line 300  Line 425 
425  #       }  #       }
426    
427          $base_line = $head_end_line;          $base_line = $head_end_line;
428          splice( @$html, $base_line, 0, "<BASE href=\"$base_url/\">\n" );          #
429            # RDO 2005-1006. Remove this so proxying works better.
430            #
431    #        splice( @$html, $base_line, 0, "<BASE href=\"$base_url/\">\n" );
432      }      }
433    
434      #      #
# Line 350  Line 478 
478      #  Figure out where to insert The SEED tail.  Before </body>,      #  Figure out where to insert The SEED tail.  Before </body>,
479      #  or before </html>, or at end of page.      #  or before </html>, or at end of page.
480      #      #
   
481      my @tags = ();      my @tags = ();
482        # Check for a tracing queue.
483        my $traceString = QTrace("HTML");
484        if ($traceString) {
485            push @tags, $traceString;
486        }
487      for ($i=0; ($i < @$html) && ($html->[$i] !~ /\<\/body\>/i); $i++) {}      for ($i=0; ($i < @$html) && ($html->[$i] !~ /\<\/body\>/i); $i++) {}
488      if ($i >= @$html)        # </body> not found; look for </html>      if ($i >= @$html)        # </body> not found; look for </html>
489      {      {
# Line 374  Line 505 
505          splice( @$html, $i, 0, @tags );          splice( @$html, $i, 0, @tags );
506      }      }
507    
508      # RAE the chomp will return any new lines at the ends of elements in the array, and then we can join  with a "\n"      # RAE the chomp will return any new lines at the ends of elements in the array,
509      # this is because somethings put newlines in, and others don't. This should make nicer looking html      # and then we can join  with a "\n". This is because somethings put newlines in,
510        # and others don't. This should make nicer looking html
511        #
512      #chomp(@$html);      #chomp(@$html);
513      #print join "\n", @$html;      #print join "\n", @$html;
514        #
515      # Apparently the above still breaks things. This is the correct code:      # Apparently the above still breaks things. This is the correct code:
516      print @$html;  
517        foreach $_ (@$html)
518        {
519            print $_;
520  }  }
521    
522    }
523    
524    
525    =head1 make_table
526    
527    The main method to convert an array into a table.
528    
529    The col_hdrs are set to the <th> headers, the $tab is an array of arrays. The first is the rows, and the second is the columns. The title is the title of the table.
530    
531    The options define the settings for the table such as border, width, and class for css formatting. If the option "excelfile" is set to a filename that will be created in FIG_Config::temp, and the link included that allows the user to download the file as an excel file.
532    
533    =cut
534    
535  sub make_table {  sub make_table {
536      my($col_hdrs,$tab,$title, %options ) = @_;      my($col_hdrs,$tab,$title, %options ) = @_;
537      my(@tab);      my(@tab);
538    
539      my $border = defined $options{border} ? "border=\"$options{border}\"" : "border";      my $border = defined $options{border} ? "border=\"$options{border}\"" : "border";
540      push( @tab, "\n<table $border>\n",      my $width = defined $options{width} ? "width=\"$options{width}\"" : undef;
541        my $class = defined $options{class} ? "class=\"$options{class}\"" : undef;
542        push( @tab, "\n<table $border $width $class>\n",
543                  "\t<caption><b>$title</b></caption>\n",                  "\t<caption><b>$title</b></caption>\n",
544                  "\t<tr>\n\t\t"                  "\t<tr>\n\t\t"
545                . join( "\n", map { &expand($_, "th") } @$col_hdrs )                . join( "\n", map { &expand($_, "th") } @$col_hdrs )
# Line 405  Line 556 
556              );              );
557      }      }
558      push(@tab,"</table>\n");      push(@tab,"</table>\n");
559    
560        # excelfile should be appropriate for a filename (no spaces/special characters)
561        if (defined $options{"excelfile"}) {push @tab, $raelib->tab2excel($col_hdrs,$tab,$title,\%options,$options{"excelfile"})}
562    
563      return join("",@tab);      return join("",@tab);
564  }  }
565    
566    sub abstract_coupling_table {
567        my($cgi,$prot,$coupling) = @_;
568        my %fc;
569    
570        my $col_hdrs = ["coupled to","Score","Type of Coupling", "Type-specific Data"];
571        my $tab = [];
572        my %by_peg;
573        foreach my $x (@$coupling)
574        {
575            my($peg2,$psc,$type,$extra) = @$x;
576            if (($type !~ /^[ID]FC$/) || (! $fc{$peg2}))
577            {
578                if ($type =~  /^[ID]FC$/)
579                {
580                    $fc{$peg2} = 1;
581                }
582    
583                $by_peg{$peg2} += $psc;
584            }
585        }
586    
587        foreach my $x (sort { ($by_peg{$b->[0]} <=> $by_peg{$a->[0]})
588                              or ($a->[0] cmp $b->[0])
589                              or ($b->[1] <=> $a->[1])
590                              or ($a->[2] cmp $b->[2]) } @$coupling)
591        {
592            my($peg2,$psc,$type,$extra) = @$x;
593            push(@$tab,[&fid_link($cgi,$peg2,1),$psc,$type,&set_prot_links($cgi,join(", ",@$extra))]);
594        }
595    
596    
597         my $help = "<a href=\"Html/abstract_coupling.html\" target=\"SEED_or_SPROUT_help\">for help</a>";
598    #    my @html = &make_table($col_hdrs,$tab,"Abstract Coupling Data for $prot");
599    #    push(@html,"<hr>\n",$cgi->h3($help),"<br>");
600    #    return @html;
601    
602        return &make_table($col_hdrs,$tab,"Abstract Coupling Data for $prot [$help]");
603    }
604    
605  sub expand {  sub expand {
606      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
607      my($x, $tag) = @_;      my($x, $tag) = @_;
608    
609      $tag = "td" unless $tag;      $tag = "td" unless $tag;
610      my $endtag=$tag;      my $endtag=$tag;
611      # RAE modified this so that you can pass in a reference to an array where the first element is the data to  
612      # display and the second element is optional things like colspan and align. Note that in this case you need to include the td      # RAE modified this so that you can pass in a reference to an array where
613        # the first element is the data to display and the second element is optional
614        # things like colspan and align. Note that in this case you need to include the td
615      # use something like ["some data to appear", "td colspan=4 bgcolor=gray"]      # use something like ["some data to appear", "td colspan=4 bgcolor=gray"]
616      if (ref($x) eq "ARRAY") {($x, $tag)=@$x; if ($tag =~ /td/) {$endtag = "td"}}  
617        # per GJO's request modified this line so it can take any tag.
618        if ( ref($x) eq "ARRAY" ) { ($x, $tag) = @$x; $tag =~ /^(\S+)/; $endtag = $1 }
619    
620      if ($x =~ /^\@([^:]+)\:(.*)$/)      if ($x =~ /^\@([^:]+)\:(.*)$/)
621      {      {
# Line 429  Line 627 
627      }      }
628  }  }
629    
630    
631    =head2 merge_table_rows()
632    
633    Merge table rows together. This will merge a table so that adjacent cells with the same content will only be shown once.
634    
635    Something like this:
636    
637        -----------------------
638        |    1     |    a     |
639        -----------------------
640        |    1     |    b     |
641        -----------------------
642        |    2     |    c     |
643        -----------------------
644        |    3     |    d     |
645        -----------------------
646        |    4     |    d     |
647        -----------------------
648        |    5     |    d     |
649        -----------------------
650    
651    Will become:
652    
653        -----------------------
654        |          |    a     |
655        |    1     |-----------
656        |          |    b     |
657        -----------------------
658        |    2     |    c     |
659        -----------------------
660        |    3     |          |
661        ------------          |
662        |    4     |    5     |
663        ------------          |
664        |    5     |          |
665        -----------------------
666    
667    
668    The method takes two arguments. The reference to the array that is the table ($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.
669    
670     $tab=&HTML::merge_table_rows($tab);
671    
672     or
673    
674     $skip=(1=>1, 3=>1, 5=>1);
675     $tab=&HTML::merge_table_rows($tab, $skip);  # will merge all columns except 1, 3 and 5. Note the first column in the table is #0
676    
677    
678    =cut
679    
680    
681    
682    
683    sub merge_table_rows {
684     # RAE:
685     # Experimental piece of code. We often want to have rows or columns were cells are merged. It just looks so much nicer
686     # this block should merge adjacent rows that have the same text in them.
687     # use like this:
688     #      $tab=&HTML::merge_table_rows($tab);
689     # before you do a make_table call
690    
691     my $self=shift if UNIVERSAL::isa($_[0],__PACKAGE__);
692     my ($tab, $skip)=@_;
693    
694     my $newtable;
695     my $lastrow;
696     my $rowspan;
697     my $refs;
698    
699     for (my $y=0; $y <= $#$tab; $y++) {
700     #$y is the row in the table;
701      for (my $x=0; $x <= $#{$tab->[$y]}; $x++) {
702       # this is the user definable columns not to merge
703       if ($skip->{$x})
704       {
705        $newtable->[$y]->[$x] = $tab->[$y]->[$x];
706        next;
707       }
708    
709       #$x is the column in the table
710       # if the column in the row we are looking at is the same as the column in the previous row, we don't add
711       # this cell to $newtable. Instead we increment the rowspan of the previous row by one
712    
713       # handle cells that are references to arrays
714       if (ref($tab->[$y]->[$x]) eq "ARRAY") {$refs->[$y]->[$x]=$tab->[$y]->[$x]->[1]; $tab->[$y]->[$x]=$tab->[$y]->[$x]->[0]}
715    
716       # now we go back through the table looking where to draw the merge line:
717       my $lasty=$y;
718       while ($lasty >= 0 && $tab->[$y]->[$x] eq $tab->[$lasty]->[$x]) {$lasty--}
719       $lasty++; # this is the last identical cell. If lasty==y it is the current cell, so we just save the data. Otherwise we increment the rowspan
720       if ($lasty == $y) {
721        # we always want to have something in rows that may otherwise be empty but should be there (see below)
722        unless ($tab->[$y]->[$x]) {$tab->[$y]->[$x]=" &nbsp; "}
723        $newtable->[$y]->[$x] = $tab->[$y]->[$x];
724       }
725       else {$rowspan->[$lasty]->[$x]++}
726      }
727     }
728    
729     # now just join everything back together
730     for (my $y=0; $y <= $#$tab; $y++) {
731      for (my $x=0; $x <= $#{$tab->[$y]}; $x++) {
732       if ($rowspan->[$y]->[$x]) {
733        if ($refs->[$y]->[$x]) {$refs->[$y]->[$x] .= " rowspan=". ($rowspan->[$y]->[$x]+1)}
734        else {$refs->[$y]->[$x] = "td rowspan=". ($rowspan->[$y]->[$x]+1)}
735        $newtable->[$y]->[$x]=[$newtable->[$y]->[$x], $refs->[$y]->[$x]];
736       }
737       elsif ($newtable->[$y]->[$x] && $refs->[$y]->[$x]) {
738        $newtable->[$y]->[$x]=[$newtable->[$y]->[$x], $refs->[$y]->[$x]];
739       }
740      }
741     }
742    
743    
744     # finally we have to remove any completely empty cells that have been added by the array mechanism
745     # (e.g. if you define $a->[2] then $a->[0] and $a->[1] are now undef).
746     # that is why in the loop above I replace empty cells with nbsp. They are now not undef!
747     # I am sure that Gary can do this in one line, but I am hacking.
748     my @trimmed;
749     foreach my $a (@$newtable) {
750      my @row;
751      foreach my $b (@$a) {
752       push @row, $b if ($b);
753      }
754      push @trimmed, \@row;
755     }
756    
757     return \@trimmed;
758    }
759    
760    
761    
762    
763  sub set_ec_links {  sub set_ec_links {
764      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
765      my($cgi,$x) = @_;      my($cgi,$x) = @_;
# Line 479  Line 810 
810      my($cgi,$fid,$local,$just_url) = @_;      my($cgi,$fid,$local,$just_url) = @_;
811      my($n);      my($n);
812    
813        my $top = top_link();
814    
815      if ($fid =~ /^fig\|\d+\.\d+\.([a-z]+)\.(\d+)/)      if ($fid =~ /^fig\|\d+\.\d+\.([a-z]+)\.(\d+)/)
816      {      {
817          if ($local)          if ($local)
# Line 496  Line 829 
829          {          {
830              $n = $fid;              $n = $fid;
831          }          }
832          if ($1 ne "peg") { return $n }  
833            my $link;
834            my $new_framework = $cgi->param('new_framework') ? 1 : 0;
835            #added to format prophage and path island links to feature.cgi
836            if ($1 ne "peg")
837            {
838               my $user = $cgi->param('user');
839               if (! $user) { $user = "" }
840               my $sprout = $cgi->param('SPROUT') ? "&SPROUT=1" : "";
841               $link = "$top/feature.cgi?feature=$fid&user=$user$trans$sprout";
842               $link =~ s/[a-z_A-Z0-9]+\.cgi\?/feature.cgi?/;
843            }
844            else
845            {
846          my $user = $cgi->param('user');          my $user = $cgi->param('user');
847          if (! $user) { $user = "" }          if (! $user) { $user = "" }
848          my $trans = $cgi->param('translate') ? "&translate=1" : "";          my $trans = $cgi->param('translate') ? "&translate=1" : "";
849          my $sprout = $cgi->param('SPROUT') ? "&SPROUT=1" : "";          my $sprout = $cgi->param('SPROUT') ? "&SPROUT=1" : "";
850          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,;  
851    
852    ### This used to be
853    ###     my $link = &FIG::cgi_url . "/protein.cgi?prot=$fid&user=$user$trans$sprout";
854    ###
855    ### The cost became prohibitive in the subsystem spreadsheets.  Hence, we cache the value
856    ###
857    ### RAO
858    
859                #if (! $cgi_url) { $cgi_url = &FIG::cgi_url }
860                #$link = $cgi_url . "/protein.cgi?prot=$fid&user=$user$trans$sprout";
861                $link = "$top/protein.cgi?prot=$fid&user=$user$trans$sprout\&new_framework=$new_framework";
862                $link =~ s/[a-z_A-Z0-9]+\.cgi\?/protein.cgi?/;
863            }
864          if ($just_url)          if ($just_url)
865          {          {
866              return $link;              return $link;
867          }          }
868          else          else
869          {          {
870              return "<a href=$link>$n</a>";              return "<a href='$link'>$n</a>";
871          }          }
872      }      }
873      return $fid;      return $fid;
# Line 527  Line 880 
880      return $family;      return $family;
881  }  }
882    
 use URI::Escape;  
883    
884  sub get_html {  sub get_html {
885      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
# Line 547  Line 899 
899          my $response = $ua->request($request);          my $response = $ua->request($request);
900          $out = $response->content;          $out = $response->content;
901      }      }
902      else  
903        if ($type =~/get/i)
904      {      {
905          @args = ();          @args = ();
906          foreach $x (@$kv_pairs)          foreach $x (@$kv_pairs)
# Line 644  Line 997 
997          $after = $3;          $after = $3;
998          return &set_prot_links($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,$after);
999      }      }
1000      elsif ($x =~ /^(.*)\b([NXYZA]P_[0-9\.]+)\b(.*)/s)      elsif ($x =~ /^(.*)\b([NXYZA][PM]_[0-9\.]+)\b(.*)/s)
1001      {      {
1002          $before = $1;          $before = $1;
1003          $match = $2;          $match = $2;
# Line 658  Line 1011 
1011          $after = $3;          $after = $3;
1012          return &set_prot_links($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,$after);
1013      }      }
1014        elsif ($x =~ /^(.*)(tigr\|\w+)(.*)/s)
1015        {
1016            $before = $1;
1017            $match = $2;
1018            $after = $3;
1019            return &set_prot_links($cgi,$before) . &HTML::tigr_link($cgi,$match) . &set_prot_links($cgi,$after);
1020        }
1021        elsif ($x =~ /^(.*)\b(eric\|\S+)\b(.*)/s)
1022        {
1023            $before = $1;
1024            $match = $2;
1025            $after = $3;
1026            return &set_prot_links($cgi,$before) . &HTML::eric_link($cgi,$match) . &set_prot_links($cgi,$after);
1027        }
1028    
1029        elsif ($x =~ /^(.*)\b(bhb\|.*?)\b(.*)/s)
1030        {
1031            $before = $1;
1032            $match = $2;
1033            $after = $3;
1034            return &set_prot_links($cgi,$before) . &HTML::bhb_link($cgi,$match) . &set_prot_links($cgi,$after);
1035        }
1036    
1037        elsif ($x =~ /^(.*)\b(apidb\|[0-9\.a-z_]+)\b(.*)/s)
1038        {
1039            $before = $1;
1040            $match = $2;
1041            $after = $3;
1042            return &set_prot_links($cgi,$before) . &HTML::apidb_link($cgi,$match) . &set_prot_links($cgi,$after);
1043        }
1044    
1045        elsif ($x =~ /^(.*)\b(patric\|.*?)\b(.*)/s)
1046        {
1047            $before = $1;
1048            $match = $2;
1049            $after = $3;
1050            return &set_prot_links($cgi,$before) . &HTML::patric_link($cgi,$match) . &set_prot_links($cgi,$after);
1051        }
1052    
1053        elsif ($x =~ /^(.*)\b(vbrc\|.*?)\b(.*)/s)
1054        {
1055            $before = $1;
1056            $match = $2;
1057            $after = $3;
1058            return &set_prot_links($cgi,$before) . &HTML::vbrc_link($cgi,$match) . &set_prot_links($cgi,$after);
1059        }
1060    
1061        elsif ($x =~ /^(.*)\b(vectorbase\|.*?)\b(.*)/s)
1062        {
1063            $before = $1;
1064            $match = $2;
1065            $after = $3;
1066            return &set_prot_links($cgi,$before) . &HTML::vectorbase_link($cgi,$match) . &set_prot_links($cgi,$after);
1067        }
1068      elsif ($x =~  /^(.*)(uni\|[A-Z0-9]{6})(.*)/s)      elsif ($x =~  /^(.*)(uni\|[A-Z0-9]{6})(.*)/s)
1069      {      {
1070          $before = $1;          $before = $1;
# Line 686  Line 1093 
1093          $after = $3;          $after = $3;
1094          return &set_prot_links($cgi,$before) . &HTML::kegg_link($cgi,$match) . &set_prot_links($cgi,$after);          return &set_prot_links($cgi,$before) . &HTML::kegg_link($cgi,$match) . &set_prot_links($cgi,$after);
1095      }      }
1096        elsif ($x =~ /^(.*)(Ensembl[a-zA-Z]+:[a-zA-Z_0-9\.]+)(.*)/s)
1097        {
1098            $before = $1;
1099            $match = $2;
1100            $after = $3;
1101            return &set_prot_links($cgi,$before) . &HTML::ensembl_link($cgi,$match) . &set_prot_links($cgi,$after);
1102        }
1103        elsif ($x =~ /^(.*)(EntrezGene:[a-zA-Z_0-9\.]+)(.*)/s)
1104        {
1105            $before = $1;
1106            $match = $2;
1107            $after = $3;
1108            return &set_prot_links($cgi,$before) . &HTML::entrezgene_link($cgi,$match) . &set_prot_links($cgi,$after);
1109        }
1110        elsif ($x =~ /^(.*)(MIM:[a-zA-Z_0-9\.]+)(.*)/s)
1111        {
1112            $before = $1;
1113            $match = $2;
1114            $after = $3;
1115            return &set_prot_links($cgi,$before) . &HTML::mim_link($cgi,$match) . &set_prot_links($cgi,$after);
1116        }
1117        elsif ($x =~ /^(.*)(HGNC:[a-zA-Z_0-9\.]+)(.*)/s)
1118        {
1119            $before = $1;
1120            $match = $2;
1121            $after = $3;
1122            return &set_prot_links($cgi,$before) . &HTML::hgnc_link($cgi,$match) . &set_prot_links($cgi,$after);
1123        }
1124        elsif ($x =~ /^(.*)(UniGene:[a-zA-Z_0-9\.]+)(.*)/s)
1125        {
1126            $before = $1;
1127            $match = $2;
1128            $after = $3;
1129            return &set_prot_links($cgi,$before) . &HTML::unigene_link($cgi,$match) . &set_prot_links($cgi,$after);
1130        }
1131    # IPI stopped working. turn off for now.
1132    #    elsif ($x =~ /^(.*)(IPI:[a-zA-Z_0-9\.]+)(.*)/s)
1133    #    {
1134    #        $before = $1;
1135    #        $match = $2;
1136    #        $after = $3;
1137    #        return &set_prot_links($cgi,$before) . &HTML::ipi_link($cgi,$match) . &set_prot_links($cgi,$after);
1138    #    }
1139        elsif ($x =~ /^(.*)(WP:[a-zA-Z_0-9\.]+)(.*)/s)
1140        {
1141            #wormbase
1142    
1143            $before = $1;
1144            $match = $2;
1145            $after = $3;
1146            return &set_prot_links($cgi,$before) . &HTML::wp_link($cgi,$match) . &set_prot_links($cgi,$after);
1147        }
1148        elsif ($x =~ /^(.*)(FB:[a-zA-Z_0-9\.]+)(.*)/s)
1149        {
1150            #flybase
1151    
1152            $before = $1;
1153            $match = $2;
1154            $after = $3;
1155            return &set_prot_links($cgi,$before) . &HTML::fb_link($cgi,$match) . &set_prot_links($cgi,$after);
1156        }
1157        elsif ($x =~ /^(.*)(FlyBaseORFNames:[a-zA-Z_0-9\.]+)(.*)/s)
1158        {
1159            #flybase
1160    
1161            $before = $1;
1162            $match = $2;
1163            $after = $3;
1164            return &set_prot_links($cgi,$before) . &HTML::fborf_link($cgi,$match) . &set_prot_links($cgi,$after);
1165        }
1166        elsif ($x =~ /^(.*)(SGD_LOCUS:[a-zA-Z_0-9\.]+)(.*)/s)
1167        {
1168            #flybase
1169    
1170            $before = $1;
1171            $match = $2;
1172            $after = $3;
1173            return &set_prot_links($cgi,$before) . &HTML::sgd_link($cgi,$match) . &set_prot_links($cgi,$after);
1174        }
1175      return $x;      return $x;
1176  }  }
1177    
# Line 697  Line 1183 
1183      {      {
1184          return "<a href=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=protein&cmd=search&term=$id>$id</a>";          return "<a href=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=protein&cmd=search&term=$id>$id</a>";
1185      }      }
1186        elsif ($id =~ /^[NXYZA]M_/)
1187        {
1188            return "<a href=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=nuccore&cmd=search&term=$id>$id</a>";
1189        }
1190  }  }
1191    
1192  sub gi_link {  sub gi_link {
# Line 710  Line 1200 
1200      return $gi;      return $gi;
1201  }  }
1202    
1203    sub tigr_link {
1204        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1205        my($cgi,$tigr) = @_;
1206    
1207        if ($tigr =~ /^tigr\|(NT|ntbp|ntbpA|BA|BMAA|BXB|GBA)(\w+)$/)
1208        {
1209            my $id=$1.$2;
1210            return "<a href=\"http://pathema.tigr.org/tigr-scripts/pathema/shared/GenePage.cgi?locus=$id\">$tigr</a> (Pathema)";
1211        }
1212        elsif ($tigr =~ /^tigr\|(\S+)$/)
1213        {
1214            return "<a href=\"http://www.tigr.org/tigr-scripts/CMR2/GenePage.spl?locus=$1\">$tigr</a>";
1215        }
1216        return $tigr;
1217    }
1218    
1219    sub eric_link {
1220        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1221        my($cgi,$eric) = @_;
1222    
1223        if ($eric =~ /^eric\|(\S+)/)
1224        {
1225            return "<a href=\"https://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=$1\">$eric</a>";
1226        }
1227        return $eric;
1228    }
1229    
1230    sub bhb_link {
1231        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1232        my($cgi,$bhb) = @_;
1233    
1234        return "<a href=\"http://www.biohealthbase.org\">$bhb</a>";
1235    }
1236    
1237    sub apidb_link {
1238        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1239        my($cgi,$api) = @_;
1240    
1241        if ($api =~ /apidb\|(.*?)\.(.*)$/)
1242        {
1243            return "<a href=\"http://www.apidb.org/cgi-bin/redirect.cgi?taxon_id=$1&source_id=$2\">$api</a>";
1244        }
1245        return $api;
1246    }
1247    
1248    sub patric_link {
1249        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1250        my($cgi,$patric) = @_;
1251    
1252        if ($patric =~ /patric\|(.*)/)
1253        {
1254            return "<a href=\"https://patric.vbi.vt.edu/software/curationTool/gep/pgiCuration.php?locus_name=$1\">$patric</a>";
1255        }
1256        return $patric;
1257    }
1258    
1259    sub vbrc_link {
1260        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1261        my($cgi,$vbrc) = @_;
1262    
1263        if ($vbrc =~ /vbrc\|(.*)/)
1264        {
1265            return "<a href=\"http://www.biovirus.org/gene_detail.asp?name=$1\">$vbrc</a>";
1266        }
1267        return $vbrc;
1268    }
1269    
1270    sub vectorbase_link {
1271        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1272        my($cgi,$vec) = @_;
1273        return "<a href=\"http://www.vectorbase.org\">$vec</a>";
1274    }
1275    
1276    
1277  sub uni_link {  sub uni_link {
1278      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1279      my($cgi,$uni) = @_;      my($cgi,$uni) = @_;
1280    
1281      if ($uni =~ /^uni\|(\S+)$/)      if ($uni =~ /^uni\|(\S+)$/)
1282      {      {
1283          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>";
1284            return "<a href='http://www.ebi.uniprot.org/uniprot-srv/uniProtView.do?proteinAc=$1'>$uni</a>";
1285      }      }
1286      return $uni;      return $uni;
1287  }  }
# Line 754  Line 1319 
1319      return $kegg;      return $kegg;
1320  }  }
1321    
1322    sub ensembl_link {
1323        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1324        my($cgi,$ensembl) = @_;
1325    
1326        if ($ensembl =~ /^(\S+):(\S+)$/)
1327        {
1328            my $what=$1;
1329            my $key=$2;
1330            my $idx="All";
1331            if ($what eq "EnsemblGene") { $idx = "Gene" }
1332            if ($what eq "EnsemblTranscript") { $idx = "All" }
1333            if ($what eq "EnsemblProtein") { $idx = "All" }
1334    
1335            #I really want to get right to the transcript and peptide pages, but
1336            #can't see how to do that without knowing the org name too, which
1337            #I don't know at this point. (ensembl org name, not real org name)
1338    
1339            return "<a href=http://www.ensembl.org/Homo_sapiens/searchview?species=all&idx=$idx&q=$key>$ensembl</a>";
1340        }
1341        return $ensembl;
1342    }
1343    
1344    sub entrezgene_link {
1345        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1346        my($cgi,$entrezgene) = @_;
1347    
1348        if ($entrezgene =~ /^EntrezGene:(\S+)$/)
1349        {
1350            return "<a href=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=full_report&list_uids=$1>$entrezgene</a>";
1351        }
1352        return $entrezgene;
1353    }
1354    
1355    sub mim_link {
1356        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1357        my($cgi,$mim) = @_;
1358    
1359        if ($mim =~ /^MIM:(\S+)$/)
1360        {
1361            return "<a href=http://www3.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=$1>$mim</a>";
1362        }
1363        return $mim;
1364    }
1365    
1366    sub hgnc_link {
1367        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1368        my($cgi,$hgnc) = @_;
1369    
1370        if ($hgnc =~ /^HGNC:(\S+)$/)
1371        {
1372            return "<a href=http://www.gene.ucl.ac.uk/cgi-bin/nomenclature/searchgenes.pl?field=symbol&anchor=equals&match=$1&symbol_search=Search&number=50&format=html&sortby=symbol>$hgnc</a>";
1373        }
1374        return $mim;
1375    }
1376    
1377    sub unigene_link {
1378        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1379        my($cgi,$unigene) = @_;
1380    
1381        if ($unigene =~ /^UniGene:(\S+)$/)
1382        {
1383            return "<a href=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unigene&cmd=search&term=$1>$unigene</a>";
1384        }
1385        return $unigene;
1386    }
1387    
1388    sub ipi_link {
1389        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1390        my($cgi,$ipi) = @_;
1391    
1392        if ($ipi =~ /^IPI:(\S+)$/)
1393        {
1394            return "<a href=http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-id+AEoS1R8Jnn+-e+[IPI:\'$1\']+-qnum+1+-enum+1>$ipi</a>";
1395        }
1396        return $ipi;
1397    }
1398    
1399    sub wp_link {
1400        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1401        my($cgi,$wp) = @_;
1402    
1403        #wormbase
1404    
1405        if ($wp =~ /^WP:(\S+)$/)
1406        {
1407            return "<a href=http://www.wormbase.org/db/searches/basic?class=Any&query=$1&Search=Search>$wp</a>";
1408        }
1409        return $wp;
1410    }
1411    
1412    sub fb_link {
1413        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1414        my($cgi,$fb) = @_;
1415    
1416        #flybase
1417    
1418        if ($fb =~ /^FB:(\S+)$/)
1419        {
1420            return "<a href=http://flybase.bio.indiana.edu/.bin/fbidq.html?$1>$fb</a>";
1421        }
1422        return $fb;
1423    }
1424    
1425    sub fborf_link {
1426        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1427        my($cgi,$fb) = @_;
1428    
1429        #flybase
1430    
1431        if ($fb =~ /^FlyBaseORFNames:(\S+)$/)
1432        {
1433            return "<a href=http://flybase.bio.indiana.edu/.bin/fbidq.html?$1>$fb</a>";
1434        }
1435        return $fb;
1436    }
1437    
1438    sub sgd_link {
1439        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1440        my($cgi,$sgd) = @_;
1441    
1442        #yeast
1443    
1444        if ($sgd =~ /^SGD_LOCUS:(\S+)$/)
1445        {
1446            return "<a href=http://db.yeastgenome.org/cgi-bin/locus.pl?locus=$1>$sgd</a>";
1447        }
1448        return $sgd;
1449    }
1450    
1451    
1452    
1453    
1454  sub set_map_links {  sub set_map_links {
1455      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1456      my($cgi,$x) = @_;      my($cgi,$x) = @_;
# Line 771  Line 1468 
1468      return $x;      return $x;
1469  }  }
1470    
1471    
1472    
1473  sub map_link {  sub map_link {
1474      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1475      my($cgi,$map,$org) = @_;      my($cgi,$map,$org) = @_;
# Line 778  Line 1477 
1477      $user = $cgi->param('user');      $user = $cgi->param('user');
1478      $user = $user ? $user : "";      $user = $user ? $user : "";
1479      $org = $org ? $org : "";      $org = $org ? $org : "";
1480      my $url = "$FIG_Config::cgi_url/show_kegg_map.cgi?user=$user&map=$map&org=$org";  
1481        my $url = "show_kegg_map.cgi?user=$user&map=$map&org=$org";
1482    #rel    my $url = &FIG::cgi_url() . "/show_kegg_map.cgi?user=$user&map=$map&org=$org";
1483      my $link = "<a href=\"$url\">$map</a>";      my $link = "<a href=\"$url\">$map</a>";
1484      return $link;      return $link;
1485  }  }
1486    
 sub javascript {  
     shift if UNIVERSAL::isa($_[0],__PACKAGE__);  
         #### MODIFIED BY RAE TO ADD JAVA SUPPORT FOR CHECK ALL/UNCHECK ALL  
         # This routine takes three arguments, $html, $form, and $button  
         # $html is the ref to the array with the html in it  
         # $form is the name of the form. This must be added whenever start_form is called  
         # by including a -name entry. This is only used for the javascript  
         # $button is the name of the button that should be checked/unchecked.  
         #  
         # 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.  
   
         # Note that the other change is I added a -name=>'fig_checked' to the start_form  
         # field. The name is needed for the java script.  
         #  
   
           $java_script=<<EOF;  
   <SCRIPT LANGUAGE="JavaScript">  
   <!-- Begin  
   function checkAll(field)  
   {  
    for (i = 0; i < field.length; i++)  
    field[i].checked = true ;  
   }  
   
   function checkFirst(field)  
   {  
    for (i = 0; i < field.length/2; i++)  
    field[i].checked = true;  
   }  
   
   function checkSecond(field)  
   {  
    for (i=Math.round(field.length/2); i < field.length; i++)  
    field[i].checked = true ;  
   }  
   
   function uncheckAll(field)  
   {  
    for (i = 0; i < field.length; i++)  
    field[i].checked = false ;  
   }  
   //  End -->  
   </script>  
 EOF  
         return $java_script;  
 }  
   
1487  sub java_buttons {  sub java_buttons {
1488      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1489    ## ADDED BY RAE    ## ADDED BY RAE
# Line 856  Line 1506 
1506      my($sub_link);      my($sub_link);
1507    
1508      my $user = $cgi->param('user');      my $user = $cgi->param('user');
1509        my $esc_sub = uri_escape( $sub );
1510        $sub =~ s/\_/ /g;
1511      if ($user)      if ($user)
1512      {      {
1513          $sub_link = "<a href=./subsys.cgi?ssa_name=$sub&request=show_ssa&user=$user>$sub</a>";          $sub_link = "<a href=./subsys.cgi?ssa_name=$esc_sub&request=show_ssa&user=$user>$sub</a>";
1514      }      }
1515      else      else
1516      {      {
1517          $sub_link = $sub;          $sub_link = "<a href=\"display_subsys.cgi?ssa_name=$esc_sub&request=show_ssa&sort=by_phylo\">$sub</a>";
1518      }      }
1519      return $sub_link;      return $sub_link;
1520  }  }
1521    
1522  1  sub reaction_link {
1523        my($reaction) = @_;
1524    
1525        if ($reaction =~ /^R\d+/)
1526        {
1527            return "<a href=\"http://www.genome.ad.jp/dbget-bin/www_bget?rn+$reaction\" target=reaction$$>$reaction</a>";
1528        }
1529        return $reaction;
1530    }
1531    
1532    sub html_for_assignments {
1533        my($fig,$user,$peg_sets) = @_;
1534        my $i;
1535    
1536        my @vals = ();
1537        my $set = 1;
1538        foreach $peg_set (@$peg_sets)
1539        {
1540            for ($i=0; ($i < @$peg_set); $i++)
1541            {
1542                $peg = $peg_set->[$i];
1543                push(@vals,'show=' . join("@",($set,$i+1,$peg,&FIG::abbrev($fig->org_of($peg)),"")));
1544            }
1545            $set++;
1546        }
1547    
1548        $ENV{'REQUEST_METHOD'} = 'GET';
1549        $ENV{'QUERY_STRING'} = join('&',('request=show_commentary',"uni=1","user=$user",@vals));
1550        my $out = join("",`$FIG_Config::fig/CGI/chromosomal_clusters.cgi`);
1551        $out =~ s/^.*?<form/<form/si;
1552        $out =~ s/^(.*)<table.*/$1/si;
1553        return $out;
1554    }
1555    
1556    =head1 rss_feed
1557    
1558    Add something to the RSS feed. The rss feeds are stored in the Html directory, and there are several RSS feeds:
1559            SEED.rss                - everything gets written here
1560            SEEDgenomes.rss                 - whenever a genome is added to the SEED
1561            SEEDsubsystems.rss      - whenever a subsystem is edited (or should this be added?)
1562    
1563    
1564    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.
1565    
1566    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.
1567    
1568    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.
1569    
1570    The has can have these keys:
1571    
1572    REQUIRED:
1573    title       : the title. This is usually what is seen by the user in the pull down menu
1574    description : a more complete description that is often seen is rss viewers but not always
1575    link        : link to the item that was added/edited
1576    All other keys are treated as optional RSS arguments and written to the file.
1577    
1578    At most, $max_entries recent entries are stored in the rss file, and this is currently 50.
1579    
1580    RSS files are quite simple, and contain some standard header information, and then individual items surrounded by an <item> </item> tag. Note that there is also an initial title/description/link set that describes the file.
1581    
1582    
1583    =cut
1584    
1585    sub rss_feed {
1586     shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1587     my ($files, $args)=@_;
1588    
1589     # how many entries to store in the file
1590     my $max_entries=50;
1591    
1592     foreach my $a (keys %$args) {if ($a =~ /^-(.*)/) {my $b=$1; $args->{$b}=$args->{$a}; delete $args->{$a}}}
1593    
1594     my $filepath=$FIG_Config::fig."/CGI/Html/rss";
1595     # check for the directory and if not, make it
1596     mkdir $filepath unless (-d $filepath);
1597    
1598     # note that $info is a hash of references to hashes that are written out as headers in the file
1599     my $info=
1600     {
1601      "SEED.rss" =>
1602       {
1603            title           => "The SEED",
1604            description     => "Latest news from the SEED",
1605            link            => "Html/rss/SEED.rss",
1606       },
1607    
1608      "SEEDsubsystems.rss" =>
1609      {
1610            title           => "SEED Subsystems",
1611            description     => "Recently updated SEED subsystems",
1612            link            => "Html/rss/SEEDsubsystems.rss",
1613      },
1614    
1615      "SEEDsubsystems.rss" =>
1616      {
1617            title           => "SEED Genomes",
1618            description     => "Genomes recently added to the SEED",
1619            link            => &FIG::cgi_url()."/Html/rss/SEEDsubsystems.rss",
1620      },
1621    
1622     };
1623    
1624    
1625     # build the new xml
1626     my $xml = "\t<item>\n";
1627     foreach my $qw ("title", "description", "link") {
1628      unless ($args->{$qw}) {
1629       print STDERR "You need to include a $qw tag in your RSS description\n";
1630       return(0);
1631      }
1632      # we need to do something a bit funky with the link. We can't have ampersands in the <link> </link> in valid html
1633      # so we are going to pull out the links and uri_escape just the part after the .cgi
1634      if ($qw eq "link")
1635      {
1636       $args->{$qw} =~ /^(.*?\.cgi.)(.*)$/;
1637       $args->{$qw} = $1.uri_escape($2) if ($1 && $2);
1638      }
1639    
1640      $xml .= "\t\t<$qw>".$args->{$qw}."</$qw>\n";
1641      delete $args->{$qw};
1642     }
1643    
1644     foreach my $tag (grep {!/type/i} keys %$args)
1645     {
1646      $xml .= "\t\t<$tag>".$args->{$tag}."</$tag>\n";
1647     }
1648    
1649     $xml .= "\t</item>\n";
1650    
1651    
1652     my @files=("SEED.rss");
1653     if ($args->{"type"}) {push @files, "SEED.$type.rss"}
1654    
1655     foreach my $file ("SEED.rss", @$files)
1656     {
1657      if (-e "$filepath/$file")
1658      {
1659       my @out; # the new content of the file
1660       my $itemcount=0; # how many <item> </item>'s are we keeping
1661       my $initem; # are we in an item?
1662       open(IN, "$filepath/$file") || die "Can't open $filepath/$file";
1663       while (<IN>)
1664       {
1665        if (/\<item\>/) {
1666         push @out, $xml, unless ($itemcount);
1667         $itemcount++;
1668         $initem=1;
1669        }
1670        if (/\<\/item\>/) {$initem=0; next if ($itemcount > $max_entries)}
1671        next if ($initem && $itemcount > $max_entries);
1672        push @out, $_;
1673       }
1674       close IN;
1675       open(OUT, ">$filepath/$file") || die "Can't open $filepath/$file for writing";
1676       print OUT @out;
1677      }
1678      else
1679      {
1680       open(OUT, ">$filepath/$file") || die "Can't open $filepath/$file for writing";
1681       print OUT "<?xml version=\"1.0\"?>\n<rss version=\"2.0\">\n<channel>\n";
1682       if ($info->{$file})
1683       {
1684         # we're going to sanity check each of the three options we output, just to be sure
1685         foreach my $qw ("title", "description", "link")
1686         {
1687           if ($info->{$file}->{$qw})
1688           {
1689              print OUT "<$qw>", $info->{$file}->{$qw}, "</$qw>\n";
1690           } else {
1691              print STDERR "Please add a $qw for $file\n"; print OUT "<$qw>$file</$qw>\n";
1692           }
1693         }
1694       }
1695       else {
1696        print STDERR "Please define title, link, and description information for $file\n";
1697        print OUT "<title>$file</title>\n<description>An RSS feed</description>\n<link>", &FIG::cgi_url, "</link>\n";
1698       }
1699       print OUT "\n", $xml;
1700       print OUT "\n", "</channel>\n</rss>\n"
1701      }
1702     }
1703    }
1704    
1705    
1706    
1707    1;
1708    

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