$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;
# add it to a SeqDiff container object
# and create links to and from RNA level variant objects
DESCRIPTIONThe 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.
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AUTHOR - Heikki LehvaslaihoEmail: heikki-at-bioperl-dot-org
APPENDIXThe 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(); 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
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 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