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
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[email protected] - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list: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:
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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