/ 
bioperl-1.2.2
/ Bio::Expression::FeatureSet

NAME

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

SYNOPSIS

#

DESCRIPTION

A set of DNA/RNA features.

FEEDBACK

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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.

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

_initialize

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

type

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

id

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

standard_deviation

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

quantitation

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

quantitation_units

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

presence

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

add_feature

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

this_feature

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

each_feature

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

is_qc

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