Reference

Bio::Expression::FeatureGroup(3pm)

a set of DNA/RNA features. ISA Bio::Expression::FeatureI

NAME

Bio::Expression::FeatureGroup - a set of DNA/RNA features. ISA Bio::Expression::FeatureI

SYNOPSIS

#

DESCRIPTION

A set of DNA/RNA features.

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.

  [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:

[email protected]

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:

  http://bugzilla.open-bio.org/

AUTHOR

Allen Day <[email protected]>

APPENDIX

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

new

 Title   : new
 Usage   : $featuregroup = Bio::Expression::FeatureGroup->new(%args);
 Function: create a new featuregroup object
 Returns : a Bio::Expression::FeatureGroup object
 Args    : an optional hash of parameters to be used in initialization:
           -id    --  the featuregroup ID
           -type  --  the featuregroup type

_initialize

 Title   : _initialize
 Usage   : $featuregroup->_initialize(@args);
 Function: initialize the featuregroup object
 Returns : nothing
 Args    : @args

type

 Title   : type
 Usage   : $featuregroup->type($optional_arg);
 Function: get/set the type of the featuregroup
 Comments: this is probably going to be a string like
           "quality control", "mismatch blah blah", etc.
 Returns : the featuregroup type
 Args    : a new value for the featuregroup type

id

 Title   : id
 Usage   : $featuregroup->id($optional_arg);
 Function: get/set the id of the featuregroup
 Returns : the featuregroup id
 Args    : a new value for the featuregroup id

standard_deviation

 Title   : standard_deviation
 Usage   : $featuregroup->standard_deviation($optional_arg);
 Function: get/set the standard deviation of the featuregroup value
 Returns : the featuregroup standard deviation
 Args    : a new value for the featuregroup standard deviation
 Notes   : this method does no calculation, it merely holds a value

quantitation

 Title   : quantitation
 Usage   : $featuregroup->quantitation($optional_arg);
 Function: get/set the quantitation of the featuregroup
 Returns : the featuregroup's quantitated value
 Args    : a new value for the featuregroup's quantitated value
 Notes   : this method does no calculation, it merely holds a value

quantitation_units

 Title   : quantitation_units
 Usage   : $featuregroup->quantitation_units($optional_arg);
 Function: get/set the quantitation units of the featuregroup
 Returns : the featuregroup's quantitated value units
 Args    : a new value for the featuregroup's quantitated value units

presence

 Title   : presence
 Usage   : $featuregroup->presence($optional_arg);
 Function: get/set the presence call of the featuregroup
 Returns : the featuregroup's presence call
 Args    : a new value for the featuregroup's presence call

add_feature

 Title   : add_feature
 Usage   : $feature_copy = $featuregroup->add_feature($feature);
 Function: add a feature to the featuregroup
 Returns : see this_feature()
 Args    : a Bio::Expression::FeatureI compliant object

this_feature

 Title   : this_feature
 Usage   : $feature = $featuregroup->this_feature
 Function: access the last feature added to the featuregroup
 Returns : the last feature added to the featuregroup
 Args    : none

each_feature

 Title   : each_feature
 Usage   : @features = $featuregroup->each_feature
 Function: returns a list of Bio::Expression::FeatureI compliant
           objects
 Returns : a list of objects
 Args    : none

each_feature_quantitation

 Title   : each_feature_quantitation
 Usage   : @featurequantitions = $featuregroup->each_feature_quantitation;
 Function: returns an list of quantitations of the features in the featuregroup
 Returns : a list of numeric values
 Args    : none

is_qc

 Title   : is_qc
 Usage   : $is_quality_control = $featuregroup->is_qc
 Function: get/set whether or not the featuregroup is used for quality control purposes
 Returns : a boolean (equivalent)
 Args    : a new value

History