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revision 1.23, Tue Apr 3 12:24:31 2007 UTC revision 1.24, Tue Apr 10 03:48:49 2007 UTC
# Line 1057  Line 1057 
1057    
1058          if (!$seen{$genome, $sname, $role})          if (!$seen{$genome, $sname, $role})
1059          {          {
1060              push(@{$genome_index->{$genome}, [$sname, $role]});              push(@{$genome_index->{$genome}}, [$sname, $role]);
1061          }          }
1062    
1063      }      }
# Line 1161  Line 1161 
1161      my $fig     = $self->{_fig};      my $fig     = $self->{_fig};
1162      my $newG    = $self->{_genome};      my $newG    = $self->{_genome};
1163      my $newGdir = $self->{_orgdir};      my $newGdir = $self->{_orgdir};
1164      my $max     = $max ? $max : 10000;      $max     = $max ? $max : 10000;
1165      my $maxP    = $maxP ? $maxP : 1.0e-5;      $maxP    = $maxP ? $maxP : 1.0e-5;
1166      $select     = $select ? $select : "all";      $select     = $select ? $select : "all";
1167    
1168      my $sims_file = "$newGdir/expanded_similarities";      my $sims_file = "$newGdir/expanded_similarities";
# Line 1176  Line 1176 
1176              my($id1,$id2,$iden,$f1,$f2,$f3,$b1,$e1,$b2,$e2,$psc,$bsc,$ln1,$ln2) = split(/\t/,$_);              my($id1,$id2,$iden,$f1,$f2,$f3,$b1,$e1,$b2,$e2,$psc,$bsc,$ln1,$ln2) = split(/\t/,$_);
1177              push(@flips, bless ( [$id2,$id1,$iden,$f1,$f2,$f3,$b2,$e2,$b1,$e1,$psc,$bsc,$ln2,$ln1],'Sim'));              push(@flips, bless ( [$id2,$id1,$iden,$f1,$f2,$f3,$b2,$e2,$b1,$e1,$psc,$bsc,$ln2,$ln1],'Sim'));
1178          }          }
1179          my @flips = sort { $b->bsc <=> $a->bsc } @flips;          @flips = sort { $b->bsc <=> $a->bsc } @flips;
1180          my @old = $fig->sims($peg,$max,$maxP,$select);          my @old = $fig->sims($peg,$max,$maxP,$select);
1181          my @old = sort { $b->bsc <=> $a->bsc } @old;          @old = sort { $b->bsc <=> $a->bsc } @old;
1182    
1183          my @merged = ();          my @merged = ();
1184          my $i1 = 0;          my $i1 = 0;
# Line 1233  Line 1233 
1233      my $fig     = $self->{_fig};      my $fig     = $self->{_fig};
1234      my $newG    = $self->{_genome};      my $newG    = $self->{_genome};
1235      my $newGdir = $self->{_orgdir};      my $newGdir = $self->{_orgdir};
1236      my $max     = $max ? $max : 10000;      $max     = $max ? $max : 10000;
1237      my $maxP    = $maxP ? $maxP : 1.0e-5;      $maxP    = $maxP ? $maxP : 1.0e-5;
1238      $select     = $select ? $select : "all";      $select     = $select ? $select : "all";
1239    
1240      if (($peg =~ /^fig\|(\d+\.\d+)/) && ($1 eq $newG))      if (($peg =~ /^fig\|(\d+\.\d+)/) && ($1 eq $newG))

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