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.\"
.IX Title "Bio::SeqEvolution::EvolutionI 3pm"
.TH Bio::SeqEvolution::EvolutionI 3pm "2018-10-27" "perl v5.26.2" "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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.SH "NAME"
Bio::SeqEvolution::EvolutionI \- the interface for evolving sequences
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&    # not an instantiable class
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This is the interface that all classes that mutate sequence objects in
constant fashion must implement. A good example is
Bio::SeqEvolution::DNAPoint.
.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 list.  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
of 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"
.IX Header "AUTHOR"
.Vb 1
\&  Heikki Lehvaslaiho E<lt>heikki at bioperl dot orgE<gt>
.Ve
.SH "CONTRIBUTORS"
.IX Header "CONTRIBUTORS"
Additional contributor's names and emails here
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
.SS "annotation"
.IX Subsection "annotation"
.Vb 8
\& Title   : annotation
\& Usage   : $obj\->annotation($newval)
\& Function: Get the annotation collection for this annotatable object.
\& Example :
\& Returns : a Bio::AnnotationCollectionI implementing object, or undef
\& Args    : on set, new value (a Bio::AnnotationCollectionI
\&           implementing object, optional) (an implementation may not
\&           support changing the annotation collection)
.Ve
.PP
See Bio::AnnotationCollectionI
.SS "seq"
.IX Subsection "seq"
.Vb 5
\& Title   : seq
\& Usage   : $obj\->seq($newval)
\& Function: Set the sequence object for the original sequence
\& Returns : The sequence object
\& Args    : newvalue (optional)
.Ve
.PP
Setting this will reset mutation and generated mutation counters.
.SS "next_seq"
.IX Subsection "next_seq"
.Vb 5
\&  Title   : next_seq
\&  Usage   : $obj\->next_seq
\&  Function: Evolve the reference sequence to desired level
\&  Returns : A new sequence object mutated from the reference sequence
\&  Args    : \-
.Ve
.SS "mutate"
.IX Subsection "mutate"
.Vb 5
\&  Title   : mutate
\&  Usage   : $obj\->mutate
\&  Function: mutate the sequence at the given location according to the model
\&  Returns : true
\&  Args    : integer, start location of the mutation, required argument
.Ve
.PP
Called from \fInext_seq()\fR.