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revision 1.626, Mon Oct 1 15:33:11 2007 UTC revision 1.627, Thu Oct 4 19:48:40 2007 UTC
# Line 6944  Line 6944 
6944      return FIGRules::NetCouplingData('coupled_to', id1 => $peg);      return FIGRules::NetCouplingData('coupled_to', id1 => $peg);
6945  }  }
6946    
6947    sub net_in_pch_pin_with_and_evidence {
6948        my($self, $peg) = @_;
6949        return FIGRules::NetCouplingData('in_pch_pin_with_and_evidence', id1 => $peg);
6950    }
6951    
6952  sub net_coupling_evidence  sub net_coupling_evidence
6953  {  {
6954      my($self, $peg1, $peg2) = @_;      my($self, $peg1, $peg2) = @_;
# Line 9411  Line 9416 
9416    
9417  =cut  =cut
9418    
9419  sub in_pch_pin_with {  sub in_pch_pin_with_old {
9420      my($self,$peg) = @_;      my($self,$peg) = @_;
9421      my($set,$id,%in);      my($set,$id,%in);
9422    
9423      return $self->in_set_with($peg,"pch_pins","pin");      return $self->in_set_with($peg,"pch_pins","pin");
9424  }  }
9425    
9426    sub in_pch_pin_with
9427    {
9428        my($self, $peg1, $diverse) = @_;
9429    
9430        my @all = $self->in_pch_pin_with_and_evidence($peg1);
9431        warn "Got all=" . Dumper(\@all);
9432        if ($diverse)
9433        {
9434            return map { $_->[0] } grep { $_->[1] == 1 } @all;
9435        }
9436        else
9437        {
9438            return map { $_->[0] } @all;
9439        }
9440    }
9441    
9442    sub in_pch_pin_with_and_evidence
9443    {
9444        my($self,$peg1) = @_;
9445    
9446        if ($FIG_Config::use_pch_server)
9447        {
9448            warn "returning net pch\n";
9449            return $self->net_in_pch_pin_with_and_evidence($peg1);
9450        }
9451    
9452        my $rdbH = $self->db_handle;
9453        if ($rdbH->table_exists('pchs') && $self->is_complete(&FIG::genome_of($peg1)))
9454        {
9455            my $res = $rdbH->SQL(qq(SELECT peg3, max(rep)
9456                                    FROM pchs
9457                                    WHERE peg1 = ?
9458                                    GROUP BY peg3
9459                                   ), undef, $peg1);
9460            return @$res;
9461        }
9462    }
9463    
9464    
9465    
9466  =head3 add_pch_pins  =head3 add_pch_pins
9467    
9468  usage: $fig->add_pch_pins($file)  usage: $fig->add_pch_pins($file)
# Line 15405  Line 15450 
15450    
15451  =head3 perform_subsystem_salvage  =head3 perform_subsystem_salvage
15452    
15453  C<< my $glist = [['273035.1', '273035.4']]; >>      my $glist = [['273035.1', '273035.4']];
15454  C<< my $pmap = { 'fig|273035.1.peg.1' => 'fig|273035.4.peg.4', ... }; >>      my $pmap = { 'fig|273035.1.peg.1' => 'fig|273035.4.peg.4', ... };
15455  C<< $fig->perform_subsystem_salvage($glist, $pmap); >>      $fig->perform_subsystem_salvage($glist, $pmap);
15456    
15457  For each subsystem in this SEED, perform a subsystem salvage operation for each old-genome / new-genome pair in $glist.  For each subsystem in this SEED, perform a subsystem salvage operation for each old-genome / new-genome pair in $glist.
15458  This operation will determine if the old genome exists in the subsystem. If it does, the new genome is  This operation will determine if the old genome exists in the subsystem. If it does, the new genome is
# Line 15542  Line 15587 
15587    
15588   my $version=subsystem_version($subsystem_name)   my $version=subsystem_version($subsystem_name)
15589    
15590   returns the current version of the subsystem.  Returns the current version of the subsystem.
15591    
15592  =cut  =cut
15593    

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