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revision 1.85, Sat Jan 28 04:23:48 2006 UTC revision 1.123, Tue Apr 29 05:43:12 2008 UTC
# Line 17  Line 17 
17    
18  package HTML;  package HTML;
19    
20    use strict;
21  use Tracer;  use Tracer;
22  use FIG;  use FIG;
23    use FIGRules;
24  use Carp;  use Carp;
25  use Data::Dumper;  use Data::Dumper;
26  use LWP::UserAgent;  use LWP::UserAgent;
# Line 27  Line 29 
29  use URI::URL;  use URI::URL;
30  use HTTP::Request::Common;  use HTTP::Request::Common;
31  use POSIX;  use POSIX;
32    use CGI;
33    
34    #use raelib; # now used for the excel function, that should eventually end up in here. Way too experimental!
35    my $raelib;
36    
37    
38  my $top_link_cache;  my $top_link_cache;
# Line 53  Line 59 
59    
60      my @parts = split(/\//, $ENV{SCRIPT_NAME});      my @parts = split(/\//, $ENV{SCRIPT_NAME});
61      my $top;      my $top;
62      if ($parts[-2] eq 'FIG')      if (defined $parts[-2] && $parts[-2] eq 'FIG')
63      {      {
64          $top = '.';          $top = '.';
65  #       warn "toplevel @parts\n";  #       warn "toplevel @parts\n";
66      }      }
67      elsif ($parts[-3] eq 'FIG')      elsif (defined $parts[-3] && $parts[-3] eq 'FIG')
68      {      {
69          $top = '..';          $top = '..';
70  #       warn "subdir @parts\n";  #       warn "subdir @parts\n";
# Line 78  Line 84 
84      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
85      my($additional_insert, $user, %options ) = @_;      my($additional_insert, $user, %options ) = @_;
86    
87        local $/ = "\n";
88    
89      my $header_name = $options{header_name} ? $options{header_name} : "html.hdr";      my $header_name = $options{header_name} ? $options{header_name} : "html.hdr";
90      my $tail_name = $options{tail_name} ? $options{tail_name} : "html.tail";      my $tail_name = $options{tail_name} ? $options{tail_name} : "html.tail";
91    
# Line 156  Line 164 
164  sub show_page {  sub show_page {
165      #warn "SHOWPAGE: cgi=", Dumper(@_);      #warn "SHOWPAGE: cgi=", Dumper(@_);
166      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
167      my($cgi,$html,$no_home, $alt_header, $css, $javasrc, $cookie) = @_;      my($cgi,$html,$no_home, $alt_header, $css, $javasrc, $cookie, $options) = @_;
168      my $i;      my $i;
169        Trace("Setting top link.") if T(3);
170      my $top = top_link();      my $top = top_link();
171    
172      # ARGUMENTS:      # ARGUMENTS:
# Line 171  Line 179 
179      #               the sheet named "Sans Serif" is considered to the the first alternate, and if this is not set it points at $FIG_Config::HTML/css/sanserif.css      #               the sheet named "Sans Serif" is considered to the the first alternate, and if this is not set it points at $FIG_Config::HTML/css/sanserif.css
180      #     $javasrc is a reference to an array of URLs to javascripts to be included (e.g. "FIG/Html/css/styleswitcher.js")      #     $javasrc is a reference to an array of URLs to javascripts to be included (e.g. "FIG/Html/css/styleswitcher.js")
181      #     $cookie is the name and value of the cookie to set. Note that you should probably use raelib->cookie to get/set your cookies      #     $cookie is the name and value of the cookie to set. Note that you should probably use raelib->cookie to get/set your cookies
182        #     $options is a reference to a hash of options that you can pass around the pages
183      #      #
184      # Find the HTML header      # Find the HTML header
185      #      #
186        Trace("Reading tail.") if T(3);
187        my $tail_name = $options->{tail_name} ? $options->{tail_name} : "html.tail";
188      my $html_tail_file = "./Html/$tail_name";      my $html_tail_file = "./Html/$tail_name";
189      if (! -f $html_tail_file)      if (! -f $html_tail_file)
190      {      {
191          $html_tail_file = "$FIG_Config::fig/CGI/Html/$tail_name";          $html_tail_file = "$FIG_Config::fig/CGI/Html/$tail_name";
192      }      }
193        Trace("Extracting user name and header data.") if T(3);
194      my $user = $cgi->param('user') || "";      my $user = $cgi->param('user') || "";
195      my @html_hdr;      my @html_hdr;
196      if ($alt_header && ref($alt_header) eq "ARRAY")      if ($alt_header && ref($alt_header) eq "ARRAY")
# Line 189  Line 199 
199      }      }
200      else      else
201      {      {
202          @html_hdr = compute_html_header(undef,$user);          @html_hdr = compute_html_header(undef,$user,%$options);
203      }      }
204    
205      # 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 197  Line 207 
207    
208      # Note: 3/10/05 commented this line out pending the discussion of adding cookies into the seed that we are waiting to see about      # Note: 3/10/05 commented this line out pending the discussion of adding cookies into the seed that we are waiting to see about
209      # to add cookies back in replace these two header lines with each other      # to add cookies back in replace these two header lines with each other
210        #my $hdr_thing = $cgi->header(-cookie=>$cookie);
211      #print $cgi->header(-cookie=>$cookie);      my $hdr_thing = $cgi->header();
212      print $cgi->header();      Trace("Printing HTML header: $hdr_thing.") if T(3);
213        print $hdr_thing;
214        Trace("Header printed.") if T(3);
215      #      #
216      #  The SEED header file goes immediately after <BODY>.  Figure out      #  The SEED header file goes immediately after <BODY>.  Figure out
217      #  what parts of the HTML document skeleton are there, and fill in      #  what parts of the HTML document skeleton are there, and fill in
# Line 245  Line 256 
256      my $body_line = -1;      my $body_line = -1;
257      my $last_head_line = -1;  #  If no head tags are found, text goes at top.      my $last_head_line = -1;  #  If no head tags are found, text goes at top.
258      my $done = 0;      my $done = 0;
259        Trace("Processing special cases.") if T(3);
260      for ( $i = 0; $i < @$html; $i++ )      for ( $i = 0; $i < @$html; $i++ )
261      {      {
262          #  Some special cases:          #  Some special cases:
# Line 291  Line 302 
302    
303      if ( 1 )      if ( 1 )
304      {      {
305            Trace("Sanity checks in progress.") if T(3);
306          if ( $html_line >= 0 )          if ( $html_line >= 0 )
307          {          {
308              if ( ( $head_line >= 0 ) && ( $html_line > $head_line ) )              if ( ( $head_line >= 0 ) && ( $html_line > $head_line ) )
309              {              {
310                  print STDERR "<HTML> tag follows <HEAD> tag\n";                  Trace("<HTML> tag follows <HEAD> tag.") if T(1);
311              }              }
312              if ( ( $head_end_line >= 0 ) && ( $html_line > $head_end_line ) )              if ( ( $head_end_line >= 0 ) && ( $html_line > $head_end_line ) )
313              {              {
314                  print STDERR "<HTML> tag follows </HEAD> tag\n";                  Trace("<HTML> tag follows </HEAD> tag.") if T(1);
315              }              }
316          }          }
317          if ( $head_line >= 0 )          if ( $head_line >= 0 )
318          {          {
319              if ( ( $head_end_line >= 0 ) && ( $head_line > $head_end_line ) )              if ( ( $head_end_line >= 0 ) && ( $head_line > $head_end_line ) )
320              {              {
321                  print STDERR "<HEAD> tag follows </HEAD> tag\n";                  Trace("<HEAD> tag follows </HEAD> tag.") if T(1);
322              }              }
323          }          }
324      }      }
325        Trace("Sanity checks complete.") if T(3);
326      #      #
327      #  Okay.  Let's put in the html header file, and missing tags:      #  Okay.  Let's put in the html header file, and missing tags:
328      #      #
# Line 321  Line 333 
333      #  Note if no buttons are added we still (at the moment) add the script,      #  Note if no buttons are added we still (at the moment) add the script,
334      #  but it only adds a little text (495 characters) to the html and noone will notice!      #  but it only adds a little text (495 characters) to the html and noone will notice!
335      #  RAE: This is now deprecated because everything is in an external file, FIG.js, included later      #  RAE: This is now deprecated because everything is in an external file, FIG.js, included later
   
336      if ( $body_line < 0 )      if ( $body_line < 0 )
337      {      {
338          $body_line = $last_head_line + 1;          $body_line = $last_head_line + 1;
339            Trace("Splicing body line at $body_line.") if T(3);
340          splice( @$html, $body_line, 0, "<BODY>\n" );          splice( @$html, $body_line, 0, "<BODY>\n" );
341      }      }
342    
# Line 334  Line 346 
346    
347      if (@html_hdr)      if (@html_hdr)
348      {      {
349            Trace("Splicing SEED page header after $body_line.") if T(3);
350          splice( @$html, $body_line + 1, 0, @html_hdr );          splice( @$html, $body_line + 1, 0, @html_hdr );
351      }      }
352    
# Line 344  Line 357 
357      if ( $head_end_line < 0 )      if ( $head_end_line < 0 )
358      {      {
359          $head_end_line = $body_line;          $head_end_line = $body_line;
360            Trace("Splicing header terminater at $body_line.") if T(3);
361          splice( @$html, $body_line, 0, "</HEAD>\n" );          splice( @$html, $body_line, 0, "</HEAD>\n" );
362      }      }
363    
# Line 353  Line 367 
367      # 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:
368      #      #
369      # <link rel='stylesheet' title='default' href='/css/default.css' type='text/css'>      # <link rel='stylesheet' title='default' href='/css/default.css' type='text/css'>
370        Trace("Formatting CSS.") if T(3);
371      # convert the default key to the right case. and eliminate dups      # convert the default key to the right case. and eliminate dups
372      foreach my $k (keys %$css) {if (lc($k) eq "default") {$css->{'Default'}=$css->{$k}}}      foreach my $k (keys %$css) {if (lc($k) eq "default") {$css->{'Default'}=$css->{$k}}}
373    
# Line 383  Line 397 
397    
398      # 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
399      # it will reduce our overhead.      # it will reduce our overhead.
400        Trace("Formatting javascript.") if T(3);
401      # $javasrc must be a ref to an array with urls (absolute or relative) to the javascripts      # $javasrc must be a ref to an array with urls (absolute or relative) to the javascripts
402      push @$javasrc, "Html/css/FIG.js";      push @$javasrc, "Html/css/FIG.js";
403      foreach my $script (@$javasrc) {      foreach my $script (@$javasrc) {
404          $csstext .= "<script src=\"$script\" type=\"text/javascript\"></script>\n";          $csstext .= "<script src=\"$script\" type=\"text/javascript\"></script>\n";
405      }      }
406    
407        Trace("Re-splicing the header terminator at $head_end_line.") if T(3);
   
408      splice( @$html, $head_end_line, 1, "$csstext</HEAD>\n" );  # note here I am replacing the </head> line. Could be bad...? But it doesn't increment everything else.      splice( @$html, $head_end_line, 1, "$csstext</HEAD>\n" );  # note here I am replacing the </head> line. Could be bad...? But it doesn't increment everything else.
409    
410      #      #
# Line 409  Line 422 
422          # BASE href needs to be absolute. RDO.          # BASE href needs to be absolute. RDO.
423          #          #
424          #          #
425          $base_url = &FIG::cgi_url;  #        $base_url = &FIG::cgi_url;
426  #       my $base_url = $FIG_Config::cgi_base;  #       my $base_url = $FIG_Config::cgi_base;
427  #       if ( ! $base_url )                      # if cgi_base was not defined  #       if ( ! $base_url )                      # if cgi_base was not defined
428  #       {  #       {
# Line 432  Line 445 
445      if ( $html_line < 0 )      if ( $html_line < 0 )
446      {      {
447          $html_line = 0;          $html_line = 0;
448            Trace("Splicing the HTML tag at $html_line.") if T(3);
449          splice( @$html, $html_line, 0, "<HTML>\n" );          splice( @$html, $html_line, 0, "<HTML>\n" );
450      }      }
451    
# Line 442  Line 456 
456      if ( $head_line < 0 )      if ( $head_line < 0 )
457      {      {
458          $head_line = $html_line + 1;          $head_line = $html_line + 1;
459            Trace("Splicing the HEAD tag at $head_line.") if T(3);
460          splice( @$html, $head_line, 0, "<HEAD>\n" );          splice( @$html, $head_line, 0, "<HEAD>\n" );
461      }      }
462    
463      #      #
464      #  Place FIG search link at bottom of page      #  Place FIG search link at bottom of page
465      #      #
466        Trace("Placing FIG search link.") if T(3);
467      my @tail = -f $html_tail_file ? `cat $html_tail_file` : ();      my @tail = -f $html_tail_file ? `cat $html_tail_file` : ();
468      if (! $no_home)      if (! $no_home)
469      {      {
# Line 459  Line 474 
474      #      #
475      # See if we have a site-specific tail (for disclaimers, etc).      # See if we have a site-specific tail (for disclaimers, etc).
476      #      #
477        Trace("Placing site tail.") if T(3);
478      my $site_tail = "$FIG_Config::fig_disk/config/site_tail.html";      my $site_tail = "$FIG_Config::fig_disk/config/site_tail.html";
479      my $site_fh;      my $site_fh;
480      if (open($site_fh, "<$site_tail"))      if (open($site_fh, "<$site_tail"))
# Line 473  Line 488 
488      #  or before </html>, or at end of page.      #  or before </html>, or at end of page.
489      #      #
490      my @tags = ();      my @tags = ();
491      # Check for a tracing queue.      Trace("Processing closing tags.") if T(3);
     my $traceString = QTrace("HTML");  
     if ($traceString) {  
         push @tags, $traceString;  
     }  
492      for ($i=0; ($i < @$html) && ($html->[$i] !~ /\<\/body\>/i); $i++) {}      for ($i=0; ($i < @$html) && ($html->[$i] !~ /\<\/body\>/i); $i++) {}
493      if ($i >= @$html)        # </body> not found; look for </html>      if ($i >= @$html)        # </body> not found; look for </html>
494      {      {
# Line 492  Line 503 
503    
504      if ( @tail )      if ( @tail )
505      {      {
506            Trace("Splicing tail.") if T(3);
507          splice( @$html, $i, 0, @tail, @tags );          splice( @$html, $i, 0, @tail, @tags );
508      }      }
509      elsif ( @tags )      elsif ( @tags )
510      {      {
511            Trace("Splicing tags.") if T(3);
512          splice( @$html, $i, 0, @tags );          splice( @$html, $i, 0, @tags );
513      }      }
514    
515        Trace("Printing the HTML array.") if T(3);
516      # RAE the chomp will return any new lines at the ends of elements in the array,      # RAE the chomp will return any new lines at the ends of elements in the array,
517      # and then we can join  with a "\n". This is because somethings put newlines in,      # and then we can join  with a "\n". This is because somethings put newlines in,
518      # and others don't. This should make nicer looking html      # and others don't. This should make nicer looking html
# Line 507  Line 521 
521      # print join "\n", @$html;      # print join "\n", @$html;
522      #      #
523      # Apparently the above still breaks things. This is the correct code:      # Apparently the above still breaks things. This is the correct code:
   
524      foreach $_ (@$html)      foreach $_ (@$html)
525      {      {
526          print $_;          my $line = $_;
527            if (T(4)) {
528                my $escapedLine = CGI::escapeHTML($line);
529                Trace("Printing:\n$escapedLine") if T(4);
530            }
531            print $line;
532      }      }
533    
534  }  }
535    
536    
537    =head1 make_table
538    
539    The main method to convert an array into a table.
540    
541    The col_hdrs are set to the <th> headers, the $tab is an array of arrays. The first is the rows, and the second is the columns. The title is the title of the table.
542    
543    The options define the settings for the table such as border, width, and class for css formatting. If the option "excelfile" is set to a filename that will be created in FIG_Config::temp, and the link included that allows the user to download the file as an excel file.
544    
545    =cut
546    
547  sub make_table {  sub make_table {
548      my($col_hdrs,$tab,$title, %options ) = @_;      my($col_hdrs,$tab,$title, %options ) = @_;
549      my(@tab);      my(@tab);
550    
551      my $border = defined $options{border} ? "border=\"$options{border}\"" : "border";      my $border = defined $options{border} ? "border=\"$options{border}\"" : "border";
552      my $width = defined $options{width} ? "width=\"$options{width}\"" : undef;      my $width = defined $options{width} ? "width=\"$options{width}\"" : "";
553      my $class = defined $options{class} ? "class=\"$options{class}\"" : undef;      my $class = defined $options{class} ? "class=\"$options{class}\"" : "";
554      push( @tab, "\n<table $border $width $class>\n",      push( @tab, "\n<table $border $width $class>\n",
555                  "\t<caption><b>$title</b></caption>\n",                  "\t<caption><b>$title</b></caption>\n",
556                  "\t<tr>\n\t\t"                  "\t<tr>\n\t\t"
# Line 539  Line 568 
568              );              );
569      }      }
570      push(@tab,"</table>\n");      push(@tab,"</table>\n");
571    
572        # excelfile should be appropriate for a filename (no spaces/special characters)
573        if (defined $options{"excelfile"}) {
574            if (! defined($raelib)) {
575                require raelib;
576                $raelib = new raelib;
577            }
578            push @tab, $raelib->tab2excel($col_hdrs,$tab,$title,\%options,$options{"excelfile"})}
579    
580      return join("",@tab);      return join("",@tab);
581  }  }
582    
# Line 780  Line 818 
818      return "<a href=$link>$role</a>";      return "<a href=$link>$role</a>";
819  }  }
820    
821  #  =head2 fid_link
822  # Local means to eliminate the fig|org.peg from the  
823  # text of the link.  Get a link to a fid.
824  #  
825    use: my $html=&HTML::fid_link($cgi, $fid, Local, Just_URL, Full_Path);
826    
827    Local is a boolean means to eliminate the fig|org.peg from the text of the link.
828    
829    Just_URL will only return the URL and not the HTML code. The default is to return the full code.
830    
831    Full_Path is a boolean that will get the full path to the URL not just a relative path. This is required in pages where the base href changes (e.g. if an image is imported like on the metabolic pages).
832    
833    =cut
834    
835    
836  sub fid_link {  sub fid_link {
837      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
838      my($cgi,$fid,$local,$just_url) = @_;      my($cgi,$fid,$local,$just_url,$fullpath) = @_;
839        Trace("Creating link for feature $fid.") if T(4);
840        my $err=join(" ", $cgi,$fid,$local,$just_url,$fullpath);
841        if (FIGRules::nmpdr_mode($cgi)) {
842            # We're NMPDR. Compute the link to the seed viewer feature page.
843            my $link = "seedviewer.cgi?page=Annotation;feature=$fid";
844            if ($fullpath) {
845                # Full-path mode: add the base URL.
846                $link = "$FIG_Config::cgi_url/$link";
847            }
848            if ($just_url) {
849                # URL-only mode: return the link.
850                return $link;
851            } else {
852                # HTML mode. We need to compute the link text.
853                my $text = $fid;
854                # If we're in local mode, we remove everything but the final number from the fig ID.
855                if ($local) {
856                    $fid =~ s/^.+\.//;
857                }
858                # Return the full HTML for the link.
859                return "<a href=\"$link\">$text</a>";
860            }
861        }
862      my($n);      my($n);
863    
864      my $top = top_link();      my $top = top_link();
865        if ($fullpath) {$top=$FIG_Config::cgi_url}
866    
867      if ($fid =~ /^fig\|\d+\.\d+\.([a-z]+)\.(\d+)/)      if ($fid =~ /^fig\|\d+\.\d+\.([a-zA-Z]+)\.(\d+)/)
868      {      {
869          if ($local)          if ($local)
870          {          {
# Line 810  Line 883 
883          }          }
884    
885          my $link;          my $link;
886            my $new_framework = $cgi->param('new_framework') ? 1 : 0;
887          #added to format prophage and path island links to feature.cgi          #added to format prophage and path island links to feature.cgi
888          if ($1 ne "peg")          my $sprout = $cgi->param('SPROUT') ? "&SPROUT=1" : "";
889            my $virt = "&48hr_job=" . $cgi->param("48hr_job");
890            Trace("Sprout mode is \"$sprout\".") if T(4);
891            if ($1 ne "peg" && ! $sprout)
892          {          {
893               Trace("Creating feature link for $fid.") if T(4);
894             my $user = $cgi->param('user');             my $user = $cgi->param('user');
895             if (! $user) { $user = "" }             if (! $user) { $user = "" }
896             my $sprout = $cgi->param('SPROUT') ? "&SPROUT=1" : "";             $link = "$top/feature.cgi?feature=$fid&user=$user$sprout$virt";
            $link = "$top/feature.cgi?feature=$fid&user=$user$trans$sprout";  
897             $link =~ s/[a-z_A-Z0-9]+\.cgi\?/feature.cgi?/;             $link =~ s/[a-z_A-Z0-9]+\.cgi\?/feature.cgi?/;
898          }          }
899          else          else
900          {          {
901                Trace("Creating protein link for $fid.") if T(4);
902              my $user = $cgi->param('user');              my $user = $cgi->param('user');
903              if (! $user) { $user = "" }              if (! $user) { $user = "" }
904              my $trans = $cgi->param('translate') ? "&translate=1" : "";              my $trans = $cgi->param('translate') ? "&translate=1" : "";
# Line 836  Line 914 
914    
915              #if (! $cgi_url) { $cgi_url = &FIG::cgi_url }              #if (! $cgi_url) { $cgi_url = &FIG::cgi_url }
916              #$link = $cgi_url . "/protein.cgi?prot=$fid&user=$user$trans$sprout";              #$link = $cgi_url . "/protein.cgi?prot=$fid&user=$user$trans$sprout";
917              $link = "$top/protein.cgi?prot=$fid&user=$user$trans$sprout";              $link = "$top/protein.cgi?prot=$fid&user=$user$trans$sprout$virt\&new_framework=$new_framework";
918              $link =~ s/[a-z_A-Z0-9]+\.cgi\?/protein.cgi?/;              $link =~ s/[a-z_A-Z0-9]+\.cgi\?/protein.cgi?/;
919          }          }
920          if ($just_url)          if ($just_url)
# Line 845  Line 923 
923          }          }
924          else          else
925          {          {
926              return "<a href=$link>$n</a>";              return "<a href='$link'>$n</a>";
927          }          }
928      }      }
929      return $fid;      return $fid;
# Line 858  Line 936 
936      return $family;      return $family;
937  }  }
938    
939    =head2 evidence_codes_explain
940    
941    Given an evidence code, returns a string that explains this eveidence code.
942    
943    =cut
944    
945    sub evidence_codes_explain {
946     my($ec)=@_;
947     return unless ($ec);
948    
949     $ec=uc($ec);
950     return "IDA: Inferred from Direct Assay" if ($ec =~ /IDA/);
951     return "IGI: Inferred from Genetic Interaction" if ($ec =~ /IGI/);
952     return "TAS: Traceable Author Statement" if ($ec =~ /TAS/);
953     return "ISU: in subsystem unique" if ($ec =~ /ISU/);
954     return "$ec: in subsystem duplicates" if ($ec =~ /IDU/);
955     return "$ec: in cluster with" if ($ec =~ /ICW/);
956     return "FF: in FIGfam" if ($ec =~ /FF/);
957     return "CWN: clustered with nonhypothetical" if ($ec =~ /CWN/);
958     return "CWH: clustered, but only with hypotheticals" if ($ec =~ /CWH/);
959     return "DLIT: literature references to this gene exist" if ($ec =~ /DLIT/);
960     return "ILIT: no references to this gene exist, but they do to other genes with the same functional role" if ($ec =~ /ILIT/);
961     return "$ec: unknown!";
962    }
963    
964  sub get_html {  sub get_html {
965      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
# Line 877  Line 979 
979          my $response = $ua->request($request);          my $response = $ua->request($request);
980          $out = $response->content;          $out = $response->content;
981      }      }
982      else  
983        if ($type =~/get/i)
984      {      {
985          @args = ();          @args = ();
986          foreach $x (@$kv_pairs)          foreach $x (@$kv_pairs)
# Line 889  Line 992 
992          {          {
993              $url .= "?" . join("&",@args);              $url .= "?" . join("&",@args);
994          }          }
995          $request = new HTTP::Request('GET', $url);          my $request = new HTTP::Request('GET', $url);
996          my $response = $ua->request($request);          my $response = $ua->request($request);
997    
998          if ($response->is_success)          if ($response->is_success)
# Line 907  Line 1010 
1010    
1011  #   Now splice in a line of the form <base href=URL> to cause all relative links to work  #   Now splice in a line of the form <base href=URL> to cause all relative links to work
1012  #   properly.  Remove the header.  #   properly.  Remove the header.
1013        my $i;
1014      for ($i=0; ($i < @output) && ($output[$i] !~ /^\s*\</); $i++) {}      for ($i=0; ($i < @output) && ($output[$i] !~ /^\s*\</); $i++) {}
1015      if ($i < @output)      if ($i < @output) {
     {  
   
1016          splice(@output,0,$i);          splice(@output,0,$i);
1017      }      }
1018    
# Line 927  Line 1028 
1028  sub trim_output {  sub trim_output {
1029      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1030      my($out) = @_;      my($out) = @_;
1031      my $i;      my ($i, $j);
1032    
1033      for ($i=0; ($i < @$out) && ($out->[$i] !~ /^\</); $i++) {}      for ($i=0; ($i < @$out) && ($out->[$i] !~ /^\</); $i++) {}
1034      splice(@$out,0,$i);      splice(@$out,0,$i);
# Line 956  Line 1057 
1057      for ($j=$i-1; ($j > 0) && ($out->[$j] !~ /FIG search/); $j--) {}      for ($j=$i-1; ($j > 0) && ($out->[$j] !~ /FIG search/); $j--) {}
1058      if ($j > 0)      if ($j > 0)
1059      {      {
1060            #
1061            # Hm. We would have tried using the options here:
1062            # my $tail_name = $options{tail_name} ? $options{tail_name} : "html.tail";
1063            # but they're not passed in. So use the default html.tail.
1064            #
1065            my $html_tail_file = "./Html/html.tail";
1066          my @tmp = `cat $html_tail_file`;          my @tmp = `cat $html_tail_file`;
1067          my $n = @tmp;          my $n = @tmp;
1068          splice(@$out,$j-$n,$n+1);          splice(@$out,$j-$n,$n+1);
1069      }      }
1070  }  }
1071    
1072    =head2 alias_url
1073    
1074    Returns the url that links to an external page showing information about the given alias.
1075    The type of the alias will be determined by the prefix (i.e. 'tr|' for Trembl) If the type
1076    cannot be determined, the function will return undef.
1077    
1078    use: my $html=&HTML::alias_url($alias, $type);
1079    
1080    =cut
1081    
1082    sub alias_url {
1083      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1084    
1085      my ($id, $type) = @_;
1086    
1087      if ($type eq "SEED") { # 1
1088        return "http://seed-viewer.theseed.org/linkin.cgi?id=$id";
1089      }
1090      elsif ($type eq "UniProt") {
1091        return "http://www.uniprot.org/entry/$id";
1092      }
1093      elsif ($type eq "UniProt_ac") { # 2
1094        return "http://www.uniprot.org/entry/$id";
1095      }
1096      elsif ($type eq "UniProt_id") { # 3
1097        return "http://www.uniprot.org/entry/$id";
1098      }
1099      elsif ($type eq "EntrezGene") { # 4
1100        return "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&id=$id";
1101      }
1102      elsif ($type eq "RefSeq") { # 5
1103        return "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&id=$id";
1104      }
1105      elsif ($type eq "GIID") { # 6
1106        return "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&id=$id";
1107      }
1108      elsif ($type eq "NCBI") {
1109        return "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&id=$id";
1110      }
1111      elsif ($type eq "PDB") { # 7
1112        $id =~ s/\:\w//;
1113        return "http://www.rcsb.org/pdb/explore/explore.do?structureId=$id";
1114      }
1115      elsif ($type eq "PFAM") { # 8
1116        return "http://pfam.janelia.org/family?acc=$id";
1117      }
1118      elsif ($type eq "GO") { # 9
1119        return "http://amigo.geneontology.org/cgi-bin/amigo/go.cgi?view=details&search_constraint=terms&depth=0&query=$id";
1120      }
1121      elsif ($type eq "PIRSF") { # 10
1122        return "http://pir.georgetown.edu/cgi-bin/ipcSF?id=$id";
1123      }
1124      elsif ($type eq "IPI") { # 11
1125        return "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+[IPI-AllText:".$id."*]+-lv+30+-view+SeqSimpleView+-page+qResult";
1126      }
1127      elsif ($type eq "UniRef_100") { # 12
1128        return "http://www.uniprot.org/entry/$id";
1129      }
1130      elsif ($type eq "UniRef_90") { # 13
1131        return "http://www.uniprot.org/entry/$id";
1132      }
1133      elsif ($type eq "UniRef_50") { # 14
1134        return "http://www.uniprot.org/entry/$id";
1135      }
1136      elsif ($type eq "UniParc") { # 15
1137        return "http://www.uniprot.org/entry/$id";
1138      }
1139      elsif ($type eq "PIR-PSD") { # 16
1140        return "http://pir.georgetown.edu/cgi-bin/pir_psd_get.pl?id=$id";
1141      }
1142      elsif ($type eq "Taxon_ID") { # 17
1143        return "http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=$id";
1144      }
1145      elsif ($type eq "OMIM") { # 18
1146        return "http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=$id";
1147      }
1148      elsif ($type eq "UniGene") { # 19
1149        return "http://www.ncbi.nlm.nih.gov/sites/entrez?db=unigene&cmd=search&term=$id";
1150      }
1151      elsif ($type eq "Ensemble_ID") { # 20
1152        #return "$id";
1153      }
1154      elsif ($type eq "PMID") { # 21
1155        return "http://www.ncbi.nlm.nih.gov/pubmed/$id";
1156      }
1157      elsif ($type eq "EMBL_DNA_AC") { # 22
1158        return "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBL:".$id."]+-newId";
1159      }
1160      elsif ($type eq "EMBL_Protein_AC") { # 23
1161        $id =~ s/\.\d//;
1162        return "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[{EMBL}-ProteinID:".$id."]";
1163      }
1164      elsif ($type eq "CMR") { # 24
1165        if ($id =~ /^\d+$/) {
1166          return "http://cmr.jcvi.org/cgi-bin/CMR/shared/GenePage.cgi?type=PID&acc=".$id;
1167        } else {
1168          return "http://cmr.jcvi.org/tigr-scripts/CMR/shared/GenePage.cgi?locus=".$id;
1169        }
1170      }
1171    
1172      return undef;
1173    }
1174    
1175  sub set_prot_links {  sub set_prot_links {
1176      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1177      my($cgi,$x) = @_;      my($cgi,$x) = @_;
# Line 988  Line 1198 
1198          $after = $3;          $after = $3;
1199          return &set_prot_links($cgi,$before) . &HTML::gi_link($cgi,$match) . &set_prot_links($cgi,$after);          return &set_prot_links($cgi,$before) . &HTML::gi_link($cgi,$match) . &set_prot_links($cgi,$after);
1200      }      }
1201      elsif ($x =~ /^(.*)(tigr\|[0-9a-zA-Z]+)(.*)/s)      elsif ($x =~ /^(.*)(img\|\d+)(.*)/s)
1202        {
1203            $before = $1;
1204            $match = $2;
1205            $after = $3;
1206            return &set_prot_links($cgi,$before) . &HTML::img_link($cgi,$match) . &set_prot_links($cgi,$after);
1207        }
1208        elsif ($x =~ /^(.*)(tigr\|\w+)(.*)/s)
1209        {
1210            $before = $1;
1211            $match = $2;
1212            $after = $3;
1213            return &set_prot_links($cgi,$before) . &HTML::tigr_link($cgi,$match) . &set_prot_links($cgi,$after);
1214        }
1215        elsif ($x =~ /^(.*)(tigrcmr\|\w+)(.*)/s)
1216      {      {
1217          $before = $1;          $before = $1;
1218          $match = $2;          $match = $2;
# Line 1003  Line 1227 
1227          return &set_prot_links($cgi,$before) . &HTML::eric_link($cgi,$match) . &set_prot_links($cgi,$after);          return &set_prot_links($cgi,$before) . &HTML::eric_link($cgi,$match) . &set_prot_links($cgi,$after);
1228      }      }
1229    
1230      elsif ($x =~ /^(.*)\bbhb\|.*?\b(.*)/s)      elsif ($x =~ /^(.*)\b(bhb\|.*?)\b(.*)/s)
1231      {      {
1232          $before = $1;          $before = $1;
1233          $match = $2;          $match = $2;
# Line 1011  Line 1235 
1235          return &set_prot_links($cgi,$before) . &HTML::bhb_link($cgi,$match) . &set_prot_links($cgi,$after);          return &set_prot_links($cgi,$before) . &HTML::bhb_link($cgi,$match) . &set_prot_links($cgi,$after);
1236      }      }
1237    
1238      elsif ($x =~ /^(.*)\bapidb\|.*?\..*\b(.*)/s)      elsif ($x =~ /^(.*)\b(apidb\|[0-9\.a-z_]+)\b(.*)/s)
1239      {      {
1240          $before = $1;          $before = $1;
1241          $match = $2;          $match = $2;
# Line 1019  Line 1243 
1243          return &set_prot_links($cgi,$before) . &HTML::apidb_link($cgi,$match) . &set_prot_links($cgi,$after);          return &set_prot_links($cgi,$before) . &HTML::apidb_link($cgi,$match) . &set_prot_links($cgi,$after);
1244      }      }
1245    
1246      elsif ($x =~ /^(.*)\bpatric\|.*?\b(.*)/s)      elsif ($x =~ /^(.*)\b(patric\|.*?)\b(.*)/s)
1247      {      {
1248          $before = $1;          $before = $1;
1249          $match = $2;          $match = $2;
# Line 1027  Line 1251 
1251          return &set_prot_links($cgi,$before) . &HTML::patric_link($cgi,$match) . &set_prot_links($cgi,$after);          return &set_prot_links($cgi,$before) . &HTML::patric_link($cgi,$match) . &set_prot_links($cgi,$after);
1252      }      }
1253    
1254      elsif ($x =~ /^(.*)\bvbrc\|.*?\b(.*)/s)      elsif ($x =~ /^(.*)\b(vbrc\|.*?)\b(.*)/s)
1255      {      {
1256          $before = $1;          $before = $1;
1257          $match = $2;          $match = $2;
# Line 1035  Line 1259 
1259          return &set_prot_links($cgi,$before) . &HTML::vbrc_link($cgi,$match) . &set_prot_links($cgi,$after);          return &set_prot_links($cgi,$before) . &HTML::vbrc_link($cgi,$match) . &set_prot_links($cgi,$after);
1260      }      }
1261    
1262      elsif ($x =~ /^(.*)\bvectorbase\|.*?\b(.*)/s)      elsif ($x =~ /^(.*)\b(vectorbase\|.*?)\b(.*)/s)
1263      {      {
1264          $before = $1;          $before = $1;
1265          $match = $2;          $match = $2;
# Line 1091  Line 1315 
1315          $after = $3;          $after = $3;
1316          return &set_prot_links($cgi,$before) . &HTML::mim_link($cgi,$match) . &set_prot_links($cgi,$after);          return &set_prot_links($cgi,$before) . &HTML::mim_link($cgi,$match) . &set_prot_links($cgi,$after);
1317      }      }
1318      elsif ($x =~ /^(.*)(UniGene:[a-zA-Z_0-9\.]+)(.*)/s)      elsif ($x =~ /^(.*)(HGNC:[a-zA-Z_0-9\.]+)(.*)/s)
1319      {      {
1320          $before = $1;          $before = $1;
1321          $match = $2;          $match = $2;
1322          $after = $3;          $after = $3;
1323          return &set_prot_links($cgi,$before) . &HTML::unigene_link($cgi,$match) . &set_prot_links($cgi,$after);          return &set_prot_links($cgi,$before) . &HTML::hgnc_link($cgi,$match) . &set_prot_links($cgi,$after);
1324      }      }
1325      elsif ($x =~ /^(.*)(IPI:[a-zA-Z_0-9\.]+)(.*)/s)      elsif ($x =~ /^(.*)(UniGene:[a-zA-Z_0-9\.]+)(.*)/s)
1326      {      {
1327          $before = $1;          $before = $1;
1328          $match = $2;          $match = $2;
1329          $after = $3;          $after = $3;
1330          return &set_prot_links($cgi,$before) . &HTML::ipi_link($cgi,$match) . &set_prot_links($cgi,$after);          return &set_prot_links($cgi,$before) . &HTML::unigene_link($cgi,$match) . &set_prot_links($cgi,$after);
1331      }      }
1332    # IPI stopped working. turn off for now.
1333    #    elsif ($x =~ /^(.*)(IPI:[a-zA-Z_0-9\.]+)(.*)/s)
1334    #    {
1335    #        $before = $1;
1336    #        $match = $2;
1337    #        $after = $3;
1338    #        return &set_prot_links($cgi,$before) . &HTML::ipi_link($cgi,$match) . &set_prot_links($cgi,$after);
1339    #    }
1340      elsif ($x =~ /^(.*)(WP:[a-zA-Z_0-9\.]+)(.*)/s)      elsif ($x =~ /^(.*)(WP:[a-zA-Z_0-9\.]+)(.*)/s)
1341      {      {
1342          #wormbase          #wormbase
# Line 1141  Line 1373 
1373          $after = $3;          $after = $3;
1374          return &set_prot_links($cgi,$before) . &HTML::sgd_link($cgi,$match) . &set_prot_links($cgi,$after);          return &set_prot_links($cgi,$before) . &HTML::sgd_link($cgi,$match) . &set_prot_links($cgi,$after);
1375      }      }
1376        elsif ($x =~ /^(.*)(tr\|[a-zA-Z0-9]+)(.*)/s)
1377        {
1378    
1379          $before = $1;
1380          $match = $2;
1381          $after = $3;
1382    
1383          return &set_prot_links($cgi,$before) .  &HTML::trembl_link($cgi,$match) . &set_prot_links($cgi,$after);
1384        }
1385      return $x;      return $x;
1386  }  }
1387    
1388    sub trembl_link {
1389        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1390        my($cgi,$id) = @_;
1391    
1392        if ($id =~ /^tr\|(.*)/) {
1393          return "<a href='http://ca.expasy.org/uniprot/$1' target=_blank>$id</a>";
1394        } else {
1395          return "invalid call to trembl link";
1396        }
1397    }
1398    
1399  sub refseq_link {  sub refseq_link {
1400      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1401      my($cgi,$id) = @_;      my($cgi,$id) = @_;
1402    
1403      if ($id =~ /^[NXYZA]P_/)      if ($id =~ /^[NXYZA]P_/)
1404      {      {
1405          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>";
1406      }      }
1407      elsif ($id =~ /^[NXYZA]M_/)      elsif ($id =~ /^[NXYZA]M_/)
1408      {      {
1409          return "<a href=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=nuccore&cmd=search&term=$id>$id</a>";          return "<a href='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=nuccore&cmd=search&term=$id' target=_blank>$id</a>";
1410      }      }
1411  }  }
1412    
# Line 1164  Line 1416 
1416    
1417      if ($gi =~ /^gi\|(\d+)$/)      if ($gi =~ /^gi\|(\d+)$/)
1418      {      {
1419          return "<a href=http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=Protein&list_uids=$1&dopt=GenPept>$gi</a>";          return "<a href='http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=Protein&list_uids=$1&dopt=GenPept' target=_blank>$gi</a>";
1420      }      }
1421      return $gi;      return $gi;
1422  }  }
# Line 1176  Line 1428 
1428      if ($tigr =~ /^tigr\|(NT|ntbp|ntbpA|BA|BMAA|BXB|GBA)(\w+)$/)      if ($tigr =~ /^tigr\|(NT|ntbp|ntbpA|BA|BMAA|BXB|GBA)(\w+)$/)
1429      {      {
1430          my $id=$1.$2;          my $id=$1.$2;
1431          return "<a href=\"http://pathema.tigr.org/tigr-scripts/pathema/shared/GenePage.cgi?locus=$id\">$tigr</a> (Pathema)";          return "<a href=\"http://pathema.tigr.org/tigr-scripts/pathema/shared/GenePage.cgi?locus=$id\" target=_blank>$tigr</a> (Pathema)";
1432      }      }
1433      elsif ($tigr =~ /^tigr\|(\S+)$/)      elsif ($tigr =~ /^tigr(cmr)?\|(\S+)$/)
1434      {      {
1435          return "<a href=\"http://www.tigr.org/tigr-scripts/CMR2/GenePage.spl?locus=$1\">$tigr</a>";          return "<a href=\"http://www.tigr.org/tigr-scripts/CMR2/GenePage.spl?locus=$2\" target=_blank>$tigr</a>";
1436      }      }
1437      return $tigr;      return $tigr;
1438  }  }
# Line 1191  Line 1443 
1443    
1444      if ($eric =~ /^eric\|(\S+)/)      if ($eric =~ /^eric\|(\S+)/)
1445      {      {
1446          return "<a href=\"https://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=$1\">$eric</a>";          return "<a href=\"https://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=$1\" target=_blank>$eric</a>";
1447      }      }
1448      return $eric;      return $eric;
1449  }  }
# Line 1200  Line 1452 
1452      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1453      my($cgi,$bhb) = @_;      my($cgi,$bhb) = @_;
1454    
1455      return "<a href=\"http://www.biohealthbase.org\">$bhb</a>";      return "<a href=\"http://www.biohealthbase.org\" target=_blank>$bhb</a>";
1456  }  }
1457    
1458  sub apidb_link {  sub apidb_link {
# Line 1209  Line 1461 
1461    
1462      if ($api =~ /apidb\|(.*?)\.(.*)$/)      if ($api =~ /apidb\|(.*?)\.(.*)$/)
1463      {      {
1464          return "<a href=\"http://www.apidb.org/cgi-bin/redirect.cgi?taxon_id=$1&source_id=$2\">$api</a>";          return "<a href=\"http://www.apidb.org/cgi-bin/redirect.cgi?taxon_id=$1&source_id=$2\" target=_blank>$api</a>";
1465      }      }
1466      return $api;      return $api;
1467  }  }
# Line 1220  Line 1472 
1472    
1473      if ($patric =~ /patric\|(.*)/)      if ($patric =~ /patric\|(.*)/)
1474      {      {
1475          return "<a href=\"https://patric.vbi.vt.edu/software/curationTool/gep/pgiCuration.php?locus_name=$1\">$patric</a>";          return "<a href=\"https://patric.vbi.vt.edu/software/curationTool/gep/pgiCuration.php?locus_name=$1\" target=_blank>$patric</a>";
1476      }      }
1477      return $patric;      return $patric;
1478  }  }
# Line 1231  Line 1483 
1483    
1484      if ($vbrc =~ /vbrc\|(.*)/)      if ($vbrc =~ /vbrc\|(.*)/)
1485      {      {
1486          return "<a href=\"http://www.biovirus.org/gene_detail.asp?name=$1\">$vbrc</a>";          return "<a href=\"http://www.biovirus.org/gene_detail.asp?name=$1\" target=_blank>$vbrc</a>";
1487      }      }
1488      return $vbrc;      return $vbrc;
1489  }  }
# Line 1239  Line 1491 
1491  sub vectorbase_link {  sub vectorbase_link {
1492      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1493      my($cgi,$vec) = @_;      my($cgi,$vec) = @_;
1494      return "<a href=\"http://www.vectorbase.org\">$vec</a>";      return "<a href=\"http://www.vectorbase.org\" target=_blank>$vec</a>";
1495  }  }
1496    
1497    
# Line 1249  Line 1501 
1501    
1502      if ($uni =~ /^uni\|(\S+)$/)      if ($uni =~ /^uni\|(\S+)$/)
1503      {      {
1504          return "<a href=http://www.pir.uniprot.org/cgi-bin/upEntry?id=$1>$uni</a>";          #return "<a href=http://www.pir.uniprot.org/cgi-bin/upEntry?id=$1>$uni</a>";
1505            return "<a href='http://www.ebi.uniprot.org/uniprot-srv/uniProtView.do?proteinAc=$1' target=_blank>$uni</a>";
1506      }      }
1507      return $uni;      return $uni;
1508  }  }
# Line 1260  Line 1513 
1513    
1514      if ($sp =~ /^sp\|(\S+)$/)      if ($sp =~ /^sp\|(\S+)$/)
1515      {      {
1516          return "<a href=http://us.expasy.org/cgi-bin/get-sprot-entry?$1>$sp</a>";          return "<a href='http://us.expasy.org/cgi-bin/get-sprot-entry?$1' target=_blank>$sp</a>";
1517      }      }
1518      return $sp;      return $sp;
1519  }  }
# Line 1271  Line 1524 
1524    
1525      if ($pir =~ /^pirnr\|(NF\d+)$/)      if ($pir =~ /^pirnr\|(NF\d+)$/)
1526      {      {
1527          return "<a href=http://pir.georgetown.edu/cgi-bin/nfEntry.pl?id=$1>$pir</a>";          return "<a href='http://pir.georgetown.edu/cgi-bin/nfEntry.pl?id=$1' target=_blank>$pir</a>";
1528      }      }
1529      return $pir;      return $pir;
1530  }  }
# Line 1282  Line 1535 
1535    
1536      if ($kegg =~ /^kegg\|([^:]+):(\S+)$/)      if ($kegg =~ /^kegg\|([^:]+):(\S+)$/)
1537      {      {
1538          return "<a href=http://www.genome.ad.jp/dbget-bin/www_bget?$1+$2>$kegg</a>";          return "<a href='http://www.genome.ad.jp/dbget-bin/www_bget?$1+$2' target=_blank>$kegg</a>";
1539      }      }
1540      return $kegg;      return $kegg;
1541  }  }
1542    
1543    sub img_link {
1544        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1545        my($cgi,$img) = @_;
1546    
1547        if ($img =~ /^img\|(\S+)$/)
1548        {
1549            return "<a href='http://img.jgi.doe.gov/cgi-bin/pub/main.cgi?page=geneDetail&gene_oid=$1' target=_blank>$img</a>";
1550        }
1551        return $img;
1552    }
1553    
1554  sub ensembl_link {  sub ensembl_link {
1555      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1556      my($cgi,$ensembl) = @_;      my($cgi,$ensembl) = @_;
# Line 1295  Line 1559 
1559      {      {
1560          my $what=$1;          my $what=$1;
1561          my $key=$2;          my $key=$2;
1562          my $idx="all";          my $idx="All";
1563          if ($what eq "EnsemblGene") { $idx = "Gene" }          if ($what eq "EnsemblGene") { $idx = "Gene" }
1564          if ($what eq "EnsemblTranscript") { $idx = "all" }          if ($what eq "EnsemblTranscript") { $idx = "All" }
1565          if ($what eq "EnsemblProtein") { $idx = "all" }          if ($what eq "EnsemblProtein") { $idx = "All" }
1566    
1567          #I really want to get right to the transcript and peptide pages, but          #I really want to get right to the transcript and peptide pages, but
1568          #can't see how to do that without knowing the org name too, which          #can't see how to do that without knowing the org name too, which
1569          #I don't know at this point. (ensembl org name, not real org name)          #I don't know at this point. (ensembl org name, not real org name)
1570    
1571          return "<a href=http://www.ensembl.org/Homo_sapiens/textview?species=all&idx=$idx&q=$key>$ensembl</a>";          return "<a href='http://www.ensembl.org/Homo_sapiens/searchview?species=all&idx=$idx&q=$key' target=_blank>$ensembl</a>";
1572      }      }
1573      return $ensembl;      return $ensembl;
1574  }  }
# Line 1315  Line 1579 
1579    
1580      if ($entrezgene =~ /^EntrezGene:(\S+)$/)      if ($entrezgene =~ /^EntrezGene:(\S+)$/)
1581      {      {
1582          return "<a href=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=full_report&list_uids=$1>$entrezgene</a>";          return "<a href='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=full_report&list_uids=$1' target=_blank>$entrezgene</a>";
1583      }      }
1584      return $entrezgene;      return $entrezgene;
1585  }  }
# Line 1326  Line 1590 
1590    
1591      if ($mim =~ /^MIM:(\S+)$/)      if ($mim =~ /^MIM:(\S+)$/)
1592      {      {
1593          return "<a href=http://www3.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=$1>$mim</a>";          return "<a href='http://www3.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=$1' target=_blank>$mim</a>";
1594      }      }
1595      return $mim;      return $mim;
1596  }  }
1597    
1598    sub hgnc_link {
1599        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1600        my($cgi,$hgnc) = @_;
1601    
1602        if ($hgnc =~ /^HGNC:(\S+)$/)
1603        {
1604            return "<a href='http://www.gene.ucl.ac.uk/cgi-bin/nomenclature/searchgenes.pl?field=symbol&anchor=equals&match=$1&symbol_search=Search&number=50&format=html&sortby=symbol' target=_blank>$hgnc</a>";
1605        }
1606    
1607        return $hgnc;
1608    }
1609    
1610  sub unigene_link {  sub unigene_link {
1611      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1612      my($cgi,$unigene) = @_;      my($cgi,$unigene) = @_;
1613    
1614      if ($unigene =~ /^UniGene:(\S+)$/)      if ($unigene =~ /^UniGene:(\S+)$/)
1615      {      {
1616          return "<a href=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unigene&cmd=search&term=$1>$unigene</a>";          return "<a href='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unigene&cmd=search&term=$1' target=_blank>$unigene</a>";
1617      }      }
1618      return $unigene;      return $unigene;
1619  }  }
# Line 1348  Line 1624 
1624    
1625      if ($ipi =~ /^IPI:(\S+)$/)      if ($ipi =~ /^IPI:(\S+)$/)
1626      {      {
1627          return "<a href=http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-id+AEoS1R8Jnn+-e+[IPI:\'$1\']+-qnum+1+-enum+1>$ipi</a>";          return "<a href='http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-id+AEoS1R8Jnn+-e+[IPI:\'$1\']+-qnum+1+-enum+1' target=_blank>$ipi</a>";
1628      }      }
1629      return $ipi;      return $ipi;
1630  }  }
# Line 1361  Line 1637 
1637    
1638      if ($wp =~ /^WP:(\S+)$/)      if ($wp =~ /^WP:(\S+)$/)
1639      {      {
1640          return "<a href=http://www.wormbase.org/db/searches/basic?class=Any&query=$1&Search=Search>$wp</a>";          return "<a href='http://www.wormbase.org/db/searches/basic?class=Any&query=$1&Search=Search' target=_blank>$wp</a>";
1641      }      }
1642      return $wp;      return $wp;
1643  }  }
# Line 1374  Line 1650 
1650    
1651      if ($fb =~ /^FB:(\S+)$/)      if ($fb =~ /^FB:(\S+)$/)
1652      {      {
1653          return "<a href=http://flybase.bio.indiana.edu/.bin/fbidq.html?$1>$fb</a>";          return "<a href='http://flybase.bio.indiana.edu/.bin/fbidq.html?$1' target=_blank>$fb</a>";
1654      }      }
1655      return $fb;      return $fb;
1656  }  }
# Line 1387  Line 1663 
1663    
1664      if ($fb =~ /^FlyBaseORFNames:(\S+)$/)      if ($fb =~ /^FlyBaseORFNames:(\S+)$/)
1665      {      {
1666          return "<a href=http://flybase.bio.indiana.edu/.bin/fbidq.html?$1>$fb</a>";          return "<a href='http://flybase.bio.indiana.edu/.bin/fbidq.html?$1' target=_blank>$fb</a>";
1667      }      }
1668      return $fb;      return $fb;
1669  }  }
# Line 1400  Line 1676 
1676    
1677      if ($sgd =~ /^SGD_LOCUS:(\S+)$/)      if ($sgd =~ /^SGD_LOCUS:(\S+)$/)
1678      {      {
1679          return "<a href=http://db.yeastgenome.org/cgi-bin/locus.pl?locus=$1>$sgd</a>";          return "<a href='http://db.yeastgenome.org/cgi-bin/locus.pl?locus=$1' target=_blank>$sgd</a>";
1680      }      }
1681      return $sgd;      return $sgd;
1682  }  }
# Line 1431  Line 1707 
1707      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1708      my($cgi,$map,$org) = @_;      my($cgi,$map,$org) = @_;
1709    
1710      $user = $cgi->param('user');      my $user = $cgi->param('user');
1711      $user = $user ? $user : "";      $user = $user ? $user : "";
1712      $org = $org ? $org : "";      $org = $org ? $org : "";
1713    
# Line 1449  Line 1725 
1725    # -name => field and the checkbox name    # -name => field and the checkbox name
1726    my ($form, $button)=@_;    my ($form, $button)=@_;
1727    
1728    $java_script="<input type=\"button\" name=\"CheckAll\" value=\"Check All\"\nonClick=\"checkAll(document.$form.$button)\">\n";    my $java_script="<input type=\"button\" name=\"CheckAll\" value=\"Check All\"\nonClick=\"checkAll(document.$form.$button)\">\n";
1729    $java_script.="<input type=\"button\" name=\"CheckFirst\" value=\"Check First Half\"\nonClick=\"checkFirst(document.$form.$button)\">\n";    $java_script.="<input type=\"button\" name=\"CheckFirst\" value=\"Check First Half\"\nonClick=\"checkFirst(document.$form.$button)\">\n";
1730    $java_script.="<input type=\"button\" name=\"CheckSecond\" value=\"Check Second Half\"\nonClick=\"checkSecond(document.$form.$button)\">\n";    $java_script.="<input type=\"button\" name=\"CheckSecond\" value=\"Check Second Half\"\nonClick=\"checkSecond(document.$form.$button)\">\n";
1731    $java_script.="<input type=\"button\" name=\"UnCheckAll\" value=\"Uncheck All\"\nonClick=\"uncheckAll(document.$form.$button)\">\n";    $java_script.="<input type=\"button\" name=\"UnCheckAll\" value=\"Uncheck All\"\nonClick=\"uncheckAll(document.$form.$button)\">\n";
# Line 1457  Line 1733 
1733    return $java_script;    return $java_script;
1734  }  }
1735    
1736    =head3 sub_link
1737    
1738        my $htmlText = HTML::sub_link($cgi, $sub, gid);
1739    
1740    Create a subsystem link. The link will be to the display page if there is no
1741    user or we are in SPROUT mode; otherwise it will be to the edit page.
1742    
1743    =over 4
1744    
1745    =item cgi
1746    
1747    CGI query object for the current web session. The parameters of special interest
1748    are C<SPROUT> and C<user>. If the user is non-blank and SPROUT mode is 0, then
1749    the subsystem's edit page will be shown rather than its display page.
1750    
1751    =item sub
1752    
1753    Name of the desired subsystem. It will be cleaned of underscores before the
1754    hyperlink is applied.
1755    
1756    =item gid
1757    
1758    Genome ID to be specified as the focus.
1759    
1760    =back
1761    
1762    =cut
1763    
1764  sub sub_link {  sub sub_link {
1765        # Allow call as an instance in addition to the authorized method.
1766      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
1767      my($cgi,$sub) = @_;      # Get the parameters.
1768      my($sub_link);      my ($cgi, $sub, $gid) = @_;
1769        # Declare the return variable.
1770        my $retVal;
1771        # Clean the subsystem name for display purposes. This is a very
1772        # different thing from URL-escaping.
1773        my $cleaned = CGI::escapeHTML($sub);
1774        $cleaned =~ s/_/ /g;
1775        # URL-escape the subsystem name for use in the link.
1776        my $linkable = uri_escape($sub);
1777        # Determine the mode. Note we use the little OR trick to insure that
1778        # we have the correct value for plugging into the output link.
1779        my $user = $cgi->param('user') || "";
1780        my $sproutMode = $cgi->param('SPROUT') || 0;
1781        if ($user && ! $sproutMode) {
1782            # A SEED user is calling, so we go to the edit page.
1783            $retVal = "<a href=\"subsys.cgi?ssa_name=$linkable&request=show_ssa&user=$user\">$cleaned</a>";
1784        } else {
1785            # A visitor or SPROUT user is calling, so we go to the display page.
1786            $retVal = "<a href=\"display_subsys.cgi?ssa_name=$linkable;request=show_ssa;sort=by_phylo;focus=$gid;SPROUT=$sproutMode\">$cleaned</a>";
1787        }
1788        # Return the result.
1789        return $retVal;
1790    }
1791    
1792      my $user = $cgi->param('user');  sub reaction_map_link {
1793      my $esc_sub = uri_escape( $sub );      my($mapID, @reaction_list) = @_;
1794      $sub =~ s/\_/ /g;      if($mapID =~ /\d+/)
1795      if ($user)      {
1796            my $reactions = join "+", @reaction_list;
1797            if ($reactions ne "")
1798            {
1799                $reactions = "+".$reactions;
1800            }
1801    
1802            return "<a href=http://www.genome.jp/dbget-bin/show_pathway?rn$mapID$reactions>$mapID</a>";
1803        }
1804        else
1805      {      {
1806          $sub_link = "<a href=./subsys.cgi?ssa_name=$esc_sub&request=show_ssa&user=$user>$sub</a>";          return $mapID;
1807        }
1808    }
1809    
1810    sub compound_link {
1811        my($compound) = @_;
1812        if($compound =~ /^C\d+/)
1813        {
1814            return "<a href=\"javascript:void(0)\"onclick=\"window.open('http://www.genome.jp/dbget-bin/www_bget?compound+$compound','$&','height=640,width=800,scrollbars=yes,toolbar=yes,status=yes,resizable=yes')\">$compound</a>";
1815      }      }
1816      else      else
1817      {      {
1818          $sub_link = "<a href=\"display_subsys.cgi?ssa_name=$esc_sub&request=show_ssa&sort=by_phylo\">$sub</a>";          return $compound;
1819      }      }
     return $sub_link;  
1820  }  }
1821    
1822    
1823  sub reaction_link {  sub reaction_link {
1824      my($reaction) = @_;      my($reaction) = @_;
1825        if ($reaction =~ /^(\*)?(R\d+)/)
     if ($reaction =~ /^R\d+/)  
1826      {      {
1827          return "<a href=\"http://www.genome.ad.jp/dbget-bin/www_bget?rn+$reaction\" target=reaction$$>$reaction</a>";          # return "<a href=\"http://www.genome.ad.jp/dbget-bin/www_bget?rn+$2\" target=reaction$$>$reaction</a>";
1828            return "<a href=\"javascript:void(0)\"onclick=\"window.open('http://www.genome.ad.jp/dbget-bin/www_bget?rn+$reaction','$&','height=640,width=800,scrollbars=yes,toolbar=yes,status=yes,resizable=yes')\">$reaction</a>";
1829      }      }
1830      return $reaction;      return $reaction;
1831  }  }
1832    
1833    
1834  sub html_for_assignments {  sub html_for_assignments {
1835      my($fig,$user,$peg_sets) = @_;      my($fig,$user,$peg_sets) = @_;
1836      my $i;      my $i;
1837    
1838      my @vals = ();      my @vals = ();
1839      my $set = 1;      my $set = 1;
1840      foreach $peg_set (@$peg_sets)      foreach my $peg_set (@$peg_sets)
1841      {      {
1842          for ($i=0; ($i < @$peg_set); $i++)          for ($i=0; ($i < @$peg_set); $i++)
1843          {          {
1844              $peg = $peg_set->[$i];              my $peg = $peg_set->[$i];
1845              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)),"")));
1846          }          }
1847          $set++;          $set++;
# Line 1607  Line 1952 
1952    
1953    
1954   my @files=("SEED.rss");   my @files=("SEED.rss");
1955   if ($args->{"type"}) {push @files, "SEED.$type.rss"}   if ($args->{"type"}) {
1956        my $type = $args->{type};
1957        push @files, "SEED.$type.rss"
1958    }
1959    
1960   foreach my $file ("SEED.rss", @$files)   foreach my $file ("SEED.rss", @$files)
1961   {   {

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