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bio::seqevolution::evolutioni(3pm) [debian man page]

Bio::SeqEvolution::EvolutionI(3pm)			User Contributed Perl Documentation			Bio::SeqEvolution::EvolutionI(3pm)

NAME

       Bio::SeqEvolution::EvolutionI - the interface for evolving sequences

SYNOPSIS

	   # not an instantiable class

DESCRIPTION

       This is the interface that all classes that mutate sequence objects in constant fashion must implement. A good example is
       Bio::SeqEvolution::DNAPoint.

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 list.  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 of the bugs and their resolution. Bug reports can be submitted via the
       web:

	 https://redmine.open-bio.org/projects/bioperl/

AUTHOR

	 Heikki Lehvaslaiho E<lt>heikki at bioperl dot orgE<gt>

CONTRIBUTORS

       Additional contributor's names and emails here

APPENDIX

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

   annotation
	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)

       See Bio::AnnotationCollectionI

   seq
	Title	: seq
	Usage	: $obj->seq($newval)
	Function: Set the sequence object for the original sequence
	Returns : The sequence object
	Args	: newvalue (optional)

       Setting this will reset mutation and generated mutation counters.

   next_seq
	 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	 : -

   mutate
	 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

       Called from next_seq().

perl v5.14.2							    2012-03-02					Bio::SeqEvolution::EvolutionI(3pm)

Check Out this Related Man Page

Bio::SeqIO::ztr(3pm)					User Contributed Perl Documentation				      Bio::SeqIO::ztr(3pm)

NAME

       Bio::SeqIO::ztr - ztr trace sequence input/output stream

SYNOPSIS

       Do not use this module directly.  Use it via the Bio::SeqIO class.

DESCRIPTION

       This object can transform Bio::Seq objects to and from ztr trace files.

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 one
       of 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/

AUTHORS - Aaron Mackey
       Email: amackey@virginia.edu

APPENDIX

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

   next_seq
	Title	: next_seq
	Usage	: $seq = $stream->next_seq()
	Function: returns the next sequence in the stream
	Returns : Bio::Seq::Quality object
	Args	: NONE

   write_seq
	Title	: write_seq
	Usage	: $stream->write_seq(@seq)
	Function: writes the $seq object into the stream
	Returns : 1 for success and 0 for error
	Args	: Bio::Seq object

   compression
	Title	: compression
	Usage	: $stream->compression(3);
	Function: determines the level of ZTR compression
	Returns : the current (or newly set) value.
	Args	: 1, 2 or 3 - any other (defined) value will cause the compression
		  to be reset to the default of 2.

perl v5.14.2							    2012-03-02						      Bio::SeqIO::ztr(3pm)
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