From 29d935e1a955e0f81faf6037d68c07478688394c Mon Sep 17 00:00:00 2001 From: cjfields Date: Wed, 10 Dec 2008 05:51:24 +0000 Subject: [PATCH] update deprecation list svn path=/bioperl-live/trunk/; revision=15130 --- DEPRECATED | 31 +++++++++++++++++-------------- 1 file changed, 17 insertions(+), 14 deletions(-) diff --git a/DEPRECATED b/DEPRECATED index af553ae3a..c61a1c6ac 100644 --- a/DEPRECATED +++ b/DEPRECATED @@ -10,29 +10,32 @@ Bio::Tools::Blast::HSP 1.0 1.1 use Bio::Search::HSP::GenericHSP Bio::Tools::Blast::Sbjct 1.0 1.1 use Bio::Search::Hit::GenericHit Bio::Tools::Blast::HTML 1.0 1.1 use Bio::SearchIO::Writer::HTMLWriter Bio::Tools::SeqAnal 1.0 1.1 used only by deprecated Bio::Tools::Blast -Bio::Tools::WWW 1.1 1.1.1 Just a collection of links Bio::UnivAln 1.0 1.1 use Bio::SimpleAlign +Bio::Tools::WWW 1.1 1.1.1 Just a collection of links +Bio::Root::Err 1.5.2 1.5.2 Bio::Root* redundant classes +Bio::Root::Global 1.5.2 1.5.2 Bio::Root* redundant classes +Bio::Root::IOManager 1.5.2 1.5.2 Bio::Root* redundant classes +Bio::Root::Object 1.5.2 1.5.2 Bio::Root* redundant classes +Bio::Root::Utilities 1.5.2 1.5.2 Bio::Root* redundant classes +Bio::Root::Vector 1.5.2 1.5.2 Bio::Root* redundant classes +Bio::Root::Xref 1.5.2 1.5.2 Bio::Root* redundant classes Bio::Tools::RestrictionEnzyme 1.5 1.6 use Bio::Restriction Bio::Tools::BPlite 1.5 1.6 use Bio::SearchIO Bio::Tools::BPpsilite 1.5 1.6 use Bio::SearchIO Bio::Tools::BPbl2seq 1.5 1.6 use Bio::SearchIO Bio::Ontology::SimpleGOEngine 1.5.1 1.6 use Bio::Ontology::OBOEngine +Bio::Factory::ResultFactoryI 1.5.2 1.6 Superseded by Bio::Factory::ObjectFactory +Bio::Factory::HitFactoryI 1.5.2 1.6 Superseded by Bio::Factory::ObjectFactory +Bio::Graph 1.5.2 1.6 Superseded by bioperl-network +Bio::Tools::WebBlat 1.5.2 1.6 Requested that this not be maintained +Bio::DB::XEMBL 1.5.2 1.6 Service no longer available; use DBFetch +Bio::DB::XEMBLService 1.5.2 1.6 Service no longer available; use DBFetch Bio::Taxonomy 1.5.1 1.7 use Bio::Taxon & Bio::Tree::Tree Bio::Taxonomy::Node 1.5.1 1.7 renamed Bio::Taxon Bio::Taxonomy::Taxon 1.5.1 1.7 use Bio::Taxon Bio::Taxonomy::Tree 1.5.1 1.7 use Bio::Taxon & Bio::Tree::Tree Bio::Taxonomy::FactoryI 1.5.1 1.7 Redundant, no implementors Bio::Search::Processor 1.5.1 1.7 Superseded by Bio::SearchIO -Bio::Factory::ResultFactoryI 1.5.2 1.6 Superseded by Bio::Factory::ObjectFactory -Bio::Factory::HitFactoryI 1.5.2 1.6 Superseded by Bio::Factory::ObjectFactory -Bio::Graph 1.5.2 1.6 Superseded by bioperl-network -Bio::Root::Err 1.5.2 1.5.2 Bio::Root* redundant classes -Bio::Root::Global 1.5.2 1.5.2 Bio::Root* redundant classes -Bio::Root::IOManager 1.5.2 1.5.2 Bio::Root* redundant classes -Bio::Root::Object 1.5.2 1.5.2 Bio::Root* redundant classes -Bio::Root::Utilities 1.5.2 1.5.2 Bio::Root* redundant classes -Bio::Root::Vector 1.5.2 1.5.2 Bio::Root* redundant classes -Bio::Root::Xref 1.5.2 1.5.2 Bio::Root* redundant classes -Bio::Tools::WebBlat 1.5.2 1.5.3 Requested that this not be maintained -Bio::DB::XEMBL 1.5.2 ? Service no longer available; use DBFetch -Bio::DB::XEMBLService 1.5.2 ? Service no longer available; use DBFetch +Bio::Tools::RNAMotif 1.5.2 1.7 Superseded by Bio::SearchIO::rnamotif +Bio::Tools::Infernal 1.5.2 1.7 Superseded by Bio::SearchIO::infernal +Bio::Tools::ERPIN 1.5.2 1.7 Superseded by Bio::SearchIO::erpin -- 2.11.4.GIT