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)	__mul__() (in SeqMat)	_get_entry_dbs() (in Bio.TogoWS)
__add__() (in MultipleSeqAlignment)	__ne__() (in Chain)	_get_entry_fields() (in Bio.TogoWS)
__add__() (in Chain)	__ne__() (in Hetero)	_get_entry_formats() (in Bio.TogoWS)
__add__() (in Vector)	__ne__() (in Organism)	_get_fields() (in Bio.TogoWS)
__add__() (in Confidence)	__ne__() (in Reaction)	_get_frag_frame() (in BlastTabParser)
__add__() (in RestrictionBatch)	__ne__() (in Graph)	_get_frag_strand() (in BlastTabParser)
__add__() (in RestrictionType)	__ne__() (in HashSet)	_get_gly_cb_vector() (in _AbstractHSExposure)
__add__() (in SeqMap)	__ne__() (in MultiGraph)	_get_header() (in PDBParser)
__add__() (in MutableSeq)	__ne__() (in Confidence)	_get_icode() (in MMCIFParser)
__add__() (in Seq)	__ne__() (in RestrictionType)	_get_id() (in Chain)
__add__() (in UnknownSeq)	__ne__() (in OrderedDict)	_get_id() (in BlastTabParser)
__add__() (in SeqRecord)	__neg__() (in Vector)	_get_illumina_quality_str() (in Bio.SeqIO.QualityIO)
__add__() (in SeqMat)	__neg__() (in Confidence)	_get_indices() (in Nexus)
__add__() (in DBSeq)	__new__() (in AfterPosition)	_get_inter_coords() (in Bio.SearchIO.ExonerateIO.exonerate_text)
__call__() (in AbstractCommandline)	__new__() (in BeforePosition)	_get_jitter() (in ColorSpiral)
__call__() (in affine_penalty)	__new__() (in BetweenPosition)	_get_journal() (in Bio.PDB.parse_pdb_header')
__call__() (in dictionary_match)	__new__() (in ExactPosition)	_get_letter_freqs() (in SummaryInfo)
__call__() (in identity_match)	__new__() (in OneOfPosition)	_get_meta_data() (in StockholmIterator)
__cmp__() (in HasStopCodon)	__new__() (in WithinPosition)	_get_motif_dict() (in MotifFinder)
__cmp__() (in MutableSeq)	__next_section() (in PrintFormat)	_get_new_organism() (in DiversitySelection)
__cmp__() (in Seq)	__nonzero__() (in Clade)	_get_nexus_block() (in Nexus)
__contains__() (in Chain)	__nonzero__() (in Hit)	_get_num_motifs() (in SchemaFactory)
__contains__() (in Crystal)	__nonzero__() (in HSP)	_get_ontology_id() (in DatabaseLoader)
__contains__() (in _IndexedSeqFileDict)	__nonzero__() (in QueryResult)	_get_opts() (in GenePopController)
__contains__() (in _SQLiteManySeqFilesDict)	__nonzero__() (in FeatureLocation)	_get_parameter() (in AbstractCommandline)
__contains__() (in AbstractPropertyMap)	__nonzero__() (in SeqFeature)	_get_path() (in FDistController)
__contains__() (in Chain)	__nonzero__() (in SeqRecord)	_get_phred_quality() (in Bio.SeqIO.QualityIO)
__contains__() (in DisorderedEntityWrapper)	__parse_hit_table() (in FastaM10Parser)	_get_raw_qresult() (in BlastTabIndexer)
__contains__() (in Entity)	__pos__() (in Confidence)	_get_raw_qresult_commented() (in BlastTabIndexer)
__contains__() (in FragmentMapper)	__pow__() (in Vector)	_get_read_region() (in Bio.SeqIO.SffIO)
__contains__() (in Vector)	__pow__() (in Confidence)	_get_read_time() (in Bio.SeqIO.SffIO)
__contains__() (in HashSet)	__process_feature() (in Feature)	_get_read_xy() (in Bio.SeqIO.SffIO)
__contains__() (in Events)	__radd__() (in Chain)	_get_ref() (in SeqFeature)
__contains__() (in RestrictionBatch)	__radd__() (in Confidence)	_get_ref_db() (in SeqFeature)
__contains__() (in Hit)	__radd__() (in MutableSeq)	_get_references() (in Bio.PDB.parse_pdb_header')
__contains__() (in HSP)	__radd__() (in Seq)	_get_row_dict() (in Bio.SearchIO.ExonerateIO.exonerate_text)
__contains__() (in QueryResult)	__radd__() (in UnknownSeq)	_get_sanger_quality_str() (in Bio.SeqIO.QualityIO)
__contains__() (in Seq)	__radd__() (in SeqRecord)	_get_scodon_moves() (in Bio.SearchIO.ExonerateIO.exonerate_text)
__contains__() (in FeatureLocation)	__radd__() (in DBSeq)	_get_seq_str_and_check_alphabet() (in Seq)
__contains__() (in SeqFeature)	__rdiv__() (in Confidence)	_get_seq_string() (in SequenceWriter)
__contains__() (in SeqRecord)	__rdiv__() (in RestrictionBatch)	_get_seqfeature_dbxref() (in DatabaseLoader)
__contains__() (in BioSeqDatabase)	__rdiv__() (in RestrictionType)	_get_signature_dict() (in SignatureFinder)
__contains__() (in DBServer)	__rdivmod__() (in Confidence)	_get_solexa_quality_str() (in Bio.SeqIO.QualityIO)
__create_motif() (in Bio.Motif.Parsers.MEME)	__read() (in Bio.ExPASy.Enzyme)	_get_strand() (in HSPFragment)
__del__() (in _InMemoryIndex)	__read() (in Bio.ExPASy.Prodoc)	_get_strand() (in FeatureLocation)
__del__() (in _ShelveIndex)	__read() (in Bio.ExPASy.Prosite)	_get_strand() (in SeqFeature)
__del__() (in _FileIterator)	__read_alphabet() (in Bio.Motif.Parsers.MEME)	_get_taxon_id() (in DatabaseLoader)
__del__() (in RebaseUpdate)	__read_alphabet() (in Bio.motifs.meme)	_get_taxon_id_from_ncbi_lineage() (in DatabaseLoader)
__del_annotations() (in DBSeqRecord)	__read_command() (in Bio.Motif.Parsers.MEME)	_get_taxon_id_from_ncbi_taxon_id() (in DatabaseLoader)
__del_dbxrefs() (in DBSeqRecord)	__read_command() (in Bio.motifs.meme)	_get_taxonomy() (in Clade)
__del_features() (in DBSeqRecord)	__read_copyright_line() (in Bio.ExPASy.Prodoc)	_get_temp_file() (in FDistController)
__del_seq() (in DBSeqRecord)	__read_database_and_motifs() (in Bio.Motif.Parsers.MAST)	_get_term_id() (in DatabaseLoader)
__delitem__() (in Chain)	__read_database_and_motifs() (in Bio.motifs.mast)	_get_unique_parent_pairs() (in NeighborSearch)
__delitem__() (in Crystal)	__read_datafile() (in Bio.Motif.Parsers.MEME)	_get_unique_schema() (in SchemaFactory)
__delitem__() (in _InMemoryIndex)	__read_datafile() (in Bio.motifs.meme)	_get_v_final() (in ColorSpiral)
__delitem__() (in Chain)	__read_hit_alignment() (in Bio.Compass)	_get_v_init() (in ColorSpiral)
__delitem__() (in Entity)	__read_lengths() (in Bio.Compass)	_get_values() (in Tree)
__delitem__() (in Events)	__read_motif_name() (in Bio.Motif.Parsers.MEME)	_gp_float() (in Bio.PopGen.GenePop.Controller)
__delitem__() (in Hit)	__read_motif_name() (in Bio.motifs.meme)	_gp_int() (in Bio.PopGen.GenePop.Controller)
__delitem__() (in HSP)	__read_motif_sequences() (in Bio.Motif.Parsers.MEME)	_Graph (in Bio.Graphics.GenomeDiagram)
__delitem__() (in QueryResult)	__read_motif_sequences() (in Bio.motifs.meme)	_GraphSet (in Bio.Graphics.GenomeDiagram)
__delitem__() (in MutableSeq)	__read_motif_statistics() (in Bio.motifs.meme)	_guess_consensus_alphabet() (in SummaryInfo)
__delitem__() (in OrderedDict)	__read_names() (in Bio.Compass)	_handle_complex() (in Bio.Phylo.PhyloXMLIO)
__delitem__() (in BioSeqDatabase)	__read_positive_alignment() (in Bio.Compass)	_handle_convert() (in Bio.SeqIO._convert)
__delitem__() (in DBServer)	__read_profilewidth() (in Bio.Compass)	_handle_PDB_exception() (in PDBParser)
__div__() (in Vector)	__read_prosite_reference_line() (in Bio.ExPASy.Prodoc)	_handle_simple() (in Bio.Phylo.PhyloXMLIO)
__div__() (in Confidence)	__read_query_alignment() (in Bio.Compass)	_HeaderConsumer (in Bio.Blast.NCBIStandalone)
__div__() (in RestrictionBatch)	__read_reference_line() (in Bio.ExPASy.Prodoc)	_HEADFMT (in Bio.SeqIO.AbiIO)
__div__() (in RestrictionType)	__read_reference_start() (in Bio.ExPASy.Prodoc)	_hit_end_get() (in HSP)
__divmod__() (in Confidence)	__read_scores() (in Bio.Compass)	_hit_end_get() (in HSPFragment)
__enter__() (in UndoHandle)	__read_section_i() (in Bio.Motif.Parsers.MAST)	_hit_end_set() (in HSPFragment)
__eq__() (in Chain)	__read_section_i() (in Bio.motifs.mast)	_hit_frame_get() (in HSPFragment)
__eq__() (in Hetero)	__read_section_ii() (in Bio.Motif.Parsers.MAST)	_hit_frame_set() (in HSPFragment)
__eq__() (in Organism)	__read_section_ii() (in Bio.motifs.mast)	_hit_get() (in HSPFragment)
__eq__() (in Reaction)	__read_section_iii() (in Bio.Motif.Parsers.MAST)	_hit_inter_ranges_get() (in HSP)
__eq__() (in Graph)	__read_section_iii() (in Bio.motifs.mast)	_hit_inter_spans_get() (in HSP)
__eq__() (in HashSet)	__read_sequence_names() (in Bio.Motif.Parsers.MEME)	_hit_range_get() (in HSP)
__eq__() (in MultiGraph)	__read_sequences() (in Bio.motifs.meme)	_hit_range_get() (in HSPFragment)
__eq__() (in Confidence)	__read_text_line() (in Bio.ExPASy.Prodoc)	_hit_set() (in HSPFragment)
__eq__() (in FormattedSeq)	__read_threshold() (in Bio.Compass)	_hit_span_get() (in HSP)
__eq__() (in RestrictionType)	__read_version() (in Bio.Motif.Parsers.MAST)	_hit_span_get() (in HSPFragment)
__eq__() (in OrderedDict)	__read_version() (in Bio.Motif.Parsers.MEME)	_hit_start_get() (in HSP)
__exit__() (in UndoHandle)	__read_version() (in Bio.motifs.mast)	_hit_start_get() (in HSPFragment)
__float__() (in Confidence)	__read_version() (in Bio.motifs.meme)	_hit_start_set() (in HSPFragment)
__floordiv__() (in Confidence)	__reduce__() (in OrderedDict)	_hit_strand_get() (in HSPFragment)
__floordiv__() (in RestrictionType)	__regex (in Bio.Compass)	_hit_strand_set() (in HSPFragment)
__format__() (in Alignment)	__repr__() (in Alignment)	_HitPlaceholder (in Bio.SearchIO.HmmerIO.hmmer2_text)
__format__() (in Tree)	__repr__() (in Alphabet)	_HRE_ANNOT_LINE (in Bio.SearchIO.HmmerIO.hmmer3_text)
__format__() (in SeqRecord)	__repr__() (in AlphabetEncoder)	_HRE_ID_LINE (in Bio.SearchIO.HmmerIO.hmmer3_text)
__ge__() (in Organism)	__repr__() (in AbstractCommandline)	_HRE_VALIDATE (in Bio.SearchIO.HmmerIO.hmmer3_text)
__ge__() (in Confidence)	__repr__() (in ApplicationError)	_hsh (in Bio.SeqIO.SffIO)
__ge__() (in RestrictionType)	__repr__() (in Crystal)	_HSP_ALIGN_LINE (in Bio.SearchIO.HmmerIO.hmmer2_text)
__get_annotations() (in DBSeqRecord)	__repr__() (in Hetero)	_HSP_ATTR_MAP (in Bio.SearchIO.FastaIO)
__get_dbxrefs() (in DBSeqRecord)	__repr__() (in Query)	_HSPConsumer (in Bio.Blast.NCBIStandalone)
__get_features() (in DBSeqRecord)	__repr__() (in DictionaryElement)	_hw_func() (in Bio.PopGen.GenePop.Controller)
__get_seq() (in DBSeqRecord)	__repr__() (in IntegerElement)	_hydrogen (in Bio.PDB.Dice)
__getattr__() (in AlphabetEncoder)	__repr__() (in ListElement)	_identifier_split() (in StockholmIterator)
__getattr__() (in AmbiguousCodonTable)	__repr__() (in StringElement)	_identity_matcher() (in Bio.Phylo.BaseTree)
__getattr__() (in QueryRow)	__repr__() (in StructureElement)	_iis_solve_delta() (in Bio.MaxEntropy)
__getattr__() (in UndoHandle)	__repr__() (in UnicodeElement)	_ImgtScanner (in Bio.GenBank.Scanner)
__getattr__() (in _BaseGenBankConsumer)	__repr__() (in Record)	_incomplete_gamma() (in Bio.Phylo.PAML.chi2)
__getattr__() (in Feature)	__repr__() (in FSSPSumRec)	_indent() (in Bio.Phylo.PhyloXMLIO)
__getattr__() (in DisorderedEntityWrapper)	__repr__() (in PosAlign)	_indent_genbank() (in Bio.GenBank.Record)
__getattr__() (in AbstractConsumer)	__repr__() (in fff_rec)	_index (in Bio.SearchIO)
__getattr__() (in TaggingConsumer)	__repr__() (in _IndexedSeqFileDict)	_index (in Bio.SeqIO)
__getattr__() (in _SeqLength)	__repr__() (in _SQLiteManySeqFilesDict)	_index_diff() (in ScoreDistribution)
__getitem__() (in PSSM)	__repr__() (in Atom)	_index_diff() (in ScoreDistribution)
__getitem__() (in Alignment)	__repr__() (in DisorderedAtom)	_IndexedSeqFileDict
__getitem__() (in MultipleSeqAlignment)	__repr__() (in Chain)	_IndexedSeqFileProxy
__getitem__() (in Chain)	__repr__() (in Fragment)	_INDEXER_MAP (in Bio.SearchIO)
__getitem__() (in Crystal)	__repr__() (in Model)	_info_factory() (in Writer)
__getitem__() (in AmbiguousForwardTable)	__repr__() (in Select)	_inhibitor() (in Record)
__getitem__() (in fff_rec)	__repr__() (in Polypeptide)	_init_from_text() (in ProtsimLine)
__getitem__() (in _IndexedSeqFileDict)	__repr__() (in DisorderedResidue)	_init_from_text() (in STSLine)
__getitem__() (in _SQLiteManySeqFilesDict)	__repr__() (in Residue)	_init_from_text() (in SequenceLine)
__getitem__() (in Diagram)	__repr__() (in Structure)	_init_table_h() (in Bio.SeqUtils.CheckSum)
__getitem__() (in FeatureSet)	__repr__() (in Vector)	_init_zero() (in SeqMat)
__getitem__() (in GraphData)	__repr__() (in Interaction)	_InMemoryIndex (in Bio.Index)
__getitem__() (in GraphSet)	__repr__() (in Network)	_InMemoryIndex__version (in _InMemoryIndex)
__getitem__() (in Track)	__repr__() (in Reaction)	_InMemoryIndex__version_key (in _InMemoryIndex)
__getitem__() (in Motif)	__repr__() (in Graph)	_insdc_feature_location_string() (in Bio.SeqIO.InsdcIO)
__getitem__() (in AbstractPropertyMap)	__repr__() (in HashSet)	_insdc_feature_position_string() (in Bio.SeqIO.InsdcIO)
__getitem__() (in Chain)	__repr__() (in MultiGraph)	_insdc_location_string_ignoring_strand_and_subfeatures() (in Bio.SeqIO.InsdcIO)
__getitem__() (in DisorderedEntityWrapper)	__repr__() (in System)	_InsdcWriter (in Bio.SeqIO.InsdcIO)
__getitem__() (in Entity)	__repr__() (in BranchColor)	_insert_seqfeature_location() (in DatabaseLoader)
__getitem__() (in FragmentMapper)	__repr__() (in TreeElement)	_int() (in Bio.Phylo.PhyloXMLIO)
__getitem__() (in Vector)	__repr__() (in Analysis)	_inter_ranges_get() (in HSP)
__getitem__() (in Clade)	__repr__() (in FormattedSeq)	_inter_spans_get() (in HSP)
__getitem__() (in Events)	__repr__() (in RestrictionBatch)	_invoke_blast() (in Bio.Blast.NCBIStandalone)
__getitem__() (in Phyloxml)	__repr__() (in RestrictionType)	_io (in Bio.Phylo)
__getitem__() (in FormattedSeq)	__repr__() (in Hit)	_is_completely_disordered() (in StructureBuilder)
__getitem__() (in Index)	__repr__() (in HSP)	_is_connected() (in CaPPBuilder)
__getitem__() (in SeqMap)	__repr__() (in HSPFragment)	_is_connected() (in PPBuilder)
__getitem__() (in SeqMapIndex)	__repr__() (in QueryResult)	_is_header() (in PhylipIterator)
__getitem__() (in Hit)	__repr__() (in MutableSeq)	_is_int_or_long() (in Bio._py3k)
__getitem__() (in HSP)	__repr__() (in Seq)	_is_protein() (in Bio.SearchIO.BlatIO)
__getitem__() (in HSPFragment)	__repr__() (in UnknownSeq)	_ITERATOR_MAP (in Bio.SearchIO)
__getitem__() (in QueryResult)	__repr__() (in AbstractPosition)	_journal_line() (in Reference)
__getitem__() (in MutableSeq)	__repr__() (in AfterPosition)	_keywords_line() (in Record)
__getitem__() (in Seq)	__repr__() (in BeforePosition)	_kill_comments_and_break_lines() (in Bio.Nexus.Nexus)
__getitem__() (in UnknownSeq)	__repr__() (in BetweenPosition)	_length() (in MEMEInstance)
__getitem__() (in InterlacedSequenceIterator)	__repr__() (in ExactPosition)	_level_traverse() (in Bio.Phylo.BaseTree)
__getitem__() (in SeqRecord)	__repr__() (in FeatureLocation)	_LinearDrawer (in Bio.Graphics.GenomeDiagram)
__getitem__() (in Record)	__repr__() (in OneOfPosition)	_list_from_csv() (in Bio.SearchIO.BlatIO)
__getitem__() (in GenericPositionMatrix)	__repr__() (in PositionGap)	_ln_gamma_function() (in Bio.Phylo.PAML.chi2)
__getitem__() (in Record)	__repr__() (in Reference)	_load_annotations() (in DatabaseLoader)
__getitem__() (in DBSeq)	__repr__() (in SeqFeature)	_load_bgzf_block() (in Bio.bgzf)
__getitem__() (in BioSeqDatabase)	__repr__() (in UnknownPosition)	_load_bioentry_date() (in DatabaseLoader)
__getitem__() (in DBServer)	__repr__() (in WithinPosition)	_load_bioentry_table() (in DatabaseLoader)
__gt__() (in Organism)	__repr__() (in SeqRecord)	_load_biosequence() (in DatabaseLoader)
__gt__() (in Confidence)	__repr__() (in ProtsimLine)	_load_block() (in BgzfReader)
__gt__() (in RestrictionType)	__repr__() (in Record)	_load_comment() (in DatabaseLoader)
__hash__() (in Interaction)	__repr__() (in STSLine)	_load_dbxrefs() (in DatabaseLoader)
__hash__() (in Reaction)	__repr__() (in SequenceLine)	_load_reference() (in DatabaseLoader)
__hash__() (in Confidence)	__repr__() (in AlignmentColumn)	_load_seqfeature() (in DatabaseLoader)
__hash__() (in RestrictionType)	__repr__() (in OrderedDict)	_load_seqfeature_basic() (in DatabaseLoader)
__hash__() (in Seq)	__repr__() (in BioSeqDatabase)	_load_seqfeature_dbxref() (in DatabaseLoader)
__hash__() (in UnknownPosition)	__repr__() (in DBServer)	_load_seqfeature_locations() (in DatabaseLoader)
__iadd__() (in Chain)	__reversed__() (in OrderedDict)	_load_seqfeature_qualifiers() (in DatabaseLoader)
__iadd__() (in RestrictionBatch)	__rfloordiv__() (in Confidence)	_local() (in Bio.Phylo.PhyloXMLIO)
__iadd__() (in SeqMap)	__rfloordiv__() (in RestrictionType)	_local_reserved_names (in Bio.Application)
__init_() (in Interaction)	__rmod__() (in Confidence)	_locus_line() (in Record)
__init__() (in Record)	__rmul__() (in Confidence)	_log_transform() (in HiddenMarkovModel)
__init__() (in PSSM)	__rpow__() (in Confidence)	_logsum() (in Bio.MarkovModel)
__init__() (in SummaryInfo)	__rshift__() (in RestrictionType)	_logvecadd() (in Bio.MarkovModel)
__init__() (in ClustalOmegaCommandline)	__rsub__() (in Confidence)	_LONG_SHORT_MAP (in Bio.SearchIO.BlastIO.blast_tab)
__init__() (in ClustalwCommandline)	__rtruediv__() (in Confidence)	_lower() (in Alphabet)
__init__() (in DialignCommandline)	__rtruediv__() (in RestrictionType)	_lower() (in AlphabetEncoder)
__init__() (in MafftCommandline)	__set_annotations() (in DBSeqRecord)	_lower() (in Gapped)
__init__() (in MuscleCommandline)	__set_dbxrefs() (in DBSeqRecord)	_lower() (in HasStopCodon)
__init__() (in PrankCommandline)	__set_features() (in DBSeqRecord)	_lpad() (in Bio.pairwise2)
__init__() (in ProbconsCommandline)	__set_seq() (in DBSeqRecord)	_lpad_until_equal() (in Bio.pairwise2)
__init__() (in TCoffeeCommandline)	__setattr__() (in AbstractCommandline)	_Mafft (in Bio.Align.Applications)
__init__() (in Alignment)	__setattr__() (in QueryRow)	_make_ambiguous_ranges() (in Bio.Data.IUPACData)
__init__() (in MultipleSeqAlignment)	__setitem__() (in Chain)	_make_callback() (in EventGenerator)
__init__() (in AlignmentIterator)	__setitem__() (in Crystal)	_make_fragment_list() (in Bio.PDB.FragmentMapper')
__init__() (in AlignmentWriter)	__setitem__() (in StructureElement)	_make_list() (in PrintFormat)
__init__() (in SequentialAlignmentWriter)	__setitem__() (in _IndexedSeqFileDict)	_make_list_only() (in PrintFormat)
__init__() (in AlphabetEncoder)	__setitem__() (in _InMemoryIndex)	_make_map() (in PrintFormat)
__init__() (in Gapped)	__setitem__() (in DisorderedEntityWrapper)	_make_map_only() (in PrintFormat)
__init__() (in HasStopCodon)	__setitem__() (in Vector)	_make_mmcif_dict() (in MMCIF2Dict)
__init__() (in AbstractCommandline)	__setitem__() (in Events)	_make_nocut() (in PrintFormat)
__init__() (in ApplicationError)	__setitem__() (in Hit)	_make_nocut_only() (in PrintFormat)
__init__() (in _AbstractParameter)	__setitem__() (in HSP)	_make_number() (in PrintFormat)
__init__() (in _Argument)	__setitem__() (in QueryResult)	_make_number_only() (in PrintFormat)
__init__() (in _Option)	__setitem__() (in MutableSeq)	_make_position() (in Bio.SeqIO.SwissIO)
__init__() (in _Switch)	__setitem__() (in _RestrictedDict)	_make_ranges() (in Bio.Data.IUPACData)
__init__() (in BlastallCommandline)	__setitem__() (in OrderedDict)	_make_score_matrix_fast() (in Bio.cpairwise2)
__init__() (in BlastpgpCommandline)	__skip_unused_lines() (in Bio.Motif.Parsers.MEME)	_make_score_matrix_generic() (in Bio.pairwise2)
__init__() (in FastacmdCommandline)	__skip_unused_lines() (in Bio.motifs.meme)	_make_seqfeature() (in Bio.SeqIO.SwissIO)
__init__() (in NcbiblastformatterCommandline)	__str__() (in PSSM)	_make_triplets() (in Bio.SearchIO.ExonerateIO._base)
__init__() (in NcbiblastnCommandline)	__str__() (in Alignment)	_make_unicode_into_string() (in BioSQL.BioSeq)
__init__() (in NcbiblastpCommandline)	__str__() (in AbstractCommandline)	_make_unique() (in Bio.Nexus.Nexus)
__init__() (in NcbiblastxCommandline)	__str__() (in ApplicationError)	_maketrans() (in Bio.Seq)
__init__() (in NcbipsiblastCommandline)	__str__() (in _AbstractParameter)	_map() (in FragmentMapper)
__init__() (in NcbirpsblastCommandline)	__str__() (in _Argument)	_map_fragment_list() (in Bio.PDB.FragmentMapper')
__init__() (in NcbirpstblastnCommandline)	__str__() (in _Option)	_mass() (in Record)
__init__() (in NcbitblastnCommandline)	__str__() (in _Switch)	_matrix() (in Nexus)
__init__() (in NcbitblastxCommandline)	__str__() (in Alignment)	_medline_line() (in Reference)
__init__() (in RpsBlastCommandline)	__str__() (in Description)	_mft (in Bio.SeqIO.SffIO)
__init__() (in _BlastAllOrPgpCommandLine)	__str__() (in HSP)	_MIN_HIT_FIELDS (in Bio.SearchIO.BlastIO.blast_tab)
__init__() (in _BlastCommandLine)	__str__() (in Chain)	_MIN_QUERY_FIELDS (in Bio.SearchIO.BlastIO.blast_tab)
__init__() (in _NcbibaseblastCommandline)	__str__() (in Crystal)	_mle() (in Bio.MarkovModel)
__init__() (in _Ncbiblast2SeqCommandline)	__str__() (in Hetero)	_mod1() (in Blunt)
__init__() (in _NcbiblastCommandline)	__str__() (in CodonTable)	_mod1() (in Ov3)
__init__() (in _NcbiblastMain2SeqCommandline)	__str__() (in InputRecord)	_mod1() (in Ov5)
__init__() (in BlastErrorParser)	__str__() (in CorruptedXMLError)	_mod1() (in Unknown)
__init__() (in BlastParser)	__str__() (in NotXMLError)	_mod2() (in Ambiguous)
__init__() (in Iterator)	__str__() (in ValidationError)	_mod2() (in Defined)
__init__() (in PSIBlastParser)	__str__() (in Record)	_mod2() (in NotDefined)
__init__() (in _BlastConsumer)	__str__() (in _IndexedSeqFileDict)	_model (in Bio.SearchIO)
__init__() (in _BlastErrorConsumer)	__str__() (in Organism)	_modify() (in NoCut)
__init__() (in _PSIBlastConsumer)	__str__() (in Feature)	_modify() (in OneCut)
__init__() (in BlastParser)	__str__() (in Record)	_modify() (in TwoCuts)
__init__() (in _XMLparser)	__str__() (in Reference)	_Motif (in Bio.Motif)
__init__() (in BlastTableEntry)	__str__() (in Record)	_motifname() (in MEMEInstance)
__init__() (in BlastTableReader)	__str__() (in Diagram)	_Muscle (in Bio.Align.Applications)
__init__() (in BlastTableRec)	__str__() (in FeatureSet)	_name() (in Record)
__init__() (in Alignment)	__str__() (in GraphData)	_name() (in Record)
__init__() (in Blast)	__str__() (in GraphSet)	_name_n_vector() (in Nexus)
__init__() (in DatabaseReport)	__str__() (in Track)	_NcbibaseblastCommandline (in Bio.Blast.Applications)
__init__() (in Description)	__str__() (in Record)	_Ncbiblast2SeqCommandline (in Bio.Blast.Applications)
__init__() (in HSP)	__str__() (in Record)	_NcbiblastCommandline (in Bio.Blast.Applications)
__init__() (in Header)	__str__() (in MarkovModel)	_NcbiblastMain2SeqCommandline (in Bio.Blast.Applications)
__init__() (in MultipleAlignment)	__str__() (in Motif)	_neighbor_test() (in Bio.KDTree.KDTree')
__init__() (in PSIBlast)	__str__() (in AbstractLayer)	_nice_case() (in Bio.PDB.parse_pdb_header')
__init__() (in Parameters)	__str__() (in Tree)	_nid_line() (in Record)
__init__() (in Round)	__str__() (in Interaction)	_nodetype_to_code (in Bio.SCOP)
__init__() (in CAPSMap)	__str__() (in Network)	_NON_STICKY_ATTRS (in _BaseSearchObject)
__init__() (in DifferentialCutsite)	__str__() (in Reaction)	_NON_STICKY_ATTRS (in Hit)
__init__() (in Record)	__str__() (in Graph)	_NON_STICKY_ATTRS (in HSP)
__init__() (in Record)	__str__() (in HashSet)	_NON_STICKY_ATTRS (in QueryResult)
__init__() (in Chain)	__str__() (in MultiGraph)	_normalize() (in Bio.MarkovModel)
__init__() (in Crystal)	__str__() (in System)	_normalize_spaces() (in _BaseGenBankConsumer)
__init__() (in Hetero)	__str__() (in BranchColor)	_Novoalign (in Bio.Sequencing.Applications)
__init__() (in AmbiguousCodonTable)	__str__() (in Clade)	_ns() (in Bio.Phylo.PhyloXMLIO)
__init__() (in AmbiguousForwardTable)	__str__() (in Tree)	_null (in Bio.SeqIO.SffIO)
__init__() (in CodonTable)	__str__() (in Accession)	_numoccurrences() (in MEMEMotif)
__init__() (in NCBICodonTable)	__str__() (in Date)	_object_matcher() (in Bio.Phylo.BaseTree)
__init__() (in Create)	__str__() (in Id)	_oneof_location (in Bio.GenBank)
__init__() (in Insert)	__str__() (in MolSeq)	_oneof_position (in Bio.GenBank)
__init__() (in IterationCursor)	__str__() (in Phyloxml)	_open() (in Bio.Entrez)
__init__() (in Query)	__str__() (in Polygon)	_open() (in Bio.SCOP)
__init__() (in QueryAll)	__str__() (in Taxonomy)	_open() (in Bio.TogoWS)
__init__() (in QueryGeneric)	__str__() (in Uri)	_open_scop_file() (in Bio.SCOP)
__init__() (in QueryRow)	__str__() (in Record)	_Option (in Bio.Application)
__init__() (in QuerySingle)	__str__() (in FileRecord)	_OPTION_GAP_EXTENSION (in Bio.Wise.psw)
__init__() (in DiffseqCommandline)	__str__() (in Record)	_OPTION_GAP_START (in Bio.Wise.psw)
__init__() (in EInvertedCommandline)	__str__() (in RestrictionBatch)	_OPTION_SCORES (in Bio.Wise.psw)
__init__() (in ETandemCommandline)	__str__() (in RestrictionType)	_options() (in Nexus)
__init__() (in Est2GenomeCommandline)	__str__() (in Record)	_ordereddict (in Bio._py3k)
__init__() (in FConsenseCommandline)	__str__() (in Record)	_organism_line() (in Record)
__init__() (in FDNADistCommandline)	__str__() (in Record)	_origin_line() (in Record)
__init__() (in FDNAParsCommandline)	__str__() (in Domain)	_overdraw_subcomponents() (in AnnotatedChromosomeSegment)
__init__() (in FNeighborCommandline)	__str__() (in Record)	_overdraw_subcomponents() (in ChromosomeSegment)
__init__() (in FProtDistCommandline)	__str__() (in Node)	_pad() (in Bio.pairwise2)
__init__() (in FProtParsCommandline)	__str__() (in Residues)	_pad_until_equal() (in Bio.pairwise2)
__init__() (in FSeqBootCommandline)	__str__() (in Hit)	_pair_location (in Bio.GenBank)
__init__() (in FTreeDistCommandline)	__str__() (in HSP)	_pair_replacement() (in SummaryInfo)
__init__() (in FuzznucCommandline)	__str__() (in HSPFragment)	_paml (in Bio.Phylo.PAML)
__init__() (in IepCommandline)	__str__() (in QueryResult)	_ParametersConsumer (in Bio.Blast.NCBIStandalone)
__init__() (in NeedleCommandline)	__str__() (in MutableSeq)	_parse() (in _DescriptionConsumer)
__init__() (in NeedleallCommandline)	__str__() (in Seq)	_Parse() (in BlastTableReader)
__init__() (in PalindromeCommandline)	__str__() (in UnknownSeq)	_parse() (in Tree)
__init__() (in Primer3Commandline)	__str__() (in AfterPosition)	_parse() (in PDBParser)
__init__() (in PrimerSearchCommandline)	__str__() (in BeforePosition)	_parse() (in Residues)
__init__() (in SeqmatchallCommandline)	__str__() (in BetweenPosition)	_parse() (in BlastXmlIndexer)
__init__() (in SeqretCommandline)	__str__() (in FeatureLocation)	_parse() (in SearchIndexer)
__init__() (in StretcherCommandline)	__str__() (in OneOfPosition)	_parse_alignment_header() (in _BaseExonerateParser)
__init__() (in TranalignCommandline)	__str__() (in PositionGap)	_parse_aln_block() (in Hmmer3TextParser)
__init__() (in WaterCommandline)	__str__() (in Reference)	_parse_baseml (in Bio.Phylo.PAML)
__init__() (in _EmbossCommandLine)	__str__() (in SeqFeature)	_parse_clade() (in Parser)
__init__() (in _EmbossMinimalCommandLine)	__str__() (in WithinPosition)	_parse_codeml (in Bio.Phylo.PAML)
__init__() (in Primers)	__str__() (in SeqRecord)	_parse_commented_qresult() (in BlastTabParser)
__init__() (in Record)	__str__() (in SeqMat)	_parse_comments() (in BlastTabParser)
__init__() (in Amplifier)	__str__() (in Statistics)	_parse_coordinates() (in PDBParser)
__init__() (in InputRecord)	__str__() (in ColumnUnit)	_parse_database() (in BlastTableReader)
__init__() (in OutputRecord)	__str__() (in Instances)	_parse_fields() (in BlastTableReader)
__init__() (in CorruptedXMLError)	__str__() (in Motif)	_parse_fields_line() (in BlastTabParser)
__init__() (in DataHandler)	__str__() (in GenericPositionMatrix)	_parse_hit() (in BlastXmlParser)
__init__() (in NotXMLError)	__str__() (in Record)	_parse_hit() (in FastaM10Parser)
__init__() (in StructureElement)	__str__() (in DBSeq)	_parse_hit() (in Hmmer3TextParser)
__init__() (in ValidationError)	__sub__() (in Atom)	_parse_hit_or_query_line() (in Bio.SearchIO.ExonerateIO._base)
__init__() (in Record)	__sub__() (in DisorderedEntityWrapper)	_parse_hsp() (in BlastXmlParser)
__init__() (in Record)	__sub__() (in Fragment)	_parse_iteration() (in BlastTableReader)
__init__() (in Reference)	__sub__() (in Vector)	_parse_list() (in Nexus)
__init__() (in Record)	__sub__() (in Confidence)	_parse_nexus_block() (in Nexus)
__init__() (in ContentHandler)	__sub__() (in SeqMat)	_parse_pdb_header_list() (in Bio.PDB.parse_pdb_header')
__init__() (in Parser)	__truediv__() (in Confidence)	_parse_phylogeny() (in Parser)
__init__() (in Record)	__truediv__() (in RestrictionType)	_parse_preamble() (in BlastXmlParser)
__init__() (in FSSPAlignDict)	__version (in _InMemoryIndex)	_parse_preamble() (in FastaM10Parser)
__init__() (in FSSPAlignRec)	__version (in _ShelveIndex)	_parse_preamble() (in Hmmer3TextParser)
__init__() (in FSSPHeader)	__version_key (in _InMemoryIndex)	_parse_qblast_ref_page() (in Bio.Blast.NCBIWWW)
__init__() (in FSSPSumRec)	__version_key (in _ShelveIndex)	_parse_qresult() (in BlastTabParser)
__init__() (in FSSPMultAlign)	__warningregistry__ (in Bio.Blast.NCBIStandalone)	_parse_qresult() (in BlastXmlParser)
__init__() (in PosAlign)	__warningregistry__ (in Bio.HotRand)	_parse_qresult() (in BlatPslParser)
__init__() (in fff_rec)	__warningregistry__ (in Bio.MarkovModel)	_parse_qresult() (in _BaseExonerateParser)
__init__() (in UndoHandle)	__warningregistry__ (in Bio.Motif)	_parse_qresult() (in FastaM10Parser)
__init__() (in _IndexedSeqFileDict)	__warningregistry__ (in Bio.ParserSupport)	_parse_qresult() (in Hmmer3DomtabParser)
__init__() (in _SQLiteManySeqFilesDict)	__warningregistry__ (in Bio.Pathway.Rep.HashSet)	_parse_qresult() (in Hmmer3TabParser)
__init__() (in SafeFitnessCrossover)	__warningregistry__ (in Bio.Search)	_parse_qresult() (in Hmmer3TextParser)
__init__() (in GeneralPointCrossover)	__warningregistry__ (in Bio.SearchIO)	_parse_query() (in BlastTableReader)
__init__() (in InterleaveCrossover)	__warningregistry__ (in Bio.UniGene.UniGene)	_parse_result_row() (in BlastTabParser)
__init__() (in SinglePointCrossover)	_abi_parse_header() (in Bio.SeqIO.AbiIO)	_parse_row() (in BlatPslParser)
__init__() (in TwoPointCrossover)	_abi_trim() (in Bio.SeqIO.AbiIO)	_parse_row() (in Hmmer3DomtabParser)
__init__() (in UniformCrossover)	_AbiTrimIterator() (in Bio.SeqIO.AbiIO)	_parse_row() (in Hmmer3TabParser)
__init__() (in GenerationEvolver)	_AbstractDrawer (in Bio.Graphics.GenomeDiagram)	_parse_sequence() (in Parser)
__init__() (in SteadyStateEvolver)	_AbstractHSExposure (in Bio.PDB.HSExposure)	_parse_subtree() (in Parser)
__init__() (in SafeFitnessMutation)	_AbstractParameter (in Bio.Application)	_parse_tag() (in Parser)
__init__() (in ConversionMutation)	_accept() (in _PPBuilder)	_parse_tag_data() (in Bio.SeqIO.AbiIO)
__init__() (in SinglePositionMutation)	_accession_line() (in Record)	_parse_taxonomy() (in Parser)
__init__() (in Organism)	_add() (in ScoreDistribution)	_parse_tree() (in Parser)
__init__() (in AmbiguousRepair)	_add() (in ScoreDistribution)	_parse_version() (in BlastTableReader)
__init__() (in AbstractSelection)	_add_bioentry_dbxref() (in DatabaseLoader)	_parse_yn00 (in Bio.Phylo.PAML)
__init__() (in DiversitySelection)	_add_dbxref() (in DatabaseLoader)	_parser (in _BaseExonerateIndexer)
__init__() (in RouletteWheelSelection)	_add_feature() (in _RecordConsumer)	_parsers (in Bio.Motif)
__init__() (in TournamentSelection)	_add_motif() (in MotifFinder)	_pathway() (in Record)
__init__() (in FeatureParser)	_add_nodedata() (in Tree)	_pathway() (in Record)
__init__() (in Iterator)	_add_numbering_table() (in FSSPAlign)	_pdbid_re (in Bio.SCOP.Residues)
__init__() (in Feature)	_add_seqfeature_dbxref() (in DatabaseLoader)	_phred_to_illumina_quality_str (in Bio.SeqIO.QualityIO)
__init__() (in Qualifier)	_add_sig() (in SignatureFinder)	_phred_to_sanger_quality_str (in Bio.SeqIO.QualityIO)
__init__() (in Record)	_add_subtree() (in Tree)	_phred_to_solexa_quality_str (in Bio.SeqIO.QualityIO)
__init__() (in Reference)	_AddTellHandle (in Bio.SeqIO.SffIO)	_PHYLIP_ID_WIDTH (in Bio.AlignIO.PhylipIO)
__init__() (in RecordParser)	_adjust_aa_seq() (in Bio.SearchIO.ExonerateIO._base)	_Phyml (in Bio.Phylo.Applications)
__init__() (in InsdcScanner)	_adjust_charlabels() (in Nexus)	_pid_line() (in Record)
__init__() (in _BaseGenBankConsumer)	_adjust_coords() (in BlastTabWriter)	_pir_alphabets (in Bio.SeqIO.PirIO)
__init__() (in _FeatureConsumer)	_adjust_lines() (in Bio.Nexus.Nexus)	_place_labels() (in Bio.Graphics.BasicChromosome)
__init__() (in _RecordConsumer)	_adjust_output() (in BlastTabWriter)	_populate_meta_data() (in StockholmIterator)
__init__() (in FeatureValueCleaner)	_adjust_output() (in BlastXmlWriter)	_possibly_complemented_complex_location (in Bio.GenBank)
__init__() (in Record)	_alb_line2coords() (in Bio.Wise.dnal)	_POSTGRES_RULES_PRESENT (in BioSQL.BioSeqDatabase)
__init__() (in AnnotatedChromosomeSegment)	_align() (in Bio.pairwise2)	_PostgreSQL_dbutils (in BioSQL.DBUtils)
__init__() (in Chromosome)	_AlignAce (in Bio.Motif.Applications)	_postorder_traverse() (in Bio.Phylo.BaseTree)
__init__() (in ChromosomeSegment)	_alignace (in Bio.motifs.applications)	_powers_of_36 (in Bio.SeqIO.SffIO)
__init__() (in Organism)	_AlignmentConsumer (in Bio.Blast.NCBIStandalone)	_PPBuilder (in Bio.PDB.Polypeptide)
__init__() (in TelomereSegment)	_all_blank() (in MarkovModelBuilder)	_Prank (in Bio.Align.Applications)
__init__() (in _ChromosomeComponent)	_all_pseudo() (in MarkovModelBuilder)	_PRECISION (in Bio.pairwise2)
__init__() (in ColorSpiral)	_allowed_lookups (in BioSQL.BioSeqDatabase)	_preorder_traverse() (in Bio.Phylo.BaseTree)
__init__() (in ComparativeScatterPlot)	_aln_get() (in HSPFragment)	_prep_coord() (in HSPFragment)
__init__() (in ChromosomeCounts)	_ALN_MARK (in _BaseExonerateParser)	_prep_fields() (in BlastTabParser)
__init__() (in BarChartDistribution)	_ALN_MARK (in ExonerateCigarParser)	_prep_frame() (in HSPFragment)
__init__() (in DistributionPage)	_ALN_MARK (in ExonerateTextParser)	_prep_strand() (in HSPFragment)
__init__() (in LineDistribution)	_ALN_MARK (in ExonerateVulgarParser)	_print_name() (in TaggingConsumer)
__init__() (in AbstractDrawer)	_aln_span_get() (in HSP)	_Probcons (in Bio.Align.Applications)
__init__() (in CircularDrawer)	_aln_span_get() (in HSPFragment)	_process() (in Record)
__init__() (in ColorTranslator)	_aln_span_set() (in HSPFragment)	_process() (in Record)
__init__() (in CrossLink)	_alphabet_from_input() (in FreqTable)	_process() (in Record)
__init__() (in Diagram)	_alphabet_from_matrix() (in SeqMat)	_process() (in Record)
__init__() (in Feature)	_alphabet_get() (in HSPFragment)	_process() (in SeqMap)
__init__() (in FeatureSet)	_alphabet_set() (in HSPFragment)	_product() (in Record)
__init__() (in GraphData)	_any() (in Bio.Wise.dnal)	_project_line() (in Record)
__init__() (in GraphSet)	_append() (in MultipleSeqAlignment)	_PSIBlastConsumer (in Bio.Blast.NCBIStandalone)
__init__() (in LinearDrawer)	_apply_block_structure() (in Nexus)	_PTR_ID_DESC_SEQLEN (in Bio.SearchIO.FastaIO)
__init__() (in Track)	_argmaxes() (in Bio.MarkovModel)	_PTR_ROW_CHECK (in Bio.SearchIO.BlatIO)
__init__() (in AbstractDPAlgorithms)	_Argument (in Bio.Application)	_pubmed_line() (in Reference)
__init__() (in LogDPAlgorithms)	_as_bytes() (in Bio._py3k)	_pvalue() (in MEMEInstance)
__init__() (in ScaledDPAlgorithms)	_as_unicode() (in Bio._py3k)	_pwm (in Bio.Motif)
__init__() (in HiddenMarkovModel)	_assign_atom_mass() (in Atom)	_pwm (in Bio.motifs)
__init__() (in MarkovModelBuilder)	_assign_element() (in Atom)	_pwm_calculate() (in Motif)
__init__() (in AbstractTrainer)	_ATOM_FORMAT_STRING (in Bio.PDB.PDBIO')	_py3k (in Bio)
__init__() (in BaumWelchTrainer)	_atom_name_dict (in Bio.PDB.Residue)	_QRE_ID_LEN (in Bio.SearchIO.HmmerIO.hmmer3_text)
__init__() (in KnownStateTrainer)	_attr_DBRef() (in SeqXmlIterator)	_QRE_ID_LEN_PTN (in Bio.SearchIO.HmmerIO.hmmer3_text)
__init__() (in TrainingSequence)	_attr_entry() (in SeqXmlIterator)	_qresult_index() (in BlastTabIndexer)
__init__() (in HotCache)	_attr_property() (in SeqXmlIterator)	_qresult_index_commented() (in BlastTabIndexer)
__init__() (in HotRandom)	_attr_seqXML() (in SeqXmlIterator)	_query_end_get() (in HSP)
__init__() (in _InMemoryIndex)	_attr_species() (in SeqXmlIterator)	_query_end_get() (in HSPFragment)
__init__() (in _ShelveIndex)	_attribute_matcher() (in Bio.Phylo.BaseTree)	_query_end_set() (in HSPFragment)
__init__() (in KDTree)	_attributes() (in XMLRecordIterator)	_query_frame_get() (in HSPFragment)
__init__() (in Record)	_augment_blast_hsp() (in Bio.SearchIO.BlastIO.blast_tab)	_query_frame_set() (in HSPFragment)
__init__() (in Record)	_authors_line() (in Reference)	_query_get() (in HSPFragment)
__init__() (in LogisticRegression)	_backward() (in Bio.MarkovModel)	_query_id_idx (in Hmmer3DomtabHmmhitIndexer)
__init__() (in MarkovModel)	_backward_recursion() (in AbstractDPAlgorithms)	_query_id_idx (in Hmmer3DomtabHmmqueryIndexer)
__init__() (in MaxEntropy)	_backward_recursion() (in ScaledDPAlgorithms)	_query_id_idx (in Hmmer3TabIndexer)
__init__() (in AlignAceCommandline)	_base (in Bio.SearchIO.ExonerateIO)	_query_inter_ranges_get() (in HSP)
__init__() (in CompareAceCommandline)	_base (in Bio.SearchIO.HmmerIO)	_query_inter_spans_get() (in HSP)
__init__() (in XXmotifCommandline)	_base (in Bio.SearchIO._model)	_query_mark (in _BaseExonerateIndexer)
__init__() (in Record)	_base_count_line() (in Record)	_query_mark (in ExonerateCigarIndexer)
__init__() (in Record)	_BASE_URL (in Bio.TogoWS)	_query_mark (in ExonerateTextIndexer)
__init__() (in MEMEInstance)	_BaseExonerateIndexer (in Bio.SearchIO.ExonerateIO._base)	_query_mark (in ExonerateVulgarIndexer)
__init__() (in MEMEMotif)	_BaseExonerateParser (in Bio.SearchIO.ExonerateIO._base)	_query_range_get() (in HSP)
__init__() (in MEMERecord)	_BaseGenBankConsumer	_query_range_get() (in HSPFragment)
__init__() (in ScoreDistribution)	_BaseHmmerTextIndexer (in Bio.SearchIO.HmmerIO._base)	_query_re (in _HSPConsumer)
__init__() (in Motif)	_BaseHSP (in Bio.SearchIO._model._base)	_query_set() (in HSPFragment)
__init__() (in Peaklist)	_BaseSearchObject (in Bio.SearchIO._model._base)	_query_span_get() (in HSP)
__init__() (in XpkEntry)	_baum_welch() (in Bio.MarkovModel)	_query_span_get() (in HSPFragment)
__init__() (in NaiveBayes)	_baum_welch_one() (in Bio.MarkovModel)	_query_start_get() (in HSP)
__init__() (in AbstractLayer)	_between_location (in Bio.GenBank)	_query_start_get() (in HSPFragment)
__init__() (in HiddenLayer)	_bgzf_eof (in Bio.bgzf)	_query_start_set() (in HSPFragment)
__init__() (in InputLayer)	_bgzf_header (in Bio.bgzf)	_query_strand_get() (in HSPFragment)
__init__() (in OutputLayer)	_bgzf_magic (in Bio.bgzf)	_query_strand_set() (in HSPFragment)
__init__() (in BasicNetwork)	_binary_to_string_handle() (in Bio._py3k)	_random_norm() (in Bio.MarkovModel)
__init__() (in MotifCoder)	_BinaryFormats (in Bio.SeqIO)	_Raxml (in Bio.Phylo.Applications)
__init__() (in MotifFinder)	_BlastAllOrPgpCommandLine (in Bio.Blast.Applications)	_re_alb_line2coords (in Bio.Wise.dnal)
__init__() (in PatternIO)	_BlastCommandLine (in Bio.Blast.Applications)	_RE_ALN_ROW (in Bio.SearchIO.ExonerateIO.exonerate_text)
__init__() (in PatternRepository)	_BlastConsumer (in Bio.Blast.NCBIStandalone)	_RE_ATTR (in Bio.SearchIO.FastaIO)
__init__() (in DifferentialSchemaFitness)	_BlastErrorConsumer (in Bio.Blast.NCBIStandalone)	_RE_CIGAR (in Bio.SearchIO.ExonerateIO.exonerate_cigar)
__init__() (in GeneticAlgorithmFinder)	_BlastXmlGenerator (in Bio.SearchIO.BlastIO.blast_xml)	_re_complex_compound (in Bio.GenBank)
__init__() (in MostCountSchemaFitness)	_boundaries() (in Analysis)	_re_complex_location (in Bio.GenBank)
__init__() (in RandomMotifGenerator)	_build_align_cmdline() (in Bio.Wise)	_RE_EXON (in Bio.SearchIO.ExonerateIO.exonerate_text)
__init__() (in Schema)	_build_comments() (in BlastTabWriter)	_RE_EXON_LEN (in Bio.SearchIO.ExonerateIO.exonerate_text)
__init__() (in SchemaCoder)	_build_dnal_cmdline() (in Bio.Wise.dnal)	_RE_FLAVS (in Bio.SearchIO.FastaIO)
__init__() (in SchemaFactory)	_build_exp_freq_mat() (in Bio.SubsMat)	_RE_GAPOPEN (in Bio.SearchIO.BlastIO.blast_tab)
__init__() (in SchemaFinder)	_build_header() (in BlatPslWriter)	_RE_ID_DESC_SEQLEN (in Bio.SearchIO.FastaIO)
__init__() (in SimpleFinisher)	_build_header() (in Hmmer3DomtabHmmhitWriter)	_RE_ID_DESC_SEQLEN_IDX (in Bio.SearchIO.FastaIO)
__init__() (in SignatureCoder)	_build_header() (in Hmmer3TabWriter)	_RE_NER (in Bio.SearchIO.ExonerateIO.exonerate_text)
__init__() (in SignatureFinder)	_build_log_odds_mat() (in Bio.SubsMat)	_RE_NER_LEN (in Bio.SearchIO.ExonerateIO.exonerate_text)
__init__() (in ValidationIncreaseStop)	_build_obs_freq_mat() (in Bio.SubsMat)	_re_oneof_position (in Bio.GenBank)
__init__() (in ExampleManager)	_build_row() (in BlatPslWriter)	_RE_OPT (in Bio.SearchIO.HmmerIO.hmmer3_text)
__init__() (in TrainingExample)	_build_row() (in Hmmer3DomtabHmmhitWriter)	_RE_PROGRAM (in Bio.SearchIO.HmmerIO.hmmer3_text)
__init__() (in Block)	_build_row() (in Hmmer3TabWriter)	_re_prop_name (in Bio.Application)
__init__() (in CharBuffer)	_build_rows() (in BlastTabWriter)	_RE_ROW_CHECK (in Bio.SearchIO.BlatIO)
__init__() (in Commandline)	_build_structure() (in MMCIFParser)	_RE_ROW_CHECK_IDX (in Bio.SearchIO.BlatIO)
__init__() (in Nexus)	_build_subs_mat() (in Bio.SubsMat)	_RE_SCODON_END (in Bio.SearchIO.ExonerateIO.exonerate_text)
__init__() (in StepMatrix)	_BYTEFMT (in Bio.SeqIO.AbiIO)	_RE_SCODON_START (in Bio.SearchIO.ExonerateIO.exonerate_text)
__init__() (in Chain)	_bytes_BC (in Bio.bgzf)	_re_search() (in Bio.Blast.NCBIStandalone)
__init__() (in Node)	_bytes_newline (in Bio.bgzf)	_RE_SHIFTS (in Bio.SearchIO.ExonerateIO._base)
__init__() (in NodeData)	_bytes_to_string() (in Bio._py3k)	_re_simple_compound (in Bio.GenBank)
__init__() (in Tree)	_calc_diversities_fis() (in GenePopController)	_re_simple_location (in Bio.GenBank)
__init__() (in AbstractAtomPropertyMap)	_calc_empirical_expects() (in Bio.MaxEntropy)	_RE_TRANS (in Bio.SearchIO.ExonerateIO._base)
__init__() (in AbstractPropertyMap)	_calc_f_sharp() (in Bio.MaxEntropy)	_re_unit (in Bio.Wise.psw)
__init__() (in AbstractResiduePropertyMap)	_calc_ibd() (in GenePopController)	_RE_VCOMP (in Bio.SearchIO.ExonerateIO.exonerate_vulgar)
__init__() (in Atom)	_calc_millibad() (in Bio.SearchIO.BlatIO)	_RE_VERSION (in Bio.SearchIO.BlastIO.blast_xml)
__init__() (in DisorderedAtom)	_calc_model_expects() (in Bio.MaxEntropy)	_RE_VERSION (in Bio.SearchIO.HmmerIO.hmmer3_text)
__init__() (in Chain)	_calc_p_class_given_x() (in Bio.MaxEntropy)	_RE_VULGAR (in Bio.SearchIO.ExonerateIO.exonerate_vulgar)
__init__() (in DSSP)	_calc_score() (in Bio.SearchIO.BlatIO)	_re_within_position (in Bio.GenBank)
__init__() (in ChainSelector)	_calculate_emissions() (in Bio.HMM.MarkovModel)	_reaction() (in Record)
__init__() (in DisorderedEntityWrapper)	_calculate_from_transitions() (in Bio.HMM.MarkovModel)	_read() (in Motif)
__init__() (in Entity)	_calculate_s_value() (in ScaledDPAlgorithms)	_read() (in Bio.SwissProt)
__init__() (in Fragment)	_calculate_to_transitions() (in Bio.HMM.MarkovModel)	_read() (in Bio.UniGene)
__init__() (in FragmentMapper)	_case_less() (in Alphabet)	_read_alignment() (in ExonerateTextParser)
__init__() (in ExposureCN)	_changeset() (in Nexus)	_read_allele_freq_table() (in Bio.PopGen.GenePop.Controller)
__init__() (in HSExposureCA)	_chargeR() (in IsoelectricPoint)	_read_cc() (in Bio.SwissProt)
__init__() (in HSExposureCB)	_charlabels() (in Nexus)	_read_dicts() (in Bio.NMR.xpktools)
__init__() (in _AbstractHSExposure)	_charpartition() (in Nexus)	_read_dr() (in Bio.SwissProt)
__init__() (in MMCIF2Dict)	_charset() (in Nexus)	_read_dt() (in Bio.SwissProt)
__init__() (in Model)	_charstatelabels() (in Nexus)	_read_fragments() (in Bio.PDB.FragmentMapper')
__init__() (in NACCESS)	_check_alphabet() (in Motif)	_read_ft() (in Bio.SwissProt)
__init__() (in NACCESS_atomic)	_check_bases() (in Bio.Restriction.Restriction)	_read_headed_triangle_matrix() (in Bio.PopGen.GenePop.Controller)
__init__() (in NeighborSearch)	_check_is_public() (in Bio.DocSQL)	_read_id() (in Bio.SwissProt)
__init__() (in PDBIO)	_check_length() (in Motif)	_read_key_value() (in Bio.Geo)
__init__() (in PDBList)	_check_str() (in Bio.Phylo.PhyloXML)	_read_oh() (in Bio.SwissProt)
__init__() (in PDBParser)	_check_taxlabels() (in Nexus)	_read_ox() (in Bio.SwissProt)
__init__() (in PSEA)	_check_type_compatible() (in Bio.Alphabet)	_read_rc() (in Bio.SwissProt)
__init__() (in CaPPBuilder)	_check_value() (in AbstractCommandline)	_read_rn() (in Bio.SwissProt)
__init__() (in PPBuilder)	_chop_end_codes() (in Bio.PDB.parse_pdb_header')	_read_rx() (in Bio.SwissProt)
__init__() (in _PPBuilder)	_chop_end_misc() (in Bio.PDB.parse_pdb_header')	_read_table() (in Bio.PopGen.GenePop.Controller)
__init__() (in DisorderedResidue)	_ChromosomeComponent (in Bio.Graphics.BasicChromosome)	_read_triangle_matrix() (in Bio.PopGen.GenePop.Controller)
__init__() (in Residue)	_CircularDrawer (in Bio.Graphics.GenomeDiagram)	_read_until() (in Hmmer3TextParser)
__init__() (in ResidueDepth)	_CKDTree (in Bio.KDTree)	_read_vertex_array() (in Bio.PDB.ResidueDepth')
__init__() (in Structure)	_clade_complex_types (in Parser)	_readers (in Bio.Motif)
__init__() (in StructureAlignment)	_clade_list_types (in Parser)	_readline_and_check_start() (in Bio.MarkovModel)
__init__() (in StructureBuilder)	_clade_tracked_tags (in Parser)	_RecordConsumer
__init__() (in Superimposer)	_class_matcher() (in Bio.Phylo.BaseTree)	_recover_alignments() (in Bio.pairwise2)
__init__() (in Vector)	_classify_alphabet_for_nexus() (in NexusWriter)	_reference_line() (in Reference)
__init__() (in EventGenerator)	_classname() (in Record)	_relpath() (in Bio.Phylo.PAML._paml)
__init__() (in TaggingConsumer)	_clean_alignments() (in Bio.pairwise2)	_remark_line() (in Reference)
__init__() (in Network)	_clean_attrib() (in Bio.Phylo.PhyloXMLIO)	_remove_garbage() (in GenePopController)
__init__() (in Reaction)	_clean_blocks() (in Bio.SearchIO.ExonerateIO.exonerate_text)	_remove_newlines() (in _BaseGenBankConsumer)
__init__() (in Graph)	_clean_location() (in _BaseGenBankConsumer)	_remove_spaces() (in _BaseGenBankConsumer)
__init__() (in HashSet)	_clean_translation() (in FeatureValueCleaner)	_reorient_starts() (in Bio.SearchIO.BlatIO)
__init__() (in MultiGraph)	_clear() (in SVDSuperimposer)	_replace_parenthesized_ambigs() (in Bio.Nexus.Nexus)
__init__() (in System)	_clear_parameter() (in AbstractCommandline)	_replace_wspace() (in Bio.Phylo.PhyloXMLIO)
__init__() (in PhymlCommandline)	_ClustalOmega (in Bio.Align.Applications)	_reserved_names (in Bio.Application)
__init__() (in RaxmlCommandline)	_Clustalw (in Bio.Align.Applications)	_resolve() (in Nexus)
__init__() (in BranchColor)	_CMDLINE_DNAL (in Bio.Wise.dnal)	_RestrictedDict (in Bio.SeqRecord)
__init__() (in Clade)	_CMDLINE_FGREP_COUNT (in Bio.Wise.dnal)	_retrieve_annotations() (in BioSQL.BioSeq)
__init__() (in Tree)	_CMDLINE_PSW (in Bio.Wise.psw)	_retrieve_comment() (in BioSQL.BioSeq)
__init__() (in Clade)	_codeset() (in Nexus)	_retrieve_dbxrefs() (in BioSQL.BioSeq)
__init__() (in Tree)	_codonposset() (in Nexus)	_retrieve_features() (in BioSQL.BioSeq)
__init__() (in Parser)	_cofactor() (in Record)	_retrieve_location_qualifier_value() (in BioSQL.BioSeq)
__init__() (in Writer)	_col_ave() (in Bio.NMR.NOEtools)	_retrieve_qualifier_value() (in BioSQL.BioSeq)
__init__() (in Paml)	_collapse_wspace() (in Bio.Phylo.PhyloXMLIO)	_retrieve_reference() (in BioSQL.BioSeq)
__init__() (in Baseml)	_color_from_count() (in ChromosomeCounts)	_retrieve_seq() (in BioSQL.BioSeq)
__init__() (in Codeml)	_color_trans (in Bio.Graphics.BasicChromosome)	_retrieve_taxon() (in BioSQL.BioSeq)
__init__() (in Yn00)	_Colors (in Bio.Graphics.GenomeDiagram)	_rev_modify() (in NoCut)
__init__() (in Accession)	_COLUMN_FRAG (in Bio.SearchIO.BlastIO.blast_tab)	_rev_modify() (in OneCut)
__init__() (in Annotation)	_COLUMN_HIT (in Bio.SearchIO.BlastIO.blast_tab)	_rev_modify() (in TwoCuts)
__init__() (in BinaryCharacters)	_COLUMN_HSP (in Bio.SearchIO.BlastIO.blast_tab)	_rms() (in SVDSuperimposer)
__init__() (in BranchColor)	_COLUMN_QRESULT (in Bio.SearchIO.BlastIO.blast_tab)	_rna_complement_table (in Bio.Seq)
__init__() (in Clade)	_combine_args() (in Bio.Phylo.BaseTree)	_run_genepop() (in GenePopController)
__init__() (in CladeRelation)	_combine_matchers() (in Bio.Phylo.BaseTree)	_run_program() (in Async)
__init__() (in Confidence)	_comment() (in Record)	_run_program() (in Local)
__init__() (in Date)	_comment_line() (in Record)	_safe_float() (in Bio.Blast.NCBIStandalone)
__init__() (in Distribution)	_comp_coords() (in Bio.SearchIO.ExonerateIO.exonerate_text)	_safe_int() (in Bio.Blast.NCBIStandalone)
__init__() (in DomainArchitecture)	_comp_intron_lens() (in Bio.SearchIO.ExonerateIO.exonerate_text)	_savedata() (in Record)
__init__() (in Events)	_comp_split_codons() (in Bio.SearchIO.ExonerateIO.exonerate_text)	_savekmeans() (in Record)
__init__() (in Id)	_compact4nexus() (in Bio.Nexus.Nexus)	_savetree() (in Bio.Cluster)
__init__() (in MolSeq)	_complex_location (in Bio.GenBank)	_sbjct_re (in _HSPConsumer)
__init__() (in Other)	_compute_gapopen_num() (in Bio.SearchIO.BlastIO.blast_tab)	_scan_alignment_header() (in _Scanner)
__init__() (in Phylogeny)	_consensus_alphabet() (in Bio.Alphabet)	_scan_alignments() (in _Scanner)
__init__() (in Phyloxml)	_consensus_base_alphabet() (in Bio.Alphabet)	_scan_database_report() (in _Scanner)
__init__() (in Point)	_consrtm_line() (in Reference)	_scan_descriptions() (in _Scanner)
__init__() (in Polygon)	_consume_entry() (in BlastTableReader)	_scan_header() (in _Scanner)
__init__() (in Property)	_consume_header() (in BlastTableReader)	_scan_hsp() (in _Scanner)
__init__() (in ProteinDomain)	_contents() (in Bio.NaiveBayes)	_scan_hsp_alignment() (in _Scanner)
__init__() (in Reference)	_contig_line() (in Record)	_scan_hsp_header() (in _Scanner)
__init__() (in Sequence)	_convert (in Bio.SeqIO)	_scan_masterslave_alignment() (in _Scanner)
__init__() (in SequenceRelation)	_convert_formats (in Bio.TogoWS)	_scan_one_pairwise_alignment() (in _Scanner)
__init__() (in Taxonomy)	_convert_genepop_to_fdist() (in Bio.PopGen.FDist.Utils)	_scan_pairwise_alignments() (in _Scanner)
__init__() (in Uri)	_convert_genepop_to_fdist_big() (in Bio.PopGen.FDist.Utils)	_scan_parameters() (in _Scanner)
__init__() (in Parser)	_convert_genepop_to_fdist_big_old() (in Bio.PopGen.FDist.Utils)	_scan_rounds() (in _Scanner)
__init__() (in Writer)	_convert_to_python_numbers() (in _BaseGenBankConsumer)	_Scanner (in Bio.Blast.NCBIStandalone)
__init__() (in Async)	_converter (in Bio.SeqIO._convert)	_schema_from_motif() (in SchemaFactory)
__init__() (in DirectoryRetriever)	_copy_and_check() (in Bio.MarkovModel)	_score() (in MEMEInstance)
__init__() (in FileRetriever)	_correct_matrix() (in SeqMat)	_SCORE_GAP_EXTENSION (in Bio.Wise.dnal)
__init__() (in Local)	_count_codons() (in CodonAdaptationIndex)	_SCORE_GAP_START (in Bio.Wise.dnal)
__init__() (in FDistAsync)	_count_emissions() (in KnownStateTrainer)	_SCORE_MATCH (in Bio.Wise.dnal)
__init__() (in SplitFDist)	_count_transitions() (in KnownStateTrainer)	_SCORE_MISMATCH (in Bio.Wise.dnal)
__init__() (in FDistController)	_create_hits() (in Hmmer3TextParser)	_search() (in NonPalindromic)
__init__() (in Record)	_create_hsp() (in Bio.SearchIO.BlatIO)	_search() (in Palindromic)
__init__() (in GenePopController)	_create_hsp() (in Bio.SearchIO.ExonerateIO._base)	_search_db_names (in Bio.TogoWS)
__init__() (in _FileIterator)	_CrossLink (in Bio.Graphics.GenomeDiagram)	_secure_name() (in _XMLparser)
__init__() (in _GenePopCommandline)	_crossover() (in GeneralPointCrossover)	_security_check_parameters() (in Bio.Blast.NCBIStandalone)
__init__() (in EasyController)	_crossover() (in InterleaveCrossover)	_segment_line() (in Record)
__init__() (in FileRecord)	_crossover() (in TwoCrossover)	_select_charged() (in IsoelectricPoint)
__init__() (in Record)	_current_track_start_end() (in AbstractDrawer)	_SeqIO_to_alignment_iterator() (in Bio.AlignIO)
__init__() (in Record)	_data_map() (in Bio.NMR.NOEtools)	_SeqLength (in Bio.Search)
__init__() (in SimCoalCache)	_DatabaseReportConsumer (in Bio.Blast.NCBIStandalone)	_seqmatrix2strmatrix() (in Bio.Nexus.Nexus)
__init__() (in SimCoalCache)	_db_source_line() (in Record)	_seqname() (in MEMEInstance)
__init__() (in SimCoalController)	_dblink_line() (in Record)	_sequence_line() (in Record)
__init__() (in PrintFormat)	_dblinks() (in Record)	_serialize() (in Bio.Phylo.PhyloXMLIO)
__init__() (in Analysis)	_dblinks() (in Record)	_set() (in Nexus)
__init__() (in FormattedSeq)	_dbutils (in BioSQL.DBUtils)	_set_a() (in ColorSpiral)
__init__() (in RestrictionBatch)	_DEFAULT_FIELDS (in Bio.SearchIO.BlastIO.blast_tab)	_set_b() (in ColorSpiral)
__init__() (in RestrictionType)	_default_wrap() (in Bio.KEGG)	_set_color() (in Clade)
__init__() (in DictionaryBuilder)	_definition_line() (in Record)	_set_colors_and_shapes() (in ComparativeScatterPlot)
__init__() (in TypeCompiler)	_del_confidence() (in Clade)	_set_confidence() (in Clade)
__init__() (in newenzyme)	_del_confidence() (in Phylogeny)	_set_confidence() (in Phylogeny)
__init__() (in ConnectionError)	_DescriptionConsumer (in Bio.Blast.NCBIStandalone)	_set_frame() (in Bio.SearchIO.ExonerateIO._base)
__init__() (in FtpNameError)	_determine_position() (in BarChartDistribution)	_set_hsp_seqs() (in Bio.SearchIO.FastaIO)
__init__() (in FtpPasswordError)	_diagnose_error() (in BlastErrorParser)	_set_jitter() (in ColorSpiral)
__init__() (in RebaseUpdate)	_Diagram (in Bio.Graphics.GenomeDiagram)	_set_kind() (in AlignmentColumn)
__init__() (in Astral)	_Dialign (in Bio.Align.Applications)	_set_per_letter_annotations() (in SeqRecord)
__init__() (in Index)	_dict_str2bool() (in Bio.Phylo.PhyloXMLIO)	_set_qresult_hits() (in Bio.SearchIO.FastaIO)
__init__() (in Record)	_digest() (in CAPSMap)	_set_ref() (in SeqFeature)
__init__() (in Record)	_digest_with() (in CAPSMap)	_set_ref_db() (in SeqFeature)
__init__() (in Record)	_dimensions() (in Nexus)	_set_rel_paths() (in Paml)
__init__() (in Domain)	_DIRFMT (in Bio.SeqIO.AbiIO)	_set_rel_paths() (in Baseml)
__init__() (in Record)	_disease() (in Record)	_set_rel_paths() (in Codeml)
__init__() (in Node)	_dist() (in Bio.KDTree.KDTree')	_set_seq() (in HSPFragment)
__init__() (in Res)	_dna_complement_table (in Bio.Seq)	_set_seq() (in SeqRecord)
__init__() (in SeqMap)	_domain_re (in Bio.SCOP)	_set_strand() (in FeatureLocation)
__init__() (in SeqMapIndex)	_draw_arc() (in CircularDrawer)	_set_strand() (in SeqFeature)
__init__() (in Residues)	_draw_arc_arrow() (in CircularDrawer)	_set_taxonomy() (in Clade)
__init__() (in Scop)	_draw_arc_line() (in CircularDrawer)	_set_up_genetic_algorithm() (in GeneticAlgorithmFinder)
__init__() (in SVDSuperimposer)	_draw_arc_poly() (in CircularDrawer)	_set_up_wheel() (in RouletteWheelSelection)
__init__() (in Algorithm)	_draw_distributions() (in DistributionPage)	_set_v_final() (in ColorSpiral)
__init__() (in Database)	_draw_label() (in Chromosome)	_set_v_init() (in ColorSpiral)
__init__() (in HSP)	_draw_label() (in ChromosomeSegment)	_sff (in Bio.SeqIO.SffIO)
__init__() (in HSPSeq)	_draw_labels() (in Chromosome)	_sff_do_slow_index() (in Bio.SeqIO.SffIO)
__init__() (in Hit)	_draw_legend() (in Organism)	_sff_file_header() (in Bio.SeqIO.SffIO)
__init__() (in HomologySeq)	_draw_legend() (in DistributionPage)	_sff_find_roche_index() (in Bio.SeqIO.SffIO)
__init__() (in Query)	_draw_scatter_plot() (in ComparativeScatterPlot)	_sff_read_raw_record() (in Bio.SeqIO.SffIO)
__init__() (in Search)	_draw_segment() (in ChromosomeSegment)	_sff_read_roche_index() (in Bio.SeqIO.SffIO)
__init__() (in TableInfo)	_draw_segment() (in TelomereSegment)	_sff_read_seq_record() (in Bio.SeqIO.SffIO)
__init__() (in _SeqLength)	_draw_sigil_arrow() (in CircularDrawer)	_SffTrimIterator() (in Bio.SeqIO.SffIO)
__init__() (in BlastTabIndexer)	_draw_sigil_arrow() (in LinearDrawer)	_ShelveIndex (in Bio.Index)
__init__() (in BlastTabParser)	_draw_sigil_big_arrow() (in CircularDrawer)	_ShelveIndex__version (in _ShelveIndex)
__init__() (in BlastTabWriter)	_draw_sigil_big_arrow() (in LinearDrawer)	_ShelveIndex__version_key (in _ShelveIndex)
__init__() (in BlastTextParser)	_draw_sigil_box() (in CircularDrawer)	_shift() (in AfterPosition)
__init__() (in BlastXmlIndexer)	_draw_sigil_box() (in LinearDrawer)	_shift() (in BeforePosition)
__init__() (in BlastXmlParser)	_draw_sigil_cut_corner_box() (in CircularDrawer)	_shift() (in BetweenPosition)
__init__() (in BlastXmlWriter)	_draw_sigil_jaggy() (in CircularDrawer)	_shift() (in ExactPosition)
__init__() (in _BlastXmlGenerator)	_draw_sigil_jaggy() (in LinearDrawer)	_shift() (in FeatureLocation)
__init__() (in BlatPslIndexer)	_draw_sigil_octo() (in LinearDrawer)	_shift() (in OneOfPosition)
__init__() (in BlatPslParser)	_draw_subcomponents() (in ChromosomeSegment)	_shift() (in SeqFeature)
__init__() (in BlatPslWriter)	_draw_title() (in Organism)	_shift() (in UnknownPosition)
__init__() (in _BaseExonerateParser)	_draw_title() (in ComparativeScatterPlot)	_shift() (in WithinPosition)
__init__() (in FastaM10Indexer)	_draw_title() (in BarChartDistribution)	_simple_location (in Bio.GenBank)
__init__() (in FastaM10Parser)	_draw_title() (in DistributionPage)	_solexa_to_illumina_quality_str (in Bio.SeqIO.QualityIO)
__init__() (in _BaseHmmerTextIndexer)	_drop() (in Ambiguous)	_solexa_to_sanger_quality_str (in Bio.SeqIO.QualityIO)
__init__() (in Hmmer2TextParser)	_drop() (in Defined)	_solexa_to_solexa_quality_str (in Bio.SeqIO.QualityIO)
__init__() (in Hmmer3DomtabHmmhitWriter)	_drop() (in NotDefined)	_solo_location (in Bio.GenBank)
__init__() (in Hmmer3TabParser)	_dssp_cys (in Bio.PDB.DSSP')	_sort() (in Chain)
__init__() (in Hmmer3TabWriter)	_DTD_OPT (in Bio.SearchIO.BlastIO.blast_xml)	_sort() (in Model)
__init__() (in Hmmer3TextParser)	_effector() (in Record)	_sort() (in Residue)
__init__() (in SearchIndexer)	_elem_AAseq() (in SeqXmlIterator)	_sort() (in Structure)
__init__() (in Hit)	_elem_description() (in SeqXmlIterator)	_sort_keys() (in Bio.NMR.xpktools)
__init__() (in HSP)	_elem_DNAseq() (in SeqXmlIterator)	_sort_keys_by_values() (in Bio.Nexus.Nexus)
__init__() (in HSPFragment)	_ELEM_FRAG (in Bio.SearchIO.BlastIO.blast_xml)	_sorted_attrs() (in Bio.Phylo.BaseTree)
__init__() (in QueryResult)	_ELEM_HIT (in Bio.SearchIO.BlastIO.blast_xml)	_source_line() (in Record)
__init__() (in MutableSeq)	_ELEM_HSP (in Bio.SearchIO.BlastIO.blast_xml)	_SPCTAGS (in Bio.SeqIO.AbiIO)
__init__() (in Seq)	_ELEM_META (in Bio.SearchIO.BlastIO.blast_xml)	_split_accessions() (in _BaseGenBankConsumer)
__init__() (in UnknownSeq)	_ELEM_QRESULT_FALLBACK (in Bio.SearchIO.BlastIO.blast_xml)	_split_contig() (in _InsdcWriter)
__init__() (in FeatureLocation)	_ELEM_QRESULT_OPT (in Bio.SearchIO.BlastIO.blast_xml)	_split_fragment() (in Bio.SearchIO.ExonerateIO._base)
__init__() (in PositionGap)	_elem_RNAseq() (in SeqXmlIterator)	_split_id() (in PhylipIterator)
__init__() (in Reference)	_eliminate() (in Nexus)	_split_id() (in RelaxedPhylipIterator)
__init__() (in SeqFeature)	_embl_convert_fasta() (in Bio.SeqIO._convert)	_split_keywords() (in _BaseGenBankConsumer)
__init__() (in FastaWriter)	_EmbossCommandLine (in Bio.Emboss.Applications)	_split_multi_line() (in _InsdcWriter)
__init__() (in InterlacedSequenceIterator)	_EmbossMinimalCommandLine (in Bio.Emboss.Applications)	_split_namespace() (in Bio.Phylo.PhyloXMLIO)
__init__() (in SequenceIterator)	_empty_bytes_string (in Bio.SearchIO.BlastIO.blast_xml)	_split_reference_locations() (in _FeatureConsumer)
__init__() (in SequenceWriter)	_empty_bytes_string (in Bio.bgzf)	_split_taxonomy() (in _BaseGenBankConsumer)
__init__() (in SequentialSequenceWriter)	_end_BlastOutput_db() (in BlastParser)	_spring_layout() (in Bio.Graphics.BasicChromosome)
__init__() (in PhdWriter)	_end_BlastOutput_hits() (in BlastParser)	_SQLiteManySeqFilesDict
__init__() (in QualPhredWriter)	_end_BlastOutput_program() (in BlastParser)	_srt (in Bio.SeqIO.SffIO)
__init__() (in SeqXmlIterator)	_end_BlastOutput_query_def() (in BlastParser)	_start() (in MEMEInstance)
__init__() (in SeqXmlWriter)	_end_BlastOutput_query_ID() (in BlastParser)	_start_Hit() (in BlastParser)
__init__() (in XMLRecordIterator)	_end_BlastOutput_query_len() (in BlastParser)	_start_Hsp() (in BlastParser)
__init__() (in SffWriter)	_end_BlastOutput_reference() (in BlastParser)	_start_Iteration() (in BlastParser)
__init__() (in _AddTellHandle)	_end_BlastOutput_version() (in BlastParser)	_STATE_CONS_BLOCK (in Bio.SearchIO.FastaIO)
__init__() (in Parser)	_end_Hit() (in BlastParser)	_STATE_HIT_BLOCK (in Bio.SearchIO.FastaIO)
__init__() (in IntelliGeneticsRandomAccess)	_end_Hit_accession() (in BlastParser)	_STATE_NONE (in Bio.SearchIO.FastaIO)
__init__() (in SeqFileRandomAccess)	_end_Hit_def() (in BlastParser)	_STATE_QUERY_BLOCK (in Bio.SearchIO.FastaIO)
__init__() (in SequentialSeqFileRandomAccess)	_end_Hit_id() (in BlastParser)	_statelabels() (in Nexus)
__init__() (in SffRandomAccess)	_end_Hit_len() (in BlastParser)	_stateset() (in Nexus)
__init__() (in SeqRecord)	_end_Hsp_align_len() (in BlastParser)	_stitch_rows() (in Bio.SearchIO.ExonerateIO.exonerate_text)
__init__() (in _RestrictedDict)	_end_Hsp_bit_score() (in BlastParser)	_str2bool() (in Bio.Phylo.PhyloXMLIO)
__init__() (in CodonAdaptationIndex)	_end_Hsp_evalue() (in BlastParser)	_str_aln() (in HSPFragment)
__init__() (in IsoelectricPoint)	_end_Hsp_gaps() (in BlastParser)	_str_hsp_header() (in _BaseHSP)
__init__() (in ProteinAnalysis)	_end_Hsp_hit_frame() (in BlastParser)	_str_line() (in Alignment)
__init__() (in ACEFileRecord)	_end_Hsp_hit_from() (in BlastParser)	_strand() (in MEMEInstance)
__init__() (in Contig)	_end_Hsp_hit_to() (in BlastParser)	_STRAND_MAP (in Bio.SearchIO.ExonerateIO._base)
__init__() (in Reads)	_end_Hsp_hseq() (in BlastParser)	_string_as_base_36() (in Bio.SeqIO.SffIO)
__init__() (in af)	_end_Hsp_identity() (in BlastParser)	_string_matcher() (in Bio.Phylo.BaseTree)
__init__() (in bs)	_end_Hsp_midline() (in BlastParser)	_string_to_bytes() (in Bio._py3k)
__init__() (in ct)	_end_Hsp_positive() (in BlastParser)	_stroke_and_fill_colors() (in Bio.Graphics.GenomeDiagram._AbstractDrawer)
__init__() (in ds)	_end_Hsp_qseq() (in BlastParser)	_structures() (in Record)
__init__() (in qa)	_end_Hsp_query_frame() (in BlastParser)	_structures() (in Record)
__init__() (in rd)	_end_Hsp_query_from() (in BlastParser)	_sub_set() (in Analysis)
__init__() (in rt)	_end_Hsp_query_to() (in BlastParser)	_substrate() (in Record)
__init__() (in wa)	_end_Hsp_score() (in BlastParser)	_SUPPORTED_FIELDS (in Bio.SearchIO.BlastIO.blast_tab)
__init__() (in wr)	_end_Iteration() (in BlastParser)	_Switch (in Bio.Application)
__init__() (in NovoalignCommandline)	_end_Iteration_query_def() (in BlastParser)	_sysname() (in Record)
__init__() (in Record)	_end_Iteration_query_ID() (in BlastParser)	_table_h (in Bio.SeqUtils.CheckSum)
__init__() (in FreqTable)	_end_Iteration_query_len() (in BlastParser)	_taxlabels() (in Nexus)
__init__() (in SeqMat)	_end_Parameters_expect() (in BlastParser)	_taxpartition() (in Nexus)
__init__() (in Record)	_end_Parameters_filter() (in BlastParser)	_taxset() (in Nexus)
__init__() (in Record)	_end_Parameters_gap_extend() (in BlastParser)	_TCoffee (in Bio.Align.Applications)
__init__() (in Reference)	_end_Parameters_gap_open() (in BlastParser)	_test() (in Bio.Align.Applications._ClustalOmega)
__init__() (in ProtsimLine)	_end_Parameters_matrix() (in BlastParser)	_test() (in Bio.Align.Applications._Clustalw)
__init__() (in Record)	_end_Parameters_sc_match() (in BlastParser)	_test() (in Bio.Align.Applications._Dialign)
__init__() (in STSLine)	_end_Parameters_sc_mismatch() (in BlastParser)	_test() (in Bio.Align.Applications._Muscle)
__init__() (in SequenceLine)	_end_Statistics_db_len() (in BlastParser)	_test() (in Bio.Align.Applications._Prank)
__init__() (in Statistics)	_end_Statistics_db_num() (in BlastParser)	_test() (in Bio.Align.Applications._Probcons)
__init__() (in AlignmentColumn)	_end_Statistics_eff_space() (in BlastParser)	_test() (in Bio.Align.Applications._TCoffee)
__init__() (in ColumnUnit)	_end_Statistics_entropy() (in BlastParser)	_test() (in Bio.Align.Generic)
__init__() (in OrderedDict)	_end_Statistics_hsp_len() (in BlastParser)	_test() (in Bio.Application)
__init__() (in BgzfReader)	_end_Statistics_kappa() (in BlastParser)	_test() (in Bio.Blast.Applications)
__init__() (in BgzfWriter)	_end_Statistics_lambda() (in BlastParser)	_test() (in Bio.DocSQL)
__init__() (in kNN)	_entry() (in Record)	_test() (in Bio.Emboss.Applications)
__init__() (in Instances)	_entry() (in Record)	_test() (in Bio.Entrez)
__init__() (in Motif)	_entry_db_fields (in Bio.TogoWS)	_test() (in Bio.KDTree.KDTree')
__init__() (in Record)	_entry_db_formats (in Bio.TogoWS)	_test() (in Bio.Motif.Applications._AlignAce)
__init__() (in AlignAceCommandline)	_entry_db_names (in Bio.TogoWS)	_test() (in Bio.Motif.Applications._XXmotif)
__init__() (in CompareAceCommandline)	_enzyme() (in Record)	_test() (in Bio.Motif)
__init__() (in XXmotifCommandline)	_eof() (in _Scanner)	_test() (in Bio.PDB.Selection)
__init__() (in Record)	_escape_filename() (in Bio.Application)	_test() (in Bio.Seq)
__init__() (in GenericPositionMatrix)	_eval_feature_fn() (in Bio.MaxEntropy)	_test() (in Bio.SeqUtils.MeltingTemp)
__init__() (in PositionWeightMatrix)	_evalue() (in MEMEMotif)	_test() (in Bio.SeqUtils)
__init__() (in Instance)	_exp_freq_table_from_obs_freq() (in Bio.SubsMat)	_test() (in Bio.Sequencing.Applications._Novoalign)
__init__() (in Motif)	_exp_logsum() (in Bio.MarkovModel)	_test() (in Bio.Statistics.lowess)
__init__() (in Record)	_EXTRACT (in Bio.SeqIO.AbiIO)	_test() (in Bio.Wise)
__init__() (in ScoreDistribution)	_extract_alignment() (in Bio.SearchIO.FastaIO)	_test() (in Bio.Wise.dnal)
__init__() (in Record)	_extract_alignment_region() (in Bio.AlignIO.FastaIO)	_test() (in Bio.Wise.psw)
__init__() (in affine_penalty)	_fails_conditions() (in Bio.ParserSupport)	_test() (in Bio.motifs.applications._alignace)
__init__() (in dictionary_match)	_fastq_convert_fasta() (in Bio.SeqIO._convert)	_test() (in Bio.motifs.applications._xxmotif)
__init__() (in identity_match)	_fastq_convert_qual() (in Bio.SeqIO._convert)	_test() (in Bio.pairwise2)
__init__() (in DBSeq)	_fastq_convert_tab() (in Bio.SeqIO._convert)	_test_dist() (in PPBuilder)
__init__() (in DBSeqRecord)	_fastq_generic() (in Bio.SeqIO._convert)	_test_equivalence() (in StructureAlignment)
__init__() (in Adaptor)	_fastq_generic2() (in Bio.SeqIO._convert)	_test_global_hz_both() (in GenePopController)
__init__() (in BioSeqDatabase)	_fastq_illumina_convert_fastq_illumina() (in Bio.SeqIO._convert)	_test_normal() (in Analysis)
__init__() (in DBServer)	_fastq_illumina_convert_fastq_sanger() (in Bio.SeqIO._convert)	_test_pop_hz_both() (in GenePopController)
__init__() (in Generic_dbutils)	_fastq_illumina_convert_fastq_solexa() (in Bio.SeqIO._convert)	_test_reverse() (in Analysis)
__init__() (in DatabaseLoader)	_fastq_illumina_convert_qual() (in Bio.SeqIO._convert)	_THREECODE (in Bio.SeqUtils)
__init__() (in DatabaseRemover)	_fastq_sanger_convert_fastq_illumina() (in Bio.SeqIO._convert)	_time_denominators (in Bio.SeqIO.SffIO)
__int__() (in Confidence)	_fastq_sanger_convert_fastq_sanger() (in Bio.SeqIO._convert)	_title() (in Nexus)
__iter__() (in Alignment)	_fastq_sanger_convert_fastq_solexa() (in Bio.SeqIO._convert)	_title_line() (in Reference)
__iter__() (in AlignmentIterator)	_fastq_sanger_convert_qual() (in Bio.SeqIO._convert)	_to_fasta() (in Motif)
__iter__() (in Iterator)	_fastq_solexa_convert_fastq_illumina() (in Bio.SeqIO._convert)	_to_horizontal_matrix() (in Motif)
__iter__() (in Query)	_fastq_solexa_convert_fastq_sanger() (in Bio.SeqIO._convert)	_to_jaspar_pfm() (in Motif)
__iter__() (in UndoHandle)	_fastq_solexa_convert_fastq_solexa() (in Bio.SeqIO._convert)	_to_transfac() (in Motif)
__iter__() (in _IndexedSeqFileDict)	_fastq_solexa_convert_qual() (in Bio.SeqIO._convert)	_to_vertical_matrix() (in Motif)
__iter__() (in _IndexedSeqFileProxy)	_Feature (in Bio.Graphics.GenomeDiagram)	_toobj() (in _InMemoryIndex)
__iter__() (in _SQLiteManySeqFilesDict)	_FeatureConsumer	_tostr() (in _InMemoryIndex)
__iter__() (in Iterator)	_features_line() (in Record)	_Track (in Bio.Graphics.GenomeDiagram)
__iter__() (in AbstractPropertyMap)	_FeatureSet (in Bio.Graphics.GenomeDiagram)	_trackA() (in CrossLink)
__iter__() (in DisorderedEntityWrapper)	_feed_feature_table() (in InsdcScanner)	_trackB() (in CrossLink)
__iter__() (in Entity)	_feed_first_line() (in EmblScanner)	_train_iis() (in Bio.MaxEntropy)
__iter__() (in Clade)	_feed_first_line() (in GenBankScanner)	_transfer_attrs() (in _BaseSearchObject)
__iter__() (in Events)	_feed_first_line() (in InsdcScanner)	_translate() (in Nexus)
__iter__() (in Other)	_feed_first_line_new() (in EmblScanner)	_translate_id() (in AbstractAtomPropertyMap)
__iter__() (in Phyloxml)	_feed_first_line_old() (in EmblScanner)	_translate_id() (in AbstractPropertyMap)
__iter__() (in _FileIterator)	_feed_header_lines() (in EmblScanner)	_translate_id() (in AbstractResiduePropertyMap)
__iter__() (in BlastTabIndexer)	_feed_header_lines() (in GenBankScanner)	_translate_id() (in Chain)
__iter__() (in BlastTabParser)	_feed_header_lines() (in InsdcScanner)	_translate_str() (in Bio.Seq)
__iter__() (in BlastTextParser)	_feed_misc_lines() (in EmblScanner)	_tree() (in Nexus)
__iter__() (in BlastXmlIndexer)	_feed_misc_lines() (in GenBankScanner)	_treepartition() (in Nexus)
__iter__() (in BlastXmlParser)	_feed_misc_lines() (in InsdcScanner)	_treeset() (in Nexus)
__iter__() (in BlatPslIndexer)	_feed_seq_length() (in EmblScanner)	_treesort() (in Bio.Cluster)
__iter__() (in BlatPslParser)	_fgrep_count() (in Bio.Wise.dnal)	_try_open_read() (in Bio.NMR.xpktools)
__iter__() (in _BaseExonerateIndexer)	_FileIterator (in Bio.PopGen.GenePop.Controller)	_try_open_write() (in Bio.NMR.xpktools)
__iter__() (in _BaseExonerateParser)	_filter_search() (in TreeMixin)	_ungap() (in Bio.Alphabet)
__iter__() (in FastaM10Indexer)	_find_global_start() (in Bio.pairwise2)	_unhandled() (in _BaseGenBankConsumer)
__iter__() (in FastaM10Parser)	_find_local_start() (in Bio.pairwise2)	_unhandled() (in AbstractConsumer)
__iter__() (in Hmmer2TextIndexer)	_find_min_max() (in ComparativeScatterPlot)	_unhandled_section() (in AbstractConsumer)
__iter__() (in Hmmer2TextParser)	_find_start() (in Bio.pairwise2)	_uniform_norm() (in Bio.MarkovModel)
__iter__() (in Hmmer3TabIndexer)	_find_start_entry() (in Bio.NMR.xpktools)	_unique_label() (in Bio.Nexus.Nexus)
__iter__() (in Hmmer3TabParser)	_fix_name_class() (in DatabaseLoader)	_unknown_nexus_block() (in Nexus)
__iter__() (in Hmmer3TextIndexer)	_flag (in Bio.SeqIO.SffIO)	_Update (in Bio.Restriction)
__iter__() (in Hmmer3TextParser)	_flip() (in AfterPosition)	_upper() (in Alphabet)
__iter__() (in Hit)	_flip() (in BeforePosition)	_upper() (in AlphabetEncoder)
__iter__() (in HSP)	_flip() (in BetweenPosition)	_upper() (in Gapped)
__iter__() (in QueryResult)	_flip() (in ExactPosition)	_upper() (in HasStopCodon)
__iter__() (in FeatureLocation)	_flip() (in FeatureLocation)	_utils (in Bio.Phylo)
__iter__() (in SeqFeature)	_flip() (in OneOfPosition)	_utils (in Bio.SearchIO)
__iter__() (in InterlacedSequenceIterator)	_flip() (in SeqFeature)	_utils (in Bio)
__iter__() (in SequenceIterator)	_flip() (in UnknownPosition)	_utree() (in Nexus)
__iter__() (in XMLRecordIterator)	_flip() (in WithinPosition)	_valid_UAN_read_name (in Bio.SeqIO.SffIO)
__iter__() (in EmblRandomAccess)	_flip_codons() (in Bio.SearchIO.ExonerateIO.exonerate_text)	_validate() (in AbstractCommandline)
__iter__() (in FastqRandomAccess)	_float() (in Bio.Phylo.PhyloXMLIO)	_validate() (in NcbiblastformatterCommandline)
__iter__() (in GenBankRandomAccess)	_force_alphabet() (in Bio.AlignIO)	_validate() (in NcbiblastnCommandline)
__iter__() (in IntelliGeneticsRandomAccess)	_force_alphabet() (in Bio.SeqIO)	_validate() (in NcbipsiblastCommandline)
__iter__() (in SequentialSeqFileRandomAccess)	_format() (in Nexus)	_validate() (in NcbirpsblastCommandline)
__iter__() (in SffRandomAccess)	_format_date() (in Bio.PDB.parse_pdb_header')	_validate() (in _BlastCommandLine)
__iter__() (in SwissRandomAccess)	_FormatToIterator (in Bio.AlignIO)	_validate() (in _Ncbiblast2SeqCommandline)
__iter__() (in TabRandomAccess)	_FormatToIterator (in Bio.SeqIO)	_validate() (in _NcbiblastCommandline)
__iter__() (in UniprotRandomAccess)	_FormatToRandomAccess (in Bio.SeqIO._index)	_validate() (in _NcbiblastMain2SeqCommandline)
__iter__() (in SeqRecord)	_FormatToWriter (in Bio.AlignIO)	_validate() (in SeqretCommandline)
__iter__() (in OrderedDict)	_FormatToWriter (in Bio.SeqIO)	_validate() (in _EmbossCommandLine)
__iter__() (in BgzfReader)	_formula() (in Record)	_validate_cols() (in BlatPslParser)
__iter__() (in BioSeqDatabase)	_forward() (in Bio.MarkovModel)	_validate_fragment() (in HSP)
__iter__() (in DBServer)	_forward_recursion() (in AbstractDPAlgorithms)	_validate_hsp() (in Hit)
__le__() (in Organism)	_forward_recursion() (in ScaledDPAlgorithms)	_validate_incompatibilities() (in _NcbibaseblastCommandline)
__le__() (in Confidence)	_FRAGMENT_FILE (in Bio.PDB.FragmentMapper')	_verify_alphabet() (in Bio.Alphabet)
__le__() (in RestrictionType)	_fragment_re (in Bio.SCOP.Residues)	_version_line() (in Record)
__len__() (in Alignment)	_freq_from_count() (in FreqTable)	_viterbi() (in Bio.MarkovModel)
__len__() (in Chain)	_from_horiz_matrix() (in Motif)	_walk() (in Tree)
__len__() (in Crystal)	_from_jaspar_pfm() (in Motif)	_weight_list() (in ProteinAnalysis)
__len__() (in Hetero)	_from_jaspar_sites() (in Motif)	_wgs_line() (in Record)
__len__() (in Primers)	_from_pfm() (in Bio.Motif)	_wgs_scafld_line() (in Record)
__len__() (in fff_rec)	_from_sites() (in Bio.Motif)	_within_location (in Bio.GenBank)
__len__() (in _IndexedSeqFileDict)	_from_vert_matrix() (in Motif)	_within_position (in Bio.GenBank)
__len__() (in _SQLiteManySeqFilesDict)	_full_to_half() (in SeqMat)	_wrap_kegg() (in Bio.KEGG)
__len__() (in AbstractDrawer)	_function_matcher() (in Bio.Phylo.BaseTree)	_wrap_location() (in _InsdcWriter)
__len__() (in FeatureSet)	_gen_loci() (in Bio.PopGen.SimCoal.Template)	_wrapped_genbank() (in Bio.GenBank.Record)
__len__() (in GraphData)	_gen_random_array() (in Bio.HMM.MarkovModel)	_write() (in Bio.Graphics)
__len__() (in GraphSet)	_genbank_convert_fasta() (in Bio.SeqIO._convert)	_write() (in Motif)
__len__() (in Motif)	_GenePopCommandline (in Bio.PopGen.GenePop.Controller)	_write_block() (in BgzfWriter)
__len__() (in AbstractPropertyMap)	_generate_intfile() (in FDistController)	_write_comment() (in EmblWriter)
__len__() (in DisorderedEntityWrapper)	_generate_locs() (in GeneralPointCrossover)	_write_comment() (in GenBankWriter)
__len__() (in Entity)	_generate_locs() (in InterleaveCrossover)	_write_contig() (in EmblWriter)
__len__() (in Fragment)	_generate_locs() (in TwoCrossover)	_write_contig() (in GenBankWriter)
__len__() (in HashSet)	_genes() (in Record)	_write_dbxrefs() (in SeqXmlWriter)
__len__() (in Clade)	_get_a() (in ColorSpiral)	_write_description() (in SeqXmlWriter)
__len__() (in Events)	_get_all_letters() (in SummaryInfo)	_write_elem_block() (in BlastXmlWriter)
__len__() (in Phyloxml)	_get_annotation_str() (in _InsdcWriter)	_write_feature() (in _InsdcWriter)
__len__() (in FormattedSeq)	_get_atom_line() (in PDBIO)	_write_feature_qualifier() (in _InsdcWriter)
__len__() (in RestrictionType)	_get_b() (in ColorSpiral)	_write_hits() (in BlastXmlWriter)
__len__() (in Hit)	_get_base_alphabet() (in Bio.Alphabet)	_write_hsps() (in BlastXmlWriter)
__len__() (in _SeqLength)	_get_base_letters() (in SummaryInfo)	_write_index() (in SffWriter)
__len__() (in Hit)	_get_base_replacements() (in SummaryInfo)	_write_kegg() (in Bio.KEGG)
__len__() (in HSP)	_get_bioentry_dbxref() (in DatabaseLoader)	_WRITE_MAPS (in Bio.SearchIO.BlastIO.blast_xml)
__len__() (in HSPFragment)	_get_block_coords() (in Bio.SearchIO.ExonerateIO.exonerate_text)	_write_multi_entries() (in GenBankWriter)
__len__() (in QueryResult)	_get_blocks() (in Bio.SearchIO.ExonerateIO.exonerate_text)	_write_multi_line() (in EmblWriter)
__len__() (in MutableSeq)	_get_cb() (in HSExposureCA)	_write_multi_line() (in GenBankWriter)
__len__() (in Seq)	_get_cb() (in HSExposureCB)	_write_param() (in BlastXmlWriter)
__len__() (in UnknownSeq)	_get_cb() (in _AbstractHSExposure)	_write_preamble() (in BlastXmlWriter)
__len__() (in FeatureLocation)	_get_child_as() (in Bio.Phylo.PhyloXMLIO)	_write_properties() (in SeqXmlWriter)
__len__() (in SeqFeature)	_get_child_text() (in Bio.Phylo.PhyloXMLIO)	_write_qresults() (in BlastXmlWriter)
__len__() (in InterlacedSequenceIterator)	_get_children_as() (in Bio.Phylo.PhyloXMLIO)	_write_record() (in StockholmWriter)
__len__() (in SeqRecord)	_get_children_text() (in Bio.Phylo.PhyloXMLIO)	_write_references() (in EmblWriter)
__len__() (in Motif)	_get_color() (in Clade)	_write_references() (in GenBankWriter)
__len__() (in DBSeq)	_get_cols() (in Bio.Blast.NCBIStandalone)	_write_seq() (in SeqXmlWriter)
__len__() (in BioSeqDatabase)	_get_column_info_content() (in SummaryInfo)	_write_sequence() (in EmblWriter)
__len__() (in DBServer)	_get_command_lines() (in Bio.Nexus.Nexus)	_write_sequence() (in GenBankWriter)
__long__() (in Confidence)	_get_confidence() (in Clade)	_write_single_line() (in EmblWriter)
__lt__() (in Organism)	_get_confidence() (in Phylogeny)	_write_single_line() (in GenBankWriter)
__lt__() (in Confidence)	_get_convert_formats() (in Bio.TogoWS)	_write_species() (in SeqXmlWriter)
__lt__() (in RestrictionType)	_get_coords() (in HSP)	_write_the_first_line() (in GenBankWriter)
__marker (in QueryResult)	_get_coords() (in Bio.Wise.dnal)	_write_the_first_lines() (in EmblWriter)
__mod__() (in Confidence)	_get_data_division() (in EmblWriter)	_WRITER_MAP (in Bio.SearchIO)
__mod__() (in RestrictionType)	_get_data_division() (in GenBankWriter)	_XMLparser (in Bio.Blast.NCBIXML)
__mul__() (in Vector)	_get_date() (in GenBankWriter)	_XXmotif (in Bio.Motif.Applications)
__mul__() (in Confidence)	_get_dbxref_id() (in DatabaseLoader)	_xxmotif (in Bio.motifs.applications)