/ 
bioperl-db-0.1 UNAUTHORIZED RELEASE
/ Bio::DB::Map::SQL::MapAdaptor

NAME

Bio::DB::Map::SQL::MapAdaptor - DESCRIPTION of Object

SYNOPSIS

Give standard usage here

DESCRIPTION

Describe the object here

FEEDBACK

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bioperl-l@bioperl.org             - General discussion
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Reporting Bugs

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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 _

get

Title   : get
Usage   : my $map = $adaptor->get(-id => $mapid); OR
          my $map = $adaptor->get(-name => $name); 
Function: finds the map based on a criteria
Returns : Bio::DB::Map::MapI object
Args    : -id => mapid OR
          -name => mapname

write

Title   : write
Usage   : $mapadaptor->write($map);
Function: adds a new map to the database
Returns : Bio::DB::Map::MapI object
Args    : Bio::DB::Map::MapI object

get_mapids_hash

Title   : get_mapids_hash
Usage   : my %mapnames = $adaptor->get_mapids_hash();
Function: returns a hash of mapnames => mapids and mapids => mapnames
Returns : hash which 
Args    : none

get_markers_for_region

 Title   : get_markers_for_region
 Usage   : my @markers = $map->get_markers_for_region('-start' => $start,
						      '-end'   => $end);
 Function: returns a list of markers for this map that fall between
           start and end in this map\'s units.  Omitting 'start' will
           default to the beginning of the map, omitting 'end' will
           default to the end of map.
 Returns : List of Bio::DB::Map::MarkerI objects
 Args    : -start => starting point or region (in units of this map)
           -end   => ending point of region (in units of this map)
           -chrom => chromosome [1,22,X,Y]
           -id    => map id

get_next_marker

 Title   : get_next_marker
 Usage   : my $marker = $map->get_next_marker(-marker => $marker,
					      -direction => 1);
 Function: returns the next marker(s) (by markerid) in the map based on the given marker
           and either a positive or negative direction
 Returns : Array of markerid or empty array if error or none found 
 Args    : -mapid     => mapid
           -markerid  => markerid
           -direction => [1,-1] (default 1)          
           -number    => number of markers to get (default 1)

get_Chrom_length

Title   : get_Chrom_length
Usage   : my $len = $map->get_Chrom_Length()
Function: Returns the length of a chromosome for a Map in the map\'s units
Returns : float
Args    : map id, chromsome

get_all_markerids_for_map

Title   : get_all_markerids_for_map
Usage   : my @markerids = $mapadaptor->get_all_markerid_for_map($mapid);
Function: returns a list of marker ids which are associated with a map
Returns : list of markerids
Args    : $mapid

create_ePCR_DB

Title   : create_ePCRDB
Usage   : $mapadaptor->create_ePCR_DB ( $mapid, $fh );
Function: writes an ePCR format database to $fh based on a mapid
Returns : boolean on success
Args    : mapid to build db on
          filehandle to write to
                     someday will add option to write each chrom
                     to different file

# Later on maps may become a bit more dynamic, ie collections of # markers, so perhaps we'll want to do this based on a mapobj