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# Line 1  Line 1 
1    #
2    # Copyright (c) 2003-2006 University of Chicago and Fellowship
3    # for Interpretations of Genomes. All Rights Reserved.
4    #
5    # This file is part of the SEED Toolkit.
6    #
7    # The SEED Toolkit is free software. You can redistribute
8    # it and/or modify it under the terms of the SEED Toolkit
9    # Public License.
10    #
11    # You should have received a copy of the SEED Toolkit Public License
12    # along with this program; if not write to the University of Chicago
13    # at info@ci.uchicago.edu or the Fellowship for Interpretation of
14    # Genomes at veronika@thefig.info or download a copy from
15    # http://www.theseed.org/LICENSE.TXT.
16    #
17    
18  package HTML;  package HTML;
19    
20    use strict;
21    use Tracer;
22    use FIG;
23  use Carp;  use Carp;
24  use Data::Dumper;  use Data::Dumper;
25  use LWP::UserAgent;  use LWP::UserAgent;
26  use LWP::Simple;  use LWP::Simple;
27    use URI::Escape;  # uri_escape()
28  use URI::URL;  use URI::URL;
29  use HTTP::Request::Common;  use HTTP::Request::Common;
30    use POSIX;
31    
32    #use raelib; # now used for the excel function, that should eventually end up in here. Way too experimental!
33    my $raelib;
34    
35    
36    my $top_link_cache;
37    
38    
39    sub new
40    {
41        my($class) = @_;
42    
43        my $self = {};
44    
45        return bless $self, $class;
46    }
47    
48    sub top_link
49    {
50    
51        #
52        # Determine if this is a toplevel cgi or one in one of the subdirs (currently
53        # just /p2p).
54        #
55    
56        return $top_link_cache if ($top_link_cache);
57    
58        my @parts = split(/\//, $ENV{SCRIPT_NAME});
59        my $top;
60        if (defined $parts[-2] && $parts[-2] eq 'FIG')
61        {
62            $top = '.';
63    #       warn "toplevel @parts\n";
64        }
65        elsif (defined $parts[-3] && $parts[-3] eq 'FIG')
66        {
67            $top = '..';
68    #       warn "subdir @parts\n";
69        }
70        else
71        {
72            $top = $FIG_Config::cgi_base;
73    #       warn "other @parts\n";
74        }
75    
76        $top_link_cache = $top;
77        return $top;
78    }
79    
80    sub compute_html_header
81    {
82        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
83        my($additional_insert, $user, %options ) = @_;
84    
85        local $/ = "\n";
86    
87        my $header_name = $options{header_name} ? $options{header_name} : "html.hdr";
88        my $tail_name = $options{tail_name} ? $options{tail_name} : "html.tail";
89    
90        my $html_hdr_file = "./Html/$header_name";
91        if (! -f $html_hdr_file)
92        {
93            $html_hdr_file = "$FIG_Config::fig/CGI/Html/$header_name";
94        }
95        my @html_hdr = &FIG::file_read($html_hdr_file);
96    
97        # for my $k (sort keys %ENV) { warn "$k = $ENV{$k}\n"; }
98    
99        #
100        # Determine if this is a toplevel cgi or one in one of the subdirs (currently
101        # just /p2p).
102        #
103    
104        my @parts = split(/\//, $ENV{SCRIPT_NAME});
105        my $top;
106        if ($parts[-2] eq 'FIG')
107        {
108            $top = '.';
109    #       warn "toplevel @parts\n";
110        }
111        elsif ($parts[-3] eq 'FIG')
112        {
113            $top = '..';
114    #       warn "subdir @parts\n";
115        }
116        else
117        {
118            $top = $FIG_Config::cgi_base;
119    #       warn "other @parts\n";
120        }
121    
122        $options{no_fig_search} or push( @html_hdr, "<br><a href=\"$top/index.cgi?user=$user\">FIG search</a>\n" );
123    
124        if (@html_hdr)
125        {
126            my $insert_stuff;
127    
128            if (not $options{no_release_info})
129            {
130                my @ver = &FIG::file_head("$FIG_Config::fig_disk/CURRENT_RELEASE", 1);
131                my $ver = $ver[0];
132                chomp $ver;
133                if ($ver =~ /^cvs\.(\d+)$/)
134                {
135                    my $d = asctime(localtime($1));
136                    chomp($d);
137                    $ver .=  " ($d)";
138                }
139                my $host = &FIG::get_local_hostname();
140                $insert_stuff = "SEED version <b>$ver</b> on $host";
141            }
142    
143            if ($additional_insert)
144            {
145                $insert_stuff .= "<br>" . $additional_insert;
146            }
147    
148            for $_ (@html_hdr)
149            {
150                s,(href|img\s+src)="/FIG/,$1="$top/,g;
151                    s,(\?user\=)\",$1$user",;
152                if ($_ eq "<!-- HEADER_INSERT -->\n")
153                {
154                    $_ = $insert_stuff;
155                }
156            }
157        }
158    
159        return @html_hdr;
160    }
161    
162  sub show_page {  sub show_page {
163      my($cgi,$html,$no_home) = @_;      #warn "SHOWPAGE: cgi=", Dumper(@_);
164        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
165        my($cgi,$html,$no_home, $alt_header, $css, $javasrc, $cookie, $options) = @_;
166      my $i;      my $i;
167    
168        my $top = top_link();
169    
170        # ARGUMENTS:
171        #     $cgi is the CGI method
172        #     $html is an array with all the html in it. It is just joined by "\n" (and not <br> or <p>
173        #     $no_home eliminates ONLY the bottom FIG search link in a page
174        #     $alt_header is a reference to an array for an alternate header banner that you can replace the standard one with
175        #     $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
176        #               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
177        #               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
178        #     $javasrc is a reference to an array of URLs to javascripts to be included (e.g. "FIG/Html/css/styleswitcher.js")
179        #     $cookie is the name and value of the cookie to set. Note that you should probably use raelib->cookie to get/set your cookies
180        #     $options is a reference to a hash of options that you can pass around the pages
181      #      #
182      # Find the HTML header      # Find the HTML header
183      #      #
184    
185      my $html_hdr_file = "./Html/html.hdr";      my $tail_name = $options->{tail_name} ? $options->{tail_name} : "html.tail";
186      if (! -f $html_hdr_file)      my $html_tail_file = "./Html/$tail_name";
187        if (! -f $html_tail_file)
188      {      {
189          $html_hdr_file = "$FIG_Config::fig/CGI/Html/html.hdr";          $html_tail_file = "$FIG_Config::fig/CGI/Html/$tail_name";
190      }      }
191    
192      my $html_tail_file = "./Html/html.tail";      my $user = $cgi->param('user') || "";
193      if (! -f $html_tail_file)      my @html_hdr;
194        if ($alt_header && ref($alt_header) eq "ARRAY")
195        {
196           @html_hdr = @$alt_header;
197        }
198        else
199      {      {
200          $html_tail_file = "$FIG_Config::fig/CGI/Html/html.tail";          @html_hdr = compute_html_header(undef,$user,%$options);
201      }      }
202    
203        # RAE: I am offloading the handling of cookies to CGI.pm since I don't know how they are set up.
204        # This modification adds the cookies if necessary
205    
206      print $cgi->header;      # Note: 3/10/05 commented this line out pending the discussion of adding cookies into the seed that we are waiting to see about
207        # to add cookies back in replace these two header lines with each other
208    
209        #print $cgi->header(-cookie=>$cookie);
210        print $cgi->header();
211    
212      #      #
213      #  The SEED header file goes immediately after <BODY>.  Figure out      #  The SEED header file goes immediately after <BODY>.  Figure out
# Line 46  Line 225 
225                       meta     => 1,                       meta     => 1,
226                       nextid   => 1,                       nextid   => 1,
227                       style    => 1,                       style    => 1,
228                       title    => 1                       title    => 1,
229                     );                     );
230    
231      #      #
# Line 89  Line 268 
268          if ( $html->[$i] =~ /\<body[^0-9a-z]/i )          if ( $html->[$i] =~ /\<body[^0-9a-z]/i )
269          {          {
270              $body_line = $i;              $body_line = $i;
271              $last;              last;
272          }          }
273    
274          #  Now the general case.          #  Now the general case.
# Line 145  Line 324 
324      #      #
325      #  <BODY> goes after last head line      #  <BODY> goes after last head line
326      #      #
327        #  RAE:
328        #  Added the javascript for the buttons immediately after body.
329        #  Note if no buttons are added we still (at the moment) add the script,
330        #  but it only adds a little text (495 characters) to the html and noone will notice!
331        #  RAE: This is now deprecated because everything is in an external file, FIG.js, included later
332    
333      if ( $body_line < 0 )      if ( $body_line < 0 )
334      {      {
# Line 156  Line 340 
340      #  Seed page header (if it exists) goes after <BODY>      #  Seed page header (if it exists) goes after <BODY>
341      #      #
342    
343      if ( -f $html_hdr_file )      if (@html_hdr)
344      {      {
345          splice( @$html, $body_line + 1, 0, `cat $html_hdr_file` );          splice( @$html, $body_line + 1, 0, @html_hdr );
346      }      }
347    
348      #      #
# Line 171  Line 355 
355          splice( @$html, $body_line, 0, "</HEAD>\n" );          splice( @$html, $body_line, 0, "</HEAD>\n" );
356      }      }
357    
358        # RAE:
359        # Add css here
360        # Note that at the moment I define these two sheets here. I think this should
361        # be moved out, but I want to try it and see what happens.  css has the format:
362        #
363        # <link rel='stylesheet' title='default' href='/css/default.css' type='text/css'>
364    
365        # convert the default key to the right case. and eliminate dups
366        foreach my $k (keys %$css) {if (lc($k) eq "default") {$css->{'Default'}=$css->{$k}}}
367    
368        if (!$css || !$css->{'Default'})
369        {
370           $css->{'Default'} = "Html/css/default.css";
371        }
372        if (!$css->{"Sans Serif"})
373        {
374           $css->{'Sans Serif'} = "Html/css/sanserif.css";
375        }
376    
377        my $csstext = "<link rel='stylesheet' title='default' href='".$css->{'Default'}."' type='text/css'>\n";
378        $csstext   .= "<link rel='alternate stylesheet' title='Sans Serif' href='".$css->{'Sans Serif'}."' type='text/css'>\n";
379    
380        foreach my $k (keys %$css)
381        {
382           next if (lc($k) eq "default" || lc($k) eq "sans serif");
383           $csstext .= "<link rel='alternate stylesheet' title='$k' href='".$css->{$k}."' type='text/css'>\n";
384        }
385    
386        $csstext   .= "<link rel='alternate'  title='SEED RSS feeds' href='Html/rss/SEED.rss' type='application/rss+xml'>\n";
387    
388        # RAE: also added support for external javascripts here.
389        # we are cluttering the HTML code with all the javascripts when they could easily be in external files
390        # this solution allows us to source other files
391    
392        # the file FIG.js contains most of the java script we use routinely. Every browser will just cache this and so
393        # it will reduce our overhead.
394    
395        # $javasrc must be a ref to an array with urls (absolute or relative) to the javascripts
396        push @$javasrc, "Html/css/FIG.js";
397        foreach my $script (@$javasrc) {
398            $csstext .= "<script src=\"$script\" type=\"text/javascript\"></script>\n";
399        }
400    
401    
402    
403        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.
404    
405      #      #
406      #  <BASE ...> goes before </HEAD>      #  <BASE ...> goes before </HEAD>
407      #      #
# Line 183  Line 414 
414          #  only, or every update?), I provide an alternative derivation          #  only, or every update?), I provide an alternative derivation
415          #  from $cgi_url. -- GJO          #  from $cgi_url. -- GJO
416          #          #
417            # BASE href needs to be absolute. RDO.
418          my $base_url = $FIG_Config::cgi_base;          #
419          if ( ! $base_url )                      # if cgi_base was not defined          #
420          {  #        $base_url = &FIG::cgi_url;
421              $base_url = $FIG_Config::cgi_url;   # get the full cgi url  #       my $base_url = $FIG_Config::cgi_base;
422              $base_url =~ s~^http://[^/]*~~;     # remove protocol and host  #       if ( ! $base_url )                      # if cgi_base was not defined
423              $base_url =~ m~/$~ || $base_url =~ s~$~/~; # check trailing slash  #       {
424          }  #           $base_url = $FIG_Config::cgi_url;   # get the full cgi url
425    #           $base_url =~ s~^http://[^/]*~~;     # remove protocol and host
426    #           $base_url =~ m~/$~ || $base_url =~ s~$~/~; # check trailing slash
427    #       }
428    
429          $base_line = $head_end_line;          $base_line = $head_end_line;
430          splice( @$html, $base_line, 0, "<BASE href=\"$base_url\">\n" );          #
431            # RDO 2005-1006. Remove this so proxying works better.
432            #
433    #        splice( @$html, $base_line, 0, "<BASE href=\"$base_url/\">\n" );
434      }      }
435    
436      #      #
# Line 228  Line 465 
465      }      }
466    
467      #      #
468        # See if we have a site-specific tail (for disclaimers, etc).
469        #
470    
471        my $site_tail = "$FIG_Config::fig_disk/config/site_tail.html";
472        my $site_fh;
473        if (open($site_fh, "<$site_tail"))
474        {
475            push(@tail, <$site_fh>);
476            close($site_fh);
477        }
478    
479        #
480      #  Figure out where to insert The SEED tail.  Before </body>,      #  Figure out where to insert The SEED tail.  Before </body>,
481      #  or before </html>, or at end of page.      #  or before </html>, or at end of page.
482      #      #
   
483      my @tags = ();      my @tags = ();
484        # Check for a tracing queue.
485        my $traceString = QTrace("HTML");
486        if ($traceString) {
487            push @tags, $traceString;
488        }
489      for ($i=0; ($i < @$html) && ($html->[$i] !~ /\<\/body\>/i); $i++) {}      for ($i=0; ($i < @$html) && ($html->[$i] !~ /\<\/body\>/i); $i++) {}
490      if ($i >= @$html)        # </body> not found; look for </html>      if ($i >= @$html)        # </body> not found; look for </html>
491      {      {
# Line 255  Line 507 
507          splice( @$html, $i, 0, @tags );          splice( @$html, $i, 0, @tags );
508      }      }
509    
510      print @$html;      # RAE the chomp will return any new lines at the ends of elements in the array,
511        # and then we can join  with a "\n". This is because somethings put newlines in,
512        # and others don't. This should make nicer looking html
513        #
514        # chomp(@$html);
515        # print join "\n", @$html;
516        #
517        # Apparently the above still breaks things. This is the correct code:
518    
519        foreach $_ (@$html)
520        {
521            print $_;
522        }
523    
524  }  }
525    
526    
527    =head1 make_table
528    
529    The main method to convert an array into a table.
530    
531    The col_hdrs are set to the <th> headers, the $tab is an array of arrays. The first is the rows, and the second is the columns. The title is the title of the table.
532    
533    The options define the settings for the table such as border, width, and class for css formatting. If the option "excelfile" is set to a filename that will be created in FIG_Config::temp, and the link included that allows the user to download the file as an excel file.
534    
535    =cut
536    
537  sub make_table {  sub make_table {
538      my($col_hdrs,$tab,$title,$instr) = @_;      my($col_hdrs,$tab,$title, %options ) = @_;
539      my(@tab);      my(@tab);
540    
541      push( @tab, "\n<table border>\n",      my $border = defined $options{border} ? "border=\"$options{border}\"" : "border";
542        my $width = defined $options{width} ? "width=\"$options{width}\"" : "";
543        my $class = defined $options{class} ? "class=\"$options{class}\"" : "";
544        push( @tab, "\n<table $border $width $class>\n",
545                  "\t<caption><b>$title</b></caption>\n",                  "\t<caption><b>$title</b></caption>\n",
546                  "\t<tr>\n\t\t<th>"                  "\t<tr>\n\t\t"
547                . join( "</th>\n\t\t<th>", @$col_hdrs )                . join( "\n", map { &expand($_, "th") } @$col_hdrs )
548                . "</th>\n\t</tr>\n"                . "\n\t</tr>\n"
549          );          );
550      my($i,$nowrap);      my($i);
   
     for ($i=0; ($i < @$instr) && ($instr->[$i] !~ /nowrap/); $i++) {}  
     $nowrap = ($i == @$instr) ? "" : " nowrap";  
551    
552      my $row;      my $row;
553      foreach $row (@$tab)      foreach $row (@$tab)
554      {      {
555          push( @tab, "\t<tr>\n"          push( @tab, "\t<tr>\n"
556                    . join( "\n", map { &expand($_,$nowrap) } @$row )                    . join( "\n", map { &expand($_) } @$row )
557                    . "\n\t</tr>\n"                    . "\n\t</tr>\n"
558              );              );
559      }      }
560      push(@tab,"</table>\n");      push(@tab,"</table>\n");
561    
562        # excelfile should be appropriate for a filename (no spaces/special characters)
563        if (defined $options{"excelfile"}) {
564            if (! defined($raelib)) {
565                require raelib;
566                $raelib = new raelib;
567            }
568            push @tab, $raelib->tab2excel($col_hdrs,$tab,$title,\%options,$options{"excelfile"})}
569    
570      return join("",@tab);      return join("",@tab);
571  }  }
572    
573    sub abstract_coupling_table {
574        my($cgi,$prot,$coupling) = @_;
575        my %fc;
576    
577        my $col_hdrs = ["coupled to","Score","Type of Coupling", "Type-specific Data"];
578        my $tab = [];
579        my %by_peg;
580        foreach my $x (@$coupling)
581        {
582            my($peg2,$psc,$type,$extra) = @$x;
583            if (($type !~ /^[ID]FC$/) || (! $fc{$peg2}))
584            {
585                if ($type =~  /^[ID]FC$/)
586                {
587                    $fc{$peg2} = 1;
588                }
589    
590                $by_peg{$peg2} += $psc;
591            }
592        }
593    
594        foreach my $x (sort { ($by_peg{$b->[0]} <=> $by_peg{$a->[0]})
595                              or ($a->[0] cmp $b->[0])
596                              or ($b->[1] <=> $a->[1])
597                              or ($a->[2] cmp $b->[2]) } @$coupling)
598        {
599            my($peg2,$psc,$type,$extra) = @$x;
600            push(@$tab,[&fid_link($cgi,$peg2,1),$psc,$type,&set_prot_links($cgi,join(", ",@$extra))]);
601        }
602    
603    
604         my $help = "<a href=\"Html/abstract_coupling.html\" target=\"SEED_or_SPROUT_help\">for help</a>";
605    #    my @html = &make_table($col_hdrs,$tab,"Abstract Coupling Data for $prot");
606    #    push(@html,"<hr>\n",$cgi->h3($help),"<br>");
607    #    return @html;
608    
609        return &make_table($col_hdrs,$tab,"Abstract Coupling Data for $prot [$help]");
610    }
611    
612  sub expand {  sub expand {
613      my($x,$nowrap) = @_;      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
614        my( $x, $tag ) = @_;
615    
616        $tag = "td" unless $tag;
617        my $endtag = $tag;
618    
619        # RAE modified this so that you can pass in a reference to an array where
620        # the first element is the data to display and the second element is optional
621        # things like colspan and align. Note that in this case you need to include the td
622        # use something like ["some data to appear", "td colspan=4 bgcolor=gray"]
623    
624        # per GJO's request modified this line so it can take any tag.
625        if ( ref($x) eq "ARRAY" ) { ($x, $tag) = @$x; $tag =~ /^(\S+)/; $endtag = $1 }
626    
627      if ($x =~ /^\@([^:]+)\:([^:]+)\:(.*)$/)      if ( $x =~ /^\@([^:]+)\:(.*)$/ )
628      {      {
629          return "\t\t<td$nowrap $1=\"$2\">$3</td>";          return "\t\t<$tag $1>$2</$endtag>";
630      }      }
631      else      else
632      {      {
633          return "\t\t<td$nowrap>$x</td>";          return "\t\t<$tag>$x</$endtag>";
634        }
635    }
636    
637    
638    =head2 merge_table_rows()
639    
640    Merge table rows together. This will merge a table so that adjacent cells with the same content will only be shown once.
641    
642    Something like this:
643    
644        -----------------------
645        |    1     |    a     |
646        -----------------------
647        |    1     |    b     |
648        -----------------------
649        |    2     |    c     |
650        -----------------------
651        |    3     |    d     |
652        -----------------------
653        |    4     |    d     |
654        -----------------------
655        |    5     |    d     |
656        -----------------------
657    
658    Will become:
659    
660        -----------------------
661        |          |    a     |
662        |    1     |-----------
663        |          |    b     |
664        -----------------------
665        |    2     |    c     |
666        -----------------------
667        |    3     |          |
668        ------------          |
669        |    4     |    5     |
670        ------------          |
671        |    5     |          |
672        -----------------------
673    
674    
675    The method takes two arguments. The reference to the array that is the table ($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.
676    
677     $tab=&HTML::merge_table_rows($tab);
678    
679     or
680    
681     $skip=(1=>1, 3=>1, 5=>1);
682     $tab=&HTML::merge_table_rows($tab, $skip);  # will merge all columns except 1, 3 and 5. Note the first column in the table is #0
683    
684    
685    =cut
686    
687    
688    
689    
690    sub merge_table_rows {
691     # RAE:
692     # Experimental piece of code. We often want to have rows or columns were cells are merged. It just looks so much nicer
693     # this block should merge adjacent rows that have the same text in them.
694     # use like this:
695     #      $tab=&HTML::merge_table_rows($tab);
696     # before you do a make_table call
697    
698     my $self=shift if UNIVERSAL::isa($_[0],__PACKAGE__);
699     my ($tab, $skip)=@_;
700    
701     my $newtable;
702     my $lastrow;
703     my $rowspan;
704     my $refs;
705    
706     for (my $y=0; $y <= $#$tab; $y++) {
707     #$y is the row in the table;
708      for (my $x=0; $x <= $#{$tab->[$y]}; $x++) {
709       # this is the user definable columns not to merge
710       if ($skip->{$x})
711       {
712        $newtable->[$y]->[$x] = $tab->[$y]->[$x];
713        next;
714       }
715    
716       #$x is the column in the table
717       # if the column in the row we are looking at is the same as the column in the previous row, we don't add
718       # this cell to $newtable. Instead we increment the rowspan of the previous row by one
719    
720       # handle cells that are references to arrays
721       if (ref($tab->[$y]->[$x]) eq "ARRAY") {$refs->[$y]->[$x]=$tab->[$y]->[$x]->[1]; $tab->[$y]->[$x]=$tab->[$y]->[$x]->[0]}
722    
723       # now we go back through the table looking where to draw the merge line:
724       my $lasty=$y;
725       while ($lasty >= 0 && $tab->[$y]->[$x] eq $tab->[$lasty]->[$x]) {$lasty--}
726       $lasty++; # this is the last identical cell. If lasty==y it is the current cell, so we just save the data. Otherwise we increment the rowspan
727       if ($lasty == $y) {
728        # we always want to have something in rows that may otherwise be empty but should be there (see below)
729        unless ($tab->[$y]->[$x]) {$tab->[$y]->[$x]=" &nbsp; "}
730        $newtable->[$y]->[$x] = $tab->[$y]->[$x];
731       }
732       else {$rowspan->[$lasty]->[$x]++}
733      }
734     }
735    
736     # now just join everything back together
737     for (my $y=0; $y <= $#$tab; $y++) {
738      for (my $x=0; $x <= $#{$tab->[$y]}; $x++) {
739       if ($rowspan->[$y]->[$x]) {
740        if ($refs->[$y]->[$x]) {$refs->[$y]->[$x] .= " rowspan=". ($rowspan->[$y]->[$x]+1)}
741        else {$refs->[$y]->[$x] = "td rowspan=". ($rowspan->[$y]->[$x]+1)}
742        $newtable->[$y]->[$x]=[$newtable->[$y]->[$x], $refs->[$y]->[$x]];
743       }
744       elsif ($newtable->[$y]->[$x] && $refs->[$y]->[$x]) {
745        $newtable->[$y]->[$x]=[$newtable->[$y]->[$x], $refs->[$y]->[$x]];
746       }
747      }
748     }
749    
750    
751     # finally we have to remove any completely empty cells that have been added by the array mechanism
752     # (e.g. if you define $a->[2] then $a->[0] and $a->[1] are now undef).
753     # that is why in the loop above I replace empty cells with nbsp. They are now not undef!
754     # I am sure that Gary can do this in one line, but I am hacking.
755     my @trimmed;
756     foreach my $a (@$newtable) {
757      my @row;
758      foreach my $b (@$a) {
759       push @row, $b if ($b);
760      }
761      push @trimmed, \@row;
762     }
763    
764     return \@trimmed;
765    }
766    
767    
768    
769    
770    sub set_ec_links {
771        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
772        my($cgi,$x) = @_;
773        my($before,$match,$after);
774    
775        if ($x =~ /^(.*)(EC \d+\.\d+\.\d+\.\d+)(.*)/s)
776        {
777            $before = $1;
778            $match = $2;
779            $after = $3;
780            return &set_ec_links($cgi,$before) . &HTML::ec_link($match) . &set_ec_links($cgi,$after);
781      }      }
782        return $x;
783  }  }
784    
785  sub ec_link {  sub ec_link {
786        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
787      my($role) = @_;      my($role) = @_;
788    
789      if ($role =~ /(\d+\.\d+\.\d+\.\d+)/)      if ($role =~ /(\d+\.\d+\.\d+\.\d+)/)
# Line 312  Line 797 
797  }  }
798    
799  sub role_link {  sub role_link {
800        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
801      my($cgi,$role) = @_;      my($cgi,$role) = @_;
802    
803      my $roleR = ($role =~ /^(\d+\.\d+\.\d+\.\d+)\s+-\s+/) ? $1 : $role;      my $roleR = ($role =~ /^(\d+\.\d+\.\d+\.\d+)\s+-\s+/) ? $1 : $role;
# Line 322  Line 808 
808      return "<a href=$link>$role</a>";      return "<a href=$link>$role</a>";
809  }  }
810    
811    =head2 fid_link
812    
813    Get a link to a fid.
814    
815    use: my $html=&HTML::fid_link($cgi, $fid, Local, Just_URL, Full_Path);
816    
817    Local is a boolean means to eliminate the fig|org.peg from the text of the link.
818    
819    Just_URL will only return the URL and not the HTML code. The default is to return the full code.
820    
821    Full_Path is a boolean that will get the full path to the URL not just a relative path. This is required in pages where the base href changes (e.g. if an image is imported like on the metabolic pages).
822    
823    =cut
824    
825    
826  sub fid_link {  sub fid_link {
827      my($cgi,$fid,$local,$just_url) = @_;      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
828        my($cgi,$fid,$local,$just_url,$fullpath) = @_;
829        Trace("Creating link for feature $fid.") if T(4);
830        my $err=join(" ", $cgi,$fid,$local,$just_url,$fullpath);
831    
832      my($n);      my($n);
833    
834        my $top = top_link();
835        if ($fullpath) {$top=$FIG_Config::cgi_url}
836    
837      if ($fid =~ /^fig\|\d+\.\d+\.([a-z]+)\.(\d+)/)      if ($fid =~ /^fig\|\d+\.\d+\.([a-z]+)\.(\d+)/)
838      {      {
839          if ($local)          if ($local)
# Line 343  Line 851 
851          {          {
852              $n = $fid;              $n = $fid;
853          }          }
854          if ($1 ne "peg") { return $n }  
855            my $link;
856            my $new_framework = $cgi->param('new_framework') ? 1 : 0;
857            #added to format prophage and path island links to feature.cgi
858            my $sprout = $cgi->param('SPROUT') ? "&SPROUT=1" : "";
859            Trace("Sprout mode is \"$sprout\".") if T(4);
860            if ($1 ne "peg" && ! $sprout)
861            {
862               Trace("Creating feature link for $fid.") if T(4);
863               my $user = $cgi->param('user');
864               if (! $user) { $user = "" }
865               $link = "$top/feature.cgi?feature=$fid&user=$user$sprout";
866               $link =~ s/[a-z_A-Z0-9]+\.cgi\?/feature.cgi?/;
867            }
868            else
869            {
870                Trace("Creating protein link for $fid.") if T(4);
871          my $user = $cgi->param('user');          my $user = $cgi->param('user');
872          if (! $user) { $user = "" }          if (! $user) { $user = "" }
873          my $trans = $cgi->param('translate') ? "&translate=1" : "";          my $trans = $cgi->param('translate') ? "&translate=1" : "";
874          my $link = $cgi->url() . "?prot=$fid&user=$user$trans";              my $sprout = $cgi->param('SPROUT') ? "&SPROUT=1" : "";
875          $link =~ s/[a-z_A-Z]+\.cgi\?/protein.cgi?/;  ###a
876    
877    ### This used to be
878    ###     my $link = &FIG::cgi_url . "/protein.cgi?prot=$fid&user=$user$trans$sprout";
879    ###
880    ### The cost became prohibitive in the subsystem spreadsheets.  Hence, we cache the value
881    ###
882    ### RAO
883    
884                #if (! $cgi_url) { $cgi_url = &FIG::cgi_url }
885                #$link = $cgi_url . "/protein.cgi?prot=$fid&user=$user$trans$sprout";
886                $link = "$top/protein.cgi?prot=$fid&user=$user$trans$sprout\&new_framework=$new_framework";
887                $link =~ s/[a-z_A-Z0-9]+\.cgi\?/protein.cgi?/;
888            }
889          if ($just_url)          if ($just_url)
890          {          {
891              return $link;              return $link;
892          }          }
893          else          else
894          {          {
895              return "<a href=$link>$n</a>";              return "<a href='$link'>$n</a>";
896          }          }
897      }      }
898      return $fid;      return $fid;
899  }  }
900    
901  sub family_link {  sub family_link {
902        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
903      my($family,$user) = @_;      my($family,$user) = @_;
904    
905      return $family;      return $family;
906  }  }
907    
 use URI::Escape;  
908    
909  sub get_html {  sub get_html {
910        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
911      my( $url, $type, $kv_pairs) = @_;      my( $url, $type, $kv_pairs) = @_;
912      my( $encoded, $ua, $args, @args, $out, @output, $x );      my( $encoded, $ua, $args, @args, $out, @output, $x );
913    
914      $ua = new LWP::UserAgent;      $ua = new LWP::UserAgent;
915      $ua->timeout( 900 );      $ua->timeout( 900 );
   
916      if ($type =~/post/i)      if ($type =~/post/i)
917      {      {
918          $args = [];          $args = [];
# Line 387  Line 924 
924          my $response = $ua->request($request);          my $response = $ua->request($request);
925          $out = $response->content;          $out = $response->content;
926      }      }
927      else  
928        if ($type =~/get/i)
929      {      {
930          @args = ();          @args = ();
931          foreach $x (@$kv_pairs)          foreach $x (@$kv_pairs)
# Line 399  Line 937 
937          {          {
938              $url .= "?" . join("&",@args);              $url .= "?" . join("&",@args);
939          }          }
940          $request = new HTTP::Request('GET', $url);          my $request = new HTTP::Request('GET', $url);
941          my $response = $ua->request($request);          my $response = $ua->request($request);
942    
943          if ($response->is_success)          if ($response->is_success)
# Line 417  Line 955 
955    
956  #   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
957  #   properly.  Remove the header.  #   properly.  Remove the header.
958        my $i;
959      for ($i=0; ($i < @output) && ($output[$i] !~ /^\s*\</); $i++) {}      for ($i=0; ($i < @output) && ($output[$i] !~ /^\s*\</); $i++) {}
960      if ($i < @output)      if ($i < @output) {
     {  
   
961          splice(@output,0,$i);          splice(@output,0,$i);
962      }      }
963    
# Line 435  Line 971 
971  }  }
972    
973  sub trim_output {  sub trim_output {
974        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
975      my($out) = @_;      my($out) = @_;
976      my $i;      my ($i, $j);
977    
978      for ($i=0; ($i < @$out) && ($out->[$i] !~ /^\</); $i++) {}      for ($i=0; ($i < @$out) && ($out->[$i] !~ /^\</); $i++) {}
979      splice(@$out,0,$i);      splice(@$out,0,$i);
# Line 465  Line 1002 
1002      for ($j=$i-1; ($j > 0) && ($out->[$j] !~ /FIG search/); $j--) {}      for ($j=$i-1; ($j > 0) && ($out->[$j] !~ /FIG search/); $j--) {}
1003      if ($j > 0)      if ($j > 0)
1004      {      {
1005            #
1006            # Hm. We would have tried using the options here:
1007            # my $tail_name = $options{tail_name} ? $options{tail_name} : "html.tail";
1008            # but they're not passed in. So use the default html.tail.
1009            #
1010            my $html_tail_file = "./Html/html.tail";
1011          my @tmp = `cat $html_tail_file`;          my @tmp = `cat $html_tail_file`;
1012          my $n = @tmp;          my $n = @tmp;
1013          splice(@$out,$j-$n,$n+1);          splice(@$out,$j-$n,$n+1);
# Line 472  Line 1015 
1015  }  }
1016    
1017  sub set_prot_links {  sub set_prot_links {
1018        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1019      my($cgi,$x) = @_;      my($cgi,$x) = @_;
1020      my($before,$match,$after);      my($before,$match,$after);
1021    
1022      if ($x =~ /^(.*)(fig\|\d+\.\d+\.peg\.\d+)(.*)$/)      if ($x =~ /^(.*)(fig\|\d+\.\d+\.peg\.\d+)(.*)/s)
1023      {      {
1024          $before = $1;          $before = $1;
1025          $match = $2;          $match = $2;
1026          $after = $3;          $after = $3;
1027          return &set_prot_links($cgi,$before) . &HTML::fid_link($cgi,$match) . &set_prot_links($cgi,$after) . "\n";          return &set_prot_links($cgi,$before) . &HTML::fid_link($cgi,$match) . &set_prot_links($cgi,$after);
1028      }      }
1029      elsif ($x =~ /^(.*)(gi\|\d+)(.*)$/)      elsif ($x =~ /^(.*)\b([NXYZA][PM]_[0-9\.]+)\b(.*)/s)
1030      {      {
1031          $before = $1;          $before = $1;
1032          $match = $2;          $match = $2;
1033          $after = $3;          $after = $3;
1034          return &set_prot_links($cgi,$before) . &HTML::gi_link($cgi,$match) . &set_prot_links($cgi,$after) . "\n";          return &set_prot_links($cgi,$before) . &HTML::refseq_link($cgi,$match) . &set_prot_links($cgi,$after);
1035      }      }
1036      elsif ($x =~ /^(.*)(sp\|[A-Z0-9]{6})(.*)$/)      elsif ($x =~ /^(.*)(gi\|\d+)(.*)/s)
1037      {      {
1038          $before = $1;          $before = $1;
1039          $match = $2;          $match = $2;
1040          $after = $3;          $after = $3;
1041          return &set_prot_links($cgi,$before) . &HTML::sp_link($cgi,$match) . &set_prot_links($cgi,$after) . "\n";          return &set_prot_links($cgi,$before) . &HTML::gi_link($cgi,$match) . &set_prot_links($cgi,$after);
1042      }      }
1043      elsif ($x =~ /^(.*)(pirnr\|NF\d+)(.*)$/)      elsif ($x =~ /^(.*)(tigr\|\w+)(.*)/s)
1044      {      {
1045          $before = $1;          $before = $1;
1046          $match = $2;          $match = $2;
1047          $after = $3;          $after = $3;
1048          return &set_prot_links($cgi,$before) . &HTML::pir_link($cgi,$match) . &set_prot_links($cgi,$after) . "\n";          return &set_prot_links($cgi,$before) . &HTML::tigr_link($cgi,$match) . &set_prot_links($cgi,$after);
1049      }      }
1050      return $x;      elsif ($x =~ /^(.*)\b(eric\|\S+)\b(.*)/s)
1051        {
1052            $before = $1;
1053            $match = $2;
1054            $after = $3;
1055            return &set_prot_links($cgi,$before) . &HTML::eric_link($cgi,$match) . &set_prot_links($cgi,$after);
1056  }  }
1057    
1058  sub gi_link {      elsif ($x =~ /^(.*)\b(bhb\|.*?)\b(.*)/s)
     my($cgi,$gi) = @_;  
   
     if ($gi =~ /^gi\|(\d+)$/)  
1059      {      {
1060          return "<a href=http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=Protein&list_uids=$1&dopt=GenPept>$gi</a>";          $before = $1;
1061      }          $match = $2;
1062      return $gi;          $after = $3;
1063            return &set_prot_links($cgi,$before) . &HTML::bhb_link($cgi,$match) . &set_prot_links($cgi,$after);
1064  }  }
1065    
1066  sub sp_link {      elsif ($x =~ /^(.*)\b(apidb\|[0-9\.a-z_]+)\b(.*)/s)
     my($cgi,$sp) = @_;  
   
     if ($sp =~ /^sp\|(\S+)$/)  
1067      {      {
1068          return "<a href=http://us.expasy.org/cgi-bin/get-sprot-entry?$1>$sp</a>";          $before = $1;
1069      }          $match = $2;
1070      return $sp;          $after = $3;
1071            return &set_prot_links($cgi,$before) . &HTML::apidb_link($cgi,$match) . &set_prot_links($cgi,$after);
1072        }
1073    
1074        elsif ($x =~ /^(.*)\b(patric\|.*?)\b(.*)/s)
1075        {
1076            $before = $1;
1077            $match = $2;
1078            $after = $3;
1079            return &set_prot_links($cgi,$before) . &HTML::patric_link($cgi,$match) . &set_prot_links($cgi,$after);
1080        }
1081    
1082        elsif ($x =~ /^(.*)\b(vbrc\|.*?)\b(.*)/s)
1083        {
1084            $before = $1;
1085            $match = $2;
1086            $after = $3;
1087            return &set_prot_links($cgi,$before) . &HTML::vbrc_link($cgi,$match) . &set_prot_links($cgi,$after);
1088        }
1089    
1090        elsif ($x =~ /^(.*)\b(vectorbase\|.*?)\b(.*)/s)
1091        {
1092            $before = $1;
1093            $match = $2;
1094            $after = $3;
1095            return &set_prot_links($cgi,$before) . &HTML::vectorbase_link($cgi,$match) . &set_prot_links($cgi,$after);
1096        }
1097        elsif ($x =~  /^(.*)(uni\|[A-Z0-9]{6})(.*)/s)
1098        {
1099            $before = $1;
1100            $match = $2;
1101            $after = $3;
1102            return &set_prot_links($cgi,$before) . &HTML::uni_link($cgi,$match) . &set_prot_links($cgi,$after);
1103        }
1104        elsif ($x =~ /^(.*)(sp\|[A-Z0-9]{6})(.*)/s)
1105        {
1106            $before = $1;
1107            $match = $2;
1108            $after = $3;
1109            return &set_prot_links($cgi,$before) . &HTML::sp_link($cgi,$match) . &set_prot_links($cgi,$after);
1110        }
1111        elsif ($x =~ /^(.*)(pirnr\|NF\d+)(.*)/s)
1112        {
1113            $before = $1;
1114            $match = $2;
1115            $after = $3;
1116            return &set_prot_links($cgi,$before) . &HTML::pir_link($cgi,$match) . &set_prot_links($cgi,$after);
1117        }
1118        elsif ($x =~ /^(.*)(kegg\|[a-z]{2,4}:[a-zA-Z_0-9]+)(.*)/s)
1119        {
1120            $before = $1;
1121            $match = $2;
1122            $after = $3;
1123            return &set_prot_links($cgi,$before) . &HTML::kegg_link($cgi,$match) . &set_prot_links($cgi,$after);
1124        }
1125        elsif ($x =~ /^(.*)(Ensembl[a-zA-Z]+:[a-zA-Z_0-9\.]+)(.*)/s)
1126        {
1127            $before = $1;
1128            $match = $2;
1129            $after = $3;
1130            return &set_prot_links($cgi,$before) . &HTML::ensembl_link($cgi,$match) . &set_prot_links($cgi,$after);
1131        }
1132        elsif ($x =~ /^(.*)(EntrezGene:[a-zA-Z_0-9\.]+)(.*)/s)
1133        {
1134            $before = $1;
1135            $match = $2;
1136            $after = $3;
1137            return &set_prot_links($cgi,$before) . &HTML::entrezgene_link($cgi,$match) . &set_prot_links($cgi,$after);
1138        }
1139        elsif ($x =~ /^(.*)(MIM:[a-zA-Z_0-9\.]+)(.*)/s)
1140        {
1141            $before = $1;
1142            $match = $2;
1143            $after = $3;
1144            return &set_prot_links($cgi,$before) . &HTML::mim_link($cgi,$match) . &set_prot_links($cgi,$after);
1145        }
1146        elsif ($x =~ /^(.*)(HGNC:[a-zA-Z_0-9\.]+)(.*)/s)
1147        {
1148            $before = $1;
1149            $match = $2;
1150            $after = $3;
1151            return &set_prot_links($cgi,$before) . &HTML::hgnc_link($cgi,$match) . &set_prot_links($cgi,$after);
1152        }
1153        elsif ($x =~ /^(.*)(UniGene:[a-zA-Z_0-9\.]+)(.*)/s)
1154        {
1155            $before = $1;
1156            $match = $2;
1157            $after = $3;
1158            return &set_prot_links($cgi,$before) . &HTML::unigene_link($cgi,$match) . &set_prot_links($cgi,$after);
1159        }
1160    # IPI stopped working. turn off for now.
1161    #    elsif ($x =~ /^(.*)(IPI:[a-zA-Z_0-9\.]+)(.*)/s)
1162    #    {
1163    #        $before = $1;
1164    #        $match = $2;
1165    #        $after = $3;
1166    #        return &set_prot_links($cgi,$before) . &HTML::ipi_link($cgi,$match) . &set_prot_links($cgi,$after);
1167    #    }
1168        elsif ($x =~ /^(.*)(WP:[a-zA-Z_0-9\.]+)(.*)/s)
1169        {
1170            #wormbase
1171    
1172            $before = $1;
1173            $match = $2;
1174            $after = $3;
1175            return &set_prot_links($cgi,$before) . &HTML::wp_link($cgi,$match) . &set_prot_links($cgi,$after);
1176        }
1177        elsif ($x =~ /^(.*)(FB:[a-zA-Z_0-9\.]+)(.*)/s)
1178        {
1179            #flybase
1180    
1181            $before = $1;
1182            $match = $2;
1183            $after = $3;
1184            return &set_prot_links($cgi,$before) . &HTML::fb_link($cgi,$match) . &set_prot_links($cgi,$after);
1185        }
1186        elsif ($x =~ /^(.*)(FlyBaseORFNames:[a-zA-Z_0-9\.]+)(.*)/s)
1187        {
1188            #flybase
1189    
1190            $before = $1;
1191            $match = $2;
1192            $after = $3;
1193            return &set_prot_links($cgi,$before) . &HTML::fborf_link($cgi,$match) . &set_prot_links($cgi,$after);
1194        }
1195        elsif ($x =~ /^(.*)(SGD_LOCUS:[a-zA-Z_0-9\.]+)(.*)/s)
1196        {
1197            #flybase
1198    
1199            $before = $1;
1200            $match = $2;
1201            $after = $3;
1202            return &set_prot_links($cgi,$before) . &HTML::sgd_link($cgi,$match) . &set_prot_links($cgi,$after);
1203        }
1204        elsif ($x =~ /^(.*)(tr\|[a-zA-Z0-9]+)(.*)/s)
1205        {
1206    
1207          $before = $1;
1208          $match = $2;
1209          $after = $3;
1210    
1211          return &set_prot_links($cgi,$before) .  &HTML::trembl_link($cgi,$match) . &set_prot_links($cgi,$after);
1212        }
1213        return $x;
1214    }
1215    
1216    sub trembl_link {
1217        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1218        my($cgi,$id) = @_;
1219    
1220        if ($id =~ /^tr\|(.*)/) {
1221          return "<a href='http://ca.expasy.org/uniprot/$1' target=_blank>$id</a>";
1222        } else {
1223          return "invalid call to trembl link";
1224        }
1225    }
1226    
1227    sub refseq_link {
1228        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1229        my($cgi,$id) = @_;
1230    
1231        if ($id =~ /^[NXYZA]P_/)
1232        {
1233            return "<a href='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=protein&cmd=search&term=$id' target=_blank>$id</a>";
1234        }
1235        elsif ($id =~ /^[NXYZA]M_/)
1236        {
1237            return "<a href='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=nuccore&cmd=search&term=$id' target=_blank>$id</a>";
1238        }
1239    }
1240    
1241    sub gi_link {
1242        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1243        my($cgi,$gi) = @_;
1244    
1245        if ($gi =~ /^gi\|(\d+)$/)
1246        {
1247            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>";
1248        }
1249        return $gi;
1250    }
1251    
1252    sub tigr_link {
1253        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1254        my($cgi,$tigr) = @_;
1255    
1256        if ($tigr =~ /^tigr\|(NT|ntbp|ntbpA|BA|BMAA|BXB|GBA)(\w+)$/)
1257        {
1258            my $id=$1.$2;
1259            return "<a href=\"http://pathema.tigr.org/tigr-scripts/pathema/shared/GenePage.cgi?locus=$id\" target=_blank>$tigr</a> (Pathema)";
1260        }
1261        elsif ($tigr =~ /^tigr\|(\S+)$/)
1262        {
1263            return "<a href=\"http://www.tigr.org/tigr-scripts/CMR2/GenePage.spl?locus=$1\" target=_blank>$tigr</a>";
1264        }
1265        return $tigr;
1266    }
1267    
1268    sub eric_link {
1269        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1270        my($cgi,$eric) = @_;
1271    
1272        if ($eric =~ /^eric\|(\S+)/)
1273        {
1274            return "<a href=\"https://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=$1\" target=_blank>$eric</a>";
1275        }
1276        return $eric;
1277    }
1278    
1279    sub bhb_link {
1280        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1281        my($cgi,$bhb) = @_;
1282    
1283        return "<a href=\"http://www.biohealthbase.org\" target=_blank>$bhb</a>";
1284    }
1285    
1286    sub apidb_link {
1287        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1288        my($cgi,$api) = @_;
1289    
1290        if ($api =~ /apidb\|(.*?)\.(.*)$/)
1291        {
1292            return "<a href=\"http://www.apidb.org/cgi-bin/redirect.cgi?taxon_id=$1&source_id=$2\" target=_blank>$api</a>";
1293        }
1294        return $api;
1295    }
1296    
1297    sub patric_link {
1298        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1299        my($cgi,$patric) = @_;
1300    
1301        if ($patric =~ /patric\|(.*)/)
1302        {
1303            return "<a href=\"https://patric.vbi.vt.edu/software/curationTool/gep/pgiCuration.php?locus_name=$1\" target=_blank>$patric</a>";
1304        }
1305        return $patric;
1306    }
1307    
1308    sub vbrc_link {
1309        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1310        my($cgi,$vbrc) = @_;
1311    
1312        if ($vbrc =~ /vbrc\|(.*)/)
1313        {
1314            return "<a href=\"http://www.biovirus.org/gene_detail.asp?name=$1\" target=_blank>$vbrc</a>";
1315        }
1316        return $vbrc;
1317    }
1318    
1319    sub vectorbase_link {
1320        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1321        my($cgi,$vec) = @_;
1322        return "<a href=\"http://www.vectorbase.org\" target=_blank>$vec</a>";
1323    }
1324    
1325    
1326    sub uni_link {
1327        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1328        my($cgi,$uni) = @_;
1329    
1330        if ($uni =~ /^uni\|(\S+)$/)
1331        {
1332            #return "<a href=http://www.pir.uniprot.org/cgi-bin/upEntry?id=$1>$uni</a>";
1333            return "<a href='http://www.ebi.uniprot.org/uniprot-srv/uniProtView.do?proteinAc=$1' target=_blank>$uni</a>";
1334        }
1335        return $uni;
1336    }
1337    
1338    sub sp_link {
1339        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1340        my($cgi,$sp) = @_;
1341    
1342        if ($sp =~ /^sp\|(\S+)$/)
1343        {
1344            return "<a href='http://us.expasy.org/cgi-bin/get-sprot-entry?$1' target=_blank>$sp</a>";
1345        }
1346        return $sp;
1347  }  }
1348    
1349  sub pir_link {  sub pir_link {
1350        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1351      my($cgi,$pir) = @_;      my($cgi,$pir) = @_;
1352    
1353      if ($pir =~ /^pirnr\|(NF\d+)$/)      if ($pir =~ /^pirnr\|(NF\d+)$/)
1354      {      {
1355          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>";
1356      }      }
1357      return $pir;      return $pir;
1358  }  }
1359    
1360    sub kegg_link {
1361        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1362        my($cgi,$kegg) = @_;
1363    
1364        if ($kegg =~ /^kegg\|([^:]+):(\S+)$/)
1365        {
1366            return "<a href='http://www.genome.ad.jp/dbget-bin/www_bget?$1+$2' target=_blank>$kegg</a>";
1367        }
1368        return $kegg;
1369    }
1370    
1371    sub ensembl_link {
1372        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1373        my($cgi,$ensembl) = @_;
1374    
1375        if ($ensembl =~ /^(\S+):(\S+)$/)
1376        {
1377            my $what=$1;
1378            my $key=$2;
1379            my $idx="All";
1380            if ($what eq "EnsemblGene") { $idx = "Gene" }
1381            if ($what eq "EnsemblTranscript") { $idx = "All" }
1382            if ($what eq "EnsemblProtein") { $idx = "All" }
1383    
1384            #I really want to get right to the transcript and peptide pages, but
1385            #can't see how to do that without knowing the org name too, which
1386            #I don't know at this point. (ensembl org name, not real org name)
1387    
1388            return "<a href='http://www.ensembl.org/Homo_sapiens/searchview?species=all&idx=$idx&q=$key' target=_blank>$ensembl</a>";
1389        }
1390        return $ensembl;
1391    }
1392    
1393    sub entrezgene_link {
1394        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1395        my($cgi,$entrezgene) = @_;
1396    
1397        if ($entrezgene =~ /^EntrezGene:(\S+)$/)
1398        {
1399            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>";
1400        }
1401        return $entrezgene;
1402    }
1403    
1404    sub mim_link {
1405        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1406        my($cgi,$mim) = @_;
1407    
1408        if ($mim =~ /^MIM:(\S+)$/)
1409        {
1410            return "<a href='http://www3.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=$1' target=_blank>$mim</a>";
1411        }
1412        return $mim;
1413    }
1414    
1415    sub hgnc_link {
1416        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1417        my($cgi,$hgnc) = @_;
1418    
1419        if ($hgnc =~ /^HGNC:(\S+)$/)
1420        {
1421            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>";
1422        }
1423    
1424        return $hgnc;
1425    }
1426    
1427    sub unigene_link {
1428        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1429        my($cgi,$unigene) = @_;
1430    
1431        if ($unigene =~ /^UniGene:(\S+)$/)
1432        {
1433            return "<a href='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unigene&cmd=search&term=$1' target=_blank>$unigene</a>";
1434        }
1435        return $unigene;
1436    }
1437    
1438    sub ipi_link {
1439        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1440        my($cgi,$ipi) = @_;
1441    
1442        if ($ipi =~ /^IPI:(\S+)$/)
1443        {
1444            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>";
1445        }
1446        return $ipi;
1447    }
1448    
1449    sub wp_link {
1450        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1451        my($cgi,$wp) = @_;
1452    
1453        #wormbase
1454    
1455        if ($wp =~ /^WP:(\S+)$/)
1456        {
1457            return "<a href='http://www.wormbase.org/db/searches/basic?class=Any&query=$1&Search=Search' target=_blank>$wp</a>";
1458        }
1459        return $wp;
1460    }
1461    
1462    sub fb_link {
1463        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1464        my($cgi,$fb) = @_;
1465    
1466        #flybase
1467    
1468        if ($fb =~ /^FB:(\S+)$/)
1469        {
1470            return "<a href='http://flybase.bio.indiana.edu/.bin/fbidq.html?$1' target=_blank>$fb</a>";
1471        }
1472        return $fb;
1473    }
1474    
1475    sub fborf_link {
1476        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1477        my($cgi,$fb) = @_;
1478    
1479        #flybase
1480    
1481        if ($fb =~ /^FlyBaseORFNames:(\S+)$/)
1482        {
1483            return "<a href='http://flybase.bio.indiana.edu/.bin/fbidq.html?$1' target=_blank>$fb</a>";
1484        }
1485        return $fb;
1486    }
1487    
1488    sub sgd_link {
1489        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1490        my($cgi,$sgd) = @_;
1491    
1492        #yeast
1493    
1494        if ($sgd =~ /^SGD_LOCUS:(\S+)$/)
1495        {
1496            return "<a href='http://db.yeastgenome.org/cgi-bin/locus.pl?locus=$1' target=_blank>$sgd</a>";
1497        }
1498        return $sgd;
1499    }
1500    
1501    
1502    
1503    
1504    sub set_map_links {
1505        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1506        my($cgi,$x) = @_;
1507        my($before,$match,$after);
1508    
1509        my $org = ($cgi->param('org') || $cgi->param('genome') || "");
1510    
1511        if ($x =~ /^(.*)(MAP\d+)(.*)/s)
1512        {
1513            $before = $1;
1514            $match = $2;
1515            $after = $3;
1516            return &set_map_links($cgi,$before) . &map_link($cgi,$match,$org) . &set_map_links($cgi,$after);
1517        }
1518        return $x;
1519    }
1520    
1521    
1522    
1523    sub map_link {
1524        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1525        my($cgi,$map,$org) = @_;
1526    
1527        my $user = $cgi->param('user');
1528        $user = $user ? $user : "";
1529        $org = $org ? $org : "";
1530    
1531        my $url = "show_kegg_map.cgi?user=$user&map=$map&org=$org";
1532    #rel    my $url = &FIG::cgi_url() . "/show_kegg_map.cgi?user=$user&map=$map&org=$org";
1533        my $link = "<a href=\"$url\">$map</a>";
1534        return $link;
1535    }
1536    
1537    sub java_buttons {
1538        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1539      ## ADDED BY RAE
1540      # Provides code to include check all/first half/second half/none for javascrspt
1541      # this takes two variables - the form name provided in start_form with the
1542      # -name => field and the checkbox name
1543      my ($form, $button)=@_;
1544    
1545      my $java_script="<input type=\"button\" name=\"CheckAll\" value=\"Check All\"\nonClick=\"checkAll(document.$form.$button)\">\n";
1546      $java_script.="<input type=\"button\" name=\"CheckFirst\" value=\"Check First Half\"\nonClick=\"checkFirst(document.$form.$button)\">\n";
1547      $java_script.="<input type=\"button\" name=\"CheckSecond\" value=\"Check Second Half\"\nonClick=\"checkSecond(document.$form.$button)\">\n";
1548      $java_script.="<input type=\"button\" name=\"UnCheckAll\" value=\"Uncheck All\"\nonClick=\"uncheckAll(document.$form.$button)\">\n";
1549    
1550      return $java_script;
1551    }
1552    
1553    =head3 sub_link
1554    
1555    C<< my $htmlText = HTML::sub_link($cgi, $sub); >>
1556    
1557    Create a subsystem link. The link will be to the display page if there is no
1558    user or we are in SPROUT mode; otherwise it will be to the edit page.
1559    
1560    =over 4
1561    
1562    =item cgi
1563    
1564    CGI query object for the current web session. The parameters of special interest
1565    are C<SPROUT> and C<user>. If the user is non-blank and SPROUT mode is 0, then
1566    the subsystem's edit page will be shown rather than its display page.
1567    
1568    =item sub
1569    
1570    Name of the desired subsystem. It will be cleaned of underscores before the
1571    hyperlink is applied.
1572    
1573    =back
1574    
1575    =cut
1576    
1577    sub sub_link {
1578        # Allow call as an instance in addition to the authorized method.
1579        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1580        # Get the parameters.
1581        my ($cgi, $sub) = @_;
1582        # Declare the return variable.
1583        my $retVal;
1584        # Clean the subsystem name for display purposes. This is a very
1585        # different thing from URL-escaping.
1586        my $cleaned = CGI::escapeHtml($sub);
1587        $cleaned =~ s/_/ /g;
1588        # URL-escape the subsystem name for use in the link.
1589        my $linkable = uri_escape($sub);
1590        # Determine the mode. Note we use the little OR trick to insure that
1591        # we have the correct value for plugging into the output link.
1592        my $user = $cgi->param('user') || "";
1593        my $sproutMode = $cgi->param('SPROUT') || 0;
1594        if ($user && ! $sproutMode) {
1595            # A SEED user is calling, so we go to the edit page.
1596            $retVal = "<a href=\"subsys.cgi?ssa_name=$linkable&request=show_ssa&user=$user\">$cleaned</a>";
1597        } else {
1598            # A visitor or SPROUT user is calling, so we go to the display page.
1599            $retVal = "<a href=\"display_subsys.cgi?ssa_name=$linkable;request=show_ssa;sort=by_phylo;SPROUT=$sproutMode\">$cleaned</a>";
1600        }
1601        # Return the result.
1602        return $retVal;
1603    }
1604    
1605    
1606    sub reaction_link {
1607        my($reaction) = @_;
1608        if ($reaction =~ /^(\*)?(R\d+)/)
1609        {
1610            return "<a href=\"http://www.genome.ad.jp/dbget-bin/www_bget?rn+$2\" target=reaction$$>$reaction</a>";
1611        }
1612        return $reaction;
1613    }
1614    
1615    
1616    sub html_for_assignments {
1617        my($fig,$user,$peg_sets) = @_;
1618        my $i;
1619    
1620        my @vals = ();
1621        my $set = 1;
1622        foreach my $peg_set (@$peg_sets)
1623        {
1624            for ($i=0; ($i < @$peg_set); $i++)
1625            {
1626                my $peg = $peg_set->[$i];
1627                push(@vals,'show=' . join("@",($set,$i+1,$peg,&FIG::abbrev($fig->org_of($peg)),"")));
1628            }
1629            $set++;
1630        }
1631    
1632        $ENV{'REQUEST_METHOD'} = 'GET';
1633        $ENV{'QUERY_STRING'} = join('&',('request=show_commentary',"uni=1","user=$user",@vals));
1634        my $out = join("",`$FIG_Config::fig/CGI/chromosomal_clusters.cgi`);
1635        $out =~ s/^.*?<form/<form/si;
1636        $out =~ s/^(.*)<table.*/$1/si;
1637        return $out;
1638    }
1639    
1640    =head1 rss_feed
1641    
1642    Add something to the RSS feed. The rss feeds are stored in the Html directory, and there are several RSS feeds:
1643            SEED.rss                - everything gets written here
1644            SEEDgenomes.rss                 - whenever a genome is added to the SEED
1645            SEEDsubsystems.rss      - whenever a subsystem is edited (or should this be added?)
1646    
1647    
1648    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.
1649    
1650    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.
1651    
1652    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.
1653    
1654    The has can have these keys:
1655    
1656    REQUIRED:
1657    title       : the title. This is usually what is seen by the user in the pull down menu
1658    description : a more complete description that is often seen is rss viewers but not always
1659    link        : link to the item that was added/edited
1660    All other keys are treated as optional RSS arguments and written to the file.
1661    
1662    At most, $max_entries recent entries are stored in the rss file, and this is currently 50.
1663    
1664    RSS files are quite simple, and contain some standard header information, and then individual items surrounded by an <item> </item> tag. Note that there is also an initial title/description/link set that describes the file.
1665    
1666    
1667    =cut
1668    
1669    sub rss_feed {
1670     shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1671     my ($files, $args)=@_;
1672    
1673     # how many entries to store in the file
1674     my $max_entries=50;
1675    
1676     foreach my $a (keys %$args) {if ($a =~ /^-(.*)/) {my $b=$1; $args->{$b}=$args->{$a}; delete $args->{$a}}}
1677    
1678     my $filepath=$FIG_Config::fig."/CGI/Html/rss";
1679     # check for the directory and if not, make it
1680     mkdir $filepath unless (-d $filepath);
1681    
1682     # note that $info is a hash of references to hashes that are written out as headers in the file
1683     my $info=
1684     {
1685      "SEED.rss" =>
1686       {
1687            title           => "The SEED",
1688            description     => "Latest news from the SEED",
1689            link            => "Html/rss/SEED.rss",
1690       },
1691    
1692      "SEEDsubsystems.rss" =>
1693      {
1694            title           => "SEED Subsystems",
1695            description     => "Recently updated SEED subsystems",
1696            link            => "Html/rss/SEEDsubsystems.rss",
1697      },
1698    
1699      "SEEDsubsystems.rss" =>
1700      {
1701            title           => "SEED Genomes",
1702            description     => "Genomes recently added to the SEED",
1703            link            => &FIG::cgi_url()."/Html/rss/SEEDsubsystems.rss",
1704      },
1705    
1706     };
1707    
1708    
1709     # build the new xml
1710     my $xml = "\t<item>\n";
1711     foreach my $qw ("title", "description", "link") {
1712      unless ($args->{$qw}) {
1713       print STDERR "You need to include a $qw tag in your RSS description\n";
1714       return(0);
1715      }
1716      # we need to do something a bit funky with the link. We can't have ampersands in the <link> </link> in valid html
1717      # so we are going to pull out the links and uri_escape just the part after the .cgi
1718      if ($qw eq "link")
1719      {
1720       $args->{$qw} =~ /^(.*?\.cgi.)(.*)$/;
1721       $args->{$qw} = $1.uri_escape($2) if ($1 && $2);
1722      }
1723    
1724      $xml .= "\t\t<$qw>".$args->{$qw}."</$qw>\n";
1725      delete $args->{$qw};
1726     }
1727    
1728     foreach my $tag (grep {!/type/i} keys %$args)
1729     {
1730      $xml .= "\t\t<$tag>".$args->{$tag}."</$tag>\n";
1731     }
1732    
1733     $xml .= "\t</item>\n";
1734    
1735    
1736     my @files=("SEED.rss");
1737     if ($args->{"type"}) {
1738        my $type = $args->{type};
1739        push @files, "SEED.$type.rss"
1740    }
1741    
1742     foreach my $file ("SEED.rss", @$files)
1743     {
1744      if (-e "$filepath/$file")
1745      {
1746       my @out; # the new content of the file
1747       my $itemcount=0; # how many <item> </item>'s are we keeping
1748       my $initem; # are we in an item?
1749       open(IN, "$filepath/$file") || die "Can't open $filepath/$file";
1750       while (<IN>)
1751       {
1752        if (/\<item\>/) {
1753         push @out, $xml, unless ($itemcount);
1754         $itemcount++;
1755         $initem=1;
1756        }
1757        if (/\<\/item\>/) {$initem=0; next if ($itemcount > $max_entries)}
1758        next if ($initem && $itemcount > $max_entries);
1759        push @out, $_;
1760       }
1761       close IN;
1762       open(OUT, ">$filepath/$file") || die "Can't open $filepath/$file for writing";
1763       print OUT @out;
1764      }
1765      else
1766      {
1767       open(OUT, ">$filepath/$file") || die "Can't open $filepath/$file for writing";
1768       print OUT "<?xml version=\"1.0\"?>\n<rss version=\"2.0\">\n<channel>\n";
1769       if ($info->{$file})
1770       {
1771         # we're going to sanity check each of the three options we output, just to be sure
1772         foreach my $qw ("title", "description", "link")
1773         {
1774           if ($info->{$file}->{$qw})
1775           {
1776              print OUT "<$qw>", $info->{$file}->{$qw}, "</$qw>\n";
1777           } else {
1778              print STDERR "Please add a $qw for $file\n"; print OUT "<$qw>$file</$qw>\n";
1779           }
1780         }
1781       }
1782       else {
1783        print STDERR "Please define title, link, and description information for $file\n";
1784        print OUT "<title>$file</title>\n<description>An RSS feed</description>\n<link>", &FIG::cgi_url, "</link>\n";
1785       }
1786       print OUT "\n", $xml;
1787       print OUT "\n", "</channel>\n</rss>\n"
1788      }
1789     }
1790    }
1791    
1792    
1793    
1794    1;
1795    
 1  

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