[Gusdev-gusdev] fixing GBParser to add topology

[Fidel S. <fi...@vb...>]

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 ----