Bio::PopGen MarkerI
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Summary
Bio::PopGen::MarkerI - A Population Genetic conceptual marker
Package variables
No package variables defined.
Inherit
Bio::AnnotatableI Bio::Root::RootI
Synopsis
# Get a Bio::PopGen::MarkerI somehow - like using a Bio::PopGen::Marker
  my $name = $marker->name();            # marker name
my $description = $marker->description(); # description
my $type = $marker->type(); # coded type of the marker
my $unique_id = $marker->unique_id; # optional unique ID
my @alleles = $marker->get_Alleles(); # the known alleles my %allele_freqs = $marker->get_Allele_Frequencies(); # keys are marker names # vals are frequencies # may change to handle multiple populations
Description
This is the basic interface for Markers which one can associate
alleles with for calculating Theta and Pi.
Methods
nameDescriptionCode
descriptionDescriptionCode
typeDescriptionCode
unique_idDescriptionCode
annotationDescriptionCode
get_AllelesDescriptionCode
get_Allele_FrequenciesDescriptionCode
Methods description
namecode    nextTop
 Title   : name
Usage : my $name = $marker->name();
Function: Get the name of the marker
Returns : string representing the name of the marker
Args :
descriptioncodeprevnextTop
 Title   : description
Usage : my $desc = $marker->description
Function: Get the marker description free text
Returns : string
Args : [optional] string
typecodeprevnextTop
 Title   : type
Usage : my $type = $marker->type;
Function: Get coded string for marker type
Returns : string
Args : [optional] string
unique_idcodeprevnextTop
 Title   : unique_id
Usage : my $id = $marker->unique_id;
Function: Get the unique marker ID
Returns : unique ID string
Args : [optional ] string
annotationcodeprevnextTop
 Title   : annotation
Usage : $obj->annotation($seq_obj)
Function: retrieve the attached annotation object
Returns : Bio::AnnotationCollectionI or none;
See Bio::AnnotationCollectionI and Bio::Annotation::Collection
for more information. This method comes through extension from
Bio::AnnotatableI.
get_AllelescodeprevnextTop
 Title   : get_Alleles
Usage : my @alleles = $marker->get_Alleles();
Function: Get the available marker alleles if they are known and stored
Returns : Array of strings
Args : none
get_Allele_FrequenciescodeprevnextTop
 Title   : get_Allele_Frequencies
Usage : my %allele_freqs = $marker->get_Allele_Frequencies;
Function: Get the alleles and their frequency (set relative to
a given population - you may want to create different
markers with the same name for different populations
with this current implementation
Returns : Associative array (hash) where keys are the names of the alleles
Args : none
Methods code
namedescriptionprevnextTop
sub name {
   $_[0]->throw_not_implemented();
}
descriptiondescriptionprevnextTop
sub description {
    $_[0]->throw_not_implemented();
}
typedescriptionprevnextTop
sub type {
   my ($self) = @_;
   $self->throw_not_implemented();
}
unique_iddescriptionprevnextTop
sub unique_id {
   my ($self) = @_;
    $self->throw_not_implemented();
}
annotationdescriptionprevnextTop
sub annotation {
   my ($self,@args) = @_;
   $self->throw_not_implemented();
}
get_AllelesdescriptionprevnextTop
sub get_Alleles {
   my ($self) = @_;
   $self->throw_not_implemented();
}
get_Allele_FrequenciesdescriptionprevnextTop
sub get_Allele_Frequencies {
   my ($self) = @_;
    $self->throw_not_implemented();
}

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 list. 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
of the bugs and their resolution. Bug reports can be submitted via
email or the web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Jason StajichTop
Email jason-at-bioperl.org
CONTRIBUTORSTop
Matthew Hahn, matthew.hahn-at-duke.edu
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _