Bio::SeqFeature::Computation(3pm)			User Contributed Perl Documentation			 Bio::SeqFeature::Computation(3pm)

NAME

       Bio::SeqFeature::Computation - Computation SeqFeature

SYNOPSIS

	  $feat = Bio::SeqFeature::Computation->new(
				       -start => 10, -end => 100,
				       -strand => -1, -primary => 'repeat',
				       -program_name => 'GeneMark',
				       -program_date => '12-5-2000',
				       -program_version => 'x.y',
				       -database_name => 'Arabidopsis',
				       -database_date => '12-dec-2000',
				       -computation_id => 2231,
				       -score	 => { no_score => 334 } );

DESCRIPTION

       Bio::SeqFeature::Computation extends the Generic seqfeature object with a set of computation related fields and a more flexible set of
       storing more types of score and subseqfeatures. It is compatible with the Generic SeqFeature object.

       The new way of storing score values is similar to the tag structure in the Generic object. For storing sets of subseqfeatures the array
       containg the subseqfeatures is now a hash which contains arrays of seqfeatures Both the score and subSeqfeature methods can be called in
       exactly the same way, the value's will be stored as a 'default' score or subseqfeature.

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/

AUTHOR - Ewan Birney, Mark Fiers
       Ewan Birney <birney@sanger.ac.uk> Mark Fiers <m.w.e.j.fiers@plant.wag-ur.nl>

DEVELOPERS

       This class has been written with an eye out of inheritance. The fields the actual object hash are:

	  _gsf_sub_hash  = reference to a hash containing sets of sub arrays
	  _gsf_score_hash= reference to a hash for the score values

APPENDIX

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

   has_score
	Title	: has_score
	Usage	: $value = $self->has_score('some_score')
	Function: Tests wether a feature contains a score
	Returns : TRUE if the SeqFeature has the score,
		  and FALSE otherwise.
	Args	: The name of a score

   add_score_value
	Title	: add_score_value
	Usage	: $self->add_score_value('P_value',224);
	Returns : TRUE on success
	Args	: score (string) and value (any scalar)

   score
	Title	: score
	Usage	: $value = $comp_obj->score()
		  $comp_obj->score($value)
	Function: Returns the 'default' score or sets the 'default' score
		  This method exist for compatibility options
		  It would equal ($comp_obj->each_score_value('default'))[0];
	Returns : A value
	Args	: (optional) a new value for the 'default' score

   each_score_value
	Title	: each_score_value
	Usage	: @values = $gsf->each_score_value('note');
	Function: Returns a list of all the values stored
		  under a particular score.
	Returns : A list of scalars
	Args	: The name of the score

   all_scores
	Title	: all_scores
	Usage	: @scores = $feat->all_scores()
	Function: Get a list of all the scores in a feature
	Returns : An array of score names
	Args	: none

   remove_score
	Title	: remove_score
	Usage	: $feat->remove_score('some_score')
	Function: removes a score from this feature
	Returns : nothing
	Args	: score (string)

   computation_id
	Title	: computation_id
	Usage	: $computation_id = $feat->computation_id()
		  $feat->computation_id($computation_id)
	Function: get/set on program name information
	Returns : string
	Args	: none if get, the new value if set

   program_name
	Title	: program_name
	Usage	: $program_name = $feat->program_name()
		  $feat->program_name($program_name)
	Function: get/set on program name information
	Returns : string
	Args	: none if get, the new value if set

   program_date
	Title	: program_date
	Usage	: $program_date = $feat->program_date()
		  $feat->program_date($program_date)
	Function: get/set on program date information
	Returns : date (string)
	Args	: none if get, the new value if set

   program_version
	Title	: program_version
	Usage	: $program_version = $feat->program_version()
		  $feat->program_version($program_version)
	Function: get/set on program version information
	Returns : date (string)
	Args	: none if get, the new value if set

   database_name
	Title	: database_name
	Usage	: $database_name = $feat->database_name()
		  $feat->database_name($database_name)
	Function: get/set on program name information
	Returns : string
	Args	: none if get, the new value if set

   database_date
	Title	: database_date
	Usage	: $database_date = $feat->database_date()
		  $feat->database_date($database_date)
	Function: get/set on program date information
	Returns : date (string)
	Args	: none if get, the new value if set

   database_version
	Title	: database_version
	Usage	: $database_version = $feat->database_version()
		  $feat->database_version($database_version)
	Function: get/set on program version information
	Returns : date (string)
	Args	: none if get, the new value if set

   sub_SeqFeature_type
	Title	: sub_SeqFeature_type
	Usage	: $sub_SeqFeature_type = $feat->sub_SeqFeature_type()
		  $feat->sub_SeqFeature_type($sub_SeqFeature_type)
	Function: sub_SeqFeature_type is automatically set when adding
		  a sub_computation (sub_SeqFeature) to a computation object
	Returns : sub_SeqFeature_type (string)
	Args	: none if get, the new value if set

   all_sub_SeqFeature_types
	Title	: all_Sub_SeqFeature_types
	Usage	: @all_sub_seqfeature_types = $comp->all_Sub_SeqFeature_types();
	Function: Returns an array with all subseqfeature types
	Returns : An array
	Args	: none

   sub_SeqFeature
	Title	: sub_SeqFeature('sub_feature_type')
	Usage	: @feats = $feat->sub_SeqFeature();
		  @feats = $feat->sub_SeqFeature('sub_feature_type');
	Function: Returns an array of sub Sequence Features of a specific
		  type or, if the type is ommited, all sub Sequence Features
	Returns : An array
	Args	: (optional) a sub_SeqFeature type (ie exon, pattern)

   add_sub_SeqFeature
	Title	: add_sub_SeqFeature
	Usage	: $feat->add_sub_SeqFeature($subfeat);
		  $feat->add_sub_SeqFeature($subfeat,'sub_seqfeature_type')
		  $feat->add_sub_SeqFeature($subfeat,'EXPAND')
		  $feat->add_sub_SeqFeature($subfeat,'EXPAND','sub_seqfeature_type')
	Function: adds a SeqFeature into a specific subSeqFeature array.
		  with no 'EXPAND' qualifer, subfeat will be tested
		  as to whether it lies inside the parent, and throw
		  an exception if not.
		  If EXPAND is used, the parents start/end/strand will
		  be adjusted so that it grows to accommodate the new
		  subFeature,
		  optionally a sub_seqfeature type can be defined.
	Returns : nothing
	Args	: An object which has the SeqFeatureI interface
		: (optional) 'EXPAND'
		: (optional) 'sub_SeqFeature_type'

   flush_sub_SeqFeature
	Title	: flush_sub_SeqFeature
	Usage	: $sf->flush_sub_SeqFeature
		  $sf->flush_sub_SeqFeature('sub_SeqFeature_type');
	Function: Removes all sub SeqFeature or all sub SeqFeatures
		  of a specified type
		  (if you want to remove a more specific subset, take
		   an array of them all, flush them, and add
		   back only the guys you want)
	Example :
	Returns : none
	Args	: none

perl v5.14.2							    2012-03-02					 Bio::SeqFeature::Computation(3pm)