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revision 1.92, Tue Mar 1 13:13:52 2005 UTC revision 1.93, Thu Mar 3 23:54:03 2005 UTC
# Line 1048  Line 1048 
1048                        "</TH>\n\t</TR>\n"                        "</TH>\n\t</TR>\n"
1049              );              );
1050    
1051            #  Grouping by genome is hard to see.  This is an attempt to make it more obvious
1052            #  by consolidating the "Organism" for all rows in which it is repeated.  -- GJO
1053    
1054            my $sim;
1055            my ( $id2, $genome, $org, $color, $info, $prev_genome, $prev_sim );
1056            foreach $sim ( @sims ) {
1057                $id2  = $sim->id2;
1058                if ( $group_by_genome && ( ( $genome ) = $id2 =~ /fig\|(\d+\.\d+)\./ )
1059                                      && ( $genome eq $prev_genome ) )
1060                {
1061                    $prev_sim->[-1]->[2]++;         # Increase row span of org
1062                    push @$sim, [ "", $color, 0 ];  # No org name, prev_color, no row span
1063                }
1064                else
1065                {
1066                    ( $org, $color ) = org_and_color_of( $fig_or_sprout, $id2 );
1067                    push @$sim, [ html_enc( $org ), $color, 1 ];
1068                    $prev_genome = $genome || "";
1069                    $prev_sim = $sim;
1070                }
1071            }
1072    
1073          #  Add the table data, row-by-row          #  Add the table data, row-by-row
1074    
1075          my $alia = (! $hide_alias);          my $alia = (! $hide_alias);
         my $sim;  
1076          foreach $sim ( @sims ) {          foreach $sim ( @sims ) {
1077              my $id2  = $sim->id2;              my $id2  = $sim->id2;
1078    
# Line 1101  Line 1122 
1122              my $color2  = match_color( $b2, $e2, $ln2 );              my $color2  = match_color( $b2, $e2, $ln2 );
1123              my $radio   = $user ? shift @from : undef;              my $radio   = $user ? shift @from : undef;
1124              my $func2   = html_enc( scalar &trans_function_of( $cgi, $fig_or_sprout, $id2, $user ) );              my $func2   = html_enc( scalar &trans_function_of( $cgi, $fig_or_sprout, $id2, $user ) );
1125              ## RAE Added color3. This will color function tables that do not match the original  
1126                ## RAE Added color3. This will color function cells that do not match the original
1127              ## annotation. This makes is a lot easier to see what is different (e.g. caps/spaces, etc)              ## annotation. This makes is a lot easier to see what is different (e.g. caps/spaces, etc)
1128              my $color3="#FFFFFF";              my $color3  = ( $func2 eq $current_func ) ? "#FFFFFF" : "#FFDEAD";
             unless ($func2 eq $current_func) {$color3="#FFDEAD"}  
1129    
1130              if ($funcF && $funcF ne $func2) { $func2 = "$funcF<br>$func2" }              if ( $funcF && ( $funcF ne $func2 ) ) { $func2 = "$funcF<br>$func2" }
1131    
1132              #              # Retrieve the Organism data that was pushed on the end of the sim:
1133              # Colorize organisms:              my ( $org, $oc, $rowspan ) = @{$sim->[-1]};
             #  
             # my $org     = html_enc( &org_of($fig_or_sprout, $id2 ) );  
             my ($org,$oc) = &org_and_color_of($fig_or_sprout, $id2 );  
             $org        = html_enc( $org );  
1134    
1135              my $aliases = $alia ? html_enc( join( ", ", &feature_aliasesL($fig_or_sprout,$id2) ) )              my $aliases = $alia ? html_enc( join( ", ", &feature_aliasesL($fig_or_sprout,$id2) ) )
1136                                  : undef;                                  : undef;
# Line 1139  Line 1156 
1156                            #                            #
1157                            #  Colorize organism by Domain                            #  Colorize organism by Domain
1158                            #                            #
1159                            # "\t\t<TD>$org</TD>\n",                            $rowspan ? "\t\t<TD Rowspan=$rowspan Bgcolor=$oc>$org</TD>\n" : (),
                           "\t\t<TD Bgcolor=$oc>$org</TD>\n",  
1160                            $alia ? "\t\t<TD>$aliases</TD>\n" : (),                            $alia ? "\t\t<TD>$aliases</TD>\n" : (),
1161                            "\t</TR>\n"                            "\t</TR>\n"
1162                  );                  );
# Line 1328  Line 1344 
1344      Just FIG IDs:<input type=checkbox name=just_fig value=1 $chk_just_fig>      Just FIG IDs:<input type=checkbox name=just_fig value=1 $chk_just_fig>
1345      Show Env. samples:<input type=checkbox name=show_env value=1 $chk_show_env>      Show Env. samples:<input type=checkbox name=show_env value=1 $chk_show_env>
1346      Hide aliases:<input type=checkbox name=hide_alias value=1 $chk_hide_alias>      Hide aliases:<input type=checkbox name=hide_alias value=1 $chk_hide_alias>
1347      Group by Genome:<input type=checkbox name=group_by_genome value=1 $chk_group_by_genome><br />      Group by genome:<input type=checkbox name=group_by_genome value=1 $chk_group_by_genome><br />
1348  </FORM>  </FORM>
1349  End_Short_Form  End_Short_Form
1350    
# Line 1384  Line 1400 
1400      Just FIG IDs:<input type=checkbox name=just_fig value=1 $chk_just_fig>      Just FIG IDs:<input type=checkbox name=just_fig value=1 $chk_just_fig>
1401      Show Env. samples:<input type=checkbox name=show_env value=1 $chk_show_env>      Show Env. samples:<input type=checkbox name=show_env value=1 $chk_show_env>
1402      Hide aliases:<input type=checkbox name=hide_alias value=1 $chk_hide_alias>      Hide aliases:<input type=checkbox name=hide_alias value=1 $chk_hide_alias>
1403      Group by Genome:<input type=checkbox name=group_by_genome value=1 $chk_group_by_genome><br />      Group by genome:<input type=checkbox name=group_by_genome value=1 $chk_group_by_genome><br />
1404  End_Default_Options  End_Default_Options
1405    
1406          #  Extra options          #  Extra options
# Line 1393  Line 1409 
1409      <input type=hidden name=extra_opt value=\"$extra_opt\">      <input type=hidden name=extra_opt value=\"$extra_opt\">
1410    
1411      Min similarity:<input type=text name=min_sim size=5 value=$min_sim>      Min similarity:<input type=text name=min_sim size=5 value=$min_sim>
1412      As defined by      as defined by
1413      <select name=sim_meas>      <select name=sim_meas>
1414          <option value=id  $chk_sim_meas_id>identities</option>          <option value=id  $chk_sim_meas_id>identities</option>
1415          <!--  Hide unimplimented options          <!--  Hide unimplimented options

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