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

NAME

       Bio::Map::FPCMarker - An central map object representing a marker

SYNOPSIS

          # get the marker object of $marker from the Bio::Map::FPCMarker
          my $markerobj = $physical->get_markerobj($marker);

          # acquire all the clones that hit this marker
          foreach my $clone ($markerobj->each_cloneid()) {
              print "   +++$clone\n";
          }

          # find the position of this marker in $contig
          print "Position in contig $contig"," = ",$markerobj->position($contig),
                "\n";

          # find the group of the marker
          print "Group : ",$markerobj->group();

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

DESCRIPTION

       This object handles the notion of a marker.  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::FPCMarker->new
                             (
                              -name    => $marker,
                              -type    => $type,
                              -global  => $global,
                              -frame   => $frame,
                              -group   => $group,
                              -subgroup=> $subgroup,
                              -anchor  => $anchor,
                              -clones  => \%clones,
                              -contigs => \%contigs,
                              -position => \%markerpos,
                      -remark => $remark
                              );

        Function: Initialize a new Bio::Map::FPCMarker object
                  Most people will not use this directly but get Markers
                  through L<Bio::MapIO::fpc>
        Returns : L<Bio::Map::FPCMarker> object
        Args    : -name     => marker name string,
                      -type     => type string,
                      -global   => global position for marker,
                      -frame    => boolean if marker is framework or placement,
                      -group    => group number for marker,
                      -subgroup => subgroup number of marker,
                      -anchor   => boolean if marker is anchored,
                      -clones   => all the clone elements in map (hashref),
                      -contigs  => all the contig elements (hasref),
                      -position => mapping of marker names to map position (hasref),
                  -remark   => remarks, separated by newlines

Access Methods

       These methods let you get and set the member variables

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

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

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

   anchor
        Title   : anchor
        Usage   : my $anchor = $markerobj->anchor();
        Function: indicate if the Marker is anchored or not (True | False)
        Returns : scalar representing the anchor (1 | 0) for this marker
        Args    : none to get, OR 1|0 to set

   framework
        Title   : framework
        Usage   : $frame = $markerobj->framework();
        Function: indicate if the Marker is framework or placement (1 | 0)
        Returns : scalar representing if the marker is framework
                  (1 if framework, 0 if placement)
        Args    : none to get, OR 1|0 to set

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

   subgroup
        Title   : subgroup
        Usage   : $subgroup = $marker->subgroup();
        Function: Get/set the subgroup for this marker. 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 : scalar representing the subgroup of this marker
        Args    : none to get, OR string to set

   position
        Title   : position
        Usage   : $markerpos = $markerobj->position($ctg);
        Function: get the position of the marker in the contig
        Returns : scalar representing the position of the markernumber of
                  the contig
        Args    : $ctg is necessary to look for the position of the marker
                  in that contig.

        *** This has nothing to do with an actual Bio::Map::PositionI object ***

   remark
        Title   : remark
        Usage   : $markerremark = $markerobj->remark();
        Function: get the remarks for this marker
        Returns : scalar of newline-separated markers
        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_contigid
        Title   : each_contigid
        Usage   : my @contigs = $map->each_contigid();
        Function: retrieves all the contig ids in a map unordered
        Returns : list of strings (ids)
        Args    : none

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

   set_clones
        Title   : set_clones
        Usage   : $marker->set_clones(\%clones)
        Function: Set the clone ids 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_contigs
        Title   : set_contigs
        Usage   : $marker->set_contigs(\%contigs)
        Function: Set the contig ids hashref
        Returns : None
        Args    : Hashref of contig ids

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

   set_positions
        Title   : set_positions
        Usage   : $marker->set_positions(\%markerpos)
        Function: Set the positions hashref
        Returns : None
        Args    : Hashref of marker positions

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