Identifier Index

[ A B C D E F G H I J K L M N O P Q R S T U V W X Y Z _ ]

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__abs__() (in Confidence)	__package__ (in Bio.Graphics)	_gaf20iterator() (in Bio.UniProt.GOA)
__add__() (in MultipleSeqAlignment)	__package__ (in Bio.HMM.DynamicProgramming)	_gen_random_array() (in Bio.HMM.MarkovModel)
__add__() (in Chain)	__package__ (in Bio.HMM.MarkovModel)	_genbank_convert_fasta() (in Bio.SeqIO._convert)
__add__() (in Vector)	__package__ (in Bio.HMM.Trainer)	_GenePopCommandline (in Bio.PopGen.GenePop.Controller)
__add__() (in Confidence)	__package__ (in Bio.HMM.Utilities)	_generate_full_id() (in Entity)
__add__() (in RestrictionBatch)	__package__ (in Bio.HMM)	_genes() (in Record)
__add__() (in RestrictionType)	__package__ (in Bio.Index)	_get_a() (in ColorSpiral)
__add__() (in SeqMap)	__package__ (in Bio.KDTree.KDTree')	_get_aa_regex() (in Bio.codonalign)
__add__() (in MutableSeq)	__package__ (in Bio.KDTree._CKDTree)	_get_all_letters() (in SummaryInfo)
__add__() (in Seq)	__package__ (in Bio.KDTree)	_get_aln_slice_coords() (in Bio.SearchIO.FastaIO)
__add__() (in UnknownSeq)	__package__ (in Bio.KEGG.Compound)	_get_annotation_str() (in _InsdcWriter)
__add__() (in CompoundLocation)	__package__ (in Bio.KEGG.Enzyme)	_get_atom_line() (in PDBIO)
__add__() (in FeatureLocation)	__package__ (in Bio.KEGG.Gene)	_get_atom_radius() (in Bio.PDB.ResidueDepth')
__add__() (in SeqRecord)	__package__ (in Bio.KEGG.KGML.KGML_parser)	_get_attribute_value() (in Bio.SeqIO.SnapGeneIO)
__add__() (in SeqMat)	__package__ (in Bio.KEGG.KGML.KGML_pathway)	_get_b() (in ColorSpiral)
__add__() (in CodonAlignment)	__package__ (in Bio.KEGG.KGML)	_get_base_alphabet() (in Bio.Alphabet)
__add__() (in PlateRecord)	__package__ (in Bio.KEGG.Map)	_get_base_letters() (in SummaryInfo)
__add__() (in WellRecord)	__package__ (in Bio.KEGG.REST)	_get_base_replacements() (in SummaryInfo)
__add__() (in DBSeq)	__package__ (in Bio.KEGG)	_get_bioentry_dbxref() (in DatabaseLoader)
__add_compounds() (in KGMLCanvas)	__package__ (in Bio.LogisticRegression)	_get_block_coords() (in Bio.SearchIO.ExonerateIO.exonerate_text)
__add_genes() (in KGMLCanvas)	__package__ (in Bio.MarkovModel)	_get_blocks() (in Bio.SearchIO.ExonerateIO.exonerate_text)
__add_graphics() (in KGMLCanvas)	__package__ (in Bio.MaxEntropy)	_get_cb() (in HSExposureCA)
__add_labels() (in KGMLCanvas)	__package__ (in Bio.Medline)	_get_cb() (in HSExposureCB)
__add_maps() (in KGMLCanvas)	__package__ (in Bio.NMR.NOEtools)	_get_cb() (in _AbstractHSExposure)
__add_orthologs() (in KGMLCanvas)	__package__ (in Bio.NMR)	_get_child_as() (in Bio.Phylo.PhyloXMLIO)
__add_reaction_entries() (in KGMLCanvas)	__package__ (in Bio.NMR.xpktools)	_get_child_text() (in Bio.Phylo.PhyloXMLIO)
__add_relations() (in KGMLCanvas)	__package__ (in Bio.NaiveBayes)	_get_child_value() (in Bio.SeqIO.SnapGeneIO)
__and__() (in _BitString)	__package__ (in Bio.Nexus.Nexus)	_get_children_as() (in Bio.Phylo.PhyloXMLIO)
__array_finalize__() (in Array)	__package__ (in Bio.Nexus.Nodes)	_get_children_text() (in Bio.Phylo.PhyloXMLIO)
__array_prepare__() (in Array)	__package__ (in Bio.Nexus.StandardData)	_get_codon2codon_matrix() (in Bio.codonalign.codonalignment)
__array_ufunc__() (in Array)	__package__ (in Bio.Nexus.Trees)	_get_codon_fold() (in Bio.codonalign.codonseq)
__array_wrap__() (in Array)	__package__ (in Bio.Nexus)	_get_codon_list() (in Bio.codonalign.codonseq)
__bool__() (in Clade)	__package__ (in Bio.Nexus.cnexus)	_get_codon_rec() (in Bio.codonalign)
__bool__() (in Hit)	__package__ (in Bio.PDB.AbstractPropertyMap)	_get_color() (in Clade)
__bool__() (in HSP)	__package__ (in Bio.PDB.Atom)	_get_cols() (in Bio.SearchIO._legacy.NCBIStandalone)
__bool__() (in QueryResult)	__package__ (in Bio.PDB.Chain)	_get_column_info_content() (in SummaryInfo)
__bool__() (in SeqFeature)	__package__ (in Bio.PDB.DSSP')	_get_command_lines() (in Bio.Nexus.Nexus)
__bool__() (in SeqRecord)	__package__ (in Bio.PDB.Dice)	_get_comment() (in Bio.Phylo.NewickIO)
__call__() (in AbstractCommandline)	__package__ (in Bio.PDB.Entity)	_get_confidence() (in Clade)
__call__() (in affine_penalty)	__package__ (in Bio.PDB.FragmentMapper')	_get_confidence() (in Phylogeny)
__call__() (in dictionary_match)	__package__ (in Bio.PDB.HSExposure)	_get_convert_formats() (in Bio.TogoWS)
__call__() (in identity_match)	__package__ (in Bio.PDB.MMCIF2Dict)	_get_coords() (in HSP)
__check_data() (in Bio.Cluster)	__package__ (in Bio.PDB.MMCIFParser')	_get_coords() (in Bio.Wise.dnal)
__check_distancematrix() (in Bio.Cluster)	__package__ (in Bio.PDB.Model)	_get_data_division() (in EmblWriter)
__check_existing_db() (in MafIndex)	__package__ (in Bio.PDB.NACCESS)	_get_data_division() (in GenBankWriter)
__check_index() (in Bio.Cluster)	__package__ (in Bio.PDB.NeighborSearch')	_get_date() (in GenBankWriter)
__check_initialid() (in Bio.Cluster)	__package__ (in Bio.PDB.PDBExceptions)	_get_dbxref_id() (in DatabaseLoader)
__check_mask() (in Bio.Cluster)	__package__ (in Bio.PDB.PDBIO')	_get_entry_dbs() (in Bio.TogoWS)
__check_weight() (in Bio.Cluster)	__package__ (in Bio.PDB.PDBList')	_get_entry_fields() (in Bio.TogoWS)
__cmp__() (in PairwiseAlignment)	__package__ (in Bio.PDB.PDBParser')	_get_entry_formats() (in Bio.TogoWS)
__contains__() (in Array)	__package__ (in Bio.PDB.PSEA)	_get_fields() (in Bio.TogoWS)
__contains__() (in Chain)	__package__ (in Bio.PDB.Polypeptide)	_get_frag_frame() (in BlastTabParser)
__contains__() (in Crystal)	__package__ (in Bio.PDB.QCPSuperimposer)	_get_frag_strand() (in BlastTabParser)
__contains__() (in AmbiguousForwardTable)	__package__ (in Bio.PDB.QCPSuperimposer.qcprotmodule)	_get_fragments_coord() (in Bio.SearchIO.ExonerateIO._base)
__contains__() (in _IndexedSeqFileDict)	__package__ (in Bio.PDB.Residue)	_get_fragments_phase() (in Bio.SearchIO.ExonerateIO._base)
__contains__() (in _SQLiteManySeqFilesDict)	__package__ (in Bio.PDB.ResidueDepth')	_get_gap_char() (in SummaryInfo)
__contains__() (in AbstractPropertyMap)	__package__ (in Bio.PDB.Selection)	_get_gly_cb_vector() (in _AbstractHSExposure)
__contains__() (in Chain)	__package__ (in Bio.PDB.Structure)	_get_header() (in PDBParser)
__contains__() (in DisorderedEntityWrapper)	__package__ (in Bio.PDB.StructureAlignment')	_get_id() (in Chain)
__contains__() (in Entity)	__package__ (in Bio.PDB.StructureBuilder)	_get_id() (in BlastTabParser)
__contains__() (in FragmentMapper)	__package__ (in Bio.PDB.Superimposer')	_get_illumina_quality_str() (in Bio.SeqIO.QualityIO)
__contains__() (in Vector)	__package__ (in Bio.PDB)	_get_indices() (in Nexus)
__contains__() (in Events)	__package__ (in Bio.PDB.kdtrees)	_get_inter_coords() (in Bio.SearchIO.ExonerateIO.exonerate_text)
__contains__() (in RestrictionBatch)	__package__ (in Bio.PDB.mmcifio)	_get_jitter() (in ColorSpiral)
__contains__() (in Hit)	__package__ (in Bio.PDB.parse_pdb_header')	_get_journal() (in Bio.PDB.parse_pdb_header')
__contains__() (in HSP)	__package__ (in Bio.PDB.vectors)	_get_kappa_t() (in Bio.codonalign.codonseq)
__contains__() (in QueryResult)	__package__ (in Bio.Pathway.Rep.Graph)	_get_label_asym_id() (in MMCIFIO)
__contains__() (in Seq)	__package__ (in Bio.Pathway.Rep.MultiGraph)	_get_letter_freqs() (in SummaryInfo)
__contains__() (in CompoundLocation)	__package__ (in Bio.Pathway.Rep)	_get_location_operator() (in SeqFeature)
__contains__() (in FeatureLocation)	__package__ (in Bio.Pathway)	_get_meta_data() (in StockholmIterator)
__contains__() (in SeqFeature)	__package__ (in Bio.Phylo.Applications._Fasttree)	_get_neighbors() (in NNITreeSearcher)
__contains__() (in SeqRecord)	__package__ (in Bio.Phylo.Applications._Phyml)	_get_nexus_block() (in Nexus)
__contains__() (in PlateRecord)	__package__ (in Bio.Phylo.Applications._Raxml)	_get_ontology_id() (in DatabaseLoader)
__contains__() (in BioSeqDatabase)	__package__ (in Bio.Phylo.Applications)	_get_opts() (in GenePopController)
__contains__() (in DBServer)	__package__ (in Bio.Phylo.BaseTree)	_get_parameter() (in AbstractCommandline)
__del__() (in _InMemoryIndex)	__package__ (in Bio.Phylo.CDAO)	_get_per_column_annotations() (in MultipleSeqAlignment)
__del__() (in _ShelveIndex)	__package__ (in Bio.Phylo.Consensus)	_get_phred_quality() (in Bio.SeqIO.QualityIO)
__del__() (in _FileIterator)	__package__ (in Bio.Phylo.NeXML)	_get_pi() (in Bio.codonalign.codonseq)
__del_annotations() (in DBSeqRecord)	__package__ (in Bio.Phylo.NeXMLIO)	_get_Q() (in Bio.codonalign.codonseq)
__del_dbxrefs() (in DBSeqRecord)	__package__ (in Bio.Phylo.Newick)	_get_raw_qresult() (in BlastTabIndexer)
__del_features() (in DBSeqRecord)	__package__ (in Bio.Phylo.NewickIO)	_get_raw_qresult_commented() (in BlastTabIndexer)
__del_seq() (in DBSeqRecord)	__package__ (in Bio.Phylo.NexusIO)	_get_read_region() (in Bio.SeqIO.SffIO)
__delitem__() (in Chain)	__package__ (in Bio.Phylo.PAML)	_get_read_time() (in Bio.SeqIO.SffIO)
__delitem__() (in Crystal)	__package__ (in Bio.Phylo.PAML._paml)	_get_read_xy() (in Bio.SeqIO.SffIO)
__delitem__() (in _InMemoryIndex)	__package__ (in Bio.Phylo.PAML._parse_baseml)	_get_record() (in MafIndex)
__delitem__() (in Chain)	__package__ (in Bio.Phylo.PAML._parse_codeml)	_get_ref() (in SeqFeature)
__delitem__() (in Entity)	__package__ (in Bio.Phylo.PAML._parse_yn00)	_get_ref_db() (in SeqFeature)
__delitem__() (in Events)	__package__ (in Bio.Phylo.PAML.baseml)	_get_references() (in Bio.PDB.parse_pdb_header')
__delitem__() (in _Matrix)	__package__ (in Bio.Phylo.PAML.chi2)	_get_row_dict() (in Bio.SearchIO.ExonerateIO.exonerate_text)
__delitem__() (in Hit)	__package__ (in Bio.Phylo.PAML.codeml)	_get_sanger_quality_str() (in Bio.SeqIO.QualityIO)
__delitem__() (in HSP)	__package__ (in Bio.Phylo.PAML.yn00)	_get_scodon_moves() (in Bio.SearchIO.ExonerateIO.exonerate_text)
__delitem__() (in QueryResult)	__package__ (in Bio.Phylo.PhyloXML)	_get_seq_str_and_check_alphabet() (in Seq)
__delitem__() (in MutableSeq)	__package__ (in Bio.Phylo.PhyloXMLIO)	_get_seq_string() (in SequenceWriter)
__delitem__() (in PlateRecord)	__package__ (in Bio.Phylo.TreeConstruction)	_get_seq_string() (in Bio.SeqIO.Interfaces)
__delitem__() (in BioSeqDatabase)	__package__ (in Bio.Phylo)	_get_seqfeature_dbxref() (in DatabaseLoader)
__delitem__() (in DBServer)	__package__ (in Bio.Phylo._cdao_owl)	_get_shift_anchor_re() (in Bio.codonalign)
__div__() (in Confidence)	__package__ (in Bio.Phylo._io)	_get_solexa_quality_str() (in Bio.SeqIO.QualityIO)
__div__() (in RestrictionBatch)	__package__ (in Bio.Phylo._utils)	_get_strand() (in HSPFragment)
__div__() (in RestrictionType)	__package__ (in Bio.PopGen.GenePop.Controller)	_get_strand() (in CompoundLocation)
__divmod__() (in Confidence)	__package__ (in Bio.PopGen.GenePop.EasyController)	_get_strand() (in FeatureLocation)
__doc__ (in Node)	__package__ (in Bio.PopGen.GenePop.FileParser)	_get_strand() (in SeqFeature)
__draw_arrow() (in KGMLCanvas)	__package__ (in Bio.PopGen.GenePop.LargeFileParser)	_get_string_tag() (in Bio.SeqIO.AbiIO)
__enter__() (in UndoHandle)	__package__ (in Bio.PopGen.GenePop.Utils)	_get_subgraph() (in Bio.codonalign.codonalignment)
__enter__() (in BgzfReader)	__package__ (in Bio.PopGen.GenePop)	_get_taxon_id() (in DatabaseLoader)
__enter__() (in BgzfWriter)	__package__ (in Bio.PopGen)	_get_taxon_id_from_ncbi_lineage() (in DatabaseLoader)
__eq__() (in PairwiseAlignment)	__package__ (in Bio.Restriction.PrintFormat)	_get_taxon_id_from_ncbi_taxon_id() (in DatabaseLoader)
__eq__() (in Chain)	__package__ (in Bio.Restriction.Restriction)	_get_taxonomy() (in Clade)
__eq__() (in Hetero)	__package__ (in Bio.Restriction.Restriction_Dictionary)	_get_term_id() (in DatabaseLoader)
__eq__() (in NoneElement)	__package__ (in Bio.Restriction)	_get_topology() (in GenBankWriter)
__eq__() (in Atom)	__package__ (in Bio.SCOP.Cla)	_get_TV() (in Bio.codonalign.codonseq)
__eq__() (in Entity)	__package__ (in Bio.SCOP.Des)	_get_unique_parent_pairs() (in NeighborSearch)
__eq__() (in Reaction)	__package__ (in Bio.SCOP.Dom)	_get_v_final() (in ColorSpiral)
__eq__() (in Graph)	__package__ (in Bio.SCOP.Hie)	_get_v_init() (in ColorSpiral)
__eq__() (in MultiGraph)	__package__ (in Bio.SCOP.Raf)	_get_values() (in Tree)
__eq__() (in Confidence)	__package__ (in Bio.SCOP.Residues)	_getbgcolor() (in Graphics)
__eq__() (in FormattedSeq)	__package__ (in Bio.SCOP)	_getcoords() (in Graphics)
__eq__() (in RestrictionType)	__package__ (in Bio.SVDSuperimposer)	_getentry1() (in Relation)
__eq__() (in MutableSeq)	__package__ (in Bio.SearchIO.BlastIO)	_getentry2() (in Relation)
__eq__() (in Seq)	__package__ (in Bio.SearchIO.BlastIO.blast_tab)	_getfgcolor() (in Graphics)
__eq__() (in CompoundLocation)	__package__ (in Bio.SearchIO.BlastIO.blast_text)	_getheight() (in Graphics)
__eq__() (in FeatureLocation)	__package__ (in Bio.SearchIO.BlastIO.blast_xml)	_getid() (in Component)
__eq__() (in Reference)	__package__ (in Bio.SearchIO.BlatIO)	_getid() (in Entry)
__eq__() (in SeqRecord)	__package__ (in Bio.SearchIO.ExonerateIO)	_getid() (in Reaction)
__eq__() (in Motif)	__package__ (in Bio.SearchIO.ExonerateIO._base)	_getname() (in Entry)
__eq__() (in PlateRecord)	__package__ (in Bio.SearchIO.ExonerateIO.exonerate_cigar)	_getname() (in Pathway)
__eq__() (in WellRecord)	__package__ (in Bio.SearchIO.ExonerateIO.exonerate_text)	_getnames() (in Reaction)
__exit__() (in UndoHandle)	__package__ (in Bio.SearchIO.ExonerateIO.exonerate_vulgar)	_getnumber() (in Pathway)
__exit__() (in BgzfReader)	__package__ (in Bio.SearchIO.FastaIO)	_getreaction() (in Entry)
__exit__() (in BgzfWriter)	__package__ (in Bio.SearchIO.HHsuiteIO)	_getwidth() (in Graphics)
__float__() (in Confidence)	__package__ (in Bio.SearchIO.HHsuiteIO.hhsuite2_text)	_getx() (in Graphics)
__floordiv__() (in Confidence)	__package__ (in Bio.SearchIO.HmmerIO)	_gety() (in Graphics)
__floordiv__() (in RestrictionType)	__package__ (in Bio.SearchIO.HmmerIO._base)	_gp_float() (in Bio.PopGen.GenePop.Controller)
__format__() (in MultipleSeqAlignment)	__package__ (in Bio.SearchIO.HmmerIO.hmmer2_text)	_gp_int() (in Bio.PopGen.GenePop.Controller)
__format__() (in PairwiseAlignment)	__package__ (in Bio.SearchIO.HmmerIO.hmmer3_domtab)	_gpa10iterator() (in Bio.UniProt.GOA)
__format__() (in Array)	__package__ (in Bio.SearchIO.HmmerIO.hmmer3_tab)	_gpa11iterator() (in Bio.UniProt.GOA)
__format__() (in Tree)	__package__ (in Bio.SearchIO.HmmerIO.hmmer3_text)	_gpi10iterator() (in Bio.UniProt.GOA)
__format__() (in SeqRecord)	__package__ (in Bio.SearchIO.InterproscanIO)	_gpi11iterator() (in Bio.UniProt.GOA)
__ge__() (in PairwiseAlignment)	__package__ (in Bio.SearchIO.InterproscanIO.interproscan_xml)	_Graph (in Bio.Graphics.GenomeDiagram)
__ge__() (in Atom)	__package__ (in Bio.SearchIO)	_GraphSet (in Bio.Graphics.GenomeDiagram)
__ge__() (in Chain)	__package__ (in Bio.SearchIO._index)	_grey (in Bio.Graphics.GenomeDiagram._Track)
__ge__() (in DisorderedEntityWrapper)	__package__ (in Bio.SearchIO._legacy.NCBIStandalone)	_guess_consensus_alphabet() (in SummaryInfo)
__ge__() (in Entity)	__package__ (in Bio.SearchIO._legacy.ParserSupport)	_handle_complex() (in Bio.Phylo.PhyloXMLIO)
__ge__() (in Confidence)	__package__ (in Bio.SearchIO._legacy)	_handle_convert() (in Bio.SeqIO._convert)
__ge__() (in RestrictionType)	__package__ (in Bio.SearchIO._model)	_handle_PDB_exception() (in PDBParser)
__ge__() (in MutableSeq)	__package__ (in Bio.SearchIO._model._base)	_handle_simple() (in Bio.Phylo.PhyloXMLIO)
__ge__() (in Seq)	__package__ (in Bio.SearchIO._model.hit)	_header (in ClustalIterator)
__ge__() (in SeqRecord)	__package__ (in Bio.SearchIO._model.hsp)	_header (in EmbossIterator)
__get_annotations() (in DBSeqRecord)	__package__ (in Bio.SearchIO._model.query)	_header (in MsfIterator)
__get_dbxrefs() (in DBSeqRecord)	__package__ (in Bio.SearchIO._utils)	_header (in PhylipIterator)
__get_features() (in DBSeqRecord)	__package__ (in Bio.Seq)	_header (in SequentialPhylipIterator)
__get_seq() (in DBSeqRecord)	__package__ (in Bio.SeqFeature)	_header (in StockholmIterator)
__getattr__() (in AlphabetEncoder)	__package__ (in Bio.SeqIO.AbiIO)	_HeaderConsumer (in Bio.SearchIO._legacy.NCBIStandalone)
__getattr__() (in AmbiguousCodonTable)	__package__ (in Bio.SeqIO.AceIO)	_HEADFMT (in Bio.SeqIO.AbiIO)
__getattr__() (in UndoHandle)	__package__ (in Bio.SeqIO.FastaIO)	_height_of() (in DistanceTreeConstructor)
__getattr__() (in _BaseGenBankConsumer)	__package__ (in Bio.SeqIO.GckIO)	_hit_end_get() (in HSP)
__getattr__() (in Feature)	__package__ (in Bio.SeqIO.IgIO)	_hit_end_get() (in HSPFragment)
__getattr__() (in DisorderedEntityWrapper)	__package__ (in Bio.SeqIO.InsdcIO)	_hit_end_set() (in HSPFragment)
__getattr__() (in AbstractConsumer)	__package__ (in Bio.SeqIO.Interfaces)	_hit_frame_get() (in HSPFragment)
__getattr__() (in TaggingConsumer)	__package__ (in Bio.SeqIO.NibIO)	_hit_frame_set() (in HSPFragment)
__getitem__() (in PSSM)	__package__ (in Bio.SeqIO.PdbIO)	_hit_get() (in HSPFragment)
__getitem__() (in MultipleSeqAlignment)	__package__ (in Bio.SeqIO.PhdIO)	_hit_inter_ranges_get() (in HSP)
__getitem__() (in PairwiseAlignments)	__package__ (in Bio.SeqIO.PirIO)	_hit_inter_spans_get() (in HSP)
__getitem__() (in Array)	__package__ (in Bio.SeqIO.QualityIO)	_hit_key_func() (in Bio.SearchIO._model.query)
__getitem__() (in Chain)	__package__ (in Bio.SeqIO.SeqXmlIO)	_hit_range_get() (in HSP)
__getitem__() (in Crystal)	__package__ (in Bio.SeqIO.SffIO)	_hit_range_get() (in HSPFragment)
__getitem__() (in AmbiguousForwardTable)	__package__ (in Bio.SeqIO.SnapGeneIO)	_hit_set() (in HSPFragment)
__getitem__() (in fff_rec)	__package__ (in Bio.SeqIO.SwissIO)	_hit_span_get() (in HSP)
__getitem__() (in _IndexedSeqFileDict)	__package__ (in Bio.SeqIO.TabIO)	_hit_span_get() (in HSPFragment)
__getitem__() (in _SQLiteManySeqFilesDict)	__package__ (in Bio.SeqIO.UniprotIO)	_hit_start_get() (in HSP)
__getitem__() (in Diagram)	__package__ (in Bio.SeqIO.XdnaIO)	_hit_start_get() (in HSPFragment)
__getitem__() (in FeatureSet)	__package__ (in Bio.SeqIO)	_hit_start_set() (in HSPFragment)
__getitem__() (in GraphData)	__package__ (in Bio.SeqIO._convert)	_hit_strand_get() (in HSPFragment)
__getitem__() (in GraphSet)	__package__ (in Bio.SeqIO._index)	_hit_strand_set() (in HSPFragment)
__getitem__() (in Track)	__package__ (in Bio.SeqRecord)	_HitPlaceholder (in Bio.SearchIO.HmmerIO.hmmer2_text)
__getitem__() (in StandardData)	__package__ (in Bio.SeqUtils.CheckSum)	_hour (in Bio.phenotype.phen_micro)
__getitem__() (in AbstractPropertyMap)	__package__ (in Bio.SeqUtils.CodonUsage)	_HRE_ANNOT_LINE (in Bio.SearchIO.HmmerIO.hmmer3_text)
__getitem__() (in Chain)	__package__ (in Bio.SeqUtils.CodonUsageIndices)	_HRE_ID_LINE (in Bio.SearchIO.HmmerIO.hmmer3_text)
__getitem__() (in DisorderedEntityWrapper)	__package__ (in Bio.SeqUtils.IsoelectricPoint)	_HRE_VALIDATE (in Bio.SearchIO.HmmerIO.hmmer3_text)
__getitem__() (in Entity)	__package__ (in Bio.SeqUtils.MeltingTemp)	_hsh (in Bio.SeqIO.SffIO)
__getitem__() (in FragmentMapper)	__package__ (in Bio.SeqUtils.ProtParam)	_HSP_ALIGN_LINE (in Bio.SearchIO.HmmerIO.hmmer2_text)
__getitem__() (in Vector)	__package__ (in Bio.SeqUtils.ProtParamData)	_HSP_ATTR_MAP (in Bio.SearchIO.FastaIO)
__getitem__() (in Clade)	__package__ (in Bio.SeqUtils)	_HSPConsumer (in Bio.SearchIO._legacy.NCBIStandalone)
__getitem__() (in Events)	__package__ (in Bio.SeqUtils.lcc)	_hw_func() (in Bio.PopGen.GenePop.Controller)
__getitem__() (in Phyloxml)	__package__ (in Bio.Sequencing.Ace)	_hydrogen (in Bio.PDB.Dice)
__getitem__() (in _Matrix)	__package__ (in Bio.Sequencing.Applications._Novoalign)	_identifier_split() (in Bio.AlignIO.MauveIO)
__getitem__() (in FormattedSeq)	__package__ (in Bio.Sequencing.Applications)	_identifier_split() (in StockholmIterator)
__getitem__() (in Index)	__package__ (in Bio.Sequencing.Applications._bwa)	_identity_matcher() (in Bio.Phylo.BaseTree)
__getitem__() (in SeqMap)	__package__ (in Bio.Sequencing.Applications._samtools)	_ids (in MauveIterator)
__getitem__() (in SeqMapIndex)	__package__ (in Bio.Sequencing.Phd)	_igam() (in Bio.codonalign.chisq)
__getitem__() (in Hit)	__package__ (in Bio.Sequencing)	_igamc() (in Bio.codonalign.chisq)
__getitem__() (in HSP)	__package__ (in Bio.Statistics)	_iis_solve_delta() (in Bio.MaxEntropy)
__getitem__() (in HSPFragment)	__package__ (in Bio.Statistics.lowess)	_ImgtScanner (in Bio.GenBank.Scanner)
__getitem__() (in QueryResult)	__package__ (in Bio.SubsMat.FreqTable)	_incomplete_gamma() (in Bio.Phylo.PAML.chi2)
__getitem__() (in MutableSeq)	__package__ (in Bio.SubsMat.MatrixInfo)	_indent() (in Bio.Phylo.PhyloXMLIO)
__getitem__() (in Seq)	__package__ (in Bio.SubsMat)	_indent_genbank() (in Bio.GenBank.Record)
__getitem__() (in UnknownSeq)	__package__ (in Bio.SwissProt.KeyWList)	_index (in Bio.SearchIO)
__getitem__() (in SeqRecord)	__package__ (in Bio.SwissProt)	_index (in Bio.SeqIO)
__getitem__() (in CodonAlignment)	__package__ (in Bio.TogoWS)	_index_diff() (in ScoreDistribution)
__getitem__() (in CodonSeq)	__package__ (in Bio.UniGene)	_IndexedSeqFileDict (in Bio.File)
__getitem__() (in Record)	__package__ (in Bio.UniProt.GOA)	_IndexedSeqFileProxy (in Bio.File)
__getitem__() (in GenericPositionMatrix)	__package__ (in Bio.UniProt)	_INDEXER_MAP (in Bio.SearchIO)
__getitem__() (in Record)	__package__ (in Bio.Wise)	_info_factory() (in Writer)
__getitem__() (in Record)	__package__ (in Bio.Wise.dnal)	_inhibitor() (in Record)
__getitem__() (in PlateRecord)	__package__ (in Bio.Wise.psw)	_init_from_text() (in ProtsimLine)
__getitem__() (in WellRecord)	__package__ (in Bio)	_init_from_text() (in STSLine)
__getitem__() (in DBSeq)	__package__ (in Bio._py3k)	_init_from_text() (in SequenceLine)
__getitem__() (in BioSeqDatabase)	__package__ (in Bio._utils)	_init_table_h() (in Bio.SeqUtils.CheckSum)
__getitem__() (in DBServer)	__package__ (in Bio.bgzf)	_init_zero() (in SeqMat)
__getnewargs__() (in BetweenPosition)	__package__ (in Bio.codonalign)	_initialize_directory() (in DataHandler)
__getnewargs__() (in OneOfPosition)	__package__ (in Bio.codonalign.chisq)	_InMemoryIndex (in Bio.Index)
__getnewargs__() (in WithinPosition)	__package__ (in Bio.codonalign.codonalignment)	_InMemoryIndex__version (in _InMemoryIndex)
__global_tag_listing (in Bio.SeqIO.AbiIO)	__package__ (in Bio.codonalign.codonalphabet)	_InMemoryIndex__version_key (in _InMemoryIndex)
__gt__() (in PairwiseAlignment)	__package__ (in Bio.codonalign.codonseq)	_inner_product() (in QCPSuperimposer)
__gt__() (in Atom)	__package__ (in Bio.cpairwise2)	_input_type_checker() (in NcbimakeblastdbCommandline)
__gt__() (in Chain)	__package__ (in Bio.kNN)	_insdc_feature_position_string() (in Bio.SeqIO.InsdcIO)
__gt__() (in DisorderedEntityWrapper)	__package__ (in Bio.motifs)	_insdc_location_string() (in Bio.SeqIO.InsdcIO)
__gt__() (in Entity)	__package__ (in Bio.motifs._pwm)	_insdc_location_string_ignoring_strand_and_subfeatures() (in Bio.SeqIO.InsdcIO)
__gt__() (in Confidence)	__package__ (in Bio.motifs.alignace)	_InsdcWriter (in Bio.SeqIO.InsdcIO)
__gt__() (in RestrictionType)	__package__ (in Bio.motifs.applications)	_insert_location() (in DatabaseLoader)
__gt__() (in MutableSeq)	__package__ (in Bio.motifs.applications._xxmotif)	_INSTRUMENT_SPECIFIC_TAGS (in Bio.SeqIO.AbiIO)
__gt__() (in Seq)	__package__ (in Bio.motifs.clusterbuster)	_int() (in Bio.Phylo.PhyloXMLIO)
__gt__() (in SeqRecord)	__package__ (in Bio.motifs.jaspar)	_inter_ranges_get() (in HSP)
__hash__ (in SeqRecord)	__package__ (in Bio.motifs.mast)	_inter_spans_get() (in HSP)
__hash__() (in Atom)	__package__ (in Bio.motifs.matrix)	_interface_specific_adaptors (in BioSQL.BioSeqDatabase)
__hash__() (in Entity)	__package__ (in Bio.motifs.meme)	_interpolate() (in WellRecord)
__hash__() (in Interaction)	__package__ (in Bio.motifs.minimal)	_io (in Bio.Phylo)
__hash__() (in Reaction)	__package__ (in Bio.motifs.pfm)	_is_completely_disordered() (in StructureBuilder)
__hash__() (in Confidence)	__package__ (in Bio.motifs.thresholds)	_is_connected() (in CaPPBuilder)
__hash__() (in RestrictionType)	__package__ (in Bio.motifs.transfac)	_is_connected() (in PPBuilder)
__hash__() (in Seq)	__package__ (in Bio.motifs.xms)	_is_header() (in PhylipIterator)
__hash__() (in UnknownPosition)	__package__ (in Bio.pairwise2)	_is_int() (in Bio.Phylo.Applications._Fasttree)
__hash__() (in Motif)	__package__ (in Bio.phenotype)	_is_int_or_long() (in Bio._py3k)
__iadd__() (in Chain)	__package__ (in Bio.phenotype.phen_micro)	_is_latest_version() (in JASPAR5)
__iadd__() (in RestrictionBatch)	__package__ (in Bio.phenotype.pm_fitting)	_is_numeric() (in Bio.Phylo.Applications._Fasttree)
__iadd__() (in SeqMap)	__package__ (in Bio.trie)	_is_numeric() (in Bio.Phylo.TreeConstruction)
__imul__() (in MutableSeq)	__package__ (in Bio.triefind)	_is_protein() (in Bio.SearchIO.BlatIO)
__imul__() (in Seq)	__package__ (in BioSQL.BioSeq)	_is_well() (in PlateRecord)
__imul__() (in UnknownSeq)	__package__ (in BioSQL.BioSeqDatabase)	_ITERATOR_MAP (in Bio.SearchIO)
__imul__() (in DBSeq)	__package__ (in BioSQL.DBUtils)	_journal_line() (in Reference)
__init_() (in Interaction)	__package__ (in BioSQL.Loader)	_key_error() (in Bio.SeqUtils.MeltingTemp)
__init__() (in ParserError)	__package__ (in BioSQL)	_keywords_line() (in Record)
__init__() (in Record)	__parse_hit_table() (in FastaM10Parser)	_kill_comments_and_break_lines() (in Bio.Nexus.Nexus)
__init__() (in PSSM)	__pos__() (in Confidence)	_legacy (in Bio.SearchIO)
__init__() (in SummaryInfo)	__pow__() (in Vector)	_level_traverse() (in Bio.Phylo.BaseTree)
__init__() (in ClustalOmegaCommandline)	__pow__() (in Confidence)	_likelihood_func() (in Bio.codonalign.codonseq)
__init__() (in ClustalwCommandline)	__process_feature() (in Feature)	_LinearDrawer (in Bio.Graphics.GenomeDiagram)
__init__() (in DialignCommandline)	__radd__() (in Chain)	_link() (in Nexus)
__init__() (in MSAProbsCommandline)	__radd__() (in Confidence)	_list_diamond() (in Bio.SearchIO.BlastIO.blast_tab)
__init__() (in MafftCommandline)	__radd__() (in MutableSeq)	_list_from_csv() (in Bio.SearchIO.BlatIO)
__init__() (in MuscleCommandline)	__radd__() (in Seq)	_list_semicol() (in Bio.SearchIO.BlastIO.blast_tab)
__init__() (in PrankCommandline)	__radd__() (in UnknownSeq)	_ln_gamma_function() (in Bio.Phylo.PAML.chi2)
__init__() (in ProbconsCommandline)	__radd__() (in CompoundLocation)	_load_annotations() (in DatabaseLoader)
__init__() (in TCoffeeCommandline)	__radd__() (in FeatureLocation)	_load_bgzf_block() (in Bio.bgzf)
__init__() (in MultipleSeqAlignment)	__radd__() (in SeqRecord)	_load_bioentry_date() (in DatabaseLoader)
__init__() (in PairwiseAlignment)	__radd__() (in DBSeq)	_load_bioentry_table() (in DatabaseLoader)
__init__() (in PairwiseAlignments)	__rand__() (in _BitString)	_load_biosequence() (in DatabaseLoader)
__init__() (in AlignmentIterator)	__rdiv__() (in Confidence)	_load_block() (in BgzfReader)
__init__() (in AlignmentWriter)	__rdiv__() (in RestrictionBatch)	_load_comment() (in DatabaseLoader)
__init__() (in SequentialAlignmentWriter)	__rdiv__() (in RestrictionType)	_load_dbxrefs() (in DatabaseLoader)
__init__() (in MafIndex)	__rdivmod__() (in Confidence)	_load_index() (in _SQLiteManySeqFilesDict)
__init__() (in MauveWriter)	__read() (in Bio.ExPASy.Enzyme)	_load_reference() (in DatabaseLoader)
__init__() (in AlphabetEncoder)	__read() (in Bio.ExPASy.Prodoc)	_load_seqfeature() (in DatabaseLoader)
__init__() (in Gapped)	__read() (in Bio.ExPASy.Prosite)	_load_seqfeature_basic() (in DatabaseLoader)
__init__() (in HasStopCodon)	__read() (in Bio.ExPASy.cellosaurus)	_load_seqfeature_dbxref() (in DatabaseLoader)
__init__() (in AbstractCommandline)	__read_alphabet() (in Bio.motifs.meme)	_load_seqfeature_locations() (in DatabaseLoader)
__init__() (in ApplicationError)	__read_command() (in Bio.motifs.meme)	_load_seqfeature_qualifiers() (in DatabaseLoader)
__init__() (in _AbstractParameter)	__read_copyright_line() (in Bio.ExPASy.Prodoc)	_local() (in Bio.Phylo.PhyloXMLIO)
__init__() (in _Argument)	__read_datafile() (in Bio.motifs.meme)	_local_reserved_names (in Bio.Application)
__init__() (in _Option)	__read_hit_alignment() (in Bio.Compass)	_locus_line() (in Record)
__init__() (in _StaticArgument)	__read_lengths() (in Bio.Compass)	_log_transform() (in HiddenMarkovModel)
__init__() (in _Switch)	__read_metadata() (in Bio.motifs.mast)	_logsum() (in Bio.MarkovModel)
__init__() (in NcbiblastformatterCommandline)	__read_motif_name() (in Bio.motifs.meme)	_logvecadd() (in Bio.MarkovModel)
__init__() (in NcbiblastnCommandline)	__read_motif_sequences() (in Bio.motifs.meme)	_LONG_SHORT_MAP (in Bio.SearchIO.BlastIO.blast_tab)
__init__() (in NcbiblastpCommandline)	__read_motif_statistics() (in Bio.motifs.meme)	_lower() (in Alphabet)
__init__() (in NcbiblastxCommandline)	__read_names() (in Bio.Compass)	_lower() (in AlphabetEncoder)
__init__() (in NcbideltablastCommandline)	__read_positive_alignment() (in Bio.Compass)	_lower() (in Gapped)
__init__() (in NcbimakeblastdbCommandline)	__read_profilewidth() (in Bio.Compass)	_lower() (in HasStopCodon)
__init__() (in NcbipsiblastCommandline)	__read_prosite_reference_line() (in Bio.ExPASy.Prodoc)	_lower() (in ThreeLetterProtein)
__init__() (in NcbirpsblastCommandline)	__read_query_alignment() (in Bio.Compass)	_lwl85() (in Bio.codonalign.codonseq)
__init__() (in NcbirpstblastnCommandline)	__read_reference_line() (in Bio.ExPASy.Prodoc)	_Mafft (in Bio.Align.Applications)
__init__() (in NcbitblastnCommandline)	__read_reference_start() (in Bio.ExPASy.Prodoc)	_make_ambiguous_ranges() (in Bio.Data.IUPACData)
__init__() (in NcbitblastxCommandline)	__read_scores() (in Bio.Compass)	_make_dssp_dict() (in Bio.PDB.DSSP')
__init__() (in _NcbibaseblastCommandline)	__read_sequences() (in Bio.motifs.mast)	_make_fragment_list() (in Bio.PDB.FragmentMapper')
__init__() (in _Ncbiblast2SeqCommandline)	__read_sequences() (in Bio.motifs.meme)	_make_list() (in PrintFormat)
__init__() (in _NcbiblastCommandline)	__read_text_line() (in Bio.ExPASy.Prodoc)	_make_list_only() (in PrintFormat)
__init__() (in _NcbiblastMain2SeqCommandline)	__read_threshold() (in Bio.Compass)	_make_map() (in PrintFormat)
__init__() (in BlastParser)	__read_version() (in Bio.motifs.meme)	_make_map_only() (in PrintFormat)
__init__() (in _XMLparser)	__regex (in Bio.Compass)	_make_nocut() (in PrintFormat)
__init__() (in BlastTableEntry)	__repr__() (in MultipleSeqAlignment)	_make_nocut_only() (in PrintFormat)
__init__() (in BlastTableReader)	__repr__() (in Array)	_make_number() (in PrintFormat)
__init__() (in BlastTableRec)	__repr__() (in MafIndex)	_make_number_only() (in PrintFormat)
__init__() (in Alignment)	__repr__() (in Alphabet)	_make_position() (in Bio.SeqIO.SwissIO)
__init__() (in Blast)	__repr__() (in AlphabetEncoder)	_make_ranges() (in Bio.Data.IUPACData)
__init__() (in DatabaseReport)	__repr__() (in AbstractCommandline)	_make_score_matrix_fast() (in Bio.cpairwise2)
__init__() (in Description)	__repr__() (in ApplicationError)	_make_score_matrix_generic() (in Bio.pairwise2)
__init__() (in DescriptionExt)	__repr__() (in Crystal)	_make_seqfeature() (in Bio.SeqIO.SwissIO)
__init__() (in DescriptionExtItem)	__repr__() (in Hetero)	_make_tree() (in Parser)
__init__() (in HSP)	__repr__() (in NCBICodonTable)	_make_triplets() (in Bio.SearchIO.ExonerateIO._base)
__init__() (in Header)	__repr__() (in DictionaryElement)	_make_unicode_into_string() (in BioSQL.BioSeq)
__init__() (in MultipleAlignment)	__repr__() (in IntegerElement)	_make_unique() (in Bio.Nexus.Nexus)
__init__() (in PSIBlast)	__repr__() (in ListElement)	_maketrans() (in Bio.Seq)
__init__() (in Parameters)	__repr__() (in NoneElement)	_map() (in FragmentMapper)
__init__() (in Round)	__repr__() (in StringElement)	_map_fragment_list() (in Bio.PDB.FragmentMapper')
__init__() (in CAPSMap)	__repr__() (in UnicodeElement)	_mass() (in Record)
__init__() (in DifferentialCutsite)	__repr__() (in Record)	_Matrix (in Bio.Phylo.TreeConstruction)
__init__() (in Record)	__repr__() (in Record)	_matrix() (in Nexus)
__init__() (in Record)	__repr__() (in FSSPSumRec)	_measurements (in Bio.phenotype.phen_micro)
__init__() (in Chain)	__repr__() (in PosAlign)	_medline_line() (in Reference)
__init__() (in Crystal)	__repr__() (in fff_rec)	_merge_aa2re() (in Bio.codonalign)
__init__() (in Hetero)	__repr__() (in _IndexedSeqFileDict)	_mft (in Bio.SeqIO.SffIO)
__init__() (in AmbiguousCodonTable)	__repr__() (in _SQLiteManySeqFilesDict)	_MIN_HIT_FIELDS (in Bio.SearchIO.BlastIO.blast_tab)
__init__() (in AmbiguousForwardTable)	__repr__() (in Feature)	_MIN_QUERY_FIELDS (in Bio.SearchIO.BlastIO.blast_tab)
__init__() (in CodonTable)	__repr__() (in Qualifier)	_ml() (in Bio.codonalign.codonseq)
__init__() (in NCBICodonTable)	__repr__() (in Atom)	_mle() (in Bio.MarkovModel)
__init__() (in DiffseqCommandline)	__repr__() (in DisorderedAtom)	_mod1() (in Blunt)
__init__() (in EInvertedCommandline)	__repr__() (in Chain)	_mod1() (in Ov3)
__init__() (in ETandemCommandline)	__repr__() (in Fragment)	_mod1() (in Ov5)
__init__() (in Est2GenomeCommandline)	__repr__() (in Model)	_mod1() (in Unknown)
__init__() (in FConsenseCommandline)	__repr__() (in Select)	_mod2() (in Ambiguous)
__init__() (in FDNADistCommandline)	__repr__() (in Polypeptide)	_mod2() (in Defined)
__init__() (in FDNAParsCommandline)	__repr__() (in DisorderedResidue)	_mod2() (in NotDefined)
__init__() (in FNeighborCommandline)	__repr__() (in Residue)	_modeError (in Bio.Affy.CelFile)
__init__() (in FProtDistCommandline)	__repr__() (in Structure)	_model (in Bio.SearchIO)
__init__() (in FProtParsCommandline)	__repr__() (in Vector)	_modify() (in NoCut)
__init__() (in FSeqBootCommandline)	__repr__() (in Interaction)	_modify() (in OneCut)
__init__() (in FTreeDistCommandline)	__repr__() (in Network)	_modify() (in TwoCuts)
__init__() (in FuzznucCommandline)	__repr__() (in Reaction)	_MSAProbs (in Bio.Align.Applications)
__init__() (in FuzzproCommandline)	__repr__() (in Graph)	_Muscle (in Bio.Align.Applications)
__init__() (in IepCommandline)	__repr__() (in MultiGraph)	_name() (in Record)
__init__() (in NeedleCommandline)	__repr__() (in System)	_name() (in Record)
__init__() (in NeedleallCommandline)	__repr__() (in BranchColor)	_name() (in Record)
__init__() (in PalindromeCommandline)	__repr__() (in TreeElement)	_name_n_vector() (in Nexus)
__init__() (in Primer3Commandline)	__repr__() (in _BitString)	_NcbibaseblastCommandline (in Bio.Blast.Applications)
__init__() (in PrimerSearchCommandline)	__repr__() (in _Matrix)	_Ncbiblast2SeqCommandline (in Bio.Blast.Applications)
__init__() (in SeqmatchallCommandline)	__repr__() (in Analysis)	_NcbiblastCommandline (in Bio.Blast.Applications)
__init__() (in SeqretCommandline)	__repr__() (in FormattedSeq)	_NcbiblastMain2SeqCommandline (in Bio.Blast.Applications)
__init__() (in StretcherCommandline)	__repr__() (in RestrictionBatch)	_ng86() (in Bio.codonalign.codonseq)
__init__() (in TranalignCommandline)	__repr__() (in RestrictionType)	_nice_case() (in Bio.PDB.parse_pdb_header')
__init__() (in WaterCommandline)	__repr__() (in Hit)	_nid_line() (in Record)
__init__() (in _EmbossCommandLine)	__repr__() (in HSP)	_nni() (in NNITreeSearcher)
__init__() (in _EmbossMinimalCommandLine)	__repr__() (in HSPFragment)	_NO_DOTS (in Bio.AlignIO.PhylipIO)
__init__() (in Primers)	__repr__() (in QueryResult)	_NO_SEQRECORD_COMPARISON (in Bio.SeqRecord)
__init__() (in Record)	__repr__() (in MutableSeq)	_node_method_name() (in _XMLparser)
__init__() (in Amplifier)	__repr__() (in Seq)	_nodetype_to_code (in Bio.SCOP)
__init__() (in InputRecord)	__repr__() (in UnknownSeq)	_NON_STICKY_ATTRS (in _BaseSearchObject)
__init__() (in OutputRecord)	__repr__() (in AbstractPosition)	_NON_STICKY_ATTRS (in Hit)
__init__() (in CorruptedXMLError)	__repr__() (in AfterPosition)	_NON_STICKY_ATTRS (in HSP)
__init__() (in DataHandler)	__repr__() (in BeforePosition)	_NON_STICKY_ATTRS (in QueryResult)
__init__() (in DictionaryElement)	__repr__() (in BetweenPosition)	_normalize() (in Bio.MarkovModel)
__init__() (in ListElement)	__repr__() (in CompoundLocation)	_normalize_spaces() (in _BaseGenBankConsumer)
__init__() (in NoneElement)	__repr__() (in ExactPosition)	_Novoalign (in Bio.Sequencing.Applications)
__init__() (in NotXMLError)	__repr__() (in FeatureLocation)	_ns() (in Bio.Phylo.PhyloXMLIO)
__init__() (in ValidationError)	__repr__() (in OneOfPosition)	_null (in Bio.SeqIO.SffIO)
__init__() (in Record)	__repr__() (in PositionGap)	_object_matcher() (in Bio.Phylo.BaseTree)
__init__() (in Record)	__repr__() (in Reference)	_on_root_node() (in BlastParser)
__init__() (in Reference)	__repr__() (in SeqFeature)	_oneof_location (in Bio.GenBank)
__init__() (in Record)	__repr__() (in UnknownPosition)	_oneof_position (in Bio.GenBank)
__init__() (in ContentHandler)	__repr__() (in WithinPosition)	_open() (in Bio.Entrez)
__init__() (in Parser)	__repr__() (in SeqRecord)	_open() (in Bio.SCOP)
__init__() (in Record)	__repr__() (in ProtsimLine)	_open() (in Bio.TogoWS)
__init__() (in Record)	__repr__() (in Record)	_open_for_random_access() (in Bio.File)
__init__() (in FSSPAlignDict)	__repr__() (in STSLine)	_open_scop_file() (in Bio.SCOP)
__init__() (in FSSPAlignRec)	__repr__() (in SequenceLine)	_Option (in Bio.Application)
__init__() (in FSSPHeader)	__repr__() (in AlignmentColumn)	_OPTION_GAP_EXTENSION (in Bio.Wise.psw)
__init__() (in FSSPSumRec)	__repr__() (in ColumnUnit)	_OPTION_GAP_START (in Bio.Wise.psw)
__init__() (in FSSPMultAlign)	__repr__() (in CodonAlphabet)	_OPTION_SCORES (in Bio.Wise.psw)
__init__() (in PosAlign)	__repr__() (in PlateRecord)	_options() (in Nexus)
__init__() (in fff_rec)	__repr__() (in WellRecord)	_organism_line() (in Record)
__init__() (in UndoHandle)	__repr__() (in BioSeqDatabase)	_origin_line() (in Record)
__init__() (in _IndexedSeqFileDict)	__repr__() (in DBServer)	_other (in Bio.phenotype.phen_micro)
__init__() (in _SQLiteManySeqFilesDict)	__rfloordiv__() (in Confidence)	_overdraw_subcomponents() (in AnnotatedChromosomeSegment)
__init__() (in FeatureParser)	__rfloordiv__() (in RestrictionType)	_overdraw_subcomponents() (in ChromosomeSegment)
__init__() (in Iterator)	__rmod__() (in Confidence)	_packet_handlers (in Bio.SeqIO.SnapGeneIO)
__init__() (in Feature)	__rmul__() (in Confidence)	_PacketIterator (in Bio.SeqIO.SnapGeneIO)
__init__() (in Qualifier)	__rmul__() (in MutableSeq)	_pair_location (in Bio.GenBank)
__init__() (in Record)	__rmul__() (in Seq)	_pair_replacement() (in SummaryInfo)
__init__() (in Reference)	__rmul__() (in UnknownSeq)	_pairwise() (in DistanceCalculator)
__init__() (in RecordParser)	__rmul__() (in SeqMat)	_paml (in Bio.Phylo.PAML)
__init__() (in InsdcScanner)	__rmul__() (in DBSeq)	_ParametersConsumer (in Bio.SearchIO._legacy.NCBIStandalone)
__init__() (in _BaseGenBankConsumer)	__ror__() (in _BitString)	_parent_dir (in Bio)
__init__() (in _FeatureConsumer)	__rpow__() (in Confidence)	_Parse() (in BlastTableReader)
__init__() (in _RecordConsumer)	__rshift__() (in RestrictionType)	_parse() (in Tree)
__init__() (in FeatureValueCleaner)	__rsub__() (in Confidence)	_parse() (in PDBParser)
__init__() (in Record)	__rtruediv__() (in Confidence)	_parse() (in Residues)
__init__() (in AnnotatedChromosomeSegment)	__rtruediv__() (in RestrictionBatch)	_parse() (in BlastXmlIndexer)
__init__() (in Chromosome)	__rtruediv__() (in RestrictionType)	_parse() (in SearchIndexer)
__init__() (in ChromosomeSegment)	__rxor__() (in _BitString)	_parse() (in _DescriptionConsumer)
__init__() (in Organism)	__set_annotations() (in DBSeqRecord)	_parse_alignment_header() (in _BaseExonerateParser)
__init__() (in TelomereSegment)	__set_dbxrefs() (in DBSeqRecord)	_parse_aln_block() (in Hmmer3TextParser)
__init__() (in _ChromosomeComponent)	__set_features() (in DBSeqRecord)	_parse_baseml (in Bio.Phylo.PAML)
__init__() (in ColorSpiral)	__set_seq() (in DBSeqRecord)	_parse_clade() (in Parser)
__init__() (in ComparativeScatterPlot)	__setattr__() (in PairwiseAligner)	_parse_codeml (in Bio.Phylo.PAML)
__init__() (in ChromosomeCounts)	__setattr__() (in AbstractCommandline)	_parse_commented_qresult() (in BlastTabParser)
__init__() (in BarChartDistribution)	__setitem__() (in Array)	_parse_comments() (in BlastTabParser)
__init__() (in DistributionPage)	__setitem__() (in Chain)	_parse_confidence() (in Bio.Phylo.NewickIO)
__init__() (in LineDistribution)	__setitem__() (in Crystal)	_parse_cookie_packet() (in Bio.SeqIO.SnapGeneIO)
__init__() (in AbstractDrawer)	__setitem__() (in _IndexedSeqFileDict)	_parse_coordinates() (in PDBParser)
__init__() (in CircularDrawer)	__setitem__() (in _InMemoryIndex)	_parse_database() (in BlastTableReader)
__init__() (in ColorTranslator)	__setitem__() (in DisorderedEntityWrapper)	_parse_dna_packet() (in Bio.SeqIO.SnapGeneIO)
__init__() (in CrossLink)	__setitem__() (in Vector)	_parse_feature_description() (in Bio.SeqIO.XdnaIO)
__init__() (in Diagram)	__setitem__() (in Events)	_parse_features_packet() (in Bio.SeqIO.SnapGeneIO)
__init__() (in Feature)	__setitem__() (in DistanceMatrix)	_parse_fields() (in BlastTableReader)
__init__() (in FeatureSet)	__setitem__() (in _Matrix)	_parse_fields_line() (in BlastTabParser)
__init__() (in GraphData)	__setitem__() (in Hit)	_parse_header() (in InterproscanXmlParser)
__init__() (in GraphSet)	__setitem__() (in HSP)	_parse_hit() (in BlastXmlParser)
__init__() (in LinearDrawer)	__setitem__() (in QueryResult)	_parse_hit() (in FastaM10Parser)
__init__() (in Track)	__setitem__() (in MutableSeq)	_parse_hit() (in Hmmer3TextParser)
__init__() (in KGMLCanvas)	__setitem__() (in _RestrictedDict)	_parse_hit() (in InterproscanXmlParser)
__init__() (in AbstractDPAlgorithms)	__setitem__() (in PlateRecord)	_parse_hit_block() (in Hhsuite2TextParser)
__init__() (in LogDPAlgorithms)	__setitem__() (in WellRecord)	_parse_hit_match_block() (in Hhsuite2TextParser)
__init__() (in ScaledDPAlgorithms)	__skip_unused_lines() (in Bio.motifs.meme)	_parse_hit_or_query_line() (in Bio.SearchIO.ExonerateIO._base)
__init__() (in HiddenMarkovModel)	__str__() (in PSSM)	_parse_hsp() (in BlastXmlParser)
__init__() (in MarkovModelBuilder)	__str__() (in MultipleSeqAlignment)	_parse_hsp() (in InterproscanXmlParser)
__init__() (in AbstractTrainer)	__str__() (in PairwiseAlignment)	_parse_iteration() (in BlastTableReader)
__init__() (in BaumWelchTrainer)	__str__() (in Array)	_parse_list() (in Nexus)
__init__() (in KnownStateTrainer)	__str__() (in AbstractCommandline)	_parse_nexus_block() (in Nexus)
__init__() (in TrainingSequence)	__str__() (in ApplicationError)	_parse_notes_packet() (in Bio.SeqIO.SnapGeneIO)
__init__() (in _InMemoryIndex)	__str__() (in _AbstractParameter)	_parse_pdb_header_list() (in Bio.PDB.parse_pdb_header')
__init__() (in _ShelveIndex)	__str__() (in _Argument)	_parse_phylogeny() (in Parser)
__init__() (in KDTree)	__str__() (in _ArgumentList)	_parse_preamble() (in BlastXmlParser)
__init__() (in Record)	__str__() (in _Option)	_parse_preamble() (in FastaM10Parser)
__init__() (in Record)	__str__() (in _StaticArgument)	_parse_preamble() (in Hhsuite2TextParser)
__init__() (in Record)	__str__() (in _Switch)	_parse_preamble() (in Hmmer3TextParser)
__init__() (in KGMLParser)	__str__() (in Alignment)	_parse_primers_packet() (in Bio.SeqIO.SnapGeneIO)
__init__() (in Component)	__str__() (in Description)	_parse_qblast_ref_page() (in Bio.Blast.NCBIWWW)
__init__() (in Entry)	__str__() (in DescriptionExtItem)	_parse_qresult() (in BlastTabParser)
__init__() (in Graphics)	__str__() (in HSP)	_parse_qresult() (in BlastXmlParser)
__init__() (in Pathway)	__str__() (in Chain)	_parse_qresult() (in BlatPslParser)
__init__() (in Reaction)	__str__() (in Crystal)	_parse_qresult() (in _BaseExonerateParser)
__init__() (in Relation)	__str__() (in Hetero)	_parse_qresult() (in FastaM10Parser)
__init__() (in LogisticRegression)	__str__() (in CodonTable)	_parse_qresult() (in Hhsuite2TextParser)
__init__() (in MarkovModel)	__str__() (in InputRecord)	_parse_qresult() (in Hmmer3DomtabParser)
__init__() (in MaxEntropy)	__str__() (in CorruptedXMLError)	_parse_qresult() (in Hmmer3TabParser)
__init__() (in Peaklist)	__str__() (in NotXMLError)	_parse_qresult() (in Hmmer3TextParser)
__init__() (in XpkEntry)	__str__() (in ValidationError)	_parse_qresult() (in InterproscanXmlParser)
__init__() (in NaiveBayes)	__str__() (in Record)	_parse_query() (in BlastTableReader)
__init__() (in Block)	__str__() (in Record)	_parse_remark_465() (in Bio.PDB.parse_pdb_header')
__init__() (in CharBuffer)	__str__() (in _IndexedSeqFileDict)	_parse_result_row() (in BlastTabParser)
__init__() (in Commandline)	__str__() (in Feature)	_parse_row() (in BlatPslParser)
__init__() (in Nexus)	__str__() (in Qualifier)	_parse_row() (in Hmmer3DomtabParser)
__init__() (in StepMatrix)	__str__() (in Record)	_parse_row() (in Hmmer3TabParser)
__init__() (in Chain)	__str__() (in Reference)	_parse_sequence() (in Parser)
__init__() (in Node)	__str__() (in Record)	_parse_tag_data() (in Bio.SeqIO.AbiIO)
__init__() (in StandardData)	__str__() (in Diagram)	_parse_taxonomy() (in Parser)
__init__() (in NodeData)	__str__() (in FeatureSet)	_parse_tree() (in Parser)
__init__() (in Tree)	__str__() (in GraphData)	_parse_version() (in BlastTableReader)
__init__() (in AbstractAtomPropertyMap)	__str__() (in GraphSet)	_parse_xrefs() (in InterproscanXmlParser)
__init__() (in AbstractPropertyMap)	__str__() (in Track)	_parse_yn00 (in Bio.Phylo.PAML)
__init__() (in AbstractResiduePropertyMap)	__str__() (in Record)	_parser (in _BaseExonerateIndexer)
__init__() (in Atom)	__str__() (in Record)	_part() (in Bio.Phylo.Consensus)
__init__() (in DisorderedAtom)	__str__() (in Record)	_pathway() (in Record)
__init__() (in Chain)	__str__() (in Entry)	_pathway() (in Record)
__init__() (in DSSP)	__str__() (in Pathway)	_pdbid_re (in Bio.SCOP.Residues)
__init__() (in ChainSelector)	__str__() (in Reaction)	_phred_to_illumina_quality_str (in Bio.SeqIO.QualityIO)
__init__() (in DisorderedEntityWrapper)	__str__() (in Relation)	_phred_to_sanger_quality_str (in Bio.SeqIO.QualityIO)
__init__() (in Entity)	__str__() (in MarkovModel)	_phred_to_solexa_quality_str (in Bio.SeqIO.QualityIO)
__init__() (in Fragment)	__str__() (in StandardData)	_PHYLIP_ID_WIDTH (in Bio.AlignIO.PhylipIO)
__init__() (in FragmentMapper)	__str__() (in Tree)	_Phyml (in Bio.Phylo.Applications)
__init__() (in ExposureCN)	__str__() (in Interaction)	_pid_line() (in Record)
__init__() (in HSExposureCA)	__str__() (in Network)	_pir_alphabets (in Bio.SeqIO.PirIO)
__init__() (in HSExposureCB)	__str__() (in Reaction)	_place_labels() (in Bio.Graphics.BasicChromosome)
__init__() (in _AbstractHSExposure)	__str__() (in Graph)	_plate (in Bio.phenotype.phen_micro)
__init__() (in MMCIF2Dict)	__str__() (in MultiGraph)	_platesPrefix (in Bio.phenotype.phen_micro)
__init__() (in FastMMCIFParser)	__str__() (in System)	_platesPrefixMammalian (in Bio.phenotype.phen_micro)
__init__() (in MMCIFParser)	__str__() (in BranchColor)	_populate_meta_data() (in StockholmIterator)
__init__() (in Model)	__str__() (in Clade)	_position (in Bio.phenotype.phen_micro)
__init__() (in NACCESS)	__str__() (in Tree)	_possibly_complemented_complex_location (in Bio.GenBank)
__init__() (in NACCESS_atomic)	__str__() (in Accession)	_POSTGRES_RULES_PRESENT (in BioSQL.BioSeqDatabase)
__init__() (in NeighborSearch)	__str__() (in Date)	_PostgreSQL_dbutils (in BioSQL.DBUtils)
__init__() (in PDBIO)	__str__() (in Id)	_postorder_traverse() (in Bio.Phylo.BaseTree)
__init__() (in PDBList)	__str__() (in MolSeq)	_powers_of_36 (in Bio.SeqIO.SffIO)
__init__() (in PDBParser)	__str__() (in Phyloxml)	_PPBuilder (in Bio.PDB.Polypeptide)
__init__() (in PSEA)	__str__() (in Polygon)	_Prank (in Bio.Align.Applications)
__init__() (in CaPPBuilder)	__str__() (in Taxonomy)	_PRECISION (in Bio.pairwise2)
__init__() (in PPBuilder)	__str__() (in Uri)	_preorder_traverse() (in Bio.Phylo.BaseTree)
__init__() (in _PPBuilder)	__str__() (in _Matrix)	_prep_coord() (in HSPFragment)
__init__() (in QCPSuperimposer)	__str__() (in FileRecord)	_prep_fields() (in BlastTabParser)
__init__() (in DisorderedResidue)	__str__() (in Record)	_prep_frame() (in HSPFragment)
__init__() (in Residue)	__str__() (in RestrictionBatch)	_prep_strand() (in HSPFragment)
__init__() (in ResidueDepth)	__str__() (in RestrictionType)	_prim() (in Bio.codonalign.codonalignment)
__init__() (in Structure)	__str__() (in Record)	_print_default_format_warning() (in PDBList)
__init__() (in StructureAlignment)	__str__() (in Record)	_print_name() (in TaggingConsumer)
__init__() (in StructureBuilder)	__str__() (in Record)	_Probcons (in Bio.Align.Applications)
__init__() (in Superimposer)	__str__() (in Domain)	_process() (in Record)
__init__() (in MMCIFIO)	__str__() (in Record)	_process() (in Record)
__init__() (in StructureDecoder)	__str__() (in Node)	_process() (in Record)
__init__() (in MMTFIO)	__str__() (in Residues)	_process() (in Record)
__init__() (in Vector)	__str__() (in Hit)	_process() (in SeqMap)
__init__() (in Network)	__str__() (in HSP)	_process_score_line() (in Hhsuite2TextParser)
__init__() (in Reaction)	__str__() (in HSPFragment)	_product() (in Record)
__init__() (in Graph)	__str__() (in QueryResult)	_PROGRAM (in Bio.SearchIO.HHsuiteIO.hhsuite2_text)
__init__() (in MultiGraph)	__str__() (in MutableSeq)	_project_line() (in Record)
__init__() (in System)	__str__() (in Seq)	_PSIBlastConsumer (in Bio.SearchIO._legacy.NCBIStandalone)
__init__() (in FastTreeCommandline)	__str__() (in UnknownSeq)	_PTR_ID_DESC_SEQLEN (in Bio.SearchIO.FastaIO)
__init__() (in PhymlCommandline)	__str__() (in AfterPosition)	_PTR_ROW_CHECK (in Bio.SearchIO.BlatIO)
__init__() (in RaxmlCommandline)	__str__() (in BeforePosition)	_pubmed_line() (in Reference)
__init__() (in BranchColor)	__str__() (in BetweenPosition)	_pwm (in Bio.motifs)
__init__() (in Clade)	__str__() (in CompoundLocation)	_py3k (in Bio)
__init__() (in Tree)	__str__() (in ExactPosition)	_python_make_score_matrix_fast() (in Bio.pairwise2)
__init__() (in Clade)	__str__() (in FeatureLocation)	_python_rint() (in Bio.pairwise2)
__init__() (in Tree)	__str__() (in OneOfPosition)	_q() (in Bio.KEGG.REST)
__init__() (in Parser)	__str__() (in PositionGap)	_q() (in Bio.codonalign.codonseq)
__init__() (in Writer)	__str__() (in Reference)	_QRE_ID_LEN (in Bio.SearchIO.HmmerIO.hmmer3_text)
__init__() (in Clade)	__str__() (in SeqFeature)	_QRE_ID_LEN_PTN (in Bio.SearchIO.HmmerIO.hmmer3_text)
__init__() (in Tree)	__str__() (in WithinPosition)	_qresult_index() (in BlastTabIndexer)
__init__() (in Parser)	__str__() (in SeqRecord)	_qresult_index_commented() (in BlastTabIndexer)
__init__() (in Writer)	__str__() (in SeqMat)	_query_end_get() (in HSP)
__init__() (in Clade)	__str__() (in Statistics)	_query_end_get() (in HSPFragment)
__init__() (in Tree)	__str__() (in CodonAlignment)	_query_end_set() (in HSPFragment)
__init__() (in Parser)	__str__() (in Instances)	_query_frame_get() (in HSPFragment)
__init__() (in Writer)	__str__() (in Motif)	_query_frame_set() (in HSPFragment)
__init__() (in Paml)	__str__() (in Record)	_query_get() (in HSPFragment)
__init__() (in Baseml)	__str__() (in Motif)	_query_id_idx (in Hmmer3DomtabHmmhitIndexer)
__init__() (in Codeml)	__str__() (in Record)	_query_id_idx (in Hmmer3DomtabHmmqueryIndexer)
__init__() (in Yn00)	__str__() (in JASPAR5)	_query_id_idx (in Hmmer3TabIndexer)
__init__() (in Accession)	__str__() (in GenericPositionMatrix)	_query_inter_ranges_get() (in HSP)
__init__() (in Annotation)	__str__() (in Record)	_query_inter_spans_get() (in HSP)
__init__() (in BinaryCharacters)	__str__() (in Record)	_query_mark (in _BaseExonerateIndexer)
__init__() (in BranchColor)	__str__() (in Record)	_query_mark (in ExonerateCigarIndexer)
__init__() (in Clade)	__str__() (in PlateRecord)	_query_mark (in ExonerateTextIndexer)
__init__() (in CladeRelation)	__str__() (in WellRecord)	_query_mark (in ExonerateVulgarIndexer)
__init__() (in Confidence)	__str__() (in DBSeq)	_query_range_get() (in HSP)
__init__() (in Date)	__sub__() (in Atom)	_query_range_get() (in HSPFragment)
__init__() (in Distribution)	__sub__() (in DisorderedEntityWrapper)	_query_re (in _HSPConsumer)
__init__() (in DomainArchitecture)	__sub__() (in Fragment)	_query_set() (in HSPFragment)
__init__() (in Events)	__sub__() (in Vector)	_query_span_get() (in HSP)
__init__() (in Id)	__sub__() (in Confidence)	_query_span_get() (in HSPFragment)
__init__() (in MolSeq)	__sub__() (in SeqMat)	_query_start_get() (in HSP)
__init__() (in Other)	__sub__() (in PlateRecord)	_query_start_get() (in HSPFragment)
__init__() (in Phylogeny)	__sub__() (in WellRecord)	_query_start_set() (in HSPFragment)
__init__() (in Phyloxml)	__truediv__() (in Vector)	_query_strand_get() (in HSPFragment)
__init__() (in Point)	__truediv__() (in Confidence)	_query_strand_set() (in HSPFragment)
__init__() (in Polygon)	__truediv__() (in RestrictionBatch)	_random_norm() (in Bio.MarkovModel)
__init__() (in Property)	__truediv__() (in RestrictionType)	_Raxml (in Bio.Phylo.Applications)
__init__() (in ProteinDomain)	__version (in _InMemoryIndex)	_re_alb_line2coords (in Bio.Wise.dnal)
__init__() (in Reference)	__version (in _ShelveIndex)	_RE_ALN_ROW (in Bio.SearchIO.ExonerateIO.exonerate_text)
__init__() (in Sequence)	__version_key (in _InMemoryIndex)	_RE_ATTR (in Bio.SearchIO.FastaIO)
__init__() (in SequenceRelation)	__version_key (in _ShelveIndex)	_RE_CIGAR (in Bio.SearchIO.ExonerateIO.exonerate_cigar)
__init__() (in Taxonomy)	__warningregistry__ (in Bio.Align.substitution_matrices)	_re_complex_compound (in Bio.GenBank)
__init__() (in Uri)	__warningregistry__ (in Bio.Alphabet)	_re_complex_location (in Bio.GenBank)
__init__() (in Parser)	__warningregistry__ (in Bio.Index)	_RE_END_EXC (in Bio.SearchIO.FastaIO)
__init__() (in Writer)	__warningregistry__ (in Bio.KDTree)	_RE_EXON (in Bio.SearchIO.ExonerateIO.exonerate_text)
__init__() (in DistanceCalculator)	__warningregistry__ (in Bio.Statistics)	_RE_EXON_LEN (in Bio.SearchIO.ExonerateIO.exonerate_text)
__init__() (in DistanceMatrix)	__warningregistry__ (in Bio.codonalign)	_RE_FLAVS (in Bio.SearchIO.FastaIO)
__init__() (in DistanceTreeConstructor)	__warningregistry__ (in Bio.phenotype)	_RE_GAPOPEN (in Bio.SearchIO.BlastIO.blast_tab)
__init__() (in NNITreeSearcher)	__warningregistry__ (in Bio.triefind)	_RE_HIT_BLOCK_DESC (in Bio.SearchIO.HHsuiteIO.hhsuite2_text)
__init__() (in ParsimonyScorer)	__xor__() (in _BitString)	_RE_HIT_BLOCK_START (in Bio.SearchIO.HHsuiteIO.hhsuite2_text)
__init__() (in ParsimonyTreeConstructor)	_abi_parse_header() (in Bio.SeqIO.AbiIO)	_RE_ID_DESC_PAIRS_PATTERN (in Bio.SearchIO.BlastIO.blast_xml)
__init__() (in _Matrix)	_abi_trim() (in Bio.SeqIO.AbiIO)	_RE_ID_DESC_PATTERN (in Bio.SearchIO.BlastIO.blast_xml)
__init__() (in GenePopController)	_AbiTrimIterator() (in Bio.SeqIO.AbiIO)	_RE_ID_DESC_SEQLEN (in Bio.SearchIO.FastaIO)
__init__() (in _FileIterator)	_AbstractDrawer (in Bio.Graphics.GenomeDiagram)	_RE_ID_DESC_SEQLEN_IDX (in Bio.SearchIO.FastaIO)
__init__() (in _GenePopCommandline)	_AbstractHSExposure (in Bio.PDB.HSExposure)	_RE_MATCH_BLOCK_HIT_SEQ (in Bio.SearchIO.HHsuiteIO.hhsuite2_text)
__init__() (in EasyController)	_AbstractParameter (in Bio.Application)	_RE_MATCH_BLOCK_QUERY_SEQ (in Bio.SearchIO.HHsuiteIO.hhsuite2_text)
__init__() (in FileRecord)	_accept() (in _PPBuilder)	_RE_NER (in Bio.SearchIO.ExonerateIO.exonerate_text)
__init__() (in Record)	_accession_line() (in Record)	_RE_NER_LEN (in Bio.SearchIO.ExonerateIO.exonerate_text)
__init__() (in Record)	_add() (in ScoreDistribution)	_re_oneof_position (in Bio.GenBank)
__init__() (in PrintFormat)	_add_bioentry_dbxref() (in DatabaseLoader)	_RE_OPT (in Bio.SearchIO.HmmerIO.hmmer3_text)
__init__() (in Analysis)	_add_dbxref() (in DatabaseLoader)	_RE_PROGRAM (in Bio.SearchIO.HmmerIO.hmmer3_text)
__init__() (in FormattedSeq)	_add_feature() (in _RecordConsumer)	_re_prop_name (in Bio.Application)
__init__() (in RestrictionBatch)	_add_nodedata() (in Tree)	_RE_QUERY (in Bio.SearchIO.HHsuiteIO.hhsuite2_text)
__init__() (in RestrictionType)	_add_numbering_table() (in FSSPAlign)	_RE_ROW_CHECK (in Bio.SearchIO.BlatIO)
__init__() (in Astral)	_add_seqfeature_dbxref() (in DatabaseLoader)	_RE_ROW_CHECK_IDX (in Bio.SearchIO.BlatIO)
__init__() (in Index)	_add_subtree() (in Tree)	_RE_SCODON_END (in Bio.SearchIO.ExonerateIO.exonerate_text)
__init__() (in Record)	_AddTellHandle (in Bio.SeqIO.SffIO)	_RE_SCODON_START (in Bio.SearchIO.ExonerateIO.exonerate_text)
__init__() (in Record)	_adjust_aa_seq() (in Bio.SearchIO.ExonerateIO._base)	_re_search() (in Bio.SearchIO._legacy.NCBIStandalone)
__init__() (in Record)	_adjust_charlabels() (in Nexus)	_RE_SHIFTS (in Bio.SearchIO.ExonerateIO._base)
__init__() (in Domain)	_adjust_coords() (in BlastTabWriter)	_re_simple_compound (in Bio.GenBank)
__init__() (in Record)	_adjust_lines() (in Bio.Nexus.Nexus)	_re_simple_location (in Bio.GenBank)
__init__() (in Node)	_adjust_output() (in BlastTabWriter)	_RE_START_EXC (in Bio.SearchIO.FastaIO)
__init__() (in Res)	_adjust_output() (in BlastXmlWriter)	_RE_TRANS (in Bio.SearchIO.ExonerateIO._base)
__init__() (in SeqMap)	_alb_line2coords() (in Bio.Wise.dnal)	_re_unit (in Bio.Wise.psw)
__init__() (in SeqMapIndex)	_align() (in QCPSuperimposer)	_RE_VCOMP (in Bio.SearchIO.ExonerateIO.exonerate_vulgar)
__init__() (in Residues)	_align() (in Bio.pairwise2)	_RE_VERSION (in Bio.SearchIO.BlastIO.blast_xml)
__init__() (in Scop)	_align_shift_recs() (in Bio.codonalign)	_RE_VERSION (in Bio.SearchIO.HmmerIO.hmmer3_text)
__init__() (in SVDSuperimposer)	_aligners (in Bio.Align)	_RE_VULGAR (in Bio.SearchIO.ExonerateIO.exonerate_vulgar)
__init__() (in BlastTabIndexer)	_AlignmentConsumer (in Bio.SearchIO._legacy.NCBIStandalone)	_re_within_position (in Bio.GenBank)
__init__() (in BlastTabParser)	_all_blank() (in MarkovModelBuilder)	_reaction() (in Record)
__init__() (in BlastTabWriter)	_all_pseudo() (in MarkovModelBuilder)	_read() (in Bio.SeqIO.GckIO)
__init__() (in BlastTextParser)	_allowed_lookups (in BioSQL.BioSeqDatabase)	_read() (in Bio.SeqIO.XdnaIO)
__init__() (in BlastXmlIndexer)	_aln_get() (in HSPFragment)	_read() (in Bio.SwissProt)
__init__() (in BlastXmlParser)	_ALN_MARK (in _BaseExonerateParser)	_read() (in Bio.UniGene)
__init__() (in BlastXmlWriter)	_ALN_MARK (in ExonerateCigarParser)	_read_alignment() (in ExonerateTextParser)
__init__() (in _BlastXmlGenerator)	_ALN_MARK (in ExonerateTextParser)	_read_allele_freq_table() (in Bio.PopGen.GenePop.Controller)
__init__() (in BlatPslIndexer)	_ALN_MARK (in ExonerateVulgarParser)	_read_alphabet() (in Bio.motifs.minimal)
__init__() (in BlatPslParser)	_aln_span_get() (in HSP)	_read_background() (in Bio.motifs.minimal)
__init__() (in BlatPslWriter)	_aln_span_get() (in HSPFragment)	_read_cc() (in Bio.SwissProt)
__init__() (in _BaseExonerateParser)	_aln_span_set() (in HSPFragment)	_read_dicts() (in Bio.NMR.xpktools)
__init__() (in FastaM10Indexer)	_alphabet_from_input() (in FreqTable)	_read_dr() (in Bio.SwissProt)
__init__() (in FastaM10Parser)	_alphabet_from_matrix() (in SeqMat)	_read_dt() (in Bio.SwissProt)
__init__() (in Hhsuite2TextParser)	_alphabet_get() (in HSPFragment)	_read_feature() (in Bio.SeqIO.XdnaIO)
__init__() (in _BaseHmmerTextIndexer)	_alphabet_set() (in HSPFragment)	_read_fragments() (in Bio.PDB.FragmentMapper')
__init__() (in Hmmer2TextParser)	_append() (in MultipleSeqAlignment)	_read_ft() (in Bio.SwissProt)
__init__() (in Hmmer3DomtabHmmhitWriter)	_apply_block_structure() (in Nexus)	_read_headed_triangle_matrix() (in Bio.PopGen.GenePop.Controller)
__init__() (in Hmmer3TabParser)	_argmaxes() (in Bio.MarkovModel)	_read_header() (in Bio._utils)
__init__() (in Hmmer3TabWriter)	_Argument (in Bio.Application)	_read_id() (in Bio.SwissProt)
__init__() (in Hmmer3TextParser)	_ArgumentList (in Bio.Application)	_read_jaspar() (in Bio.motifs.jaspar)
__init__() (in InterproscanXmlParser)	_as_bytes() (in Bio._py3k)	_read_key_value() (in Bio.Geo)
__init__() (in SearchIndexer)	_as_unicode() (in Bio._py3k)	_read_kw() (in Bio.SwissProt)
__init__() (in BlastErrorParser)	_assign_atom_mass() (in Atom)	_read_lpm() (in Bio.motifs.minimal)
__init__() (in BlastParser)	_assign_element() (in Atom)	_read_motif_name() (in Bio.motifs.minimal)
__init__() (in Iterator)	_ATOM_FORMAT_STRING (in Bio.PDB.PDBIO')	_read_motif_statistics() (in Bio.motifs.minimal)
__init__() (in PSIBlastParser)	_atom_name_dict (in Bio.PDB.Residue)	_read_oh() (in Bio.SwissProt)
__init__() (in _BlastConsumer)	_atomic_radii (in Bio.PDB.ResidueDepth')	_read_overhang() (in Bio.SeqIO.XdnaIO)
__init__() (in _BlastErrorConsumer)	_attr_DBRef() (in SeqXmlIterator)	_read_ox() (in Bio.SwissProt)
__init__() (in _PSIBlastConsumer)	_attr_entry() (in SeqXmlIterator)	_read_p4string() (in Bio.SeqIO.GckIO)
__init__() (in _Scanner)	_attr_property() (in SeqXmlIterator)	_read_packet() (in Bio.SeqIO.GckIO)
__init__() (in TaggingConsumer)	_attr_seqXML() (in SeqXmlIterator)	_read_pe() (in Bio.SwissProt)
__init__() (in Hit)	_attr_species() (in SeqXmlIterator)	_read_pfm() (in Bio.motifs.jaspar)
__init__() (in HSP)	_attribute_matcher() (in Bio.Phylo.BaseTree)	_read_pfm_four_columns() (in Bio.motifs.pfm)
__init__() (in HSPFragment)	_attributes() (in XMLRecordIterator)	_read_pfm_four_rows() (in Bio.motifs.pfm)
__init__() (in QueryResult)	_augment_blast_hsp() (in Bio.SearchIO.BlastIO.blast_tab)	_read_pstring() (in Bio.SeqIO.GckIO)
__init__() (in MutableSeq)	_authors_line() (in Reference)	_read_pstring() (in Bio.SeqIO.XdnaIO)
__init__() (in Seq)	_backward() (in Bio.MarkovModel)	_read_pstring_as_integer() (in Bio.SeqIO.XdnaIO)
__init__() (in UnknownSeq)	_backward_recursion() (in AbstractDPAlgorithms)	_read_rc() (in Bio.SwissProt)
__init__() (in CompoundLocation)	_backward_recursion() (in ScaledDPAlgorithms)	_read_rn() (in Bio.SwissProt)
__init__() (in FeatureLocation)	_base (in Bio.SearchIO.ExonerateIO)	_read_rx() (in Bio.SwissProt)
__init__() (in PositionGap)	_base (in Bio.SearchIO.HmmerIO)	_read_sites() (in Bio.motifs.jaspar)
__init__() (in Reference)	_base (in Bio.SearchIO._model)	_read_table() (in Bio.PopGen.GenePop.Controller)
__init__() (in SeqFeature)	_base_count_line() (in Record)	_read_triangle_matrix() (in Bio.PopGen.GenePop.Controller)
__init__() (in FastaTwoLineWriter)	_BASE_URL (in Bio.TogoWS)	_read_until() (in Hhsuite2TextParser)
__init__() (in FastaWriter)	_BaseExonerateIndexer (in Bio.SearchIO.ExonerateIO._base)	_read_until() (in Hmmer3TextParser)
__init__() (in SequenceIterator)	_BaseExonerateParser (in Bio.SearchIO.ExonerateIO._base)	_read_version() (in Bio.motifs.minimal)
__init__() (in SequenceWriter)	_BaseGenBankConsumer	_read_vertex_array() (in Bio.PDB.ResidueDepth')
__init__() (in SequentialSequenceWriter)	_BaseHmmerTextIndexer (in Bio.SearchIO.HmmerIO._base)	_readline_and_check_start() (in Bio.MarkovModel)
__init__() (in NibWriter)	_BaseHSP (in Bio.SearchIO._model._base)	_RecordConsumer
__init__() (in PhdWriter)	_BaseSearchObject (in Bio.SearchIO._model._base)	_recover_alignments() (in Bio.pairwise2)
__init__() (in PirWriter)	_baum_welch() (in Bio.MarkovModel)	_reference_line() (in Reference)
__init__() (in QualPhredWriter)	_baum_welch_one() (in Bio.MarkovModel)	_region2bin() (in MafIndex)
__init__() (in SeqXmlIterator)	_between_location (in Bio.GenBank)	_remark_line() (in Reference)
__init__() (in SeqXmlWriter)	_bgzf_eof (in Bio.bgzf)	_remove_newlines() (in _BaseGenBankConsumer)
__init__() (in XMLRecordIterator)	_bgzf_header (in Bio.bgzf)	_remove_spaces() (in _BaseGenBankConsumer)
__init__() (in SffWriter)	_bgzf_magic (in Bio.bgzf)	_reorient_starts() (in Bio.SearchIO.BlatIO)
__init__() (in _AddTellHandle)	_binary_to_string_handle() (in Bio._py3k)	_replace_parenthesized_ambigs() (in Bio.Nexus.Nexus)
__init__() (in _PacketIterator)	_BinaryFormats (in Bio.SeqIO)	_replace_wspace() (in Bio.Phylo.PhyloXMLIO)
__init__() (in Parser)	_BitString (in Bio.Phylo.Consensus)	_requires_newline() (in MMCIFIO)
__init__() (in IntelliGeneticsRandomAccess)	_bitstring_topology() (in Bio.Phylo.Consensus)	_requires_quote() (in MMCIFIO)
__init__() (in SeqFileRandomAccess)	_BlastConsumer (in Bio.SearchIO._legacy.NCBIStandalone)	_reserved_names (in Bio.Application)
__init__() (in SequentialSeqFileRandomAccess)	_BlastErrorConsumer (in Bio.SearchIO._legacy.NCBIStandalone)	_reset_full_id() (in Entity)
__init__() (in SffRandomAccess)	_BlastXmlGenerator (in Bio.SearchIO.BlastIO.blast_xml)	_resolve() (in Nexus)
__init__() (in SeqRecord)	_boundaries() (in Analysis)	_RestrictedDict (in Bio.SeqRecord)
__init__() (in _RestrictedDict)	_build_align_cmdline() (in Bio.Wise)	_restrictionbatch (in Bio.Restriction.Restriction)
__init__() (in CodonAdaptationIndex)	_build_comments() (in BlastTabWriter)	_retrieve_annotations() (in BioSQL.BioSeq)
__init__() (in IsoelectricPoint)	_build_dnal_cmdline() (in Bio.Wise.dnal)	_retrieve_comment() (in BioSQL.BioSeq)
__init__() (in ProteinAnalysis)	_build_exp_freq_mat() (in Bio.SubsMat)	_retrieve_dbxrefs() (in BioSQL.BioSeq)
__init__() (in ACEFileRecord)	_build_header() (in BlatPslWriter)	_retrieve_features() (in BioSQL.BioSeq)
__init__() (in Contig)	_build_header() (in Hmmer3DomtabHmmhitWriter)	_retrieve_location_qualifier_value() (in BioSQL.BioSeq)
__init__() (in Reads)	_build_header() (in Hmmer3TabWriter)	_retrieve_qualifier_value() (in BioSQL.BioSeq)
__init__() (in af)	_build_index() (in _SQLiteManySeqFilesDict)	_retrieve_reference() (in BioSQL.BioSeq)
__init__() (in bs)	_build_log_odds_mat() (in Bio.SubsMat)	_retrieve_seq() (in BioSQL.BioSeq)
__init__() (in ct)	_build_obs_freq_mat() (in Bio.SubsMat)	_retrieve_seq_len() (in BioSQL.BioSeq)
__init__() (in ds)	_build_protein_matrix() (in DistanceCalculator)	_retrieve_taxon() (in BioSQL.BioSeq)
__init__() (in qa)	_build_row() (in BlatPslWriter)	_rev_modify() (in NoCut)
__init__() (in rd)	_build_row() (in Hmmer3DomtabHmmhitWriter)	_rev_modify() (in OneCut)
__init__() (in rt)	_build_row() (in Hmmer3TabWriter)	_rev_modify() (in TwoCuts)
__init__() (in wa)	_build_rows() (in BlastTabWriter)	_reverse_matrices() (in Bio.pairwise2)
__init__() (in wr)	_build_structure() (in FastMMCIFParser)	_rms() (in QCPSuperimposer)
__init__() (in NovoalignCommandline)	_build_structure() (in MMCIFParser)	_rms() (in SVDSuperimposer)
__init__() (in BwaAlignCommandline)	_build_subs_mat() (in Bio.SubsMat)	_rna_complement_table (in Bio.Seq)
__init__() (in BwaBwaswCommandline)	_bwa (in Bio.Sequencing.Applications)	_run_genepop() (in GenePopController)
__init__() (in BwaIndexCommandline)	_BYTEFMT (in Bio.SeqIO.AbiIO)	_safe_float() (in Bio.SearchIO._legacy.NCBIStandalone)
__init__() (in BwaMemCommandline)	_bytes_BC (in Bio.bgzf)	_safe_int() (in Bio.SearchIO._legacy.NCBIStandalone)
__init__() (in BwaSampeCommandline)	_bytes_bytearray_to_str() (in Bio._py3k)	_sample (in Bio.phenotype.phen_micro)
__init__() (in BwaSamseCommandline)	_bytes_to_string() (in Bio._py3k)	_samtools (in Bio.Sequencing.Applications)
__init__() (in SamtoolsCalmdCommandline)	_calc_diversities_fis() (in GenePopController)	_save_dict() (in MMCIFIO)
__init__() (in SamtoolsCatCommandline)	_calc_empirical_expects() (in Bio.MaxEntropy)	_save_structure() (in MMCIFIO)
__init__() (in SamtoolsFaidxCommandline)	_calc_f_sharp() (in Bio.MaxEntropy)	_save_structure() (in MMTFIO)
__init__() (in SamtoolsFixmateCommandline)	_calc_ibd() (in GenePopController)	_savedata() (in Record)
__init__() (in SamtoolsIdxstatsCommandline)	_calc_millibad() (in Bio.SearchIO.BlatIO)	_savekmeans() (in Record)
__init__() (in SamtoolsIndexCommandline)	_calc_model_expects() (in Bio.MaxEntropy)	_savetree() (in Record)
__init__() (in SamtoolsMergeCommandline)	_calc_p_class_given_x() (in Bio.MaxEntropy)	_sbjct_re (in _HSPConsumer)
__init__() (in SamtoolsMpileupCommandline)	_calc_score() (in Bio.SearchIO.BlatIO)	_scan_alignment_header() (in _Scanner)
__init__() (in SamtoolsPhaseCommandline)	_calculate() (in Bio.motifs.matrix)	_scan_alignments() (in _Scanner)
__init__() (in SamtoolsReheaderCommandline)	_calculate_emissions() (in Bio.HMM.MarkovModel)	_scan_database_report() (in _Scanner)
__init__() (in SamtoolsRmdupCommandline)	_calculate_from_transitions() (in Bio.HMM.MarkovModel)	_scan_descriptions() (in _Scanner)
__init__() (in SamtoolsTargetcutCommandline)	_calculate_s_value() (in ScaledDPAlgorithms)	_scan_header() (in _Scanner)
__init__() (in SamtoolsVersion0xSortCommandline)	_calculate_to_transitions() (in Bio.HMM.MarkovModel)	_scan_hsp() (in _Scanner)
__init__() (in SamtoolsVersion1xSortCommandline)	_case_less() (in Alphabet)	_scan_hsp_alignment() (in _Scanner)
__init__() (in SamtoolsViewCommandline)	_cdao_owl (in Bio.Phylo)	_scan_hsp_header() (in _Scanner)
__init__() (in Record)	_chain_id_iterator() (in MMTFIO)	_scan_masterslave_alignment() (in _Scanner)
__init__() (in FreqTable)	_changeset() (in Nexus)	_scan_one_pairwise_alignment() (in _Scanner)
__init__() (in SeqMat)	_chargeR() (in IsoelectricPoint)	_scan_pairwise_alignments() (in _Scanner)
__init__() (in Record)	_charlabels() (in Nexus)	_scan_parameters() (in _Scanner)
__init__() (in Record)	_charpartition() (in Nexus)	_scan_rounds() (in _Scanner)
__init__() (in Reference)	_charset() (in Nexus)	_Scanner (in Bio.SearchIO._legacy.NCBIStandalone)
__init__() (in ProtsimLine)	_charstatelabels() (in Nexus)	_score_e_re (in Bio.SearchIO._legacy.NCBIStandalone)
__init__() (in Record)	_check() (in Bio.SeqUtils.MeltingTemp)	_SCORE_GAP_EXTENSION (in Bio.Wise.dnal)
__init__() (in STSLine)	_check_bases() (in Bio.Restriction.Restriction)	_SCORE_GAP_START (in Bio.Wise.dnal)
__init__() (in SequenceLine)	_check_corr() (in Bio.codonalign)	_SCORE_MATCH (in Bio.Wise.dnal)
__init__() (in Statistics)	_check_eof() (in Bio.SeqIO.SffIO)	_SCORE_MISMATCH (in Bio.Wise.dnal)
__init__() (in AlignmentColumn)	_check_mode() (in Bio.SeqIO.SffIO)	_search() (in NonPalindromic)
__init__() (in ColumnUnit)	_check_str() (in Bio.Phylo.PhyloXML)	_search() (in Palindromic)
__init__() (in BgzfReader)	_check_taxlabels() (in Nexus)	_search_db_names (in Bio.TogoWS)
__init__() (in BgzfWriter)	_check_type_compatible() (in Bio.Alphabet)	_segment_line() (in Record)
__init__() (in CodonAlignment)	_check_value() (in AbstractCommandline)	_select (in Bio.PDB.PDBIO')
__init__() (in CodonSeq)	_chop_end_codes() (in Bio.PDB.parse_pdb_header')	_select (in Bio.PDB.mmcifio)
__init__() (in kNN)	_chop_end_misc() (in Bio.PDB.parse_pdb_header')	_select (in Bio.PDB.mmtf.mmtfio)
__init__() (in Instances)	_ChromosomeComponent (in Bio.Graphics.BasicChromosome)	_select_charged() (in IsoelectricPoint)
__init__() (in Motif)	_CircularDrawer (in Bio.Graphics.GenomeDiagram)	_seq_topologies (in Bio.SeqIO.XdnaIO)
__init__() (in Record)	_CKDTree (in Bio.KDTree)	_seq_types (in Bio.SeqIO.XdnaIO)
__init__() (in XXmotifCommandline)	_clade_complex_types (in Parser)	_SeqIO_to_alignment_iterator() (in Bio.AlignIO)
__init__() (in Motif)	_clade_list_types (in Parser)	_seqmatrix2strmatrix() (in Bio.Nexus.Nexus)
__init__() (in Record)	_clade_to_bitstr() (in Bio.Phylo.Consensus)	_sequence_line() (in Record)
__init__() (in JASPAR5)	_clade_tracked_tags (in Parser)	_serialize() (in Bio.Phylo.PhyloXMLIO)
__init__() (in Record)	_class_matcher() (in Bio.Phylo.BaseTree)	_set() (in Nexus)
__init__() (in GenericPositionMatrix)	_classify_alphabet_for_nexus() (in NexusWriter)	_set_a() (in ColorSpiral)
__init__() (in PositionWeightMatrix)	_classname() (in Record)	_set_b() (in ColorSpiral)
__init__() (in Instance)	_clean() (in Bio.SeqIO.Interfaces)	_set_color() (in Clade)
__init__() (in Motif)	_clean_alignments() (in Bio.pairwise2)	_set_colors_and_shapes() (in ComparativeScatterPlot)
__init__() (in Record)	_clean_attrib() (in Bio.Phylo.PhyloXMLIO)	_set_confidence() (in Clade)
__init__() (in Record)	_clean_blocks() (in Bio.SearchIO.ExonerateIO.exonerate_text)	_set_confidence() (in Phylogeny)
__init__() (in ScoreDistribution)	_clean_location() (in _BaseGenBankConsumer)	_set_frame() (in Bio.SearchIO.ExonerateIO._base)
__init__() (in Record)	_clean_translation() (in FeatureValueCleaner)	_set_header_application() (in BlastParser)
__init__() (in XMSScanner)	_cleaner (in Bio.GenBank)	_set_header_database() (in BlastParser)
__init__() (in affine_penalty)	_clear() (in QCPSuperimposer)	_set_header_query() (in BlastParser)
__init__() (in dictionary_match)	_clear() (in SVDSuperimposer)	_set_header_query_id() (in BlastParser)
__init__() (in identity_match)	_clear_parameter() (in AbstractCommandline)	_set_header_query_letters() (in BlastParser)
__init__() (in JsonWriter)	_ClustalOmega (in Bio.Align.Applications)	_set_header_reference() (in BlastParser)
__init__() (in PlateRecord)	_Clustalw (in Bio.Align.Applications)	_set_header_version() (in BlastParser)
__init__() (in WellRecord)	_cluster (in Bio.Cluster)	_set_hsp_align_len() (in BlastParser)
__init__() (in DBSeq)	_CMDLINE_DNAL (in Bio.Wise.dnal)	_set_hsp_bit_score() (in BlastParser)
__init__() (in DBSeqRecord)	_CMDLINE_FGREP_COUNT (in Bio.Wise.dnal)	_set_hsp_e_value() (in BlastParser)
__init__() (in Adaptor)	_CMDLINE_PSW (in Bio.Wise.psw)	_set_hsp_gaps() (in BlastParser)
__init__() (in BioSeqDatabase)	_codeset() (in Nexus)	_set_hsp_hit_frame() (in BlastParser)
__init__() (in DBServer)	_codonposset() (in Nexus)	_set_hsp_hit_from() (in BlastParser)
__init__() (in _CursorWrapper)	_codons2re() (in Bio.codonalign)	_set_hsp_hit_strand() (in BlastParser)
__init__() (in Generic_dbutils)	_cofactor() (in Record)	_set_hsp_hit_to() (in BlastParser)
__init__() (in DatabaseLoader)	_col_ave() (in Bio.NMR.NOEtools)	_set_hsp_identity() (in BlastParser)
__init__() (in DatabaseRemover)	_collapse_wspace() (in Bio.Phylo.PhyloXMLIO)	_set_hsp_midline() (in BlastParser)
__int__() (in Confidence)	_color_from_count() (in ChromosomeCounts)	_set_hsp_positive() (in BlastParser)
__iter__() (in MultipleSeqAlignment)	_color_trans (in Bio.Graphics.BasicChromosome)	_set_hsp_query_end() (in BlastParser)
__iter__() (in PairwiseAlignments)	_Colors (in Bio.Graphics.GenomeDiagram)	_set_hsp_query_frame() (in BlastParser)
__iter__() (in AlignmentIterator)	_COLUMN_FRAG (in Bio.SearchIO.BlastIO.blast_tab)	_set_hsp_query_seq() (in BlastParser)
__iter__() (in UndoHandle)	_COLUMN_HIT (in Bio.SearchIO.BlastIO.blast_tab)	_set_hsp_query_start() (in BlastParser)
__iter__() (in _IndexedSeqFileDict)	_COLUMN_HSP (in Bio.SearchIO.BlastIO.blast_tab)	_set_hsp_query_strand() (in BlastParser)
__iter__() (in _IndexedSeqFileProxy)	_COLUMN_QRESULT (in Bio.SearchIO.BlastIO.blast_tab)	_set_hsp_score() (in BlastParser)
__iter__() (in _SQLiteManySeqFilesDict)	_combine_args() (in Bio.Phylo.BaseTree)	_set_hsp_seqs() (in Bio.SearchIO.FastaIO)
__iter__() (in Iterator)	_combine_matchers() (in Bio.Phylo.BaseTree)	_set_hsp_subject_seq() (in BlastParser)
__iter__() (in StandardData)	_comment() (in Record)	_set_jitter() (in ColorSpiral)
__iter__() (in AbstractPropertyMap)	_comment_line() (in Record)	_set_kind() (in AlignmentColumn)
__iter__() (in DisorderedAtom)	_comp_coords() (in Bio.SearchIO.ExonerateIO.exonerate_text)	_set_location_operator() (in SeqFeature)
__iter__() (in DisorderedEntityWrapper)	_comp_intron_lens() (in Bio.SearchIO.ExonerateIO.exonerate_text)	_set_parameters_expect() (in BlastParser)
__iter__() (in Entity)	_comp_split_codons() (in Bio.SearchIO.ExonerateIO.exonerate_text)	_set_parameters_filter() (in BlastParser)
__iter__() (in Clade)	_compact4nexus() (in Bio.Nexus.Nexus)	_set_parameters_gap_extend() (in BlastParser)
__iter__() (in Events)	_complex_location (in Bio.GenBank)	_set_parameters_gap_penalties() (in BlastParser)
__iter__() (in Other)	_compute_gapopen_num() (in Bio.SearchIO.BlastIO.blast_tab)	_set_parameters_matrix() (in BlastParser)
__iter__() (in Phyloxml)	_consensus_alphabet() (in Bio.Alphabet)	_set_parameters_sc_match() (in BlastParser)
__iter__() (in _FileIterator)	_consensus_base_alphabet() (in Bio.Alphabet)	_set_parameters_sc_mismatch() (in BlastParser)
__iter__() (in BlastTabIndexer)	_consrtm_line() (in Reference)	_set_per_column_annotations() (in MultipleSeqAlignment)
__iter__() (in BlastTabParser)	_construct_cgi() (in Bio.Entrez)	_set_per_letter_annotations() (in SeqRecord)
__iter__() (in BlastTextParser)	_construct_params() (in Bio.Entrez)	_set_qresult_hits() (in Bio.SearchIO.FastaIO)
__iter__() (in BlastXmlIndexer)	_consume_entry() (in BlastTableReader)	_set_record_hits() (in BlastParser)
__iter__() (in BlastXmlParser)	_consume_header() (in BlastTableReader)	_set_record_query_def() (in BlastParser)
__iter__() (in BlatPslIndexer)	_contents() (in Bio.NaiveBayes)	_set_record_query_id() (in BlastParser)
__iter__() (in BlatPslParser)	_contig_line() (in Record)	_set_record_query_letters() (in BlastParser)
__iter__() (in _BaseExonerateIndexer)	_convert (in Bio.SeqIO)	_set_ref() (in SeqFeature)
__iter__() (in _BaseExonerateParser)	_convert_formats (in Bio.TogoWS)	_set_ref_db() (in SeqFeature)
__iter__() (in FastaM10Indexer)	_convert_key() (in Array)	_set_rel_paths() (in Paml)
__iter__() (in FastaM10Parser)	_convert_list() (in _CursorWrapper)	_set_rel_paths() (in Baseml)
__iter__() (in Hhsuite2TextParser)	_convert_to_python_numbers() (in _BaseGenBankConsumer)	_set_rel_paths() (in Codeml)
__iter__() (in Hmmer2TextIndexer)	_convert_tuple() (in _CursorWrapper)	_set_seq() (in HSPFragment)
__iter__() (in Hmmer2TextParser)	_converter (in Bio.SeqIO._convert)	_set_seq() (in SeqRecord)
__iter__() (in Hmmer3TabIndexer)	_copy_and_check() (in Bio.MarkovModel)	_set_statistics_db_len() (in BlastParser)
__iter__() (in Hmmer3TabParser)	_correct_matrix() (in SeqMat)	_set_statistics_db_num() (in BlastParser)
__iter__() (in Hmmer3TextIndexer)	_count_clades() (in Bio.Phylo.Consensus)	_set_statistics_eff_space() (in BlastParser)
__iter__() (in Hmmer3TextParser)	_count_codons() (in CodonAdaptationIndex)	_set_statistics_entropy() (in BlastParser)
__iter__() (in InterproscanXmlParser)	_count_diff_NG86() (in Bio.codonalign.codonseq)	_set_statistics_hsp_len() (in BlastParser)
__iter__() (in Iterator)	_count_diff_YN00() (in Bio.codonalign.codonseq)	_set_statistics_kappa() (in BlastParser)
__iter__() (in Hit)	_count_emissions() (in KnownStateTrainer)	_set_statistics_lambda() (in BlastParser)
__iter__() (in HSP)	_count_replacement() (in Bio.codonalign.codonalignment)	_set_strand() (in CompoundLocation)
__iter__() (in QueryResult)	_count_site_NG86() (in Bio.codonalign.codonseq)	_set_strand() (in FeatureLocation)
__iter__() (in CompoundLocation)	_count_site_YN00() (in Bio.codonalign.codonseq)	_set_strand() (in SeqFeature)
__iter__() (in FeatureLocation)	_count_transitions() (in KnownStateTrainer)	_set_taxonomy() (in Clade)
__iter__() (in SeqFeature)	_create_hits() (in Hmmer3TextParser)	_set_v_final() (in ColorSpiral)
__iter__() (in SequenceIterator)	_create_hsp() (in Bio.SearchIO.BlatIO)	_set_v_init() (in ColorSpiral)
__iter__() (in XMLRecordIterator)	_create_hsp() (in Bio.SearchIO.ExonerateIO._base)	_set_zero_diagonal() (in DistanceMatrix)
__iter__() (in _PacketIterator)	_create_qresult() (in Hhsuite2TextParser)	_setbgcolor() (in Graphics)
__iter__() (in EmblRandomAccess)	_CrossLink (in Bio.Graphics.GenomeDiagram)	_setcoords() (in Graphics)
__iter__() (in FastqRandomAccess)	_csvData (in Bio.phenotype.phen_micro)	_setentry1() (in Relation)
__iter__() (in GenBankRandomAccess)	_current_track_start_end() (in AbstractDrawer)	_setentry2() (in Relation)
__iter__() (in IntelliGeneticsRandomAccess)	_CursorWrapper (in BioSQL.BioSeqDatabase)	_setfgcolor() (in Graphics)
__iter__() (in SequentialSeqFileRandomAccess)	_data_map() (in Bio.NMR.NOEtools)	_setheight() (in Graphics)
__iter__() (in SffRandomAccess)	_DatabaseReportConsumer (in Bio.SearchIO._legacy.NCBIStandalone)	_setid() (in Component)
__iter__() (in SwissRandomAccess)	_datafile (in Bio.phenotype.phen_micro)	_setid() (in Entry)
__iter__() (in TabRandomAccess)	_db_source_line() (in Record)	_setid() (in Reaction)
__iter__() (in UniprotRandomAccess)	_dblink_line() (in Record)	_setname() (in Entry)
__iter__() (in SeqRecord)	_dblinks() (in Record)	_setname() (in Pathway)
__iter__() (in BgzfReader)	_dblinks() (in Record)	_setnames() (in Reaction)
__iter__() (in PlateRecord)	_dblinks() (in Record)	_setnumber() (in Pathway)
__iter__() (in WellRecord)	_dbutils (in BioSQL.DBUtils)	_setreaction() (in Entry)
__iter__() (in BioSeqDatabase)	_decode() (in Bio.SeqIO.SnapGeneIO)	_setup_blast_v1() (in BlastParser)
__iter__() (in DBServer)	_DEFAULT_FIELDS (in Bio.SearchIO.BlastIO.blast_tab)	_setup_blast_v2() (in BlastParser)
__le__() (in PairwiseAlignment)	_default_wrap() (in Bio.KEGG)	_setupTime (in Bio.phenotype.phen_micro)
__le__() (in Atom)	_definition() (in Record)	_setwidth() (in Graphics)
__le__() (in Chain)	_definition_line() (in Record)	_setx() (in Graphics)
__le__() (in DisorderedEntityWrapper)	_del_confidence() (in Clade)	_sety() (in Graphics)
__le__() (in Entity)	_del_confidence() (in Phylogeny)	_sff (in Bio.SeqIO.SffIO)
__le__() (in Confidence)	_delbgcolor() (in Graphics)	_sff_do_slow_index() (in Bio.SeqIO.SffIO)
__le__() (in RestrictionType)	_delcoords() (in Graphics)	_sff_file_header() (in Bio.SeqIO.SffIO)
__le__() (in MutableSeq)	_delentry1() (in Relation)	_sff_find_roche_index() (in Bio.SeqIO.SffIO)
__le__() (in Seq)	_delentry2() (in Relation)	_sff_read_raw_record() (in Bio.SeqIO.SffIO)
__le___() (in SeqRecord)	_delfgcolor() (in Graphics)	_sff_read_roche_index() (in Bio.SeqIO.SffIO)
__len__() (in MultipleSeqAlignment)	_delheight() (in Graphics)	_sff_read_seq_record() (in Bio.SeqIO.SffIO)
__len__() (in PairwiseAlignments)	_delid() (in Component)	_SffTrimIterator() (in Bio.SeqIO.SffIO)
__len__() (in MafIndex)	_delid() (in Entry)	_ShelveIndex (in Bio.Index)
__len__() (in Chain)	_delid() (in Reaction)	_ShelveIndex__version (in _ShelveIndex)
__len__() (in Crystal)	_delname() (in Entry)	_ShelveIndex__version_key (in _ShelveIndex)
__len__() (in Hetero)	_delname() (in Pathway)	_shift() (in AfterPosition)
__len__() (in Primers)	_delnames() (in Reaction)	_shift() (in BeforePosition)
__len__() (in fff_rec)	_delnumber() (in Pathway)	_shift() (in BetweenPosition)
__len__() (in _IndexedSeqFileDict)	_delreaction() (in Entry)	_shift() (in CompoundLocation)
__len__() (in _SQLiteManySeqFilesDict)	_delwidth() (in Graphics)	_shift() (in ExactPosition)
__len__() (in AbstractDrawer)	_delx() (in Graphics)	_shift() (in FeatureLocation)
__len__() (in FeatureSet)	_dely() (in Graphics)	_shift() (in OneOfPosition)
__len__() (in GraphData)	_DescriptionConsumer (in Bio.SearchIO._legacy.NCBIStandalone)	_shift() (in SeqFeature)
__len__() (in GraphSet)	_determine_position() (in BarChartDistribution)	_shift() (in UnknownPosition)
__len__() (in StandardData)	_diagnose_error() (in BlastErrorParser)	_shift() (in WithinPosition)
__len__() (in AbstractPropertyMap)	_Diagram (in Bio.Graphics.GenomeDiagram)	_simple_location (in Bio.GenBank)
__len__() (in DisorderedEntityWrapper)	_Dialign (in Bio.Align.Applications)	_solexa_to_illumina_quality_str (in Bio.SeqIO.QualityIO)
__len__() (in Entity)	_dict_str2bool() (in Bio.Phylo.PhyloXMLIO)	_solexa_to_sanger_quality_str (in Bio.SeqIO.QualityIO)
__len__() (in Fragment)	_diff_codon() (in Bio.codonalign.codonseq)	_solexa_to_solexa_quality_str (in Bio.SeqIO.QualityIO)
__len__() (in Clade)	_digest() (in CAPSMap)	_solo_bond (in Bio.GenBank)
__len__() (in Events)	_digest_with() (in CAPSMap)	_solo_location (in Bio.GenBank)
__len__() (in Phyloxml)	_dijkstra() (in Bio.codonalign.codonalignment)	_sort_keys_by_values() (in Bio.Nexus.Nexus)
__len__() (in _Matrix)	_dimensions() (in Nexus)	_sorted_attrs() (in Bio.Phylo.BaseTree)
__len__() (in FormattedSeq)	_DIRFMT (in Bio.SeqIO.AbiIO)	_source_line() (in Record)
__len__() (in RestrictionType)	_disease() (in Record)	_split_accessions() (in _BaseGenBankConsumer)
__len__() (in Hit)	_dna_complement_table (in Bio.Seq)	_split_contig() (in _InsdcWriter)
__len__() (in HSP)	_domain_re (in Bio.SCOP)	_split_fragment() (in Bio.SearchIO.ExonerateIO._base)
__len__() (in HSPFragment)	_draw_arc() (in CircularDrawer)	_split_id() (in PhylipIterator)
__len__() (in QueryResult)	_draw_arc_arrow() (in CircularDrawer)	_split_id() (in RelaxedPhylipIterator)
__len__() (in MutableSeq)	_draw_arc_line() (in CircularDrawer)	_split_keywords() (in _BaseGenBankConsumer)
__len__() (in Seq)	_draw_arc_poly() (in CircularDrawer)	_split_multi_line() (in _InsdcWriter)
__len__() (in UnknownSeq)	_draw_distributions() (in DistributionPage)	_split_namespace() (in Bio.Phylo.PhyloXMLIO)
__len__() (in CompoundLocation)	_draw_label() (in Chromosome)	_split_reference_locations() (in _FeatureConsumer)
__len__() (in FeatureLocation)	_draw_label() (in ChromosomeSegment)	_split_taxonomy() (in _BaseGenBankConsumer)
__len__() (in SeqFeature)	_draw_labels() (in Chromosome)	_splitline() (in MMCIF2Dict)
__len__() (in SeqRecord)	_draw_legend() (in Organism)	_spring_layout() (in Bio.Graphics.BasicChromosome)
__len__() (in Motif)	_draw_legend() (in DistributionPage)	_SQLiteManySeqFilesDict (in Bio.File)
__len__() (in PlateRecord)	_draw_scatter_plot() (in ComparativeScatterPlot)	_srt (in Bio.SeqIO.SffIO)
__len__() (in WellRecord)	_draw_segment() (in ChromosomeSegment)	_start_blast_record() (in BlastParser)
__len__() (in DBSeq)	_draw_segment() (in TelomereSegment)	_start_hit() (in BlastParser)
__len__() (in BioSeqDatabase)	_draw_sigil_arrow() (in CircularDrawer)	_start_hit_descr_item() (in BlastParser)
__len__() (in DBServer)	_draw_sigil_arrow() (in LinearDrawer)	_start_hsp() (in BlastParser)
__long__() (in Confidence)	_draw_sigil_big_arrow() (in CircularDrawer)	_STATE_CONS_BLOCK (in Bio.SearchIO.FastaIO)
__lt__() (in PairwiseAlignment)	_draw_sigil_big_arrow() (in LinearDrawer)	_STATE_HIT_BLOCK (in Bio.SearchIO.FastaIO)
__lt__() (in Atom)	_draw_sigil_box() (in CircularDrawer)	_STATE_NONE (in Bio.SearchIO.FastaIO)
__lt__() (in Chain)	_draw_sigil_box() (in LinearDrawer)	_STATE_QUERY_BLOCK (in Bio.SearchIO.FastaIO)
__lt__() (in DisorderedEntityWrapper)	_draw_sigil_cut_corner_box() (in CircularDrawer)	_statelabels() (in Nexus)
__lt__() (in Entity)	_draw_sigil_jaggy() (in CircularDrawer)	_stateset() (in Nexus)
__lt__() (in Confidence)	_draw_sigil_jaggy() (in LinearDrawer)	_StaticArgument (in Bio.Application)
__lt__() (in RestrictionType)	_draw_sigil_octo() (in LinearDrawer)	_stitch_rows() (in Bio.SearchIO.ExonerateIO.exonerate_text)
__lt__() (in MutableSeq)	_draw_subcomponents() (in ChromosomeSegment)	_str2bool() (in Bio.Phylo.PhyloXMLIO)
__lt__() (in Seq)	_draw_title() (in Organism)	_str_aln() (in HSPFragment)
__lt__() (in SeqRecord)	_draw_title() (in ComparativeScatterPlot)	_str_hsp_header() (in _BaseHSP)
__maf_indexer() (in MafIndex)	_draw_title() (in BarChartDistribution)	_str_line() (in MultipleSeqAlignment)
__make_diagram() (in Bio.motifs.mast)	_draw_title() (in DistributionPage)	_strainName (in Bio.phenotype.phen_micro)
__make_new_index() (in MafIndex)	_drop() (in Ambiguous)	_strainNumber (in Bio.phenotype.phen_micro)
__marker (in QueryResult)	_drop() (in Defined)	_strainType (in Bio.phenotype.phen_micro)
__mod__() (in Confidence)	_drop() (in NotDefined)	_STRAND_MAP (in Bio.SearchIO.ExonerateIO._base)
__mod__() (in RestrictionType)	_dssp_cys (in Bio.PDB.DSSP')	_string_as_base_36() (in Bio.SeqIO.SffIO)
__mul__() (in Vector)	_DTD_OPT (in Bio.SearchIO.BlastIO.blast_xml)	_string_matcher() (in Bio.Phylo.BaseTree)
__mul__() (in Confidence)	_effector() (in Record)	_string_to_bytes() (in Bio._py3k)
__mul__() (in MutableSeq)	_elem_AAseq() (in SeqXmlIterator)	_stroke_and_fill_colors() (in Bio.Graphics.GenomeDiagram._AbstractDrawer)
__mul__() (in Seq)	_elem_description() (in SeqXmlIterator)	_struct_wrap() (in Bio.KEGG)
__mul__() (in UnknownSeq)	_elem_DNAseq() (in SeqXmlIterator)	_structures() (in Record)
__mul__() (in SeqMat)	_ELEM_FRAG (in Bio.SearchIO.BlastIO.blast_xml)	_structures() (in Record)
__mul__() (in DBSeq)	_ELEM_FRAG (in Bio.SearchIO.InterproscanIO.interproscan_xml)	_sub_clade() (in Bio.Phylo.Consensus)
__ne__() (in PairwiseAlignment)	_ELEM_HIT (in Bio.SearchIO.BlastIO.blast_xml)	_sub_placeholder() (in Sqlite_dbutils)
__ne__() (in Chain)	_ELEM_HIT (in Bio.SearchIO.InterproscanIO.interproscan_xml)	_sub_set() (in Analysis)
__ne__() (in Hetero)	_ELEM_HSP (in Bio.SearchIO.BlastIO.blast_xml)	_substrate() (in Record)
__ne__() (in NoneElement)	_ELEM_HSP (in Bio.SearchIO.InterproscanIO.interproscan_xml)	_SUPPORTED_FIELDS (in Bio.SearchIO.BlastIO.blast_tab)
__ne__() (in Atom)	_ELEM_META (in Bio.SearchIO.BlastIO.blast_xml)	_Switch (in Bio.Application)
__ne__() (in Entity)	_ELEM_QRESULT_FALLBACK (in Bio.SearchIO.BlastIO.blast_xml)	_sysname() (in Record)
__ne__() (in Reaction)	_ELEM_QRESULT_OPT (in Bio.SearchIO.BlastIO.blast_xml)	_table_h (in Bio.SeqUtils.CheckSum)
__ne__() (in Graph)	_elem_RNAseq() (in SeqXmlIterator)	_taxlabels() (in Nexus)
__ne__() (in MultiGraph)	_eliminate() (in Nexus)	_taxpartition() (in Nexus)
__ne__() (in Confidence)	_embl_convert_fasta() (in Bio.SeqIO._convert)	_taxset() (in Nexus)
__ne__() (in RestrictionType)	_EmbossCommandLine (in Bio.Emboss.Applications)	_TCoffee (in Bio.Align.Applications)
__ne__() (in MutableSeq)	_EmbossMinimalCommandLine (in Bio.Emboss.Applications)	_test() (in Bio.Application)
__ne__() (in Seq)	_empty_bytes_string (in Bio.SearchIO.BlastIO.blast_xml)	_test() (in Bio.Blast.Applications)
__ne__() (in CompoundLocation)	_empty_DNA (in Bio.Restriction.Restriction)	_test() (in Bio.Seq)
__ne__() (in FeatureLocation)	_encode_options() (in Bio.Entrez)	_test() (in Bio.Wise)
__ne__() (in Reference)	_end_blast_record() (in BlastParser)	_test() (in Bio.Wise.dnal)
__ne__() (in SeqRecord)	_end_description_accession() (in BlastParser)	_test() (in Bio.Wise.psw)
__ne__() (in PlateRecord)	_end_description_id() (in BlastParser)	_test_dist() (in PPBuilder)
__ne__() (in WellRecord)	_end_description_sciname() (in BlastParser)	_test_equivalence() (in StructureAlignment)
__neg__() (in Vector)	_end_description_taxid() (in BlastParser)	_test_global_hz_both() (in GenePopController)
__neg__() (in Confidence)	_end_description_title() (in BlastParser)	_test_normal() (in Analysis)
__new__() (in Array)	_end_hit() (in BlastParser)	_test_pop_hz_both() (in GenePopController)
__new__() (in IntegerElement)	_end_hit_descr_item() (in BlastParser)	_test_reverse() (in Analysis)
__new__() (in StringElement)	_end_hsp() (in BlastParser)	_time_denominators (in Bio.SeqIO.SffIO)
__new__() (in UnicodeElement)	_END_OF_FILE_MARKER (in Bio.SearchIO.HHsuiteIO.hhsuite2_text)	_title() (in Nexus)
__new__() (in _BitString)	_entry() (in Record)	_title_line() (in Reference)
__new__() (in AfterPosition)	_entry() (in Record)	_tokenize() (in MMCIF2Dict)
__new__() (in BeforePosition)	_entry() (in Record)	_toobj() (in _InMemoryIndex)
__new__() (in BetweenPosition)	_entry_db_fields (in Bio.TogoWS)	_toOPM() (in Bio.phenotype.phen_micro)
__new__() (in ExactPosition)	_entry_db_formats (in Bio.TogoWS)	_tostr() (in _InMemoryIndex)
__new__() (in OneOfPosition)	_entry_db_names (in Bio.TogoWS)	_Track (in Bio.Graphics.GenomeDiagram)
__new__() (in WithinPosition)	_enzyme() (in Record)	_trackA() (in CrossLink)
__next__() (in PairwiseAlignments)	_eof() (in _Scanner)	_trackB() (in CrossLink)
__next__() (in ClustalIterator)	_equal_topology() (in Bio.Phylo.Consensus)	_train_iis() (in Bio.MaxEntropy)
__next__() (in EmbossIterator)	_escape_filename() (in Bio.Application)	_transfer_attrs() (in _BaseSearchObject)
__next__() (in AlignmentIterator)	_eval_feature_fn() (in Bio.MaxEntropy)	_translate() (in Nexus)
__next__() (in MauveIterator)	_exp_freq_table_from_obs_freq() (in Bio.SubsMat)	_translate_id() (in AbstractAtomPropertyMap)
__next__() (in MsfIterator)	_exp_logsum() (in Bio.MarkovModel)	_translate_id() (in AbstractPropertyMap)
__next__() (in PhylipIterator)	_EXTRACT (in Bio.SeqIO.AbiIO)	_translate_id() (in AbstractResiduePropertyMap)
__next__() (in SequentialPhylipIterator)	_extract_alignment_region() (in Bio.AlignIO.FastaIO)	_translate_id() (in Chain)
__next__() (in StockholmIterator)	_extract_ids_and_descs() (in Bio.SearchIO.BlastIO.blast_xml)	_translate_str() (in Bio.Seq)
__next__() (in BlastTableReader)	_fails_conditions() (in Bio.SearchIO._legacy.ParserSupport)	_tree() (in Nexus)
__next__() (in UndoHandle)	_fastq_convert_fasta() (in Bio.SeqIO._convert)	_tree_to_bitstrs() (in Bio.Phylo.Consensus)
__next__() (in Iterator)	_fastq_convert_qual() (in Bio.SeqIO._convert)	_treepartition() (in Nexus)
__next__() (in CharBuffer)	_fastq_convert_tab() (in Bio.SeqIO._convert)	_treeset() (in Nexus)
__next__() (in StandardData)	_fastq_generic() (in Bio.SeqIO._convert)	_ucscbin() (in MafIndex)
__next__() (in _FileIterator)	_fastq_generic2() (in Bio.SeqIO._convert)	_ungap() (in Bio.Alphabet)
__next__() (in Iterator)	_fastq_illumina_convert_fastq_illumina() (in Bio.SeqIO._convert)	_unhandled() (in _BaseGenBankConsumer)
__next__() (in SequenceIterator)	_fastq_illumina_convert_fastq_sanger() (in Bio.SeqIO._convert)	_unhandled() (in AbstractConsumer)
__next__() (in _PacketIterator)	_fastq_illumina_convert_fastq_solexa() (in Bio.SeqIO._convert)	_unhandled_section() (in AbstractConsumer)
__next__() (in BgzfReader)	_fastq_illumina_convert_qual() (in Bio.SeqIO._convert)	_uniform_norm() (in Bio.MarkovModel)
__next_section() (in PrintFormat)	_fastq_sanger_convert_fastq_illumina() (in Bio.SeqIO._convert)	_unique_label() (in Bio.Nexus.Nexus)
__nonzero__() (in CompoundLocation)	_fastq_sanger_convert_fastq_sanger() (in Bio.SeqIO._convert)	_universal_read_mode (in Bio._py3k)
__nonzero__() (in FeatureLocation)	_fastq_sanger_convert_fastq_solexa() (in Bio.SeqIO._convert)	_unknown_nexus_block() (in Nexus)
__or__() (in _BitString)	_fastq_sanger_convert_qual() (in Bio.SeqIO._convert)	_update() (in PlateRecord)
__package__ (in Bio.Affy.CelFile)	_fastq_solexa_convert_fastq_illumina() (in Bio.SeqIO._convert)	_update_ecitmatch_variables() (in Bio.Entrez)
__package__ (in Bio.Affy)	_fastq_solexa_convert_fastq_sanger() (in Bio.SeqIO._convert)	_update_left_right_taxon_values() (in DatabaseLoader)
__package__ (in Bio.Align.AlignInfo)	_fastq_solexa_convert_fastq_solexa() (in Bio.SeqIO._convert)	_update_pKs_tables() (in IsoelectricPoint)
__package__ (in Bio.Align.Applications._ClustalOmega)	_fastq_solexa_convert_qual() (in Bio.SeqIO._convert)	_upper() (in Alphabet)
__package__ (in Bio.Align.Applications._Clustalw)	_Fasttree (in Bio.Phylo.Applications)	_upper() (in AlphabetEncoder)
__package__ (in Bio.Align.Applications._Dialign)	_Feature (in Bio.Graphics.GenomeDiagram)	_upper() (in Gapped)
__package__ (in Bio.Align.Applications._MSAProbs)	_FeatureConsumer	_upper() (in HasStopCodon)
__package__ (in Bio.Align.Applications._Mafft)	_features_line() (in Record)	_upper() (in ThreeLetterProtein)
__package__ (in Bio.Align.Applications._Muscle)	_FeatureSet (in Bio.Graphics.GenomeDiagram)	_utils (in Bio.Phylo)
__package__ (in Bio.Align.Applications._Prank)	_feed_feature_table() (in InsdcScanner)	_utils (in Bio.SearchIO)
__package__ (in Bio.Align.Applications._Probcons)	_feed_first_line() (in EmblScanner)	_utils (in Bio)
__package__ (in Bio.Align.Applications._TCoffee)	_feed_first_line() (in GenBankScanner)	_utree() (in Nexus)
__package__ (in Bio.Align.Applications)	_feed_first_line() (in InsdcScanner)	_valid_UAN_read_name (in Bio.SeqIO.SffIO)
__package__ (in Bio.Align)	_feed_first_line() (in _ImgtScanner)	_validate() (in AbstractCommandline)
__package__ (in Bio.Align._aligners)	_feed_first_line_new() (in EmblScanner)	_validate() (in NcbiblastformatterCommandline)
__package__ (in Bio.Align.substitution_matrices)	_feed_first_line_old() (in EmblScanner)	_validate() (in NcbiblastnCommandline)
__package__ (in Bio.AlignIO.ClustalIO)	_feed_first_line_patents() (in EmblScanner)	_validate() (in NcbimakeblastdbCommandline)
__package__ (in Bio.AlignIO.EmbossIO)	_feed_first_line_patents_kipo() (in EmblScanner)	_validate() (in NcbipsiblastCommandline)
__package__ (in Bio.AlignIO.FastaIO)	_feed_header_lines() (in EmblScanner)	_validate() (in NcbirpsblastCommandline)
__package__ (in Bio.AlignIO.Interfaces)	_feed_header_lines() (in GenBankScanner)	_validate() (in _Ncbiblast2SeqCommandline)
__package__ (in Bio.AlignIO.MafIO)	_feed_header_lines() (in InsdcScanner)	_validate() (in _NcbiblastCommandline)
__package__ (in Bio.AlignIO.MauveIO)	_feed_misc_lines() (in EmblScanner)	_validate() (in _NcbiblastMain2SeqCommandline)
__package__ (in Bio.AlignIO.MsfIO)	_feed_misc_lines() (in GenBankScanner)	_validate() (in SeqretCommandline)
__package__ (in Bio.AlignIO.NexusIO)	_feed_misc_lines() (in InsdcScanner)	_validate() (in _EmbossCommandLine)
__package__ (in Bio.AlignIO.PhylipIO)	_feed_seq_length() (in EmblScanner)	_validate_cols() (in BlatPslParser)
__package__ (in Bio.AlignIO.StockholmIO)	_fetch_counts_matrix() (in JASPAR5)	_validate_fragment() (in HSP)
__package__ (in Bio.AlignIO)	_fetch_internal_id() (in JASPAR5)	_validate_hsp() (in Hit)
__package__ (in Bio.Alphabet.IUPAC)	_fetch_internal_id_list() (in JASPAR5)	_validate_incompatibilities() (in _NcbibaseblastCommandline)
__package__ (in Bio.Alphabet.Reduced)	_fetch_latest_version() (in JASPAR5)	_verify_alphabet() (in Bio.Alphabet)
__package__ (in Bio.Alphabet)	_fetch_motif_by_internal_id() (in JASPAR5)	_version_line() (in Record)
__package__ (in Bio.Application)	_fgrep_count() (in Bio.Wise.dnal)	_viterbi() (in Bio.MarkovModel)
__package__ (in Bio.Blast.Applications)	_file (in Bio.phenotype.phen_micro)	_walk() (in Tree)
__package__ (in Bio.Blast.NCBIWWW)	_FileIterator (in Bio.PopGen.GenePop.Controller)	_weight_list() (in ProteinAnalysis)
__package__ (in Bio.Blast.NCBIXML)	_filter_search() (in TreeMixin)	_wgs_line() (in Record)
__package__ (in Bio.Blast.ParseBlastTable)	_find_gap_open() (in Bio.pairwise2)	_wgs_scafld_line() (in Record)
__package__ (in Bio.Blast.Record)	_find_min_max() (in ComparativeScatterPlot)	_within_location (in Bio.GenBank)
__package__ (in Bio.Blast)	_find_start() (in Bio.pairwise2)	_within_position (in Bio.GenBank)
__package__ (in Bio.CAPS)	_find_start_entry() (in Bio.NMR.xpktools)	_wrap_kegg() (in Bio.KEGG)
__package__ (in Bio.Cluster)	_finish_backtrace() (in Bio.pairwise2)	_wrap_location() (in _InsdcWriter)
__package__ (in Bio.Cluster._cluster)	_first_defined() (in Bio.Graphics.GenomeDiagram._Diagram)	_wrapped_genbank() (in Bio.GenBank.Record)
__package__ (in Bio.Compass)	_fix_name_class() (in DatabaseLoader)	_write() (in Bio.Graphics)
__package__ (in Bio.Crystal)	_flag (in Bio.SeqIO.SffIO)	_write_block() (in BgzfWriter)
__package__ (in Bio.Data.CodonTable)	_flip() (in AfterPosition)	_write_comment() (in EmblWriter)
__package__ (in Bio.Data.IUPACData)	_flip() (in BeforePosition)	_write_comment() (in GenBankWriter)
__package__ (in Bio.Data.SCOPData)	_flip() (in BetweenPosition)	_write_contig() (in EmblWriter)
__package__ (in Bio.Data)	_flip() (in CompoundLocation)	_write_contig() (in GenBankWriter)
__package__ (in Bio.Emboss.Applications)	_flip() (in ExactPosition)	_write_dbxrefs() (in SeqXmlWriter)
__package__ (in Bio.Emboss.Primer3)	_flip() (in FeatureLocation)	_write_description() (in SeqXmlWriter)
__package__ (in Bio.Emboss.PrimerSearch)	_flip() (in OneOfPosition)	_write_elem_block() (in BlastXmlWriter)
__package__ (in Bio.Emboss)	_flip() (in SeqFeature)	_write_feature() (in _InsdcWriter)
__package__ (in Bio.Entrez.Parser)	_flip() (in UnknownPosition)	_write_feature_qualifier() (in _InsdcWriter)
__package__ (in Bio.Entrez)	_flip() (in WithinPosition)	_write_hits() (in BlastXmlWriter)
__package__ (in Bio.ExPASy.Enzyme)	_flip_codons() (in Bio.SearchIO.ExonerateIO.exonerate_text)	_write_hsps() (in BlastXmlWriter)
__package__ (in Bio.ExPASy.Prodoc)	_float() (in Bio.Phylo.PhyloXMLIO)	_write_index() (in SffWriter)
__package__ (in Bio.ExPASy.Prosite)	_force_alphabet() (in Bio.AlignIO)	_write_kegg() (in Bio.KEGG)
__package__ (in Bio.ExPASy.ScanProsite)	_force_alphabet() (in Bio.SeqIO)	_write_keywords() (in EmblWriter)
__package__ (in Bio.ExPASy)	_format() (in Nexus)	_WRITE_MAPS (in Bio.SearchIO.BlastIO.blast_xml)
__package__ (in Bio.ExPASy.cellosaurus)	_format_1D() (in Array)	_write_multi_entries() (in GenBankWriter)
__package__ (in Bio.FSSP.FSSPTools)	_format_2D() (in Array)	_write_multi_line() (in EmblWriter)
__package__ (in Bio.FSSP)	_format_comment() (in Bio.Phylo.NewickIO)	_write_multi_line() (in GenBankWriter)
__package__ (in Bio.FSSP.fssp_rec)	_format_date() (in Bio.PDB.parse_pdb_header')	_write_param() (in BlastXmlWriter)
__package__ (in Bio.File)	_format_generalized() (in PairwiseAlignment)	_write_preamble() (in BlastXmlWriter)
__package__ (in Bio.GenBank.Record)	_format_mmcif_col() (in MMCIFIO)	_write_properties() (in SeqXmlWriter)
__package__ (in Bio.GenBank.Scanner)	_format_psl() (in PairwiseAlignment)	_write_pstring() (in XdnaWriter)
__package__ (in Bio.GenBank)	_FormatToIterator (in Bio.AlignIO)	_write_qresults() (in BlastXmlWriter)
__package__ (in Bio.GenBank.utils)	_FormatToIterator (in Bio.SeqIO)	_write_record() (in MafWriter)
__package__ (in Bio.Geo.Record)	_FormatToIterator (in Bio.phenotype)	_write_record() (in MauveWriter)
__package__ (in Bio.Geo)	_FormatToRandomAccess (in Bio.SeqIO._index)	_write_record() (in StockholmWriter)
__package__ (in Bio.Graphics.BasicChromosome)	_FormatToString (in Bio.SeqIO)	_write_references() (in EmblWriter)
__package__ (in Bio.Graphics.ColorSpiral)	_FormatToWriter (in Bio.AlignIO)	_write_references() (in GenBankWriter)
__package__ (in Bio.Graphics.Comparative)	_FormatToWriter (in Bio.SeqIO)	_write_seq() (in SeqXmlWriter)
__package__ (in Bio.Graphics.DisplayRepresentation)	_FormatToWriter (in Bio.phenotype)	_write_sequence() (in EmblWriter)
__package__ (in Bio.Graphics.Distribution)	_formula() (in Record)	_write_sequence() (in GenBankWriter)
__package__ (in Bio.Graphics.GenomeDiagram._AbstractDrawer)	_forward() (in Bio.MarkovModel)	_write_single_line() (in EmblWriter)
__package__ (in Bio.Graphics.GenomeDiagram._CircularDrawer)	_forward_recursion() (in AbstractDPAlgorithms)	_write_single_line() (in GenBankWriter)
__package__ (in Bio.Graphics.GenomeDiagram._Colors)	_forward_recursion() (in ScaledDPAlgorithms)	_write_species() (in SeqXmlWriter)
__package__ (in Bio.Graphics.GenomeDiagram._CrossLink)	_FRAGMENT_FILE (in Bio.PDB.FragmentMapper')	_write_the_first_line() (in GenBankWriter)
__package__ (in Bio.Graphics.GenomeDiagram._Diagram)	_fragment_re (in Bio.SCOP.Residues)	_write_the_first_lines() (in EmblWriter)
__package__ (in Bio.Graphics.GenomeDiagram._Feature)	_freq_from_count() (in FreqTable)	_write_tree() (in Writer)
__package__ (in Bio.Graphics.GenomeDiagram._FeatureSet)	_full_to_half() (in SeqMat)	_WRITER_MAP (in Bio.SearchIO)
__package__ (in Bio.Graphics.GenomeDiagram._Graph)	_function_matcher() (in Bio.Phylo.BaseTree)	_XMLparser (in Bio.Blast.NCBIXML)
__package__ (in Bio.Graphics.GenomeDiagram._GraphSet)	_G_test() (in Bio.codonalign.codonalignment)	_xxmotif (in Bio.motifs.applications)
__package__ (in Bio.Graphics.GenomeDiagram._LinearDrawer)	_gaf10byproteiniterator() (in Bio.UniProt.GOA)	_yn00() (in Bio.codonalign.codonseq)
__package__ (in Bio.Graphics.GenomeDiagram._Track)	_gaf10iterator() (in Bio.UniProt.GOA)
__package__ (in Bio.Graphics.GenomeDiagram)	_gaf20byproteiniterator() (in Bio.UniProt.GOA)