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revision 1.53, Fri Mar 4 23:16:43 2005 UTC revision 1.54, Sat Mar 5 04:29:59 2005 UTC
# Line 745  Line 745 
745      push(@$html,$cgi->checkbox(-name => 'ignore_alt', -value => 1, -override => 1, -label => 'ignore alternatives', -checked => ($cgi->param('ignore_alt'))),$cgi->br);      push(@$html,$cgi->checkbox(-name => 'ignore_alt', -value => 1, -override => 1, -label => 'ignore alternatives', -checked => ($cgi->param('ignore_alt'))),$cgi->br);
746      push(@$html,$cgi->checkbox(-name => 'ext_ids', -value => 1, -checked => 0, -label => 'use external ids'),$cgi->br);      push(@$html,$cgi->checkbox(-name => 'ext_ids', -value => 1, -checked => 0, -label => 'use external ids'),$cgi->br);
747      push(@$html,$cgi->checkbox(-name => 'show_clusters', -value => 1, -checked => 0, -override => 1,-label => 'show clusters'),$cgi->br);      push(@$html,$cgi->checkbox(-name => 'show_clusters', -value => 1, -checked => 0, -override => 1,-label => 'show clusters'),$cgi->br);
     push(@$html,$cgi->checkbox(-name => 'pirsf_color', -value => 1, -checked => 0, -override => 1,-label => 'show PIR superfamilies'),$cgi->br);  
748      my $opt=$fig->get_tags("genome"); # all the tags we know about      my $opt=$fig->get_tags("genome"); # all the tags we know about
749      my @options=sort {uc($a) cmp uc($b)} keys %$opt;      my @options=sort {uc($a) cmp uc($b)} keys %$opt;
750      unshift(@options, undef); # a blank field at the start      unshift(@options, undef); # a blank field at the start
751      push(@$html,$cgi->popup_menu(-name => 'color_by_ga', -values=>\@options), "   color by an organism's attribute",$cgi->br);      push(@$html,"color rows by each organism's attribute:   ", $cgi->popup_menu(-name => 'color_by_ga', -values=>\@options), $cgi->br);
752    
753        $opt=$fig->get_tags("peg"); # all the peg tags
754        @options=sort {uc($a) cmp uc($b)} keys %$opt;
755        unshift(@options, undef);
756        push(@$html,"color columns by each PEGs attribute:   ", $cgi->popup_menu(-name => 'color_by_peg_tag', -values=>\@options), $cgi->br);
757    
758      push(@$html,$cgi->checkbox(-name => 'show_missing', -value => 1, -checked => 0, -override => 1,-label => 'show missing'),$cgi->br);      push(@$html,$cgi->checkbox(-name => 'show_missing', -value => 1, -checked => 0, -override => 1,-label => 'show missing'),$cgi->br);
759    
760      push(@$html,$cgi->checkbox(-name => 'show_missing_including_matches', -value => 1, -checked => 0, -override => 1,-label => 'show missing with matches'),      push(@$html,$cgi->checkbox(-name => 'show_missing_including_matches', -value => 1, -checked => 0, -override => 1,-label => 'show missing with matches'),
# Line 1390  Line 1395 
1395                    }                    }
1396                 }                 }
1397              }              }
1398              if ($cgi->param("pirsf_color"))              if ($cgi->param("color_by_peg_tag"))
1399              {              {
1400               ($color_of, $superscript, $tagvalcolor) = color_by_tag($fig, \@pegs, $color_of, $tagvalcolor, "PIRSF");               ($color_of, $superscript, $tagvalcolor) = color_by_tag($fig, \@pegs, $color_of, $tagvalcolor, $cgi->param("color_by_peg_tag"));
1401              }              }
1402              foreach $cell (@cells)              foreach $cell (@cells)
1403              {              {
# Line 1605  Line 1610 
1610   foreach my $t (keys %$tagvalcolor) {($tagvalcolor->{$t} > $count) ? $count=$tagvalcolor->{$t} : 1}   foreach my $t (keys %$tagvalcolor) {($tagvalcolor->{$t} > $count) ? $count=$tagvalcolor->{$t} : 1}
1611   $count++; # this should now be the next number to assign   $count++; # this should now be the next number to assign
1612   foreach my $peg (@$pegs) {   foreach my $peg (@$pegs) {
1613    next unless (my @attr=$fig->feature_attributes($peg));    next unless (my @attr=$fig->get_attributes($peg));
1614    foreach my $attr (@attr) {    foreach my $attr (@attr) {
1615       next unless (defined $attr);
1616     my ($tag, $val, $link)=@$attr;     my ($tag, $val, $link)=@$attr;
1617     next unless ($tag eq $want);     next unless ($tag eq $want);
1618     if ($tagvalcolor->{$val}) {     if ($tagvalcolor->{$val}) {

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