[Bioperl-guts-l] bioperl-network/Bio/Network/IO psi.pm,1.7,1.8

[Brian Osborne]

Update of /home/repository/bioperl/bioperl-network/Bio/Network/IO
In directory dev.open-bio.org:/tmp/cvs-serv21019/Bio/Network/IO

Modified Files:
	psi.pm 
Log Message:
Allow a node to use a DIP id as an accession

Index: psi.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-network/Bio/Network/IO/psi.pm,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** psi.pm	1 Oct 2006 20:36:43 -0000	1.7
--- psi.pm	1 Oct 2006 21:45:17 -0000	1.8
***************
*** 294,303 ****
  	# Make new species object if doesn't already exist
  	if ( !exists($species{$taxid}) ) {
! 		my $common     =  $org->first_child('names')->first_child('shortLabel')->text;
! 		my $full       =  $org->first_child('names')->first_child('fullName')->text;
! 		my $sp_obj     = Bio::Species->new(-ncbi_taxid     => $taxid,
! 													  -name => $full,
! 													  -common_name    => $common
! 													 );
  		$species{$taxid} = $sp_obj;
  	}
--- 294,303 ----
  	# Make new species object if doesn't already exist
  	if ( !exists($species{$taxid}) ) {
! 		my $common =  $org->first_child('names')->first_child('shortLabel')->text;
! 		my $full   =  $org->first_child('names')->first_child('fullName')->text;
! 		my $sp_obj = Bio::Species->new(-ncbi_taxid  => $taxid,
! 												 -name        => $full,
! 												 -common_name => $common
! 												);
  		$species{$taxid} = $sp_obj;
  	}
***************
*** 310,314 ****
  	$prim_id = defined ($ids{'GI'}) ?  $ids{'GI'} : '';
  	$acc = $ids{'RefSeq'} || 
! 	       $ids{'SWP'} || 
  			 $ids{'Swiss-Prot'} || # db name from HPRD
  			 $ids{'Ref-Seq'} ||    # db name from HPRD
--- 310,314 ----
  	$prim_id = defined ($ids{'GI'}) ?  $ids{'GI'} : '';
  	$acc = $ids{'RefSeq'} || 
! 	       $ids{'SWP'} ||        # DIP's name for Swissprot
  			 $ids{'Swiss-Prot'} || # db name from HPRD
  			 $ids{'Ref-Seq'} ||    # db name from HPRD
***************
*** 316,320 ****
  			 $ids{'PIR'} ||
  			 $ids{'intact'} ||     # db name from IntAct
! 			 $ids{'psi-mi'};       # db name from IntAct
  
  	# Get description line - certain files, like PSI XML from HPRD, have
--- 316,321 ----
  			 $ids{'PIR'} ||
  			 $ids{'intact'} ||     # db name from IntAct
! 			 $ids{'psi-mi'} ||     # db name from IntAct
! 			 $ids{'DIP'};          # DIP node name
  
  	# Get description line - certain files, like PSI XML from HPRD, have
***************
*** 331,335 ****
  	my $ac = Bio::Annotation::Collection->new();	
  	for my $db (keys %ids) {
! 		next if $ids{$db} eq $acc;
  		next if $ids{$db} eq $prim_id;
  		my $an = Bio::Annotation::DBLink->new( -database   => $db,
--- 332,336 ----
  	my $ac = Bio::Annotation::Collection->new();	
  	for my $db (keys %ids) {
! 		next if $ids{$db} eq $acc; print "desc $desc\n" unless $acc; 
  		next if $ids{$db} eq $prim_id;
  		my $an = Bio::Annotation::DBLink->new( -database   => $db,