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Bio::DB::Map::Marker
Marker object suitable for mapping

Bio::DB::Map::Marker - Marker object suitable for mapping


NAME

Bio::DB::Map::Marker - Marker object suitable for mapping


SYNOPSIS

Give standard usage here


DESCRIPTION

Describe the object here


FEEDBACK

Mailing Lists

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/MailList.shtml             - About the mailing lists

Reporting Bugs

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@bioperl.org

  http://bioperl.org/bioperl-bugs/


AUTHOR - Jason Stajich

Email jason@chg.mc.duke.edu

Describe contact details here


APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new


 Title   : new

 Usage   : my $marker = new Bio::DB::Map::Marker(@params)

 Function: 

 Returns : 

 Args    : -id    => db id,

           -locus => locus,

           -probe => probe,

           -chrom => chrom,

           -pcrfwd=> Fwd PCR primer,

           -pcrrev=> Rev PCR primer,

           -length=> product length,

           -type  => Marker type ('rh', 'msat', 'snp')

           -adaptor => Bio::DB::Map::SQL::MarkerAdaptor object

=cut

sub new { my ($class,@args) = @_; my $self = $class->SUPER::new(@args); # initialize $self->{'_positions'} = {}; $self->{'_aliases'} = {};


    my ($id,$locus,$probe,$chrom, $fwd,

        $rev,$type,$length,$adaptor) = 

        $self->_rearrange([qw(ID LOCUS PROBE CHROM 

                              PCRFWD PCRREV TYPE 

                              LENGTH ADAPTOR)],@args);

    $self->id($id);

    $self->locus($locus);

    $self->chrom($chrom);

    $self->probe($probe);

    $self->pcrfwd($fwd);

    $self->pcrrev($rev);

    $self->type($type);

    $self->length($length);

    $self->adaptor($adaptor);

    return $self;

}

add_alias


 Title   : add_alias

 Usage   : $marker->add_alias($alias,'whitehead');

 Function: adds an alias for a marker

 Returns : nothing

 Args    : alias to add, 

           source alias is from (optional)

get_source_for_alias


 Title   : get_source_for_alias

 Usage   : my $source = $marker->get_source_for_alias($alias);

 Function: Returns the source for a specific alias if stored

 Returns : string

 Args    : alias

is_alias


 Title   : is_alias

 Usage   : if ( $marker->is_alias($alias) )

 Function: test whether or not a specific name is an alias for a marker

 Returns : boolean

 Args    : alias

each_alias


 Title   : each_alias

 Usage   : my @aliases = $marker->each_alias();

 Function: Get a list of all the aliases for a marker

 Returns : array

 Args    : none

remove_alias


 Title   : remove_alias

 Usage   : $marker->remove_alias($alias);

 Function: Remove a specific alias from a marker

 Returns : nothing

 Args    : alias

add_position


 Title   : add_position

 Usage   : $marker->add_position($position, $map);

 Function: Stores the position of a marker on specific map

           A marker can only have 1 position on a map

 Returns : void

 Args    : position - marker position

           map      - map name

=cut

sub add_position { my($self,$position,$map) = @_; $map = lc $map; $self->{'_positions'}->{$map} = $position; }

each_positions


 Title   : each_positions

 Usage   : my @positions = $marker->each_position();

 Function: returns a list of hashes, one per map,

           Hashes have 2 keys, 'map' and 'position'

 Returns : array of hashes

 Args    : none

get_position


 Title   : get_position

 Usage   : my $pos = $marker->get_position($map);

 Function: return the position of a marker on a specific map

 Returns : position

 Args    : map name

id


 Title   : id

 Usage   : my $id = $marker->id

 Function: Get/Set Marker id

 Returns : integer

 Args    : integer (optional)

chrom


 Title   : chrom

 Usage   : my $chrom = $marker->chrom

 Function: Get/Set Marker Chromosome

 Returns : Chromosome value

 Args    : 1-24, X,Y (optional)

locus


 Title   : locus

 Usage   : $obj->locus($newval)

 Function: 

 Example : 

 Returns : value of locus

 Args    : newvalue (optional)

probe


 Title   : probe

 Usage   : $obj->probe($newval)

 Function: 

 Example : 

 Returns : value of probe

 Args    : newvalue (optional)

pcrfwd


 Title   : pcrfwd

 Usage   : $obj->pcrfwd($newval)

 Function: 

 Example : 

 Returns : value of pcrfwd

 Args    : newvalue (optional)

pcrrev


 Title   : pcrrev

 Usage   : $obj->pcrrev($newval)

 Function: 

 Example : 

 Returns : value of pcrrev

 Args    : newvalue (optional)

type


 Title   : type

 Usage   : $obj->type($newval)

 Function: 

 Example : 

 Returns : value of type

 Args    : newvalue (optional)

length


 Title   : length

 Usage   : $obj->length($newval)

 Function: 

 Example : 

 Returns : value of length

 Args    : newvalue (optional)

adaptor


 Title   : adaptor

 Usage   : $obj->adaptor($newval)

 Function: 

 Example : 

 Returns : value of adaptor

 Args    : newvalue (optional)
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