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BioPerl-DB-1.006900
River stage zero No dependents
++
Author image Christopher Fields
and 1 contributors

Changes for version 1.6.900

  • [2958] - association table alias is not honored [maj]
  • [2624] - Bio::SeqFeature::Generic scores not persisted [cjfields]
  • [2573] - Ontology tests failing [cjfields]
  • [2572] - get_dblinks in load_seqdatabase.pl is deprecated [cjfields]
  • small doc fixes
  • 1.6.0, 1.6.1
  • [bug 2092] - Now uses correct Bio::Species syntax [1.6.1]
  • [bug 2757] - patch for error handling [maj]
  • small POD fixes

Documentation

drop_mysql_biosql_test_dbs
load_ontology.pl
load_seqdatabase.pl
add-term-annot.pl

Modules

Bio::BioEntry
DESCRIPTION of Object
Bio::DB::BioDB
class creating the adaptor factory for a particular database
Bio::DB::BioSQL::AnnotationCollectionAdaptor
DESCRIPTION of Object
Bio::DB::BioSQL::BaseDriver
DESCRIPTION of Object
Bio::DB::BioSQL::BasePersistenceAdaptor
DESCRIPTION of Object
Bio::DB::BioSQL::BioNamespaceAdaptor
DESCRIPTION of Object
Bio::DB::BioSQL::BiosequenceAdaptor
DESCRIPTION of Object
Bio::DB::BioSQL::ClusterAdaptor
DESCRIPTION of Object
Bio::DB::BioSQL::CommentAdaptor
DESCRIPTION of Object
Bio::DB::BioSQL::DBAdaptor
Object representing an instance of a bioperl database
Bio::DB::BioSQL::DBLinkAdaptor
DBLink Adaptor
Bio::DB::BioSQL::LocationAdaptor
DESCRIPTION of Object
Bio::DB::BioSQL::MultiDB
Bio::DB::BioSQL::OBDA
Bio::DB::BioSQL::OntologyAdaptor
DB Adaptor for Ontology objects
Bio::DB::BioSQL::Oracle::AnnotationCollectionAdaptorDriver
DESCRIPTION of Object
Bio::DB::BioSQL::Oracle::BasePersistenceAdaptorDriver
DESCRIPTION of Object
Bio::DB::BioSQL::Oracle::BiosequenceAdaptorDriver
DESCRIPTION of Object
Bio::DB::BioSQL::Oracle::PathAdaptorDriver
DESCRIPTION of Object
Bio::DB::BioSQL::Oracle::SpeciesAdaptorDriver
DESCRIPTION of Object
Bio::DB::BioSQL::Oracle::TermAdaptorDriver
DESCRIPTION of Object
Bio::DB::BioSQL::PathAdaptor
DESCRIPTION of Object
Bio::DB::BioSQL::Pg::AnnotationCollectionAdaptorDriver
DESCRIPTION of Object
Bio::DB::BioSQL::Pg::BasePersistenceAdaptorDriver
DESCRIPTION of Object
Bio::DB::BioSQL::Pg::BiosequenceAdaptorDriver
DESCRIPTION of Object
Bio::DB::BioSQL::Pg::PathAdaptorDriver
DESCRIPTION of Object
Bio::DB::BioSQL::Pg::SpeciesAdaptorDriver
DESCRIPTION of Object
Bio::DB::BioSQL::Pg::TermAdaptorDriver
DESCRIPTION of Object
Bio::DB::BioSQL::PrimarySeqAdaptor
DESCRIPTION of Object
Bio::DB::BioSQL::ReferenceAdaptor
DESCRIPTION of Object
Bio::DB::BioSQL::RelationshipAdaptor
DESCRIPTION of Object
Bio::DB::BioSQL::SeqAdaptor
DESCRIPTION of Object
Bio::DB::BioSQL::SeqFeatureAdaptor
DESCRIPTION of Object
Bio::DB::BioSQL::SimpleValueAdaptor
DESCRIPTION of Object
Bio::DB::BioSQL::SpeciesAdaptor
DESCRIPTION of Object
Bio::DB::BioSQL::TermAdaptor
DESCRIPTION of Object
Bio::DB::BioSQL::mysql::AnnotationCollectionAdaptorDriver
DESCRIPTION of Object
Bio::DB::BioSQL::mysql::BasePersistenceAdaptorDriver
DESCRIPTION of Object
Bio::DB::BioSQL::mysql::BiosequenceAdaptorDriver
DESCRIPTION of Object
Bio::DB::BioSQL::mysql::PathAdaptorDriver
DESCRIPTION of Object
Bio::DB::BioSQL::mysql::SpeciesAdaptorDriver
DESCRIPTION of Object
Bio::DB::BioSQL::mysql::TermAdaptorDriver
DESCRIPTION of Object
Bio::DB::CacheServer::SeqDB
Caching DB object
Bio::DB::DBAdaptorI
DESCRIPTION of Interface
Bio::DB::DBContextI
Interface for a class implementing a database context
Bio::DB::DBD
DESCRIPTION of Interface
Bio::DB::DBI
DESCRIPTION of Interface
Bio::DB::DBI::Oracle
DESCRIPTION of Object
Bio::DB::DBI::Pg
DESCRIPTION of Object
Bio::DB::DBI::Transaction
DESCRIPTION of Object
Bio::DB::DBI::TransactionListener
a simple transaction listener
Bio::DB::DBI::base
base class for drivers implementing Bio::DB::DBI
Bio::DB::DBI::mysql
DESCRIPTION of Object
Bio::DB::EasyArgv
Bio::DB::PersistenceAdaptorI
DESCRIPTION of Interface
Bio::DB::Persistent::BioNamespace
DESCRIPTION of Object
Bio::DB::Persistent::ObjectRellMapperI
DESCRIPTION of Interface
Bio::DB::Persistent::PersistentObject
makes a given object persistent
Bio::DB::Persistent::PersistentObjectFactory
DESCRIPTION of Object
Bio::DB::Persistent::PrimarySeq
Proxy object for database PrimarySeq representations
Bio::DB::Persistent::Seq
Proxy object for database PrimarySeq representations
Bio::DB::Persistent::SeqFeature
Proxy object for database SeqFeatureI representations
Bio::DB::PersistentObjectI
DESCRIPTION of Interface
Bio::DB::Query::AbstractQuery
Abstract Query class
Bio::DB::Query::BioQuery
Object representing a query on a bioperldb
Bio::DB::Query::DBQueryResult
DESCRIPTION of Object
Bio::DB::Query::PrebuiltResult
DESCRIPTION of Object
Bio::DB::Query::QueryConstraint
a constraint on a variable value in a query
Bio::DB::Query::QueryResultI
DESCRIPTION of Interface
Bio::DB::Query::SqlGenerator
Object representing an SQL Query
Bio::DB::Query::SqlQuery
Object representing an SQL Query
Bio::DB::SimpleDBContext
a base implementation of Bio::DB::DBContextI

Other files