NAME

       Bio::Map::Contig - A MapI implementation handling the contigs of a Physical Map (such as
       FPC)

SYNOPSIS

           # get the contig object of $contig from the Bio::Map::Physical
           my $ctgobj = $physical->get_contigobj($contig);

           # acquire all the markers that lie in this contig
           foreach my $marker ($ctgobj->each_markerid()) {
               print "   +++$marker\n";
           }

           # find the group of this contig
           print "Group: ",$ctgobj->group(),"\n";

           # find the range of this contig
           print "RANGE: start:",$ctgobj->range()->start(),"\tend: ",
                  $ctgobj->range()->end(),"\n";

           # find the position of this contig in $group (chromosome)
           print "Position in Group $group"," = ",$ctgobj->position($group),"\n";

DESCRIPTION

       This is an implementation of Bio::Map::MapI.  It handles the essential storage of name,
       species, type, and units as well as in memory representation of the elements of a map.

       Bio::Map::Contig has been tailored to work for FPC physical maps, but could probably be
       used for others as well (with the appropriate MapIO module).

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://github.com/bioperl/bioperl-live/issues

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::Contig->new
                             (
                              -name    => $name,
                              -chr_remark   => $cremark,
                              -user_remark  => $uremark,
                              -trace_remark => $tremark,
                              -group   => $group,
                              -subgroup=> $subgroup,
                              -anchor  => $anchor,
                              -markers => \%markers,
                              -clones  => \%clones,
                              -position => $pos
                              -range    => Bio::Range->new(-start =>$s,-end=>$e),
                              );

        Function: Initialize a new Bio::Map::Contig object
                  Most people will not use this directly but get Markers
                  through L<Bio::MapIO::fpc>
        Returns : L<Bio::Map::Contig> object
        Args    : ( -name    => name string,
                    -chr_remark   => chr remark string,
                    -user_remark  => userremark string,
                    -trace_remark => tremark string,
                    -group   => group string,
                    -subgroup=> subgroup string,
                    -anchor  => boolean if this is anchored or not,
                    -markers => hashref of contained markers,
                    -clones  => hashref of contained clones,
                    -position => position
                    -range    => L<Bio::Range>

   Modifier methods
       All methods present in Bio::Map::SimpleMap are implemented by this class.  Most of the
       methods are inherited from SimpleMap.  The following methods have been modified to reflect
       the needs of physical maps.

   chr_remark
        Title   : chr_remark
        Usage   : my $chrremark = $contigobj->chr_remark();
        Function: Get/set the group remark for this contig
        Returns : scalar representing the current group_remark of this contig
        Args    : none to get, OR string to set

   user_remark
        Title   : user_remark
        Usage   : my $userremark = $contigobj->user_remark();
        Function: Get/set the user remark for this contig
        Returns : scalar representing the current user_remark of this contig
        Args    : none to get, OR string to set

   trace_remark
        Title   : trace_remark
        Usage   : my $traceremark = $contigobj->trace_remark();
        Function: Get/set the trace remark for this contig
        Returns : scalar representing the current trace_remark of this contig
        Args    : none to get, OR string to set

   range
        Title   : range
        Usage   : my $range = $contigobj->range();
        Function: Get/set the range for this Contig
        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

   position
        Title   : position
        Usage   : $ctgpos = $contigobj->position();
        Function: Get/set the position of the contig in the group
        Returns : scalar representing the position of the contig in the group
        Args    : none to get, OR string to set

   anchor
        Title   : anchor
        Usage   : $ctganchor = $contig->anchor();
        Function: Get/set the anchor value for this Contig (True | False)
        Returns : scalar representing the anchor (1 | 0) for this contig
        Args    : none to get, OR string to set

   group
        Title   : group
        Usage   : $groupno = $contigobj->group();
        Function: Get/set 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 contig
        Args    : none

   subgroup
        Title   : subgroup
        Usage   : $subgroup = $contig->subgroup();
        Function: Get/set the subgroup for this contig. This is a generic term:
                  subgroup here could represent subgroup of a Chromosome or of a
                  Linkage Group. The user must take care of which subgroup he/she is
                  querying for.
        Returns : A scalar representing the subgroup of this contig
        Args    : none

   each_cloneid
        Title   : each_cloneid
        Usage   : my @clones  = $map->each_cloneid();
        Function: retrieves all the clone ids in a map unordered
        Returns : list of strings (ids)
        Args    : none

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

   each_markerid
        Title   : each_markerid
        Usage   : my @markers = $map->each_markerid();
        Function: retrieves all the marker ids 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_clones
        Title   : set_clones
        Usage   : $marker->set_clones(\%clones)
        Function: Set the clones hashref
        Returns : None
        Args    : Hashref of clone ids

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

   set_markers
        Title   : markers
        Usage   : $obj->set_markers($newval)
        Function: Set list of Markers (hashref)
        Returns : None
        Args    : Hashref of marker ids

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