diff variant_effect_predictor/Bio/Expression/FeatureI.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Expression/FeatureI.pm	Thu Apr 11 02:01:53 2013 -0400
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+# $Id: FeatureI.pm,v 1.3 2002/10/30 23:15:23 allenday Exp $
+# BioPerl module for Bio::Expression::FeatureI
+#
+# Copyright Allen Day <[e-mail]>, Stan Nelson <[e-mail]>
+# Human Genetics, UCLA Medical School, University of California, Los Angeles
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::Expression::FeatureI - an interface class for DNA/RNA features
+
+=head1 SYNOPSIS
+
+Do not use this module directly
+
+=head1 DESCRIPTION
+
+This provides a standard bioperl interface class for representing
+DNA and RNA features.  It cannot be instantiated directly, but serves
+as an abstract base class for implementors.
+
+=head1 FEEDBACK
+
+=head2 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.
+
+  [e-mail]            - General discussion
+  http://bioperl.org/MailList.shtml - About the mailing lists
+
+=head2 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:
+
+  [e-mail]
+  http://bugzilla.bioperl.org/
+
+=head1 AUTHOR
+
+Allen Day E<lt>[e-mail]<gt>
+
+=head1 APPENDIX
+
+The rest of the documentation details each of the object
+methods. Internal methods are usually preceded with a _
+
+=cut
+
+# Let the code begin...
+package Bio::Expression::FeatureI;
+
+use strict;
+use Bio::Root::Root;
+
+use base qw(Bio::Root::Root Bio::PrimarySeqI);
+use vars qw($DEBUG);
+
+=head2 quantitation()
+
+  Title   : value
+  Usage   : $val = $ftr->quantitation()
+  Function: get/set the feature's quantitation
+  Returns : A numeric value
+  Args    : a new numeric value (optional)
+
+=cut
+
+sub quantitation {
+  shift->throw_not_implemented();
+}
+
+=head2 quantitation_units()
+
+  Title   : quantitation_units
+  Usage   : $units = $ftr->quantitation_units()
+  Function: get/set the units of the feature's quantitation
+  Returns : A string or undef
+  Args    : a new string (optional)
+
+=cut
+
+sub quantitation_units {
+  shift->throw_not_implemented();
+}
+
+=head2 standard_deviation()
+
+  Title   : standard_deviation
+  Usage   : $std_dev = $ftr->standard_deviation()
+  Function: get/set the feature's standard deviation of quantitation()
+  Returns : A numeric value
+  Args    : a new numeric value (optional)
+  Comments: no calculation is done here
+
+=cut
+
+sub standard_deviation {
+  shift->throw_not_implemented();
+}
+
+=head2 sample_count()
+
+  Title   : sample_count
+  Usage   : $sample_count = $ftr->sample_count()
+  Function: get/set the number of samples used to calculate
+            quantitation()
+  Returns : An integer
+  Args    : a new integer (optional)
+
+=cut
+
+sub sample_count {
+  shift->throw_not_implemented();
+}
+
+1;