Bio::Variation Allele
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Summary
Bio::Variation::Allele - Sequence object with allele-specific attributes
Package variables
No package variables defined.
Inherit
Bio::DBLinkContainerI Bio::PrimarySeq
Synopsis
  $allele1 = Bio::Variation::Allele->new ( -seq => 'A',
-id => 'AC00001.1',
-alphabet => 'dna',
-is_reference => 1
);
Description
List of alleles describe known sequence alternatives in a variable region.
Alleles are contained in Bio::Variation::VariantI complying objects.
See Bio::Variation::VariantI for details.
Bio::Varation::Alleles are PrimarySeqI complying objects which can
contain database cross references as specified in
Bio::DBLinkContainerI interface, too.
A lot of the complexity with dealing with Allele objects are caused by
null alleles; Allele objects that have zero length sequence string.
In addition describing the allele by its sequence , it possible to
give describe repeat structure within the sequence. This done using
methods repeat_unit (e.g. 'ca') and repeat_count (e.g. 7).
Methods
new
No description
Code
is_referenceDescriptionCode
add_DBLinkDescriptionCode
each_DBLinkDescriptionCode
repeat_unitDescriptionCode
repeat_countDescriptionCode
countDescriptionCode
frequencyDescriptionCode
Methods description
is_referencecode    nextTop
 Title   : is_reference
Usage : $obj->is_reference()
Function: sets and returns boolean values.
Unset values return false.
Example : $obj->is_reference()
Returns : boolean
Args : optional true of false value
add_DBLinkcodeprevnextTop
 Title   : add_DBLink
Usage : $self->add_DBLink($ref)
Function: adds a link object
Example :
Returns :
Args :
each_DBLinkcodeprevnextTop
 Title   : each_DBLink
Usage : foreach $ref ( $self->each_DBlink() )
Function: gets an array of DBlink of objects
Example :
Returns :
Args :
repeat_unitcodeprevnextTop
 Title   : repeat_unit
Usage : $obj->repeat_unit('ca');
Function:
Sets and returns the sequence of the repeat_unit the allele is composed of. Example : Returns : string Args : string
repeat_countcodeprevnextTop
 Title   : repeat_count
Usage : $obj->repeat_count();
Function:
Sets and returns the number of repeat units in the allele. Example : Returns : string Args : string
countcodeprevnextTop
 Title   : count
Usage : $obj->count();
Function:
Sets and returns the number of times this allele was observed. Example : Returns : string Args : string
frequencycodeprevnextTop
 Title   : frequency
Usage : $obj->frequency();
Function:
Sets and returns the frequency of the allele in the observed population. Example : Returns : string Args : string
Methods code
newdescriptionprevnextTop
sub new {
    my($class, @args) = @_;
    my $self = $class->SUPER::new(@args);

    my($is_reference, $repeat_unit, $repeat_count) =
	   $self->_rearrange([qw(IS_REFERENCE
				 REPEAT_UNIT
				 REPEAT_COUNT
				 )],
			     @args);

    $is_reference && $self->is_reference($is_reference);
    $repeat_unit && $self->repeat_unit($repeat_unit);
    $repeat_count && $self->repeat_count($repeat_count);

    return $self; # success - we hope!
}
is_referencedescriptionprevnextTop
sub is_reference {
    my ($self,$value) = @_;
    if( defined $value) {
	$value ? ($value = 1) : ($value = 0);
	$self->{'is_reference'} = $value;
    }
    if( ! exists $self->{'is_reference'} ) {
	return 0;
    } 
    else {
	return $self->{'is_reference'};
    }
}
add_DBLinkdescriptionprevnextTop
sub add_DBLink {
   my ($self,$com) = @_;
   if( ! $com->isa('Bio::Annotation::DBLink') ) {
       $self->throw("Is not a link object but a  [$com]");
   }
   push(@{$self->{'link'}},$com);
}
each_DBLinkdescriptionprevnextTop
sub each_DBLink {
   my ($self) = @_;   
   return @{$self->{'link'}};
}
repeat_unitdescriptionprevnextTop
sub repeat_unit {
    my ($self,$value) = @_;
    if( defined $value) {
	$self->{'repeat_unit'} = $value;
    }
    if ($self->{'seq'} && $self->{'repeat_unit'} && $self->{'repeat_count'} ) {
	$self->warn("Repeats do not add up!") 
	    if ( $self->{'repeat_unit'} x $self->{'repeat_count'})  ne $self->{'seq'};
    }
    return $self->{'repeat_unit'};
}
repeat_countdescriptionprevnextTop
sub repeat_count {
    my ($self,$value) = @_;
    if( defined $value) {
	if (  not $value =~ /^\d+$/ ) {
	    $self->throw("[$value] for repeat_count has to be a positive integer\n");
	} else {
	    $self->{'repeat_count'} = $value;
	}
    }
    if ($self->{'seq'} && $self->{'repeat_unit'} && $self->{'repeat_count'} ) {
	$self->warn("Repeats do not add up!") 
	    if ( $self->{'repeat_unit'} x $self->{'repeat_count'})  ne $self->{'seq'};
    }
    return $self->{'repeat_count'};
}
countdescriptionprevnextTop
sub count {
    my ($self,$value) = @_;
    if( defined $value) {
	if (  not $value =~ /^\d+$/ ) {
	    $self->throw("[$value] for count has to be a positive integer\n");
	} else {
	    $self->{'count'} = $value;
	}
    }
    return $self->{'count'};
}
frequencydescriptionprevnextTop
sub frequency {
    my ($self,$value) = @_;
    if( defined $value) {
	if (  not $value =~ /^\d+$/ ) {
	    $self->throw("[$value] for frequency has to be a positive integer\n");
	} else {
	    $self->{'frequency'} = $value;
	}
    }
    return $self->{'frequency'};
}


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 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/
AUTHOR - Heikki LehvaslaihoTop
Email: heikki-at-bioperl-dot-org
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _