Bio::Variation SNP
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Summary
Bio::Variation::SNP - submitted SNP
Package variables
Privates (from "my" definitions)
%OK_AUTOLOAD = ( id => '', type => '', observed => [], seq_5 => '', seq_3 => '', ncbi_build => '', ncbi_chr_hits => '', ncbi_ctg_hits => '', ncbi_seq_loc => '', ucsc_build => '', ucsc_chr_hits => '', ucsc_ctg_hits => '', heterozygous => '', heterozygous_SE => '', validated => '', genotype => '', handle => '', batch_id => '', method => '', locus_id => '', symbol => '', mrna => '', protein => '', functional_class => '', )
Included modules
Bio::Root::Root
Inherit
Bio::Variation::Allele Bio::Variation::SeqDiff
Synopsis
  $SNP = Bio::Variation::SNP->new ();
Description
Inherits from Bio::Variation::SeqDiff and Bio::Variation::Allele, with
additional methods that are (db)SNP specific (ie, refSNP/subSNP IDs, batch
IDs, validation methods).
Methods
AUTOLOAD
No description
Code
is_subsnpDescriptionCode
subsnpDescriptionCode
add_subsnpDescriptionCode
each_subsnpDescriptionCode
Methods description
is_subsnpcode    nextTop
 Title   : is_subsnp
Usage : $is = $snp->is_subsnp()
Function: returns 1 if $snp is a subSNP
Returns : 1 or undef
Args : NONE
subsnpcodeprevnextTop
 Title   : subsnp
Usage : $subsnp = $snp->subsnp()
Function: returns the currently active subSNP of $snp
Returns : Bio::Variation::SNP
Args : NONE
add_subsnpcodeprevnextTop
 Title   : add_subsnp
Usage : $subsnp = $snp->add_subsnp()
Function: pushes the previous value returned by subsnp() onto a stack,
accessible with each_subsnp().
Sets return value of subsnp() to a new Bio::Variation::SNP
object, and returns that object.
Returns : Bio::Varitiation::SNP
Args : NONE
each_subsnpcodeprevnextTop
 Title   : each_subsnp
Usage : @subsnps = $snp->each_subsnp()
Function: returns a list of the subSNPs of a refSNP
Returns : list
Args : NONE
Methods code
AUTOLOADdescriptionprevnextTop
sub AUTOLOAD {
	my $self = shift;
	my $param = $AUTOLOAD;
	$param =~ s/.*:://;
	$self->throw(__PACKAGE__." doesn't implement $param") unless defined $OK_AUTOLOAD{$param};

	if( ref $OK_AUTOLOAD{$param} eq 'ARRAY' ) {
		push @{$self->{$param}}, shift if @_;
		return $self->{$param}->[scalar(@{$self->{$param}}) - 1];
	} else {
		$self->{$param} = shift if @_;
		return $self->{$param};
	}
}


#foreach my $slot (keys %RWSLOT){
# no strict "refs"; #add class methods to package
# *$slot = sub {
# shift;
# $RWSLOT{$slot} = shift if @_;
# return $RWSLOT{$slot};
# };
#
}
is_subsnpdescriptionprevnextTop
sub is_subsnp {
	return shift->{is_subsnp};
}
subsnpdescriptionprevnextTop
sub subsnp {
	my $self = shift;
	return $self->{subsnps}->[ scalar($self->each_subsnp) - 1 ];
}
add_subsnpdescriptionprevnextTop
sub add_subsnp {
	my $self = shift;
	$self->throw("add_subsnp(): cannot add subSNP to subSNP, only to refSNP")
            if $self->is_subsnp;

	my $subsnp = Bio::Variation::SNP->new;
	push @{$self->{subsnps}}, $subsnp;
	$self->subsnp->{is_subsnp} = 1;
	return $self->subsnp;
}
each_subsnpdescriptionprevnextTop
sub each_subsnp {
	my $self = shift;
	$self->throw("each_subsnp(): cannot be called on a subSNP")
            if $self->is_subsnp;
	return @{$self->{subsnps}};
}

1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
  bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support Top
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
Reporting BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via the
web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHORTop
Allen Day <allenday@ucla.edu>
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
get/set-able methodsTop
 Usage   : $is = $snp->method()
Function: for getting/setting attributes
Returns : a value. probably a scalar.
Args : if you're trying to set an attribute, pass in the new value.
Methods: -------- id type observed seq_5 seq_3 ncbi_build ncbi_chr_hits ncbi_ctg_hits ncbi_seq_loc ucsc_build ucsc_chr_hits ucsc_ctg_hits heterozygous heterozygous_SE validated genotype handle batch_id method locus_id symbol mrna protein functional_class