[Bioperl-guts-l] bioperl-live/Bio AlignIO.pm,1.40,1.41

Brian Osborne bosborne at pub.open-bio.org
Thu Mar 16 19:13:13 EST 2006


Update of /home/repository/bioperl/bioperl-live/Bio
In directory pub.open-bio.org:/tmp/cvs-serv8959/Bio

Modified Files:
	AlignIO.pm 
Log Message:
Minor edits


Index: AlignIO.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/AlignIO.pm,v
retrieving revision 1.40
retrieving revision 1.41
diff -C2 -d -r1.40 -r1.41
*** AlignIO.pm	9 Oct 2005 14:53:05 -0000	1.40
--- AlignIO.pm	17 Mar 2006 00:13:11 -0000	1.41
***************
*** 12,16 ****
  #
  # History
- # October 18, 1999  SeqIO largely rewritten by Lincoln Stein
  # September, 2000 AlignIO written by Peter Schattner
  
--- 12,15 ----
***************
*** 79,87 ****
      use Bio::AlignIO;
  
!      # read from standard input
      $stream = Bio::AlignIO->newFh(-format => 'Fasta');
  
      while ( $aln = <$stream> ) {
! 	# do something with $aln
      }
  
--- 78,86 ----
      use Bio::AlignIO;
  
!     # read from standard input
      $stream = Bio::AlignIO->newFh(-format => 'Fasta');
  
      while ( $aln = <$stream> ) {
! 	     # do something with $aln
      }
  
***************
*** 156,160 ****
     nexus       Swofford et al NEXUS format
     pfam        Pfam sequence alignment format
!    phylip      Felsenstein's PHYLIP format
     prodom      prodom (protein domain) format
     psi         PSI-BLAST format
--- 155,159 ----
     nexus       Swofford et al NEXUS format
     pfam        Pfam sequence alignment format
!    phylip      Felsenstein PHYLIP format
     prodom      prodom (protein domain) format
     psi         PSI-BLAST format
***************
*** 199,203 ****
  By default, all files (or filehandles) opened for writing alignments
  will be flushed after each write_aln() making the file immediately
! usable.  If you don't need this facility and would like to marginally
  improve the efficiency of writing multiple sequences to the same file
  (or filehandle), pass the -flush option '0' or any other value that
--- 198,202 ----
  By default, all files (or filehandles) opened for writing alignments
  will be flushed after each write_aln() making the file immediately
! usable.  If you do not need this facility and would like to marginally
  improve the efficiency of writing multiple sequences to the same file
  (or filehandle), pass the -flush option '0' or any other value that
***************
*** 282,286 ****
   Title   : new
   Usage   : $stream = Bio::AlignIO->new(-file => $filename,
!                                        '-format' => 'Format')
   Function: Returns a new seqstream
   Returns : A Bio::AlignIO::Handler initialised with 
--- 281,285 ----
   Title   : new
   Usage   : $stream = Bio::AlignIO->new(-file => $filename,
!                                        -format => 'Format')
   Function: Returns a new seqstream
   Returns : A Bio::AlignIO::Handler initialised with 



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