[Bio] / FigKernelPackages / FigGFF.pm Repository:
ViewVC logotype

Diff of /FigKernelPackages/FigGFF.pm

Parent Directory Parent Directory | Revision Log Revision Log | View Patch Patch

revision 1.11, Sun Apr 24 16:33:26 2005 UTC revision 1.12, Fri Apr 29 20:48:51 2005 UTC
# Line 710  Line 710 
710      # are we case sensitive? I don't think so      # are we case sensitive? I don't think so
711      $verb=lc($verb);      $verb=lc($verb);
712    
713      if ($verb eq "genome")      if ($verb eq "genome_id")
714      {      {
715          $self->current_file->genome_id($rest[0]);          $self->current_file->genome_id($rest[0]);
716          $self->current_file->genome_name($rest[1]);      }
717        elsif ($verb eq "name")
718        {
719            $self->current_file->genome_name($rest[0]);
720      }      }
721      elsif ($verb eq "genome_md5")      elsif ($verb eq "genome_md5")
722      {      {
723          $self->current_file->set_genome_checksum(@rest[0,1]);          $self->current_file->set_genome_checksum($rest[0]);
724      }      }
725      elsif ($verb eq "project")      elsif ($verb eq "project")
726      {      {
# Line 726  Line 729 
729      }      }
730      elsif ($verb eq "taxonomy")      elsif ($verb eq "taxonomy")
731      {      {
732          $self->current_file->taxonomy($rest);          $self->current_file->taxonomy($rest[0]);
733        }
734        elsif ($verb eq "taxon_id")
735        {
736            $self->current_file->taxon_id($rest[0]);
737      }      }
738      elsif ($verb eq "anno_start")      elsif ($verb eq "anno_start")
739      {      {
# Line 900  Line 907 
907    
908  map { $GFF_Tags{$_} = 1 } @GFF_Tags;  map { $GFF_Tags{$_} = 1 } @GFF_Tags;
909    
910  __PACKAGE__->mk_accessors(qw(fig seqid source type start end score strand phase attributes genome fig_id),  __PACKAGE__->mk_accessors(qw(fig seqid source type start end score strand phase attributes
911                                 genome fig_id),
912                            @GFF_Tags);                            @GFF_Tags);
913    
914    
# Line 979  Line 987 
987  use strict;  use strict;
988  use base qw(Class::Accessor);  use base qw(Class::Accessor);
989    
990  __PACKAGE__->mk_accessors(qw(fig filename features feature_index anno_start anno_end));  __PACKAGE__->mk_accessors(qw(fig filename features feature_index anno_start anno_end taxon_id genome_id));
991    
992  #  #
993  # Package to hold the contents of a GFF file, and to hold the code  # Package to hold the contents of a GFF file, and to hold the code
# Line 997  Line 1005 
1005          features => [],          features => [],
1006          contigs  => [],          contigs  => [],
1007          feature_index => {},          feature_index => {},
1008          genome_checksum => {},          genome_checksum => '',
1009          contig_checksum => {},          contig_checksum => {},
1010          features_by_genome => {},          features_by_genome => {},
1011      };      };
# Line 1022  Line 1030 
1030    
1031  sub genome_checksum  sub genome_checksum
1032  {  {
     my($self, $genome) = @_;  
   
     return $self->{genome_checksum}->{$genome};  
 }  
   
 sub genome_checksums  
 {  
1033      my($self) = @_;      my($self) = @_;
1034    
1035      return [map { [$_, $self->{genome_checksum}->{$_}] } keys(%{$self->{genome_checksum}})];      return $self->{genome_checksum};
1036  }  }
1037    
1038  sub set_genome_checksum  sub set_genome_checksum
1039  {  {
1040      my($self, $genome, $md5sum) = @_;      my($self, $md5sum) = @_;
1041      $self->{genome_checksum}->{$genome} = $md5sum;      $self->{genome_checksum} = $md5sum;
1042  }  }
1043    
1044  sub set_contig_checksum  sub set_contig_checksum

Legend:
Removed from v.1.11  
changed lines
  Added in v.1.12

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3