[Bioperl-guts-l] bioperl-live/Bio/SearchIO/Writer GbrowseGFF.pm, 1.17, 1.18

Christopher John Fields cjfields at dev.open-bio.org
Sun Jul 8 21:35:42 EDT 2007


Update of /home/repository/bioperl/bioperl-live/Bio/SearchIO/Writer
In directory dev.open-bio.org:/tmp/cvs-serv28757

Modified Files:
	GbrowseGFF.pm 
Log Message:
Use double quotes to interpolate

Index: GbrowseGFF.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/SearchIO/Writer/GbrowseGFF.pm,v
retrieving revision 1.17
retrieving revision 1.18
diff -C2 -d -r1.17 -r1.18
*** GbrowseGFF.pm	14 Jun 2007 14:16:14 -0000	1.17
--- GbrowseGFF.pm	9 Jul 2007 01:35:40 -0000	1.18
***************
*** 97,101 ****
       $self->{'signif'} ) = $self->_rearrange([qw(E_VALUE OUTPUT_CIGAR PREFIX
  						 OUTPUT_SIGNIF)], @args);
!     $self->{'_evalue'} && warn( 'use of the -e_value argument is deprecated.  In future, use $writer->filter("type", \&code)  instead.\n\tparsing will proceed correctly with this e_value\n');
      $self->{Gbrowse_HSPID} = 0;
      $self->{Gbrowse_HITID} = 0;
--- 97,101 ----
       $self->{'signif'} ) = $self->_rearrange([qw(E_VALUE OUTPUT_CIGAR PREFIX
  						 OUTPUT_SIGNIF)], @args);
!     $self->{'_evalue'} && warn( "Use of the -e_value argument is deprecated.\nIn future, use \$writer->filter(\"type\", \&code) instead.\n\tparsing will proceed correctly with this e_value\n");
      $self->{Gbrowse_HSPID} = 0;
      $self->{Gbrowse_HITID} = 0;
***************
*** 150,154 ****
  				       MATCH_TAG HSP_TAG
  				       PREFIX)], @args);
!     warn $reference if $reference;
      $reference ||='hit'; # default is that the hit sequence (db sequence) becomes the reference sequence.  I think this is fairly typical...
      $match_tag ||= $Defaults{'MatchTag'}; # default is the generic 'match' tag.
--- 150,154 ----
  				       MATCH_TAG HSP_TAG
  				       PREFIX)], @args);
!     $self->warn($reference) if $reference; 
      $reference ||='hit'; # default is that the hit sequence (db sequence) becomes the reference sequence.  I think this is fairly typical...
      $match_tag ||= $Defaults{'MatchTag'}; # default is the generic 'match' tag.



More information about the Bioperl-guts-l mailing list