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

Diff of /FigKernelPackages/FIGO.pm

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

revision 1.25, Wed Sep 26 03:40:10 2007 UTC revision 1.26, Wed Sep 26 04:03:48 2007 UTC
# Line 366  Line 366 
366    
367  =item USAGE:  =item USAGE:
368    
369  C<< my $org = GenomeO->new($figO, $tax_id); >>  C<< my $orgO = GenomeO->new($figO, $tax_id); >>
370    
371  =item RETURNS:  =item RETURNS:
372    
373      A new GenomeO object.      A new "GenomeO" object.
374    
375  =back  =back
376    
# Line 393  Line 393 
393    
394  =item USAGE:  =item USAGE:
395    
396  C<< my $tax_id = $org->id(); >>  C<< my $tax_id = $orgO->id(); >>
397    
398  =item RETURNS:  =item RETURNS:
399    
400      Taxonomy-ID of GenomeO object.      Taxonomy-ID of "GenomeO" object.
401    
402  =back  =back
403    
# Line 417  Line 417 
417    
418  =item USAGE:  =item USAGE:
419    
420  C<< $gs = $genome->genus_species(); >>  C<< $gs = $orgO->genus_species(); >>
421    
422  =item RETURNS:  =item RETURNS:
423    
# Line 439  Line 439 
439    
440  =head3 taxonomy_of  =head3 taxonomy_of
441    
442    =over 4
443    
444    =item FUNCTION:
445    
446    Return the TAXONOMY string of a "GenomeO" object.
447    
448    =item USAGE:
449    
450    C<< my $taxonomy = $orgO->taxonomy_of(); >>
451    
452    =item RETURNS:
453    
454    TAXONOMY string.
455    
456    =back
457    
458  =cut  =cut
459    
460  sub taxonomy_of {  sub taxonomy_of {
# Line 447  Line 463 
463      my $figO = $self->{_figO};      my $figO = $self->{_figO};
464      my $fig  = $figO->{_fig};      my $fig  = $figO->{_fig};
465    
466      return $fig->taxonomy_of($self->id());      return $fig->taxonomy_of($self->{_id});
467  }  }
468    
469    
# Line 479  Line 495 
495    
496  =head3 features_of  =head3 features_of
497    
498    =over 4
499    
500    =item FUNCTION:
501    
502    Returns a list of "FeatureO" objects contained in a "GenomeO" object.
503    
504    =item USAGE:
505    
506    C<< my @featureOs = $orgO->features_of();        #...Fetch all features >>
507    
508    or
509    
510    C<< my @featureOs = $orgO->features_of('peg');   #...Fetch only PEGs >>
511    
512    =item RETURNS:
513    
514    List of "FeatureO" objects.
515    
516    =back
517    
518  =cut  =cut
519    
520  sub features_of {  sub features_of {

Legend:
Removed from v.1.25  
changed lines
  Added in v.1.26

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3