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revision 1.39, Thu Jul 20 05:37:45 2006 UTC revision 1.40, Mon Aug 14 04:57:29 2006 UTC
# Line 60  Line 60 
60      $fig_or_sprout = new FIG;      $fig_or_sprout = new FIG;
61      unshift @$html, "<TITLE>The SEED Signature Genes Page</TITLE>\n";      unshift @$html, "<TITLE>The SEED Signature Genes Page</TITLE>\n";
62  }  }
63    my $qflag = 0;
64  my $tracing = $cgi->param('TRACE');  my $tracing = $cgi->param('TRACE');
65  if ($tracing) {  if ($tracing) {
66      TSetup($tracing, $cgi->param('TTYPE'));      my $type = $cgi->param('TTYPE');
67        TSetup($tracing, $type);
68        if ($type eq 'QUEUE') { $qflag = 1; }
69  }  }
70    
71  my @tmp = grep { $_ =~ /^\d+\.\d+$/ } $cgi->param;  my @tmp = grep { $_ =~ /^\d+\.\d+$/ } $cgi->param;
# Line 220  Line 223 
223  if ($is_sprout) {  if ($is_sprout) {
224      # For sprout, we use a template.      # For sprout, we use a template.
225      my $template = "$FIG_Config::template_url/Sigs_tmpl.php";      my $template = "$FIG_Config::template_url/Sigs_tmpl.php";
226      my $result = PageBuilder::Build($template, { data => join("\n", @$html) }, "Html");      my $traceList = ($qflag ? QTrace("html") : "");
227        my $result = PageBuilder::Build($template, { data => join("\n", @$html),
228                                                     tracing => $traceList }, "Html");
229      print "CONTENT-TYPE: text/html\n\n";      print "CONTENT-TYPE: text/html\n\n";
230      print $result;      print $result;
231  } else {  } else {
# Line 270  Line 275 
275      my %set2  = map { $_ => 1 } @$set2;      my %set2  = map { $_ => 1 } @$set2;
276    
277      my(%hits_set1,%hits_set2,@hits,$sim,$id2,$peg);      my(%hits_set1,%hits_set2,@hits,$sim,$id2,$peg);
278        my $pegCount = 0;
279        my $simCount = 0;
280      foreach $peg ($fig_or_sprout->all_features($given,"peg"))      foreach $peg ($fig_or_sprout->all_features($given,"peg"))
281      {      {
282            $pegCount++;
283          undef %hits_set1; undef %hits_set2;          undef %hits_set1; undef %hits_set2;
284          $hits_set1{&FIG::genome_of($peg)} = 1;          $hits_set1{&FIG::genome_of($peg)} = 1;
285          Trace("Processing $peg.") if T(3);          Trace("Processing $peg.") if T(4);
286          foreach $sim ($is_sprout ? $fig_or_sprout->bbhs($peg, $sim_cutoff) : $fig_or_sprout->sims($peg, 1000, $sim_cutoff, "fig"))          foreach $sim ($is_sprout ? $fig_or_sprout->bbhs($peg, $sim_cutoff) : $fig_or_sprout->sims($peg, 1000, $sim_cutoff, "fig"))
287          {          {
288                $simCount++;
289              $id2          = $is_sprout ? $sim->[0] : $sim->[1];              $id2          = $is_sprout ? $sim->[0] : $sim->[1];
290              Trace("SIG tool sim check for $peg vs. $id2.") if T(4);              Trace("SIG tool sim check for $peg vs. $id2.") if T(4);
291              if ($id2 =~ /^fig\|(\d+\.\d+)/)              if ($id2 =~ /^fig\|(\d+\.\d+)/)
# Line 303  Line 311 
311              push(@hits,[$peg,$sc,scalar $fig_or_sprout->function_of($peg)]);              push(@hits,[$peg,$sc,scalar $fig_or_sprout->function_of($peg)]);
312          }          }
313      }      }
314      Trace(scalar(@hits) . " hits found by differentiator.") if T(3);      Trace(scalar(@hits) . " hits found by differentiator off of $simCount sims for $pegCount pegs with cutoff $sim_cutoff.") if T(3);
315      return @hits;      return @hits;
316  }  }
317    

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