[Bioperl-l] bioperl-live: audit of FIXME/???/TODO/etc and undef/die

[Torsten Seemann]

David,

>  From running the deobfuscator on bioperl-live, I've found some  
> formatting inconsistencies in the POD of some modules which are hard  
> for the deobfuscator to parse. I've corrected some of these in my  
> working (checked-out) copy of bioperl-live.

Please check them in.

I have written a script to audit all Perl modules to ensure the NAME in 
the POD matches the Perl module and has the correct capitilization.

% cd bioperl-live/maintenance
% ./check_NAMEs.pl

Here's the current buggy ones, before your commits AFAIK.

Bio::IdCollectionI
Bio::Location::SplitLocationI
Bio::Search::Result::PullResultI
Bio::Search::HSP::HmmpfamHSP
Bio::Search::Hit::HmmpfamHit
Bio::Expression::FeatureGroup::FeatureGroupMas50
Bio::Expression::FeatureSet::FeatureSetMas50
Bio::DB::EUtilities::Cookie
Bio::DB::GFF::Adaptor::berkeleydb
Bio::DB::GFF::Adaptor::biofetch_oracle
Bio::DB::GFF::Adaptor::dbi::pg_fts
Bio::DB::GFF::Adaptor::memory::feature_serializer
Bio::DB::SeqFeature::Store::bdb
Bio::DB::SeqFeature::Store::DBI::Iterator
Bio::Matrix::PSM::SiteMatrixI
Bio::Matrix::PSM::ProtPsm
Bio::Matrix::PSM::IO::psiblast
Bio::Matrix::PSM::IO::transfac
Bio::Matrix::PSM::IO::meme
Bio::Graphics::Util
Bio::Graphics::Glyph::ex
Bio::Graphics::Glyph::three_letters
Bio::Graphics::Glyph::arrow
Bio::Graphics::Glyph::ruler_arrow
Bio::Graphics::Glyph::flag
Bio::Phenotype::Measure
Bio::Phenotype::PhenotypeI
Bio::Phenotype::Phenotype
Bio::Phenotype::Correlate
Bio::Phenotype::OMIM::MiniMIMentry
Bio::Phenotype::OMIM::OMIMparser
Bio::Phenotype::OMIM::OMIMentry
Bio::Phenotype::OMIM::OMIMentryAllelicVariant
Bio::SeqIO::qual
Bio::SeqIO::genbank
Bio::OntologyIO::simplehierarchy
Bio::OntologyIO::InterProParser
Bio::OntologyIO::soflat
Bio::OntologyIO::dagflat
Bio::OntologyIO::obo
Bio::OntologyIO::goflat
Bio::OntologyIO::Handlers::InterProHandler
Bio::Tools::pICalculator
Bio::Tools::ECnumber
Bio::SeqFeature::Gene::GeneStructureI
Bio::SeqFeature::Gene::Poly_A_site
Bio::Seq::SeqFastaSpeedFactory
Bio::Ontology::RelationshipI
Bio::Ontology::TermI
Bio::Ontology::InterProTerm
Bio::Ontology::RelationshipType
Bio::Ontology::OBOterm
Bio::Ontology::OBOEngine
Bio::Ontology::PathI
Bio::Ontology::OntologyEngineI
Bio::Ontology::Path
Bio::Ontology::GOterm
Bio::Ontology::Term
Bio::Ontology::SimpleGOEngine
Bio::Ontology::Relationship
Bio::Ontology::SimpleGOEngine::GraphAdaptor
Bio::Ontology::SimpleGOEngine::GraphAdaptor02

-- 
Dr Torsten Seemann               http://www.vicbioinformatics.com
Victorian Bioinformatics Consortium, Monash University, Australia