Provided by: libbio-perl-perl_1.7.2-2_all bug


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


          $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;
          my $a2 = Bio::Variation::Allele->new;
          $a2->seq($mut) if $mut;

          print  "\n";

          # add it to a SeqDiff container object

          # and create links to and from RNA level variant objects


       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


   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.
                  - General discussion  - About the mailing lists

       Please direct usage questions or support issues to the mailing list:

       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:

AUTHOR - Heikki Lehvaslaiho

       Email:  heikki-at-bioperl-dot-org


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

        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

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

                   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

        Example :
        Returns : string
        Args    : string

        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

        Title   : trivname
        Usage   : $self->trivname

                  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