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.\" ========================================================================
.\"
.IX Title "Bio::Variation::AAChange 3pm"
.TH Bio::Variation::AAChange 3pm "2021-03-04" "perl v5.32.1" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
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.nh
.SH "NAME"
Bio::Variation::AAChange \- Sequence change class for polypeptides
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 8
\&   $aamut = Bio::Variation::AAChange\->new
\&       (\*(Aq\-start\*(Aq         => $start,
\&        \*(Aq\-end\*(Aq           => $end,
\&        \*(Aq\-length\*(Aq        => $len,
\&        \*(Aq\-proof\*(Aq         => $proof,
\&        \*(Aq\-isMutation\*(Aq    => 1,
\&        \*(Aq\-mut_number\*(Aq    => $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  "\en";
\&
\&   # 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);
.Ve
.SH "DESCRIPTION"
.IX Header "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.
.PP
If the variation described by a AAChange object has a known
Bio::Variation::RNAAChange object, create the link with method
\&\fBAAChange()\fR. See Bio::Variation::AAChange for more information.
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHOR \- Heikki Lehvaslaiho"
.IX Header "AUTHOR - Heikki Lehvaslaiho"
Email:  heikki-at-bioperl-dot-org
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
.SS "RNAChange"
.IX Subsection "RNAChange"
.Vb 6
\& 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
.Ve
.SS "label"
.IX Subsection "label"
.Vb 3
\& 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
\&            \*(AqMutation event controlled vocabulary\*(Aq in
\&            http://www.ebi.ac.uk/mutations/recommendations/mutevent.html.
\&
\& Example : 
\& Returns : string
\& Args    : string
.Ve
.SS "similarity_score"
.IX Subsection "similarity_score"
.Vb 6
\& 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
.Ve
.SS "trivname"
.IX Subsection "trivname"
.Vb 3
\& 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 \*(Aqtrivial name\*(Aq of the mutation. Trivial name is
\&           specified in Antonorakis & MDI Nomenclature Working Group:
\&           Human Mutation 11:1\-3, 1998.
\&
\& Returns : string
.Ve