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This commit was manufactured by cvs2svn to create tag

'bioperl-1-2-1-rc1'.

svn path=/bioperl-live/tags/bioperl-1-2-1-rc1/; revision=5805
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commit 1f6b71d16f3734cbdade9937e52794e97a0ff31f 1 parent 467ab38
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61 Bio/Expression/ProbeI.pm
@@ -1,61 +0,0 @@
-# $Id$
-# BioPerl module for Bio::Expression::ProbeI
-#
-# Copyright Allen Day <allenday@ucla.edu>, Stan Nelson <snelson@ucla.edu>
-# Human Genetics, UCLA Medical School, University of California, Los Angeles
-
-# POD documentation - main docs before the code
-
-=head1 NAME
-
-Bio::Expression::ProbeI - an interface class for DNA/RNA probes
-
-=head1 SYNOPSIS
-
-Do not use this module directly
-
-=head1 DESCRIPTION
-
-This class ISA Bio::Expression::FeatureI, nothing more.
-
-=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.
-
- bioperl-l@bioperl.org - 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:
-
- bioperl-bugs@bio.perl.org
- http://bio.perl.org/bioperl-bugs/
-
-=head1 AUTHOR
-
-Allen Day E<lt>allenday@ucla.eduE<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::ProbeI;
-
-use strict;
-use Bio::Root::Root;
-
-use base qw(Bio::Expression::FeatureI);
-use vars qw($DEBUG);
-
-1;
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130 t/OntologyEngine.t
@@ -1,130 +0,0 @@
-# -*-Perl-*-
-## Bioperl Test Harness Script for Modules
-## $Id$
-
-# Before `make install' is performed this script should be runnable with
-# `make test'. After `make install' it should work as `perl test.t'
-
-use strict;
-BEGIN {
- # to handle systems with no installed Test module
- # we include the t dir (where a copy of Test.pm is located)
- # as a fallback
- eval { require Test; };
- if( $@ ) {
- use lib 't';
- }
- use Test;
- plan tests => 22;
-}
-
-use Bio::Ontology::Term;
-use Bio::Ontology::Relationship;
-use Bio::Ontology::RelationshipType;
-use Bio::Ontology::SimpleOntologyEngine;
-use Bio::Ontology::Ontology;
-
-my $ont = Bio::Ontology::Ontology->new(-name => "My Ontology");
-
-my $eng = Bio::Ontology::SimpleOntologyEngine->new();
-$ont->engine($eng);
-ok( $eng->isa( "Bio::Ontology::OntologyEngineI" ) );
-ok ($ont->engine, $eng);
-
-my @terms = (
- [-identifier => "IPR000001",
- -name => "Kringle",
- -definition => "Kringles are autonomous structural domains ...",
- -ontology => $ont
- ],
- [-identifier => "IPR000002",
- -name => "Cdc20/Fizzy",
- -definition => "The Cdc20/Fizzy region is almost always ...",
- -ontology => $ont
- ],
- [-identifier => "IPR000003",
- -name => "Retinoid X receptor",
- -definition => "Steroid or nuclear hormone receptors ...",
- -ontology => $ont
- ],
- [-identifier => "IPR000004",
- -name => "Test4",
- -definition => "Test4 definition ...",
- -ontology => $ont
- ],
- );
-
-for(my $i = 0; $i < @terms; $i++) {
- $terms[$i] = Bio::Ontology::Term->new(@{$terms[$i]});
- $ont->add_term($terms[$i]);
-}
-
-my $rel_type = Bio::Ontology::RelationshipType->get_instance("IS_A", $ont);
-my $rel_type1 = Bio::Ontology::RelationshipType->get_instance("PART_OF", $ont);
-
-my @rels = (
- [-parent_term => $terms[0],
- -child_term => $terms[1],
- -relationship_type => $rel_type,
- -ontology => $ont,
- ],
- [-parent_term => $terms[1],
- -child_term => $terms[2],
- -relationship_type => $rel_type,
- -ontology => $ont,
- ],
- [-parent_term => $terms[0],
- -child_term => $terms[3],
- -relationship_type => $rel_type,
- -ontology => $ont,
- ],
- [-parent_term => $terms[3],
- -child_term => $terms[2],
- -relationship_type => $rel_type,
- -ontology => $ont,
- ],
- );
-
-for(my $i = 0; $i < @rels; $i++) {
- $rels[$i] = Bio::Ontology::Relationship->new(@{$rels[$i]});
- $ont->add_relationship($rels[$i]);
-}
-
-my @child_terms = $ont->get_child_terms($terms[0]);
-ok (scalar(@child_terms), 2);
-ok( $child_terms[0], $terms[1] );
-my @child_terms1 = $ont->get_child_terms($terms[0], $rel_type);
-ok (scalar(@child_terms), 2);
-ok( $child_terms1[0], $terms[1] );
-ok (scalar($ont->get_child_terms($terms[0], $rel_type1)), 0);
-
-my @descendant_terms = $ont->get_descendant_terms($terms[0]);
-ok( scalar(@descendant_terms), 3);
-ok( $descendant_terms[1], $terms[2] );
-
-my @descendant_terms1 = $ont->get_descendant_terms($terms[0], $rel_type);
-ok( $descendant_terms1[1], $terms[2] );
-ok (scalar(@descendant_terms1), 3);
-ok (scalar($ont->get_descendant_terms($terms[0], $rel_type1)), 0);
-
-my @parent_terms = $ont->get_parent_terms($terms[1]);
-ok (scalar(@parent_terms), 1);
-ok( $parent_terms[0], $terms[0] );
-
-my @ancestor_terms = $ont->get_ancestor_terms($terms[2]);
-ok( $ancestor_terms[0], $terms[0] );
-ok (scalar(@ancestor_terms), 3);
-ok (scalar($ont->get_ancestor_terms($terms[2], $rel_type)), 3);
-ok (scalar($ont->get_ancestor_terms($terms[2], $rel_type1)), 0);
-
-my @leaf_terms = $ont->get_leaf_terms();
-# print scalar(@leaf_terms)."\n";
-ok (scalar(@leaf_terms), 1);
-ok( $leaf_terms[0], $terms[2]);
-
-my @root_terms = $ont->get_root_terms();
-# print scalar(@root_terms)."\n";
-ok (scalar(@root_terms), 1);
-ok( $root_terms[0], $terms[0]);
-
-#print $ont->engine->to_string();
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28 t/data/noninterleaved.phy
@@ -1,28 +0,0 @@
- 4 297
-SBP-5.05 CCTCAGATCA CTCTTTGGCA ACGACCCCTT GTCACAATAA AGATAGGGGG
- GCAACTAAAG GAAGCTCTAT TAGATACAGG AGCAGATGAT ACAGTATTAG
- AAGAAATGAA TTTGCCAGGA AGATGGAAAC CAAAAATGAT AGGGGGAATT
- GGAGGGTTTA TCAAAGTAAA ACAGTATGAT CAGATACCCA TAGAGATCTG
- TGGACATAAA GCTATAGGTA CAGTATTAGT AGGACCCACA CCTGTCAATA
- TAATTGGAAG AAATCTGTTG ACTCAGATTG GTTGCACTTT AAATTTT
-
-SBP-5.21_S CCTCAGATCA CTCTTTGGCA ACGACCCCTC GTCACAATAA AGGTAGGGGG
- GCAACTAAAG GAAGCTCTAT TAGATACAGG AGCAGATGAT ACAGTATTAG
- AAGACATGAA TTTGCCAGGA AGATGGAAAC CAAAAATGAT AGGGGGAATT
- GGAGGGTTTA TCAAAGTAAG ACAGTATGAT CAGATACCCA TAGAGATCTG
- TGGACATAAA GCTATAGGTA CAGTATTAGT AGGACCCACA CCTGTCAATA
- TAATTGGAAG AAATCTGTTG ACTCAGATTG GTTGCACTTT AAATTTT
-
-SBP-5.04_2 CCTCAGATCA CTCTTTGGCA ACGACCCCTC GTCACAATAA AGATAGGGGG
- GCAACTAAAG GAAGCTCTAT TAGATACAGG AGCAGATGAT ACAGTATTAG
- AAGAAATGAA TTTGCCAGGA AGATGGAAAC CAAAAATGAT AGGGGGAATT
- GGAGGGTTTA TCAAAGTAAG ACAGTATGAT CAGATACCCA TAGAGATCTG
- TGGACATAAA GCTATAGGTA CAGTATTAGT AGGACCCACA CCTGTCAATA
- TAATTGGAAG AAATCTGTTG ACTCAGATTG GTTGCACTTT AAATTTT
-
-REC_SBP0.2 CCTCAGATCA CTCTTTGGCA ACGACCCCTC GTCACAATAA AGATAGGGGG
- GCAACTAAAG GAAGCTCTAT TAGATACAGG AGCAGATGAT ACAGTATTAG
- AGGAAACGAA TTTGCCAGGA AGATGGAAAC CAAAAATGAT AGGGGGAATT
- GGAGGGTTTA TCAAAGTAAG ACAGTATGAT CAGATACCCA TAGAGATCTG
- TGGACATAAA GCTATAGGTA CAGTATTAGT AGGACCCACA CCTGTCAATA
- TAATTGGAAG AAATCTGTTG ACTCAGATTG GTTGCACTTT AAATTTT
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