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Member Bio::EnsEMBL::Compara::BaseGenomicAlignSet::reference_slice ()
. Returntype : Bio::EnsEMBL::Slice object Exceptions : Caller : general Status : Stable

Member Bio::EnsEMBL::Compara::DBSQL::GenomicAlignBlockAdaptor::fetch_all_by_MethodLinkSpeciesSet_DnaFrag_GroupType ()

! Use Bio::EnsEMBL::Compara::GenomicAlignBlockAdaptor->fetch_all_by_MethodLinkSpeciesSet_DnaFrag method instead

Member Bio::EnsEMBL::Compara::DBSQL::MemberAdaptor::fetch_by_source_taxon ()
: use fetch_all_by_source_taxon instead

Member Bio::EnsEMBL::Compara::DBSQL::MethodLinkSpeciesSetAdaptor::fetch_all_by_genome_db_id ()
: Use the fetch_all_by_GenomeDB methodsinstead

Member Bio::EnsEMBL::Compara::DBSQL::MethodLinkSpeciesSetAdaptor::fetch_all_by_method_link_id ()
: Use the fetch_all_by_method_link_type method instead

Member Bio::EnsEMBL::Compara::DBSQL::MethodLinkSpeciesSetAdaptor::fetch_all_by_method_link_id_genome_db_id ()
: Use the fetch_all_by_method_link_type_GenomeDB method instead

Member Bio::EnsEMBL::Compara::DBSQL::MethodLinkSpeciesSetAdaptor::fetch_all_by_method_link_id_GenomeDB ()
: Use the fetch_all_by_method_link_type_GenomeDB method instead

Member Bio::EnsEMBL::Compara::DBSQL::MethodLinkSpeciesSetAdaptor::fetch_all_by_method_link_type_genome_db_id ()
: Use the fetch_all_by_method_link_type_GenomeDB method instead

Member Bio::EnsEMBL::Compara::DBSQL::MethodLinkSpeciesSetAdaptor::fetch_by_method_link_id_genome_db_ids ()
: Use the fetch_by_method_link_type_GenomeDBs method instead

Member Bio::EnsEMBL::Compara::DBSQL::MethodLinkSpeciesSetAdaptor::fetch_by_method_link_id_GenomeDBs ()
: Use the fetch_by_method_link_type_GenomeDBs method instead!

Member Bio::EnsEMBL::Compara::DnaFrag::end ()
! Use Bio::EnsEMBL::Compara::DnaFrag->length() method instead

Member Bio::EnsEMBL::Compara::DnaFrag::start ()
! All Bio::EnsEMBL::Compara::DnaFrag objects start in 1

Member Bio::EnsEMBL::Compara::GenomicAlignBlock::requesting_slice ()
! Use Bio::EnsEMBL::Compara::GenomicAlignBlock->reference_slice() method instead

Member Bio::EnsEMBL::Compara::GenomicAlignBlock::resulting_genomic_aligns ()
! Use Bio::EnsEMBL::Compara::GenomicAlignBlock->get_all_non_reference_genomic_align() method instead

Member Bio::EnsEMBL::Compara::GenomicAlignBlock::starting_genomic_align ()
! Use Bio::EnsEMBL::Compara::GenomicAlignBlock->reference_genomic_align() method instead

Member Bio::EnsEMBL::Compara::GenomicAlignBlock::starting_genomic_align_id ()
! Use Bio::EnsEMBL::Compara::GenomicAlignBlock->reference_genomic_align_id() method instead

Member Bio::EnsEMBL::Compara::GenomicAlignTree::genomic_align_array ()
Returntype : listref of Bio::EnsEMBL::Compara::GenomicAlign objects Exceptions : none Caller : general Status : Stable

Member Bio::EnsEMBL::Compara::GenomicAlignTree::get_all_GenomicAligns ()
Returntype : listref of Bio::EnsEMBL::Compara::GenomicAlign objects Exceptions : none Caller : general Status : Stable

Member Bio::EnsEMBL::Compara::SyntenyRegion::stable_id ()
: SyntenyRegions don't have any stable id.