[Bioperl-guts-l] bioperl-live/Bio/AlignIO arp.pm, 1.1, 1.2 mase.pm, 1.14, 1.15 metafasta.pm, 1.8, 1.9

Christopher John Fields cjfields at dev.open-bio.org
Tue Jan 16 14:31:07 EST 2007


Update of /home/repository/bioperl/bioperl-live/Bio/AlignIO
In directory dev.open-bio.org:/tmp/cvs-serv1805

Modified Files:
	arp.pm mase.pm metafasta.pm 
Log Message:
fix for filehandle IO

Index: arp.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/AlignIO/arp.pm,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** arp.pm	11 Nov 2006 23:08:12 -0000	1.1
--- arp.pm	16 Jan 2007 19:31:05 -0000	1.2
***************
*** 120,124 ****
      # alignments only returned if they contain sequences
      return $aln if $aln->no_sequences;
!     return 0;
  }
  
--- 120,124 ----
      # alignments only returned if they contain sequences
      return $aln if $aln->no_sequences;
!     return;
  }
  

Index: metafasta.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/AlignIO/metafasta.pm,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** metafasta.pm	28 Oct 2006 01:54:17 -0000	1.8
--- metafasta.pm	16 Jan 2007 19:31:05 -0000	1.9
***************
*** 154,161 ****
  	}
      }
!     return $aln;
  }
  
- 
  =head2 write_aln
  
--- 154,161 ----
  	}
      }
!     return $aln if $aln->no_sequences;
! 	return;
  }
  
  =head2 write_aln
  

Index: mase.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/AlignIO/mase.pm,v
retrieving revision 1.14
retrieving revision 1.15
diff -C2 -d -r1.14 -r1.15
*** mase.pm	26 Sep 2006 22:03:05 -0000	1.14
--- mase.pm	16 Jan 2007 19:31:05 -0000	1.15
***************
*** 111,115 ****
  	}
  
! 	$add = new Bio::LocatableSeq('-seq'=>$seq,
  			    '-id'=>$name,
  			    '-start'=>$start,
--- 111,115 ----
  	}
  
! 	$add = Bio::LocatableSeq->new('-seq'=>$seq,
  			    '-id'=>$name,
  			    '-start'=>$start,
***************
*** 128,132 ****
     }
  
!    return $aln;
  }
  
--- 128,133 ----
     }
  
!    return $aln if $aln->no_sequences;
!    return;
  }
  



More information about the Bioperl-guts-l mailing list