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 containing 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://github.com/bioperl/bioperl-live/issues

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 whether 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

get_SeqFeature_type

 Title   : get_SeqFeature_type
 Usage   : $SeqFeature_type = $feat->get_SeqFeature_type()
           $feat->get_SeqFeature_type($SeqFeature_type)
 Function: Get SeqFeature type which is automatically set when adding
           a computation (SeqFeature) to a computation object
 Returns : SeqFeature_type (string)
 Args    : none if get, the new value if set

get_all_SeqFeature_types

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

get_SeqFeatures

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

add_SeqFeature

 Title   : add_SeqFeature
 Usage   : $feat->add_SeqFeature($subfeat);
           $feat->add_SeqFeature($subfeat,'seqfeature_type')
           $feat->add_SeqFeature($subfeat,'EXPAND')
           $feat->add_SeqFeature($subfeat,'EXPAND','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 seqfeature type can be defined.
 Returns : nothing
 Args    : An object which has the SeqFeatureI interface
           (optional) 'EXPAND'
           (optional) 'SeqFeature_type'

remove_SeqFeatures

 Title   : remove_SeqFeatures
 Usage   : $sf->remove_SeqFeatures
           $sf->remove_SeqFeatures('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