Provided by: libbio-perl-perl_1.6.901-2_all bug

NAME

       Bio::LiveSeq::Mutation - Mutation event descriptor class

SYNOPSIS

         # full descrition of a point mutation
         $mutation1a = Bio::LiveSeq::Mutation->new ( -seq => 'A',
                                                     -seqori => 'T',
                                                     -pos  => 100,
                                                     -len => 1 # optional, defaults to length(seq)
                                                    );

         # minimal information for a point mutation
         $mutation1b = Bio::LiveSeq::Mutation->new ( -seq => 'A',
                                                     -pos  => 100
                                                     );
         # insertion
         $mutation2 = Bio::LiveSeq::Mutation->new ( -seq => 'ATT',
                                                    -pos  => 100,
                                                    -len => 0
                                                    );
         # deletion
         $mutation3 = Bio::LiveSeq::Mutation->new ( -seq => '',  # optional
                                                    -seqori => 'TTG',  # optional
                                                    -pos  => 100
                                                    -len => 3
                                                    );
         # complex
         $mutation4 = Bio::LiveSeq::Mutation->new ( -seq => 'CC',
                                                    -seqori => 'TTG',  # optional
                                                    -pos  => 100
                                                    -len => 3
                                                    );

DESCRIPTION

       This class describes a local mutation event using minimalistic description.  It is not
       necessary to know anything about the original sequence. You need to give the changed
       sequence, the position of the mutation in the (unidentified) reference sequence, and the
       length of the affected subsequence in the reference sequence. If the original allele
       sequence is given, the objects applying the mutation into the reference sequence (e.g.
       Bio::LiveSeq::Mutator) might check for its validity.

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 _

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

                   Sets and returns the mutated sequence. No checking is done
                   to validate the symbols.

        Example :
        Returns : string
        Args    : integer

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

                   Sets and returns the original subsequence in the reference
                   sequence. No checking is done to validate the symbols.
                   Optional value.

        Example :
        Returns : string
        Args    : string

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

                   Sets and returns the position of the first element in the
                   sequence.

        Example :
        Returns : string
        Args    : integer

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

                   Sets and returns the len of the affected original allele
                   sequence.  If value is not set, defaults to the length of
                   the mutated sequence (seq).

        Example :
        Returns : string
        Args    : string

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

                   Sets and returns the label of the affected original allele
                   location. Label is a stable identifier whereas location
                   can be changed by mutations. Label comes from
                   l<Bio::LiveSeq::Gene>.

        Example :
        Returns : string
        Args    : string

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

                   Sets and returns the transcript position of the mutation.
                   Set when associated with a reference sequence. Value
                   depends on reference molecule and the co-ordinate system
                   used.

        Example :
        Returns : string
        Args    : integer

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

                   Sets and returns the position of the mutation in an array
                   of mutations to be issued. Set after the validity of the
                   mutation has been confirmed.

        Example :
        Returns : string
        Args    : integer

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

                   Sets and returns the prelabel of the affected original allele
                   location. Prelabel is a stable identifier whereas location
                   can be changed by mutations. Prelabel comes from
                   l<Bio::LiveSeq::Gene>.

        Example :
        Returns : string
        Args    : string

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

                   Sets and returns the postlabel of the affected original allele
                   location. Postlabel is a stable identifier whereas location
                   can be changed by mutations. Postlabel comes from
                   l<Bio::LiveSeq::Gene>.

        Example :
        Returns : string
        Args    : string

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

                   Sets and returns the lastlabel of the affected original allele
                   location. Lastlabel is a stable identifier whereas location
                   can be changed by mutations. Lastlabel comes from
                   l<Bio::LiveSeq::Gene>.

        Example :
        Returns : string
        Args    : string