Bio::Map::fpcmarker - An central map object representing a marker
## 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 the Bio::Map::Position manpage and the Bio::Map::PositionI manpage for more information.
This object handles the notion of a marker.
This object is intended to be used by a map parser like fpc.pm.
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.
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.
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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:
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Email will@agcol.arizona.edu
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
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
These methods let you get and set the member variables
Title : name Usage : my $name = $markerobj->name(); Function: get the name for this marker Returns : scalar representing the current name of this marker Args : none
Title : global Usage : my $type = $markerobj->global(); Function: get the global position for this marker Returns : scalar representing the current global position of this marker Args : none
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
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
Title : group
Usage : $grpno = $markerobj->group();
Function: get 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
Title : subgroup
Usage : $subgroup = $marker->subgroup();
Function: get 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
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.
Title : each_<element>id
Usage : my @clones = $markerobj->each_cloneid();
my @contigs = $markerobj->each_contigid();
Function: retrieves all the elements in a map unordered
Returns : list of Bio::Map::MappableI ids (names)
Args : type of elements you want (clones, contigs)