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revision 1.93, Sat Jul 16 00:41:58 2005 UTC revision 1.94, Wed Jul 20 02:05:10 2005 UTC
# Line 895  Line 895 
895      push(@$html,$cgi->checkbox(-name => 'check_problems', -value => 1, -checked => 0, -override => 1,-label => 'show PEGs in roles that do not match precisely'),$cgi->br);      push(@$html,$cgi->checkbox(-name => 'check_problems', -value => 1, -checked => 0, -override => 1,-label => 'show PEGs in roles that do not match precisely'),$cgi->br);
896      if ($can_alter)      if ($can_alter)
897      {      {
898          push(@$html,$cgi->checkbox(-name => 'add_solid', -value => 1, -checked => 0, -override => 1,-label => 'Add Genomes with Solid Hits'),$cgi->br);          push(@$html,$cgi->checkbox(-name => 'add_solid', -value => 1, -checked => 0, -override => 1,-label => 'add genomes with solid hits'),$cgi->br);
899      }      }
900    
901      push(@$html,$cgi->checkbox(-name => 'show_coupled_fast', -value => 1, -checked => 0, -override => 1,-label => 'show coupled PEGs fast [depends on existing pins/clusters]'),$cgi->br);      push(@$html,$cgi->checkbox(-name => 'show_coupled_fast', -value => 1, -checked => 0, -override => 1,-label => 'show coupled PEGs fast [depends on existing pins/clusters]'),$cgi->br);
902    
903      push(@$html,$cgi->checkbox(-name => 'show_coupled', -value => 1, -checked => 0, -override => 1,-label => 'show coupled PEGs[figure 2 minutes per PEG in spreadsheet]'),$cgi->br);      push(@$html,$cgi->checkbox(-name => 'show_coupled', -value => 1, -checked => 0, -override => 1,-label => 'show coupled PEGs[figure 2 minutes per PEG in spreadsheet]'),$cgi->br);
904    
905      # RAE Hide -1 variants      # RAE Hide -1 variants
906      push(@$html,$cgi->checkbox(-name => 'show_minus1', -value=> 1, -checked => 0, -label => 'Show -1 variants'),$cgi->br);      push(@$html,$cgi->checkbox(-name => 'show_minus1', -value=> 1, -checked => 0, -label => 'show -1 variants'),$cgi->br);
907      push(@$html,$cgi->hr,  
908                  $cgi->br,"Column (specify the number of the column): ",      #  Alignment functions:
909                  $cgi->textfield(-name => "col_to_align", -size => 7),  
910        push @$html, $cgi->hr,
911                     # $cgi->br, "Column (specify the number of the column): ",
912                     # $cgi->textfield(-name => "col_to_align", -size => 7),
913                     "For sequences in a column (i.e., role): ",
914                     $cgi->popup_menu( -name   => 'col_to_align',
915                                       -values => [ map {   $_->[0]            } @roles ],
916                                       -labels => { map { ( $_->[0], $_->[1] ) } @roles }
917                                     ),
918                  $cgi->br,                  $cgi->br,
919                  $cgi->submit(-value => "Just show Sequences in Column",                   $cgi->submit(-value => "Show Sequences in Column",
920                               -name => "show_sequences_in_column"),                               -name => "show_sequences_in_column"),
921                  $cgi->br,                  $cgi->br,
922                  $cgi->submit(-value => "Align Column",                   $cgi->submit(-value => "Align Sequences in Column",
923                               -name => "align_column"),                               -name => "align_column"),
924                  $cgi->br,                  $cgi->br,
925                  $cgi->br,"Realign subgroup within a column (adding homologs): ",                  $cgi->br,"Realign subgroup within a column (adding homologs): ",
# Line 918  Line 928 
928                  $cgi->textfield(-name => "include_homo", -size => 10)," (leave blank to see just column)",                  $cgi->textfield(-name => "include_homo", -size => 10)," (leave blank to see just column)",
929                  " Max homologous seqs: ",$cgi->textfield(-name => "max_homo", -value => 100, -size => 6),                  " Max homologous seqs: ",$cgi->textfield(-name => "max_homo", -value => 100, -size => 6),
930                  $cgi->br,                  $cgi->br,
931                  $cgi->submit(-value => "Realign Column",                   $cgi->submit(-value => "Realign Sequences in Column",
932                               -name => "realign_column"),                               -name => "realign_column"),
933                  $cgi->hr                   $cgi->hr;
              );  
934    
935       # RAE: A new function to reannotate a single column       # RAE: A new function to reannotate a single column
936       # I don't understand how you get CGI.pm to reset (and never have).       # I don't understand how you get CGI.pm to reset (and never have).

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