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BioPerl-1.007000_006
River stage two • 60 direct dependents • 65 total dependents
/ Bio::SeqFeature::Computation

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://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 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

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 ommited, 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