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Bio::DB::Map::Map
DESCRIPTION of Object

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


NAME

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


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 _

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]

=cut

sub get_markers_for_region{ my ($self,@args) = @_;




   my ( $start, $end,$chrom ) = $self->_rearrange([qw(START END CHROM)], 

                                                  @args);

   $start = 0 unless defined $start;

   if( !defined $end ) {

       $end = $self->chrom_length($self->id, $chrom);

   }

   my @markers = $self->adaptor->get_markers_for_region('-id'    => $self->id,

                                                        '-start' => $start,

                                                        '-end'   => $end,

                                                        '-chrom' => $chrom);

   return @markers;

}

get_next_marker


 Title   : get_next_marker

 Usage   : my $marker = $map->get_next_marker(-marker    => $marker,

                                              -direction => 1);

 Function: returns the next marker in the map based on the given marker

           and either a positive or negative direction

 Returns : Bio::DB::Map::MarkerI object or undef 

 Args    : -marker    => $marker Bio::DB::Map::MarkerI object to start with

           -direction => [1,-1]

           -number    => number of markers to retrieve

=cut

sub get_next_marker { my ($self,@args) = @_; my ($marker,$direction,$number) = $self->_rearrange([qw(MARKER DIRECTION NUMBER)], @args); my @markers = $self->adaptor->get_next_marker('-markerid' => $marker->id, '-mapid' => $self->id, '-direction' => $direction, '-number' => $number); return @markers; }

chrom_length


 Title   : chrom_length

 Usage   : my $len = $map->chrom_length()

 Function: Returns the length of a chromosome in a Map in the map\'s units

 Returns : float

 Args    : none

Get/Set Methods

id


 Title   : id

 Usage   : $obj->id($newval)

 Function: 

 Example : 

 Returns : value of id

 Args    : newvalue (optional)

name


 Title   : name

 Usage   : $obj->name($newval)

 Function: 

 Example : 

 Returns : value of name

 Args    : newvalue (optional)

units


 Title   : units

 Usage   : $obj->units($newval)

 Function: 

 Example : 

 Returns : value of units

 Args    : newvalue (optional)

adaptor


 Title   : adaptor

 Usage   : $obj->adaptor($newval)

 Function: 

 Example : 

 Returns : value of adaptor

 Args    : newvalue (optional)
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