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bio::map::positionwithsequence(3pm) [debian man page]

Bio::Map::PositionWithSequence(3pm)			User Contributed Perl Documentation		       Bio::Map::PositionWithSequence(3pm)

NAME

       Bio::Map::PositionWithSequence - A position with a sequence.

SYNOPSIS

	   use Bio::Map::PositionWithSequence;

	   my $pos = Bio::Map::PositionWithSequence->new(-map => $map,
				       -element => $element,
				       -start => 0,
				       -seq => 'ATGC');

DESCRIPTION

       Have a position with a sequence, eg. define what the binding site sequence of a certain transcription factor binding site is by modelling
       it as one of these objects with the -element assigned to a Bio::Map::TranscriptionFactor instance.

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 - Sendu Bala
       Email bix@sendu.me.uk

APPENDIX

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

   new
	Title	: new
	Usage	: my $obj = Bio::Map::PositionWithSequence->new();
	Function: Builds a new Bio::Map::PositionWithSequence object
	Returns : Bio::Map::PositionWithSequence
	Args	: -map	    => Bio::Map::GeneMap object
		  -element  => Bio::Map::Gene object
		  -relative => Bio::Map::GeneRelative object
		  -seq	    => string, length of this string will set the length
			       of this position's range

		  * If this position has no range, or if a single value can describe
		    the range *
		  -value => scalar	       : something that describes the single
						 point position or range of this
						 Position, most likely an int

		  * Or if this position has a range, at least two of *
		  -start => int 	       : value of the start co-ordinate
		  -end => int		       : value of the end co-ordinate
		  -length => int	       : length of the range

   seq
	Title	: seq
	Usage	: my $string = $obj->seq();
	Function: Get/set the sequence as a string of letters.
	Returns : scalar
	Args	: Optionally on set the new value (a string). An optional second
		  argument presets the alphabet (otherwise it will be guessed).

perl v5.14.2							    2012-03-02				       Bio::Map::PositionWithSequence(3pm)

Check Out this Related Man Page

Bio::Map::CytoMap(3pm)					User Contributed Perl Documentation				    Bio::Map::CytoMap(3pm)

NAME

       Bio::Map::CytoMap - A Bio::MapI compliant map implementation handling cytogenic bands

SYNOPSIS

	   use Bio::Map::CytoMap;
	   my $map = Bio::Map::CytoMap->new(-name => 'human1',
					     -species => $human);
	   foreach my $marker ( @markers ) { # get a list of markers somewhere
	       $map->add_element($marker);
	   }

DESCRIPTION

       This is the simple implementation of cytogenetic maps based on 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.

       For CytoMaps type is hard coded to be 'cytogeneticmap' and units are set to '' but can be set to something else.

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 - Heikki Lehvaslaiho
       Email heikki-at-bioperl-dot-org

CONTRIBUTORS

       Jason Stajich	  jason@bioperl.org Lincoln Stein      lstein@cshl.org Sendu Bala	  bix@sendu.me.uk

APPENDIX

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

   new
	Title	: new
	Usage	: my $obj = Bio::Map::CytoMap->new();
	Function: Builds a new Bio::Map::CytoMap object
	Returns : Bio::Map::CytoMap
	Args	: -name    => name of map (string)
		  -species => species for this map (Bio::Species) [optional]
		  -elements=> elements to initialize with
			      (arrayref of Bio::Map::MappableI objects) [optional]

		  -uid	   => Unique Id

   type
	Title	: type
	Usage	: my $type = $map->type
	Function: Get hard-coded Map type
	Returns : String coding Map type (always 'cyto')
	Args	: none

   length
	Title	: length
	Usage	: my $length = $map->length();
	Function: Retrieves the length of the map,
	Returns : 0 since length is not calculatable for cytogenetic maps
	Args	: none

perl v5.14.2							    2012-03-02						    Bio::Map::CytoMap(3pm)
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