[Bioperl-guts-l] bioperl-live/Bio/Assembly/IO ace.pm,1.6,1.7

Heikki Lehvaslaiho heikki at pub.open-bio.org
Wed Jul 13 08:29:18 EDT 2005


Update of /home/repository/bioperl/bioperl-live/Bio/Assembly/IO
In directory pub.open-bio.org:/tmp/cvs-serv19339/Bio/Assembly/IO

Modified Files:
	ace.pm 
Log Message:
removing Bio:Seq::SeqWithQuality in favour of Bio::Seq::Quality


Index: ace.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Assembly/IO/ace.pm,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** ace.pm	22 Apr 2004 17:22:45 -0000	1.6
--- ace.pm	13 Jul 2005 12:29:16 -0000	1.7
***************
*** 100,104 ****
  use Bio::LocatableSeq;
  use Bio::Annotation::SimpleValue;
! use Bio::Seq::PrimaryQual;
  use Bio::SeqIO;
  use Bio::SeqFeature::Generic;
--- 100,104 ----
  use Bio::LocatableSeq;
  use Bio::Annotation::SimpleValue;
! use Bio::Seq::Quality;
  use Bio::SeqIO;
  use Bio::SeqFeature::Generic;
***************
*** 198,203 ****
  	    }
  
! 	    my $qual = Bio::Seq::PrimaryQual->new(-qual=>join(" ", at quality),
! 						  -id=>$contigOBJ->id());
  	    $contigOBJ->set_consensus_quality($qual);
  	};
--- 198,203 ----
  	    }
  
! 	    my $qual = Bio::Seq::Quality->new(-qual=>join(" ", at quality),
!                                               -id=>$contigOBJ->id());
  	    $contigOBJ->set_consensus_quality($qual);
  	};



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