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revision 1.27, Wed Jul 12 06:40:30 2006 UTC revision 1.28, Wed Jul 12 20:06:38 2006 UTC
# Line 62  Line 62 
62  }  }
63  my $tracing = $cgi->param('TRACE');  my $tracing = $cgi->param('TRACE');
64  if ($tracing) {  if ($tracing) {
65      TSetup($tracing, "QUEUE");      TSetup($tracing, $cgi->param('TTYPE'));
66  }  }
67    
68  my @tmp = grep { $_ =~ /^\d+\.\d+$/ } $cgi->param;  my @tmp = grep { $_ =~ /^\d+\.\d+$/ } $cgi->param;
# Line 110  Line 110 
110                  $cgi->checkbox( -name => 'sort_by_func', -value => 1, -override => 1, -checked => 0, -label => 'Sort by Function'),                  $cgi->checkbox( -name => 'sort_by_func', -value => 1, -override => 1, -checked => 0, -label => 'Sort by Function'),
111                  $cgi->br,                  $cgi->br,
112                  $cgi->checkbox( -name => 'write_tab', -value => 1, -override => 1, -checked => 0, -label => 'Export Tab Delimited Table'),                  $cgi->checkbox( -name => 'write_tab', -value => 1, -override => 1, -checked => 0, -label => 'Export Tab Delimited Table'),
 #                $cgi->br,  
 #                $cgi->br, "Tracing: ",$cgi->textfield(-name => "TRACE", -size => 30, -value => ""),  
113                  $cgi->br,                  $cgi->br,
114                  $cgi->br,                  $cgi->br,
115                  $cgi->submit("Find the Discriminating Proteins from Given Organism"),$cgi->reset,                  $cgi->submit("Find the Discriminating Proteins from Given Organism"),$cgi->reset,
116                  $cgi->br,                  $cgi->br,
117                  $cgi->br,                  $cgi->br,
118                  $cgi->submit("Find Genes from Checked Organism and in Organisms from Set 1"),                  $cgi->submit("Find Genes from Checked Organism and in Organisms from Set 1"),
119                  " (minimum matches from Set 1: )", $cgi->textfield(-name => minN, -size => 5),                  " (minimum matches from Set 1: )", $cgi->textfield(-name => minN, -size => 5));
120        if ($cgi->param('TTYPE')) {
121            push @$html,
122                    $cgi->br,
123                    $cgi->br, "Tracing: ",$cgi->textfield(-name => "TRACE", -size => 30, -value => ""),
124                    $cgi->hidden(-name => 'TTYPE', -value => $cgi->param('TTYPE'));
125        }
126        push @$html,
127                  $cgi->end_form,                  $cgi->end_form,
128                  "\n");                  "\n";
129  }  }
130  else  else
131  {  {
# Line 263  Line 268 
268          undef %hits_set1; undef %hits_set2;          undef %hits_set1; undef %hits_set2;
269          $hits_set1{&FIG::genome_of($peg)} = 1;          $hits_set1{&FIG::genome_of($peg)} = 1;
270    
271          foreach $sim ($fig_or_sprout->sims($peg, 1000, $sim_cutoff, "fig"))          foreach $sim ($fig_or_sprout->bbhs($peg)) # sims($peg, 1000, $sim_cutoff, "fig"))
272          {          {
273              $id2          = $sim->[0]; # id2;              $id2          = $sim->[0]; # id2;
274              Trace("SIG tool sim check for $peg vs. $id2.") if T(4);              Trace("SIG tool sim check for $peg vs. $id2.") if T(4);
# Line 290  Line 295 
295              push(@hits,[$peg,$sc,scalar $fig_or_sprout->function_of($peg)]);              push(@hits,[$peg,$sc,scalar $fig_or_sprout->function_of($peg)]);
296          }          }
297      }      }
298        Trace(scalar(@hits) . " hits found by differentiator.") if T(3);
299      return @hits;      return @hits;
300  }  }
301    

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