Provided by: libbio-perl-perl_1.6.901-2_all bug

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 Bio::Map::Position and Bio::Map::PositionI 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.

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/wiki/Mailing_lists  - About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will
       be able look at the problem and quickly address it. Please include a thorough description
       of the problem with code and data examples if at all possible.

   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 the web:

         https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Gaurav Gupta

       Email gaurav@genome.arizona.edu

CONTRIBUTORS

       Sendu Bala  bix@sendu.me.uk

PROJECT LEADERS

       Jamie Hatfield      jamie@genome.arizona.edu Dr. Cari Soderlund  cari@genome.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.genome.arizona.edu

APPENDIX

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

   new
        Title   : new
        Usage   : my $clone = Bio::Map::Clone->new
                             (
                              -name    => $clone,
                              -markers => \@markers,
                              -contig  => $contig,
                              -type    => $type,
                              -bands   => $bands,
                              -gel     => $gel,
                              -group   => $group,
                              -remark  => $remark,
                              -fpnumber=> $fp_number,
                              -sequencetype  => $seq_type,
                              -sequencestatus=> $seq_status,
                              -fpcremark => $fpc_remark,
                              -matche    => \@ematch,
                              -matcha    => \@amatch,
                              -matchp    => \@pmatch,
                              -range     => Bio::Range->new(-start => $startrange,
                                                            -end   => $endrange)
                              );
        Function: Initialize a new Bio::Map::Clone object
                  Most people will not use this directly but get Clones
                  through L<Bio::MapIO::fpc>
        Returns : L<Bio::Map::Clone> object
        Args    :   -name => marker name string,
                    -markers => array ref of markers,
                    -contig  => contig name string,
                    -type    => type string,
                    -bands   => band string,
                    -gel     => gel string,
                    -group   => group name string,
                    -remark  => remark string,
                    -fpnumber=> FP number string,
                    -sequencetype  => seq type string,
                    -sequencestatus=> seq status string,
                    -fpcremark => FPC remark,
                    -matche    => array ref,
                    -matcha    => array ref,
                    -matchp    => array ref,
                    -range     => L<Bio::Range> object,

Access Methods

       These methods let you get and set the member variables

   name
        Title   : name
        Usage   : my $name = $cloneobj->name();
        Function: Get/set the name for this Clone
        Returns : scalar representing the current name of this clone
        Args    : none to get, OR string to set

   type
        Title   : type
        Usage   : my $type = $cloneobj->type();
        Function: Get/set the type for this clone
        Returns : scalar representing the current type of this clone
        Args    : none to get, OR string to set

   range
        Title   : range
        Usage   : my $range = $cloneobj->range();
        Function: Get/set 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 to get, OR Bio::Range to set

   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.

   each_match
        Title   : each_match
        Function: Synonym of the match() method.

   set_match
        Title   : set_match
        Usage   : $clone->set_match($type,$values);
        Function: Set the Matches per type
        Returns : None
        Args    : type (one of 'exact' 'approx' 'pseudo')
                  array ref of match values

   gel
        Title   : gel
        Usage   : $clonegel = $cloneobj->gel();
        Function: Get/set the gel number for this clone
        Returns : scalar representing the gel number of this clone
        Args    : none to get, OR string to set

   remark
        Title   : remark
        Usage   : $cloneremark = $cloneobj->remark();
        Function: Get/set the remark for this clone
        Returns : scalar representing the current remark of this clone
        Args    : none to get, OR string to set

   fp_number
        Title   : fp_number
        Usage   : $clonefpnumber = $cloneobj->fp_number();
        Function: Get/set the fp number for this clone
        Returns : scalar representing the fp number of this clone
        Args    : none to get, OR string to set

   sequence_type
        Title   : sequence_type
        Usage   : $cloneseqtype = $cloneobj->sequence_type();
        Function: Get/set the sequence type for this clone
        Returns : scalar representing the sequence type of this clone
        Args    : none to get, OR string to set

   sequence_status
        Title   : sequence_status
        Usage   : $cloneseqstatus = $cloneobj->sequence_status();
        Function: Get/set the sequence status for this clone
        Returns : scalar representing the sequence status of this clone
        Args    : none to get, OR string to set

   fpc_remark
        Title   : fpc_remark
        Usage   : $clonefpcremark = $cloneobj->fpc_remark();
        Function: Get/set the fpc remark for this clone
        Returns : scalar representing the fpc remark of this clone
        Args    : none to get, OR string to set

   bands
        Title   : bands
        Usage   : @clonebands = $cloneobj->bands();
        Function: Get/set 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 to get, OR string to set

   group
        Title   : group
        Usage   : $cloneobj->group($chrno);
        Function: Get/set the group number for this clone.
                  This is a generic term, used for Linkage-Groups as well as for
                  Chromosomes.
        Returns : scalar representing the group number of this clone
        Args    : none to get, OR string to set

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

   each_markerid
        Title   : each_markerid
        Usage   : @markers = $cloneobj->each_markerid();
        Function: retrieves all the elements in a map unordered
        Returns : list of strings (ids)
        Args    : none

        *** This only supplies the ids set with the set_markers method ***
        *** It has nothing to do with actual Bio::Map::MarkerI objects ***

   set_markers
        Title   : markers
        Usage   : $obj->set_markers($newval)
        Function: Set list of Marker ids (arrayref)
        Returns : None
        Args    : arrayref of strings (ids)

        *** This only sets a list of ids ***
        *** It has nothing to do with actual Bio::Map::MarkerI objects ***