Re: [Gusdev-gusdev] fixing GBParser to add topology

[Steve F. <sfi...@pc...>]

ok, thanks fidel.   we'll fold these changes in.

steve

Fidel Salas wrote:

>To get GBParser to fill-in the topology attribute, I had to make
>manual changes to two files (see below).  Creation of Perl objects
>automatically created setTopology and getTopology methods in 
>GUS::Model::DoTS::NAEntry_Row (after creating initial DB instance with
>modified schema).
>
>Fidel
>
>
>Here are the diffs:
>CBIL::Bio::GenBank::Locus
>*** /tmp/Locus.pm	Thu Mar  4 15:03:49 2004
>--- /tmp/Locus.pm-original	Thu Mar  4 15:03:49 2004
>***************
>*** 9,15 ****
>  sub setType     { $_[0]->{TYP} = $_[1]; $_[0] }
>  sub setDivision { $_[0]->{DIV} = $_[1]; $_[0] }
>  sub setDate     { $_[0]->{DAT} = $_[1]; $_[0] }
>- sub setTopology { $_[0]->{TOP} = $_[1]; $_[0] }
>  
>  sub getId       { $_[0]->{ID}  }
>  sub getLength   { $_[0]->{LEN} }
>--- 9,14 ----
>***************
>*** 16,22 ****
>  sub getType     { $_[0]->{TYP} }
>  sub getDivision { $_[0]->{DIV} }
>  sub getDate     { $_[0]->{DAT} }
>- sub getTopology { $_[0]->{TOP} }
>  
>  # ........................................
>  
>--- 15,20 ----
>***************
>*** 27,35 ****
>    my $line = $IOS->getLine();
>  
>  	my @A = split /\s+/, $line;
>!   my ( $LOCUS, $id, $length, $bp, $type, $topology, $div, $date );
>  	if (@A > 7) {
>! 		( $LOCUS, $id, $length, $bp, $type, $topology, $div, $date ) = @A;
>  	} elsif (@A == 7) {
>  		( $LOCUS, $id, $length, $bp, $type, $div, $date ) = @A;
>  	}	else {
>--- 25,33 ----
>    my $line = $IOS->getLine();
>  
>  	my @A = split /\s+/, $line;
>!   my ( $LOCUS, $id, $length, $bp, $type, $circular, $div, $date );
>  	if (@A > 7) {
>! 		( $LOCUS, $id, $length, $bp, $type, $circular, $div, $date ) = @A;
>  	} elsif (@A == 7) {
>  		( $LOCUS, $id, $length, $bp, $type, $div, $date ) = @A;
>  	}	else {
>***************
>*** 43,49 ****
>    $M->setType(     $type );
>    $M->setDivision( $div );
>    $M->setDate(     $date );
>-   $M->setTopology( $topology );
>  
>    $M;
>  }
>--- 41,46 ----
>
>
>GUS::Common::Plugin::GBParser
>*** /tmp/GBParser.pm	Thu Mar  4 15:15:26 2004
>--- /tmp/GBParser.pm~	Thu Mar  4 15:15:26 2004
>***************
>*** 348,354 ****
>    my %h = ('source_id' =>  $e->{ACCESSION}->[0]->getAccession(), 
>  	   'division' => $e->{LOCUS}->[0]->getDivision(),
>  	   'version' => $e->{VERSION}->[0]->getSeqVersion(),
>- 	   'topology' => $e->{LOCUS}->[0]->getTopology(),
>  	  ) ;
>    my $date = &formatDate($e->{LOCUS}->[0]->getDate());
>    if ($chkdif) { 
>--- 345,350 ----
>
>
>
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