Bio::Variation Allele
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Summary
Bio::Variation::Allele - Sequence object with allele-specific attributes
Package variables
Privates (from "my" definitions)
$VERSION = 1.0
Included modules
Bio::DBLinkContainerI
Bio::PrimarySeq
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
add_DBLinkDescriptionCode
countDescriptionCode
each_DBLinkDescriptionCode
frequencyDescriptionCode
is_referenceDescriptionCode
new
No description
Code
repeat_countDescriptionCode
repeat_unitDescriptionCode
Methods description
add_DBLinkcode    nextTop
 Title   : add_DBLink
Usage : $self->add_DBLink($ref)
Function: adds a link object
Example :
Returns :
Args :
countcodeprevnextTop
 Title   : count
Usage : $obj->count();
Function:
Sets and returns the number of times this allele was observed. Example : Returns : string Args : string
each_DBLinkcodeprevnextTop
 Title   : each_DBLink
Usage : foreach $ref ( $self->each_DBlink() )
Function: gets an array of DBlink of objects
Example :
Returns :
Args :
frequencycodeprevnextTop
 Title   : frequency
Usage : $obj->frequency();
Function:
Sets and returns the frequency of the allele in the observed population. Example : Returns : string Args : string
is_referencecodeprevnextTop
 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
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
repeat_unitcodeprevnextTop
 Title   : repeat_unit
Usage : $obj->repeat_unit('ca');
Function:
Sets and returns the sequence of the repeat_unit the allele is composed of. Example : Returns : string Args : string
Methods code
add_DBLinkdescriptionprevnextTop
sub add_DBLink {
   my ($self,$com) = @_;
   if( ! $com->isa('Bio::Annotation::DBLink') ) {
       $self->throw("Is not a link object but a  [$com]");
   }
   push(@{$self->{'link'}},$com);
}
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 $self->{'count'};
}
each_DBLinkdescriptionprevnextTop
sub each_DBLink {
   my ($self) = @_;   
   return @{$self->{'link'}};
}
frequencydescriptionprevnextTop
sub frequency {
    my ($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;
}
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 $self->{'is_reference'};
    }
}
newdescriptionprevnextTop
sub new {
    my($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 $self; # success - we hope!
}
repeat_countdescriptionprevnextTop
sub repeat_count {
    my ($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 $self->{'repeat_count'};
}
repeat_unitdescriptionprevnextTop
sub repeat_unit {
    my ($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'};
}
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://bio.perl.org/MailList.html - About the mailing lists
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
email or the web:
  bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.org/
AUTHOR - Heikki LehvaslaihoTop
Email: heikki@ebi.ac.uk
Address:
     EMBL Outstation, European Bioinformatics Institute
Wellcome Trust Genome Campus, Hinxton
Cambs. CB10 1SD, United Kingdom
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _