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revision 1.114, Mon Jun 6 13:25:16 2005 UTC revision 1.115, Fri Jun 10 16:08:52 2005 UTC
# Line 266  Line 266 
266      unshift @$html, "<TITLE>The SEED: Functional Coupling</TITLE>\n";      unshift @$html, "<TITLE>The SEED: Functional Coupling</TITLE>\n";
267      my $user = $cgi->param('user');      my $user = $cgi->param('user');
268      my $to   = $cgi->param('to');      my $to   = $cgi->param('to');
269      my @coup = grep { $_->[1] eq $to } &coupling_and_evidence($fig_or_sprout,$peg,5000,1.0e-10,4);      my @coup = grep { $_->[1] eq $to } &coupling_and_evidence($fig_or_sprout,$peg,5000,1.0e-10,4,1);
270    
271      if (@coup != 1) {      if (@coup != 1) {
272                  push(@$html,"<h1>Sorry, no evidence that $peg is coupled to $to</h1>\n");                  push(@$html,"<h1>Sorry, no evidence that $peg is coupled to $to</h1>\n");
# Line 347  Line 347 
347          if ($cgi->param('fcsim')) {$sim_cutoff=$cgi->param('fcsim')}          if ($cgi->param('fcsim')) {$sim_cutoff=$cgi->param('fcsim')}
348          if ($cgi->param('fccoup')) {$coupling_cutoff=$cgi->param('fccoup')}          if ($cgi->param('fccoup')) {$coupling_cutoff=$cgi->param('fccoup')}
349    
350          @fc_data = &coupling_and_evidence($fig_or_sprout,$peg,$bound,$sim_cutoff,$coupling_cutoff);          @fc_data = &coupling_and_evidence($fig_or_sprout,$peg,$bound,$sim_cutoff,$coupling_cutoff,1);
351      } else {      } else {
352          @fc_data = ();          @fc_data = ();
353      }      }
# Line 2501  Line 2501 
2501  }  }
2502    
2503  sub coupling_and_evidence {  sub coupling_and_evidence {
2504      my($fig_or_sprout,$peg,$bound,$sim_cutoff,$coupling_cutoff) = @_;      my($fig_or_sprout,$peg,$bound,$sim_cutoff,$coupling_cutoff,$try_old) = @_;
2505    
2506      return $fig_or_sprout->coupling_and_evidence($peg,$bound,$sim_cutoff,$coupling_cutoff,"keep");      return $fig_or_sprout->coupling_and_evidence($peg,$bound,$sim_cutoff,$coupling_cutoff,"keep",$try_old);
2507  }  }
2508    
2509  sub feature_locationS {  sub feature_locationS {
# Line 2537  Line 2537 
2537              {              {
2538                  $in_cluster{$peg} = "";                  $in_cluster{$peg} = "";
2539              }              }
2540                elsif ($cgi->param('fc'))
2541                {
2542                    %in_cluster = map { $_ => "" } $fig_or_sprout->in_cluster_with($peg);
2543                }
2544          }          }
2545          else          else
2546          {          {

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