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revision 1.64, Sat Oct 8 14:14:47 2005 UTC revision 1.119, Thu Dec 6 13:59:34 2007 UTC
# Line 1  Line 1 
1    #
2    # Copyright (c) 2003-2006 University of Chicago and Fellowship
3    # for Interpretations of Genomes. All Rights Reserved.
4    #
5    # This file is part of the SEED Toolkit.
6    #
7    # The SEED Toolkit is free software. You can redistribute
8    # it and/or modify it under the terms of the SEED Toolkit
9    # Public License.
10    #
11    # You should have received a copy of the SEED Toolkit Public License
12    # along with this program; if not write to the University of Chicago
13    # at info@ci.uchicago.edu or the Fellowship for Interpretation of
14    # Genomes at veronika@thefig.info or download a copy from
15    # http://www.theseed.org/LICENSE.TXT.
16    #
17    
18  package HTML;  package HTML;
19    
20    use strict;
21  use Tracer;  use Tracer;
22  use FIG;  use FIG;
23  use Carp;  use Carp;
# Line 10  Line 28 
28  use URI::URL;  use URI::URL;
29  use HTTP::Request::Common;  use HTTP::Request::Common;
30  use POSIX;  use POSIX;
31    use CGI;
32    
33    #use raelib; # now used for the excel function, that should eventually end up in here. Way too experimental!
34    my $raelib;
35    
36    
37    my $top_link_cache;
38    
39    
40  sub new  sub new
# Line 21  Line 46 
46      return bless $self, $class;      return bless $self, $class;
47  }  }
48    
49    sub top_link
50    {
51    
52        #
53        # Determine if this is a toplevel cgi or one in one of the subdirs (currently
54        # just /p2p).
55        #
56    
57        return $top_link_cache if ($top_link_cache);
58    
59        my @parts = split(/\//, $ENV{SCRIPT_NAME});
60        my $top;
61        if (defined $parts[-2] && $parts[-2] eq 'FIG')
62        {
63            $top = '.';
64    #       warn "toplevel @parts\n";
65        }
66        elsif (defined $parts[-3] && $parts[-3] eq 'FIG')
67        {
68            $top = '..';
69    #       warn "subdir @parts\n";
70        }
71        else
72        {
73            $top = $FIG_Config::cgi_base;
74    #       warn "other @parts\n";
75        }
76    
77        $top_link_cache = $top;
78        return $top;
79    }
80    
81  sub compute_html_header  sub compute_html_header
82  {  {
83      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
84      my($additional_insert, $user, %options ) = @_;      my($additional_insert, $user, %options ) = @_;
85    
86        local $/ = "\n";
87    
88      my $header_name = $options{header_name} ? $options{header_name} : "html.hdr";      my $header_name = $options{header_name} ? $options{header_name} : "html.hdr";
89      my $tail_name = $options{tail_name} ? $options{tail_name} : "html.tail";      my $tail_name = $options{tail_name} ? $options{tail_name} : "html.tail";
90    
# Line 36  Line 95 
95      }      }
96      my @html_hdr = &FIG::file_read($html_hdr_file);      my @html_hdr = &FIG::file_read($html_hdr_file);
97    
98      $options{no_fig_search} or push( @html_hdr, "<br><a href=\"index.cgi?user=$user\">FIG search</a>\n" );      # for my $k (sort keys %ENV) { warn "$k = $ENV{$k}\n"; }
99    
100        #
101        # Determine if this is a toplevel cgi or one in one of the subdirs (currently
102        # just /p2p).
103        #
104    
105        my @parts = split(/\//, $ENV{SCRIPT_NAME});
106        my $top;
107        if ($parts[-2] eq 'FIG')
108        {
109            $top = '.';
110    #       warn "toplevel @parts\n";
111        }
112        elsif ($parts[-3] eq 'FIG')
113        {
114            $top = '..';
115    #       warn "subdir @parts\n";
116        }
117        else
118        {
119            $top = $FIG_Config::cgi_base;
120    #       warn "other @parts\n";
121        }
122    
123        $options{no_fig_search} or push( @html_hdr, "<br><a href=\"$top/index.cgi?user=$user\">FIG search</a>\n" );
124    
125      if (@html_hdr)      if (@html_hdr)
126      {      {
# Line 64  Line 148 
148    
149          for $_ (@html_hdr)          for $_ (@html_hdr)
150          {          {
151              s,(href|img\s+src)="/FIG/,\1="$FIG_Config::cgi_base,g;              s,(href|img\s+src)="/FIG/,$1="$top/,g;
152              s,(\?user\=)\",$1$user",;              s,(\?user\=)\",$1$user",;
153              if ($_ eq "<!-- HEADER_INSERT -->\n")              if ($_ eq "<!-- HEADER_INSERT -->\n")
154              {              {
# Line 79  Line 163 
163  sub show_page {  sub show_page {
164      #warn "SHOWPAGE: cgi=", Dumper(@_);      #warn "SHOWPAGE: cgi=", Dumper(@_);
165      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
166      my($cgi,$html,$no_home, $alt_header, $css, $javasrc, $cookie) = @_;      my($cgi,$html,$no_home, $alt_header, $css, $javasrc, $cookie, $options) = @_;
167      my $i;      my $i;
168        Trace("Setting top link.") if T(3);
169        my $top = top_link();
170    
171      # ARGUMENTS:      # ARGUMENTS:
172      #     $cgi is the CGI method      #     $cgi is the CGI method
# Line 90  Line 176 
176      #     $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
177      #               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
178      #               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
179      #     $javasrc is a reference to an array of URLs to javascripts to be included (e.g. "/FIG/Html/css/styleswitcher.js")      #     $javasrc is a reference to an array of URLs to javascripts to be included (e.g. "FIG/Html/css/styleswitcher.js")
180      #     $cookie is the name and value of the cookie to set. Note that you should probably use raelib->cookie to get/set your cookies      #     $cookie is the name and value of the cookie to set. Note that you should probably use raelib->cookie to get/set your cookies
181        #     $options is a reference to a hash of options that you can pass around the pages
182      #      #
183      # Find the HTML header      # Find the HTML header
184      #      #
185        Trace("Reading tail.") if T(3);
186        my $tail_name = $options->{tail_name} ? $options->{tail_name} : "html.tail";
187      my $html_tail_file = "./Html/$tail_name";      my $html_tail_file = "./Html/$tail_name";
188      if (! -f $html_tail_file)      if (! -f $html_tail_file)
189      {      {
190          $html_tail_file = "$FIG_Config::fig/CGI/Html/$tail_name";          $html_tail_file = "$FIG_Config::fig/CGI/Html/$tail_name";
191      }      }
192        Trace("Extracting user name and header data.") if T(3);
193      my $user = $cgi->param('user') || "";      my $user = $cgi->param('user') || "";
194      my @html_hdr;      my @html_hdr;
195      if ($alt_header && ref($alt_header) eq "ARRAY")      if ($alt_header && ref($alt_header) eq "ARRAY")
# Line 110  Line 198 
198      }      }
199      else      else
200      {      {
201          @html_hdr = compute_html_header(undef,$user);          @html_hdr = compute_html_header(undef,$user,%$options);
202      }      }
203    
204      # RAE: I am offloading the handling of cookies to CGI.pm since I don't know how they are set up.      # RAE: I am offloading the handling of cookies to CGI.pm since I don't know how they are set up.
# Line 118  Line 206 
206    
207      # Note: 3/10/05 commented this line out pending the discussion of adding cookies into the seed that we are waiting to see about      # Note: 3/10/05 commented this line out pending the discussion of adding cookies into the seed that we are waiting to see about
208      # to add cookies back in replace these two header lines with each other      # to add cookies back in replace these two header lines with each other
209        #my $hdr_thing = $cgi->header(-cookie=>$cookie);
210      #print $cgi->header(-cookie=>$cookie);      my $hdr_thing = $cgi->header();
211      print $cgi->header();      Trace("Printing HTML header: $hdr_thing.") if T(3);
212        print $hdr_thing;
213        Trace("Header printed.") if T(3);
214      #      #
215      #  The SEED header file goes immediately after <BODY>.  Figure out      #  The SEED header file goes immediately after <BODY>.  Figure out
216      #  what parts of the HTML document skeleton are there, and fill in      #  what parts of the HTML document skeleton are there, and fill in
# Line 166  Line 255 
255      my $body_line = -1;      my $body_line = -1;
256      my $last_head_line = -1;  #  If no head tags are found, text goes at top.      my $last_head_line = -1;  #  If no head tags are found, text goes at top.
257      my $done = 0;      my $done = 0;
258        Trace("Processing special cases.") if T(3);
259      for ( $i = 0; $i < @$html; $i++ )      for ( $i = 0; $i < @$html; $i++ )
260      {      {
261          #  Some special cases:          #  Some special cases:
# Line 181  Line 270 
270          if ( $html->[$i] =~ /\<body[^0-9a-z]/i )          if ( $html->[$i] =~ /\<body[^0-9a-z]/i )
271          {          {
272              $body_line = $i;              $body_line = $i;
273              $last;              last;
274          }          }
275    
276          #  Now the general case.          #  Now the general case.
# Line 212  Line 301 
301    
302      if ( 1 )      if ( 1 )
303      {      {
304            Trace("Sanity checks in progress.") if T(3);
305          if ( $html_line >= 0 )          if ( $html_line >= 0 )
306          {          {
307              if ( ( $head_line >= 0 ) && ( $html_line > $head_line ) )              if ( ( $head_line >= 0 ) && ( $html_line > $head_line ) )
308              {              {
309                  print STDERR "<HTML> tag follows <HEAD> tag\n";                  Trace("<HTML> tag follows <HEAD> tag.") if T(1);
310              }              }
311              if ( ( $head_end_line >= 0 ) && ( $html_line > $head_end_line ) )              if ( ( $head_end_line >= 0 ) && ( $html_line > $head_end_line ) )
312              {              {
313                  print STDERR "<HTML> tag follows </HEAD> tag\n";                  Trace("<HTML> tag follows </HEAD> tag.") if T(1);
314              }              }
315          }          }
316          if ( $head_line >= 0 )          if ( $head_line >= 0 )
317          {          {
318              if ( ( $head_end_line >= 0 ) && ( $head_line > $head_end_line ) )              if ( ( $head_end_line >= 0 ) && ( $head_line > $head_end_line ) )
319              {              {
320                  print STDERR "<HEAD> tag follows </HEAD> tag\n";                  Trace("<HEAD> tag follows </HEAD> tag.") if T(1);
321              }              }
322          }          }
323      }      }
324        Trace("Sanity checks complete.") if T(3);
325      #      #
326      #  Okay.  Let's put in the html header file, and missing tags:      #  Okay.  Let's put in the html header file, and missing tags:
327      #      #
# Line 242  Line 332 
332      #  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,
333      #  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!
334      #  RAE: This is now deprecated because everything is in an external file, FIG.js, included later      #  RAE: This is now deprecated because everything is in an external file, FIG.js, included later
   
335      if ( $body_line < 0 )      if ( $body_line < 0 )
336      {      {
337          $body_line = $last_head_line + 1;          $body_line = $last_head_line + 1;
338            Trace("Splicing body line at $body_line.") if T(3);
339          splice( @$html, $body_line, 0, "<BODY>\n" );          splice( @$html, $body_line, 0, "<BODY>\n" );
340      }      }
341    
# Line 255  Line 345 
345    
346      if (@html_hdr)      if (@html_hdr)
347      {      {
348            Trace("Splicing SEED page header after $body_line.") if T(3);
349          splice( @$html, $body_line + 1, 0, @html_hdr );          splice( @$html, $body_line + 1, 0, @html_hdr );
350      }      }
351    
# Line 265  Line 356 
356      if ( $head_end_line < 0 )      if ( $head_end_line < 0 )
357      {      {
358          $head_end_line = $body_line;          $head_end_line = $body_line;
359            Trace("Splicing header terminater at $body_line.") if T(3);
360          splice( @$html, $body_line, 0, "</HEAD>\n" );          splice( @$html, $body_line, 0, "</HEAD>\n" );
361      }      }
362    
# Line 274  Line 366 
366      # be moved out, but I want to try it and see what happens.  css has the format:      # be moved out, but I want to try it and see what happens.  css has the format:
367      #      #
368      # <link rel='stylesheet' title='default' href='/css/default.css' type='text/css'>      # <link rel='stylesheet' title='default' href='/css/default.css' type='text/css'>
369        Trace("Formatting CSS.") if T(3);
370      # convert the default key to the right case. and eliminate dups      # convert the default key to the right case. and eliminate dups
371      foreach my $k (keys %$css) {if (lc($k) eq "default") {$css->{'Default'}=$css->{$k}}}      foreach my $k (keys %$css) {if (lc($k) eq "default") {$css->{'Default'}=$css->{$k}}}
372    
373      if (!$css || !$css->{'Default'})      if (!$css || !$css->{'Default'})
374      {      {
375         $css->{'Default'} = &FIG::cgi_url() . "/Html/css/default.css";         $css->{'Default'} = "Html/css/default.css";
376      }      }
377      if (!$css->{"Sans Serif"})      if (!$css->{"Sans Serif"})
378      {      {
379         $css->{'Sans Serif'} = &FIG::cgi_url() . "/Html/css/sanserif.css";         $css->{'Sans Serif'} = "Html/css/sanserif.css";
380      }      }
381    
382      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";
# Line 296  Line 388 
388         $csstext .= "<link rel='alternate stylesheet' title='$k' href='".$css->{$k}."' type='text/css'>\n";         $csstext .= "<link rel='alternate stylesheet' title='$k' href='".$css->{$k}."' type='text/css'>\n";
389      }      }
390    
391      $csstext   .= "<link rel='alternate'  title='SEED RSS feeds' href='".&FIG::cgi_url()."/Html/rss/SEED.rss' type='application/rss+xml'>\n";      $csstext   .= "<link rel='alternate'  title='SEED RSS feeds' href='Html/rss/SEED.rss' type='application/rss+xml'>\n";
392    
393      # RAE: also added support for external javascripts here.      # RAE: also added support for external javascripts here.
394      # we are cluttering the HTML code with all the javascripts when they could easily be in external files      # we are cluttering the HTML code with all the javascripts when they could easily be in external files
# Line 304  Line 396 
396    
397      # the file FIG.js contains most of the java script we use routinely. Every browser will just cache this and so      # the file FIG.js contains most of the java script we use routinely. Every browser will just cache this and so
398      # it will reduce our overhead.      # it will reduce our overhead.
399        Trace("Formatting javascript.") if T(3);
400      # $javasrc must be a ref to an array with urls (absolute or relative) to the javascripts      # $javasrc must be a ref to an array with urls (absolute or relative) to the javascripts
401      push @$javasrc, &FIG::cgi_url() . "/Html/css/FIG.js";      push @$javasrc, "Html/css/FIG.js";
402      foreach my $script (@$javasrc) {      foreach my $script (@$javasrc) {
403          $csstext .= "<script src=\"$script\" type=\"text/javascript\"></script>\n";          $csstext .= "<script src=\"$script\" type=\"text/javascript\"></script>\n";
404      }      }
405    
406        Trace("Re-splicing the header terminator at $head_end_line.") if T(3);
   
407      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.
408    
409      #      #
# Line 330  Line 421 
421          # BASE href needs to be absolute. RDO.          # BASE href needs to be absolute. RDO.
422          #          #
423          #          #
424          $base_url = &FIG::cgi_url;  #        $base_url = &FIG::cgi_url;
425  #       my $base_url = $FIG_Config::cgi_base;  #       my $base_url = $FIG_Config::cgi_base;
426  #       if ( ! $base_url )                      # if cgi_base was not defined  #       if ( ! $base_url )                      # if cgi_base was not defined
427  #       {  #       {
# Line 353  Line 444 
444      if ( $html_line < 0 )      if ( $html_line < 0 )
445      {      {
446          $html_line = 0;          $html_line = 0;
447            Trace("Splicing the HTML tag at $html_line.") if T(3);
448          splice( @$html, $html_line, 0, "<HTML>\n" );          splice( @$html, $html_line, 0, "<HTML>\n" );
449      }      }
450    
# Line 363  Line 455 
455      if ( $head_line < 0 )      if ( $head_line < 0 )
456      {      {
457          $head_line = $html_line + 1;          $head_line = $html_line + 1;
458            Trace("Splicing the HEAD tag at $head_line.") if T(3);
459          splice( @$html, $head_line, 0, "<HEAD>\n" );          splice( @$html, $head_line, 0, "<HEAD>\n" );
460      }      }
461    
462      #      #
463      #  Place FIG search link at bottom of page      #  Place FIG search link at bottom of page
464      #      #
465        Trace("Placing FIG search link.") if T(3);
466      my @tail = -f $html_tail_file ? `cat $html_tail_file` : ();      my @tail = -f $html_tail_file ? `cat $html_tail_file` : ();
467      if (! $no_home)      if (! $no_home)
468      {      {
# Line 380  Line 473 
473      #      #
474      # See if we have a site-specific tail (for disclaimers, etc).      # See if we have a site-specific tail (for disclaimers, etc).
475      #      #
476        Trace("Placing site tail.") if T(3);
477      my $site_tail = "$FIG_Config::fig_disk/config/site_tail.html";      my $site_tail = "$FIG_Config::fig_disk/config/site_tail.html";
478      my $site_fh;      my $site_fh;
479      if (open($site_fh, "<$site_tail"))      if (open($site_fh, "<$site_tail"))
# Line 394  Line 487 
487      #  or before </html>, or at end of page.      #  or before </html>, or at end of page.
488      #      #
489      my @tags = ();      my @tags = ();
490      # Check for a tracing queue.      Trace("Processing closing tags.") if T(3);
     my $traceString = QTrace("HTML");  
     if ($traceString) {  
         push @tags, $traceString;  
     }  
491      for ($i=0; ($i < @$html) && ($html->[$i] !~ /\<\/body\>/i); $i++) {}      for ($i=0; ($i < @$html) && ($html->[$i] !~ /\<\/body\>/i); $i++) {}
492      if ($i >= @$html)        # </body> not found; look for </html>      if ($i >= @$html)        # </body> not found; look for </html>
493      {      {
# Line 413  Line 502 
502    
503      if ( @tail )      if ( @tail )
504      {      {
505            Trace("Splicing tail.") if T(3);
506          splice( @$html, $i, 0, @tail, @tags );          splice( @$html, $i, 0, @tail, @tags );
507      }      }
508      elsif ( @tags )      elsif ( @tags )
509      {      {
510            Trace("Splicing tags.") if T(3);
511          splice( @$html, $i, 0, @tags );          splice( @$html, $i, 0, @tags );
512      }      }
513    
514        Trace("Printing the HTML array.") if T(3);
515      # RAE the chomp will return any new lines at the ends of elements in the array,      # RAE the chomp will return any new lines at the ends of elements in the array,
516      # and then we can join  with a "\n". This is because somethings put newlines in,      # and then we can join  with a "\n". This is because somethings put newlines in,
517      # and others don't. This should make nicer looking html      # and others don't. This should make nicer looking html
# Line 428  Line 520 
520      # print join "\n", @$html;      # print join "\n", @$html;
521      #      #
522      # Apparently the above still breaks things. This is the correct code:      # Apparently the above still breaks things. This is the correct code:
   
523      foreach $_ (@$html)      foreach $_ (@$html)
524      {      {
525          print $_;          my $line = $_;
526            if (T(4)) {
527                my $escapedLine = CGI::escapeHTML($line);
528                Trace("Printing:\n$escapedLine") if T(4);
529            }
530            print $line;
531      }      }
532    
533  }  }
534    
535    
536    =head1 make_table
537    
538    The main method to convert an array into a table.
539    
540    The col_hdrs are set to the <th> headers, the $tab is an array of arrays. The first is the rows, and the second is the columns. The title is the title of the table.
541    
542    The options define the settings for the table such as border, width, and class for css formatting. If the option "excelfile" is set to a filename that will be created in FIG_Config::temp, and the link included that allows the user to download the file as an excel file.
543    
544    =cut
545    
546  sub make_table {  sub make_table {
547      my($col_hdrs,$tab,$title, %options ) = @_;      my($col_hdrs,$tab,$title, %options ) = @_;
548      my(@tab);      my(@tab);
549    
550      my $border = defined $options{border} ? "border=\"$options{border}\"" : "border";      my $border = defined $options{border} ? "border=\"$options{border}\"" : "border";
551      my $width = defined $options{width} ? "width=\"$options{width}\"" : undef;      my $width = defined $options{width} ? "width=\"$options{width}\"" : "";
552      push( @tab, "\n<table $border $width>\n",      my $class = defined $options{class} ? "class=\"$options{class}\"" : "";
553        push( @tab, "\n<table $border $width $class>\n",
554                  "\t<caption><b>$title</b></caption>\n",                  "\t<caption><b>$title</b></caption>\n",
555                  "\t<tr>\n\t\t"                  "\t<tr>\n\t\t"
556                . join( "\n", map { &expand($_, "th") } @$col_hdrs )                . join( "\n", map { &expand($_, "th") } @$col_hdrs )
# Line 459  Line 567 
567              );              );
568      }      }
569      push(@tab,"</table>\n");      push(@tab,"</table>\n");
570    
571        # excelfile should be appropriate for a filename (no spaces/special characters)
572        if (defined $options{"excelfile"}) {
573            if (! defined($raelib)) {
574                require raelib;
575                $raelib = new raelib;
576            }
577            push @tab, $raelib->tab2excel($col_hdrs,$tab,$title,\%options,$options{"excelfile"})}
578    
579      return join("",@tab);      return join("",@tab);
580  }  }
581    
582    sub abstract_coupling_table {
583        my($cgi,$prot,$coupling) = @_;
584        my %fc;
585    
586        my $col_hdrs = ["coupled to","Score","Type of Coupling", "Type-specific Data"];
587        my $tab = [];
588        my %by_peg;
589        foreach my $x (@$coupling)
590        {
591            my($peg2,$psc,$type,$extra) = @$x;
592            if (($type !~ /^[ID]FC$/) || (! $fc{$peg2}))
593            {
594                if ($type =~  /^[ID]FC$/)
595                {
596                    $fc{$peg2} = 1;
597                }
598    
599                $by_peg{$peg2} += $psc;
600            }
601        }
602    
603        foreach my $x (sort { ($by_peg{$b->[0]} <=> $by_peg{$a->[0]})
604                              or ($a->[0] cmp $b->[0])
605                              or ($b->[1] <=> $a->[1])
606                              or ($a->[2] cmp $b->[2]) } @$coupling)
607        {
608            my($peg2,$psc,$type,$extra) = @$x;
609            push(@$tab,[&fid_link($cgi,$peg2,1),$psc,$type,&set_prot_links($cgi,join(", ",@$extra))]);
610        }
611    
612    
613         my $help = "<a href=\"Html/abstract_coupling.html\" target=\"SEED_or_SPROUT_help\">for help</a>";
614    #    my @html = &make_table($col_hdrs,$tab,"Abstract Coupling Data for $prot");
615    #    push(@html,"<hr>\n",$cgi->h3($help),"<br>");
616    #    return @html;
617    
618        return &make_table($col_hdrs,$tab,"Abstract Coupling Data for $prot [$help]");
619    }
620    
621  sub expand {  sub expand {
622      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
623      my( $x, $tag ) = @_;      my( $x, $tag ) = @_;
# Line 661  Line 817 
817      return "<a href=$link>$role</a>";      return "<a href=$link>$role</a>";
818  }  }
819    
820  #  =head2 fid_link
821  # Local means to eliminate the fig|org.peg from the  
822  # text of the link.  Get a link to a fid.
823  #  
824    use: my $html=&HTML::fid_link($cgi, $fid, Local, Just_URL, Full_Path);
825    
826    Local is a boolean means to eliminate the fig|org.peg from the text of the link.
827    
828    Just_URL will only return the URL and not the HTML code. The default is to return the full code.
829    
830    Full_Path is a boolean that will get the full path to the URL not just a relative path. This is required in pages where the base href changes (e.g. if an image is imported like on the metabolic pages).
831    
832    =cut
833    
834    
835  sub fid_link {  sub fid_link {
836      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
837      my($cgi,$fid,$local,$just_url) = @_;      my($cgi,$fid,$local,$just_url,$fullpath) = @_;
838        Trace("Creating link for feature $fid.") if T(4);
839        my $err=join(" ", $cgi,$fid,$local,$just_url,$fullpath);
840    
841      my($n);      my($n);
842    
843      if ($fid =~ /^fig\|\d+\.\d+\.([a-z]+)\.(\d+)/)      my $top = top_link();
844        if ($fullpath) {$top=$FIG_Config::cgi_url}
845    
846        if ($fid =~ /^fig\|\d+\.\d+\.([a-zA-Z]+)\.(\d+)/)
847      {      {
848          if ($local)          if ($local)
849          {          {
# Line 689  Line 862 
862          }          }
863    
864          my $link;          my $link;
865            my $new_framework = $cgi->param('new_framework') ? 1 : 0;
866          #added to format prophage and path island links to feature.cgi          #added to format prophage and path island links to feature.cgi
867          if ($1 ne "peg")          my $sprout = $cgi->param('SPROUT') ? "&SPROUT=1" : "";
868            my $virt = "&48hr_job=" . $cgi->param("48hr_job");
869            Trace("Sprout mode is \"$sprout\".") if T(4);
870            if ($1 ne "peg" && ! $sprout)
871          {          {
872               Trace("Creating feature link for $fid.") if T(4);
873             my $user = $cgi->param('user');             my $user = $cgi->param('user');
874             if (! $user) { $user = "" }             if (! $user) { $user = "" }
875             my $sprout = $cgi->param('SPROUT') ? "&SPROUT=1" : "";             $link = "$top/feature.cgi?feature=$fid&user=$user$sprout$virt";
            $link = &FIG::cgi_url . "/feature.cgi?feature=$fid&user=$user$trans$sprout";  
876             $link =~ s/[a-z_A-Z0-9]+\.cgi\?/feature.cgi?/;             $link =~ s/[a-z_A-Z0-9]+\.cgi\?/feature.cgi?/;
877          }          }
878          else          else
879          {          {
880                Trace("Creating protein link for $fid.") if T(4);
881              my $user = $cgi->param('user');              my $user = $cgi->param('user');
882              if (! $user) { $user = "" }              if (! $user) { $user = "" }
883              my $trans = $cgi->param('translate') ? "&translate=1" : "";              my $trans = $cgi->param('translate') ? "&translate=1" : "";
# Line 715  Line 893 
893    
894              #if (! $cgi_url) { $cgi_url = &FIG::cgi_url }              #if (! $cgi_url) { $cgi_url = &FIG::cgi_url }
895              #$link = $cgi_url . "/protein.cgi?prot=$fid&user=$user$trans$sprout";              #$link = $cgi_url . "/protein.cgi?prot=$fid&user=$user$trans$sprout";
896              $link = "protein.cgi?prot=$fid&user=$user$trans$sprout";              $link = "$top/protein.cgi?prot=$fid&user=$user$trans$sprout$virt\&new_framework=$new_framework";
897              $link =~ s/[a-z_A-Z0-9]+\.cgi\?/protein.cgi?/;              $link =~ s/[a-z_A-Z0-9]+\.cgi\?/protein.cgi?/;
             #  
             # Elimin the p2p part if we're in that subdir. Ugh.  
             #  
             $link =~ s,p2p/protein.cgi,protein.cgi,;  
898          }          }
899          if ($just_url)          if ($just_url)
900          {          {
# Line 728  Line 902 
902          }          }
903          else          else
904          {          {
905              return "<a href=$link>$n</a>";              return "<a href='$link'>$n</a>";
906          }          }
907      }      }
908      return $fid;      return $fid;
# Line 741  Line 915 
915      return $family;      return $family;
916  }  }
917    
918    =head2 evidence_codes_explain
919    
920    Given an evidence code, returns a string that explains this eveidence code.
921    
922    =cut
923    
924    sub evidence_codes_explain {
925     my($ec)=@_;
926     return unless ($ec);
927    
928     $ec=uc($ec);
929     return "IDA: Inferred from Direct Assay" if ($ec =~ /IDA/);
930     return "IGI: Inferred from Genetic Interaction" if ($ec =~ /IGI/);
931     return "TAS: Traceable Author Statement" if ($ec =~ /TAS/);
932     return "ISU: in subsystem unique" if ($ec =~ /ISU/);
933     return "$ec: in subsystem duplicates" if ($ec =~ /IDU/);
934     return "$ec: in cluster with" if ($ec =~ /ICW/);
935     return "FF: in FIGfam" if ($ec =~ /FF/);
936     return "CWN: clustered with nonhypothetical" if ($ec =~ /CWN/);
937     return "CWH: clustered, but only with hypotheticals" if ($ec =~ /CWH/);
938     return "DLIT: literature references to this gene exist" if ($ec =~ /DLIT/);
939     return "ILIT: no references to this gene exist, but they do to other genes with the same functional role" if ($ec =~ /ILIT/);
940     return "$ec: unknown!";
941    }
942    
943  sub get_html {  sub get_html {
944      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
# Line 760  Line 958 
958          my $response = $ua->request($request);          my $response = $ua->request($request);
959          $out = $response->content;          $out = $response->content;
960      }      }
961      else  
962        if ($type =~/get/i)
963      {      {
964          @args = ();          @args = ();
965          foreach $x (@$kv_pairs)          foreach $x (@$kv_pairs)
# Line 772  Line 971 
971          {          {
972              $url .= "?" . join("&",@args);              $url .= "?" . join("&",@args);
973          }          }
974          $request = new HTTP::Request('GET', $url);          my $request = new HTTP::Request('GET', $url);
975          my $response = $ua->request($request);          my $response = $ua->request($request);
976    
977          if ($response->is_success)          if ($response->is_success)
# Line 790  Line 989 
989    
990  #   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
991  #   properly.  Remove the header.  #   properly.  Remove the header.
992        my $i;
993      for ($i=0; ($i < @output) && ($output[$i] !~ /^\s*\</); $i++) {}      for ($i=0; ($i < @output) && ($output[$i] !~ /^\s*\</); $i++) {}
994      if ($i < @output)      if ($i < @output) {
     {  
   
995          splice(@output,0,$i);          splice(@output,0,$i);
996      }      }
997    
# Line 810  Line 1007 
1007  sub trim_output {  sub trim_output {
1008      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1009      my($out) = @_;      my($out) = @_;
1010      my $i;      my ($i, $j);
1011    
1012      for ($i=0; ($i < @$out) && ($out->[$i] !~ /^\</); $i++) {}      for ($i=0; ($i < @$out) && ($out->[$i] !~ /^\</); $i++) {}
1013      splice(@$out,0,$i);      splice(@$out,0,$i);
# Line 839  Line 1036 
1036      for ($j=$i-1; ($j > 0) && ($out->[$j] !~ /FIG search/); $j--) {}      for ($j=$i-1; ($j > 0) && ($out->[$j] !~ /FIG search/); $j--) {}
1037      if ($j > 0)      if ($j > 0)
1038      {      {
1039            #
1040            # Hm. We would have tried using the options here:
1041            # my $tail_name = $options{tail_name} ? $options{tail_name} : "html.tail";
1042            # but they're not passed in. So use the default html.tail.
1043            #
1044            my $html_tail_file = "./Html/html.tail";
1045          my @tmp = `cat $html_tail_file`;          my @tmp = `cat $html_tail_file`;
1046          my $n = @tmp;          my $n = @tmp;
1047          splice(@$out,$j-$n,$n+1);          splice(@$out,$j-$n,$n+1);
# Line 857  Line 1060 
1060          $after = $3;          $after = $3;
1061          return &set_prot_links($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,$after);
1062      }      }
1063      elsif ($x =~ /^(.*)\b([NXYZA]P_[0-9\.]+)\b(.*)/s)      elsif ($x =~ /^(.*)\b([NXYZA][PM]_[0-9\.]+)\b(.*)/s)
1064      {      {
1065          $before = $1;          $before = $1;
1066          $match = $2;          $match = $2;
# Line 871  Line 1074 
1074          $after = $3;          $after = $3;
1075          return &set_prot_links($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,$after);
1076      }      }
1077      elsif ($x =~ /^(.*)(tigr\|[0-9a-zA-Z]+)(.*)/s)      elsif ($x =~ /^(.*)(img\|\d+)(.*)/s)
1078        {
1079            $before = $1;
1080            $match = $2;
1081            $after = $3;
1082            return &set_prot_links($cgi,$before) . &HTML::img_link($cgi,$match) . &set_prot_links($cgi,$after);
1083        }
1084        elsif ($x =~ /^(.*)(tigr\|\w+)(.*)/s)
1085      {      {
1086          $before = $1;          $before = $1;
1087          $match = $2;          $match = $2;
1088          $after = $3;          $after = $3;
1089          return &set_prot_links($cgi,$before) . &HTML::tigr_link($cgi,$match) . &set_prot_links($cgi,$after);          return &set_prot_links($cgi,$before) . &HTML::tigr_link($cgi,$match) . &set_prot_links($cgi,$after);
1090      }      }
1091        elsif ($x =~ /^(.*)(tigrcmr\|\w+)(.*)/s)
1092        {
1093            $before = $1;
1094            $match = $2;
1095            $after = $3;
1096            return &set_prot_links($cgi,$before) . &HTML::tigr_link($cgi,$match) . &set_prot_links($cgi,$after);
1097        }
1098        elsif ($x =~ /^(.*)\b(eric\|\S+)\b(.*)/s)
1099        {
1100            $before = $1;
1101            $match = $2;
1102            $after = $3;
1103            return &set_prot_links($cgi,$before) . &HTML::eric_link($cgi,$match) . &set_prot_links($cgi,$after);
1104        }
1105    
1106        elsif ($x =~ /^(.*)\b(bhb\|.*?)\b(.*)/s)
1107        {
1108            $before = $1;
1109            $match = $2;
1110            $after = $3;
1111            return &set_prot_links($cgi,$before) . &HTML::bhb_link($cgi,$match) . &set_prot_links($cgi,$after);
1112        }
1113    
1114        elsif ($x =~ /^(.*)\b(apidb\|[0-9\.a-z_]+)\b(.*)/s)
1115        {
1116            $before = $1;
1117            $match = $2;
1118            $after = $3;
1119            return &set_prot_links($cgi,$before) . &HTML::apidb_link($cgi,$match) . &set_prot_links($cgi,$after);
1120        }
1121    
1122        elsif ($x =~ /^(.*)\b(patric\|.*?)\b(.*)/s)
1123        {
1124            $before = $1;
1125            $match = $2;
1126            $after = $3;
1127            return &set_prot_links($cgi,$before) . &HTML::patric_link($cgi,$match) . &set_prot_links($cgi,$after);
1128        }
1129    
1130        elsif ($x =~ /^(.*)\b(vbrc\|.*?)\b(.*)/s)
1131        {
1132            $before = $1;
1133            $match = $2;
1134            $after = $3;
1135            return &set_prot_links($cgi,$before) . &HTML::vbrc_link($cgi,$match) . &set_prot_links($cgi,$after);
1136        }
1137    
1138        elsif ($x =~ /^(.*)\b(vectorbase\|.*?)\b(.*)/s)
1139        {
1140            $before = $1;
1141            $match = $2;
1142            $after = $3;
1143            return &set_prot_links($cgi,$before) . &HTML::vectorbase_link($cgi,$match) . &set_prot_links($cgi,$after);
1144        }
1145      elsif ($x =~  /^(.*)(uni\|[A-Z0-9]{6})(.*)/s)      elsif ($x =~  /^(.*)(uni\|[A-Z0-9]{6})(.*)/s)
1146      {      {
1147          $before = $1;          $before = $1;
# Line 906  Line 1170 
1170          $after = $3;          $after = $3;
1171          return &set_prot_links($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,$after);
1172      }      }
1173        elsif ($x =~ /^(.*)(Ensembl[a-zA-Z]+:[a-zA-Z_0-9\.]+)(.*)/s)
1174        {
1175            $before = $1;
1176            $match = $2;
1177            $after = $3;
1178            return &set_prot_links($cgi,$before) . &HTML::ensembl_link($cgi,$match) . &set_prot_links($cgi,$after);
1179        }
1180        elsif ($x =~ /^(.*)(EntrezGene:[a-zA-Z_0-9\.]+)(.*)/s)
1181        {
1182            $before = $1;
1183            $match = $2;
1184            $after = $3;
1185            return &set_prot_links($cgi,$before) . &HTML::entrezgene_link($cgi,$match) . &set_prot_links($cgi,$after);
1186        }
1187        elsif ($x =~ /^(.*)(MIM:[a-zA-Z_0-9\.]+)(.*)/s)
1188        {
1189            $before = $1;
1190            $match = $2;
1191            $after = $3;
1192            return &set_prot_links($cgi,$before) . &HTML::mim_link($cgi,$match) . &set_prot_links($cgi,$after);
1193        }
1194        elsif ($x =~ /^(.*)(HGNC:[a-zA-Z_0-9\.]+)(.*)/s)
1195        {
1196            $before = $1;
1197            $match = $2;
1198            $after = $3;
1199            return &set_prot_links($cgi,$before) . &HTML::hgnc_link($cgi,$match) . &set_prot_links($cgi,$after);
1200        }
1201        elsif ($x =~ /^(.*)(UniGene:[a-zA-Z_0-9\.]+)(.*)/s)
1202        {
1203            $before = $1;
1204            $match = $2;
1205            $after = $3;
1206            return &set_prot_links($cgi,$before) . &HTML::unigene_link($cgi,$match) . &set_prot_links($cgi,$after);
1207        }
1208    # IPI stopped working. turn off for now.
1209    #    elsif ($x =~ /^(.*)(IPI:[a-zA-Z_0-9\.]+)(.*)/s)
1210    #    {
1211    #        $before = $1;
1212    #        $match = $2;
1213    #        $after = $3;
1214    #        return &set_prot_links($cgi,$before) . &HTML::ipi_link($cgi,$match) . &set_prot_links($cgi,$after);
1215    #    }
1216        elsif ($x =~ /^(.*)(WP:[a-zA-Z_0-9\.]+)(.*)/s)
1217        {
1218            #wormbase
1219    
1220            $before = $1;
1221            $match = $2;
1222            $after = $3;
1223            return &set_prot_links($cgi,$before) . &HTML::wp_link($cgi,$match) . &set_prot_links($cgi,$after);
1224        }
1225        elsif ($x =~ /^(.*)(FB:[a-zA-Z_0-9\.]+)(.*)/s)
1226        {
1227            #flybase
1228    
1229            $before = $1;
1230            $match = $2;
1231            $after = $3;
1232            return &set_prot_links($cgi,$before) . &HTML::fb_link($cgi,$match) . &set_prot_links($cgi,$after);
1233        }
1234        elsif ($x =~ /^(.*)(FlyBaseORFNames:[a-zA-Z_0-9\.]+)(.*)/s)
1235        {
1236            #flybase
1237    
1238            $before = $1;
1239            $match = $2;
1240            $after = $3;
1241            return &set_prot_links($cgi,$before) . &HTML::fborf_link($cgi,$match) . &set_prot_links($cgi,$after);
1242        }
1243        elsif ($x =~ /^(.*)(SGD_LOCUS:[a-zA-Z_0-9\.]+)(.*)/s)
1244        {
1245            #flybase
1246    
1247            $before = $1;
1248            $match = $2;
1249            $after = $3;
1250            return &set_prot_links($cgi,$before) . &HTML::sgd_link($cgi,$match) . &set_prot_links($cgi,$after);
1251        }
1252        elsif ($x =~ /^(.*)(tr\|[a-zA-Z0-9]+)(.*)/s)
1253        {
1254    
1255          $before = $1;
1256          $match = $2;
1257          $after = $3;
1258    
1259          return &set_prot_links($cgi,$before) .  &HTML::trembl_link($cgi,$match) . &set_prot_links($cgi,$after);
1260        }
1261      return $x;      return $x;
1262  }  }
1263    
1264    sub trembl_link {
1265        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1266        my($cgi,$id) = @_;
1267    
1268        if ($id =~ /^tr\|(.*)/) {
1269          return "<a href='http://ca.expasy.org/uniprot/$1' target=_blank>$id</a>";
1270        } else {
1271          return "invalid call to trembl link";
1272        }
1273    }
1274    
1275  sub refseq_link {  sub refseq_link {
1276      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1277      my($cgi,$id) = @_;      my($cgi,$id) = @_;
1278    
1279      if ($id =~ /^[NXYZA]P_/)      if ($id =~ /^[NXYZA]P_/)
1280      {      {
1281          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=$id' target=_blank>$id</a>";
1282        }
1283        elsif ($id =~ /^[NXYZA]M_/)
1284        {
1285            return "<a href='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=nuccore&cmd=search&term=$id' target=_blank>$id</a>";
1286      }      }
1287  }  }
1288    
# Line 925  Line 1292 
1292    
1293      if ($gi =~ /^gi\|(\d+)$/)      if ($gi =~ /^gi\|(\d+)$/)
1294      {      {
1295          return "<a href=http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=Protein&list_uids=$1&dopt=GenPept>$gi</a>";          return "<a href='http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=Protein&list_uids=$1&dopt=GenPept' target=_blank>$gi</a>";
1296      }      }
1297      return $gi;      return $gi;
1298  }  }
# Line 934  Line 1301 
1301      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1302      my($cgi,$tigr) = @_;      my($cgi,$tigr) = @_;
1303    
1304      if ($tigr =~ /^tigr\|([0-9a-zA-Z]+)$/)      if ($tigr =~ /^tigr\|(NT|ntbp|ntbpA|BA|BMAA|BXB|GBA)(\w+)$/)
1305        {
1306            my $id=$1.$2;
1307            return "<a href=\"http://pathema.tigr.org/tigr-scripts/pathema/shared/GenePage.cgi?locus=$id\" target=_blank>$tigr</a> (Pathema)";
1308        }
1309        elsif ($tigr =~ /^tigr(cmr)?\|(\S+)$/)
1310      {      {
1311          return "<a href=\"http://pathema.tigr.org/tigr-scripts/CMR/GenePage.cgi?locus=$1\">$tigr</a>";          return "<a href=\"http://www.tigr.org/tigr-scripts/CMR2/GenePage.spl?locus=$2\" target=_blank>$tigr</a>";
1312      }      }
1313      return $tigr;      return $tigr;
1314  }  }
1315    
1316    sub eric_link {
1317        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1318        my($cgi,$eric) = @_;
1319    
1320        if ($eric =~ /^eric\|(\S+)/)
1321        {
1322            return "<a href=\"https://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=$1\" target=_blank>$eric</a>";
1323        }
1324        return $eric;
1325    }
1326    
1327    sub bhb_link {
1328        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1329        my($cgi,$bhb) = @_;
1330    
1331        return "<a href=\"http://www.biohealthbase.org\" target=_blank>$bhb</a>";
1332    }
1333    
1334    sub apidb_link {
1335        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1336        my($cgi,$api) = @_;
1337    
1338        if ($api =~ /apidb\|(.*?)\.(.*)$/)
1339        {
1340            return "<a href=\"http://www.apidb.org/cgi-bin/redirect.cgi?taxon_id=$1&source_id=$2\" target=_blank>$api</a>";
1341        }
1342        return $api;
1343    }
1344    
1345    sub patric_link {
1346        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1347        my($cgi,$patric) = @_;
1348    
1349        if ($patric =~ /patric\|(.*)/)
1350        {
1351            return "<a href=\"https://patric.vbi.vt.edu/software/curationTool/gep/pgiCuration.php?locus_name=$1\" target=_blank>$patric</a>";
1352        }
1353        return $patric;
1354    }
1355    
1356    sub vbrc_link {
1357        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1358        my($cgi,$vbrc) = @_;
1359    
1360        if ($vbrc =~ /vbrc\|(.*)/)
1361        {
1362            return "<a href=\"http://www.biovirus.org/gene_detail.asp?name=$1\" target=_blank>$vbrc</a>";
1363        }
1364        return $vbrc;
1365    }
1366    
1367    sub vectorbase_link {
1368        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1369        my($cgi,$vec) = @_;
1370        return "<a href=\"http://www.vectorbase.org\" target=_blank>$vec</a>";
1371    }
1372    
1373    
1374  sub uni_link {  sub uni_link {
1375      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1376      my($cgi,$uni) = @_;      my($cgi,$uni) = @_;
1377    
1378      if ($uni =~ /^uni\|(\S+)$/)      if ($uni =~ /^uni\|(\S+)$/)
1379      {      {
1380          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>";
1381            return "<a href='http://www.ebi.uniprot.org/uniprot-srv/uniProtView.do?proteinAc=$1' target=_blank>$uni</a>";
1382      }      }
1383      return $uni;      return $uni;
1384  }  }
# Line 958  Line 1389 
1389    
1390      if ($sp =~ /^sp\|(\S+)$/)      if ($sp =~ /^sp\|(\S+)$/)
1391      {      {
1392          return "<a href=http://us.expasy.org/cgi-bin/get-sprot-entry?$1>$sp</a>";          return "<a href='http://us.expasy.org/cgi-bin/get-sprot-entry?$1' target=_blank>$sp</a>";
1393      }      }
1394      return $sp;      return $sp;
1395  }  }
# Line 969  Line 1400 
1400    
1401      if ($pir =~ /^pirnr\|(NF\d+)$/)      if ($pir =~ /^pirnr\|(NF\d+)$/)
1402      {      {
1403          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>";
1404      }      }
1405      return $pir;      return $pir;
1406  }  }
# Line 980  Line 1411 
1411    
1412      if ($kegg =~ /^kegg\|([^:]+):(\S+)$/)      if ($kegg =~ /^kegg\|([^:]+):(\S+)$/)
1413      {      {
1414          return "<a href=http://www.genome.ad.jp/dbget-bin/www_bget?$1+$2>$kegg</a>";          return "<a href='http://www.genome.ad.jp/dbget-bin/www_bget?$1+$2' target=_blank>$kegg</a>";
1415      }      }
1416      return $kegg;      return $kegg;
1417  }  }
1418    
1419    sub img_link {
1420        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1421        my($cgi,$img) = @_;
1422    
1423        if ($img =~ /^img\|(\S+)$/)
1424        {
1425            return "<a href='http://img.jgi.doe.gov/cgi-bin/pub/main.cgi?page=geneDetail&gene_oid=$1' target=_blank>$img</a>";
1426        }
1427        return $img;
1428    }
1429    
1430    sub ensembl_link {
1431        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1432        my($cgi,$ensembl) = @_;
1433    
1434        if ($ensembl =~ /^(\S+):(\S+)$/)
1435        {
1436            my $what=$1;
1437            my $key=$2;
1438            my $idx="All";
1439            if ($what eq "EnsemblGene") { $idx = "Gene" }
1440            if ($what eq "EnsemblTranscript") { $idx = "All" }
1441            if ($what eq "EnsemblProtein") { $idx = "All" }
1442    
1443            #I really want to get right to the transcript and peptide pages, but
1444            #can't see how to do that without knowing the org name too, which
1445            #I don't know at this point. (ensembl org name, not real org name)
1446    
1447            return "<a href='http://www.ensembl.org/Homo_sapiens/searchview?species=all&idx=$idx&q=$key' target=_blank>$ensembl</a>";
1448        }
1449        return $ensembl;
1450    }
1451    
1452    sub entrezgene_link {
1453        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1454        my($cgi,$entrezgene) = @_;
1455    
1456        if ($entrezgene =~ /^EntrezGene:(\S+)$/)
1457        {
1458            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>";
1459        }
1460        return $entrezgene;
1461    }
1462    
1463    sub mim_link {
1464        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1465        my($cgi,$mim) = @_;
1466    
1467        if ($mim =~ /^MIM:(\S+)$/)
1468        {
1469            return "<a href='http://www3.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=$1' target=_blank>$mim</a>";
1470        }
1471        return $mim;
1472    }
1473    
1474    sub hgnc_link {
1475        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1476        my($cgi,$hgnc) = @_;
1477    
1478        if ($hgnc =~ /^HGNC:(\S+)$/)
1479        {
1480            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>";
1481        }
1482    
1483        return $hgnc;
1484    }
1485    
1486    sub unigene_link {
1487        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1488        my($cgi,$unigene) = @_;
1489    
1490        if ($unigene =~ /^UniGene:(\S+)$/)
1491        {
1492            return "<a href='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unigene&cmd=search&term=$1' target=_blank>$unigene</a>";
1493        }
1494        return $unigene;
1495    }
1496    
1497    sub ipi_link {
1498        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1499        my($cgi,$ipi) = @_;
1500    
1501        if ($ipi =~ /^IPI:(\S+)$/)
1502        {
1503            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>";
1504        }
1505        return $ipi;
1506    }
1507    
1508    sub wp_link {
1509        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1510        my($cgi,$wp) = @_;
1511    
1512        #wormbase
1513    
1514        if ($wp =~ /^WP:(\S+)$/)
1515        {
1516            return "<a href='http://www.wormbase.org/db/searches/basic?class=Any&query=$1&Search=Search' target=_blank>$wp</a>";
1517        }
1518        return $wp;
1519    }
1520    
1521    sub fb_link {
1522        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1523        my($cgi,$fb) = @_;
1524    
1525        #flybase
1526    
1527        if ($fb =~ /^FB:(\S+)$/)
1528        {
1529            return "<a href='http://flybase.bio.indiana.edu/.bin/fbidq.html?$1' target=_blank>$fb</a>";
1530        }
1531        return $fb;
1532    }
1533    
1534    sub fborf_link {
1535        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1536        my($cgi,$fb) = @_;
1537    
1538        #flybase
1539    
1540        if ($fb =~ /^FlyBaseORFNames:(\S+)$/)
1541        {
1542            return "<a href='http://flybase.bio.indiana.edu/.bin/fbidq.html?$1' target=_blank>$fb</a>";
1543        }
1544        return $fb;
1545    }
1546    
1547    sub sgd_link {
1548        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1549        my($cgi,$sgd) = @_;
1550    
1551        #yeast
1552    
1553        if ($sgd =~ /^SGD_LOCUS:(\S+)$/)
1554        {
1555            return "<a href='http://db.yeastgenome.org/cgi-bin/locus.pl?locus=$1' target=_blank>$sgd</a>";
1556        }
1557        return $sgd;
1558    }
1559    
1560    
1561    
1562    
1563  sub set_map_links {  sub set_map_links {
1564      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1565      my($cgi,$x) = @_;      my($cgi,$x) = @_;
# Line 1002  Line 1577 
1577      return $x;      return $x;
1578  }  }
1579    
1580    
1581    
1582  sub map_link {  sub map_link {
1583      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1584      my($cgi,$map,$org) = @_;      my($cgi,$map,$org) = @_;
1585    
1586      $user = $cgi->param('user');      my $user = $cgi->param('user');
1587      $user = $user ? $user : "";      $user = $user ? $user : "";
1588      $org = $org ? $org : "";      $org = $org ? $org : "";
1589    
# Line 1024  Line 1601 
1601    # -name => field and the checkbox name    # -name => field and the checkbox name
1602    my ($form, $button)=@_;    my ($form, $button)=@_;
1603    
1604    $java_script="<input type=\"button\" name=\"CheckAll\" value=\"Check All\"\nonClick=\"checkAll(document.$form.$button)\">\n";    my $java_script="<input type=\"button\" name=\"CheckAll\" value=\"Check All\"\nonClick=\"checkAll(document.$form.$button)\">\n";
1605    $java_script.="<input type=\"button\" name=\"CheckFirst\" value=\"Check First Half\"\nonClick=\"checkFirst(document.$form.$button)\">\n";    $java_script.="<input type=\"button\" name=\"CheckFirst\" value=\"Check First Half\"\nonClick=\"checkFirst(document.$form.$button)\">\n";
1606    $java_script.="<input type=\"button\" name=\"CheckSecond\" value=\"Check Second Half\"\nonClick=\"checkSecond(document.$form.$button)\">\n";    $java_script.="<input type=\"button\" name=\"CheckSecond\" value=\"Check Second Half\"\nonClick=\"checkSecond(document.$form.$button)\">\n";
1607    $java_script.="<input type=\"button\" name=\"UnCheckAll\" value=\"Uncheck All\"\nonClick=\"uncheckAll(document.$form.$button)\">\n";    $java_script.="<input type=\"button\" name=\"UnCheckAll\" value=\"Uncheck All\"\nonClick=\"uncheckAll(document.$form.$button)\">\n";
# Line 1032  Line 1609 
1609    return $java_script;    return $java_script;
1610  }  }
1611    
1612    =head3 sub_link
1613    
1614        my $htmlText = HTML::sub_link($cgi, $sub, gid);
1615    
1616    Create a subsystem link. The link will be to the display page if there is no
1617    user or we are in SPROUT mode; otherwise it will be to the edit page.
1618    
1619    =over 4
1620    
1621    =item cgi
1622    
1623    CGI query object for the current web session. The parameters of special interest
1624    are C<SPROUT> and C<user>. If the user is non-blank and SPROUT mode is 0, then
1625    the subsystem's edit page will be shown rather than its display page.
1626    
1627    =item sub
1628    
1629    Name of the desired subsystem. It will be cleaned of underscores before the
1630    hyperlink is applied.
1631    
1632    =item gid
1633    
1634    Genome ID to be specified as the focus.
1635    
1636    =back
1637    
1638    =cut
1639    
1640  sub sub_link {  sub sub_link {
1641        # Allow call as an instance in addition to the authorized method.
1642      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1643      my($cgi,$sub) = @_;      # Get the parameters.
1644      my($sub_link);      my ($cgi, $sub, $gid) = @_;
1645        # Declare the return variable.
1646        my $retVal;
1647        # Clean the subsystem name for display purposes. This is a very
1648        # different thing from URL-escaping.
1649        my $cleaned = CGI::escapeHTML($sub);
1650        $cleaned =~ s/_/ /g;
1651        # URL-escape the subsystem name for use in the link.
1652        my $linkable = uri_escape($sub);
1653        # Determine the mode. Note we use the little OR trick to insure that
1654        # we have the correct value for plugging into the output link.
1655        my $user = $cgi->param('user') || "";
1656        my $sproutMode = $cgi->param('SPROUT') || 0;
1657        if ($user && ! $sproutMode) {
1658            # A SEED user is calling, so we go to the edit page.
1659            $retVal = "<a href=\"subsys.cgi?ssa_name=$linkable&request=show_ssa&user=$user\">$cleaned</a>";
1660        } else {
1661            # A visitor or SPROUT user is calling, so we go to the display page.
1662            $retVal = "<a href=\"display_subsys.cgi?ssa_name=$linkable;request=show_ssa;sort=by_phylo;focus=$gid;SPROUT=$sproutMode\">$cleaned</a>";
1663        }
1664        # Return the result.
1665        return $retVal;
1666    }
1667    
1668      my $user = $cgi->param('user');  sub reaction_map_link {
1669      if ($user)      my($mapID, @reaction_list) = @_;
1670        if($mapID =~ /\d+/)
1671        {
1672            my $reactions = join "+", @reaction_list;
1673            if ($reactions ne "")
1674      {      {
1675          my $esc_sub = uri_escape( $sub );              $reactions = "+".$reactions;
1676          $sub_link = "<a href=./subsys.cgi?ssa_name=$esc_sub&request=show_ssa&user=$user>$sub</a>";          }
1677    
1678            return "<a href=http://www.genome.jp/dbget-bin/show_pathway?rn$mapID$reactions>$mapID</a>";
1679      }      }
1680      else      else
1681      {      {
1682          $sub_link = $sub;          return $mapID;
1683      }      }
     return $sub_link;  
1684  }  }
1685    
1686    sub compound_link {
1687        my($compound) = @_;
1688        if($compound =~ /^C\d+/)
1689        {
1690            return "<a href=\"javascript:void(0)\"onclick=\"window.open('http://www.genome.jp/dbget-bin/www_bget?compound+$compound','$&','height=640,width=800,scrollbars=yes,toolbar=yes,status=yes,resizable=yes')\">$compound</a>";
1691        }
1692        else
1693        {
1694            return $compound;
1695        }
1696    }
1697    
1698    
1699  sub reaction_link {  sub reaction_link {
1700      my($reaction) = @_;      my($reaction) = @_;
1701        if ($reaction =~ /^(\*)?(R\d+)/)
     if ($reaction =~ /^R\d+/)  
1702      {      {
1703          return "<a href=\"http://www.genome.ad.jp/dbget-bin/www_bget?rn+$reaction\" target=reaction$$>$reaction</a>";          # return "<a href=\"http://www.genome.ad.jp/dbget-bin/www_bget?rn+$2\" target=reaction$$>$reaction</a>";
1704            return "<a href=\"javascript:void(0)\"onclick=\"window.open('http://www.genome.ad.jp/dbget-bin/www_bget?rn+$reaction','$&','height=640,width=800,scrollbars=yes,toolbar=yes,status=yes,resizable=yes')\">$reaction</a>";
1705      }      }
1706      return $reaction;      return $reaction;
1707  }  }
1708    
1709    
1710  sub html_for_assignments {  sub html_for_assignments {
1711      my($fig,$user,$peg_sets) = @_;      my($fig,$user,$peg_sets) = @_;
1712      my $i;      my $i;
1713    
1714      my @vals = ();      my @vals = ();
1715      my $set = 1;      my $set = 1;
1716      foreach $peg_set (@$peg_sets)      foreach my $peg_set (@$peg_sets)
1717      {      {
1718          for ($i=0; ($i < @$peg_set); $i++)          for ($i=0; ($i < @$peg_set); $i++)
1719          {          {
1720              $peg = $peg_set->[$i];              my $peg = $peg_set->[$i];
1721              push(@vals,'show=' . join("@",($set,$i+1,$peg,&FIG::abbrev($fig->org_of($peg)),"")));              push(@vals,'show=' . join("@",($set,$i+1,$peg,&FIG::abbrev($fig->org_of($peg)),"")));
1722          }          }
1723          $set++;          $set++;
# Line 1104  Line 1751 
1751  title       : the title. This is usually what is seen by the user in the pull down menu  title       : the title. This is usually what is seen by the user in the pull down menu
1752  description : a more complete description that is often seen is rss viewers but not always  description : a more complete description that is often seen is rss viewers but not always
1753  link        : link to the item that was added/edited  link        : link to the item that was added/edited
1754  All other keys are treated as optional RSS arguments and written to the file. At most, 10 recent entries are stored in the rss file.  All other keys are treated as optional RSS arguments and written to the file.
1755    
1756    At most, $max_entries recent entries are stored in the rss file, and this is currently 50.
1757    
1758  RSS files are quite simple, and contain some standard header information, and then individual items surrounded by an <item> </item> tag. Note that there is also an initial title/description/link set that describes the file.  RSS files are quite simple, and contain some standard header information, and then individual items surrounded by an <item> </item> tag. Note that there is also an initial title/description/link set that describes the file.
1759    
# Line 1114  Line 1763 
1763  sub rss_feed {  sub rss_feed {
1764   shift if UNIVERSAL::isa($_[0],__PACKAGE__);   shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1765   my ($files, $args)=@_;   my ($files, $args)=@_;
1766    
1767     # how many entries to store in the file
1768     my $max_entries=50;
1769    
1770   foreach my $a (keys %$args) {if ($a =~ /^-(.*)/) {my $b=$1; $args->{$b}=$args->{$a}; delete $args->{$a}}}   foreach my $a (keys %$args) {if ($a =~ /^-(.*)/) {my $b=$1; $args->{$b}=$args->{$a}; delete $args->{$a}}}
1771    
1772   my $filepath=$FIG_Config::fig."/CGI/Html/rss";   my $filepath=$FIG_Config::fig."/CGI/Html/rss";
# Line 1127  Line 1780 
1780     {     {
1781          title           => "The SEED",          title           => "The SEED",
1782          description     => "Latest news from the SEED",          description     => "Latest news from the SEED",
1783          link            => &FIG::cgi_url()."/Html/rss/SEED.rss",          link            => "Html/rss/SEED.rss",
1784     },     },
1785    
1786    "SEEDsubsystems.rss" =>    "SEEDsubsystems.rss" =>
1787    {    {
1788          title           => "SEED Subsystems",          title           => "SEED Subsystems",
1789          description     => "Recently updated SEED subsystems",          description     => "Recently updated SEED subsystems",
1790          link            => &FIG::cgi_url()."/Html/rss/SEEDsubsystems.rss",          link            => "Html/rss/SEEDsubsystems.rss",
1791    },    },
1792    
1793    "SEEDsubsystems.rss" =>    "SEEDsubsystems.rss" =>
# Line 1159  Line 1812 
1812    if ($qw eq "link")    if ($qw eq "link")
1813    {    {
1814     $args->{$qw} =~ /^(.*?\.cgi.)(.*)$/;     $args->{$qw} =~ /^(.*?\.cgi.)(.*)$/;
    print STDERR "Got ->>$1<<- and ->>$2<<-\n";  
1815     $args->{$qw} = $1.uri_escape($2) if ($1 && $2);     $args->{$qw} = $1.uri_escape($2) if ($1 && $2);
1816    }    }
1817    
# Line 1176  Line 1828 
1828    
1829    
1830   my @files=("SEED.rss");   my @files=("SEED.rss");
1831   if ($args->{"type"}) {push @files, "SEED.$type.rss"}   if ($args->{"type"}) {
1832        my $type = $args->{type};
1833        push @files, "SEED.$type.rss"
1834    }
1835    
1836   foreach my $file ("SEED.rss", @$files)   foreach my $file ("SEED.rss", @$files)
1837   {   {
# Line 1193  Line 1848 
1848       $itemcount++;       $itemcount++;
1849       $initem=1;       $initem=1;
1850      }      }
1851      if (/\<\/item\>/) {$initem=0; next if ($itemcount > 9)}      if (/\<\/item\>/) {$initem=0; next if ($itemcount > $max_entries)}
1852      next if ($initem && $itemcount > 9);      next if ($initem && $itemcount > $max_entries);
1853      push @out, $_;      push @out, $_;
1854     }     }
1855     close IN;     close IN;

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