bio::liveseq::translation(3pm) [debian man page]

Bio::LiveSeq::Translation(3pm)				User Contributed Perl Documentation			    Bio::LiveSeq::Translation(3pm)

NAME

       Bio::LiveSeq::Translation - Translation class for LiveSeq

SYNOPSIS

	 #documentation needed

DESCRIPTION

       This stores information about aminoacids translations of transcripts.  The implementation is that a Translation object is the translation
       of a Transcript object, with different possibilities of manipulation, different coordinate system and eventually its own ranges (protein
       domains).

AUTHOR - Joseph A.L. Insana
       Email:  Insana@ebi.ac.uk, jinsana@gmx.net

APPENDIX

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

   new
	 Title	 : new
	 Usage	 : $protein = Bio::LiveSeq::Translation->new(-transcript => $transcr);

	 Function: generates a new Bio::LiveSeq::Translation
	 Returns : reference to a new object of class Translation
	 Errorcode -1
	 Args	 : reference to an object of class Transcript

   get_Transcript
	 Title	 : valid
	 Usage	 : $transcript = $obj->get_Transcript()
	 Function: retrieves the reference to the object of class Transcript (if any)
		   attached to a LiveSeq object
	 Returns : object reference
	 Args	 : none

   aa_ranges
	 Title	 : aa_ranges
	 Usage	 : @proteinfeatures = $translation->aa_ranges()
	 Function: to retrieve all the LiveSeq AARange objects attached to a
		   Translation, usually created out of a SwissProt database entry
		   crossreferenced from an EMBL CDS feature.
	 Returns : an array
	 Args	 : none

perl v5.14.2							    2012-03-02					    Bio::LiveSeq::Translation(3pm)

Bio::LiveSeq::ChainI(3pm)				User Contributed Perl Documentation				 Bio::LiveSeq::ChainI(3pm)

NAME

       Bio::LiveSeq::ChainI - Double linked chain data structure

SYNOPSIS

	 #documentation needed

DESCRIPTION

       This class generates and manipulates generic double linked list, chain, that can be used to manage biological sequences.

       The advantages over strings or plain arrays is the ease of tracking changes (mutations) in the elements (sequence). The other side of the
       coin is that these structures need consideraly more memory, but that is cheap and constantly inceasing resource in computers.

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 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:

	 https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Joseph A.L. Insana
       Email:  Insana@ebi.ac.uk, jinsana@gmx.net

APPENDIX

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

   new
	 Title	 : new
	 Usage	 : $chain = Bio::LiveSeq::ChainI->new(-string => "thequickbrownfoxjumpsoverthelazydog",
						    -offset => 3 );
		OR $chain = Bio::LiveSeq::ChainI->new(-array => @array,
						    -offset => 3 );
	 Function: generates a new Bio::LiveSeq:ChainI
	 Returns : a new Chain
	 Args	 : string
		OR arrayreference
	       AND optional offset to create element labels

perl v5.14.2							    2012-03-02						 Bio::LiveSeq::ChainI(3pm)