[Bioperl-guts-l] bioperl-live/Bio/SeqIO qual.pm,1.24,1.25

Brian Osborne bosborne at pub.open-bio.org
Thu Oct 21 21:52:34 EDT 2004


Update of /home/repository/bioperl/bioperl-live/Bio/SeqIO
In directory pub.open-bio.org:/tmp/cvs-serv19185/Bio/SeqIO

Modified Files:
	qual.pm 
Log Message:
I like this syntax better...


Index: qual.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/SeqIO/qual.pm,v
retrieving revision 1.24
retrieving revision 1.25
diff -C2 -d -r1.24 -r1.25
*** qual.pm	21 Oct 2004 19:13:24 -0000	1.24
--- qual.pm	22 Oct 2004 01:52:32 -0000	1.25
***************
*** 207,216 ****
  	if (!$source || ( !$source->isa('Bio::Seq::SeqWithQuality') && 
  							!$source->isa('Bio::Seq::PrimaryQual')   )) {
! 		$self->throw("You must pass a Bio::Seq::SeqWithQuality or a Bio::Seq::PrimaryQual object to write_seq as a parameter named \"source\"");
  	}
! 	my $header = $source->id;
! 	$header = $source->header if (!$header &&
! 				 $source->isa('Bio::Seq::PrimaryQual'));
! 	if (!$header) { $header = "unknown"; }
  	my @quals = $source->qual();
  	# ::dumpValue(\@quals);
--- 207,214 ----
  	if (!$source || ( !$source->isa('Bio::Seq::SeqWithQuality') && 
  							!$source->isa('Bio::Seq::PrimaryQual')   )) {
! 		$self->throw("You must pass a Bio::Seq::SeqWithQuality or a Bio::Seq::PrimaryQual object to write_seq() as a parameter named \"source\"");
  	}
! 	my $header = $source->can("id") ? $source->id :
! 	  $source->can("header") ? $source->header : "unknown";
  	my @quals = $source->qual();
  	# ::dumpValue(\@quals);



More information about the Bioperl-guts-l mailing list