[Bioperl-guts-l] bioperl-live/Bio SimpleAlign.pm,1.128,1.129

Christopher John Fields cjfields at dev.open-bio.org
Mon Feb 26 13:02:53 EST 2007


Update of /home/repository/bioperl/bioperl-live/Bio
In directory dev.open-bio.org:/tmp/cvs-serv18097

Modified Files:
	SimpleAlign.pm 
Log Message:
Some POD fixes for bracket_string and sort_by_start

Index: SimpleAlign.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/SimpleAlign.pm,v
retrieving revision 1.128
retrieving revision 1.129
diff -C2 -d -r1.128 -r1.129
*** SimpleAlign.pm	26 Feb 2007 17:47:32 -0000	1.128
--- SimpleAlign.pm	26 Feb 2007 18:02:51 -0000	1.129
***************
*** 2619,2629 ****
  
  =head2 sort_by_start
! Title     : sort_by_start
! Usage     : $ali->sort_by_start
! Function  : Changes the order of the alignemnt to the start position of each
!             subalignment
! Returns   :
! Argument  :
! 
  =cut
  
--- 2619,2630 ----
  
  =head2 sort_by_start
!  
!  Title     : sort_by_start
!  Usage     : $ali->sort_by_start
!  Function  : Changes the order of the alignemnt to the start position of each
!              subalignment    
!  Returns   :
!  Argument  :
!  
  =cut
  
***************
*** 2684,2698 ****
   Returns   : BIC-formatted string
   Argument  : Required args
!                 refseq    : string (seqid) of the reference sequence used
                              as basis for comparison
!                 alleles   : array ref of two strings, both seqids
               Optional args
                  delimiters: two symbol string of left and right delimiters.
                              Only the first two symbols are used
                              default = '[]'
!                 seperator : string used as a separator.  Only the first
                              symbol is used
                              default = '/'
   Throws    : On no refseq/alleles, or invalid refseq/alleles.
  =cut
  
--- 2685,2701 ----
   Returns   : BIC-formatted string
   Argument  : Required args
!                 refseq    : string (ID) of the reference sequence used
                              as basis for comparison
!                 allele1   : string (ID) of the first allele
!                 allele2   : string (ID) of the second allele
               Optional args
                  delimiters: two symbol string of left and right delimiters.
                              Only the first two symbols are used
                              default = '[]'
!                 separator : string used as a separator.  Only the first
                              symbol is used
                              default = '/'
   Throws    : On no refseq/alleles, or invalid refseq/alleles.
+  
  =cut
  



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