Bio-FeatureIO

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lib/Bio/FeatureIO.pm  view on Meta::CPAN

 Returns : a Bio::SeqFeatureI feature object
 Args    : none

See L<Bio::Root::RootI>, L<Bio::SeqFeatureI>

=cut

sub next_feature {
   my ($self, $seq) = @_;
   $self->throw_not_implemented;
}

=head2 write_feature

 Title   : write_feature
 Usage   : $stream->write_feature($feature)
 Function: writes the $feature object into the stream
 Returns : 1 for success and 0 for error
 Args    : Bio::SeqFeature object

=cut

sub write_feature {
    my ($self, $seq) = @_;
    $self->throw_not_implemented();
}

=head2 _load_format_module

 Title   : _load_format_module
 Usage   : *INTERNAL FeatureIO stuff*
 Function: Loads up (like use) a module at run time on demand
 Example :
 Returns :
 Args    :

lib/Bio/FeatureIO/gff.pm  view on Meta::CPAN

=cut

sub next_feature_group {
  my $self = shift;

  my $feat;
  my %seen_ids;
  my @all_feats;
  my @toplevel_feats;

  $self->{group_not_done} = 1;

  while ($self->{group_not_done} && ($feat = $self->next_feature()) && defined($feat)) {
	# we start by collecting all features in the group and
	# memorizing those which have an ID attribute
    my $anno_ID = $feat->get_Annotations('ID');
	if(ref($anno_ID)) {
      my $attr_ID = $anno_ID->value;
      $self->throw("Oops! ID $attr_ID exists more than once in your file!")
		if (exists($seen_ids{$attr_ID}));
      $seen_ids{$attr_ID} = $feat;
	}
	push(@all_feats, $feat);

lib/Bio/FeatureIO/gff.pm  view on Meta::CPAN

  }

  elsif($directive eq 'FASTA' or $directive =~ /^>/){
    #next_seq() will take care of this.
    $self->fasta_mode(1);
    return;
  }

  elsif($directive eq '#'){
    #all forward references resolved
    $self->{group_not_done} = 0;
  }

  elsif($directive eq 'organism') {
    my $organism = $arg[0];
    $self->organism($organism);
  }

  else {
    $self->throw("don't know what do do with directive: '##".$directive."'");
  }

lib/Bio/FeatureIO/ptt.pm  view on Meta::CPAN

 Title   : write_feature
 Usage   : $io->write_feature($feature)
 Function: write a Bio::SeqFeatureI object in PTT format
 Example : 
 Args    : Bio::SeqFeatureI object
 Returns : 

=cut

sub write_feature {
  shift->throw_not_implemented;
}

=head2 description

 Title   : description
 Usage   : $obj->description($newval)
 Function: set/get the PTT file description for/from line one
 Example : 
 Returns : value of description (a scalar)
 Args    : on set, new value (a scalar or undef, optional)

lib/Bio/FeatureIO/vecscreen_simple.pm  view on Meta::CPAN

  Title   : write_feature
  Usage   : $io->write_feature($feature)
  Function: write a Bio::SeqFeatureI object in vecscreen -f 3 format
  Example :
  Args    : Bio::SeqFeatureI object
  Returns :

=cut

sub write_feature {
 shift->throw_not_implemented;
}


###
1;#do not remove
###

lib/Bio/SeqFeature/Annotated.pm  view on Meta::CPAN

}

############################################################

=head1 INTERFACE METHODS FOR Bio::AnnotatableI

=cut

=head2 annotation()

 Usage   : $obj->annotation($annot_obj)
 Function: Get/set the annotation collection object for annotating this
           feature.
 Returns : A Bio::AnnotationCollectionI object
 Args    : newvalue (optional)

=cut

sub annotation {
    my ($obj,$value) = @_;