Bio::Variation::VariantI(3pm)				User Contributed Perl Documentation			     Bio::Variation::VariantI(3pm)

NAME

       Bio::Variation::VariantI - Sequence Change SeqFeature abstract class

SYNOPSIS

	 #get Bio::Variant::VariantI somehow
	 print $var->restriction_changes, "
";
	 foreach $allele ($var->each_Allele) {
	     #work on Bio::Variation::Allele objects
	 }

DESCRIPTION

       This superclass defines common methods to basic sequence changes.  The instantiable classes Bio::Variation::DNAMutation,
       Bio::Variation::RNAChange and Bio::Variation::AAChange use them.  See Bio::Variation::DNAMutation, Bio::Variation::RNAChange, and
       Bio::Variation::AAChange for more information.

       These classes store information, heavy computation to detemine allele sequences is done elsewhere.

       The database cross-references are implemented as Bio::Annotation::DBLink objects. The methods to access them are defined in
       Bio::DBLinkContainerI. See Bio::Annotation::DBLink and Bio::DBLinkContainerI for details.

       Bio::Variation::VariantI redifines and extends Bio::SeqFeature::Generic for sequence variations. This class describes specific sequence
       change events. These events are always from a specific reference sequence to something different. See Bio::SeqFeature::Generic for more
       information.

       IMPORTANT: The notion of reference sequence permeates all Bio::Variation classes. This is especially important to remember when dealing
       with Alleles. In a polymorphic site, there can be a large number of alleles. One of then has to be selected to be the reference allele
       (allele_ori). ALL the rest has to be passed to the Variant using the method add_Allele, including the mutated allele in a canonical
       mutation. The IO modules and generated attributes depend on it. They ignore the allele linked to using allele_mut and circulate each Allele
       returned by each_Allele into allele_mut and calculate the changes between that and allele_ori.

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 _

   id
	Title	: id
	Usage	: $obj->id
	Function:

		  Read only method. Returns the id of the variation object.
		  The id is the id of the first DBLink object attached to this object.

	Example :
	Returns : scalar
	Args	: none

   add_Allele
	Title	: add_Allele
	Usage	: $self->add_Allele($allele)
	Function:

		   Adds one Bio::Variation::Allele into the list of alleles.
		   Note that the method forces the convention that nucleotide
		   sequence is in lower case and amino acds are in upper
		   case.

	Example :
	Returns : 1 when succeeds, 0 for failure.
	Args	: Allele object

   each_Allele
	Title	: alleles
	Usage	: $obj->each_Allele();
	Function:

		    Returns a list of Bio::Variation::Allele objects

	Example :
	Returns : list of Alleles
	Args	: none

   isMutation
	Title	: isMutation
	Usage	: print join('/', $obj->each_Allele) if not $obj->isMutation;
	Function:

		  Returns or sets the boolean value indicating that the
		  variant descibed is a canonical mutation with two alleles
		  assinged to be the original (wild type) allele and mutated
		  allele, respectively. If this value is not set, it is
		  assumed that the Variant descibes polymorphisms.

	Returns : a boolean

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

		   Links to and returns the Bio::Variation::Allele object.
		   If value is not set, returns false. All other Alleles are
		   compared to this.

		   Amino acid sequences are stored in upper case characters,
		   others in lower case.

	Example :
	Returns : string
	Args	: string

       See Bio::Variation::Allele for more.

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

		    Links to and returns the Bio::Variation::Allele
		    object.  Sets and returns the mutated allele sequence.
		    If value is not set, returns false.

		    Amino acid sequences are stored in upper case characters,
		    others in lower case.

	Example :
	Returns : string
	Args	: string

       See Bio::Variation::Allele for more.

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

		   Sets and returns the length of the affected original
		   allele sequence.  If value is not set, returns false == 0.

		   Value 0 means that the variant position is before the
		   start=end sequence position. (Value 1 would denote a point
		   mutation). This follows the convension to report an
		   insertion(2insT) in equivalent way to a corresponding
		   deletion(2delT) (Think about indel polymorpism ATC <=> AC
		   where the origianal state is not known ).

	Example :
	Returns : string
	Args	: string

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

		   Sets and returns upstream flanking sequence string.	If
		   value is not set, returns false. The sequence should be
		   >=25 characters long, if possible.

	Example :
	Returns : string or false
	Args	: string

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

		   Sets and returns dnstream flanking sequence string.	If
		   value is not set, returns false. The sequence should be
		   >=25 characters long, if possible.

	Example :
	Returns : string or false
	Args	: string

   label
	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 class 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

   status
	Title	: status
	Usage	: $obj->status()
	Function:

		  Returns the status of the sequence change object.
		  Valid values are: 'suspected' and 'proven'

	Example : $obj->status('proven');
	Returns : scalar
	Args	: valid string (optional, for setting)

   proof
	Title	: proof
	Usage	: $obj->proof()
	Function:

		  Returns the proof of the sequence change object.
		  Valid values are: 'computed' and 'experimental'.

	Example : $obj->proof('computed');
	Returns : scalar
	Args	: valid string (optional, for setting)

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

		   Sets and returns the name of the sequence region type or
		   protein domain at this location.  If value is not set,
		   returns false.

	Example :
	Returns : string
	Args	: string

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

		   Sets and returns the name of the sequence region_value or
		   protein domain at this location.  If value is not set,
		   returns false.

	Example :
	Returns : string
	Args	: string

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

		   Sets and returns the distance tot the closest region
		   (i.e. intro/exon or domain) boundary. If distance is not
		   set, returns false.

	Example :
	Returns : integer
	Args	: integer

   numbering
	Title	: numbering
	Usage	: $obj->numbering()
	Function:

		  Returns the numbering chema used locating sequnce features.
		  Valid values are: 'entry' and 'coding'

	Example : $obj->numbering('coding');
	Returns : scalar
	Args	: valid string (optional, for setting)

   mut_number
	Title	: mut_number
	Usage	: $num = $obj->mut_number;
		: $num = $obj->mut_number($number);
	Function:

		  Returns or sets the number identifying the order in which the
		  mutation has been issued. Numbers shouldstart from 1.
		  If the number has never been set, the method will return ''

		  If you want the output from IO modules look nice and, for
		  multivariant/allele variations, make sense you better set
		  this attribute.

	Returns : an integer

   SeqDiff
	Title	: SeqDiff
	Usage	: $mutobj = $obj->SeqDiff;
		: $mutobj = $obj->SeqDiff($objref);
	Function:

		  Returns or sets the link-reference to the umbrella
		  Bio::Variation::SeqDiff object.  If there is no link,
		  it will return undef

		  Note: Adding a variant into a SeqDiff object will
		  automatically set this value.

	Returns : an obj_ref or undef

       See Bio::Variation::SeqDiff for more information.

   add_DBLink
	Title	: add_DBLink
	Usage	: $self->add_DBLink($ref)
	Function: adds a link object
	Example :
	Returns :
	Args	:

   each_DBLink
	Title	: each_DBLink
	Usage	: foreach $ref ( $self->each_DBlink() )
	Function: gets an array of DBlink of objects
	Example :
	Returns :
	Args	:

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

		   Returns a string containing a list of restriction
		   enzyme changes of form +EcoRI, separated by
		   commas. Strings need to be valid restriction enzyme names
		   as stored in REBASE. allele_ori and allele_mut need to be assigned.

	Example :
	Returns : string
	Args	: string

perl v5.14.2							    2012-03-02					     Bio::Variation::VariantI(3pm)