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]
_
__add__()
(in
Chain
)
__init__()
(in
Handle_feature_qualifier
)
_end_Hsp_evalue()
(in
BlastParser
)
__add__()
(in
Location
)
__init__()
(in
Handle_features
)
_end_Hsp_gaps()
(in
BlastParser
)
__add__()
(in
Vector
)
__init__()
(in
Handle_hsp
)
_end_Hsp_hit_frame()
(in
BlastParser
)
__add__()
(in
RestrictionBatch
)
__init__()
(in
RecognizeHandler
)
_end_Hsp_hit_from()
(in
BlastParser
)
__add__()
(in
RestrictionType
)
__init__()
(in
FreqTable
)
_end_Hsp_hit_to()
(in
BlastParser
)
__add__()
(in
SeqMap
)
__init__()
(in
SeqMat
)
_end_Hsp_hseq()
(in
BlastParser
)
__add__()
(in
MutableSeq
)
__init__()
(in
ListParser
)
_end_Hsp_identity()
(in
BlastParser
)
__add__()
(in
Seq
)
__init__()
(in
Record
)
_end_Hsp_midline()
(in
BlastParser
)
__add__()
(in
Expression
)
__init__()
(in
_ListConsumer
)
_end_Hsp_positive()
(in
BlastParser
)
__add__()
(in
NullOp
)
__init__()
(in
_Scanner
)
_end_Hsp_qseq()
(in
BlastParser
)
__add__()
(in
Seq
)
__init__()
(in
Dictionary
)
_end_Hsp_query_frame()
(in
BlastParser
)
__and__()
(in
Expression
)
__init__()
(in
ExPASyDictionary
)
_end_Hsp_query_from()
(in
BlastParser
)
__call__()
(in
CelParser
)
__init__()
(in
Iterator
)
_end_Hsp_query_to()
(in
BlastParser
)
__call__()
(in
FunctionCall
)
__init__()
(in
Record
)
_end_Hsp_score()
(in
BlastParser
)
__call__()
(in
FunctionCallChain
)
__init__()
(in
RecordParser
)
_end_Iteration()
(in
BlastParser
)
__call__()
(in
GetObject
)
__init__()
(in
Reference
)
_end_Iteration_query_def()
(in
BlastParser
)
__call__()
(in
StdTerm
)
__init__()
(in
SequenceParser
)
_end_Iteration_query_ID()
(in
BlastParser
)
__call__()
(in
make_rate_limited_function
)
__init__()
(in
_RecordConsumer
)
_end_Iteration_query_len()
(in
BlastParser
)
__call__()
(in
affine_penalty
)
__init__()
(in
_SequenceConsumer
)
_end_Parameters_expect()
(in
BlastParser
)
__call__()
(in
dictionary_match
)
__init__()
(in
Transcribe
)
_end_Parameters_filter()
(in
BlastParser
)
__call__()
(in
identity_match
)
__init__()
(in
Translator
)
_end_Parameters_gap_extend()
(in
BlastParser
)
__call__()
(in
MulticallEnd
)
__init__()
(in
Iterator
)
_end_Parameters_gap_open()
(in
BlastParser
)
__call__()
(in
MulticallStart
)
__init__()
(in
RecordParser
)
_end_Parameters_matrix()
(in
BlastParser
)
__call__()
(in
RemapEnd
)
__init__()
(in
UnigeneProtsimRecord
)
_end_Parameters_sc_match()
(in
BlastParser
)
__call__()
(in
RemapStart
)
__init__()
(in
UnigeneRecord
)
_end_Parameters_sc_mismatch()
(in
BlastParser
)
__call__()
(in
CheckAssert
)
__init__()
(in
UnigeneSTSRecord
)
_end_Statistics_db_len()
(in
BlastParser
)
__call__()
(in
CheckAssertNot
)
__init__()
(in
UnigeneSequenceRecord
)
_end_Statistics_db_num()
(in
BlastParser
)
__call__()
(in
CheckGroupRef
)
__init__()
(in
_RecordConsumer
)
_end_Statistics_eff_space()
(in
BlastParser
)
__call__()
(in
SetGroupValue
)
__init__()
(in
RequestLimiter
)
_end_Statistics_entropy()
(in
BlastParser
)
__call__()
(in
_call_call
)
__init__()
(in
Statistics
)
_end_Statistics_hsp_len()
(in
BlastParser
)
__call__()
(in
_call_calltag
)
__init__()
(in
AlignmentColumn
)
_end_Statistics_kappa()
(in
BlastParser
)
__call__()
(in
print_debug
)
__init__()
(in
ColumnUnit
)
_end_Statistics_lambda()
(in
BlastParser
)
__call__()
(in
print_info
)
__init__()
(in
Writer
)
_endswith_tagtable_newline()
(in
Martel.RecordReader
)
__cmp__()
(in
HasStopCodon
)
__init__()
(in
Biblio
)
_endswith_tagtable_rest_of_line()
(in
Martel.RecordReader
)
__cmp__()
(in
Token
)
__init__()
(in
BiblioCollection
)
_entity_pattern
(in
Bio.EUtils.parse
)
__cmp__()
(in
ValueToken
)
__init__()
(in
BuildSearch
)
_entrezdate_format
(in
Bio.EUtils.parse
)
__cmp__()
(in
Organism
)
__init__()
(in
BuildSeqRecord
)
_entry()
(in
Record
)
__cmp__()
(in
Integer
)
__init__()
(in
BioCorbaDB
)
_entry()
(in
Record
)
__cmp__()
(in
Symbol
)
__init__()
(in
BioSQLDB
)
_enzyme()
(in
Record
)
__cmp__()
(in
Token
)
__init__()
(in
CGIDB
)
_EOF
(in
GenericParser
)
__cmp__()
(in
MutableSeq
)
__init__()
(in
DBGroup
)
_escape()
(in
Martel.msre_parse
)
__cmp__()
(in
AbstractPosition
)
__init__()
(in
DBObject
)
_eval_feature_fn()
(in
Bio.MaxEntropy
)
__contains__()
(in
Chain
)
__init__()
(in
DBRegistry
)
_evalue()
(in
MEMEMotif
)
__contains__()
(in
_BaseMultiDict
)
__init__()
(in
EUtilsDB
)
_exp_freq_table_from_obs_freq()
(in
Bio.SubsMat
)
__contains__()
(in
HashSet
)
__init__()
(in
IndexedFileDB
)
_exp_logsum()
(in
Bio.MarkovModel
)
__contains__()
(in
RestrictionBatch
)
__init__()
(in
FormatGroup
)
_extract_alignment_region()
(in
FastaM10Iterator
)
__contains__()
(in
_IsIn
)
__init__()
(in
FormatObject
)
_extract_pattern_hits()
(in
Bio.Prosite
)
__del__()
(in
TempFile
)
__init__()
(in
FormatRegistry
)
_extract_record()
(in
Bio.Prosite.Prodoc
)
__del__()
(in
_InMemoryIndex
)
__init__()
(in
RegisterableGroup
)
_extract_record()
(in
Bio.Prosite
)
__del__()
(in
_ShelveIndex
)
__init__()
(in
RegisterableObject
)
_fails_conditions()
(in
Bio.ParserSupport
)
__del__()
(in
KDTree
)
__init__()
(in
Registry
)
_fast_dbxref_parser_table
(in
Bio.StdHandler
)
__del__()
(in
BerkeleyDB
)
__init__()
(in
SeqDBRegistry
)
_fast_dbxref_sp_embl()
(in
Bio.StdHandler
)
__del__()
(in
MemoryFlatDB
)
__init__()
(in
Stanza
)
_fast_dbxref_sp_embl_data
(in
Bio.StdHandler
)
__del__()
(in
RebaseUpdate
)
__init__()
(in
StanzaFormat
)
_fast_dbxref_sp_general()
(in
Bio.StdHandler
)
__del__()
(in
BiblioCollection
)
__init__()
(in
make_cached_expression
)
_fast_dbxref_sp_general_data
(in
Bio.StdHandler
)
__del_annotations()
(in
DBSeqRecord
)
__init__()
(in
make_rate_limited_function
)
_fast_dbxref_sp_prosite()
(in
Bio.StdHandler
)
__del_dbxrefs()
(in
DBSeqRecord
)
__init__()
(in
kNN
)
_fast_dbxref_sp_prosite_data
(in
Bio.StdHandler
)
__del_features()
(in
DBSeqRecord
)
__init__()
(in
affine_penalty
)
_fast_quote_lookup
(in
Martel.Expression
)
__del_seq()
(in
DBSeqRecord
)
__init__()
(in
dictionary_match
)
_FeatureConsumer
__delattr__()
(in
ElementNode
)
__init__()
(in
identity_match
)
_features_line()
(in
Record
)
__delitem__()
(in
Chain
)
__init__()
(in
WriteEmbl
)
_feed_feature_table()
(in
InsdcScanner
)
__delitem__()
(in
Crystal
)
__init__()
(in
WriteFasta
)
_feed_first_line()
(in
EmblScanner
)
__delitem__()
(in
OrderedMultiDict
)
__init__()
(in
DBSeq
)
_feed_first_line()
(in
GenBankScanner
)
__delitem__()
(in
UnorderedMultiDict
)
__init__()
(in
DBSeqRecord
)
_feed_first_line()
(in
InsdcScanner
)
__delitem__()
(in
ElementNode
)
__init__()
(in
Adaptor
)
_feed_first_line_new()
(in
EmblScanner
)
__delitem__()
(in
_InMemoryIndex
)
__init__()
(in
BioSeqDatabase
)
_feed_first_line_old()
(in
EmblScanner
)
__delitem__()
(in
Chain
)
__init__()
(in
DBServer
)
_feed_header_lines()
(in
EmblScanner
)
__delitem__()
(in
MutableSeq
)
__init__()
(in
Generic_dbutils
)
_feed_header_lines()
(in
GenBankScanner
)
__delitem__()
(in
SubPattern
)
__init__()
(in
DatabaseLoader
)
_feed_header_lines()
(in
InsdcScanner
)
__delslice__()
(in
Chain
)
__init__()
(in
DatabaseRemover
)
_feed_misc_lines()
(in
EmblScanner
)
__div__()
(in
Vector
)
__init__()
(in
Callback
)
_feed_misc_lines()
(in
GenBankScanner
)
__div__()
(in
RestrictionBatch
)
__init__()
(in
DispatchHandler
)
_feed_misc_lines()
(in
InsdcScanner
)
__div__()
(in
RestrictionType
)
__init__()
(in
Dispatcher
)
_feed_seq_length()
(in
EmblScanner
)
__doc__
(in
Bio.PDB.AbstractPropertyMap
)
__init__()
(in
Multicall
)
_fgrep_count()
(in
Bio.Wise.dnal
)
__doc__
(in
Bio.PDB.Atom
)
__init__()
(in
RemapEnd
)
_find_begin_positions()
(in
Martel.RecordReader
)
__doc__
(in
Bio.PDB.Chain
)
__init__()
(in
RemapStart
)
_find_end_positions()
(in
Martel.RecordReader
)
__doc__
(in
Bio.PDB.Entity
)
__init__()
(in
Alt
)
_find_entry()
(in
Bio.Mindy.FlatDB
)
__doc__
(in
Bio.PDB.HSExposure
)
__init__()
(in
Any
)
_find_global_start()
(in
Bio.pairwise2
)
__doc__
(in
Bio.PDB.MMCIF2Dict
)
__init__()
(in
Assert
)
_find_groups()
(in
Expression
)
__doc__
(in
Bio.PDB.MMCIFParser
)
__init__()
(in
Debug
)
_find_groups()
(in
ExpressionList
)
__doc__
(in
Bio.PDB.Model
)
__init__()
(in
FastFeature
)
_find_groups()
(in
Group
)
__doc__
(in
Bio.PDB.NACCESS
)
__init__()
(in
Group
)
_find_groups()
(in
HeaderFooter
)
__doc__
(in
Bio.PDB.NeighborSearch
)
__init__()
(in
GroupRef
)
_find_groups()
(in
MaxRepeat
)
__doc__
(in
Bio.PDB.PDBExceptions
)
__init__()
(in
HeaderFooter
)
_find_groups()
(in
ParseRecords
)
__doc__
(in
Bio.PDB.Polypeptide
)
__init__()
(in
Literal
)
_find_groups()
(in
PassThrough
)
__doc__
(in
Bio.PDB.Residue
)
__init__()
(in
MaxRepeat
)
_find_index()
(in
ElementNode
)
__doc__
(in
Bio.PDB.Selection
)
__init__()
(in
NullOp
)
_find_local_start()
(in
Bio.pairwise2
)
__doc__
(in
Bio.PDB.Structure
)
__init__()
(in
ParseRecords
)
_find_min_max()
(in
ComparativeScatterPlot
)
__doc__
(in
Bio.PDB.StructureBuilder
)
__init__()
(in
PassThrough
)
_find_node()
(in
ElementNode
)
__doc__
(in
Bio.PDB
)
__init__()
(in
Seq
)
_find_quoted_words()
(in
Martel.test.test_Time
)
__eq__()
(in
Chain
)
__init__()
(in
Str
)
_find_range()
(in
Bio.Mindy.FlatDB
)
__eq__()
(in
Hetero
)
__init__()
(in
CheckAssert
)
_find_start()
(in
Bio.pairwise2
)
__eq__()
(in
CheckLinkSet
)
__init__()
(in
CheckAssertNot
)
_find_start_entry()
(in
Bio.NMR.xpktools
)
__eq__()
(in
DBIds
)
__init__()
(in
CheckGroupRef
)
_find_wanted_groupref_names()
(in
Martel.Generate
)
__eq__()
(in
Date
)
__init__()
(in
GeneratorState
)
_fitness_cmp()
(in
TournamentSelection
)
__eq__()
(in
IdCheck
)
__init__()
(in
HandleRepeatCount
)
_fix()
(in
Comment
)
__eq__()
(in
IdUrlSet
)
__init__()
(in
SetGroupValue
)
_fix_newlines()
(in
Martel
)
__eq__()
(in
Link
)
__init__()
(in
_call_call
)
_fix_varsplic_sequences()
(in
_RecordConsumer
)
__eq__()
(in
LinkSetDb
)
__init__()
(in
_call_calltag
)
_fixup_defs()
(in
Bio.Decode
)
__eq__()
(in
LinksLinkSet
)
__init__()
(in
print_debug
)
_fixup_query()
(in
ThinClient
)
__eq__()
(in
NeighborLinkSet
)
__init__()
(in
print_info
)
_fixup_sp_pattern()
(in
Bio.StdHandler
)
__eq__()
(in
ObjUrl
)
__init__()
(in
IterHeaderFooter
)
_flush_text()
(in
InterProParser
)
__eq__()
(in
Problem
)
__init__()
(in
IterRecords
)
_flush_text()
(in
NdbParser
)
__eq__()
(in
Provider
)
__init__()
(in
EventStream
)
_footer_next()
(in
HeaderFooterEventStream
)
__eq__()
(in
OrderedMultiDict
)
__init__()
(in
HeaderFooterEventStream
)
_format()
(in
Nexus
)
__eq__()
(in
UnorderedMultiDict
)
__init__()
(in
Iterate
)
_format_date()
(in
Bio.PDB.parse_pdb_header'
)
__eq__()
(in
Token
)
__init__()
(in
Iterator
)
_FormatToIterator
(in
Bio.AlignIO
)
__eq__()
(in
Reaction
)
__init__()
(in
IteratorHeaderFooter
)
_FormatToIterator
(in
Bio.SeqIO
)
__eq__()
(in
Graph
)
__init__()
(in
IteratorRecords
)
_FormatToWriter
(in
Bio.AlignIO
)
__eq__()
(in
HashSet
)
__init__()
(in
RecordEventStream
)
_FormatToWriter
(in
Bio.SeqIO
)
__eq__()
(in
MultiGraph
)
__init__()
(in
StoreEvents
)
_formula()
(in
Record
)
__eq__()
(in
FormattedSeq
)
__init__()
(in
ElementInfo
)
_forward()
(in
Bio.MarkovModel
)
__eq__()
(in
RestrictionType
)
__init__()
(in
LAX
)
_forward_recursion()
(in
ScaledDPAlgorithms
)
__filename_key
(in
Dictionary
)
__init__()
(in
HeaderFooterParser
)
_foward_recursion()
(in
AbstractDPAlgorithms
)
__filename_key
(in
Dictionary
)
__init__()
(in
Parser
)
_FRAGMENT_FILE
(in
Bio.PDB.FragmentMapper'
)
__filename_key
(in
Dictionary
)
__init__()
(in
ParserIncompleteException
)
_fragment_re
(in
Bio.SCOP.Residues'
)
__filename_key
(in
Dictionary
)
__init__()
(in
ParserPositionException
)
_freq_from_count()
(in
FreqTable
)
__filename_key
(in
Dictionary
)
__init__()
(in
RecordParser
)
_full_to_half()
(in
SeqMat
)
__floordiv__()
(in
RestrictionType
)
__init__()
(in
CountLines
)
_gen_loci()
(in
Bio.PopGen.SimCoal.Template
)
__ge__()
(in
RestrictionType
)
__init__()
(in
EndsWith
)
_generate()
(in
Martel.Generate
)
__get_annotations()
(in
DBSeqRecord
)
__init__()
(in
Everything
)
_generate_count
(in
Martel.Generate
)
__get_dbxrefs()
(in
DBSeqRecord
)
__init__()
(in
Nothing
)
_generate_intfile()
(in
FDistController
)
__get_features()
(in
DBSeqRecord
)
__init__()
(in
RecordReader
)
_generate_locs()
(in
GeneralPointCrossover
)
__get_seq()
(in
DBSeqRecord
)
__init__()
(in
StartsWith
)
_generate_locs()
(in
InterleaveCrossover
)
__getattr__
(in
KDTree
)
__init__()
(in
Until
)
_generate_locs()
(in
TwoCrossover
)
__getattr__()
(in
AlphabetEncoder
)
__init__()
(in
GroupNames
)
_genes()
(in
Record
)
__getattr__()
(in
AmbiguousCodonTable
)
__init__()
(in
Pattern
)
_get()
(in
ThinClient
)
__getattr__()
(in
QueryRow
)
__init__()
(in
SubPattern
)
_get()
(in
BioCorbaDB
)
__getattr__()
(in
ElementNode
)
__init__()
(in
Tokenizer
)
_get()
(in
BioSQLDB
)
__getattr__()
(in
SGMLHandle
)
__init__()
(in
CheckGood
)
_get()
(in
CGIDB
)
__getattr__()
(in
UndoHandle
)
__init__()
(in
Dump
)
_get()
(in
DBObject
)
__getattr__()
(in
FilteredReader
)
__init__()
(in
Storage
)
_get()
(in
EUtilsDB
)
__getattr__()
(in
Surrogate
)
__init__()
(in
CountErrors
)
_get()
(in
IndexedFileDB
)
__getattr__()
(in
Dictionary
)
__init__()
(in
CountRecords
)
_get_all_letters()
(in
SummaryInfo
)
__getattr__()
(in
Location
)
__init__()
(in
CatchFields
)
_get_array_entry()
(in
_RecordConsumer
)
__getattr__()
(in
DisorderedEntityWrapper
)
__init__()
(in
GetErrorPos
)
_get_atom_line()
(in
PDBIO
)
__getattr__()
(in
AbstractConsumer
)
__iter__()
(in
Alignment
)
_get_base_info()
(in
FormatConverter
)
__getattr__()
(in
SGMLStrippingConsumer
)
__iter__()
(in
AlignmentIterator
)
_get_base_letters()
(in
SummaryInfo
)
__getattr__()
(in
TaggingConsumer
)
__iter__()
(in
Iterator
)
_get_base_replacements()
(in
SummaryInfo
)
__getattr__()
(in
Dictionary
)
__iter__()
(in
Iterator
)
_get_bioentry_dbxref()
(in
DatabaseLoader
)
__getattr__()
(in
Prosite
)
__iter__()
(in
Query
)
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HSExposureCA
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Dictionary
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Iterator
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HSExposureCB
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BinaryOp
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IndexedFileDB
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SGMLExtractorHandle
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DBIds
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ObjectParserHandler
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Expression
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Term
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SummaryInfo
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Dictionary
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Bio.Wise.dnal
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LAX
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ElementNode
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BioCorbaDB
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PSSM
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Iterator
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BioSQLDB
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Chain
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Iterator
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DBIdsLookup
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Crystal
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Iterator
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CheckLinkSet
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BioformatDBName
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Iterator
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LinkSetDb
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UnknownDBName
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Iterator
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HistoryLookup
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AmbiguousForwardTable
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Iterator
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DatabaseLoader
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Iterator
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Iterator
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Iterator
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PDBParser
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AbstractPropertyMap
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MMCIFParser
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ElementNode
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Entity
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Chain
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fff_rec
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Iterator
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Nexus
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ForgivingDictionary
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Iterator
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Bio.PDB.parse_pdb_header'
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FeatureDict
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Iterator
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FilteredReader
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NCBIDictionary
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Iterator
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Dictionary
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Iterator
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DictLookup
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Iterator
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StockholmIterator
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OpenDB
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Iterator
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StockholmIterator
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BerkeleyDB
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Iterator
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MotifFinder
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InterlacedSequenceIterator
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DiversitySelection
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SequenceIterator
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Martel.Iterator
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Iterator
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Nexus
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DiskFlatDB
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Iterator
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ElementNode
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MemoryFlatDB
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Iterator
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SchemaFactory
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PrimaryNamespace
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Iterator
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DatabaseLoader
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PrimaryTable
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Iterate
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Bio.EUtils.parse
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SecondaryNamespace
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RestrictionType
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FDistController
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SecondaryTable
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Chain
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AbstractPropertyMap
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Crystal
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HandleRepeatCount
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Chain
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Hetero
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Bio.EUtils.DBIdsClient
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Entity
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BaseDBIdsRecordSet
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Bio.EUtils.HistoryClient
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FragmentMapper
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DBIds
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Bio.PDB.parse_pdb_header'
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MMCIF2Dict
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BaseHistoryRecordSet
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BioCorbaDB
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Vector
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DatabaseLoader
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CreateDict
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ElementNode
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SignatureFinder
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Dictionary
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fff_rec
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_RecordConsumer
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ExPASyDictionary
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NCBIDictionary
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DatabaseLoader
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Prosite
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Dictionary
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FDistController
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PrositeMatch
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BisectFile
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DatabaseLoader
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Dictionary
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AbstractPropertyMap
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NeighborSearch
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ExPASyDictionary
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Entity
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SchemaFactory
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Dictionary
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Fragment
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Tree
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Dictionary
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HashSet
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Martel
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FormattedSeq
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Dictionary
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Martel.msre_parse
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Index
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ExPASyDictionary
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SummaryInfo
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FileIndex
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PDBParser
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defaultdict
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PrositeMatch
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HeaderFooterEventStream
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SeqMapIndex
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Dictionary
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Bio.Blast.NCBIStandalone
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MutableSeq
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ExPASyDictionary
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Bio.Blast.NCBIStandalone
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Seq
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Dictionary
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Bio.PDB.Dice
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InterlacedSequenceIterator
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Dictionary
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StockholmIterator
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StockholmIterator
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FormattedSeq
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StockholmIterator
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Dictionary
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RestrictionType
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Bio.MaxEntropy
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ExPASyDictionary
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Hit
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Bio.GenBank.Record
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DBGroup
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_SeqLength
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Record
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DBObject
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MutableSeq
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UnigeneProtsimRecord
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Registry
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Seq
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UnigeneSTSRecord
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SeqDBRegistry
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InterlacedSequenceIterator
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UnigeneSequenceRecord
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DBSeq
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StockholmIterator
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Bio.SeqUtils.CheckSum
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BioSeqDatabase
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SeqRecord
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SeqMat
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DBServer
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Dictionary
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Bio.Index
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Iterate
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ExPASyDictionary
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MartelAttributeList
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DBSeq
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_InMemoryIndex
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SubPattern
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MartelAttributeList
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DatabaseLoader
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Storage
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SubPattern
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Bio.Mindy.BaseDB
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Chain
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RestrictionType
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StructureBuilder
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fff_rec
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Seq
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CaPPBuilder
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RestrictionType
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PPBuilder
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PrositeMatch
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Vector
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PhylipIterator
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SeqMap
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SeqMat
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Bio.ECell
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SubPattern
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Chain
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Martel.LAX
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RestrictionType
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Hetero
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Bio.SeqIO
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CheckLinkSet
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Location
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DBIds
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Reference
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Reaction
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Date
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Record
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IdCheck
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Bio.Nexus.Nexus
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RestrictionBatch
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IdUrlSet
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Instance
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SeqMap
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Link
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ParserIncompleteException
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LinkSetDb
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Bio.config.SeqDBRegistry
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ParserPositionException
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LinksLinkSet
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Bio.config.SeqDBRegistry
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NeighborLinkSet
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Bio.SwissProt.KeyWList
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CelConsumer
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ObjUrl
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Registry
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CelParser
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Problem
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SeqDBRegistry
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CelRecord
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Provider
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DatabaseLoader
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DatabaseLoader
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DatabaseLoader
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PSSM
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Token
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DatabaseLoader
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SummaryInfo
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Reaction
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DatabaseLoader
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FormatConverter
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Graph
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Alignment
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HashSet
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DatabaseLoader
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AlignAceCommandline
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MultiGraph
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Bio.config.FormatRegistry
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CompareAceCommandline
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RestrictionType
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Bio.config.FormatRegistry
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Motif
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Vector
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Bio.EUtils.parse
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AlignAceConsumer
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Tokenizer
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BerkeleyDB
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AlignAceParser
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PrintFormat
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Bio.config.FormatRegistry
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CompareAceConsumer
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ElementNode
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CompareAceParser
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SeqRecord
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Bio.config.SeqDBRegistry
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AlignmentIterator
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Expression
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AlignmentWriter
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Alt
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SequentialAlignmentWriter
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Expression
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AlphabetEncoder
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NullOp
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DatabaseLoader
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Gapped
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Vector
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HasStopCodon
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Chain
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Record
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AbstractCommandline
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MutableSeq
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HiddenMarkovModel
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ApplicationResult
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Seq
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Bio.MarkovModel
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_AbstractParameter
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RestrictionBatch
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Bio.MarkovModel
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BlastallCommandline
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RestrictionType
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Bio.MarkovModel
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FastacmdCommandline
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RetrieveSeqname
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Bio.Mindy.FlatDB
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BlastErrorParser
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Alignment
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Bio.Mindy.FlatDB
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BlastParser
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Bio.pairwise2
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Iterator
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AlphabetEncoder
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Bio.pairwise2
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PSIBlastParser
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Crystal
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Bio.Data.IUPACData
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_BlastConsumer
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Hetero
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Bio.config.SeqDBRegistry
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_BlastErrorConsumer
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Token
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Bio.config.SeqDBRegistry
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_PSIBlastConsumer
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EventGenerator
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BlastParser
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Query
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Martel.Expression
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BlastParser
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CheckLinkSet
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Bio.config.SeqDBRegistry
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DBIds
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Bio.PDB.FragmentMapper'
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BlastTableEntry
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Date
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Martel.Expression
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BlastTableReader
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EUtilsSearchError
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_RecordConsumer
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BlastTableRec
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IdCheck
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PrintFormat
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Alignment
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IdUrlSet
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PrintFormat
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Blast
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Link
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DatabaseReport
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LinkSetDb
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Description
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LinksLinkSet
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MMCIF2Dict
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HSP
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NeighborLinkSet
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Martel.Expression
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Header
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ObjUrl
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PrintFormat
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MultipleAlignment
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Problem
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PrintFormat
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PSIBlast
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Provider
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Parameters
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Summary
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PrintFormat
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Round
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OrderedMultiDict
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BioSQLDB
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CAPSMap
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CGIDB
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DifferentialCutsite
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AttributeList
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DBObject
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ContentModel
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Bio.Data.IUPACData
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Record
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Bio.pairwise2
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RecordParser
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Bio.pairwise2
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Bio.expressions.blast.ncbiblast
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Bio.SCOP
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Bio.SCOP
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Bio.config.SeqDBRegistry
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Bio.Application
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Bio.Wise.psw
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NCBIDictionary
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ContentModel
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Bio.pairwise2
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DTDConsumerForSourceGeneration
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ExPASyDictionary
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ExPASyDictionary
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Bio.Blast.NCBIStandalone
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ObjectParserHandler
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MutableSeq
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Tree
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PDBParser
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ReseekFile
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PSSM
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ThinClient
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Alignment
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Martel.msre_parse
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UsePOMParser
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NdbParser
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_Argument
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Bio.Ndb
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MethodHolder
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_Option
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PDBParser
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Alignment
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BlastTableReader
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SourceGen
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Description
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Martel.Parser
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EConsenseCommandline
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Record
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BlastTableReader
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EInvertedCommandline
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ClustalAlignment
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BlastTableReader
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ENeighborCommandline
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MultipleAlignCL
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Bio.EUtils.parse
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EProtDistCommandline
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Chain
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Nexus
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EProtParsCommandline
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Crystal
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Nexus
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ESeqBootCommandline
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Hetero
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Bio.PDB.parse_pdb_header'
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ETandemCommandline
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DBXRef
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Bio.Mindy.FlatDB
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Est2GenomeCommandline
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CodonTable
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Bio.Blast.NCBIWWW
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FuzznucCommandline
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Function
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BlastTableReader
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PalindromeCommandline
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ValueToken
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FastaM10Iterator
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Primer3Commandline
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Record
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Bio.Mindy.FlatDB
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PrimerSearchCommandline
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And
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Martel.msre_parse
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TranalignCommandline
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Date
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FastaM10Iterator
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WaterCommandline
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EUtilsSearchError
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Martel.Time
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Primer3Parser
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Not
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BlastTableReader
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Primer3Primers
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Or
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Bio.config.FormatRegistry
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Primer3Record
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Problem
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Bio.config.FormatRegistry
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PrimerSearchAmplifier
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Range
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Bio.Mindy.XPath
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PrimerSearchInputRecord
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Summary
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Record
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PrimerSearchOutputRecord
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Term
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Record
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PrimerSearchParser
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_BaseMultiDict
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Bio.SCOP.Residues'
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_Primer3RecordConsumer
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AttributeList
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Record
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_Primer3Scanner
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Comment
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StockholmIterator
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_PrimerSearchRecordConsumer
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ElementNode
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StockholmIterator
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_PrimerSearchScanner
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Fragments
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Martel.Generate
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DataHandler
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IndentedText
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Bio.PDB.Polypeptide
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StructureElement
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POMDocument
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Bio.pairwise2
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DataRecord
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Text
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Bio.Emboss.Primer
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EnzymeRecord
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ClassHolder
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Bio.Emboss.Primer
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Iterator
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FunctionHolder
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Bio.Emboss.Primer
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RecordParser
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MethodHolder
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Bio.Emboss.Primer
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_RecordConsumer
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SourceFile
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TaggingConsumer
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FSSPAlignDict
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PrimerSearchInputRecord
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Record
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FSSPAlignRec
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DataRecord
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Record
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FSSPHeader
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EnzymeRecord
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Record
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FSSPSumRec
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FastaAlignment
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Record
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FSSPMultAlign
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Record
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Record
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PosAlign
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Organism
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Record
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fff_rec
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Feature
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Record
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FastaAlignment
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VerboseDict
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SeqMap
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Iterator
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VerboseList
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Record
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Record
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Location
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Bio.Prosite.Pattern
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RecordParser
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Integer
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Bio.Blast.NCBIStandalone
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SequenceParser
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Symbol
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Bio.EUtils.parse
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SGMLHandle
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Feature
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Bio.EUtils.parse
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MyParser
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Record
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Reference
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SGMLStripper
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Reference
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Instance
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UndoHandle
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Record
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_HSPConsumer
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FilteredReader
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Record
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Martel.Expression
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SafeFitnessCrossover
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Record
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Bio.MarkovModel
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GeneralPointCrossover
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Record
)
_re_alb_line2coords
(in
Bio.Wise.dnal
)
__init__()
(in
InterleaveCrossover
)
__str__()
(in
Record
)
_re_align
(in
_Consumer
)
__init__()
(in
SinglePointCrossover
)
__str__()
(in
Record
)
_re_lengths
(in
_Consumer
)
__init__()
(in
TwoPointCrossover
)
__str__()
(in
Record
)
_re_names
(in
_Consumer
)
__init__()
(in
UniformCrossover
)
__str__()
(in
Token
)
_re_positive_alignment
(in
_Consumer
)
__init__()
(in
GenerationEvolver
)
__str__()
(in
Url
)
_re_profilewidth
(in
_Consumer
)
__init__()
(in
SteadyStateEvolver
)
__str__()
(in
MarkovModel
)
_re_scores
(in
_Consumer
)
__init__()
(in
SafeFitnessMutation
)
__str__()
(in
Metabolite
)
_re_search()
(in
Bio.Blast.NCBIStandalone
)
__init__()
(in
ConversionMutation
)
__str__()
(in
MetaboliteRole
)
_re_start
(in
_Consumer
)
__init__()
(in
SinglePositionMutation
)
__str__()
(in
PathwayTransform
)
_re_threshold
(in
_Consumer
)
__init__()
(in
Organism
)
__str__()
(in
Record
)
_re_unit
(in
Bio.Wise.psw
)
__init__()
(in
AmbiguousRepair
)
__str__()
(in
Location
)
_reaction()
(in
Record
)
__init__()
(in
AbstractSelection
)
__str__()
(in
Record
)
_read()
(in
ReseekFile
)
__init__()
(in
DiversitySelection
)
__str__()
(in
Record
)
_read_dicts()
(in
Bio.NMR.xpktools
)
__init__()
(in
RouletteWheelSelection
)
__str__()
(in
ExtractUrls
)
_read_fragments()
(in
Bio.PDB.FragmentMapper'
)
__init__()
(in
TournamentSelection
)
__str__()
(in
NetCatch
)
_read_key_value()
(in
Bio.Geo
)
__init__()
(in
Connection
)
__str__()
(in
AbstractLayer
)
_read_primary_table()
(in
Bio.Mindy.FlatDB
)
__init__()
(in
Feature
)
__str__()
(in
Tree
)
_read_secondary_table()
(in
Bio.Mindy.FlatDB
)
__init__()
(in
FeatureAggregate
)
__str__()
(in
Interaction
)
_read_vertex_array()
(in
Bio.PDB.ResidueDepth'
)
__init__()
(in
FeatureQuery
)
__str__()
(in
Network
)
_readline_and_check_start()
(in
Bio.MarkovModel
)
__init__()
(in
FeatureQueryRow
)
__str__()
(in
Reaction
)
_record_next()
(in
HeaderFooterEventStream
)
__init__()
(in
ArgsParser
)
__str__()
(in
Graph
)
_RecordConsumer
(in
Bio.CDD
)
__init__()
(in
Surrogate
)
__str__()
(in
HashSet
)
_RecordConsumer
(in
Bio.ECell
)
__init__()
(in
TempFile
)
__str__()
(in
MultiGraph
)
_RecordConsumer
(in
Bio.Enzyme
)
__init__()
(in
RetrieveSeqname
)
__str__()
(in
System
)
_RecordConsumer
__init__()
(in
Segment
)
__str__()
(in
Record
)
_RecordConsumer
(in
Bio.Gobase
)
__init__()
(in
FeatureDict
)
__str__()
(in
Record
)
_RecordConsumer
(in
Bio.IntelliGenetics
)
__init__()
(in
Location
)
__str__()
(in
Prosite
)
_RecordConsumer
(in
Bio.LocusLink
)
__init__()
(in
LocationFromCoords
)
__str__()
(in
PrositeMatch
)
_RecordConsumer
(in
Bio.Medline
)
__init__()
(in
LocationFromString
)
__str__()
(in
PrositeTerm
)
_RecordConsumer
__init__()
(in
LocationJoin
)
__str__()
(in
PatternHit
)
_RecordConsumer
(in
Bio.NBRF
)
__init__()
(in
FeatureParser
)
__str__()
(in
RestrictionBatch
)
_RecordConsumer
__init__()
(in
Iterator
)
__str__()
(in
RestrictionType
)
_RecordConsumer
(in
Bio.PopGen.GenePop
)
__init__()
(in
AbsoluteLocation
)
__str__()
(in
Record
)
_RecordConsumer
(in
Bio.Prosite.Prodoc
)
__init__()
(in
Between
)
__str__()
(in
Record
)
_RecordConsumer
(in
Bio.Prosite
)
__init__()
(in
FeatureName
)
__str__()
(in
Record
)
_RecordConsumer
(in
Bio.Rebase
)
__init__()
(in
Function
)
__str__()
(in
Domain
)
_RecordConsumer
(in
Bio.Saf
)
__init__()
(in
HighBound
)
__str__()
(in
Record
)
_RecordConsumer
(in
Bio.Sequencing.Ace
)
__init__()
(in
Integer
)
__str__()
(in
Node
)
_RecordConsumer
(in
Bio.Sequencing.Phd
)
__init__()
(in
LocationParser
)
__str__()
(in
Residues
)
_RecordConsumer
(in
Bio.SwissProt.SProt
)
__init__()
(in
LocationScanner
)
__str__()
(in
Record
)
_RecordConsumer
(in
Bio.UniGene
)
__init__()
(in
LowBound
)
__str__()
(in
MutableSeq
)
_recover_alignments()
(in
Bio.pairwise2
)
__init__()
(in
Path
)
__str__()
(in
Seq
)
_reference_line()
(in
Reference
)
__init__()
(in
Range
)
__str__()
(in
AfterPosition
)
_refresh()
(in
_RecordConsumer
)
__init__()
(in
Symbol
)
__str__()
(in
BeforePosition
)
_remark_line()
(in
Reference
)
__init__()
(in
Token
)
__str__()
(in
BetweenPosition
)
_remove_if_inconsistent()
(in
_RecordConsumer
)
__init__()
(in
TwoBound
)
__str__()
(in
ExactPosition
)
_remove_newlines()
(in
_BaseGenBankConsumer
)
__init__()
(in
NCBIDictionary
)
__str__()
(in
FeatureLocation
)
_remove_spaces()
(in
_BaseGenBankConsumer
)
__init__()
(in
Feature
)
__str__()
(in
OneOfPosition
)
_replace_parenthesized_ambigs()
(in
Bio.Nexus.Nexus
)
__init__()
(in
Qualifier
)
__str__()
(in
PositionGap
)
_resolve()
(in
Nexus
)
__init__()
(in
Record
)
__str__()
(in
Reference
)
_retrieve_annotations()
(in
BioSQL.BioSeq
)
__init__()
(in
Reference
)
__str__()
(in
SeqFeature
)
_retrieve_dbxrefs()
(in
BioSQL.BioSeq
)
__init__()
(in
RecordParser
)
__str__()
(in
WithinPosition
)
_retrieve_features()
(in
BioSQL.BioSeq
)
__init__()
(in
InsdcScanner
)
__str__()
(in
SeqRecord
)
_retrieve_qualifier_value()
(in
BioSQL.BioSeq
)
__init__()
(in
_BaseGenBankConsumer
)
__str__()
(in
Feature
)
_retrieve_reference()
(in
BioSQL.BioSeq
)
__init__()
(in
_FeatureConsumer
)
__str__()
(in
BadMatrix
)
_retrieve_seq()
(in
BioSQL.BioSeq
)
__init__()
(in
_RecordConsumer
)
__str__()
(in
Translator
)
_retrieve_taxon()
(in
BioSQL.BioSeq
)
__init__()
(in
FeatureValueCleaner
)
__str__()
(in
Statistics
)
_rev_modify()
(in
NoCut
)
__init__()
(in
Record
)
__str__()
(in
ColumnUnit
)
_rev_modify()
(in
OneCut
)
__init__()
(in
Dictionary
)
__str__()
(in
Registry
)
_rev_modify()
(in
TwoCuts
)
__init__()
(in
GeneRecord
)
__str__()
(in
DBSeq
)
_rms()
(in
SVDSuperimposer
)
__init__()
(in
Iterator
)
__str__()
(in
Alt
)
_run_program()
(in
Local
)
__init__()
(in
ProteinRecord
)
__str__()
(in
Any
)
_safe_asarray()
(in
Bio.MarkovModel
)
__init__()
(in
Record
)
__str__()
(in
AnyEol
)
_safe_copy_and_check()
(in
Bio.MarkovModel
)
__init__()
(in
RecordParser
)
__str__()
(in
Assert
)
_safe_float()
(in
Bio.Blast.NCBIStandalone
)
__init__()
(in
SequenceRecord
)
__str__()
(in
AtBeginning
)
_safe_int()
(in
Bio.Blast.NCBIStandalone
)
__init__()
(in
_RecordConsumer
)
__str__()
(in
AtEnd
)
_safe_log()
(in
Bio.MarkovModel
)
__init__()
(in
Chromosome
)
__str__()
(in
Debug
)
_savedata()
(in
Record
)
__init__()
(in
ChromosomeSegment
)
__str__()
(in
Dot
)
_savekmeans()
(in
Record
)
__init__()
(in
Organism
)
__str__()
(in
Expression
)
_savetree()
(in
Bio.Cluster
)
__init__()
(in
TelomereSegment
)
__str__()
(in
Group
)
_sbjct_re
(in
_HSPConsumer
)
__init__()
(in
_ChromosomeComponent
)
__str__()
(in
GroupRef
)
_scan_3d()
(in
_Scanner
)
__init__()
(in
ComparativeScatterPlot
)
__str__()
(in
Literal
)
_scan_abbreviated_pairwise_alignment()
(in
_Scanner
)
__init__()
(in
ChromosomeCounts
)
__str__()
(in
MaxRepeat
)
_scan_ac()
(in
_Scanner
)
__init__()
(in
BarChartDistribution
)
__str__()
(in
NullOp
)
_scan_ac()
(in
_Scanner
)
__init__()
(in
DistributionPage
)
__str__()
(in
PassThrough
)
_scan_accession()
(in
_Scanner
)
__init__()
(in
LineDistribution
)
__str__()
(in
Seq
)
_scan_Adeno2()
(in
_Scanner
)
__init__()
(in
AbstractDPAlgorithms
)
__str__()
(in
Str
)
_scan_alignment()
(in
_Scanner
)
__init__()
(in
LogDPAlgorithms
)
__str__()
(in
HeaderFooterParser
)
_scan_alignment_header()
(in
_Scanner
)
__init__()
(in
ScaledDPAlgorithms
)
__str__()
(in
MartelAttributeList
)
_scan_alignment_header()
(in
_Scanner
)
__init__()
(in
HiddenMarkovModel
)
__str__()
(in
Parser
)
_scan_alignments()
(in
_Scanner
)
__init__()
(in
MarkovModelBuilder
)
__str__()
(in
RecordParser
)
_scan_alignments()
(in
_Scanner
)
__init__()
(in
AbstractTrainer
)
__sub__()
(in
DBIds
)
_scan_an()
(in
_Scanner
)
__init__()
(in
BaumWelchTrainer
)
__sub__()
(in
Location
)
_scan_annotated_matches()
(in
_MASTScanner
)
__init__()
(in
KnownStateTrainer
)
__sub__()
(in
Atom
)
_scan_begin_sequence()
(in
_Scanner
)
__init__()
(in
TrainingSequence
)
__sub__()
(in
Fragment
)
_scan_blastform()
(in
_Scanner
)
__init__()
(in
HotCache
)
__sub__()
(in
Vector
)
_scan_bq_data()
(in
_Scanner
)
__init__()
(in
HotRandom
)
__sub__()
(in
SeqMat
)
_scan_bracket_tags()
(in
_Scanner
)
__init__()
(in
_InMemoryIndex
)
__sum__()
(in
SeqMat
)
_scan_ca()
(in
_Scanner
)
__init__()
(in
_ShelveIndex
)
__swig_getmethods__
(in
KDTree
)
_scan_cc()
(in
_Scanner
)
__init__()
(in
IntelliGeneticsReader
)
__swig_setmethods__
(in
KDTree
)
_scan_cc()
(in
_Scanner
)
__init__()
(in
Iterator
)
__test__
(in
Bio.EUtils.MultiDict
)
_scan_cc()
(in
_Scanner
)
__init__()
(in
Record
)
__truediv__()
(in
RestrictionType
)
_scan_cf()
(in
_Scanner
)
__init__()
(in
RecordParser
)
__unicode__()
(in
AttributeList
)
_scan_comments()
(in
_Scanner
)
__init__()
(in
_RecordConsumer
)
__unicode__()
(in
Comment
)
_scan_copyright()
(in
_Scanner
)
__init__()
(in
_Scanner
)
__unicode__()
(in
ElementNode
)
_scan_copyrights()
(in
_Scanner
)
__init__()
(in
KDTree
)
__unicode__()
(in
Fragments
)
_scan_database_info()
(in
_Scanner
)
__init__()
(in
KDTreePtr
)
__unicode__()
(in
IndentedText
)
_scan_database_report()
(in
_Scanner
)
__init__()
(in
KDTree
)
__unicode__()
(in
POMDocument
)
_scan_database_report()
(in
_Scanner
)
__init__()
(in
Record
)
__unicode__()
(in
Text
)
_scan_date_entered()
(in
_Scanner
)
__init__()
(in
Record
)
__version
(in
_InMemoryIndex
)
_scan_date_modified()
(in
_Scanner
)
__init__()
(in
Iterator
)
__version
(in
_ShelveIndex
)
_scan_de()
(in
_Scanner
)
__init__()
(in
Record
)
__version_key
(in
_InMemoryIndex
)
_scan_de()
(in
_Scanner
)
__init__()
(in
RecordParser
)
__version_key
(in
_ShelveIndex
)
_scan_de()
(in
_Scanner
)
__init__()
(in
_RecordConsumer
)
__warningregistry__
(in
Bio.Ais
)
_scan_descriptions()
(in
_Scanner
)
__init__()
(in
_Scanner
)
__warningregistry__
(in
Bio.CDD
)
_scan_descriptions()
(in
_Scanner
)
__init__()
(in
Record
)
__warningregistry__
(in
Bio.ECell
)
_scan_di()
(in
_Scanner
)
__init__()
(in
Token
)
__warningregistry__
(in
Bio.Gobase
)
_scan_dna()
(in
_Scanner
)
__init__()
(in
Url
)
__warningregistry__
(in
Bio.LocusLink
)
_scan_do()
(in
_Scanner
)
__init__()
(in
LogisticRegression
)
__warningregistry__
(in
Bio.LocusLink.locus_format
)
_scan_dr()
(in
_Scanner
)
__init__()
(in
Instance
)
__warningregistry__
(in
Bio.LocusLink.web_parse
)
_scan_dr()
(in
_Scanner
)
__init__()
(in
MEMEMotif
)
__warningregistry__
(in
Bio.MarkovModel
)
_scan_dr()
(in
_Scanner
)
__init__()
(in
Motif
)
__warningregistry__
(in
Bio.Rebase
)
_scan_dt()
(in
_Scanner
)
__init__()
(in
MASTParser
)
__warningregistry__
(in
Bio.SCOP.FileIndex
)
_scan_dt()
(in
_Scanner
)
__init__()
(in
MASTRecord
)
__warningregistry__
(in
Bio.SGMLExtractor
)
_scan_enzyme_num()
(in
_Scanner
)
__init__()
(in
MEMEParser
)
__warningregistry__
(in
Bio.SeqIO.ClustalIO
)
_scan_field()
(in
_Scanner
)
__init__()
(in
MEMERecord
)
__warningregistry__
(in
Bio.SeqIO.NexusIO
)
_scan_fns
(in
_Scanner
)
__init__()
(in
_MASTConsumer
)
__warningregistry__
(in
Bio.SeqIO.PhylipIO
)
_scan_fns
(in
_Scanner
)
__init__()
(in
_MEMEConsumer
)
__warningregistry__
(in
Bio.SeqIO.StockholmIO
)
_scan_fns
(in
_Scanner
)
__init__()
(in
MarkovModel
)
__warningregistry__
(in
Bio.WWW.ExPASy
)
_scan_footer()
(in
_Scanner
)
__init__()
(in
MaxEntropy
)
__warningregistry__
(in
Bio.WWW.InterPro
)
_scan_ft()
(in
_Scanner
)
__init__()
(in
Iterator
)
__warningregistry__
(in
Bio.WWW.NCBI
)
_scan_gene_record()
(in
_Scanner
)
__init__()
(in
Record
)
__warningregistry__
(in
Bio.WWW.SCOP
)
_scan_gn()
(in
_Scanner
)
__init__()
(in
RecordParser
)
__warningregistry__
(in
Bio.expressions
)
_scan_header()
(in
_Scanner
)
__init__()
(in
_RecordConsumer
)
__warningregistry__
(in
Bio.expressions.blast
)
_scan_header()
(in
_Scanner
)
__init__()
(in
Iterator
)
__warningregistry__
(in
Bio.expressions.blast.ncbiblast
)
_scan_header()
(in
_MASTScanner
)
__init__()
(in
Metabolite
)
__warningregistry__
(in
Bio.expressions.blast.wublast
)
_scan_header()
(in
_MEMEScanner
)
__init__()
(in
MetaboliteRole
)
__warningregistry__
(in
Bio.expressions.blocks
)
_scan_header()
(in
_Scanner
)
__init__()
(in
PathwayTransform
)
__warningregistry__
(in
Bio.expressions.embl
)
_scan_hsp()
(in
_Scanner
)
__init__()
(in
Record
)
__warningregistry__
(in
Bio.expressions.embl.embl65
)
_scan_hsp()
(in
_Scanner
)
__init__()
(in
RecordParser
)
__warningregistry__
(in
Bio.expressions.fasta
)
_scan_hsp_alignment()
(in
_Scanner
)
__init__()
(in
_RecordConsumer
)
__warningregistry__
(in
Bio.expressions.genbank
)
_scan_hsp_alignment()
(in
_Scanner
)
__init__()
(in
_Scanner
)
__warningregistry__
(in
Bio.expressions.hmmpfam
)
_scan_hsp_header()
(in
_Scanner
)
__init__()
(in
OpenDB
)
__warningregistry__
(in
Bio.expressions.swissprot
)
_scan_hsp_header()
(in
_Scanner
)
__init__()
(in
BerkeleyDB
)
__warningregistry__
(in
Bio.expressions.swissprot.ipi
)
_scan_id()
(in
_Scanner
)
__init__()
(in
PrimaryNamespace
)
__warningregistry__
(in
Bio.expressions.swissprot.speclist
)
_scan_id()
(in
_Scanner
)
__init__()
(in
SecondaryNamespace
)
__warningregistry__
(in
Bio.expressions.swissprot.sprot38
)
_scan_id()
(in
_Scanner
)
__init__()
(in
BaseFlatDB
)
__warningregistry__
(in
Bio.expressions.swissprot.sprot40
)
_scan_keywords()
(in
_Scanner
)
__init__()
(in
BisectFile
)
__warningregistry__
(in
Bio.expressions.transfac
)
_scan_kw()
(in
_Scanner
)
__init__()
(in
DiskFlatDB
)
_AbstractHSExposure
(in
Bio.PDB.HSExposure
)
_scan_Lambda()
(in
_Scanner
)
__init__()
(in
MemoryFlatDB
)
_AbstractParameter
(in
Bio.Application
)
_scan_lengths()
(in
_Scanner
)
__init__()
(in
PrimaryNamespace
)
_accept()
(in
_PPBuilder
)
_scan_line()
(in
_Scanner
)
__init__()
(in
PrimaryTable
)
_accession_line()
(in
Record
)
_scan_line()
(in
_Scanner
)
__init__()
(in
SecondaryNamespace
)
_acquire()
(in
ElementNode
)
_scan_line()
(in
_Scanner
)
__init__()
(in
SecondaryTable
)
_acquired
(in
ElementNode
)
_scan_line()
(in
_Scanner
)
__init__()
(in
Location
)
_add_bioentry_dbxref()
(in
DatabaseLoader
)
_scan_line()
(in
_Scanner
)
__init__()
(in
BaseSeqRecordIndexer
)
_add_db()
(in
Bio.EUtils.Config
)
_scan_ma()
(in
_Scanner
)
__init__()
(in
FixDocumentBuilder
)
_add_dbxref()
(in
DatabaseLoader
)
_scan_masterslave_alignment()
(in
_Scanner
)
__init__()
(in
FunctionIndexer
)
_add_diagram_for_sequence()
(in
MASTRecord
)
_scan_masterslave_alignment()
(in
_Scanner
)
__init__()
(in
SimpleIndexer
)
_add_diagram_from_buffer()
(in
_MASTConsumer
)
_scan_matches()
(in
_MASTScanner
)
__init__()
(in
GrabXPathNodes
)
_add_feature()
(in
_FeatureConsumer
)
_scan_methylation()
(in
_Scanner
)
__init__()
(in
Iterator
)
_add_feature()
(in
_RecordConsumer
)
_scan_microorganism()
(in
_Scanner
)
__init__()
(in
Record
)
_add_last_amplifier()
(in
_PrimerSearchRecordConsumer
)
_scan_motifs()
(in
_MEMEScanner
)
__init__()
(in
RecordParser
)
_add_last_primer()
(in
_Primer3RecordConsumer
)
_scan_names()
(in
_Scanner
)
__init__()
(in
_RecordConsumer
)
_add_line_to_buffer()
(in
_MASTConsumer
)
_scan_nr()
(in
_Scanner
)
__init__()
(in
_Scanner
)
_add_match()
(in
MASTRecord
)
_scan_oc()
(in
_Scanner
)
__init__()
(in
Peaklist
)
_add_match_diagram()
(in
_MASTConsumer
)
_scan_og()
(in
_Scanner
)
__init__()
(in
XpkEntry
)
_add_motif()
(in
MASTRecord
)
_scan_oh()
(in
_Scanner
)
__init__()
(in
NaiveBayes
)
_add_motif()
(in
_MASTConsumer
)
_scan_one_pairwise_alignment()
(in
_Scanner
)
__init__()
(in
Record
)
_add_motif()
(in
MotifFinder
)
_scan_one_pairwise_alignment()
(in
_Scanner
)
__init__()
(in
ExtractUrls
)
_add_motif_match()
(in
_MASTConsumer
)
_scan_os()
(in
_Scanner
)
__init__()
(in
NetCatch
)
_add_motif_with_info()
(in
_MEMEConsumer
)
_scan_ox()
(in
_Scanner
)
__init__()
(in
Url
)
_add_numbering_table()
(in
FSSPAlign
)
_scan_pa()
(in
_Scanner
)
__init__()
(in
AbstractLayer
)
_add_qualifier()
(in
_FeatureConsumer
)
_scan_pairwise_alignments()
(in
_Scanner
)
__init__()
(in
HiddenLayer
)
_add_seqfeature_dbxref()
(in
DatabaseLoader
)
_scan_pairwise_alignments()
(in
_Scanner
)
__init__()
(in
InputLayer
)
_add_sequence()
(in
MASTRecord
)
_scan_parameters()
(in
_Scanner
)
__init__()
(in
OutputLayer
)
_add_sequence_match_with_diagram()
(in
_MASTConsumer
)
_scan_parameters()
(in
_Scanner
)
__init__()
(in
BasicNetwork
)
_add_sig()
(in
SignatureFinder
)
_scan_pBR322()
(in
_Scanner
)
__init__()
(in
MotifCoder
)
_add_star_info()
(in
ClustalAlignment
)
_scan_pe()
(in
_Scanner
)
__init__()
(in
MotifFinder
)
_add_subtree()
(in
Tree
)
_scan_PhiX174()
(in
_Scanner
)
__init__()
(in
PatternIO
)
_add_version()
(in
ClustalAlignment
)
_scan_pp()
(in
_Scanner
)
__init__()
(in
PatternRepository
)
_adjust_charlabels()
(in
Nexus
)
_scan_pr()
(in
_Scanner
)
__init__()
(in
DifferentialSchemaFitness
)
_adjust_lines()
(in
Bio.Nexus.Nexus
)
_scan_pr()
(in
_Scanner
)
__init__()
(in
GeneticAlgorithmFinder
)
_alb_line2coords()
(in
Bio.Wise.dnal
)
_scan_profilewidth()
(in
_Scanner
)
__init__()
(in
MostCountSchemaFitness
)
_align()
(in
Bio.pairwise2
)
_scan_prosite_refs()
(in
_Scanner
)
__init__()
(in
RandomMotifGenerator
)
_AlignmentConsumer
(in
Bio.Blast.NCBIStandalone
)
_scan_protein_record()
(in
_Scanner
)
__init__()
(in
Schema
)
_all_blank()
(in
MarkovModelBuilder
)
_scan_prototype()
(in
_Scanner
)
__init__()
(in
SchemaCoder
)
_all_pseudo()
(in
MarkovModelBuilder
)
_scan_query_info()
(in
_Scanner
)
__init__()
(in
SchemaFactory
)
_allowed_lookups
(in
BioSQL.BioSeqDatabase
)
_scan_ra()
(in
_Scanner
)
__init__()
(in
SchemaFinder
)
_alphabet()
(in
Motif
)
_scan_rc()
(in
_Scanner
)
__init__()
(in
SimpleFinisher
)
_alphabet()
(in
MASTRecord
)
_scan_record()
(in
_Scanner
)
__init__()
(in
SignatureCoder
)
_alphabet()
(in
_MEMEConsumer
)
_scan_record()
(in
_Scanner
)
__init__()
(in
SignatureFinder
)
_alphabet_from_input()
(in
FreqTable
)
_scan_record()
(in
_Scanner
)
__init__()
(in
ValidationIncreaseStop
)
_alphabet_from_matrix()
(in
SeqMat
)
_scan_record()
(in
_Scanner
)
__init__()
(in
ExampleManager
)
_any()
(in
Bio.Wise.dnal
)
_scan_record()
(in
_Scanner
)
__init__()
(in
TrainingExample
)
_any_case()
(in
Martel.Time
)
_scan_record()
(in
_Scanner
)
__init__()
(in
Block
)
_apply_block_structure()
(in
Nexus
)
_scan_record()
(in
_Scanner
)
__init__()
(in
CharBuffer
)
_apply_clean_data()
(in
SGMLStrippingConsumer
)
_scan_record()
(in
_Scanner
)
__init__()
(in
Commandline
)
_argmaxes()
(in
Bio.MarkovModel
)
_scan_record()
(in
_Scanner
)
__init__()
(in
Nexus
)
_Argument
(in
Bio.Application
)
_scan_record()
(in
_Scanner
)
__init__()
(in
StepMatrix
)
_ATOM_FORMAT_STRING
(in
Bio.PDB.PDBIO'
)
_scan_reference()
(in
_Scanner
)
__init__()
(in
Chain
)
_atom_name_dict
(in
Bio.PDB.Residue
)
_scan_refs()
(in
_Scanner
)
__init__()
(in
Node
)
_attr_str()
(in
ElementNode
)
_scan_rl()
(in
_Scanner
)
__init__()
(in
NodeData
)
_attr_unistr()
(in
ElementNode
)
_scan_rn()
(in
_Scanner
)
__init__()
(in
Tree
)
_ATTRCLASSMAP
(in
Bio.EUtils.POM
)
_scan_rounds()
(in
_Scanner
)
__init__()
(in
AbstractAtomPropertyMap
)
_attribs_match()
(in
ElementNode
)
_scan_rounds()
(in
_Scanner
)
__init__()
(in
AbstractPropertyMap
)
_attribute_list
(in
Martel.Parser
)
_scan_rp()
(in
_Scanner
)
__init__()
(in
AbstractResiduePropertyMap
)
_AttributeType
_scan_rt()
(in
_Scanner
)
__init__()
(in
Atom
)
_ATTRTYPEMAP
(in
Bio.EUtils.POM
)
_scan_ru()
(in
_Scanner
)
__init__()
(in
DisorderedAtom
)
_authors_line()
(in
Reference
)
_scan_rx()
(in
_Scanner
)
__init__()
(in
Chain
)
_autoload()
(in
Registry
)
_scan_scores()
(in
_Scanner
)
__init__()
(in
DSSP
)
_back_translate_no_stop()
(in
Translator
)
_scan_sequence()
(in
_Scanner
)
__init__()
(in
ChainSelector
)
_backward()
(in
Bio.MarkovModel
)
_scan_sequence_data()
(in
_Scanner
)
__init__()
(in
DisorderedEntityWrapper
)
_backward_recursion()
(in
AbstractDPAlgorithms
)
_scan_sequence_data()
(in
_Scanner
)
__init__()
(in
Entity
)
_backward_recursion()
(in
ScaledDPAlgorithms
)
_scan_sequence_record()
(in
_Scanner
)
__init__()
(in
Fragment
)
_base_count_line()
(in
Record
)
_scan_source()
(in
_Scanner
)
__init__()
(in
FragmentMapper
)
_BaseGenBankConsumer
_scan_sq()
(in
_Scanner
)
__init__()
(in
ExposureCN
)
_BaseMultiDict
(in
Bio.EUtils.MultiDict
)
_scan_SV40()
(in
_Scanner
)
__init__()
(in
HSExposureCA
)
_baum_welch()
(in
Bio.MarkovModel
)
_scan_temperature()
(in
_Scanner
)
__init__()
(in
HSExposureCB
)
_baum_welch_one()
(in
Bio.MarkovModel
)
_scan_terminator()
(in
_Scanner
)
__init__()
(in
_AbstractHSExposure
)
_bit_info()
(in
Bio.expressions.blast.ncbiblast
)
_scan_terminator()
(in
_Scanner
)
__init__()
(in
MMCIF2Dict
)
_blank_buffer()
(in
_MASTConsumer
)
_scan_terminator()
(in
_Scanner
)
__init__()
(in
Model
)
_BlastConsumer
(in
Bio.Blast.NCBIStandalone
)
_scan_text()
(in
_Scanner
)
__init__()
(in
NACCESS
)
_BlastErrorConsumer
(in
Bio.Blast.NCBIStandalone
)
_scan_threshold()
(in
_Scanner
)
__init__()
(in
NACCESS_atomic
)
_bootstrap()
(in
Bio.Alphabet.IUPAC
)
_Scanner
(in
Bio.Blast.NCBIStandalone
)
__init__()
(in
NeighborSearch
)
_boundaries()
(in
Analysis
)
_Scanner
(in
Bio.Blast.NCBIWWW
)
__init__()
(in
PDBIO
)
_build_align_cmdline()
(in
Bio.Wise
)
_Scanner
(in
Bio.CDD
)
__init__()
(in
PDBList
)
_build_child_path()
(in
FormatRegistry
)
_Scanner
(in
Bio.Compass
)
__init__()
(in
PDBParser
)
_build_dnal_cmdline()
(in
Bio.Wise.dnal
)
_Scanner
(in
Bio.ECell
)
__init__()
(in
PSEA
)
_build_exp_freq_mat()
(in
Bio.SubsMat
)
_Scanner
(in
Bio.Enzyme
)
__init__()
(in
CaPPBuilder
)
_build_log_odds_mat()
(in
Bio.SubsMat
)
_Scanner
(in
Bio.Gobase
)
__init__()
(in
PPBuilder
)
_build_obs_freq_mat()
(in
Bio.SubsMat
)
_Scanner
(in
Bio.IntelliGenetics
)
__init__()
(in
_PPBuilder
)
_build_parent_path()
(in
FormatRegistry
)
_Scanner
(in
Bio.LocusLink
)
__init__()
(in
DisorderedResidue
)
_build_path()
(in
NetCatch
)
_Scanner
(in
Bio.Medline
)
__init__()
(in
Residue
)
_build_problem_mapping()
(in
Bio.EUtils.Datatypes
)
_Scanner
__init__()
(in
ResidueDepth
)
_build_reactor_entry()
(in
_RecordConsumer
)
_Scanner
(in
Bio.NBRF
)
__init__()
(in
Structure
)
_build_structure()
(in
MMCIFParser
)
_Scanner
__init__()
(in
StructureAlignment
)
_build_subs_mat()
(in
Bio.SubsMat
)
_Scanner
(in
Bio.PopGen.GenePop
)
__init__()
(in
StructureBuilder
)
_build_substance_entry()
(in
_RecordConsumer
)
_Scanner
(in
Bio.Prosite.Prodoc
)
__init__()
(in
Superimposer
)
_build_system_entry()
(in
_RecordConsumer
)
_Scanner
(in
Bio.Prosite
)
__init__()
(in
Vector
)
_cached_parser
(in
Bio.GenBank.LocationParser
)
_Scanner
(in
Bio.Rebase
)
__init__()
(in
EventGenerator
)
_cached_scanner
(in
Bio.GenBank.LocationParser
)
_Scanner
(in
Bio.Saf
)
__init__()
(in
SGMLStrippingConsumer
)
_calc_empirical_expects()
(in
Bio.MaxEntropy
)
_Scanner
(in
Bio.Sequencing.Ace
)
__init__()
(in
TaggingConsumer
)
_calc_f_sharp()
(in
Bio.MaxEntropy
)
_Scanner
(in
Bio.Sequencing.Phd
)
__init__()
(in
GenericASTBuilder
)
_calc_model_expects()
(in
Bio.MaxEntropy
)
_Scanner
(in
Bio.SwissProt.KeyWList
)
__init__()
(in
GenericASTMatcher
)
_calc_p_class_given_x()
(in
Bio.MaxEntropy
)
_Scanner
(in
Bio.SwissProt.SProt
)
__init__()
(in
GenericASTTraversal
)
_calculate_from_transitions()
(in
HiddenMarkovModel
)
_Scanner
(in
Bio.UniGene
)
__init__()
(in
GenericParser
)
_calculate_s_value()
(in
ScaledDPAlgorithms
)
_schema_from_motif()
(in
SchemaFactory
)
__init__()
(in
GenericScanner
)
_call_call
(in
Martel.Generate
)
_score()
(in
Instance
)
__init__()
(in
Network
)
_call_calltag
(in
Martel.Generate
)
_SCORE_GAP_EXTENSION
(in
Bio.Wise.dnal
)
__init__()
(in
Reaction
)
_callback()
(in
POMDocument
)
_SCORE_GAP_START
(in
Bio.Wise.dnal
)
__init__()
(in
Graph
)
_categories
(in
_Scanner
)
_SCORE_MATCH
(in
Bio.Wise.dnal
)
__init__()
(in
HashSet
)
_cgiopen()
(in
CGIDB
)
_SCORE_MISMATCH
(in
Bio.Wise.dnal
)
__init__()
(in
MultiGraph
)
_changeset()
(in
Nexus
)
_search()
(in
NonPalindromic
)
__init__()
(in
System
)
_chargeR()
(in
IsoelectricPoint
)
_search()
(in
Palindromic
)
__init__()
(in
Async
)
_charlabels()
(in
Nexus
)
_secure_name()
(in
_XMLparser
)
__init__()
(in
DirectoryRetriever
)
_charpartition()
(in
Nexus
)
_security_check_parameters()
(in
Bio.Blast.NCBIStandalone
)
__init__()
(in
FileRetriever
)
_charset()
(in
Nexus
)
_segment_line()
(in
Record
)
__init__()
(in
Local
)
_charstatelabels()
(in
Nexus
)
_select_charged()
(in
IsoelectricPoint
)
__init__()
(in
FDistAsync
)
_check_alphabet()
(in
Motif
)
_select_names()
(in
Expression
)
__init__()
(in
SplitFDist
)
_check_attrs()
(in
Bio.Std
)
_select_names()
(in
ExpressionList
)
__init__()
(in
FDistController
)
_check_duplicates()
(in
Record
)
_select_names()
(in
Group
)
__init__()
(in
Record
)
_check_for_bad_input_stream()
(in
Bio.EUtils.parse
)
_select_names()
(in
MaxRepeat
)
__init__()
(in
RecordParser
)
_check_for_cache_reset()
(in
HistoryClient
)
_select_names()
(in
NullOp
)
__init__()
(in
_RecordConsumer
)
_check_for_errors()
(in
Bio.EUtils.parse
)
_select_names()
(in
PassThrough
)
__init__()
(in
Record
)
_check_for_errors()
(in
TextLikeMixin
)
_SeqIO_to_alignment_iterator()
(in
Bio.AlignIO
)
__init__()
(in
RecordParser
)
_check_for_link_errors()
(in
Bio.EUtils.parse
)
_SeqLength
(in
Bio.Search
)
__init__()
(in
_RecordConsumer
)
_check_gapchar()
(in
Bio.Std
)
_seqmatrix2strmatrix()
(in
Bio.Nexus.Nexus
)
__init__()
(in
SimCoalCache
)
_check_invalid()
(in
HistoryLookup
)
_seqname()
(in
Instance
)
__init__()
(in
SimCoalCache
)
_check_is_public()
(in
Bio.DocSQL
)
_sequence()
(in
Instance
)
__init__()
(in
SimCoalController
)
_check_length()
(in
Motif
)
_sequence_line()
(in
Record
)
__init__()
(in
PropertyManager
)
_check_missing_header()
(in
_RecordConsumer
)
_sequence_name()
(in
_MEMEConsumer
)
__init__()
(in
Dictionary
)
_check_name()
(in
Bio.Std
)
_SequenceConsumer
(in
Bio.SwissProt.SProt
)
__init__()
(in
ExPASyDictionary
)
_check_no_buffer()
(in
ReseekFile
)
_set()
(in
Nexus
)
__init__()
(in
Iterator
)
_check_taxlabels()
(in
Nexus
)
_set()
(in
DBObject
)
__init__()
(in
Prosite
)
_check_value()
(in
AbstractCommandline
)
_set_colors_and_shapes()
(in
ComparativeScatterPlot
)
__init__()
(in
PrositeMatch
)
_CHOMP
(in
Bio.SwissProt.SProt
)
_set_current_seq()
(in
_MASTConsumer
)
__init__()
(in
PrositeTerm
)
_chomp()
(in
_RecordConsumer
)
_set_defaults()
(in
Bio.ECell
)
__init__()
(in
PatternHit
)
_chop_end_codes()
(in
Bio.PDB.parse_pdb_header'
)
_set_function()
(in
_FeatureConsumer
)
__init__()
(in
Dictionary
)
_chop_end_misc()
(in
Bio.PDB.parse_pdb_header'
)
_set_if_given()
(in
Bio.Std
)
__init__()
(in
ExPASyDictionary
)
_ChromosomeComponent
(in
Bio.Graphics.BasicChromosome
)
_set_kind()
(in
AlignmentColumn
)
__init__()
(in
Iterator
)
_class_escape()
(in
Martel.msre_parse
)
_set_location()
(in
_FeatureConsumer
)
__init__()
(in
Record
)
_classname()
(in
Record
)
_set_location_info()
(in
_FeatureConsumer
)
__init__()
(in
RecordParser
)
_clean()
(in
_RecordConsumer
)
_set_max()
(in
_RecordConsumer
)
__init__()
(in
Reference
)
_clean()
(in
_RecordConsumer
)
_set_ordering_info()
(in
_FeatureConsumer
)
__init__()
(in
_RecordConsumer
)
_clean_abbrev()
(in
Bio.config.DBRegistry
)
_set_reactor_defaults()
(in
Bio.ECell
)
__init__()
(in
Record
)
_clean_alignments()
(in
Bio.pairwise2
)
_set_up_genetic_algorithm()
(in
GeneticAlgorithmFinder
)
__init__()
(in
RecordParser
)
_clean_data()
(in
_RecordConsumer
)
_set_up_wheel()
(in
RouletteWheelSelection
)
__init__()
(in
_RecordConsumer
)
_clean_location()
(in
_BaseGenBankConsumer
)
_settag()
(in
Bio.Std
)
__init__()
(in
Dictionary
)
_clean_record()
(in
_RecordConsumer
)
_ShelveIndex
(in
Bio.Index
)
__init__()
(in
Dictionary
)
_clean_record()
(in
_RecordConsumer
)
_ShelveIndex__version
(in
_ShelveIndex
)
__init__()
(in
Iterator
)
_clean_references()
(in
_RecordConsumer
)
_ShelveIndex__version_key
(in
_ShelveIndex
)
__init__()
(in
Record
)
_clean_translation()
(in
FeatureValueCleaner
)
_skip_file_header()
(in
FastaM10Iterator
)
__init__()
(in
RecordParser
)
_clear()
(in
SVDSuperimposer
)
_skip_starstar()
(in
_Scanner
)
__init__()
(in
_RecordConsumer
)
_clear_bad_block()
(in
Bio.ECell
)
_sort()
(in
Chain
)
__init__()
(in
PrintFormat
)
_CMDLINE_DNAL
(in
Bio.Wise.dnal
)
_sort()
(in
Model
)
__init__()
(in
Analysis
)
_CMDLINE_FGREP_COUNT
(in
Bio.Wise.dnal
)
_sort()
(in
Residue
)
__init__()
(in
FormattedSeq
)
_CMDLINE_PSW
(in
Bio.Wise.psw
)
_sort()
(in
Structure
)
__init__()
(in
RestrictionBatch
)
_code_line
(in
Bio.expressions.swissprot.speclist
)
_sort_keys()
(in
Bio.NMR.xpktools
)
__init__()
(in
RestrictionType
)
_codeset()
(in
Nexus
)
_sort_keys_by_values()
(in
Bio.Nexus.Nexus
)
__init__()
(in
DictionaryBuilder
)
_codonposset()
(in
Nexus
)
_source_line()
(in
Record
)
__init__()
(in
TypeCompiler
)
_cofactor()
(in
Record
)
_split_accessions()
(in
_BaseGenBankConsumer
)
__init__()
(in
newenzyme
)
_col_ave()
(in
Bio.NMR.NOEtools
)
_split_keywords()
(in
_BaseGenBankConsumer
)
__init__()
(in
ConnectionError
)
_collapse_buffer()
(in
_MASTConsumer
)
_split_reference_locations()
(in
_FeatureConsumer
)
__init__()
(in
FtpNameError
)
_color_from_count()
(in
ChromosomeCounts
)
_split_taxonomy()
(in
_BaseGenBankConsumer
)
__init__()
(in
FtpPasswordError
)
_comma_digits
(in
Bio.expressions.blast.ncbiblast
)
_stanzaformat
(in
Bio.config
)
__init__()
(in
RebaseUpdate
)
_commandline()
(in
_MEMEConsumer
)
_START
(in
GenericParser
)
__init__()
(in
Astral
)
_comment()
(in
Record
)
_start()
(in
Instance
)
__init__()
(in
Index
)
_comment_line()
(in
Record
)
_start_Hit()
(in
BlastParser
)
__init__()
(in
Iterator
)
_common_line
(in
Bio.expressions.swissprot.speclist
)
_start_Hsp()
(in
BlastParser
)
__init__()
(in
Parser
)
_compact4nexus()
(in
Bio.Nexus.Nexus
)
_start_Iteration()
(in
BlastParser
)
__init__()
(in
Record
)
_complain_if_given()
(in
Bio.Std
)
_startswith_tagtable_newline()
(in
Martel.RecordReader
)
__init__()
(in
Iterator
)
_consensus()
(in
Motif
)
_startswith_tagtable_rest_of_line()
(in
Martel.RecordReader
)
__init__()
(in
Parser
)
_consistency_filter()
(in
_RecordConsumer
)
_statelabels()
(in
Nexus
)
__init__()
(in
Record
)
_consrtm_line()
(in
Reference
)
_stateset()
(in
Nexus
)
__init__()
(in
Iterator
)
_construct_pattern()
(in
Bio.EUtils.parse
)
_str_line()
(in
Alignment
)
__init__()
(in
Record
)
_consume_entry()
(in
BlastTableReader
)
_strand()
(in
Instance
)
__init__()
(in
Domain
)
_consume_header()
(in
BlastTableReader
)
_strip_and_combine()
(in
Bio.Emboss.Primer
)
__init__()
(in
FileIndex
)
_Consumer
(in
Bio.Compass
)
_structures()
(in
Record
)
__init__()
(in
defaultdict
)
_ContentModelGenerator
_structures()
(in
Record
)
__init__()
(in
Iterator
)
_contig_line()
(in
Record
)
_sub_set()
(in
Analysis
)
__init__()
(in
Parser
)
_convert_conc()
(in
_RecordConsumer
)
_substrate()
(in
Record
)
__init__()
(in
Record
)
_convert_to()
(in
BioCorbaDB
)
_support
(in
Bio.config
)
__init__()
(in
Node
)
_convert_to()
(in
BioSQLDB
)
_support
(in
Bio.dbdefs
)
__init__()
(in
Iterator
)
_convert_to()
(in
DBObject
)
_swig_getattr()
(in
Bio.KDTree.CKDTree
)
__init__()
(in
Parser
)
_convert_to()
(in
IndexedFileDB
)
_swig_setattr()
(in
Bio.KDTree.CKDTree
)
__init__()
(in
Res
)
_convert_to()
(in
TextLikeMixin
)
_synonym_line
(in
Bio.expressions.swissprot.speclist
)
__init__()
(in
SeqMap
)
_convert_to_python_numbers()
(in
_BaseGenBankConsumer
)
_sysname()
(in
Record
)
__init__()
(in
SeqMapIndex
)
_copy_and_check()
(in
Bio.MarkovModel
)
_table_h
(in
Bio.SeqUtils.CheckSum
)
__init__()
(in
Residues
)
_corr()
(in
Bio.MEME.Motif
)
_tabs()
(in
ElementNode
)
__init__()
(in
Scop
)
_correct_matrix()
(in
SeqMat
)
_tag_lines_tagtable
(in
Martel.RecordReader
)
__init__()
(in
LocalParser
)
_count_codons()
(in
CodonAdaptationIndex
)
_taxlabels()
(in
Nexus
)
__init__()
(in
SGMLExtractor
)
_count_emissions()
(in
KnownStateTrainer
)
_taxpartition()
(in
Nexus
)
__init__()
(in
SGMLExtractorHandle
)
_count_transitions()
(in
KnownStateTrainer
)
_taxset()
(in
Nexus
)
__init__()
(in
SVDSuperimposer
)
_crossover()
(in
GeneralPointCrossover
)
_test()
(in
Bio.DocSQL
)
__init__()
(in
Iterator
)
_crossover()
(in
InterleaveCrossover
)
_test()
(in
Bio.EUtils.MultiDict
)
__init__()
(in
Record
)
_crossover()
(in
TwoCrossover
)
_test()
(in
Bio.GFF
)
__init__()
(in
RecordParser
)
_dash_line
(in
Bio.expressions.swissprot.speclist
)
_test()
(in
Bio.Wise
)
__init__()
(in
_RecordConsumer
)
_data_map()
(in
Bio.NMR.NOEtools
)
_test()
(in
Bio.Wise.dnal
)
__init__()
(in
_Scanner
)
_database()
(in
MASTRecord
)
_test()
(in
Bio.Wise.psw
)
__init__()
(in
Algorithm
)
_database()
(in
_MASTConsumer
)
_test_dist()
(in
PPBuilder
)
__init__()
(in
Database
)
_DatabaseReportConsumer
(in
Bio.Blast.NCBIStandalone
)
_test_equivalence()
(in
StructureAlignment
)
__init__()
(in
HSP
)
_datafile()
(in
_MEMEConsumer
)
_test_normal()
(in
Analysis
)
__init__()
(in
HSPSeq
)
_date_re_match()
(in
Bio.EUtils.Datatypes
)
_test_reverse()
(in
Analysis
)
__init__()
(in
Hit
)
_db_source_line()
(in
Record
)
_text_in()
(in
_Scanner
)
__init__()
(in
HomologySeq
)
_dbids_to_id_string()
(in
Bio.EUtils.ThinClient
)
_text_in()
(in
_Scanner
)
__init__()
(in
Query
)
_dblinks()
(in
Record
)
_time_fields
(in
Martel.Time
)
__init__()
(in
Search
)
_dblinks()
(in
Record
)
_time_table
(in
Martel.Time
)
__init__()
(in
TableInfo
)
_dbutils
(in
BioSQL.DBUtils
)
_title()
(in
Nexus
)
__init__()
(in
_SeqLength
)
_decoder_cache
(in
Bio.Decode
)
_title_line()
(in
Reference
)
__init__()
(in
MutableSeq
)
_default_wrap()
(in
Bio.KEGG
)
_to_secondary_end
(in
Bio.expressions.swissprot.sprot38
)
__init__()
(in
Seq
)
_DEFAULTMAP
(in
Bio.EUtils.POM
)
_toobj()
(in
_InMemoryIndex
)
__init__()
(in
AbstractPosition
)
_definition_line()
(in
Record
)
_tostr()
(in
_InMemoryIndex
)
__init__()
(in
AfterPosition
)
_DescriptionConsumer
(in
Bio.Blast.NCBIStandalone
)
_train_iis()
(in
Bio.MaxEntropy
)
__init__()
(in
BeforePosition
)
_determine_position()
(in
BarChartDistribution
)
_translate()
(in
Nexus
)
__init__()
(in
BetweenPosition
)
_diagnose_error()
(in
BlastErrorParser
)
_translate_id()
(in
AbstractAtomPropertyMap
)
__init__()
(in
ExactPosition
)
_diagnostics
(in
RetrieveSeqname
)
_translate_id()
(in
AbstractPropertyMap
)
__init__()
(in
FeatureLocation
)
_dict()
(in
Bio.EUtils.setup
)
_translate_id()
(in
AbstractResiduePropertyMap
)
__init__()
(in
OneOfPosition
)
_digest()
(in
CAPSMap
)
_translate_id()
(in
Chain
)
__init__()
(in
PositionGap
)
_digest_with()
(in
CAPSMap
)
_tree()
(in
Nexus
)
__init__()
(in
Reference
)
_dimensions()
(in
Nexus
)
_treepartition()
(in
Nexus
)
__init__()
(in
SeqFeature
)
_dir_class()
(in
Martel.Dispatch
)
_treeset()
(in
Nexus
)
__init__()
(in
WithinPosition
)
_disease()
(in
Record
)
_treesort()
(in
Bio.Cluster
)
__init__()
(in
ClustalWriter
)
_do_callback()
(in
Martel.Parser
)
_try_open_read()
(in
Bio.NMR.xpktools
)
__init__()
(in
FastaWriter
)
_do_dispatch_callback()
(in
Martel.Parser
)
_try_open_write()
(in
Bio.NMR.xpktools
)
__init__()
(in
InterlacedSequenceIterator
)
_domain_re
(in
Bio.SCOP
)
_tuplestr()
(in
Bio.EUtils.sourcegen
)
__init__()
(in
SequenceIterator
)
_draw_distributions()
(in
DistributionPage
)
_typechecked_decoder_cache
(in
Bio.Decode
)
__init__()
(in
SequenceWriter
)
_draw_label()
(in
Chromosome
)
_uncompress_table
(in
Bio.Mindy.compression
)
__init__()
(in
SequentialSequenceWriter
)
_draw_label()
(in
ChromosomeSegment
)
_unhandled()
(in
AbstractConsumer
)
__init__()
(in
PhylipWriter
)
_draw_legend()
(in
Organism
)
_unhandled_section()
(in
AbstractConsumer
)
__init__()
(in
StockholmIterator
)
_draw_legend()
(in
DistributionPage
)
_uniform_norm()
(in
Bio.MarkovModel
)
__init__()
(in
StockholmWriter
)
_draw_scatter_plot()
(in
ComparativeScatterPlot
)
_unique_label()
(in
Bio.Nexus.Nexus
)
__init__()
(in
SeqRecord
)
_draw_segment()
(in
ChromosomeSegment
)
_unknown_nexus_block()
(in
Nexus
)
__init__()
(in
CodonAdaptationIndex
)
_draw_segment()
(in
TelomereSegment
)
_unmake_pickleable()
(in
BioSQLDB
)
__init__()
(in
IsoelectricPoint
)
_draw_subcomponents()
(in
ChromosomeSegment
)
_unmake_pickleable()
(in
CGIDB
)
__init__()
(in
MissingTable
)
_draw_title()
(in
Organism
)
_unmake_pickleable()
(in
DBObject
)
__init__()
(in
ProteinAnalysis
)
_draw_title()
(in
ComparativeScatterPlot
)
_Update
(in
Bio.Restriction
)
__init__()
(in
ACEFileRecord
)
_draw_title()
(in
BarChartDistribution
)
_use_hack
(in
Bio.Std
)
__init__()
(in
ACEParser
)
_draw_title()
(in
DistributionPage
)
_use_tag_format()
(in
Martel.Time
)
__init__()
(in
Contig
)
_drop()
(in
Ambiguous
)
_utree()
(in
Nexus
)
__init__()
(in
Iterator
)
_drop()
(in
Defined
)
_validate_attribute()
(in
ElementNode
)
__init__()
(in
Reads
)
_drop()
(in
NotDefined
)
_verify_attributes()
(in
ElementNode
)
__init__()
(in
RecordParser
)
_dssp_cys
(in
Bio.PDB.DSSP'
)
_verify_name()
(in
Martel.Expression
)
__init__()
(in
_RecordConsumer
)
_dump()
(in
Bio.Parsers.spark
)
_verify_subtypes()
(in
Bio.Decode
)
__init__()
(in
af
)
_effector()
(in
Record
)
_verify_test()
(in
Bio.Prosite.Pattern
)
__init__()
(in
bs
)
_eliminate()
(in
Nexus
)
_version()
(in
MASTRecord
)
__init__()
(in
ct
)
_empty_str()
(in
ElementNode
)
_version()
(in
_MASTConsumer
)
__init__()
(in
ds
)
_empty_unistr()
(in
ElementNode
)
_version()
(in
_MEMEConsumer
)
__init__()
(in
qa
)
_end_BlastOutput_db()
(in
BlastParser
)
_version_line()
(in
Record
)
__init__()
(in
rd
)
_end_BlastOutput_hits()
(in
BlastParser
)
_viterbi()
(in
Bio.MarkovModel
)
__init__()
(in
rt
)
_end_BlastOutput_program()
(in
BlastParser
)
_wait()
(in
ThinClient
)
__init__()
(in
wa
)
_end_BlastOutput_query_def()
(in
BlastParser
)
_walk()
(in
Tree
)
__init__()
(in
wr
)
_end_BlastOutput_query_ID()
(in
BlastParser
)
_warn()
(in
Bio.config.SeqDBRegistry
)
__init__()
(in
Iterator
)
_end_BlastOutput_query_len()
(in
BlastParser
)
_weight_list()
(in
ProteinAnalysis
)
__init__()
(in
Record
)
_end_BlastOutput_reference()
(in
BlastParser
)
_wrap_kegg()
(in
Bio.KEGG
)
__init__()
(in
RecordParser
)
_end_BlastOutput_version()
(in
BlastParser
)
_wrapped_genbank()
(in
Bio.GenBank.Record
)
__init__()
(in
_RecordConsumer
)
_end_Hit()
(in
BlastParser
)
_write_kegg()
(in
Bio.KEGG
)
__init__()
(in
StdTerm
)
_end_Hit_accession()
(in
BlastParser
)
_write_primary_table()
(in
Bio.Mindy.FlatDB
)
__init__()
(in
ConvertDispatchHandler
)
_end_Hit_def()
(in
BlastParser
)
_write_record()
(in
StockholmWriter
)
__init__()
(in
ConvertHandler
)
_end_Hit_id()
(in
BlastParser
)
_write_secondary_table()
(in
Bio.Mindy.FlatDB
)
__init__()
(in
Feature
)
_end_Hit_len()
(in
BlastParser
)
_write_text()
(in
POMDocument
)
__init__()
(in
Handle_dbxref
)
_end_Hsp_align_len()
(in
BlastParser
)
_XMLparser
(in
Bio.Blast.NCBIXML
)
__init__()
(in
Handle_feature_location
)
_end_Hsp_bit_score()
(in
BlastParser
)
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