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Bio::Expression::FeatureGroup.3pm

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.

   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:

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

AUTHOR

Allen Day <allenday@ucla.edu>

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