/ 
bioperl-1.2.3
/ Bio::Expression::FeatureGroup

NAME

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

SYNOPSIS

#

DESCRIPTION

A set of DNA/RNA features.

FEEDBACK

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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 email or the web:

bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.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