NAME

Bio::Map::clone - An central map object representing a clone

SYNOPSIS

   ## get the clone object of $clone from the Bio::Map::clone
   my $cloneobj = $physical->get_cloneobj($clone);
   ## acquire all the markers that hit this clone
   foreach my $marker ($cloneobj->each_markerid()) {
       print "   +++$marker\n";
   }

See the Bio::Map::Position manpage and the Bio::Map::PositionI manpage for more information.

DESCRIPTION

This object handles the notion of a clone. This clone will have a name and a position in a map.

This object is intended to be used by a map parser like fpc.pm.

Design principles

A MappableI is a central object in Bio::Map name space. A Map is a holder class for objects. A MappableI has a Position in a Map. A MappableI can be compared to an other MappableI using boolean methods.

Access Methods

These methods let you get and set the member variables

name

 Title   : name
 Usage   : my $name = $cloneobj->name();
 Function: get the name for this Clone
 Returns : scalar representing the current name of this clone
 Args    : none

type

 Title   : type
 Usage   : my $type = $cloneobj->type();
 Function: get the type for this clone
 Returns : scalar representing the current type of this clone
 Args    : none

number_of_bands

 Title   : number_of_bands
 Usage   : my $number_of_bands = $cloneobj->number_of_bands();
 Function: get the number of bands for this clone
 Returns : scalar representing the number of bands of this clone
 Args    : none

range

 Title   : range
 Usage   : my $range = $cloneobj->range();
 Function: get the range of the contig that this clone covers
 Returns : Bio::Range representing the current range of this contig,
           start and end of the contig can be thus found using:
           my $start = $contigobj->range()->start();
           my $end   = $contigobj->range()->end();
 Args    : none

See the Bio::Range manpage for more information.

match

 Title   : match
 Usage   : @eclone = $cloneobj->match('exact');
           @aclone = $cloneobj->match('approximate');
           @pclone = $cloneobj->match('pseudo');
 Function: get all matching clones
 Returns : list 
 Args    : scalar representing the type of clone to be 
           queried.

gel

 Title   : gel
 Usage   : $clonegel = $cloneobj->gel();
 Function: get the gel number for this clone
 Returns : scalar representing the gel number of this clone
 Args    : none

remark

 Title   : remark
 Usage   : $cloneremark = $cloneobj->remark();
 Function: get the remark for this clone
 Returns : scalar representing the current remark of this clone
 Args    : none

fp_number

 Title   : fp_number
 Usage   : $clonefpnumber = $cloneobj->fp_number();
 Function: get the fp number for this clone
 Returns : scalar representing the fp number of this clone
 Args    : none

sequence_type

 Title   : sequence_type
 Usage   : $cloneseqtype = $cloneobj->sequence_type();
 Function: get the sequence type for this clone
 Returns : scalar representing the sequence type of this clone
 Args    : none

sequence_status

 Title   : sequence_status
 Usage   : $cloneseqstatus = $cloneobj->sequence_status();
 Function: get the sequence status for this clone
 Returns : scalar representing the sequence status of this clone
 Args    : none

fpc_remark

 Title   : fpc_remark
 Usage   : $clonefpcremark = $cloneobj->fpc_remark();
 Function: get the fpc remark for this clone
 Returns : scalar representing the fpc remark of this clone
 Args    : none

band

 Title   : band
 Usage   : @clonebands = $cloneobj->bands();
 Function: get the bands for this clone
 Returns : liat representing the band of this clone, if 
           readcor = 1 while creating the MapIO object and the
           .cor exists
 Args    : none

group

 Title   : group
 Usage   : $cloneobj->group($chrno);
 Function: get the group number for this contig
           this is a generic term, used for Linkage-Groups
           as well as for Chromosomes.
 Returns : scalar representing the group number of this clone
 Args    : if provided, the group of this clone
           will be set to $chrno.

contigid

 Title   : contigid
 Usage   : my $ctg = $cloneobj->contigid();
 Function: get the contig this clone belongs to
 Returns : scalar representing the contig
 Args    : none

See the Bio::Map::Position manpage and the Bio::Map::PositionI manpage for more information.

each_markerid

 Title   : each_markerid
 Usage   : @markers = $cloneobj->each_markerid();
 Function: retrieves all the elements in a map unordered
 Returns : list of Bio::Map::MappableI ids (names)
 Args    : type of elements you want (markers)

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 of the bugs and their resolution. Bug reports can be submitted via email or the web:

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

AUTHOR - The AGCoL Staff

Email will@agcol.arizona.edu

PROJECT DESCRIPTION

The project was done in Arizona Genomics Computational Laboratory (AGCoL) at University of Arizona.

This work was funded by USDA-IFAFS grant #11180 titled ``Web Resources for the Computation and Display of Physical Mapping Data''.

For more information on this project, please refer: http://www.agcol.arizona.edu

APPENDIX

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