Bio::Location::SplitLocationI man page on Pidora

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Bio::Location::SplitLoUseroContributed Perl DoBio::Location::SplitLocationI(3)

NAME
       Bio::Location::SplitLocationI - Abstract interface of a Location on a
       Sequence which has multiple locations (start/end points)

SYNOPSIS
	 # get a SplitLocationI somehow
	   print $splitlocation->start, "..", $splitlocation->end, "\n";
	   my @sublocs = $splitlocation->sub_Location();

	   my $count = 1;
	   # print the start/end points of the sub locations
	   foreach my $location ( sort { $a->start <=> $b->start }  @sublocs ) {
		       printf "sub feature %d [%d..%d]\n", $location->start,$location->end;
	       $count++;
	   }

DESCRIPTION
       This interface encapsulates the necessary methods for representing the
       location of a sequence feature that has more that just a single
       start/end pair.	Some examples of this are the annotated exons in a
       gene or the annotated CDS in a sequence file.

FEEDBACK
       User feedback is an integral part of the evolution of this and other
       Bioperl modules. Send your comments and suggestions preferably to one
       of the Bioperl mailing lists.  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
       the bugs and their resolution.  Bug reports can be submitted via the
       web:

	 http://bugzilla.open-bio.org/

AUTHOR - Jason Stajich
       Email jason-at-bioperl-dot-org

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

   sub_Location
	Title	: sub_Location
	Usage	: @locations = $feat->sub_Location();
	Function: Returns an array of LocationI objects
	Returns : An array
	Args	: none

   splittype
	 Title	 : splittype
	 Usage	 : $splittype = $fuzzy->splittype();
	 Function: get/set the split splittype
	 Returns : the splittype of split feature (join, order)
	 Args	 : splittype to set

   is_single_sequence
	 Title	 : is_single_sequence
	 Usage	 : if($splitloc->is_single_sequence()) {
		       print "Location object $splitloc is split ".
			     "but only across a single sequence\n";
		   }
	 Function: Determine whether this location is split across a single or
		   multiple sequences.
	 Returns : TRUE if all sublocations lie on the same sequence as the root
		   location (feature), and FALSE otherwise.
	 Args	 : none

Bio::LocationI methods
       Bio::LocationI inherited methods follow

   min_start
	 Title	 : min_start
	 Usage	 : my $minstart = $location->min_start();
	 Function: Get minimum starting location of feature startpoint
	 Returns : integer or undef if no maximum starting point.
	 Args	 : none

   max_start
	 Title	 : max_start
	 Usage	 : my $maxstart = $location->max_start();
	 Function: Get maximum starting location of feature startpoint
	 Returns : integer or undef if no maximum starting point.
	 Args	 : none

   start_pos_type
	 Title	 : start_pos_type
	 Usage	 : my $start_pos_type = $location->start_pos_type();
	 Function: Get start position type (ie <,>, ^)
	 Returns : type of position coded as text
		   ('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN')
	 Args	 : none

   min_end
	 Title	 : min_end
	 Usage	 : my $minend = $location->min_end();
	 Function: Get minimum ending location of feature endpoint
	 Returns : integer or undef if no minimum ending point.
	 Args	 : none

   max_end
	 Title	 : max_end
	 Usage	 : my $maxend = $location->max_end();
	 Function: Get maximum ending location of feature endpoint
	 Returns : integer or undef if no maximum ending point.
	 Args	 : none

   end_pos_type
	 Title	 : end_pos_type
	 Usage	 : my $end_pos_type = $location->end_pos_type();
	 Function: Get end position type (ie <,>, ^)
	 Returns : type of position coded as text
		   ('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN')
	 Args	 : none

   seq_id
	 Title	 : seq_id
	 Usage	 : my $seqid = $location->seq_id();
	 Function: Get/Set seq_id that location refers to
	 Returns : seq_id
	 Args	 : [optional] seq_id value to set

   coordinate_policy
	 Title	 : coordinate_policy
	 Usage	 : $policy = $location->coordinate_policy();
		   $location->coordinate_policy($mypolicy); # set may not be possible
	 Function: Get the coordinate computing policy employed by this object.

		   See Bio::Location::CoordinatePolicyI for documentation about
		   the policy object and its use.

		   The interface *does not* require implementing classes to accept
		   setting of a different policy. The implementation provided here
		   does, however, allow to do so.

		   Implementors of this interface are expected to initialize every
		   new instance with a CoordinatePolicyI object. The implementation
		   provided here will return a default policy object if none has
		   been set yet. To change this default policy object call this
		   method as a class method with an appropriate argument. Note that
		   in this case only subsequently created Location objects will be
		   affected.

	 Returns : A Bio::Location::CoordinatePolicyI implementing object.
	 Args	 : On set, a Bio::Location::CoordinatePolicyI implementing object.

   to_FTstring
	 Title	 : to_FTstring
	 Usage	 : my $locstr = $location->to_FTstring()
	 Function: returns the FeatureTable string of this location
	 Returns : string
	 Args	 : none

perl v5.14.1			  2011-07-22  Bio::Location::SplitLocationI(3)
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