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 / 
bioperl-db-0.1
/ Bio::DB::Map::MarkerI

NAME

Bio::DB::Map::MarkerI - Interface of Marker objects

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 _

add_alias

 Title   : add_alias
 Usage   : $marker->add_alias($alias,'whitehead');
 Function: adds an alias for a marker
 Returns : nothing
 Args    : alias to add, 
           map name 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

each_position

 Title   : each_position
 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)