Bio::Variation::AAChange(3pm)				User Contributed Perl Documentation			     Bio::Variation::AAChange(3pm)

NAME

       Bio::Variation::AAChange - Sequence change class for polypeptides

SYNOPSIS

	  $aamut = Bio::Variation::AAChange->new
	      ('-start' 	=> $start,
	       '-end'		=> $end,
	       '-length'	=> $len,
	       '-proof' 	=> $proof,
	       '-isMutation'	=> 1,
	       '-mut_number'	=> $mut_number
	       );

	  my $a1 = Bio::Variation::Allele->new;
	  $a1->seq($ori) if $ori;
	  $aamut->allele_ori($a1);
	  my $a2 = Bio::Variation::Allele->new;
	  $a2->seq($mut) if $mut;
	  $aachange->add_Allele($a2);
	  $aachange->allele_mut($a2);

	  print  "
";

	  # add it to a SeqDiff container object
	  $seqdiff->add_Variant($rnachange);

	  # and create links to and from RNA level variant objects
	  $aamut->RNAChange($rnachange);
	  $rnachange->AAChange($rnachange);

DESCRIPTION

       The instantiable class Bio::Variation::RNAChange describes basic sequence changes at polypeptide  level. It uses methods defined in
       superclass Bio::Variation::VariantI, see Bio::Variation::VariantI for details.

       If the variation described by a AAChange object has a known Bio::Variation::RNAAChange object, create the link with method AAChange(). See
       Bio::Variation::AAChange for more information.

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

APPENDIX

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

   RNAChange
	Title	: RNAChange
	Usage	: $mutobj = $self->RNAChange;
		: $mutobj = $self->RNAChange($objref);
	Function: Returns or sets the link-reference to a mutation/change object.
		  If there is no link, it will return undef
	Returns : an obj_ref or undef

   label
	Title	: label
	Usage	: $obj->label();
	Function:

		   Sets and returns mutation event label(s).  If value is not
		   set, or no argument is given returns false.	Each
		   instantiable subclass of L<Bio::Variation::VariantI> needs
		   to implement this method. Valid values are listed in
		   'Mutation event controlled vocabulary' in
		   http://www.ebi.ac.uk/mutations/recommendations/mutevent.html.

	Example :
	Returns : string
	Args	: string

   similarity_score
	Title	: similarity_score
	Usage	: $self->similarity_score
	Function: Measure for evolutionary conservativeness
		  of single amino substitutions. Uses BLOSUM62.
		  Negative numbers are noncoservative changes.
	Returns : integer, undef if not single amino acid change

   trivname
	Title	: trivname
	Usage	: $self->trivname
	Function:

		  Given a Bio::Variation::AAChange object with linked
		  Bio::Variation::RNAChange and Bio::Variation::DNAMutation
		  objects, this subroutine creates a string corresponding to
		  the 'trivial name' of the mutation. Trivial name is
		  specified in Antonorakis & MDI Nomenclature Working Group:
		  Human Mutation 11:1-3, 1998.

	Returns : string

perl v5.14.2							    2012-03-02					     Bio::Variation::AAChange(3pm)