[Bioperl-l] tests needed!

[Heikki Lehvaslaiho]

The new maintenance/modules.pl script tells me that bioperl core module
count is:

Instance : 375
Interface:  95
Component: 149
--------------
Total    : 619

Running it with --untested option, gives me a list of 200 modules (see
below). This means that we still have a way to go in testing the
modules. 

The --untested option compares module names to those 'use'd in t/*.t
files, so it includes a fair number of modules that are called from
other modules. Maybe there should be an exclusion list for known cases
in the program... Feel free to improve the program as you see fit.


PLEASE, have a look at the list and if you think you are responsible,
please write tests for them and, preferably, for all public methods in
them.

If someone want to start contributing to bioperl, writing tests is a
great way to start and get the feel how everything works - or does not
work!

	-Heikki



Bio::Align::PairwiseStatistics
Bio::Align::Utilities
Bio::Annotation::AnnotationFactory
Bio::Annotation::TypeManager
Bio::Assembly::Contig
Bio::Assembly::ContigAnalysis
Bio::Assembly::IO
Bio::Assembly::Scaffold
Bio::Biblio::Article
Bio::Biblio::BiblioBase
Bio::Biblio::Book
Bio::Biblio::BookArticle
Bio::Biblio::Journal
Bio::Biblio::JournalArticle
Bio::Biblio::MedlineArticle
Bio::Biblio::MedlineBook
Bio::Biblio::MedlineBookArticle
Bio::Biblio::MedlineJournal
Bio::Biblio::MedlineJournalArticle
Bio::Biblio::Organisation
Bio::Biblio::Patent
Bio::Biblio::Person
Bio::Biblio::Proceeding
Bio::Biblio::Provider
Bio::Biblio::PubmedArticle
Bio::Biblio::PubmedBookArticle
Bio::Biblio::PubmedJournalArticle
Bio::Biblio::Ref
Bio::Biblio::Service
Bio::Biblio::TechReport
Bio::Biblio::Thesis
Bio::Biblio::WebResource
Bio::DB::Ace
Bio::DB::BioFetch
Bio::DB::DBFetch
Bio::DB::EMBL
Bio::DB::Failover
Bio::DB::FileCache
Bio::DB::Flat
Bio::DB::Flat::BDB
Bio::DB::Flat::BinarySearch
Bio::DB::GDB
Bio::DB::GFF::Aggregator
Bio::DB::GFF::Featname
Bio::DB::GFF::Feature
Bio::DB::GFF::Homol
Bio::DB::GFF::RelSegment
Bio::DB::GFF::Segment
Bio::DB::GFF::Typename
Bio::DB::GFF::Util::Binning
Bio::DB::GFF::Util::Rearrange
Bio::DB::GenBank
Bio::DB::GenPept
Bio::DB::NCBIHelper
Bio::DB::Query::GenBank
Bio::DB::Query::WebQuery
Bio::DB::RefSeq
Bio::DB::Registry
Bio::DB::SwissProt
Bio::DB::Universal
Bio::DB::XEMBL
Bio::DB::XEMBLService
Bio::Expression::FeatureSet
Bio::Factory::BlastHitFactory
Bio::Factory::BlastResultFactory
Bio::Factory::DriverFactory
Bio::Factory::GenericObjectFactory
Bio::Factory::ObjectFactory
Bio::Graphics
Bio::Graphics::Feature
Bio::Graphics::FeatureFile
Bio::Graphics::Glyph
Bio::Graphics::Glyph::Factory
Bio::Graphics::Panel
Bio::Graphics::Util
Bio::Index::Abstract
Bio::Index::AbstractSeq
Bio::Index::Blast
Bio::Index::Fastq
Bio::LiveSeq::AARange
Bio::LiveSeq::DNA
Bio::LiveSeq::Exon
Bio::LiveSeq::Gene
Bio::LiveSeq::IO::BioPerl
Bio::LiveSeq::IO::Loader
Bio::LiveSeq::IO::SRS
Bio::LiveSeq::Intron
Bio::LiveSeq::Mutator
Bio::LiveSeq::Prim_Transcript
Bio::LiveSeq::Range
Bio::LiveSeq::Repeat_Region
Bio::LiveSeq::Repeat_Unit
Bio::LiveSeq::Transcript
Bio::LiveSeq::Translation
Bio::Location::Atomic
Bio::Location::AvWithinCoordPolicy
Bio::Location::NarrowestCoordPolicy
Bio::Location::WidestCoordPolicy
Bio::Map::OrderedPosition
Bio::Map::OrderedPositionWithDistance
Bio::Ontology::InterProTerm
Bio::Ontology::OntologyStore
Bio::Ontology::Path
Bio::Ontology::RelationshipFactory
Bio::Ontology::SimpleGOEngine
Bio::OntologyIO::Handlers::InterProHandler
Bio::OntologyIO::InterProParser
Bio::PopGen::Marker
Bio::Root::Err
Bio::Root::Global
Bio::Root::HTTPget
Bio::Root::IOManager
Bio::Root::Object
Bio::Root::Utilities
Bio::Root::Vector
Bio::Root::Version
Bio::Root::Xref
Bio::Search::BlastUtils
Bio::Search::GenericDatabase
Bio::Search::HSP::BlastHSP
Bio::Search::HSP::FastaHSP
Bio::Search::HSP::GenericHSP
Bio::Search::HSP::HMMERHSP
Bio::Search::HSP::HSPFactory
Bio::Search::HSP::HSPI
Bio::Search::HSP::PsiBlastHSP
Bio::Search::HSP::WABAHSP
Bio::Search::Hit::BlastHit
Bio::Search::Hit::Fasta
Bio::Search::Hit::GenericHit
Bio::Search::Hit::HMMERHit
Bio::Search::Hit::HitFactory
Bio::Search::Hit::PsiBlastHit
Bio::Search::Iteration::GenericIteration
Bio::Search::Processor
Bio::Search::Result::BlastResult
Bio::Search::Result::GenericResult
Bio::Search::Result::HMMERResult
Bio::Search::Result::PsiBlastResult
Bio::Search::Result::ResultFactory
Bio::Search::Result::WABAResult
Bio::Search::SearchUtils
Bio::SearchDist
Bio::SearchIO::FastHitEventBuilder
Bio::SearchIO::IteratedSearchResultEventBuilder
Bio::SearchIO::SearchResultEventBuilder
Bio::SearchIO::Writer::HSPTableWriter
Bio::SearchIO::Writer::ResultTableWriter
Bio::SearchIO::Writer::TextResultWriter
Bio::Seq::BaseSeqProcessor
Bio::Seq::SeqBuilder
Bio::Seq::SeqFactory
Bio::Seq::SeqFastaSpeedFactory
Bio::SeqFeature::Collection
Bio::SeqFeature::Gene::Intron
Bio::SeqFeature::Gene::NC_Feature
Bio::SeqFeature::Gene::Promoter
Bio::SeqFeature::PositionProxy
Bio::SeqFeature::Similarity
Bio::SeqIO::FTHelper
Bio::Structure::SecStr::DSSP::Res
Bio::Structure::SecStr::STRIDE::Res
Bio::Taxonomy
Bio::Taxonomy::Taxon
Bio::Taxonomy::Tree
Bio::Tools::AlignFactory
Bio::Tools::AnalysisResult
Bio::Tools::BPlite::HSP
Bio::Tools::BPlite::Sbjct
Bio::Tools::Blast::HSP
Bio::Tools::Blast::HTML
Bio::Tools::Blast::Sbjct
Bio::Tools::Blat
Bio::Tools::Coil
Bio::Tools::ESTScan
Bio::Tools::Eponine
Bio::Tools::Gel
Bio::Tools::Grail
Bio::Tools::Hmmpfam
Bio::Tools::Phylo::Molphy
Bio::Tools::Phylo::Molphy::Result
Bio::Tools::Phylo::PAML
Bio::Tools::Phylo::PAML::Result
Bio::Tools::Prediction::Exon
Bio::Tools::Prediction::Gene
Bio::Tools::Prints
Bio::Tools::Profile
Bio::Tools::Pseudowise
Bio::Tools::Run::RemoteBlast
Bio::Tools::Run::WrapperBase
Bio::Tools::Seg
Bio::Tools::SeqAnal
Bio::Tools::Signalp
Bio::Tools::Sim4::Exon
Bio::Tools::Tmhmm
Bio::Tools::WWW
Bio::Tree::NodeNHX
Bio::Tree::Tree
Bio::TreeIO::TreeEventBuilder
Bio::Variation::SNP