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A | B | C | D | E | F | G | I | K | L | M | O | P | Q | R | S | T | U
  A  
DBEntryAdaptor (Bio::EnsEMBL::DBSQL)   MappedSliceContainer (Bio::EnsEMBL)   ScriptUtils (Bio::EnsEMBL::Utils)   
AedesAegypti (Bio::EnsEMBL::IdMapping::StableIdGenerator)   DBLoader (Bio::EnsEMBL)   Mapper (Bio::EnsEMBL)   SeqDumper (Bio::EnsEMBL::Utils)   
AlignStrainSlice (Bio::EnsEMBL)   DensityFeature (Bio::EnsEMBL)   MappingList (Bio::EnsEMBL::IdMapping)   SeqEdit (Bio::EnsEMBL)   
Analysis (Bio::EnsEMBL)   DensityFeatureAdaptor (Bio::EnsEMBL::DBSQL)   Marker (Bio::EnsEMBL::Map)   SeqFeature (Bio::EnsEMBL)   
AnalysisAdaptor (Bio::EnsEMBL::DBSQL)   DensityFeatureSet (Bio::EnsEMBL)   MarkerAdaptor (Bio::EnsEMBL::Map::DBSQL)   SeqFeatureI (Bio::EnsEMBL)   
ApiVersion (Bio::EnsEMBL)   DensityType (Bio::EnsEMBL)   MarkerFeature (Bio::EnsEMBL::Map)   SeqRegionCache (Bio::EnsEMBL::Utils)   
Archiver (Bio::EnsEMBL::IdMapping)   DensityTypeAdaptor (Bio::EnsEMBL::DBSQL)   MarkerFeatureAdaptor (Bio::EnsEMBL::Map::DBSQL)   SeqRegionSynonym (Bio::EnsEMBL)   
ArchiveStableId (Bio::EnsEMBL)   Ditag (Bio::EnsEMBL::Map)   MarkerSynonym (Bio::EnsEMBL::Map)   SeqRegionSynonymAdaptor (Bio::EnsEMBL::DBSQL)   
ArchiveStableIdAdaptor (Bio::EnsEMBL::DBSQL)   DitagAdaptor (Bio::EnsEMBL::Map::DBSQL)   MergedAdaptor (Bio::EnsEMBL::DBSQL)   Sequence (Bio::EnsEMBL::Utils)   
Argument (Bio::EnsEMBL::Utils)   DitagFeature (Bio::EnsEMBL::Map)   MetaContainer (Bio::EnsEMBL::DBSQL)   SequenceAdaptor (Bio::EnsEMBL::DBSQL)   
AssemblyExceptionFeature (Bio::EnsEMBL)   DitagFeatureAdaptor (Bio::EnsEMBL::Map::DBSQL)   MetaCoordContainer (Bio::EnsEMBL::DBSQL)   Serialisable (Bio::EnsEMBL::IdMapping)   
AssemblyExceptionFeatureAdaptor (Bio::EnsEMBL::DBSQL)   DnaAlignFeatureAdaptor (Bio::EnsEMBL::DBSQL)   MiscFeature (Bio::EnsEMBL)   IO::Serializer (Bio::EnsEMBL::Utils)   
AssemblyMapper (Bio::EnsEMBL)   DnaDnaAlignFeature (Bio::EnsEMBL)   MiscFeatureAdaptor (Bio::EnsEMBL::DBSQL)   SimpleFeature (Bio::EnsEMBL)   
AssemblyMapperAdaptor (Bio::EnsEMBL::DBSQL)   DnaPepAlignFeature (Bio::EnsEMBL)   MiscSet (Bio::EnsEMBL)   SimpleFeatureAdaptor (Bio::EnsEMBL::DBSQL)   
AssemblyProjector (Bio::EnsEMBL::Utils)   
  E  
MiscSetAdaptor (Bio::EnsEMBL::DBSQL)   Slice (Bio::EnsEMBL::Utils)   
AssemblySliceAdaptor (Bio::EnsEMBL::DBSQL)   EasyArgv (Bio::EnsEMBL::Utils)   
  O  
Slice (Bio::EnsEMBL)   
Attribute (Bio::EnsEMBL)   Converter::ens_bio (Bio::EnsEMBL::Utils)   OntologyDBAdaptor (Bio::EnsEMBL::DBSQL)   SliceAdaptor (Bio::EnsEMBL::DBSQL)   
AttributeAdaptor (Bio::EnsEMBL::DBSQL)   Converter::ens_bio_featurePair (Bio::EnsEMBL::Utils)   OntologyTerm (Bio::EnsEMBL)   SNP (Bio::EnsEMBL)   
  B  
Converter::ens_bio_seqFeature (Bio::EnsEMBL::Utils)   OntologyTermAdaptor (Bio::EnsEMBL::DBSQL)   SOTermAdaptor (Bio::EnsEMBL::DBSQL)   
BaseAdaptor (Bio::EnsEMBL::DBSQL)   InternalIdMapper::EnsemblExonGeneric (Bio::EnsEMBL::IdMapping)   OntologyXref (Bio::EnsEMBL)   SplicingEvent (Bio::EnsEMBL)   
BaseAlignFeature (Bio::EnsEMBL)   InternalIdMapper::EnsemblGeneGeneric (Bio::EnsEMBL::IdMapping)   Operon (Bio::EnsEMBL)   SplicingEventAdaptor (Bio::EnsEMBL::DBSQL)   
BaseAlignFeatureAdaptor (Bio::EnsEMBL::DBSQL)   EnsemblGeneric (Bio::EnsEMBL::IdMapping::StableIdGenerator)   OperonAdaptor (Bio::EnsEMBL::DBSQL)   SplicingEventFeature (Bio::EnsEMBL)   
BaseFeatureAdaptor (Bio::EnsEMBL::DBSQL)   InternalIdMapper::EnsemblTranscriptGeneric (Bio::EnsEMBL::IdMapping)   OperonTranscript (Bio::EnsEMBL)   SplicingEventFeatureAdaptor (Bio::EnsEMBL::DBSQL)   
InternalIdMapper::BaseMapper (Bio::EnsEMBL::IdMapping)   Entry (Bio::EnsEMBL::IdMapping)   OperonTranscriptAdaptor (Bio::EnsEMBL::DBSQL)   SplicingTranscriptPair (Bio::EnsEMBL)   
BaseMetaContainer (Bio::EnsEMBL::DBSQL)   Eprof (Bio::EnsEMBL::Utils)   
  P  
SplicingTranscriptPairAdaptor (Bio::EnsEMBL::DBSQL)   
BaseObject (Bio::EnsEMBL::IdMapping)   EprofStack (Bio::EnsEMBL::Utils)   PaddedSlice (Bio::EnsEMBL)   SqlHelper (Bio::EnsEMBL::Utils)   
BinValue (Bio::EnsEMBL::DensityPlot)   Exception (Bio::EnsEMBL::Utils)   Mapper::Pair (Bio::EnsEMBL)   StableIdEvent (Bio::EnsEMBL)   
BinValueSet (Bio::EnsEMBL::DensityPlot)   Exon (Bio::EnsEMBL)   Analysis::PairAlign (Bio::EnsEMBL)   StableIdHistoryTree (Bio::EnsEMBL)   
Converter::bio_ens (Bio::EnsEMBL::Utils)   ExonAdaptor (Bio::EnsEMBL::DBSQL)   PepDnaAlignFeature (Bio::EnsEMBL)   StableIdMapper (Bio::EnsEMBL::IdMapping)   
Converter::bio_ens_analysis (Bio::EnsEMBL::Utils)   ExonScoreBuilder (Bio::EnsEMBL::IdMapping)   PolyA (Bio::EnsEMBL::Utils)   StatementHandle (Bio::EnsEMBL::DBSQL)   
Converter::bio_ens_exon (Bio::EnsEMBL::Utils)   ExternalFeatureAdaptor (Bio::EnsEMBL::External)   PredictionExon (Bio::EnsEMBL)   Storable (Bio::EnsEMBL)   
Converter::bio_ens_featurePair (Bio::EnsEMBL::Utils)   ExternalFeatureFactoryI (Bio::EnsEMBL::DB)   PredictionExonAdaptor (Bio::EnsEMBL::DBSQL)   StrainSlice (Bio::EnsEMBL)   
Converter::bio_ens_gene (Bio::EnsEMBL::Utils)   
  F  
PredictionTranscript (Bio::EnsEMBL)   StrainSliceAdaptor (Bio::EnsEMBL::DBSQL)   
Converter::bio_ens_hit (Bio::EnsEMBL::Utils)   IO::FASTASerializer (Bio::EnsEMBL::Utils)   PredictionTranscriptAdaptor (Bio::EnsEMBL::DBSQL)   SupportingFeatureAdaptor (Bio::EnsEMBL::DBSQL)   
Converter::bio_ens_hsp (Bio::EnsEMBL::Utils)   Feature (Bio::EnsEMBL)   PristionchusPacificus (Bio::EnsEMBL::IdMapping::StableIdGenerator)   SyntenyFramework (Bio::EnsEMBL::IdMapping)   
Converter::bio_ens_predictionExon (Bio::EnsEMBL::Utils)   FeaturePair (Bio::EnsEMBL)   Analysis::Programs (Bio::EnsEMBL)   SyntenyRegion (Bio::EnsEMBL::IdMapping)   
Converter::bio_ens_predictionGene (Bio::EnsEMBL::Utils)   IO::FeatureSerializer (Bio::EnsEMBL::Utils)   ProjectionSegment (Bio::EnsEMBL)   
  T  
Converter::bio_ens_seqFeature (Bio::EnsEMBL::Utils)   FileAdaptor (Bio::EnsEMBL::DBFile)   ProteinAlignFeatureAdaptor (Bio::EnsEMBL::DBSQL)   TestUtils   
Converter::bio_ens_transcript (Bio::EnsEMBL::Utils)   
  G  
ProteinFeature (Bio::EnsEMBL)   TinyExon (Bio::EnsEMBL::IdMapping)   
BiotypeMapper (Bio::EnsEMBL::Utils)   Mapper::Gap (Bio::EnsEMBL)   ProteinFeatureAdaptor (Bio::EnsEMBL::DBSQL)   TinyFeature (Bio::EnsEMBL::IdMapping)   
BitString (Bio::EnsEMBL::Utils)   Gene (Bio::EnsEMBL::Utils::VegaCuration)   Proxy (Bio::EnsEMBL::Utils)   TinyGene (Bio::EnsEMBL::IdMapping)   
BlastAdaptor (Bio::EnsEMBL::External)   Gene (Bio::EnsEMBL)   ProxyDBConnection (Bio::EnsEMBL::DBSQL)   TinyTranscript (Bio::EnsEMBL::IdMapping)   
  C  
GeneAdaptor (Bio::EnsEMBL::DBSQL)   ProxySNPAdaptor (Bio::EnsEMBL::DBSQL)   TinyTranslation (Bio::EnsEMBL::IdMapping)   
Cache (Bio::EnsEMBL::Utils)   GeneScoreBuilder (Bio::EnsEMBL::IdMapping)   
  Q  
TopLevelAssemblyMapper (Bio::EnsEMBL)   
Cache (Bio::EnsEMBL::IdMapping)   IO::GFFSerializer (Bio::EnsEMBL::Utils)   Qtl (Bio::EnsEMBL::Map)   Transcript (Bio::EnsEMBL)   
ChainedAssemblyMapper (Bio::EnsEMBL)   GOTermAdaptor (Bio::EnsEMBL::DBSQL)   QtlAdaptor (Bio::EnsEMBL::Map::DBSQL)   Transcript (Bio::EnsEMBL::Utils::VegaCuration)   
CigarString (Bio::EnsEMBL::Utils)   
  I  
QtlFeature (Bio::EnsEMBL::Map)   TranscriptAdaptor (Bio::EnsEMBL::DBSQL)   
CircularSlice (Bio::EnsEMBL)   IdentityXref (Bio::EnsEMBL)   QtlFeatureAdaptor (Bio::EnsEMBL::Map::DBSQL)   TranscriptAlleles (Bio::EnsEMBL::Utils)   
CliHelper (Bio::EnsEMBL::Utils)   Mapper::IndelCoordinate (Bio::EnsEMBL)   
  R  
TranscriptFactory (Bio::EnsEMBL)   
CollectionAdaptor (Bio::EnsEMBL::DBFile)   Mapper::IndelPair (Bio::EnsEMBL)   Mapper::RangeRegistry (Bio::EnsEMBL)   TranscriptMapper (Bio::EnsEMBL)   
Collector (Bio::EnsEMBL::Utils)   IndividualSlice (Bio::EnsEMBL)   Registry (Bio::EnsEMBL)   TranscriptScoreBuilder (Bio::EnsEMBL::IdMapping)   
CompressedSequenceAdaptor (Bio::EnsEMBL::DBSQL)   IndividualSliceFactory (Bio::EnsEMBL)   RepeatConsensus (Bio::EnsEMBL)   TranscriptSNPs (Bio::EnsEMBL::Utils)   
ConfigRegistry (Bio::EnsEMBL::Utils)   InternalIdMapper (Bio::EnsEMBL::IdMapping)   RepeatConsensusAdaptor (Bio::EnsEMBL::DBSQL)   TranscriptSupportingFeatureAdaptor (Bio::EnsEMBL::DBSQL)   
ConfParser (Bio::EnsEMBL::Utils)   Intron (Bio::EnsEMBL)   RepeatFeature (Bio::EnsEMBL)   Translation (Bio::EnsEMBL::Utils::VegaCuration)   
ConversionSupport (Bio::EnsEMBL::Utils)   IO (Bio::EnsEMBL::Utils)   RepeatFeatureAdaptor (Bio::EnsEMBL::DBSQL)   Translation (Bio::EnsEMBL)   
Converter (Bio::EnsEMBL::Utils)   Iterator (Bio::EnsEMBL::Utils)   RepeatMaskedSlice (Bio::EnsEMBL)   TranslationAdaptor (Bio::EnsEMBL::DBSQL)   
Mapper::Coordinate (Bio::EnsEMBL)   
  K  
IO::ReportSerializer (Bio::EnsEMBL::Utils)   
  U  
CoordSystem (Bio::EnsEMBL)   KaryotypeBand (Bio::EnsEMBL)   ResultAnalyser (Bio::EnsEMBL::IdMapping)   UnconventionalTranscriptAssociation (Bio::EnsEMBL)   
CoordSystemAdaptor (Bio::EnsEMBL::DBSQL)   KaryotypeBandAdaptor (Bio::EnsEMBL::DBSQL)   Root (Bio::EnsEMBL)   UnconventionalTranscriptAssociationAdaptor (Bio::EnsEMBL::DBSQL)   
  D  
  L  
  S  
Mapper::Unit (Bio::EnsEMBL)   
DataFile (Bio::EnsEMBL)   Logger (Bio::EnsEMBL::Utils)   Scalar (Bio::EnsEMBL::Utils)   UnmappedObject (Bio::EnsEMBL)   
DataFileAdaptor (Bio::EnsEMBL::DBSQL)   LRGSlice (Bio::EnsEMBL)   SchemaConversion (Bio::EnsEMBL::Utils)   UnmappedObjectAdaptor (Bio::EnsEMBL::DBSQL)   
DBAdaptor (Bio::EnsEMBL::DBSQL)   
  M  
ScoreBuilder (Bio::EnsEMBL::IdMapping)   Upstream (Bio::EnsEMBL)   
DBConnection (Bio::EnsEMBL::DBSQL)   MapLocation (Bio::EnsEMBL::Map)   ScoredMappingMatrix (Bio::EnsEMBL::IdMapping)   URI (Bio::EnsEMBL::Utils)   
DBEntry (Bio::EnsEMBL)   MappedSlice (Bio::EnsEMBL)   
A | B | C | D | E | F | G | I | K | L | M | O | P | Q | R | S | T | U