diff variant_effect_predictor/Bio/Ontology/TermI.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Ontology/TermI.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,308 @@
+# $Id: TermI.pm,v 1.8.2.3 2003/05/27 22:00:52 lapp Exp $
+#
+# BioPerl module for Bio::Ontology::Term
+#
+# Cared for by Christian M. Zmasek <[e-mail]> or <[e-mail]>
+#
+# (c) Christian M. Zmasek, [e-mail], 2002.
+# (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002.
+#
+# You may distribute this module under the same terms as perl itself.
+# Refer to the Perl Artistic License (see the license accompanying this
+# software package, or see http://www.perl.com/language/misc/Artistic.html)
+# for the terms under which you may use, modify, and redistribute this module.
+#
+# THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
+# WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF
+# MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+#
+# You may distribute this module under the same terms as perl itself
+
+# POD documentation - main docs before the code
+
+
+=head1 NAME
+
+TermI - interface for ontology terms
+
+=head1 SYNOPSIS
+
+  #get Bio::Ontology::TermI somehow.
+
+  print $term->identifier(), "\n";
+  print $term->name(), "\n";
+  print $term->definition(), "\n";
+  print $term->is_obsolete(), "\n";
+  print $term->comment(), "\n";
+
+  foreach my $synonym ( $term->get_synonyms() ) {
+      print $synonym, "\n";
+  }
+
+
+=head1 DESCRIPTION
+
+This is "dumb" interface for ontology terms providing basic methods
+(it provides no functionality related to graphs).
+
+=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://bio.perl.org/MailList.html - 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
+
+Christian M. Zmasek
+
+Email: [e-mail]  or  [e-mail]
+
+WWW:   http://www.genetics.wustl.edu/eddy/people/zmasek/
+
+Address: 
+
+  Genomics Institute of the Novartis Research Foundation
+  10675 John Jay Hopkins Drive
+  San Diego, CA 92121
+
+=head1 APPENDIX
+
+The rest of the documentation details each of the object
+methods.
+
+=cut
+
+
+# Let the code begin...
+
+package Bio::Ontology::TermI;
+use vars qw( @ISA );
+use strict;
+use Bio::Root::RootI;
+
+@ISA = qw( Bio::Root::RootI );
+
+
+
+=head2 identifier
+
+ Title   : identifier
+ Usage   : $term->identifier( "0003947" );
+           or
+           print $term->identifier();
+ Function: Set/get for the identifier of this Term.
+ Returns : The identifier [scalar].
+ Args    : The identifier [scalar] (optional).
+
+=cut
+
+sub identifier {
+    shift->throw_not_implemented();
+} # identifier
+
+
+
+
+=head2 name
+
+ Title   : name
+ Usage   : $term->name( "N-acetylgalactosaminyltransferase" );
+           or
+           print $term->name();
+ Function: Set/get for the name of this Term.
+ Returns : The name [scalar].
+ Args    : The name [scalar] (optional).
+
+=cut
+
+sub name {
+    shift->throw_not_implemented();
+} # name
+
+
+
+
+
+=head2 definition
+
+ Title   : definition
+ Usage   : $term->definition( "Catalysis of ..." );
+           or
+           print $term->definition();
+ Function: Set/get for the definition of this Term.
+ Returns : The definition [scalar].
+ Args    : The definition [scalar] (optional).
+
+=cut
+
+sub definition {
+    shift->throw_not_implemented();
+} # definition
+
+
+
+=head2 ontology
+
+ Title   : ontology
+ Usage   : $ont = $term->ontology();
+           or 
+           $term->ontology( $ont );
+ Function: Get the ontology this term is in.
+
+           An implementation may not permit the value of this
+           attribute to be changed once it is set, since that may have
+           serious consequences (note that with the ontology in hand
+           you can query for all related terms etc).
+
+           Note for implementors: you will almost certainly have to
+           take special precaution in order not to create cyclical
+           references in memory.
+
+ Returns : The ontology of this Term as a L<Bio::Ontology::OntologyI>
+           implementing object.
+ Args    : On set, the  ontology of this Term as a L<Bio::Ontology::OntologyI>
+           implementing object or a string representing its name.
+
+=cut
+
+sub ontology {
+    shift->throw_not_implemented();
+} # ontology
+
+
+
+=head2 version
+
+ Title   : version
+ Usage   : $term->version( "1.00" );
+           or 
+           print $term->version();
+ Function: Set/get for version information.
+ Returns : The version [scalar].
+ Args    : The version [scalar] (optional).
+
+=cut
+
+sub version {
+    shift->throw_not_implemented();
+} # version
+
+
+
+
+=head2 is_obsolete
+
+ Title   : is_obsolete
+ Usage   : $term->is_obsolete( 1 );
+           or
+           if ( $term->is_obsolete() )
+ Function: Set/get for the obsoleteness of this Term.
+ Returns : the obsoleteness [0 or 1].
+ Args    : the obsoleteness [0 or 1] (optional).
+
+=cut
+
+sub is_obsolete {
+    shift->throw_not_implemented();
+} # is_obsolete
+
+
+
+=head2 comment
+
+ Title   : comment
+ Usage   : $term->comment( "Consider the term ..." );
+           or 
+           print $term->comment();
+ Function: Set/get for an arbitrary comment about this Term.
+ Returns : A comment.
+ Args    : A comment (optional).
+
+=cut
+
+sub comment {
+    shift->throw_not_implemented();
+} # comment
+
+
+
+
+=head2 get_synonyms
+
+ Title   : get_synonyms
+ Usage   : @aliases = $term->get_synonyms();
+ Function: Returns a list of aliases of this Term.
+
+           If an implementor of this interface permits modification of
+           this array property, the class should define at least
+           methods add_synonym() and remove_synonyms(), with obvious
+           functionality.
+
+ Returns : A list of aliases [array of [scalar]].
+ Args    :
+
+=cut
+
+sub get_synonyms {
+    shift->throw_not_implemented();
+} # get_synonyms
+
+=head2 get_dblinks
+
+ Title   : get_dblinks()
+ Usage   : @ds = $term->get_dblinks();
+ Function: Returns a list of each dblink of this term.
+
+           If an implementor of this interface permits modification of
+           this array property, the class should define at least
+           methods add_dblink() and remove_dblinks(), with obvious
+           functionality.
+
+ Returns : A list of dblinks [array of [scalars]].
+ Args    :
+
+=cut
+
+sub get_dblinks {
+    shift->throw_not_implemented();
+} # get_dblinks
+
+=head2 get_secondary_ids
+
+ Title   : get_secondary_ids
+ Usage   : @ids = $term->get_secondary_ids();
+ Function: Returns a list of secondary identifiers of this Term.
+
+           Secondary identifiers mostly originate from merging terms,
+           or possibly also from splitting terms.
+
+           If an implementor of this interface permits modification of
+           this array property, the class should define at least
+           methods add_secondary_id() and remove_secondary_ids(), with
+           obvious functionality.
+
+ Returns : A list of secondary identifiers [array of [scalar]]
+ Args    :
+
+=cut
+
+sub get_secondary_ids {
+    shift->throw_not_implemented();
+} # get_secondary_ids
+
+
+1;