Bio::SeqFeature::Computation - Computation SeqFeature $feat = new Bio::SeqFeature::Computation ( -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 } ); 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.

Mailing Lists
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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 email or the web: bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/ Ewan Birney <birney@sanger.ac.uk> Mark Fiers <m.w.e.j.fiers@plant.wag-ur.nl> 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 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