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Identifier Index
__add__ Method in class Bio.Crystal.Chain
__add__ Method in class Bio.Seq.MutableSeq
__add__ Method in class Bio.Seq.Seq
__add__ Method in class Martel.Expression.Expression
__add__ Method in class Martel.Expression.NullOp
__add__ Method in class Martel.Expression.Seq
__add__ Method in class __builtin__.list
__add__ Method in class __builtin__.str
__and__ Method in class Bio.EUtils.Datatypes.Expression
object Class in module __builtin__
__bases__ Variable in class __builtin__.type
__basicsize__ Variable in class __builtin__.type
__call__ Method in class Bio.Affy.CelFile.CelParser
__call__ Method in class Bio.Decode.FunctionCall
__call__ Method in class Bio.Decode.FunctionCallChain
__call__ Method in class Bio.EUtils.parse.GetObject
__call__ Method in class Bio.config._support.make_rate_limited_function
__call__ Method in class Bio.config._support.make_timed_function
__call__ Method in class Bio.pairwise2.affine_penalty
__call__ Method in class Bio.pairwise2.dictionary_match
__call__ Method in class Bio.pairwise2.identity_match
__call__ Method in class Martel.Dispatch.MulticallEnd
__call__ Method in class Martel.Dispatch.MulticallStart
__call__ Method in class Martel.Dispatch.RemapEnd
__call__ Method in class Martel.Dispatch.RemapStart
__call__ Method in class Martel.Generate.CheckAssert
__call__ Method in class Martel.Generate.CheckAssertNot
__call__ Method in class Martel.Generate.CheckGroupRef
__call__ Method in class Martel.Generate.SetGroupValue
__call__ Method in class Martel.Generate._call_call
__call__ Method in class Martel.Generate._call_calltag
__call__ Method in class Martel.Generate.print_debug
__call__ Method in class Martel.Generate.print_info
__call__ Method in class __builtin__.type
type Class in module __builtin__
__cmp__ Method in class Bio.Alphabet.HasStopCodon
__cmp__ Method in class Bio.Decode.Token
__cmp__ Method in class Bio.Decode.ValueToken
__cmp__ Method in class Bio.GA.Organism.Organism
__cmp__ Method in class Bio.Seq.MutableSeq
__cmp__ Method in class Bio.SeqFeature.AbstractPosition
__cmp__ Method in class __builtin__.dict
__cmp__ Method in class __builtin__.type
__contains__ Method in class Bio.Crystal.Chain
__contains__ Method in class Bio.EUtils.MultiDict._BaseMultiDict
__contains__ Method in class Bio.Pathway.Rep.HashSet.HashSet
__contains__ Method in class Martel.LAX._IsIn
__contains__ Method in class __builtin__.dict
__contains__ Method in class __builtin__.list
__contains__ Method in class __builtin__.str
__contains__ Method in class xml.sax.xmlreader.AttributesImpl
__del__ Method in class Bio.Index._InMemoryIndex
__del__ Method in class Bio.Index._ShelveIndex
__del__ Method in class Bio.Mindy.FlatDB.MemoryFlatDB
__del__ Method in class Bio.MultiProc.Task.Task
__del__ Method in class Bio.MultiProc.copen._ProcHandle
__del_annotations Method in class BioSQL.BioSeq.DBSeqRecord
__del_dbxrefs Method in class BioSQL.BioSeq.DBSeqRecord
__del_features Method in class BioSQL.BioSeq.DBSeqRecord
__del_seq Method in class BioSQL.BioSeq.DBSeqRecord
__delattr__ Method in class Bio.EUtils.POM.ElementNode
__delattr__ Method in class __builtin__.object
__delattr__ Method in class __builtin__.type
__delattr__ Method in class exceptions.BaseException
__delitem__ Method in class Bio.Crystal.Chain
__delitem__ Method in class Bio.Crystal.Crystal
__delitem__ Method in class Bio.EUtils.MultiDict.OrderedMultiDict
__delitem__ Method in class Bio.EUtils.MultiDict.UnorderedMultiDict
__delitem__ Method in class Bio.EUtils.POM.ElementNode
__delitem__ Method in class Bio.Index._InMemoryIndex
__delitem__ Method in class Bio.Seq.MutableSeq
__delitem__ Method in class Martel.msre_parse.SubPattern
__delitem__ Method in class __builtin__.dict
__delitem__ Method in class __builtin__.list
__delslice__ Method in class Bio.Crystal.Chain
__delslice__ Method in class Bio.Seq.MutableSeq
__delslice__ Method in class __builtin__.list
__dictoffset__ Variable in class __builtin__.type
__eq__ Method in class Bio.Crystal.Chain
__eq__ Method in class Bio.Crystal.Hetero
__eq__ Method in class Bio.EUtils.Datatypes.CheckLinkSet
__eq__ Method in class Bio.EUtils.Datatypes.DBIds
__eq__ Method in class Bio.EUtils.Datatypes.Date
__eq__ Method in class Bio.EUtils.Datatypes.IdCheck
__eq__ Method in class Bio.EUtils.Datatypes.IdUrlSet
__eq__ Method in class Bio.EUtils.Datatypes.Link
__eq__ Method in class Bio.EUtils.Datatypes.LinkSetDb
__eq__ Method in class Bio.EUtils.Datatypes.LinksLinkSet
__eq__ Method in class Bio.EUtils.Datatypes.NeighborLinkSet
__eq__ Method in class Bio.EUtils.Datatypes.ObjUrl
__eq__ Method in class Bio.EUtils.Datatypes.Problem
__eq__ Method in class Bio.EUtils.Datatypes.Provider
__eq__ Method in class Bio.EUtils.MultiDict.OrderedMultiDict
__eq__ Method in class Bio.EUtils.MultiDict.UnorderedMultiDict
__eq__ Method in class Bio.Pathway.Reaction
__eq__ Method in class Bio.Pathway.Rep.Graph.Graph
__eq__ Method in class Bio.Pathway.Rep.HashSet.HashSet
__eq__ Method in class Bio.Pathway.Rep.MultiGraph.MultiGraph
__eq__ Method in class __builtin__.dict
__eq__ Method in class __builtin__.list
__eq__ Method in class __builtin__.str
__flags__ Variable in class __builtin__.type
__ge__ Method in class __builtin__.dict
__ge__ Method in class __builtin__.list
__ge__ Method in class __builtin__.str
__get_annotations Method in class BioSQL.BioSeq.DBSeqRecord
__get_dbxrefs Method in class BioSQL.BioSeq.DBSeqRecord
__get_features Method in class BioSQL.BioSeq.DBSeqRecord
__get_seq Method in class BioSQL.BioSeq.DBSeqRecord
__getattr__ Method in class Bio.Alphabet.AlphabetEncoder
__getattr__ Method in class Bio.Data.CodonTable.AmbiguousCodonTable
__getattr__ Method in class Bio.EUtils.POM.ElementNode
__getattr__ Method in class Bio.File.SGMLHandle
__getattr__ Method in class Bio.File.UndoHandle
__getattr__ Method in class Bio.FilteredReader.FilteredReader
__getattr__ Method in class Bio.Gobase.Dictionary
__getattr__ Method in class Bio.Mindy.Location.Location
__getattr__ Method in class Bio.MultiProc.copen._PickleHandle
__getattr__ Method in class Bio.ParserSupport.AbstractConsumer
__getattr__ Method in class Bio.ParserSupport.SGMLStrippingConsumer
__getattr__ Method in class Bio.ParserSupport.TaggingConsumer
__getattr__ Method in class Bio.Prosite.Dictionary
__getattr__ Method in class Bio.Prosite.Pattern.Prosite
__getattr__ Method in class Bio.Prosite.Prodoc.Dictionary
__getattr__ Method in class Bio.Rebase.Dictionary
__getattr__ Method in class Bio.SGMLExtractor.SGMLExtractorHandle
__getattr__ Method in class Bio.Search._SeqLength
__getattr__ Method in class Bio.SeqFeature.FeatureLocation
__getattr__ Method in class Bio.SwissProt.SProt.Dictionary
__getattr__ Method in class Martel.LAX.LAX
__getattribute__ Method in class __builtin__.dict
__getattribute__ Method in class __builtin__.list
__getattribute__ Method in class __builtin__.object
__getattribute__ Method in class __builtin__.str
__getattribute__ Method in class __builtin__.type
__getattribute__ Method in class exceptions.BaseException
__getitem__ Method in class Bio.Align.AlignInfo.PSSM
__getitem__ Method in class Bio.Crystal.Chain
__getitem__ Method in class Bio.Crystal.Crystal
__getitem__ Method in class Bio.DBXRef.BioformatDBName
__getitem__ Method in class Bio.DBXRef.UnknownDBName
__getitem__ Method in class Bio.Data.CodonTable.AmbiguousForwardTable
__getitem__ Method in class Bio.EUtils.DBIdsClient.BaseDBIdsRecordSet
__getitem__ Method in class Bio.EUtils.Datatypes.DBIds
__getitem__ Method in class Bio.EUtils.HistoryClient.BaseHistoryRecordSet
__getitem__ Method in class Bio.EUtils.MultiDict._BaseMultiDict
__getitem__ Method in class Bio.EUtils.POM.ElementNode
__getitem__ Method in class Bio.FSSP.fssp_rec.fff_rec
__getitem__ Method in class Bio.FormatIO.FormatIOIterator
__getitem__ Method in class Bio.Gobase.Dictionary
__getitem__ Method in class Bio.Mindy.BaseDB.DictLookup
__getitem__ Method in class Bio.Mindy.BaseDB.OpenDB
__getitem__ Method in class Bio.Mindy.FlatDB.BisectFile
__getitem__ Method in class Bio.Mindy.FlatDB.DiskFlatDB
__getitem__ Method in class Bio.Mindy.FlatDB.MemoryFlatDB
__getitem__ Method in class Bio.Mindy.FlatDB.PrimaryNamespace
__getitem__ Method in class Bio.Mindy.FlatDB.PrimaryTable
__getitem__ Method in class Bio.Mindy.FlatDB.SecondaryNamespace
__getitem__ Method in class Bio.Mindy.FlatDB.SecondaryTable
__getitem__ Method in class Bio.PropertyManager.CreateDict
__getitem__ Method in class Bio.Prosite.Dictionary
__getitem__ Method in class Bio.Prosite.ExPASyDictionary
__getitem__ Method in class Bio.Prosite.Pattern.Prosite
__getitem__ Method in class Bio.Prosite.Pattern.PrositeMatch
__getitem__ Method in class Bio.Prosite.Prodoc.Dictionary
__getitem__ Method in class Bio.Prosite.Prodoc.ExPASyDictionary
__getitem__ Method in class Bio.PubMed.Dictionary
__getitem__ Method in class Bio.Rebase.Dictionary
__getitem__ Method in class Bio.Seq.MutableSeq
__getitem__ Method in class Bio.Seq.Seq
__getitem__ Method in class Bio.SwissProt.SProt.Dictionary
__getitem__ Method in class Bio.SwissProt.SProt.ExPASyDictionary
__getitem__ Method in class Bio.config.DBRegistry.DBGroup
__getitem__ Method in class Bio.config.DBRegistry.DBObject
__getitem__ Method in class Bio.config.Registry.Registry
__getitem__ Method in class Bio.config.SeqDBRegistry.SeqDBRegistry
__getitem__ Method in class BioSQL.BioSeq.DBSeq
__getitem__ Method in class BioSQL.BioSeqDatabase.BioSeqDatabase
__getitem__ Method in class BioSQL.BioSeqDatabase.DBServer
__getitem__ Method in class Martel.Iterator.Iterate
__getitem__ Method in class Martel.Parser.MartelAttributeList
__getitem__ Method in class Martel.msre_parse.SubPattern
__getitem__ Method in class Martel.test.support.Storage
__getitem__ Method in class __builtin__.dict
__getitem__ Method in class __builtin__.list
__getitem__ Method in class __builtin__.str
__getitem__ Method in class exceptions.BaseException
__getitem__ Method in class xml.sax._exceptions.SAXException
__getitem__ Method in class xml.sax.xmlreader.AttributesImpl
__getnewargs__ Method in class __builtin__.str
__getslice__ Method in class Bio.Crystal.Chain
__getslice__ Method in class Bio.FSSP.fssp_rec.fff_rec
__getslice__ Method in class Bio.Prosite.Pattern.Prosite
__getslice__ Method in class Bio.Prosite.Pattern.PrositeMatch
__getslice__ Method in class Bio.Seq.MutableSeq
__getslice__ Method in class Bio.Seq.Seq
__getslice__ Method in class BioSQL.BioSeq.DBSeq
__getslice__ Method in class Martel.msre_parse.SubPattern
__getslice__ Method in class __builtin__.list
__getslice__ Method in class __builtin__.str
__getslice__ Method in class exceptions.BaseException
__gt__ Method in class __builtin__.dict
__gt__ Method in class __builtin__.list
__gt__ Method in class __builtin__.str
__hash__ Method in class Bio.Pathway.Interaction
__hash__ Method in class Bio.Pathway.Reaction
__hash__ Method in class __builtin__.dict
__hash__ Method in class __builtin__.list
__hash__ Method in class __builtin__.object
__hash__ Method in class __builtin__.str
__hash__ Method in class __builtin__.type
__iadd__ Method in class Bio.Crystal.Chain
__iadd__ Method in class Martel.Parser.ParserIncompleteException
__iadd__ Method in class Martel.Parser.ParserPositionException
__iadd__ Method in class __builtin__.list
__imul__ Method in class __builtin__.list
__init_ Method in class Bio.Pathway.Interaction
__init__ Method in class Bio.Affy.CelFile.CelConsumer
__init__ Method in class Bio.Affy.CelFile.CelParser
__init__ Method in class Bio.Affy.CelFile.CelRecord
__init__ Method in class Bio.Ais.Immune
__init__ Method in class Bio.Ais.Lymphocyte
__init__ Method in class Bio.Align.AlignInfo.PSSM
__init__ Method in class Bio.Align.AlignInfo.SummaryInfo
__init__ Method in class Bio.Align.FormatConvert.FormatConverter
__init__ Method in class Bio.Align.Generic.Alignment
__init__ Method in class Bio.AlignAce.Applications.AlignAceCommandline
__init__ Method in class Bio.AlignAce.Applications.CompareAceCommandline
__init__ Method in class Bio.AlignAce.Motif.Motif
__init__ Method in class Bio.AlignAce.Parser.AlignAceConsumer
__init__ Method in class Bio.AlignAce.Parser.AlignAceParser
__init__ Method in class Bio.AlignAce.Parser.CompareAceConsumer
__init__ Method in class Bio.AlignAce.Parser.CompareAceParser
__init__ Method in class Bio.Alphabet.AlphabetEncoder
__init__ Method in class Bio.Alphabet.Gapped
__init__ Method in class Bio.Alphabet.HasStopCodon
__init__ Method in class Bio.Application.AbstractCommandline
__init__ Method in class Bio.Application.ApplicationResult
__init__ Method in class Bio.Application._AbstractParameter
__init__ Method in class Bio.Blast.Applications.BlastallCommandline
__init__ Method in class Bio.Blast.Applications.FastacmdCommandline
__init__ Method in class Bio.Blast.NCBIStandalone.BlastErrorParser
__init__ Method in class Bio.Blast.NCBIStandalone.BlastParser
__init__ Method in class Bio.Blast.NCBIStandalone.Iterator
__init__ Method in class Bio.Blast.NCBIStandalone.PSIBlastParser
__init__ Method in class Bio.Blast.NCBIStandalone._BlastConsumer
__init__ Method in class Bio.Blast.NCBIStandalone._BlastErrorConsumer
__init__ Method in class Bio.Blast.NCBIStandalone._PSIBlastConsumer
__init__ Method in class Bio.Blast.NCBIWWW.BlastParser
__init__ Method in class Bio.Blast.NCBIWWW._FormParser
__init__ Method in class Bio.Blast.NCBIXML.BlastParser
__init__ Method in class Bio.Blast.NCBIXML._XMLparser
__init__ Method in class Bio.Blast.ParseBlastTable.BlastTableEntry
__init__ Method in class Bio.Blast.ParseBlastTable.BlastTableReader
__init__ Method in class Bio.Blast.ParseBlastTable.BlastTableRec
__init__ Method in class Bio.Blast.Record.Alignment
__init__ Method in class Bio.Blast.Record.Blast
__init__ Method in class Bio.Blast.Record.DatabaseReport
__init__ Method in class Bio.Blast.Record.Description
__init__ Method in class Bio.Blast.Record.HSP
__init__ Method in class Bio.Blast.Record.Header
__init__ Method in class Bio.Blast.Record.MultipleAlignment
__init__ Method in class Bio.Blast.Record.PSIBlast
__init__ Method in class Bio.Blast.Record.Parameters
__init__ Method in class Bio.Blast.Record.Round
__init__ Method in class Bio.CAPS.CAPSMap
__init__ Method in class Bio.CAPS.DifferentialCutsite
__init__ Method in class Bio.Compass.Iterator
__init__ Method in class Bio.Compass.Record
__init__ Method in class Bio.Compass.RecordParser
__init__ Method in class Bio.Compass._Consumer
__init__ Method in class Bio.Crystal.Chain
__init__ Method in class Bio.Crystal.Crystal
__init__ Method in class Bio.Crystal.CrystalError
__init__ Method in class Bio.Crystal.Error
__init__ Method in class Bio.Crystal.Hetero
__init__ Method in class Bio.DBXRef.DBXRef
__init__ Method in class Bio.Data.CodonTable.AmbiguousCodonTable
__init__ Method in class Bio.Data.CodonTable.AmbiguousForwardTable
__init__ Method in class Bio.Data.CodonTable.CodonTable
__init__ Method in class Bio.Data.CodonTable.NCBICodonTable
__init__ Method in class Bio.Decode.DecodeParser
__init__ Method in class Bio.Decode.DecodeScanner
__init__ Method in class Bio.Decode.Float
__init__ Method in class Bio.Decode.Function
__init__ Method in class Bio.Decode.FunctionCall
__init__ Method in class Bio.Decode.FunctionCallChain
__init__ Method in class Bio.Decode.FunctionName
__init__ Method in class Bio.Decode.Integer
__init__ Method in class Bio.Decode.String
__init__ Method in class Bio.Decode.Token
__init__ Method in class Bio.Decode.ValueToken
__init__ Method in class Bio.EUtils.Config.DatabaseInfo
__init__ Method in class Bio.EUtils.DBIdsClient.BaseDBIdsRecordSet
__init__ Method in class Bio.EUtils.DBIdsClient.DBIdsClient
__init__ Method in class Bio.EUtils.DBIdsClient.DBIdsLookup
__init__ Method in class Bio.EUtils.Datatypes.BinaryOp
__init__ Method in class Bio.EUtils.Datatypes.CheckLinkSet
__init__ Method in class Bio.EUtils.Datatypes.DBIds
__init__ Method in class Bio.EUtils.Datatypes.Date
__init__ Method in class Bio.EUtils.Datatypes.DateRange
__init__ Method in class Bio.EUtils.Datatypes.EUtilsSearchError
__init__ Method in class Bio.EUtils.Datatypes.IdCheck
__init__ Method in class Bio.EUtils.Datatypes.IdUrlSet
__init__ Method in class Bio.EUtils.Datatypes.Link
__init__ Method in class Bio.EUtils.Datatypes.LinkSetDb
__init__ Method in class Bio.EUtils.Datatypes.LinksLinkSet
__init__ Method in class Bio.EUtils.Datatypes.NeighborLinkSet
__init__ Method in class Bio.EUtils.Datatypes.ObjUrl
__init__ Method in class Bio.EUtils.Datatypes.PostResult
__init__ Method in class Bio.EUtils.Datatypes.Problem
__init__ Method in class Bio.EUtils.Datatypes.Provider
__init__ Method in class Bio.EUtils.Datatypes.Range
__init__ Method in class Bio.EUtils.Datatypes.SearchResult
__init__ Method in class Bio.EUtils.Datatypes.Summary
__init__ Method in class Bio.EUtils.Datatypes.Term
__init__ Method in class Bio.EUtils.Datatypes.WithinNDays
__init__ Method in class Bio.EUtils.HistoryClient.BaseHistoryRecordSet
__init__ Method in class Bio.EUtils.HistoryClient.HistoryClient
__init__ Method in class Bio.EUtils.HistoryClient.HistoryCookie
__init__ Method in class Bio.EUtils.HistoryClient.HistoryLookup
__init__ Method in class Bio.EUtils.HistoryClient.HistoryRecord
__init__ Method in class Bio.EUtils.MultiDict.OrderedMultiDict
__init__ Method in class Bio.EUtils.MultiDict.UnorderedMultiDict
__init__ Method in class Bio.EUtils.POM.Comment
__init__ Method in class Bio.EUtils.POM.ContentModel
__init__ Method in class Bio.EUtils.POM.DTDConsumerForSourceGeneration
__init__ Method in class Bio.EUtils.POM.ElementNode
__init__ Method in class Bio.EUtils.POM.IndentedText
__init__ Method in class Bio.EUtils.POM.ObjectParserHandler
__init__ Method in class Bio.EUtils.POM.POMDocument
__init__ Method in class Bio.EUtils.POM.XMLAttribute
__init__ Method in class Bio.EUtils.POM._ContentModelGenerator
__init__ Method in class Bio.EUtils.ReseekFile.ReseekFile
__init__ Method in class Bio.EUtils.ThinClient.ThinClient
__init__ Method in class Bio.EUtils.parse.UsePOMParser
__init__ Method in class Bio.EUtils.sourcegen.ClassHolder
__init__ Method in class Bio.EUtils.sourcegen.FunctionHolder
__init__ Method in class Bio.EUtils.sourcegen.MethodHolder
__init__ Method in class Bio.EUtils.sourcegen.SourceFile
__init__ Method in class Bio.EUtils.sourcegen.SourceGen
__init__ Method in class Bio.Emboss.Applications.EConsenseCommandline
__init__ Method in class Bio.Emboss.Applications.EInvertedCommandline
__init__ Method in class Bio.Emboss.Applications.ENeighborCommandline
__init__ Method in class Bio.Emboss.Applications.EProtDistCommandline
__init__ Method in class Bio.Emboss.Applications.EProtParsCommandline
__init__ Method in class Bio.Emboss.Applications.ESeqBootCommandline
__init__ Method in class Bio.Emboss.Applications.ETandemCommandline
__init__ Method in class Bio.Emboss.Applications.Est2GenomeCommandline
__init__ Method in class Bio.Emboss.Applications.FuzznucCommandline
__init__ Method in class Bio.Emboss.Applications.PalindromeCommandline
__init__ Method in class Bio.Emboss.Applications.Primer3Commandline
__init__ Method in class Bio.Emboss.Applications.PrimerSearchCommandline
__init__ Method in class Bio.Emboss.Applications.TranalignCommandline
__init__ Method in class Bio.Emboss.Applications.WaterCommandline
__init__ Method in class Bio.Emboss.Primer.Primer3Parser
__init__ Method in class Bio.Emboss.Primer.Primer3Primers
__init__ Method in class Bio.Emboss.Primer.Primer3Record
__init__ Method in class Bio.Emboss.Primer.PrimerSearchAmplifier
__init__ Method in class Bio.Emboss.Primer.PrimerSearchInputRecord
__init__ Method in class Bio.Emboss.Primer.PrimerSearchOutputRecord
__init__ Method in class Bio.Emboss.Primer.PrimerSearchParser
__init__ Method in class Bio.Emboss.Primer._Primer3RecordConsumer
__init__ Method in class Bio.Emboss.Primer._Primer3Scanner
__init__ Method in class Bio.Emboss.Primer._PrimerSearchRecordConsumer
__init__ Method in class Bio.Emboss.Primer._PrimerSearchScanner
__init__ Method in class Bio.Enzyme.DataRecord
__init__ Method in class Bio.Enzyme.EnzymeRecord
__init__ Method in class Bio.Enzyme.Iterator
__init__ Method in class Bio.Enzyme.RecordParser
__init__ Method in class Bio.Enzyme._RecordConsumer
__init__ Method in class Bio.FSSP.FSSPAlignDict
__init__ Method in class Bio.FSSP.FSSPAlignRec
__init__ Method in class Bio.FSSP.FSSPHeader
__init__ Method in class Bio.FSSP.FSSPSumRec
__init__ Method in class Bio.FSSP.FSSPTools.FSSPMultAlign
__init__ Method in class Bio.FSSP.PosAlign
__init__ Method in class Bio.FSSP.fssp_rec.fff_rec
__init__ Method in class Bio.File.MyParser
__init__ Method in class Bio.File.SGMLHandle
__init__ Method in class Bio.File.SGMLStripper
__init__ Method in class Bio.File.UndoHandle
__init__ Method in class Bio.FilteredReader.FilteredReader
__init__ Method in class Bio.FormatIO.FormatIO
__init__ Method in class Bio.FormatIO.FormatIOIterator
__init__ Method in class Bio.GA.Crossover.General.SafeFitnessCrossover
__init__ Method in class Bio.GA.Crossover.GeneralPoint.GeneralPointCrossover
__init__ Method in class Bio.GA.Crossover.GeneralPoint.InterleaveCrossover
__init__ Method in class Bio.GA.Crossover.Point.SinglePointCrossover
__init__ Method in class Bio.GA.Crossover.TwoPoint.TwoPointCrossover
__init__ Method in class Bio.GA.Crossover.Uniform.UniformCrossover
__init__ Method in class Bio.GA.Evolver.GenerationEvolver
__init__ Method in class Bio.GA.Evolver.SteadyStateEvolver
__init__ Method in class Bio.GA.Mutation.General.SafeFitnessMutation
__init__ Method in class Bio.GA.Mutation.Simple.ConversionMutation
__init__ Method in class Bio.GA.Mutation.Simple.SinglePositionMutation
__init__ Method in class Bio.GA.Organism.Organism
__init__ Method in class Bio.GA.Repair.Stabilizing.AmbiguousRepair
__init__ Method in class Bio.GA.Selection.Abstract.AbstractSelection
__init__ Method in class Bio.GA.Selection.Diversity.DiversitySelection
__init__ Method in class Bio.GA.Selection.RouletteWheel.RouletteWheelSelection
__init__ Method in class Bio.GA.Selection.Tournament.TournamentSelection
__init__ Method in class Bio.Gobase.Dictionary
__init__ Method in class Bio.Gobase.GeneRecord
__init__ Method in class Bio.Gobase.Iterator
__init__ Method in class Bio.Gobase.ProteinRecord
__init__ Method in class Bio.Gobase.Record
__init__ Method in class Bio.Gobase.RecordParser
__init__ Method in class Bio.Gobase.SequenceRecord
__init__ Method in class Bio.Gobase._RecordConsumer
__init__ Method in class Bio.Graphics.BasicChromosome.Chromosome
__init__ Method in class Bio.Graphics.BasicChromosome.ChromosomeSegment
__init__ Method in class Bio.Graphics.BasicChromosome.Organism
__init__ Method in class Bio.Graphics.BasicChromosome.TelomereSegment
__init__ Method in class Bio.Graphics.BasicChromosome._ChromosomeComponent
__init__ Method in class Bio.Graphics.Comparative.ComparativeScatterPlot
__init__ Method in class Bio.Graphics.DisplayRepresentation.ChromosomeCounts
__init__ Method in class Bio.Graphics.Distribution.BarChartDistribution
__init__ Method in class Bio.Graphics.Distribution.DistributionPage
__init__ Method in class Bio.Graphics.Distribution.LineDistribution
__init__ Method in class Bio.HMM.DynamicProgramming.AbstractDPAlgorithms
__init__ Method in class Bio.HMM.DynamicProgramming.LogDPAlgorithms
__init__ Method in class Bio.HMM.DynamicProgramming.ScaledDPAlgorithms
__init__ Method in class Bio.HMM.MarkovModel.HiddenMarkovModel
__init__ Method in class Bio.HMM.MarkovModel.MarkovModelBuilder
__init__ Method in class Bio.HMM.Trainer.AbstractTrainer
__init__ Method in class Bio.HMM.Trainer.BaumWelchTrainer
__init__ Method in class Bio.HMM.Trainer.KnownStateTrainer
__init__ Method in class Bio.HMM.Trainer.TrainingSequence
__init__ Method in class Bio.HotRand.HotCache
__init__ Method in class Bio.HotRand.HotRandom
__init__ Method in class Bio.Index._InMemoryIndex
__init__ Method in class Bio.Index._ShelveIndex
__init__ Method in class Bio.LogisticRegression.LogisticRegression
__init__ Method in class Bio.MEME.Motif.Instance
__init__ Method in class Bio.MEME.Motif.MEMEMotif
__init__ Method in class Bio.MEME.Motif.Motif
__init__ Method in class Bio.MEME.Parser.MASTParser
__init__ Method in class Bio.MEME.Parser.MASTRecord
__init__ Method in class Bio.MEME.Parser.MEMEParser
__init__ Method in class Bio.MEME.Parser.MEMERecord
__init__ Method in class Bio.MEME.Parser._MASTConsumer
__init__ Method in class Bio.MEME.Parser._MEMEConsumer
__init__ Method in class Bio.MarkovModel.MarkovModel
__init__ Method in class Bio.MarkupEditor.MarkupEditor
__init__ Method in class Bio.MarkupEditor.MidPoint
__init__ Method in class Bio.MaxEntropy.MaxEntropy
__init__ Method in class Bio.Medline.Iterator
__init__ Method in class Bio.Medline.NLMMedlineXML.CitationParser
__init__ Method in class Bio.Medline.NLMMedlineXML._IndexerHandler
__init__ Method in class Bio.Medline.NLMMedlineXML._SavedDataHandle
__init__ Method in class Bio.Medline.Record
__init__ Method in class Bio.Medline.RecordParser
__init__ Method in class Bio.Medline._RecordConsumer
__init__ Method in class Bio.Mindy.BaseDB.OpenDB
__init__ Method in class Bio.Mindy.FlatDB.BaseFlatDB
__init__ Method in class Bio.Mindy.FlatDB.BisectFile
__init__ Method in class Bio.Mindy.FlatDB.DiskFlatDB
__init__ Method in class Bio.Mindy.FlatDB.MemoryFlatDB
__init__ Method in class Bio.Mindy.FlatDB.PrimaryNamespace
__init__ Method in class Bio.Mindy.FlatDB.PrimaryTable
__init__ Method in class Bio.Mindy.FlatDB.SecondaryNamespace
__init__ Method in class Bio.Mindy.FlatDB.SecondaryTable
__init__ Method in class Bio.Mindy.Location.Location
__init__ Method in class Bio.Mindy.SimpleSeqRecord.BaseSeqRecordIndexer
__init__ Method in class Bio.Mindy.SimpleSeqRecord.FixDocumentBuilder
__init__ Method in class Bio.Mindy.SimpleSeqRecord.FunctionIndexer
__init__ Method in class Bio.Mindy.SimpleSeqRecord.SimpleIndexer
__init__ Method in class Bio.Mindy.XPath.GrabXPathNodes
__init__ Method in class Bio.MultiProc.Scheduler.Scheduler
__init__ Method in class Bio.MultiProc.Task.Task
__init__ Method in class Bio.MultiProc.copen._PickleHandle
__init__ Method in class Bio.MultiProc.copen._ProcHandle
__init__ Method in class Bio.NMR.xpktools.Peaklist
__init__ Method in class Bio.NMR.xpktools.XpkEntry
__init__ Method in class Bio.NaiveBayes.NaiveBayes
__init__ Method in class Bio.Ndb.Record
__init__ Method in class Bio.NetCatch.ExtractUrls
__init__ Method in class Bio.NetCatch.NetCatch
__init__ Method in class Bio.NetCatch.Url
__init__ Method in class Bio.NeuralNetwork.BackPropagation.Layer.AbstractLayer
__init__ Method in class Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer
__init__ Method in class Bio.NeuralNetwork.BackPropagation.Layer.InputLayer
__init__ Method in class Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer
__init__ Method in class Bio.NeuralNetwork.BackPropagation.Network.BasicNetwork
__init__ Method in class Bio.NeuralNetwork.Gene.Motif.MotifCoder
__init__ Method in class Bio.NeuralNetwork.Gene.Motif.MotifFinder
__init__ Method in class Bio.NeuralNetwork.Gene.Pattern.PatternIO
__init__ Method in class Bio.NeuralNetwork.Gene.Pattern.PatternRepository
__init__ Method in class Bio.NeuralNetwork.Gene.Schema.DifferentialSchemaFitness
__init__ Method in class Bio.NeuralNetwork.Gene.Schema.GeneticAlgorithmFinder
__init__ Method in class Bio.NeuralNetwork.Gene.Schema.MostCountSchemaFitness
__init__ Method in class Bio.NeuralNetwork.Gene.Schema.RandomMotifGenerator
__init__ Method in class Bio.NeuralNetwork.Gene.Schema.Schema
__init__ Method in class Bio.NeuralNetwork.Gene.Schema.SchemaCoder
__init__ Method in class Bio.NeuralNetwork.Gene.Schema.SchemaFactory
__init__ Method in class Bio.NeuralNetwork.Gene.Schema.SchemaFinder
__init__ Method in class Bio.NeuralNetwork.Gene.Schema.SimpleFinisher
__init__ Method in class Bio.NeuralNetwork.Gene.Signature.SignatureCoder
__init__ Method in class Bio.NeuralNetwork.Gene.Signature.SignatureFinder
__init__ Method in class Bio.NeuralNetwork.StopTraining.ValidationIncreaseStop
__init__ Method in class Bio.NeuralNetwork.Training.ExampleManager
__init__ Method in class Bio.NeuralNetwork.Training.TrainingExample
__init__ Method in class Bio.Nexus.Nexus.Block
__init__ Method in class Bio.Nexus.Nexus.CharBuffer
__init__ Method in class Bio.Nexus.Nexus.Commandline
__init__ Method in class Bio.Nexus.Nexus.Nexus
__init__ Method in class Bio.Nexus.Nexus.StepMatrix
__init__ Method in class Bio.Nexus.Nodes.Chain
__init__ Method in class Bio.Nexus.Nodes.Node
__init__ Method in class Bio.Nexus.Trees.NodeData
__init__ Method in class Bio.Nexus.Trees.Tree
__init__ Method in class Bio.ParserSupport.EventGenerator
__init__ Method in class Bio.ParserSupport.SGMLStrippingConsumer
__init__ Method in class Bio.ParserSupport.TaggingConsumer
__init__ Method in class Bio.Parsers.spark.GenericASTBuilder
__init__ Method in class Bio.Parsers.spark.GenericASTMatcher
__init__ Method in class Bio.Parsers.spark.GenericASTTraversal
__init__ Method in class Bio.Parsers.spark.GenericParser
__init__ Method in class Bio.Parsers.spark.GenericScanner
__init__ Method in class Bio.Pathway.Network
__init__ Method in class Bio.Pathway.Reaction
__init__ Method in class Bio.Pathway.Rep.Graph.Graph
__init__ Method in class Bio.Pathway.Rep.HashSet.HashSet
__init__ Method in class Bio.Pathway.Rep.MultiGraph.MultiGraph
__init__ Method in class Bio.Pathway.System
__init__ Method in class Bio.PropertyManager.PropertyManager
__init__ Method in class Bio.Prosite.Dictionary
__init__ Method in class Bio.Prosite.ExPASyDictionary
__init__ Method in class Bio.Prosite.Iterator
__init__ Method in class Bio.Prosite.Pattern.Prosite
__init__ Method in class Bio.Prosite.Pattern.PrositeMatch
__init__ Method in class Bio.Prosite.Pattern.PrositeTerm
__init__ Method in class Bio.Prosite.PatternHit
__init__ Method in class Bio.Prosite.Prodoc.Dictionary
__init__ Method in class Bio.Prosite.Prodoc.ExPASyDictionary
__init__ Method in class Bio.Prosite.Prodoc.Iterator
__init__ Method in class Bio.Prosite.Prodoc.Record
__init__ Method in class Bio.Prosite.Prodoc.RecordParser
__init__ Method in class Bio.Prosite.Prodoc.Reference
__init__ Method in class Bio.Prosite.Prodoc._RecordConsumer
__init__ Method in class Bio.Prosite.Record
__init__ Method in class Bio.Prosite.RecordParser
__init__ Method in class Bio.Prosite._RecordConsumer
__init__ Method in class Bio.PubMed.Dictionary
__init__ Method in class Bio.Rebase.Dictionary
__init__ Method in class Bio.Rebase.Iterator
__init__ Method in class Bio.Rebase.Record
__init__ Method in class Bio.Rebase.RecordParser
__init__ Method in class Bio.Rebase._RecordConsumer
__init__ Method in class Bio.SGMLExtractor.LocalParser
__init__ Method in class Bio.SGMLExtractor.SGMLExtractor
__init__ Method in class Bio.SGMLExtractor.SGMLExtractorHandle
__init__ Method in class Bio.SVDSuperimposer.SVDSuperimposer.SVDSuperimposer
__init__ Method in class Bio.Search.Algorithm
__init__ Method in class Bio.Search.Database
__init__ Method in class Bio.Search.HSP
__init__ Method in class Bio.Search.HSPSeq
__init__ Method in class Bio.Search.Hit
__init__ Method in class Bio.Search.HomologySeq
__init__ Method in class Bio.Search.Query
__init__ Method in class Bio.Search.Search
__init__ Method in class Bio.Search.TableInfo
__init__ Method in class Bio.Search._SeqLength
__init__ Method in class Bio.Seq.MutableSeq
__init__ Method in class Bio.Seq.Seq
__init__ Method in class Bio.SeqFeature.AbstractPosition
__init__ Method in class Bio.SeqFeature.AfterPosition
__init__ Method in class Bio.SeqFeature.BeforePosition
__init__ Method in class Bio.SeqFeature.BetweenPosition
__init__ Method in class Bio.SeqFeature.ExactPosition
__init__ Method in class Bio.SeqFeature.FeatureLocation
__init__ Method in class Bio.SeqFeature.OneOfPosition
__init__ Method in class Bio.SeqFeature.PositionGap
__init__ Method in class Bio.SeqFeature.Reference
__init__ Method in class Bio.SeqFeature.SeqFeature
__init__ Method in class Bio.SeqFeature.WithinPosition
__init__ Method in class Bio.SeqRecord.SeqRecord
__init__ Method in class Bio.Sequencing.Ace.ACEFileRecord
__init__ Method in class Bio.Sequencing.Ace.ACEParser
__init__ Method in class Bio.Sequencing.Ace.Contig
__init__ Method in class Bio.Sequencing.Ace.Iterator
__init__ Method in class Bio.Sequencing.Ace.Reads
__init__ Method in class Bio.Sequencing.Ace.RecordParser
__init__ Method in class Bio.Sequencing.Ace._RecordConsumer
__init__ Method in class Bio.Sequencing.Ace.af
__init__ Method in class Bio.Sequencing.Ace.bs
__init__ Method in class Bio.Sequencing.Ace.ct
__init__ Method in class Bio.Sequencing.Ace.ds
__init__ Method in class Bio.Sequencing.Ace.qa
__init__ Method in class Bio.Sequencing.Ace.rd
__init__ Method in class Bio.Sequencing.Ace.rt
__init__ Method in class Bio.Sequencing.Ace.wa
__init__ Method in class Bio.Sequencing.Ace.wr
__init__ Method in class Bio.Sequencing.Phd.Iterator
__init__ Method in class Bio.Sequencing.Phd.Record
__init__ Method in class Bio.Sequencing.Phd.RecordParser
__init__ Method in class Bio.Sequencing.Phd._RecordConsumer
__init__ Method in class Bio.StdHandler.ConvertDispatchHandler
__init__ Method in class Bio.StdHandler.ConvertHandler
__init__ Method in class Bio.StdHandler.Feature
__init__ Method in class Bio.StdHandler.Handle_dbxref
__init__ Method in class Bio.StdHandler.Handle_feature_location
__init__ Method in class Bio.StdHandler.Handle_feature_qualifier
__init__ Method in class Bio.StdHandler.Handle_features
__init__ Method in class Bio.StdHandler.Handle_hsp
__init__ Method in class Bio.StdHandler.RecognizeHandler
__init__ Method in class Bio.SubsMat.FreqTable.FreqTable
__init__ Method in class Bio.SubsMat.SeqMat
__init__ Method in class Bio.SwissProt.KeyWList.ListParser
__init__ Method in class Bio.SwissProt.KeyWList._ListConsumer
__init__ Method in class Bio.SwissProt.SProt.Dictionary
__init__ Method in class Bio.SwissProt.SProt.ExPASyDictionary
__init__ Method in class Bio.SwissProt.SProt.Iterator
__init__ Method in class Bio.SwissProt.SProt.Record
__init__ Method in class Bio.SwissProt.SProt.RecordParser
__init__ Method in class Bio.SwissProt.SProt.Reference
__init__ Method in class Bio.SwissProt.SProt.SequenceParser
__init__ Method in class Bio.SwissProt.SProt._RecordConsumer
__init__ Method in class Bio.SwissProt.SProt._SequenceConsumer
__init__ Method in class Bio.Transcribe.Transcribe
__init__ Method in class Bio.Translate.Translator
__init__ Method in class Bio.UniGene.Iterator
__init__ Method in class Bio.UniGene.RecordParser
__init__ Method in class Bio.UniGene.UnigeneProtsimRecord
__init__ Method in class Bio.UniGene.UnigeneRecord
__init__ Method in class Bio.UniGene.UnigeneSTSRecord
__init__ Method in class Bio.UniGene.UnigeneSequenceRecord
__init__ Method in class Bio.UniGene._RecordConsumer
__init__ Method in class Bio.WWW.RequestLimiter
__init__ Method in class Bio.Writer.Writer
__init__ Method in class Bio.builders.Search.search.BuildSearch
__init__ Method in class Bio.builders.SeqRecord.sequence.BuildSeqRecord
__init__ Method in class Bio.config.DBRegistry.BioCorbaDB
__init__ Method in class Bio.config.DBRegistry.BioSQLDB
__init__ Method in class Bio.config.DBRegistry.CGIDB
__init__ Method in class Bio.config.DBRegistry.DBGroup
__init__ Method in class Bio.config.DBRegistry.DBObject
__init__ Method in class Bio.config.DBRegistry.DBRegistry
__init__ Method in class Bio.config.DBRegistry.EUtilsDB
__init__ Method in class Bio.config.DBRegistry.IndexedFileDB
__init__ Method in class Bio.config.FormatRegistry.FormatGroup
__init__ Method in class Bio.config.FormatRegistry.FormatObject
__init__ Method in class Bio.config.FormatRegistry.FormatRegistry
__init__ Method in class Bio.config.Registry.RegisterableGroup
__init__ Method in class Bio.config.Registry.RegisterableObject
__init__ Method in class Bio.config.Registry.Registry
__init__ Method in class Bio.config.SeqDBRegistry.SeqDBRegistry
__init__ Method in class Bio.config._stanzaformat.Stanza
__init__ Method in class Bio.config._stanzaformat.StanzaFormat
__init__ Method in class Bio.config._support.make_cached_expression
__init__ Method in class Bio.config._support.make_rate_limited_function
__init__ Method in class Bio.config._support.make_timed_function
__init__ Method in class Bio.kNN.kNN
__init__ Method in class Bio.pairwise2.affine_penalty
__init__ Method in class Bio.pairwise2.dictionary_match
__init__ Method in class Bio.pairwise2.identity_match
__init__ Method in class Bio.writers.SeqRecord.embl.WriteEmbl
__init__ Method in class Bio.writers.SeqRecord.fasta.WriteFasta
__init__ Method in class BioSQL.BioSeq.DBSeq
__init__ Method in class BioSQL.BioSeq.DBSeqRecord
__init__ Method in class BioSQL.BioSeqDatabase.Adaptor
__init__ Method in class BioSQL.BioSeqDatabase.BioSeqDatabase
__init__ Method in class BioSQL.BioSeqDatabase.DBServer
__init__ Method in class BioSQL.DBUtils.Generic_dbutils
__init__ Method in class BioSQL.Loader.DatabaseLoader
__init__ Method in class BioSQL.Loader.DatabaseRemover
__init__ Method in class Martel.Dispatch.Callback
__init__ Method in class Martel.Dispatch.DispatchHandler
__init__ Method in class Martel.Dispatch.Dispatcher
__init__ Method in class Martel.Dispatch.Multicall
__init__ Method in class Martel.Dispatch.RemapEnd
__init__ Method in class Martel.Dispatch.RemapStart
__init__ Method in class Martel.Expression.Alt
__init__ Method in class Martel.Expression.Any
__init__ Method in class Martel.Expression.Assert
__init__ Method in class Martel.Expression.Debug
__init__ Method in class Martel.Expression.FastFeature
__init__ Method in class Martel.Expression.Group
__init__ Method in class Martel.Expression.GroupRef
__init__ Method in class Martel.Expression.HeaderFooter
__init__ Method in class Martel.Expression.Literal
__init__ Method in class Martel.Expression.MaxRepeat
__init__ Method in class Martel.Expression.NullOp
__init__ Method in class Martel.Expression.ParseRecords
__init__ Method in class Martel.Expression.PassThrough
__init__ Method in class Martel.Expression.Seq
__init__ Method in class Martel.Expression.Str
__init__ Method in class Martel.Generate.CheckAssert
__init__ Method in class Martel.Generate.CheckAssertNot
__init__ Method in class Martel.Generate.CheckGroupRef
__init__ Method in class Martel.Generate.GeneratorState
__init__ Method in class Martel.Generate.HandleRepeatCount
__init__ Method in class Martel.Generate.SetGroupValue
__init__ Method in class Martel.Generate._call_call
__init__ Method in class Martel.Generate._call_calltag
__init__ Method in class Martel.Generate.print_debug
__init__ Method in class Martel.Generate.print_info
__init__ Method in class Martel.IterParser.IterHeaderFooter
__init__ Method in class Martel.IterParser.IterRecords
__init__ Method in class Martel.Iterator.EventStream
__init__ Method in class Martel.Iterator.HeaderFooterEventStream
__init__ Method in class Martel.Iterator.Iterate
__init__ Method in class Martel.Iterator.Iterator
__init__ Method in class Martel.Iterator.IteratorHeaderFooter
__init__ Method in class Martel.Iterator.IteratorRecords
__init__ Method in class Martel.Iterator.RecordEventStream
__init__ Method in class Martel.Iterator.StoreEvents
__init__ Method in class Martel.LAX.ElementInfo
__init__ Method in class Martel.LAX.LAX
__init__ Method in class Martel.Parser.HeaderFooterParser
__init__ Method in class Martel.Parser.Parser
__init__ Method in class Martel.Parser.ParserIncompleteException
__init__ Method in class Martel.Parser.ParserPositionException
__init__ Method in class Martel.Parser.RecordParser
__init__ Method in class Martel.RecordReader.CountLines
__init__ Method in class Martel.RecordReader.EndsWith
__init__ Method in class Martel.RecordReader.Everything
__init__ Method in class Martel.RecordReader.Nothing
__init__ Method in class Martel.RecordReader.RecordReader
__init__ Method in class Martel.RecordReader.StartsWith
__init__ Method in class Martel.RecordReader.Until
__init__ Method in class Martel.convert_re.GroupNames
__init__ Method in class Martel.msre_parse.Pattern
__init__ Method in class Martel.msre_parse.SubPattern
__init__ Method in class Martel.msre_parse.Tokenizer
__init__ Method in class Martel.test.support.CheckGood
__init__ Method in class Martel.test.support.Dump
__init__ Method in class Martel.test.support.Storage
__init__ Method in class Martel.test.test_Parser.CountErrors
__init__ Method in class Martel.test.test_Parser.CountRecords
__init__ Method in class Martel.test.test_delimiter.CatchFields
__init__ Method in class Martel.test.test_optimize.GetErrorPos
__init__ Method in class __builtin__.dict
__init__ Method in class __builtin__.list
__init__ Method in class __builtin__.object
__init__ Method in class exceptions.BaseException
__init__ Method in class exceptions.Exception
__init__ Method in class exceptions.StandardError
__init__ Method in class exceptions.TypeError
__init__ Method in class exceptions.ValueError
__init__ Method in class markupbase.ParserBase
__init__ Method in class sgmllib.SGMLParser
__init__ Method in class xml.sax._exceptions.SAXException
__init__ Method in class xml.sax.handler.ContentHandler
__init__ Method in class xml.sax.xmlreader.AttributesImpl
__init__ Method in class xml.sax.xmlreader.XMLReader
__itemsize__ Variable in class __builtin__.type
__iter__ Method in class Bio.Blast.NCBIStandalone.Iterator
__iter__ Method in class Bio.EUtils.Datatypes.BinaryOp
__iter__ Method in class Bio.EUtils.Datatypes.DBIds
__iter__ Method in class Bio.EUtils.Datatypes.Expression
__iter__ Method in class Bio.EUtils.Datatypes.Term
__iter__ Method in class Bio.EUtils.MultiDict._BaseMultiDict
__iter__ Method in class Bio.EUtils.POM.ElementNode
__iter__ Method in class Bio.Enzyme.Iterator
__iter__ Method in class Bio.Gobase.Iterator
__iter__ Method in class Bio.Medline.Iterator
__iter__ Method in class Bio.Prosite.Iterator
__iter__ Method in class Bio.Prosite.Prodoc.Iterator
__iter__ Method in class Bio.Rebase.Iterator
__iter__ Method in class Bio.Sequencing.Phd.Iterator
__iter__ Method in class Bio.SwissProt.SProt.Iterator
__iter__ Method in class Bio.UniGene.Iterator
__iter__ Method in class Martel.Iterator.Iterate
__iter__ Method in class __builtin__.dict
__iter__ Method in class __builtin__.list
__le__ Method in class __builtin__.dict
__le__ Method in class __builtin__.list
__le__ Method in class __builtin__.str
__len__ Method in class Bio.Crystal.Chain
__len__ Method in class Bio.Crystal.Crystal
__len__ Method in class Bio.Crystal.Hetero
__len__ Method in class Bio.EUtils.DBIdsClient.BaseDBIdsRecordSet
__len__ Method in class Bio.EUtils.Datatypes.DBIds
__len__ Method in class Bio.EUtils.HistoryClient.BaseHistoryRecordSet
__len__ Method in class Bio.EUtils.MultiDict._BaseMultiDict
__len__ Method in class Bio.EUtils.POM.ElementNode
__len__ Method in class Bio.FSSP.fssp_rec.fff_rec
__len__ Method in class Bio.Gobase.Dictionary
__len__ Method in class Bio.Mindy.FlatDB.BisectFile
__len__ Method in class Bio.Pathway.Rep.HashSet.HashSet
__len__ Method in class Bio.Prosite.Dictionary
__len__ Method in class Bio.Prosite.ExPASyDictionary
__len__ Method in class Bio.Prosite.Pattern.Prosite
__len__ Method in class Bio.Prosite.Pattern.PrositeMatch
__len__ Method in class Bio.Prosite.Prodoc.Dictionary
__len__ Method in class Bio.Prosite.Prodoc.ExPASyDictionary
__len__ Method in class Bio.PubMed.Dictionary
__len__ Method in class Bio.Rebase.Dictionary
__len__ Method in class Bio.Search.Hit
__len__ Method in class Bio.Search._SeqLength
__len__ Method in class Bio.Seq.MutableSeq
__len__ Method in class Bio.Seq.Seq
__len__ Method in class Bio.SwissProt.SProt.Dictionary
__len__ Method in class Bio.SwissProt.SProt.ExPASyDictionary
__len__ Method in class BioSQL.BioSeq.DBSeq
__len__ Method in class Martel.Parser.MartelAttributeList
__len__ Method in class Martel.msre_parse.SubPattern
__len__ Method in class __builtin__.dict
__len__ Method in class __builtin__.list
__len__ Method in class __builtin__.str
__len__ Method in class xml.sax.xmlreader.AttributesImpl
__lt__ Method in class __builtin__.dict
__lt__ Method in class __builtin__.list
__lt__ Method in class __builtin__.str
__maketrans Method in class Bio.Seq.Seq
__mod__ Method in class __builtin__.str
__mro__ Variable in class __builtin__.type
__mul__ Method in class Bio.SubsMat.SeqMat
__mul__ Method in class __builtin__.list
__mul__ Method in class __builtin__.str
__name__ Variable in class __builtin__.type
__ne__ Method in class Bio.Crystal.Chain
__ne__ Method in class Bio.Crystal.Hetero
__ne__ Method in class Bio.EUtils.Datatypes.CheckLinkSet
__ne__ Method in class Bio.EUtils.Datatypes.DBIds
__ne__ Method in class Bio.EUtils.Datatypes.Date
__ne__ Method in class Bio.EUtils.Datatypes.IdCheck
__ne__ Method in class Bio.EUtils.Datatypes.IdUrlSet
__ne__ Method in class Bio.EUtils.Datatypes.Link
__ne__ Method in class Bio.EUtils.Datatypes.LinkSetDb
__ne__ Method in class Bio.EUtils.Datatypes.LinksLinkSet
__ne__ Method in class Bio.EUtils.Datatypes.NeighborLinkSet
__ne__ Method in class Bio.EUtils.Datatypes.ObjUrl
__ne__ Method in class Bio.EUtils.Datatypes.Problem
__ne__ Method in class Bio.EUtils.Datatypes.Provider
__ne__ Method in class Bio.EUtils.MultiDict.OrderedMultiDict
__ne__ Method in class Bio.EUtils.MultiDict.UnorderedMultiDict
__ne__ Method in class Bio.Pathway.Reaction
__ne__ Method in class Bio.Pathway.Rep.Graph.Graph
__ne__ Method in class Bio.Pathway.Rep.HashSet.HashSet
__ne__ Method in class Bio.Pathway.Rep.MultiGraph.MultiGraph
__ne__ Method in class __builtin__.dict
__ne__ Method in class __builtin__.list
__ne__ Method in class __builtin__.str
__new__ Method in class __builtin__.basestring
__new__ Method in class __builtin__.dict
__new__ Method in class __builtin__.list
__new__ Method in class __builtin__.object
__new__ Method in class __builtin__.str
__new__ Method in class __builtin__.type
__new__ Method in class exceptions.BaseException
__new__ Method in class exceptions.Exception
__new__ Method in class exceptions.StandardError
__new__ Method in class exceptions.TypeError
__new__ Method in class exceptions.ValueError
__next Method in class Martel.msre_parse.Tokenizer
__nonzero__ Method in class Bio.EUtils.POM.ElementNode
__or__ Method in class Bio.EUtils.Datatypes.Expression
__or__ Method in class Martel.Expression.Alt
__or__ Method in class Martel.Expression.Expression
__or__ Method in class Martel.Expression.NullOp
__radd__ Method in class Bio.Crystal.Chain
__radd__ Method in class Bio.Seq.MutableSeq
__radd__ Method in class Bio.Seq.Seq
__reduce__ Method in class __builtin__.object
__reduce__ Method in class exceptions.BaseException
__reduce_ex__ Method in class __builtin__.object
__repr__ Method in class Bio.Alphabet.Alphabet
__repr__ Method in class Bio.Alphabet.AlphabetEncoder
__repr__ Method in class Bio.Crystal.Crystal
__repr__ Method in class Bio.Crystal.Hetero
__repr__ Method in class Bio.Decode.Token
__repr__ Method in class Bio.Decode.ValueToken
__repr__ Method in class Bio.EUtils.Datatypes.CheckLinkSet
__repr__ Method in class Bio.EUtils.Datatypes.DBIds
__repr__ Method in class Bio.EUtils.Datatypes.Date
__repr__ Method in class Bio.EUtils.Datatypes.EUtilsSearchError
__repr__ Method in class Bio.EUtils.Datatypes.IdCheck
__repr__ Method in class Bio.EUtils.Datatypes.IdUrlSet
__repr__ Method in class Bio.EUtils.Datatypes.Link
__repr__ Method in class Bio.EUtils.Datatypes.LinkSetDb
__repr__ Method in class Bio.EUtils.Datatypes.LinksLinkSet
__repr__ Method in class Bio.EUtils.Datatypes.NeighborLinkSet
__repr__ Method in class Bio.EUtils.Datatypes.ObjUrl
__repr__ Method in class Bio.EUtils.Datatypes.Problem
__repr__ Method in class Bio.EUtils.Datatypes.Provider
__repr__ Method in class Bio.EUtils.Datatypes.Summary
__repr__ Method in class Bio.EUtils.MultiDict.OrderedMultiDict
__repr__ Method in class Bio.EUtils.MultiDict.UnorderedMultiDict
__repr__ Method in class Bio.EUtils.POM.AttributeList
__repr__ Method in class Bio.EUtils.POM.ContentModel
__repr__ Method in class Bio.EUtils.POM.ElementNode
__repr__ Method in class Bio.EUtils.POM.IndentedText
__repr__ Method in class Bio.EUtils.POM.XMLAttribute
__repr__ Method in class Bio.EUtils.POM._AttributeType
__repr__ Method in class Bio.EUtils.POM._ContentModelGenerator
__repr__ Method in class Bio.Enzyme.EnzymeRecord
__repr__ Method in class Bio.FSSP.FSSPSumRec
__repr__ Method in class Bio.FSSP.PosAlign
__repr__ Method in class Bio.FSSP.fssp_rec.fff_rec
__repr__ Method in class Bio.Mindy.Location.Location
__repr__ Method in class Bio.Pathway.Interaction
__repr__ Method in class Bio.Pathway.Network
__repr__ Method in class Bio.Pathway.Reaction
__repr__ Method in class Bio.Pathway.Rep.Graph.Graph
__repr__ Method in class Bio.Pathway.Rep.HashSet.HashSet
__repr__ Method in class Bio.Pathway.Rep.MultiGraph.MultiGraph
__repr__ Method in class Bio.Pathway.System
__repr__ Method in class Bio.Prosite.Pattern.Prosite
__repr__ Method in class Bio.Prosite.Pattern.PrositeMatch
__repr__ Method in class Bio.Seq.MutableSeq
__repr__ Method in class Bio.Seq.Seq
__repr__ Method in class Bio.SeqRecord.SeqRecord
__repr__ Method in class Bio.UniGene.UnigeneProtsimRecord
__repr__ Method in class Bio.UniGene.UnigeneRecord
__repr__ Method in class Bio.UniGene.UnigeneSTSRecord
__repr__ Method in class Bio.UniGene.UnigeneSequenceRecord
__repr__ Method in class BioSQL.BioSeqDatabase.BioSeqDatabase
__repr__ Method in class BioSQL.BioSeqDatabase.DBServer
__repr__ Method in class Martel.Parser.MartelAttributeList
__repr__ Method in class Martel.msre_parse.SubPattern
__repr__ Method in class __builtin__.dict
__repr__ Method in class __builtin__.list
__repr__ Method in class __builtin__.object
__repr__ Method in class __builtin__.str
__repr__ Method in class __builtin__.type
__repr__ Method in class exceptions.BaseException
__reversed__ Method in class __builtin__.list
__rmod__ Method in class __builtin__.str
__rmul__ Method in class __builtin__.list
__rmul__ Method in class __builtin__.str
__set_annotations Method in class BioSQL.BioSeq.DBSeqRecord
__set_dbxrefs Method in class BioSQL.BioSeq.DBSeqRecord
__set_features Method in class BioSQL.BioSeq.DBSeqRecord
__set_seq Method in class BioSQL.BioSeq.DBSeqRecord
__setattr__ Method in class Bio.EUtils.POM.ElementNode
__setattr__ Method in class __builtin__.object
__setattr__ Method in class __builtin__.type
__setattr__ Method in class exceptions.BaseException
__setattr__ Method in class reportlab.graphics.widgetbase.PropHolder
__setitem__ Method in class Bio.Crystal.Chain
__setitem__ Method in class Bio.Crystal.Crystal
__setitem__ Method in class Bio.EUtils.MultiDict.OrderedMultiDict
__setitem__ Method in class Bio.EUtils.MultiDict.UnorderedMultiDict
__setitem__ Method in class Bio.EUtils.POM.ElementNode
__setitem__ Method in class Bio.Index._InMemoryIndex
__setitem__ Method in class Bio.Prosite.ExPASyDictionary
__setitem__ Method in class Bio.Prosite.Prodoc.ExPASyDictionary
__setitem__ Method in class Bio.PubMed.Dictionary
__setitem__ Method in class Bio.Seq.MutableSeq
__setitem__ Method in class Bio.SwissProt.SProt.ExPASyDictionary
__setitem__ Method in class Martel.msre_parse.SubPattern
__setitem__ Method in class __builtin__.dict
__setitem__ Method in class __builtin__.list
__setslice__ Method in class Bio.Crystal.Chain
__setslice__ Method in class Bio.Seq.MutableSeq
__setslice__ Method in class __builtin__.list
__setstate__ Method in class exceptions.BaseException
__slots__ Variable in class Bio.Nexus.Nexus.Nexus
__str__ Method in class Bio.Align.AlignInfo.PSSM
__str__ Method in class Bio.AlignAce.Motif.Motif
__str__ Method in class Bio.Application.AbstractCommandline
__str__ Method in class Bio.Application._Argument
__str__ Method in class Bio.Application._Option
__str__ Method in class Bio.Blast.Record.Alignment
__str__ Method in class Bio.Blast.Record.Description
__str__ Method in class Bio.Crystal.Chain
__str__ Method in class Bio.Crystal.Crystal
__str__ Method in class Bio.Crystal.Hetero
__str__ Method in class Bio.DBXRef.DBXRef
__str__ Method in class Bio.Decode.Function
__str__ Method in class Bio.Decode.ValueToken
__str__ Method in class Bio.EUtils.Datatypes.And
__str__ Method in class Bio.EUtils.Datatypes.Date
__str__ Method in class Bio.EUtils.Datatypes.EUtilsSearchError
__str__ Method in class Bio.EUtils.Datatypes.Not
__str__ Method in class Bio.EUtils.Datatypes.Or
__str__ Method in class Bio.EUtils.Datatypes.Problem
__str__ Method in class Bio.EUtils.Datatypes.Range
__str__ Method in class Bio.EUtils.Datatypes.Summary
__str__ Method in class Bio.EUtils.Datatypes.Term
__str__ Method in class Bio.EUtils.MultiDict._BaseMultiDict
__str__ Method in class Bio.EUtils.POM.AttributeList
__str__ Method in class Bio.EUtils.POM.Comment
__str__ Method in class Bio.EUtils.POM.ElementNode
__str__ Method in class Bio.EUtils.POM.Fragments
__str__ Method in class Bio.EUtils.POM.IndentedText
__str__ Method in class Bio.EUtils.POM.POMDocument
__str__ Method in class Bio.EUtils.POM.Text
__str__ Method in class Bio.EUtils.sourcegen.ClassHolder
__str__ Method in class Bio.EUtils.sourcegen.FunctionHolder
__str__ Method in class Bio.EUtils.sourcegen.MethodHolder
__str__ Method in class Bio.EUtils.sourcegen.SourceFile
__str__ Method in class Bio.Emboss.Primer.PrimerSearchInputRecord
__str__ Method in class Bio.Enzyme.DataRecord
__str__ Method in class Bio.Enzyme.EnzymeRecord
__str__ Method in class Bio.GA.Organism.Organism
__str__ Method in class Bio.InterPro.Record
__str__ Method in class Bio.MarkovModel.MarkovModel
__str__ Method in class Bio.Mindy.Location.Location
__str__ Method in class Bio.Ndb.Record
__str__ Method in class Bio.NetCatch.ExtractUrls
__str__ Method in class Bio.NetCatch.NetCatch
__str__ Method in class Bio.NeuralNetwork.BackPropagation.Layer.AbstractLayer
__str__ Method in class Bio.Nexus.Trees.Tree
__str__ Method in class Bio.Pathway.Interaction
__str__ Method in class Bio.Pathway.Network
__str__ Method in class Bio.Pathway.Reaction
__str__ Method in class Bio.Pathway.Rep.Graph.Graph
__str__ Method in class Bio.Pathway.Rep.HashSet.HashSet
__str__ Method in class Bio.Pathway.Rep.MultiGraph.MultiGraph
__str__ Method in class Bio.Pathway.System
__str__ Method in class Bio.Prosite.Pattern.Prosite
__str__ Method in class Bio.Prosite.Pattern.PrositeMatch
__str__ Method in class Bio.Prosite.Pattern.PrositeTerm
__str__ Method in class Bio.Prosite.PatternHit
__str__ Method in class Bio.Seq.MutableSeq
__str__ Method in class Bio.Seq.Seq
__str__ Method in class Bio.SeqFeature.AfterPosition
__str__ Method in class Bio.SeqFeature.BeforePosition
__str__ Method in class Bio.SeqFeature.BetweenPosition
__str__ Method in class Bio.SeqFeature.ExactPosition
__str__ Method in class Bio.SeqFeature.FeatureLocation
__str__ Method in class Bio.SeqFeature.OneOfPosition
__str__ Method in class Bio.SeqFeature.PositionGap
__str__ Method in class Bio.SeqFeature.Reference
__str__ Method in class Bio.SeqFeature.SeqFeature
__str__ Method in class Bio.SeqFeature.WithinPosition
__str__ Method in class Bio.SeqRecord.SeqRecord
__str__ Method in class Bio.StdHandler.Feature
__str__ Method in class Bio.SubsMat.BadMatrix
__str__ Method in class Bio.config.Registry.Registry
__str__ Method in class Martel.Expression.Alt
__str__ Method in class Martel.Expression.Any
__str__ Method in class Martel.Expression.AnyEol
__str__ Method in class Martel.Expression.Assert
__str__ Method in class Martel.Expression.AtBeginning
__str__ Method in class Martel.Expression.AtEnd
__str__ Method in class Martel.Expression.Debug
__str__ Method in class Martel.Expression.Dot
__str__ Method in class Martel.Expression.Expression
__str__ Method in class Martel.Expression.Group
__str__ Method in class Martel.Expression.GroupRef
__str__ Method in class Martel.Expression.Literal
__str__ Method in class Martel.Expression.MaxRepeat
__str__ Method in class Martel.Expression.NullOp
__str__ Method in class Martel.Expression.PassThrough
__str__ Method in class Martel.Expression.Seq
__str__ Method in class Martel.Expression.Str
__str__ Method in class Martel.Parser.HeaderFooterParser
__str__ Method in class Martel.Parser.MartelAttributeList
__str__ Method in class Martel.Parser.Parser
__str__ Method in class Martel.Parser.RecordParser
__str__ Method in class __builtin__.object
__str__ Method in class __builtin__.str
__str__ Method in class exceptions.BaseException
__str__ Method in class xml.sax._exceptions.SAXException
__sub__ Method in class Bio.EUtils.Datatypes.DBIds
__sub__ Method in class Bio.SubsMat.SeqMat
__subclasses__ Method in class __builtin__.type
__sum__ Method in class Bio.SubsMat.SeqMat
__unicode__ Method in class Bio.EUtils.POM.AttributeList
__unicode__ Method in class Bio.EUtils.POM.Comment
__unicode__ Method in class Bio.EUtils.POM.ElementNode
__unicode__ Method in class Bio.EUtils.POM.Fragments
__unicode__ Method in class Bio.EUtils.POM.IndentedText
__unicode__ Method in class Bio.EUtils.POM.POMDocument
__unicode__ Method in class Bio.EUtils.POM.Text
__weakrefoffset__ Variable in class __builtin__.type
_AbstractParameter Class in package Bio.Application
_acquire Method in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_acquired Variable in class Bio.EUtils.POM.ElementNode
_add_db Function in module Bio.EUtils.Config
_add_dbxref Method in class BioSQL.Loader.DatabaseLoader
_add_diagram_for_sequence Method in class Bio.MEME.Parser.MASTRecord
_add_diagram_from_buffer Method in class Bio.MEME.Parser._MASTConsumer
_add_last_amplifier Method in class Bio.Emboss.Primer._PrimerSearchRecordConsumer
_add_last_primer Method in class Bio.Emboss.Primer._Primer3RecordConsumer
_add_line_to_buffer Method in class Bio.MEME.Parser._MASTConsumer
_add_match Method in class Bio.MEME.Parser.MASTRecord
_add_match_diagram Method in class Bio.MEME.Parser._MASTConsumer
_add_motif Method in class Bio.MEME.Parser.MASTRecord
_add_motif Method in class Bio.MEME.Parser._MASTConsumer
_add_motif Method in class Bio.NeuralNetwork.Gene.Motif.MotifFinder
_add_motif_match Method in class Bio.MEME.Parser._MASTConsumer
_add_motif_with_info Method in class Bio.MEME.Parser._MEMEConsumer
_add_numbering_table Method in class Bio.FSSP.FSSPTools.FSSPAlign
_add_sequence Method in class Bio.MEME.Parser.MASTRecord
_add_sequence_match_with_diagram Method in class Bio.MEME.Parser._MASTConsumer
_add_sig Method in class Bio.NeuralNetwork.Gene.Signature.SignatureFinder
_add_subtree Method in class Bio.Nexus.Trees.Tree
_adjust_charlabels Method in class Bio.Nexus.Nexus.Nexus
_adjust_lines Function in module Bio.Nexus.Nexus
_align Function in module Bio.pairwise2
_AlignmentConsumer Class in module Bio.Blast.NCBIStandalone
_all_blank Method in class Bio.HMM.MarkovModel.MarkovModelBuilder
_all_pseudo Method in class Bio.HMM.MarkovModel.MarkovModelBuilder
_alphabet Method in class Bio.MEME.Motif.Motif
_alphabet Method in class Bio.MEME.Parser.MASTRecord
_alphabet Method in class Bio.MEME.Parser._MEMEConsumer
_alphabet_from_input Method in class Bio.SubsMat.FreqTable.FreqTable
_alphabet_from_matrix Method in class Bio.SubsMat.SeqMat
_any_case Function in module Martel.Time
_apply_block_structure Method in class Bio.Nexus.Nexus.Nexus
_apply_clean_data Method in class Bio.ParserSupport.SGMLStrippingConsumer
_argmaxes Function in module Bio.MarkovModel
_Argument Class in package Bio.Application
_attr2dict Method in class Bio.Blast.NCBIWWW._FormParser
_attr_str Method in class Bio.EUtils.POM.ElementNode
_attr_unistr Method in class Bio.EUtils.POM.ElementNode
_attribs_match Method in class Bio.EUtils.POM.ElementNode
_AttributeType Class in module Bio.EUtils.POM
_attrMap Variable in class reportlab.graphics.widgetbase.PropHolder
_attrMap Variable in class reportlab.graphics.widgetbase.PropHolder
_attrMap Variable in class reportlab.graphics.widgetbase.PropHolder
_attrMap Variable in class reportlab.graphics.widgetbase.PropHolder
_attrMap Variable in class reportlab.graphics.widgetbase.PropHolder
_attrMap Variable in class reportlab.graphics.widgetbase.PropHolder
_attrMap Variable in class reportlab.graphics.widgetbase.PropHolder
_autoload Method in class Bio.config.Registry.Registry
_back_translate_no_stop Method in class Bio.Translate.Translator
_backward Function in module Bio.MarkovModel
_backward_recursion Method in class Bio.HMM.DynamicProgramming.AbstractDPAlgorithms
_backward_recursion Method in class Bio.HMM.DynamicProgramming.ScaledDPAlgorithms
_BaseMultiDict Class in module Bio.EUtils.MultiDict
_baum_welch Function in module Bio.MarkovModel
_baum_welch_one Function in module Bio.MarkovModel
_bit_info Function in module Bio.expressions.blast.ncbiblast
_blank_buffer Method in class Bio.MEME.Parser._MASTConsumer
_BlastConsumer Class in module Bio.Blast.NCBIStandalone
_BlastErrorConsumer Class in module Bio.Blast.NCBIStandalone
_bootstrap Function in module Bio.Alphabet.IUPAC
_build_child_path Method in class Bio.config.FormatRegistry.FormatRegistry
_build_exp_freq_mat Function in package Bio.SubsMat
_build_log_odds_mat Function in package Bio.SubsMat
_build_obs_freq_mat Function in package Bio.SubsMat
_build_parent_path Method in class Bio.config.FormatRegistry.FormatRegistry
_build_path Method in class Bio.NetCatch.NetCatch
_build_problem_mapping Function in module Bio.EUtils.Datatypes
_build_subs_mat Function in package Bio.SubsMat
_calc_empirical_expects Function in module Bio.MaxEntropy
_calc_f_sharp Function in module Bio.MaxEntropy
_calc_model_expects Function in module Bio.MaxEntropy
_calc_p_class_given_x Function in module Bio.MaxEntropy
_calculate_from_transitions Method in class Bio.HMM.MarkovModel.HiddenMarkovModel
_calculate_s_value Method in class Bio.HMM.DynamicProgramming.ScaledDPAlgorithms
_call_call Class in module Martel.Generate
_call_calltag Class in module Martel.Generate
_call_fn Method in class Bio.config._support.make_timed_function
_callback Method in class Bio.EUtils.POM.POMDocument
_categories Variable in class Bio.Medline._Scanner
_cgiopen Method in class Bio.config.DBRegistry.CGIDB
_changeset Method in class Bio.Nexus.Nexus.Nexus
_charlabels Method in class Bio.Nexus.Nexus.Nexus
_charpartition Method in class Bio.Nexus.Nexus.Nexus
_charset Method in class Bio.Nexus.Nexus.Nexus
_charstatelabels Method in class Bio.Nexus.Nexus.Nexus
_check_alphabet Method in class Bio.AlignAce.Motif.Motif
_check_attrs Function in module Bio.Std
_check_for_bad_input_stream Function in module Bio.EUtils.parse
_check_for_cache_reset Method in class Bio.EUtils.HistoryClient.HistoryClient
_check_for_errors Function in module Bio.EUtils.parse
_check_for_errors Method in class Bio.config.DBRegistry.TextLikeMixin
_check_for_link_errors Function in module Bio.EUtils.parse
_check_gapchar Function in module Bio.Std
_check_invalid Method in class Bio.EUtils.HistoryClient.HistoryLookup
_check_length Method in class Bio.AlignAce.Motif.Motif
_check_name Function in module Bio.Std
_check_no_buffer Method in class Bio.EUtils.ReseekFile.ReseekFile
_check_taxlabels Method in class Bio.Nexus.Nexus.Nexus
_check_value Method in class Bio.Application.AbstractCommandline
_chomp Method in class Bio.Prosite._RecordConsumer
_chomp Method in class Bio.SwissProt.SProt._RecordConsumer
_ChromosomeComponent Class in module Bio.Graphics.BasicChromosome
_class_escape Function in module Martel.msre_parse
_clean Method in class Bio.Medline._RecordConsumer
_clean Method in class Bio.Prosite._RecordConsumer
_clean_abbrev Function in module Bio.config.DBRegistry
_clean_alignments Function in module Bio.pairwise2
_clean_data Method in class Bio.Prosite.Prodoc._RecordConsumer
_clean_record Method in class Bio.Medline._RecordConsumer
_clean_record Method in class Bio.SwissProt.SProt._RecordConsumer
_clean_references Method in class Bio.SwissProt.SProt._RecordConsumer
_cleanup Function in module Bio.MultiProc.copen
_cleanup_child Method in class Bio.MultiProc.copen._ProcHandle
_clear Method in class Bio.SVDSuperimposer.SVDSuperimposer.SVDSuperimposer
_col_ave Function in module Bio.NMR.NOEtools
_collapse_buffer Method in class Bio.MEME.Parser._MASTConsumer
_color_from_count Method in class Bio.Graphics.DisplayRepresentation.ChromosomeCounts
_commandline Method in class Bio.MEME.Parser._MEMEConsumer
_compact4nexus Function in module Bio.Nexus.Nexus
_compare Function in module Bio.MarkupEditor
_complain_if_given Function in module Bio.Std
_consensus Method in class Bio.MEME.Motif.Motif
_construct_node Function in module Bio.EUtils.POM
_construct_pattern Function in module Bio.EUtils.parse
_consume_entry Method in class Bio.Blast.ParseBlastTable.BlastTableReader
_consume_header Method in class Bio.Blast.ParseBlastTable.BlastTableReader
_Consumer Class in package Bio.Compass
_ContentModelGenerator Class in module Bio.EUtils.POM
_convert_ref Method in class sgmllib.SGMLParser
_convert_to Method in class Bio.config.DBRegistry.BioCorbaDB
_convert_to Method in class Bio.config.DBRegistry.BioSQLDB
_convert_to Method in class Bio.config.DBRegistry.DBObject
_convert_to Method in class Bio.config.DBRegistry.IndexedFileDB
_convert_to Method in class Bio.config.DBRegistry.TextLikeMixin
_copy_and_check Function in module Bio.MarkovModel
_corr Function in module Bio.MEME.Motif
_correct_matrix Method in class Bio.SubsMat.SeqMat
_count_emissions Method in class Bio.HMM.Trainer.KnownStateTrainer
_count_transitions Method in class Bio.HMM.Trainer.KnownStateTrainer
_crossover Method in class Bio.GA.Crossover.GeneralPoint.GeneralPointCrossover
_crossover Method in class Bio.GA.Crossover.GeneralPoint.InterleaveCrossover
_crossover Method in class Bio.GA.Crossover.GeneralPoint.TwoCrossover
_data_map Function in module Bio.NMR.NOEtools
_database Method in class Bio.MEME.Parser.MASTRecord
_database Method in class Bio.MEME.Parser._MASTConsumer
_DatabaseReportConsumer Class in module Bio.Blast.NCBIStandalone
_datafile Method in class Bio.MEME.Parser._MEMEConsumer
_dbids_to_id_string Function in module Bio.EUtils.ThinClient
_decl_otherchars Variable in class markupbase.ParserBase
_decl_otherchars Variable in class sgmllib.SGMLParser
_decl_otherchars Variable in class sgmllib.SGMLParser
_decl_otherchars Variable in class sgmllib.SGMLParser
_decl_otherchars Variable in class sgmllib.SGMLParser
_decl_otherchars Variable in class sgmllib.SGMLParser
_decl_otherchars Variable in class sgmllib.SGMLParser
_decl_otherchars Variable in class sgmllib.SGMLParser
_default_parser_callback Function in module Bio.EUtils.POM
_DescriptionConsumer Class in module Bio.Blast.NCBIStandalone
_determine_position Method in class Bio.Graphics.Distribution.BarChartDistribution
_diagnose_error Method in class Bio.Blast.NCBIStandalone.BlastErrorParser
_dict Function in module Bio.EUtils.setup
__filename_key Variable in class Bio.Gobase.Dictionary
__filename_key Variable in class Bio.Prosite.Dictionary
__filename_key Variable in class Bio.Prosite.Prodoc.Dictionary
__filename_key Variable in class Bio.Rebase.Dictionary
__filename_key Variable in class Bio.SwissProt.SProt.Dictionary
_digest Method in class Bio.CAPS.CAPSMap
_digest_with Method in class Bio.CAPS.CAPSMap
_dimensions Method in class Bio.Nexus.Nexus.Nexus
_dir_class Function in module Martel.Dispatch
_do_callback Function in module Martel.Parser
_do_dispatch_callback Function in module Martel.Parser
_draw_distributions Method in class Bio.Graphics.Distribution.DistributionPage
_draw_label Method in class Bio.Graphics.BasicChromosome.Chromosome
_draw_label Method in class Bio.Graphics.BasicChromosome.ChromosomeSegment
_draw_legend Method in class Bio.Graphics.BasicChromosome.Organism
_draw_legend Method in class Bio.Graphics.Distribution.DistributionPage
_draw_scatter_plot Method in class Bio.Graphics.Comparative.ComparativeScatterPlot
_draw_segment Method in class Bio.Graphics.BasicChromosome.ChromosomeSegment
_draw_segment Method in class Bio.Graphics.BasicChromosome.TelomereSegment
_draw_subcomponents Method in class Bio.Graphics.BasicChromosome.ChromosomeSegment
_draw_title Method in class Bio.Graphics.BasicChromosome.Organism
_draw_title Method in class Bio.Graphics.Comparative.ComparativeScatterPlot
_draw_title Method in class Bio.Graphics.Distribution.BarChartDistribution
_draw_title Method in class Bio.Graphics.Distribution.DistributionPage
_drawTimeResize Method in class reportlab.graphics.shapes._DrawTimeResizeable
_DrawTimeResizeable Class in module reportlab.graphics.shapes
_dump Function in module Bio.Parsers.spark
_eliminate Method in class Bio.Nexus.Nexus.Nexus
_empty_str Method in class Bio.EUtils.POM.ElementNode
_empty_unistr Method in class Bio.EUtils.POM.ElementNode
_end_BlastOutput_db Method in class Bio.Blast.NCBIXML.BlastParser
_end_BlastOutput_hits Method in class Bio.Blast.NCBIXML.BlastParser
_end_BlastOutput_program Method in class Bio.Blast.NCBIXML.BlastParser
_end_BlastOutput_query_def Method in class Bio.Blast.NCBIXML.BlastParser
_end_BlastOutput_query_ID Method in class Bio.Blast.NCBIXML.BlastParser
_end_BlastOutput_query_len Method in class Bio.Blast.NCBIXML.BlastParser
_end_BlastOutput_reference Method in class Bio.Blast.NCBIXML.BlastParser
_end_BlastOutput_version Method in class Bio.Blast.NCBIXML.BlastParser
_end_elem Function in module Bio.Medline.nlmmedline_001211_format
_end_elem Function in module Bio.Medline.nlmmedline_010319_format
_end_elem Function in module Bio.Medline.nlmmedline_011101_format
_end_elem Function in module Bio.Medline.nlmmedline_031101_format
_end_element Function in module Bio.MarkupEditor
_end_Hit Method in class Bio.Blast.NCBIXML.BlastParser
_end_Hit_accession Method in class Bio.Blast.NCBIXML.BlastParser
_end_Hit_def Method in class Bio.Blast.NCBIXML.BlastParser
_end_Hit_id Method in class Bio.Blast.NCBIXML.BlastParser
_end_Hit_len Method in class Bio.Blast.NCBIXML.BlastParser
_end_Hsp_align_len Method in class Bio.Blast.NCBIXML.BlastParser
_end_Hsp_bit_score Method in class Bio.Blast.NCBIXML.BlastParser
_end_Hsp_evalue Method in class Bio.Blast.NCBIXML.BlastParser
_end_Hsp_gaps Method in class Bio.Blast.NCBIXML.BlastParser
_end_Hsp_hit_frame Method in class Bio.Blast.NCBIXML.BlastParser
_end_Hsp_hit_from Method in class Bio.Blast.NCBIXML.BlastParser
_end_Hsp_hit_to Method in class Bio.Blast.NCBIXML.BlastParser
_end_Hsp_hseq Method in class Bio.Blast.NCBIXML.BlastParser
_end_Hsp_identity Method in class Bio.Blast.NCBIXML.BlastParser
_end_Hsp_midline Method in class Bio.Blast.NCBIXML.BlastParser
_end_Hsp_positive Method in class Bio.Blast.NCBIXML.BlastParser
_end_Hsp_qseq Method in class Bio.Blast.NCBIXML.BlastParser
_end_Hsp_query_frame Method in class Bio.Blast.NCBIXML.BlastParser
_end_Hsp_query_from Method in class Bio.Blast.NCBIXML.BlastParser
_end_Hsp_query_to Method in class Bio.Blast.NCBIXML.BlastParser
_end_Hsp_score Method in class Bio.Blast.NCBIXML.BlastParser
_end_Iteration Method in class Bio.Blast.NCBIXML.BlastParser
_end_Iteration_query_def Method in class Bio.Blast.NCBIXML.BlastParser
_end_Iteration_query_ID Method in class Bio.Blast.NCBIXML.BlastParser
_end_Iteration_query_len Method in class Bio.Blast.NCBIXML.BlastParser
_end_Parameters_expect Method in class Bio.Blast.NCBIXML.BlastParser
_end_Parameters_filter Method in class Bio.Blast.NCBIXML.BlastParser
_end_Parameters_gap_extend Method in class Bio.Blast.NCBIXML.BlastParser
_end_Parameters_gap_open Method in class Bio.Blast.NCBIXML.BlastParser
_end_Parameters_matrix Method in class Bio.Blast.NCBIXML.BlastParser
_end_Parameters_sc_match Method in class Bio.Blast.NCBIXML.BlastParser
_end_Parameters_sc_mismatch Method in class Bio.Blast.NCBIXML.BlastParser
_end_Statistics_db_len Method in class Bio.Blast.NCBIXML.BlastParser
_end_Statistics_db_num Method in class Bio.Blast.NCBIXML.BlastParser
_end_Statistics_eff_space Method in class Bio.Blast.NCBIXML.BlastParser
_end_Statistics_entropy Method in class Bio.Blast.NCBIXML.BlastParser
_end_Statistics_hsp_len Method in class Bio.Blast.NCBIXML.BlastParser
_end_Statistics_kappa Method in class Bio.Blast.NCBIXML.BlastParser
_end_Statistics_lambda Method in class Bio.Blast.NCBIXML.BlastParser
_endswith_tagtable_newline Function in module Martel.RecordReader
_endswith_tagtable_rest_of_line Function in module Martel.RecordReader
_EOF Variable in class Bio.Parsers.spark.GenericParser
_EOF Variable in class Bio.Parsers.spark.GenericParser
_EOF Variable in class Bio.Parsers.spark.GenericParser
_EOF Variable in class Bio.Parsers.spark.GenericParser
_escape Function in module Martel.msre_parse
_eval_feature_fn Function in module Bio.MaxEntropy
_evalue Method in class Bio.MEME.Motif.MEMEMotif
_exp_freq_table_from_obs_freq Function in package Bio.SubsMat
_exp_logsum Function in module Bio.MarkovModel
_extract_pattern_hits Function in package Bio.Prosite
_extract_record Function in module Bio.Prosite.Prodoc
_extract_record Function in package Bio.Prosite
_fails_conditions Function in module Bio.ParserSupport
_fast_dbxref_sp_embl Function in module Bio.StdHandler
_fast_dbxref_sp_general Function in module Bio.StdHandler
_fast_dbxref_sp_prosite Function in module Bio.StdHandler
_file_exists Function in module Bio.AlignAce.Applications
_file_exists Function in package Bio.Application
_find_begin_positions Function in module Martel.RecordReader
_find_element Function in module Bio.EUtils.POM
_find_end_positions Function in module Martel.RecordReader
_find_entry Function in module Bio.Mindy.FlatDB
_find_global_start Function in module Bio.pairwise2
_find_groups Method in class Martel.Expression.Expression
_find_groups Method in class Martel.Expression.ExpressionList
_find_groups Method in class Martel.Expression.Group
_find_groups Method in class Martel.Expression.HeaderFooter
_find_groups Method in class Martel.Expression.MaxRepeat
_find_groups Method in class Martel.Expression.ParseRecords
_find_groups Method in class Martel.Expression.PassThrough
_find_index Method in class Bio.EUtils.POM.ElementNode
_find_local_start Function in module Bio.pairwise2
_find_min_max Method in class Bio.Graphics.Comparative.ComparativeScatterPlot
_find_node Method in class Bio.EUtils.POM.ElementNode
_find_quoted_words Function in module Martel.test.test_Time
_find_range Function in module Bio.Mindy.FlatDB
_find_start Function in module Bio.pairwise2
_find_start_entry Function in module Bio.NMR.xpktools
_find_wanted_groupref_names Function in module Martel.Generate
_fitness_cmp Method in class Bio.GA.Selection.Tournament.TournamentSelection
_fix Method in class Bio.EUtils.POM.Comment
_fix_newlines Function in package Martel
_fix_varsplic_sequences Method in class Bio.SwissProt.SProt._RecordConsumer
_fixup_defs Function in module Bio.Decode
_fixup_query Method in class Bio.EUtils.ThinClient.ThinClient
_fixup_sp_pattern Function in module Bio.StdHandler
_flush_text Method in class Bio.InterPro.InterProParser
_flush_text Method in class Bio.Ndb.NdbParser
_footer_next Method in class Martel.Iterator.HeaderFooterEventStream
_format Method in class Bio.Nexus.Nexus.Nexus
_FormParser Class in module Bio.Blast.NCBIWWW
_forward Function in module Bio.MarkovModel
_forward_recursion Method in class Bio.HMM.DynamicProgramming.ScaledDPAlgorithms
_foward_recursion Method in class Bio.HMM.DynamicProgramming.AbstractDPAlgorithms
_freq_from_count Method in class Bio.SubsMat.FreqTable.FreqTable
_full_to_half Method in class Bio.SubsMat.SeqMat
_generate Function in module Martel.Generate
_generate_locs Method in class Bio.GA.Crossover.GeneralPoint.GeneralPointCrossover
_generate_locs Method in class Bio.GA.Crossover.GeneralPoint.InterleaveCrossover
_generate_locs Method in class Bio.GA.Crossover.GeneralPoint.TwoCrossover
_get Method in class Bio.EUtils.ThinClient.ThinClient
_get Method in class Bio.MarkupEditor.MarkupEditor
_get Method in class Bio.config.DBRegistry.BioCorbaDB
_get Method in class Bio.config.DBRegistry.BioSQLDB
_get Method in class Bio.config.DBRegistry.CGIDB
_get Method in class Bio.config.DBRegistry.DBObject
_get Method in class Bio.config.DBRegistry.EUtilsDB
_get Method in class Bio.config.DBRegistry.IndexedFileDB
_get_array_entry Method in class Bio.UniGene._RecordConsumer
_get_base_info Method in class Bio.Align.FormatConvert.FormatConverter
_get_base_letters Method in class Bio.Align.AlignInfo.SummaryInfo
_get_base_replacements Method in class Bio.Align.AlignInfo.SummaryInfo
_get_check_names Method in class Bio.config.DBRegistry.IndexedFileDB
_get_class Method in class Bio.EUtils.POM.ObjectParserHandler
_get_cols Function in module Bio.Blast.NCBIStandalone
_get_column_info_content Method in class Bio.Align.AlignInfo.SummaryInfo
_get_corba_client Method in class Bio.config.DBRegistry.BioCorbaDB
_get_db_module Method in class Bio.config.DBRegistry.BioSQLDB
_get_dbids Method in class Bio.EUtils.DBIdsClient.DBIdsLookup
_get_dbids Method in class Bio.EUtils.Datatypes.CheckLinkSet
_get_dbids Method in class Bio.EUtils.Datatypes.LinkSetDb
_get_dbids Method in class Bio.EUtils.HistoryClient.HistoryLookup
_get_file_format Method in class Bio.FormatIO.FormatIO
_get_first_words Function in module Bio.Mindy.FlatDB
_get_id Method in class Bio.Nexus.Nodes.Chain
_get_indices Method in class Bio.Nexus.Nexus.Nexus
_get_len_expected Method in class Bio.FilteredReader.FilteredReader
_get_letter_freqs Method in class Bio.Align.AlignInfo.SummaryInfo
_get_motif_dict Method in class Bio.NeuralNetwork.Gene.Motif.MotifFinder
_get_new_organism Method in class Bio.GA.Selection.Diversity.DiversitySelection
_get_next_text Function in module Martel.Iterator
_get_nexus_block Method in class Bio.Nexus.Nexus.Nexus
_get_ns Method in class Bio.EUtils.POM.ElementNode
_get_num_motifs Method in class Bio.NeuralNetwork.Gene.Schema.SchemaFactory
_get_ontology_id Method in class BioSQL.Loader.DatabaseLoader
_get_opt_string Function in module Bio.EUtils.parse
_get_ranges Method in class Martel.Generate.HandleRepeatCount
_get_recordset_constructor Function in module Bio.EUtils.DBIdsClient
_get_recordset_constructor Function in module Bio.EUtils.HistoryClient
_get_retriever Method in class Bio.config.DBRegistry.BioCorbaDB
_get_selected_names Function in module Bio.FormatIO
_get_signature_dict Method in class Bio.NeuralNetwork.Gene.Signature.SignatureFinder
_get_single_entry Method in class Bio.UniGene._RecordConsumer
_get_taxon_id Method in class BioSQL.Loader.DatabaseLoader
_get_term_id Method in class BioSQL.Loader.DatabaseLoader
_get_unique_schema Method in class Bio.NeuralNetwork.Gene.Schema.SchemaFactory
_get_values Method in class Bio.Nexus.Trees.Tree
_group Function in package Martel
_group Function in module Martel.msre_parse
_guess_consensus_alphabet Method in class Bio.Align.AlignInfo.SummaryInfo
_handle_sigterm Function in module Bio.MultiProc.copen
_header_next Method in class Martel.Iterator.HeaderFooterEventStream
_HeaderConsumer Class in module Bio.Blast.NCBIStandalone
_HSPConsumer Class in module Bio.Blast.NCBIStandalone
_iis_solve_delta Function in module Bio.MaxEntropy
_IndexerHandler Class in module Bio.Medline.NLMMedlineXML
_init_from_text Method in class Bio.UniGene.UnigeneProtsimRecord
_init_from_text Method in class Bio.UniGene.UnigeneSTSRecord
_init_from_text Method in class Bio.UniGene.UnigeneSequenceRecord
_init_zero Method in class Bio.SubsMat.SeqMat
_InMemoryIndex Class in module Bio.Index
_InMemoryIndex__version Variable in class Bio.Index._InMemoryIndex
_InMemoryIndex__version_key Variable in class Bio.Index._InMemoryIndex
_insert_seqfeature_location Method in class BioSQL.Loader.DatabaseLoader
_int_str Function in module Bio.Mindy.BaseDB
_IsIn Class in module Martel.LAX
_kill Method in class Bio.MultiProc.copen._ProcHandle
_kill_comments_and_break_lines Function in module Bio.Nexus.Nexus
_length Method in class Bio.MEME.Motif.Instance
_length Method in class Bio.MEME.Motif.Motif
_list_ini_files Function in module Bio.config.SeqDBRegistry
_list_ini_paths Function in module Bio.config.SeqDBRegistry
_ListConsumer Class in module Bio.SwissProt.KeyWList
_load Method in class Bio.config.Registry.Registry
_load Method in class Bio.config.SeqDBRegistry.SeqDBRegistry
_load_bioentry_date Method in class BioSQL.Loader.DatabaseLoader
_load_bioentry_table Method in class BioSQL.Loader.DatabaseLoader
_load_biosequence Method in class BioSQL.Loader.DatabaseLoader
_load_comment Method in class BioSQL.Loader.DatabaseLoader
_load_database Method in class Bio.config.DBRegistry.IndexedFileDB
_load_expression Function in module Bio.config.FormatRegistry
_load_first_existing Function in module Bio.config.FormatRegistry
_load_module Function in module Bio.EUtils.parse
_load_object Function in module Bio.config.FormatRegistry
_load_reference Method in class BioSQL.Loader.DatabaseLoader
_load_registry_objects Function in module Bio.config.SeqDBRegistry
_load_seqfeature Method in class BioSQL.Loader.DatabaseLoader
_load_seqfeature_basic Method in class BioSQL.Loader.DatabaseLoader
_load_seqfeature_locations Method in class BioSQL.Loader.DatabaseLoader
_load_seqfeature_qualifiers Method in class BioSQL.Loader.DatabaseLoader
_log_transform Method in class Bio.HMM.MarkovModel.HiddenMarkovModel
_logadd Function in module Bio.MarkovModel
_logsum Function in module Bio.MarkovModel
_logvecadd Function in module Bio.MarkovModel
_lookup_alias Function in module Bio.Mindy.FlatDB
_lookup_location Function in module Bio.Mindy.FlatDB
_lpad Function in module Bio.pairwise2
_lpad_until_equal Function in module Bio.pairwise2
_make_ambiguous_ranges Function in module Bio.Data.IUPACData
_make_biofetch_db Function in module Bio.config.SeqDBRegistry
_make_biosql_db Function in module Bio.config.SeqDBRegistry
_make_callback Method in class Bio.ParserSupport.EventGenerator
_make_fast_lookup Function in module Martel.Expression
_make_flat_db Function in module Bio.config.SeqDBRegistry
_make_group_pattern Function in module Martel.Expression
_make_no_case Function in module Martel.Expression
_make_pickleable Method in class Bio.config.DBRegistry.BioSQLDB
_make_pickleable Method in class Bio.config.DBRegistry.CGIDB
_make_pickleable Method in class Bio.config.DBRegistry.DBObject
_make_ranges Function in module Bio.Data.IUPACData
_make_score_matrix_fast Function in module Bio.pairwise2
_make_score_matrix_generic Function in module Bio.pairwise2
_make_unique Function in module Bio.Nexus.Nexus
_MASTConsumer Class in module Bio.MEME.Parser
_MASTScanner Class in module Bio.MEME.Parser
_matrix Method in class Bio.Nexus.Nexus.Nexus
_MEMEConsumer Class in module Bio.MEME.Parser
_MEMEScanner Class in module Bio.MEME.Parser
_merge_methods Function in module Martel.Dispatch
_minimize_any_range Function in module Martel.Expression
_minimize_escape_char Function in module Martel.Expression
_minimize_escape_range Function in module Martel.Expression
_mle Function in module Bio.MarkovModel
_modify_leaves Method in class Martel.Expression.Assert
_modify_leaves Method in class Martel.Expression.Expression
_modify_leaves Method in class Martel.Expression.ExpressionList
_modify_leaves Method in class Martel.Expression.Group
_modify_leaves Method in class Martel.Expression.HeaderFooter
_modify_leaves Method in class Martel.Expression.MaxRepeat
_modify_leaves Method in class Martel.Expression.ParseRecords
_modify_leaves Method in class Martel.Expression.PassThrough
_motifname Method in class Bio.MEME.Motif.Instance
_must_have Function in module Bio.Std
_must_have_set Function in module Bio.Std
_must_not_have Function in module Bio.Std
_my_urlencode Function in module Bio.config.DBRegistry
_name Method in class Bio.MEME.Motif.Motif
_name_n_vector Method in class Bio.Nexus.Nexus.Nexus
_namelist Function in module Bio.Parsers.spark
_needs_stripping Variable in class Bio.Medline._RecordConsumer
_newname Function in module Bio.MultiProc.Task
_non_empty_str Method in class Bio.EUtils.POM.ElementNode
_non_empty_unistr Method in class Bio.EUtils.POM.ElementNode
_normalize Function in module Bio.MarkovModel
_normalize_expression Function in module Bio.config.FormatRegistry
_normalize_params Method in class Bio.config.DBRegistry.CGIDB
_num_stat Function in module Bio.expressions.blast.ncbiblast
_numoccurrences Method in class Bio.MEME.Motif.Motif
_nv Function in module Bio.expressions.blast.ncbiblast
_open Function in module Bio.WWW.ExPASy
_open Function in module Bio.WWW.NCBI
_open Function in module Bio.WWW.SCOP
_openfu Function in module Bio.config.SeqDBRegistry
_Option Class in package Bio.Application
_options Method in class Bio.Nexus.Nexus.Nexus
_pad Function in module Bio.pairwise2
_pad_until_equal Function in module Bio.pairwise2
_pair_replacement Method in class Bio.Align.AlignInfo.SummaryInfo
_ParametersConsumer Class in module Bio.Blast.NCBIStandalone
_parse Method in class Bio.Blast.NCBIStandalone._DescriptionConsumer
_Parse Method in class Bio.Blast.ParseBlastTable.BlastTableReader
_parse Method in class Bio.Nexus.Trees.Tree
_parse Function in module Martel.msre_parse
_parse_blast_ref_page Function in module Bio.Blast.NCBIWWW
_parse_blast_results_page Function in module Bio.Blast.NCBIWWW
_parse_buffer Method in class Bio.MEME.Parser._MASTConsumer
_parse_chain Method in class Bio.Ndb.NdbParser
_parse_constants Function in package Bio.Ndb
_parse_database Method in class Bio.Blast.ParseBlastTable.BlastTableReader
_parse_doctype_attlist Method in class markupbase.ParserBase
_parse_doctype_element Method in class markupbase.ParserBase
_parse_doctype_entity Method in class markupbase.ParserBase
_parse_doctype_notation Method in class markupbase.ParserBase
_parse_doctype_subset Method in class markupbase.ParserBase
_parse_elements Function in module Martel.Parser
_parse_fields Method in class Bio.Blast.ParseBlastTable.BlastTableReader
_parse_iteration Method in class Bio.Blast.ParseBlastTable.BlastTableReader
_parse_link Function in module Bio.EUtils.parse
_parse_list Method in class Bio.Nexus.Nexus.Nexus
_parse_nexus_block Method in class Bio.Nexus.Nexus.Nexus
_parse_primary_table_entry Function in module Bio.Mindy.FlatDB
_parse_qblast_ref_page Function in module Bio.Blast.NCBIWWW
_parse_query Method in class Bio.Blast.ParseBlastTable.BlastTableReader
_parse_secondary_table_entry Function in module Bio.Mindy.FlatDB
_parse_sub Function in module Martel.msre_parse
_parse_time Function in module Martel.Time
_parse_version Method in class Bio.Blast.ParseBlastTable.BlastTableReader
_parses_file Function in module Bio.config.FormatRegistry
_parses_string Function in module Bio.config.FormatRegistry
_PickleHandle Class in module Bio.MultiProc.copen
_Primer3RecordConsumer Class in module Bio.Emboss.Primer
_Primer3Scanner Class in module Bio.Emboss.Primer
_PrimerSearchRecordConsumer Class in module Bio.Emboss.Primer
_PrimerSearchScanner Class in module Bio.Emboss.Primer
_print_name Method in class Bio.ParserSupport.TaggingConsumer
_ProcHandle Class in module Bio.MultiProc.copen
_PSIBlastConsumer Class in module Bio.Blast.NCBIStandalone
_pvalue Method in class Bio.MEME.Motif.Instance
_query_re Variable in class Bio.Blast.NCBIStandalone._HSPConsumer
_query_re Variable in class Bio.Blast.NCBIStandalone._HSPConsumer
_query_re Variable in class Bio.Blast.NCBIStandalone._HSPConsumer
_query_re Variable in class Bio.Blast.NCBIStandalone._HSPConsumer
_quote Function in module Martel.Expression
_random_norm Function in module Bio.MarkovModel
_re_align Variable in class Bio.Compass._Consumer
_re_lengths Variable in class Bio.Compass._Consumer
_re_names Variable in class Bio.Compass._Consumer
_re_positive_alignment Variable in class Bio.Compass._Consumer
_re_profilewidth Variable in class Bio.Compass._Consumer
_re_scores Variable in class Bio.Compass._Consumer
_re_search Function in module Bio.Blast.NCBIStandalone
_re_start Variable in class Bio.Compass._Consumer
_re_threshold Variable in class Bio.Compass._Consumer
_read Method in class Bio.EUtils.ReseekFile.ReseekFile
_read_dicts Function in module Bio.NMR.xpktools
_read_primary_table Function in module Bio.Mindy.FlatDB
_read_secondary_table Function in module Bio.Mindy.FlatDB
_readline_and_check_start Function in module Bio.MarkovModel
PublicationDBIdsRecord Class in module Bio.EUtils.DBIdsClient
SequenceDBIdsRecord Class in module Bio.EUtils.DBIdsClient
PublicationHistoryRecord Class in module Bio.EUtils.HistoryClient
SequenceHistoryRecord Class in module Bio.EUtils.HistoryClient
_record_next Method in class Martel.Iterator.HeaderFooterEventStream
_RecordConsumer Class in package Bio.Enzyme
_RecordConsumer Class in package Bio.Gobase
_RecordConsumer Class in package Bio.Medline
_RecordConsumer Class in module Bio.Prosite.Prodoc
_RecordConsumer Class in package Bio.Prosite
_RecordConsumer Class in package Bio.Rebase
_RecordConsumer Class in module Bio.Sequencing.Ace
_RecordConsumer Class in module Bio.Sequencing.Phd
_RecordConsumer Class in module Bio.SwissProt.SProt
_RecordConsumer Class in package Bio.UniGene
_recover_alignments Function in module Bio.pairwise2
_replace_parenthesized_ambigs Function in module Bio.Nexus.Nexus
_resolve Method in class Bio.Nexus.Nexus.Nexus
_retrieve_annotations Function in module BioSQL.BioSeq
_retrieve_dbxref Function in module BioSQL.BioSeq
_retrieve_dbxrefs Function in module BioSQL.BioSeq
_retrieve_features Function in module BioSQL.BioSeq
_retrieve_qualifier_value Function in module BioSQL.BioSeq
_retrieve_reference Function in module BioSQL.BioSeq
_retrieve_seq Function in module BioSQL.BioSeq
_retrieve_taxon Function in module BioSQL.BioSeq
_rms Method in class Bio.SVDSuperimposer.SVDSuperimposer.SVDSuperimposer
_run_concurrent Method in class Bio.config.DBRegistry.DBGroup
_run_serial Method in class Bio.config.DBRegistry.DBGroup
_safe_asarray Function in module Bio.MarkovModel
_safe_copy_and_check Function in module Bio.MarkovModel
_safe_float Function in module Bio.Blast.NCBIStandalone
_safe_int Function in module Bio.Blast.NCBIStandalone
_safe_log Function in module Bio.MarkovModel
_SavedDataHandle Class in module Bio.Medline.NLMMedlineXML
_scan_3d Method in class Bio.Prosite._Scanner
_scan_abbreviated_pairwise_alignment Method in class Bio.Blast.NCBIWWW._Scanner
_scan_ac Method in class Bio.Prosite._Scanner
_scan_ac Method in class Bio.SwissProt.SProt._Scanner
_scan_accession Method in class Bio.Prosite.Prodoc._Scanner
_scan_Adeno2 Method in class Bio.Rebase._Scanner
_scan_alignment Method in class Bio.Compass._Scanner
_scan_alignment_header Method in class Bio.Blast.NCBIStandalone._Scanner
_scan_alignment_header Method in class Bio.Blast.NCBIWWW._Scanner
_scan_alignments Method in class Bio.Blast.NCBIStandalone._Scanner
_scan_alignments Method in class Bio.Blast.NCBIWWW._Scanner
_scan_an Method in class Bio.Enzyme._Scanner
_scan_annotated_matches Method in class Bio.MEME.Parser._MASTScanner
_scan_begin_sequence Method in class Bio.Sequencing.Phd._Scanner
_scan_blastform Method in class Bio.Blast.NCBIWWW._Scanner
_scan_bq_data Method in class Bio.Sequencing.Ace._Scanner
_scan_bracket_tags Method in class Bio.Sequencing.Ace._Scanner
_scan_ca Method in class Bio.Enzyme._Scanner
_scan_cc Method in class Bio.Enzyme._Scanner
_scan_cc Method in class Bio.Prosite._Scanner
_scan_cc Method in class Bio.SwissProt.SProt._Scanner
_scan_cf Method in class Bio.Enzyme._Scanner
_scan_comments Method in class Bio.Sequencing.Phd._Scanner
_scan_copyright Method in class Bio.Prosite.Prodoc._Scanner
_scan_copyrights Method in class Bio.Prosite._Scanner
_scan_database_info Method in class Bio.Blast.NCBIWWW._Scanner
_scan_database_report Method in class Bio.Blast.NCBIStandalone._Scanner
_scan_database_report Method in class Bio.Blast.NCBIWWW._Scanner
_scan_date_entered Method in class Bio.Rebase._Scanner
_scan_date_modified Method in class Bio.Rebase._Scanner
_scan_de Method in class Bio.Enzyme._Scanner
_scan_de Method in class Bio.Prosite._Scanner
_scan_de Method in class Bio.SwissProt.SProt._Scanner
_scan_descriptions Method in class Bio.Blast.NCBIStandalone._Scanner
_scan_descriptions Method in class Bio.Blast.NCBIWWW._Scanner
_scan_di Method in class Bio.Enzyme._Scanner
_scan_dna Method in class Bio.Sequencing.Phd._Scanner
_scan_do Method in class Bio.Prosite._Scanner
_scan_dr Method in class Bio.Enzyme._Scanner
_scan_dr Method in class Bio.Prosite._Scanner
_scan_dr Method in class Bio.SwissProt.SProt._Scanner
_scan_dt Method in class Bio.Prosite._Scanner
_scan_dt Method in class Bio.SwissProt.SProt._Scanner
_scan_enzyme_num Method in class Bio.Rebase._Scanner
_scan_field Method in class Bio.Gobase._Scanner
_scan_fns Variable in class Bio.Enzyme._Scanner
_scan_fns Variable in class Bio.Prosite._Scanner
_scan_fns Variable in class Bio.SwissProt.SProt._Scanner
_scan_footer Method in class Bio.SwissProt.KeyWList._Scanner
_scan_ft Method in class Bio.SwissProt.SProt._Scanner
_scan_gene_record Method in class Bio.Gobase._Scanner
_scan_gn Method in class Bio.SwissProt.SProt._Scanner
_scan_header Method in class Bio.Blast.NCBIStandalone._Scanner
_scan_header Method in class Bio.Blast.NCBIWWW._Scanner
_scan_header Method in class Bio.MEME.Parser._MASTScanner
_scan_header Method in class Bio.MEME.Parser._MEMEScanner
_scan_header Method in class Bio.SwissProt.KeyWList._Scanner
_scan_hsp Method in class Bio.Blast.NCBIStandalone._Scanner
_scan_hsp Method in class Bio.Blast.NCBIWWW._Scanner
_scan_hsp_alignment Method in class Bio.Blast.NCBIStandalone._Scanner
_scan_hsp_alignment Method in class Bio.Blast.NCBIWWW._Scanner
_scan_hsp_header Method in class Bio.Blast.NCBIStandalone._Scanner
_scan_hsp_header Method in class Bio.Blast.NCBIWWW._Scanner
_scan_id Method in class Bio.Enzyme._Scanner
_scan_id Method in class Bio.Prosite._Scanner
_scan_id Method in class Bio.SwissProt.SProt._Scanner
_scan_keywords Method in class Bio.SwissProt.KeyWList._Scanner
_scan_kw Method in class Bio.SwissProt.SProt._Scanner
_scan_Lambda Method in class Bio.Rebase._Scanner
_scan_lengths Method in class Bio.Compass._Scanner
_scan_line Method in class Bio.Enzyme._Scanner
_scan_line Method in class Bio.Gobase._Scanner
_scan_line Method in class Bio.Prosite._Scanner
_scan_line Method in class Bio.Rebase._Scanner
_scan_line Method in class Bio.SwissProt.SProt._Scanner
_scan_ma Method in class Bio.Prosite._Scanner
_scan_masterslave_alignment Method in class Bio.Blast.NCBIStandalone._Scanner
_scan_masterslave_alignment Method in class Bio.Blast.NCBIWWW._Scanner
_scan_matches Method in class Bio.MEME.Parser._MASTScanner
_scan_methylation Method in class Bio.Rebase._Scanner
_scan_microorganism Method in class Bio.Rebase._Scanner
_scan_motifs Method in class Bio.MEME.Parser._MEMEScanner
_scan_name Method in class markupbase.ParserBase
_scan_names Method in class Bio.Compass._Scanner
_scan_nr Method in class Bio.Prosite._Scanner
_scan_oc Method in class Bio.SwissProt.SProt._Scanner
_scan_og Method in class Bio.SwissProt.SProt._Scanner
_scan_oh Method in class Bio.SwissProt.SProt._Scanner
_scan_one_pairwise_alignment Method in class Bio.Blast.NCBIStandalone._Scanner
_scan_one_pairwise_alignment Method in class Bio.Blast.NCBIWWW._Scanner
_scan_os Method in class Bio.SwissProt.SProt._Scanner
_scan_ox Method in class Bio.SwissProt.SProt._Scanner
_scan_pa Method in class Bio.Prosite._Scanner
_scan_pairwise_alignments Method in class Bio.Blast.NCBIStandalone._Scanner
_scan_pairwise_alignments Method in class Bio.Blast.NCBIWWW._Scanner
_scan_parameters Method in class Bio.Blast.NCBIStandalone._Scanner
_scan_parameters Method in class Bio.Blast.NCBIWWW._Scanner
_scan_pBR322 Method in class Bio.Rebase._Scanner
_scan_PhiX174 Method in class Bio.Rebase._Scanner
_scan_pr Method in class Bio.Enzyme._Scanner
_scan_profilewidth Method in class Bio.Compass._Scanner
_scan_prosite_refs Method in class Bio.Prosite.Prodoc._Scanner
_scan_protein_record Method in class Bio.Gobase._Scanner
_scan_prototype Method in class Bio.Rebase._Scanner
_scan_query_info Method in class Bio.Blast.NCBIWWW._Scanner
_scan_ra Method in class Bio.SwissProt.SProt._Scanner
_scan_rc Method in class Bio.SwissProt.SProt._Scanner
_scan_record Method in class Bio.Compass._Scanner
_scan_record Method in class Bio.Enzyme._Scanner
_scan_record Method in class Bio.Gobase._Scanner
_scan_record Method in class Bio.Medline._Scanner
_scan_record Method in class Bio.Prosite.Prodoc._Scanner
_scan_record Method in class Bio.Prosite._Scanner
_scan_record Method in class Bio.Rebase._Scanner
_scan_record Method in class Bio.Sequencing.Ace._Scanner
_scan_record Method in class Bio.Sequencing.Phd._Scanner
_scan_record Method in class Bio.SwissProt.SProt._Scanner
_scan_reference Method in class Bio.SwissProt.SProt._Scanner
_scan_refs Method in class Bio.Prosite.Prodoc._Scanner
_scan_rl Method in class Bio.SwissProt.SProt._Scanner
_scan_rn Method in class Bio.SwissProt.SProt._Scanner
_scan_rounds Method in class Bio.Blast.NCBIStandalone._Scanner
_scan_rounds Method in class Bio.Blast.NCBIWWW._Scanner
_scan_rp Method in class Bio.SwissProt.SProt._Scanner
_scan_rt Method in class Bio.SwissProt.SProt._Scanner
_scan_ru Method in class Bio.Prosite._Scanner
_scan_rx Method in class Bio.SwissProt.SProt._Scanner
_scan_scores Method in class Bio.Compass._Scanner
_scan_sequence Method in class Bio.Rebase._Scanner
_scan_sequence_data Method in class Bio.Sequencing.Ace._Scanner
_scan_sequence_data Method in class Bio.SwissProt.SProt._Scanner
_scan_sequence_record Method in class Bio.Gobase._Scanner
_scan_source Method in class Bio.Rebase._Scanner
_scan_sq Method in class Bio.SwissProt.SProt._Scanner
_scan_SV40 Method in class Bio.Rebase._Scanner
_scan_temperature Method in class Bio.Rebase._Scanner
_scan_terminator Method in class Bio.Enzyme._Scanner
_scan_terminator Method in class Bio.Prosite._Scanner
_scan_terminator Method in class Bio.SwissProt.SProt._Scanner
_scan_text Method in class Bio.Prosite.Prodoc._Scanner
_scan_threshold Method in class Bio.Compass._Scanner
_Scanner Class in module Bio.Blast.NCBIStandalone
_Scanner Class in module Bio.Blast.NCBIWWW
_Scanner Class in package Bio.Compass
_Scanner Class in package Bio.Enzyme
_Scanner Class in package Bio.Gobase
_Scanner Class in package Bio.Medline
_Scanner Class in module Bio.Prosite.Prodoc
_Scanner Class in package Bio.Prosite
_Scanner Class in package Bio.Rebase
_Scanner Class in module Bio.Sequencing.Ace
_Scanner Class in module Bio.Sequencing.Phd
_Scanner Class in module Bio.SwissProt.KeyWList
_Scanner Class in module Bio.SwissProt.SProt
_Scanner Class in package Bio.UniGene
_schema_from_motif Method in class Bio.NeuralNetwork.Gene.Schema.SchemaFactory
_score Method in class Bio.MEME.Motif.Instance
_secure_name Method in class Bio.Blast.NCBIXML._XMLparser
_select_names Method in class Martel.Expression.Expression
_select_names Method in class Martel.Expression.ExpressionList
_select_names Method in class Martel.Expression.Group
_select_names Method in class Martel.Expression.MaxRepeat
_select_names Method in class Martel.Expression.NullOp
_select_names Method in class Martel.Expression.PassThrough
_send_to_blasturl Function in module Bio.Blast.NCBIWWW
_SeqLength Class in module Bio.Search
_seqmatrix2strmatrix Function in module Bio.Nexus.Nexus
_seqname Method in class Bio.MEME.Motif.Instance
_sequence Method in class Bio.MEME.Motif.Instance
_sequence_name Method in class Bio.MEME.Parser._MEMEConsumer
_SequenceConsumer Class in module Bio.SwissProt.SProt
_set Method in class Bio.Nexus.Nexus.Nexus
_set Method in class Bio.config.DBRegistry.DBObject
_set_colors_and_shapes Method in class Bio.Graphics.Comparative.ComparativeScatterPlot
_set_current_seq Method in class Bio.MEME.Parser._MASTConsumer
_set_if_given Function in module Bio.Std
_set_up_genetic_algorithm Method in class Bio.NeuralNetwork.Gene.Schema.GeneticAlgorithmFinder
_set_up_wheel Method in class Bio.GA.Selection.RouletteWheel.RouletteWheelSelection
_settag Function in module Bio.Std
_ShelveIndex Class in module Bio.Index
_ShelveIndex__version Variable in class Bio.Index._ShelveIndex
_ShelveIndex__version_key Variable in class Bio.Index._ShelveIndex
_sort_keys Function in module Bio.NMR.xpktools
_sort_keys_by_values Function in module Bio.Nexus.Nexus
_stanzaformat Module in package Bio.config
_start Method in class Bio.MEME.Motif.Instance
_START Variable in class Bio.Parsers.spark.GenericParser
_START Variable in class Bio.Parsers.spark.GenericParser
_START Variable in class Bio.Parsers.spark.GenericParser
_START Variable in class Bio.Parsers.spark.GenericParser
_start_elem Function in module Bio.Medline.nlmmedline_001211_format
_start_elem Function in module Bio.Medline.nlmmedline_010319_format
_start_elem Function in module Bio.Medline.nlmmedline_011101_format
_start_elem Function in module Bio.Medline.nlmmedline_031101_format
_start_element Function in module Bio.MarkupEditor
_start_Hit Method in class Bio.Blast.NCBIXML.BlastParser
_start_Hsp Method in class Bio.Blast.NCBIXML.BlastParser
_start_Iteration Method in class Bio.Blast.NCBIXML.BlastParser
_startswith_tagtable_newline Function in module Martel.RecordReader
_startswith_tagtable_rest_of_line Function in module Martel.RecordReader
_statelabels Method in class Bio.Nexus.Nexus.Nexus
_stateset Method in class Bio.Nexus.Nexus.Nexus
_strand Method in class Bio.MEME.Motif.Instance
_strip_and_combine Function in module Bio.Emboss.Primer
_support Module in package Bio.config
_support Module in package Bio.dbdefs
_tabs Method in class Bio.EUtils.POM.ElementNode
_taxlabels Method in class Bio.Nexus.Nexus.Nexus
_taxpartition Method in class Bio.Nexus.Nexus.Nexus
_taxset Method in class Bio.Nexus.Nexus.Nexus
_test Function in module Bio.EUtils.MultiDict
_text_in Method in class Bio.Gobase._Scanner
_text_in Method in class Bio.Rebase._Scanner
_toobj Method in class Bio.Index._InMemoryIndex
_tostr Method in class Bio.Index._InMemoryIndex
_train_iis Function in module Bio.MaxEntropy
_translate Method in class Bio.Nexus.Nexus.Nexus
_tree Method in class Bio.Nexus.Nexus.Nexus
_treepartition Method in class Bio.Nexus.Nexus.Nexus
_treeset Method in class Bio.Nexus.Nexus.Nexus
_try_open_read Function in module Bio.NMR.xpktools
_try_open_write Function in module Bio.NMR.xpktools
_tuplestr Function in module Bio.EUtils.sourcegen
_unhandled Method in class Bio.ParserSupport.AbstractConsumer
_unhandled_section Method in class Bio.ParserSupport.AbstractConsumer
_uniform_norm Function in module Bio.MarkovModel
_unknown_nexus_block Method in class Bio.Nexus.Nexus.Nexus
_unmake_pickleable Method in class Bio.config.DBRegistry.BioSQLDB
_unmake_pickleable Method in class Bio.config.DBRegistry.CGIDB
_unmake_pickleable Method in class Bio.config.DBRegistry.DBObject
_use_tag_format Function in module Martel.Time
_utree Method in class Bio.Nexus.Nexus.Nexus
_validate_attribute Method in class Bio.EUtils.POM.ElementNode
_verify_attributes Method in class Bio.EUtils.POM.ElementNode
_verify_name Function in module Martel.Expression
_verify_subtypes Function in module Bio.Decode
_verify_test Function in module Bio.Prosite.Pattern
_version Method in class Bio.MEME.Parser.MASTRecord
_version Method in class Bio.MEME.Parser._MASTConsumer
_version Method in class Bio.MEME.Parser._MEMEConsumer
_viterbi Function in module Bio.MarkovModel
_walk Method in class Bio.Nexus.Trees.Tree
_warn Function in module Bio.config.SeqDBRegistry
_wrap_kegg Function in package Bio.KEGG
_write_kegg Function in package Bio.KEGG
_write_primary_table Function in module Bio.Mindy.FlatDB
_write_secondary_table Function in module Bio.Mindy.FlatDB
_write_text Method in class Bio.EUtils.POM.POMDocument
_XMLparser Class in module Bio.Blast.NCBIXML
abi_thumbprint Method in class Bio.Sequencing.Phd._RecordConsumer
abs Method in class Bio.FSSP.FSSPAlignDict
abs_res_num Variable in class Bio.FSSP.fssp_rec.align
Abstract Module in package Bio.GA.Selection
abstract Method in class Bio.Medline._RecordConsumer
abstract_author Method in class Bio.Medline._RecordConsumer
AbstractCommandline Class in package Bio.Application
AbstractConsumer Class in module Bio.ParserSupport
AbstractDPAlgorithms Class in module Bio.HMM.DynamicProgramming
AbstractLayer Class in module Bio.NeuralNetwork.BackPropagation.Layer
AbstractParser Class in module Bio.ParserSupport
AbstractPosition Class in module Bio.SeqFeature
AbstractSelection Class in module Bio.GA.Selection.Abstract
AbstractTrainer Class in module Bio.HMM.Trainer
acc Variable in class Bio.FSSP.fssp_rec.align
accession Method in class Bio.Prosite.Prodoc._RecordConsumer
accession Method in class Bio.Prosite._RecordConsumer
accession Method in class Bio.SwissProt.SProt._RecordConsumer
accession Method in class Bio.SwissProt.SProt._SequenceConsumer
Ace Module in package Bio.Sequencing
ACEFileRecord Class in module Bio.Sequencing.Ace
ACEParser Class in module Bio.Sequencing.Ace
acquire Method in class Martel.Dispatch.DispatchHandler
acquire Method in class Martel.Dispatch.Dispatcher
Adaptor Class in module BioSQL.BioSeqDatabase
add Method in class Bio.EUtils.POM.ElementNode
add Method in class Bio.Graphics.BasicChromosome._ChromosomeComponent
add Method in class Bio.MultiProc.Scheduler.Scheduler
add Method in class Bio.Nexus.Nexus.StepMatrix
add Method in class Bio.Nexus.Nodes.Chain
add Method in class Bio.Pathway.Rep.HashSet.HashSet
add Method in class Bio.config.FormatRegistry.FormatGroup
add Method in class Bio.config.Registry.RegisterableGroup
add Method in class Martel.Dispatch.MulticallEnd
add Method in class Martel.Dispatch.MulticallStart
add_after Method in class Bio.config.Registry.RegisterableGroup
add_align_list Method in class Bio.FSSP.FSSPAlignRec
add_attribute Method in class Bio.EUtils.sourcegen.ClassHolder
add_attribute Method in class Bio.EUtils.sourcegen.FunctionHolder
add_before Method in class Bio.config.Registry.RegisterableGroup
add_blank Method in class Bio.EUtils.sourcegen.SourceFile
add_class Method in class Bio.EUtils.sourcegen.SourceFile
add_comment Method in class Bio.EUtils.sourcegen.SourceFile
add_count Method in class Bio.Graphics.DisplayRepresentation.ChromosomeCounts
add_dbid Method in class Bio.builders.SeqRecord.sequence.BuildSeqRecord
add_dbxref Method in class Bio.builders.SeqRecord.sequence.BuildSeqRecord
add_dbxref_dbids Method in class Bio.builders.SeqRecord.sequence.BuildSeqRecord
add_description Method in class Bio.builders.SeqRecord.sequence.BuildSeqRecord
add_doc Method in class Bio.EUtils.sourcegen.SourceFile
add_edge Method in class Bio.Pathway.Rep.Graph.Graph
add_edge Method in class Bio.Pathway.Rep.MultiGraph.MultiGraph
add_entry Method in class Bio.Blast.ParseBlastTable.BlastTableRec
add_examples Method in class Bio.NeuralNetwork.Training.ExampleManager
add_feature_qualifier Method in class Bio.StdHandler.Handle_features
add_features Method in class Bio.builders.SeqRecord.sequence.BuildSeqRecord
add_filename Method in class Bio.Mindy.BaseDB.WriteDB
add_first_text_handler Function in module Bio.StdHandler
add_function Method in class Bio.EUtils.sourcegen.SourceFile
add_group Method in class Martel.Generate.GeneratorState
add_header Method in class Bio.builders.Search.search.BuildSearch
add_hsp Method in class Bio.builders.Search.search.BuildSearch
add_hsp_seqs Method in class Bio.StdHandler.Handle_hsp
add_import Method in class Bio.EUtils.sourcegen.SourceFile
add_instance Method in class Bio.AlignAce.Motif.Motif
add_instance Method in class Bio.MEME.Motif.Motif
add_instance Method in class Bio.MEME.Parser._MEMEConsumer
add_instance_from_values Method in class Bio.MEME.Motif.MEMEMotif
add_int_handler Function in module Bio.StdHandler
add_interaction Method in class Bio.Pathway.Network
add_label Method in class Bio.Graphics.DisplayRepresentation.ChromosomeCounts
add_location Method in class Bio.StdHandler.Handle_features
add_method Method in class Bio.EUtils.sourcegen.ClassHolder
add_module Method in class Bio.EUtils.POM.ObjectParserHandler
add_node Method in class Bio.Pathway.Rep.Graph.Graph
add_node Method in class Bio.Pathway.Rep.MultiGraph.MultiGraph
add_primer_set Method in class Bio.Emboss.Primer.PrimerSearchInputRecord
add_reaction Method in class Bio.Pathway.System
add_record Method in class Bio.Mindy.FlatDB.MemoryFlatDB
add_ref Method in class Bio.EUtils.POM.IDREFS
add_sequence Method in class Bio.Align.Generic.Alignment
add_sequence Method in class Bio.Nexus.Nexus.Nexus
add_sequence Method in class Bio.builders.SeqRecord.sequence.BuildSeqRecord
add_species Method in class Bio.Pathway.Network
add_stats Method in class Bio.builders.Search.search.BuildSearch
add_succ Method in class Bio.Nexus.Nodes.Node
add_table Method in class Bio.builders.Search.search.BuildSearch
add_test Method in class Martel.test.support.Storage
add_test_lines Method in class Martel.test.support.Storage
add_text Method in class Bio.EUtils.POM.Comment
add_text Method in class Bio.EUtils.POM.ElementNode
add_text Method in class Bio.EUtils.POM.IndentedText
add_text Method in class Bio.EUtils.POM.POMDocument
add_text_block_handler Function in module Bio.StdHandler
add_text_decode_handler Function in module Bio.StdHandler
add_text_dict_handler Function in module Bio.StdHandler
add_text_handler Function in module Bio.StdHandler
add_to_logodds Method in class Bio.MEME.Motif.MEMEMotif
add_to_logodds Method in class Bio.MEME.Parser._MEMEConsumer
add_to_pssm Method in class Bio.MEME.Motif.MEMEMotif
add_to_pssm Method in class Bio.MEME.Parser._MEMEConsumer
add_url Method in class Bio.NetCatch.NetCatch
add_value_handler Function in module Bio.StdHandler
addnode Method in class Bio.EUtils.POM.POMDocument
address Method in class Bio.Medline._RecordConsumer
addRule Method in class Bio.Parsers.spark.GenericParser
af Method in class Bio.Sequencing.Ace._RecordConsumer
af Class in module Bio.Sequencing.Ace
affine_penalty Class in module Bio.pairwise2
Affy Package in package Bio
AfterPosition Class in module Bio.SeqFeature
Ais Package in package Bio
Algorithm Class in module Bio.Search
Align Package in package Bio
align Method in class Bio.Blast.NCBIStandalone._HSPConsumer
align Class in module Bio.FSSP.fssp_rec
AlignAce Package in package Bio
AlignAce Function in module Bio.AlignAce.AlignAceStandalone
AlignAceCommandline Class in module Bio.AlignAce.Applications
AlignAceConsumer Class in module Bio.AlignAce.Parser
AlignAceParser Class in module Bio.AlignAce.Parser
AlignAceScanner Class in module Bio.AlignAce.Scanner
AlignAceStandalone Module in package Bio.AlignAce
AlignInfo Module in package Bio.Align
Alignment Class in module Bio.Align.Generic
Alignment Class in module Bio.Blast.Record
AlignmentHasDifferentLengthsError Class in package Bio.CAPS
all_ids Method in class Bio.Nexus.Nodes.Chain
all_letters_sum Method in class Bio.SubsMat.SeqMat
all_unambiguous Method in class Bio.NeuralNetwork.Gene.Schema.Schema
allitems Method in class Bio.EUtils.MultiDict.OrderedMultiDict
allitems Method in class Bio.EUtils.MultiDict.UnorderedMultiDict
allkeys Method in class Bio.EUtils.MultiDict.OrderedMultiDict
allkeys Method in class Bio.EUtils.MultiDict.UnorderedMultiDict
allow_all_transitions Method in class Bio.HMM.MarkovModel.MarkovModelBuilder
allow_transition Method in class Bio.HMM.MarkovModel.MarkovModelBuilder
allvalues Method in class Bio.EUtils.MultiDict.OrderedMultiDict
allvalues Method in class Bio.EUtils.MultiDict.UnorderedMultiDict
Alphabet Package in package Bio
Alphabet Class in package Bio.Alphabet
alphabet Variable in class Bio.Prosite.Pattern.Prosite
alphabet Function in module Bio.Std
alphabet_matches Variable in class Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet
AlphabetEncoder Class in package Bio.Alphabet
Alt Function in package Martel
Alt Class in module Martel.Expression
alternate_name Method in class Bio.Enzyme._RecordConsumer
ambiguity Method in class Bio.Parsers.spark.GenericParser
AmbiguousCodonTable Class in module Bio.Data.CodonTable
AmbiguousForwardTable Class in module Bio.Data.CodonTable
AmbiguousRepair Class in module Bio.GA.Repair.Stabilizing
amplifier Method in class Bio.Emboss.Primer._PrimerSearchRecordConsumer
amplifier_length Method in class Bio.Emboss.Primer._PrimerSearchRecordConsumer
amplifier_sequence Method in class Bio.Emboss.Primer._PrimerSearchRecordConsumer
And Class in module Bio.EUtils.Datatypes
annotations Class in module Bio.EUtils.Datatypes in class BioSQL.BioSeq.DBSeqRecord
Any Function in package Martel
Any Class in module Martel.Expression
AnyBut Function in package Martel
AnyEol Class in module Martel.Expression
apad Class in module Bio.EUtils.DTDs.LinkOut
append Method in class Bio.Crystal.Chain
append Method in class Bio.EUtils.POM.ElementNode
append Method in class Bio.EUtils.sourcegen.SourceFile
append Method in class Bio.Seq.MutableSeq
append Method in class Martel.msre_parse.SubPattern
append Method in class __builtin__.list
append_sets Method in class Bio.Nexus.Nexus.Nexus
Application Package in package Bio
application_name Function in module Bio.Std
application_version Function in module Bio.Std
ApplicationResult Class in package Bio.Application
Applications Module in package Bio.AlignAce
Applications Module in package Bio.Blast
Applications Module in package Bio.Emboss
args Variable in class exceptions.BaseException
args Variable in class exceptions.BaseException
args Variable in class exceptions.BaseException
args Variable in class exceptions.BaseException
args Variable in class exceptions.BaseException
args Variable in class exceptions.BaseException
args Variable in class exceptions.BaseException
args Variable in class exceptions.BaseException
args Variable in class exceptions.BaseException
args Variable in class exceptions.BaseException
args Variable in class exceptions.BaseException
args Variable in class exceptions.BaseException
args Variable in class exceptions.BaseException
args Variable in class exceptions.BaseException
args Variable in class exceptions.BaseException
args Variable in class exceptions.BaseException
args Variable in class exceptions.BaseException
args Variable in class exceptions.BaseException
args Variable in class exceptions.BaseException
args Variable in class exceptions.BaseException
args Variable in class exceptions.BaseException
args Variable in class exceptions.BaseException
args Variable in class exceptions.BaseException
args Variable in class exceptions.BaseException
args Variable in class exceptions.BaseException
args Variable in class exceptions.BaseException
asdict Function in module Bio.listfns
Assert Function in package Martel
Assert Class in module Martel.Expression
AssertNot Function in package Martel
AtBeginning Class in module Martel.Expression
AtEnd Class in module Martel.Expression
attempt_read_and_call Function in module Bio.ParserSupport
ATTLIST Variable in class Bio.EUtils.DTDs.LinkOut.IconUrl
ATTLIST Variable in class Bio.EUtils.DTDs.LinkOut.ObjectUrl
ATTLIST Variable in class Bio.EUtils.DTDs.LinkOut.Url
ATTLIST Variable in class Bio.EUtils.DTDs.LinkOut.apad
ATTLIST Variable in class Bio.EUtils.DTDs.LinkOut.pad
ATTLIST Variable in class Bio.EUtils.DTDs.LinkOut.strip
ATTLIST Variable in class Bio.EUtils.DTDs.LinkOut.subs
ATTLIST Variable in class Bio.EUtils.DTDs.eLink_020511.Id
ATTLIST Variable in class Bio.EUtils.DTDs.eSummary_020511.Item
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
ATTLIST Variable in class Bio.EUtils.POM.ElementNode
Attribute Class in module Bio.EUtils.DTDs.LinkOut
Attribute Class in module Bio.EUtils.DTDs.eLink_020511
AttributeList Class in module Bio.EUtils.POM
attributes Method in class Bio.EUtils.POM.ElementNode
AttributesImpl Class in module xml.sax.xmlreader
augment Method in class Bio.Parsers.spark.GenericParser
author Method in class Bio.Medline._RecordConsumer
autocommit Method in class BioSQL.BioSeqDatabase.Adaptor
autocommit Method in class BioSQL.DBUtils.Generic_dbutils
autocommit Method in class BioSQL.DBUtils.Pgdb_dbutils
autocommit Method in class BioSQL.DBUtils.Psycopg_dbutils
available_results Method in class Bio.Application.ApplicationResult
back_table Variable in class Bio.Data.CodonTable.CodonTable
back_table Variable in class Bio.Data.CodonTable.CodonTable
back_table Variable in class Bio.Data.CodonTable.CodonTable
back_table Variable in class Bio.Data.CodonTable.CodonTable
back_table Variable in class Bio.Data.CodonTable.CodonTable
back_transcribe Function in module Bio.Seq
back_transcribe Method in class Bio.Transcribe.Transcribe
back_transcribe Function in module Bio.utils
back_translate Method in class Bio.Translate.Translator
back_translate Function in module Bio.utils
backpropagate Method in class Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer
backpropagate Method in class Bio.NeuralNetwork.BackPropagation.Layer.InputLayer
backpropagate Method in class Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer
BackPropagation Package in package Bio.NeuralNetwork
backward_algorithm Method in class Bio.HMM.DynamicProgramming.AbstractDPAlgorithms
BadMatrix Class in package Bio.SubsMat
BarChartDistribution Class in module Bio.Graphics.Distribution
Base Class in module Bio.EUtils.DTDs.LinkOut
base_str Method in class Bio.Prosite.Pattern.PrositeTerm
BaseDB Module in package Bio.Mindy
BaseDBIdsRecordSet Class in module Bio.EUtils.DBIdsClient
BaseException Class in module exceptions
BaseFlatDB Class in module Bio.Mindy.FlatDB
BaseHistoryRecordSet Class in module Bio.EUtils.HistoryClient
BaseSeqRecordIndexer Class in module Bio.Mindy.SimpleSeqRecord
basestring Class in module __builtin__
BasicChromosome Module in package Bio.Graphics
BasicNetwork Class in module Bio.NeuralNetwork.BackPropagation.Network
BaumWelchTrainer Class in module Bio.HMM.Trainer
BeforePosition Class in module Bio.SeqFeature
begin_contig Method in class Bio.Sequencing.Ace._RecordConsumer
begin_sequence Method in class Bio.Sequencing.Phd._RecordConsumer
BetweenPosition Class in module Bio.SeqFeature
bf_search Function in module Bio.Pathway.Rep.MultiGraph
BinaryOp Class in module Bio.EUtils.Datatypes
Bio Package
BioCorbaDB Class in module Bio.config.DBRegistry
BioformatDBName Class in module Bio.DBXRef
BioSeq Module in package BioSQL
BioSeqDatabase Module in package BioSQL
BioSeqDatabase Class in module BioSQL.BioSeqDatabase
BioSQL Package
BioSQLDB Class in module Bio.config.DBRegistry
BisectFile Class in module Bio.Mindy.FlatDB
Blast Package in package Bio
blast Function in module Bio.Blast.NCBIWWW
Blast Class in module Bio.Blast.Record
blast Package in package Bio.expressions
blast_cutoff Method in class Bio.Blast.NCBIStandalone._ParametersConsumer
blastall Function in module Bio.Blast.NCBIStandalone
BlastallCommandline Class in module Bio.Blast.Applications
BlastErrorParser Class in module Bio.Blast.NCBIStandalone
BlastParser Class in module Bio.Blast.NCBIStandalone
BlastParser Class in module Bio.Blast.NCBIWWW
BlastParser Class in module Bio.Blast.NCBIXML
blastpgp Function in module Bio.Blast.NCBIStandalone
BlastTableEntry Class in module Bio.Blast.ParseBlastTable
BlastTableReader Class in module Bio.Blast.ParseBlastTable
BlastTableRec Class in module Bio.Blast.ParseBlastTable
blasturl Function in module Bio.Blast.NCBIWWW
Block Class in module Bio.Nexus.Nexus
blocks Module in package Bio.expressions
Bol Function in package Martel
bootstrap Method in class Bio.Nexus.Nexus.Nexus
bq_data Method in class Bio.Sequencing.Ace._RecordConsumer
bq_header Method in class Bio.Sequencing.Ace._RecordConsumer
branchlength2support Method in class Bio.Nexus.Trees.Tree
Brief Class in module Bio.EUtils.DTDs.LinkOut
bs Method in class Bio.Sequencing.Ace._RecordConsumer
bs Class in module Bio.Sequencing.Ace
build_align Method in class Bio.Ais.Immune
build_resnum_list Method in class Bio.FSSP.FSSPAlignDict
buildASTNode Method in class Bio.Parsers.spark.GenericASTBuilder
builders Package in package Bio
BuildSearch Class in module Bio.builders.Search.search
BuildSeqRecord Class in module Bio.builders.SeqRecord.sequence
buildState Method in class Bio.Parsers.spark.GenericParser
buildTree Method in class Bio.Parsers.spark.GenericParser
buildTree_r Method in class Bio.Parsers.spark.GenericParser
byte_concat Function in module Bio.HotRand
calc_affine_penalty Function in module Bio.pairwise2
calculate Function in module Bio.LogisticRegression
calculate Function in module Bio.MaxEntropy
calculate Function in module Bio.NaiveBayes
calculate Function in module Bio.kNN
calculate_fitness Method in class Bio.NeuralNetwork.Gene.Schema.DifferentialSchemaFitness
calculate_fitness Method in class Bio.NeuralNetwork.Gene.Schema.MostCountSchemaFitness
call Method in class Martel.Generate.HandleRepeatCount
call_method Method in class Bio.Sequencing.Phd._RecordConsumer
call_number Method in class Bio.Medline._RecordConsumer
Callback Class in module Martel.Dispatch
calltag Method in class Martel.Generate.HandleRepeatCount
capitalize Method in class __builtin__.str
CAPS Package in package Bio
CAPSMap Class in package Bio.CAPS
Capture Class in module Martel.test.test_macros
cartesian Method in class Bio.Pathway.Rep.HashSet.HashSet
cas_registry_number Method in class Bio.Medline._RecordConsumer
Case Function in package Martel
catalytic_activity Method in class Bio.Enzyme._RecordConsumer
CatchFields Class in module Martel.test.test_delimiter
category Variable in class Bio.EUtils.Datatypes.FieldNotFound
category Variable in class Bio.EUtils.Datatypes.OutputMessage
category Variable in class Bio.EUtils.Datatypes.PhraseIgnored
category Variable in class Bio.EUtils.Datatypes.PhraseNotFound
category Variable in class Bio.EUtils.Datatypes.QuotedPhraseNotFound
CDATA Class in module Bio.EUtils.POM
CelConsumer Class in module Bio.Affy.CelFile
CelFile Module in package Bio.Affy
CelParser Class in module Bio.Affy.CelFile
CelRecord Class in module Bio.Affy.CelFile
CelScanner Class in module Bio.Affy.CelFile
center Method in class __builtin__.str
CGIDB Class in module Bio.config.DBRegistry
Chain Class in package Bio.Crystal
Chain Class in module Bio.Nexus.Nodes
chain_id Variable in class Bio.FSSP.fssp_rec.align
ChainException Class in module Bio.Nexus.Nodes
characters Method in class Bio.Blast.NCBIXML._XMLparser
characters Method in class Bio.EUtils.POM.ObjectParserHandler
characters Method in class Bio.Medline.NLMMedlineXML._IndexerHandler
characters Method in class Bio.Mindy.XPath.GrabXPathNodes
characters Method in class Bio.ParserSupport.EventGenerator
characters Method in class Martel.Dispatch.Dispatcher
characters Method in class Martel.LAX.LAX
characters Method in class Martel.test.support.Dump
characters Method in class Martel.test.test_delimiter.CatchFields
characters Method in class xml.sax.handler.ContentHandler
CharBuffer Class in module Bio.Nexus.Nexus
check_assert Function in module Martel.Generate
check_assert_not Function in module Martel.Generate
check_at_beginning Function in module Martel.Generate
check_dicts Function in module Martel.test.test_attrs
check_element Function in module Martel.test.test_attrs
check_error_pos Function in module Martel.test.test_optimize
CheckAssert Class in module Martel.Generate
CheckAssertNot Class in module Martel.Generate
CheckGood Class in module Martel.test.support
checkgroup Method in class Martel.convert_re.GroupNames
checkgroup Method in class Martel.msre_parse.Pattern
CheckGroupRef Class in module Martel.Generate
CheckLinkSet Class in module Bio.EUtils.Datatypes
chem Method in class Bio.Sequencing.Phd._RecordConsumer
child_edges Method in class Bio.Pathway.Rep.Graph.Graph
child_edges Method in class Bio.Pathway.Rep.MultiGraph.MultiGraph
children Method in class Bio.Pathway.Rep.Graph.Graph
children Method in class Bio.Pathway.Rep.MultiGraph.MultiGraph
chomp Function in module Bio.Decode
chompchomp Function in module Bio.Decode
choose_format Function in module Bio.Medline.NLMMedlineXML
chromat_file Method in class Bio.Sequencing.Phd._RecordConsumer
Chromosome Class in module Bio.Graphics.BasicChromosome
CHROMOSOME Method in class Bio.UniGene._RecordConsumer
ChromosomeCounts Class in module Bio.Graphics.DisplayRepresentation
ChromosomeSegment Class in module Bio.Graphics.BasicChromosome
Citation Class in module Bio.Medline.NLMMedlineXML
CitationParser Class in module Bio.Medline.NLMMedlineXML
class_update_date Method in class Bio.Medline._RecordConsumer
ClassHolder Class in module Bio.EUtils.sourcegen
classify Function in module Bio.LogisticRegression
classify Function in module Bio.MaxEntropy
classify Function in module Bio.NaiveBayes
classify Function in module Bio.kNN
clear Method in class Bio.Crystal.Crystal
clear Method in class Bio.Index._InMemoryIndex
clear Method in class Bio.Prosite.ExPASyDictionary
clear Method in class Bio.Prosite.Prodoc.ExPASyDictionary
clear Method in class Bio.PubMed.Dictionary
clear Method in class Bio.SwissProt.SProt.ExPASyDictionary
clear Method in class __builtin__.dict
close Method in class Bio.FilteredReader.FilteredReader
close Method in class Bio.Mindy.FlatDB.MemoryFlatDB
close Method in class Bio.MultiProc.copen._ProcHandle
close Method in class BioSQL.BioSeqDatabase.Adaptor
close Method in class Martel.Parser.Parser
close Method in class Martel.Parser.RecordParser
close Method in class sgmllib.SGMLParser
closegroup Method in class Martel.convert_re.GroupNames
closegroup Method in class Martel.msre_parse.Pattern
cmp_dicts Function in module Martel.test.test_attrs
co_data Method in class Bio.Sequencing.Ace._RecordConsumer
co_header Method in class Bio.Sequencing.Ace._RecordConsumer
CodonTable Module in package Bio.Data
CodonTable Class in module Bio.Data.CodonTable
cofactor Method in class Bio.Enzyme._RecordConsumer
collapse Method in class Bio.Nexus.Nodes.Chain
collectRules Method in class Bio.Parsers.spark.GenericParser
Cols Method in class Bio.Affy.CelFile.CelConsumer
combine Function in module Bio.Nexus.Nexus
command_line Method in class Bio.AlignAce.Parser.AlignAceConsumer
Commandline Class in module Bio.Nexus.Nexus
Comment Class in module Bio.EUtils.POM
comment Method in class Bio.EUtils.POM.ElementNode
comment Method in class Bio.Enzyme._RecordConsumer
comment Method in class Bio.Prosite._RecordConsumer
comment Method in class Bio.SwissProt.SProt._RecordConsumer
comments Method in class Bio.Emboss.Primer._Primer3RecordConsumer
comments Method in class Bio.Medline._RecordConsumer
commit Method in class BioSQL.BioSeqDatabase.Adaptor
common_ancestor Method in class Bio.Nexus.Trees.Tree
Comparative Module in package Bio.Graphics
ComparativeScatterPlot Class in module Bio.Graphics.Comparative
compare Function in module Martel.test.test_Expression
compare_motifs Method in class Bio.MEME.Motif.MEMEMotif
CompareAce Function in module Bio.AlignAce.CompareAceStandalone
CompareAceCommandline Class in module Bio.AlignAce.Applications
CompareAceConsumer Class in module Bio.AlignAce.Parser
CompareAceParser Class in module Bio.AlignAce.Parser
CompareAceScanner Class in module Bio.AlignAce.Scanner
CompareAceStandalone Module in package Bio.AlignAce
Compass Package in package Bio
compile Function in module Bio.Prosite.Pattern
compile_file Function in module Bio.EUtils.dtd2py
complement Method in class Bio.Seq.MutableSeq
complement Method in class Bio.Seq.Seq
compression Module in package Bio.Mindy
compute_accum_weight Method in class Bio.Ais.Immune
Config Module in package Bio.EUtils
config Package in package Bio
consensus Function in module Bio.Nexus.Trees
constant Method in class Bio.Nexus.Nexus.Nexus
contains Method in class Bio.Alphabet.Alphabet
contains Method in class Bio.Alphabet.AlphabetEncoder
contains Method in class Bio.Alphabet.Gapped
contains Method in class Bio.Alphabet.HasStopCodon
contains Method in class Bio.Pathway.Rep.HashSet.HashSet
ContentHandler Class in module xml.sax.handler
CONTENTMODEL Variable in class Bio.EUtils.DTDs.LinkOut.Attribute
CONTENTMODEL Variable in class Bio.EUtils.DTDs.LinkOut.Base
CONTENTMODEL Variable in class Bio.EUtils.DTDs.LinkOut.Brief
CONTENTMODEL Variable in class Bio.EUtils.DTDs.LinkOut.Database
CONTENTMODEL Variable in class Bio.EUtils.DTDs.LinkOut.ExclQuery
CONTENTMODEL Variable in class Bio.EUtils.DTDs.LinkOut.IconUrl
CONTENTMODEL Variable in class Bio.EUtils.DTDs.LinkOut.InclQuery
CONTENTMODEL Variable in class Bio.EUtils.DTDs.LinkOut.Link
CONTENTMODEL Variable in class Bio.EUtils.DTDs.LinkOut.LinkId
CONTENTMODEL Variable in class Bio.EUtils.DTDs.LinkOut.LinkSet
CONTENTMODEL Variable in class Bio.EUtils.DTDs.LinkOut.Name
CONTENTMODEL Variable in class Bio.EUtils.DTDs.LinkOut.NameAbbr
CONTENTMODEL Variable in class Bio.EUtils.DTDs.LinkOut.ObjId
CONTENTMODEL Variable in class Bio.EUtils.DTDs.LinkOut.ObjectList
CONTENTMODEL Variable in class Bio.EUtils.DTDs.LinkOut.ObjectSelector
CONTENTMODEL Variable in class Bio.EUtils.DTDs.LinkOut.ObjectUrl
CONTENTMODEL Variable in class Bio.EUtils.DTDs.LinkOut.Provider
CONTENTMODEL Variable in class Bio.EUtils.DTDs.LinkOut.ProviderId
CONTENTMODEL Variable in class Bio.EUtils.DTDs.LinkOut.Query
CONTENTMODEL Variable in class Bio.EUtils.DTDs.LinkOut.Rule
CONTENTMODEL Variable in class Bio.EUtils.DTDs.LinkOut.RuleToMany
CONTENTMODEL Variable in class Bio.EUtils.DTDs.LinkOut.Separator
CONTENTMODEL Variable in class Bio.EUtils.DTDs.LinkOut.SubObjectSelector
CONTENTMODEL Variable in class Bio.EUtils.DTDs.LinkOut.SubProvider
CONTENTMODEL Variable in class Bio.EUtils.DTDs.LinkOut.SubjectType
CONTENTMODEL Variable in class Bio.EUtils.DTDs.LinkOut.Url
CONTENTMODEL Variable in class Bio.EUtils.DTDs.LinkOut.UrlName
CONTENTMODEL Variable in class Bio.EUtils.DTDs.LinkOut.apad
CONTENTMODEL Variable in class Bio.EUtils.DTDs.LinkOut.normalize
CONTENTMODEL Variable in class Bio.EUtils.DTDs.LinkOut.pad
CONTENTMODEL Variable in class Bio.EUtils.DTDs.LinkOut.strip
CONTENTMODEL Variable in class Bio.EUtils.DTDs.LinkOut.subs
CONTENTMODEL Variable in class Bio.EUtils.DTDs.LinkOut.tolower
CONTENTMODEL Variable in class Bio.EUtils.DTDs.LinkOut.toupper
CONTENTMODEL Variable in class Bio.EUtils.DTDs.eInfo_020511.Count
CONTENTMODEL Variable in class Bio.EUtils.DTDs.eInfo_020511.DbInfo
CONTENTMODEL Variable in class Bio.EUtils.DTDs.eInfo_020511.DbList
CONTENTMODEL Variable in class Bio.EUtils.DTDs.eInfo_020511.DbName
CONTENTMODEL Variable in class Bio.EUtils.DTDs.eInfo_020511.DbTo
CONTENTMODEL Variable in class Bio.EUtils.DTDs.eInfo_020511.Descriptor
CONTENTMODEL Variable in class Bio.EUtils.DTDs.eInfo_020511.ERROR
CONTENTMODEL Variable in class Bio.EUtils.DTDs.eInfo_020511.Field
CONTENTMODEL Variable in class Bio.EUtils.DTDs.eInfo_020511.FiledList
CONTENTMODEL Variable in class Bio.EUtils.DTDs.eInfo_020511.Hierarchy
CONTENTMODEL Variable in class Bio.EUtils.DTDs.eInfo_020511.IsDate
CONTENTMODEL Variable in class Bio.EUtils.DTDs.eInfo_020511.IsNumerical
CONTENTMODEL Variable in class Bio.EUtils.DTDs.eInfo_020511.Link
CONTENTMODEL Variable in class Bio.EUtils.DTDs.eInfo_020511.LinkList
CONTENTMODEL Variable in class Bio.EUtils.DTDs.eInfo_020511.Menu
CONTENTMODEL Variable in class Bio.EUtils.DTDs.eInfo_020511.MenuName
CONTENTMODEL Variable in class Bio.EUtils.DTDs.eInfo_020511.Name
CONTENTMODEL Variable in class Bio.EUtils.DTDs.eInfo_020511.SingleToken
CONTENTMODEL Variable in class Bio.EUtils.DTDs.eInfo_020511.TermCount
CONTENTMODEL Variable in class Bio.EUtils.DTDs.eInfo_020511.eInfoResult
CONTENTMODEL Variable in class Bio.EUtils.DTDs.eLink_020511.Attribute
CONTENTMODEL Variable in class Bio.EUtils.DTDs.eLink_020511.DbFrom
CONTENTMODEL Variable in class Bio.EUtils.DTDs.eLink_020511.DbTo
CONTENTMODEL Variable in class Bio.EUtils.DTDs.eLink_020511.ERROR
CONTENTMODEL Variable in class Bio.EUtils.DTDs.eLink_020511.IconUrl
CONTENTMODEL Variable in class Bio.EUtils.DTDs.eLink_020511.Id
CONTENTMODEL Variable in class Bio.EUtils.DTDs.eLink_020511.IdCheckList
CONTENTMODEL Variable in class Bio.EUtils.DTDs.eLink_020511.IdList
CONTENTMODEL Variable in class Bio.EUtils.DTDs.eLink_020511.IdUrlList
CONTENTMODEL Variable in class Bio.EUtils.DTDs.eLink_020511.IdUrlSet
CONTENTMODEL Variable in class Bio.EUtils.DTDs.eLink_020511.Info
CONTENTMODEL Variable in class Bio.EUtils.DTDs.eLink_020511.Link
CONTENTMODEL Variable in class Bio.EUtils.DTDs.eLink_020511.LinkName
CONTENTMODEL Variable in class Bio.EUtils.DTDs.eLink_020511.LinkSet
CONTENTMODEL Variable in class Bio.EUtils.DTDs.eLink_020511.LinkSetDb
CONTENTMODEL Variable in class Bio.EUtils.DTDs.eLink_020511.Name
CONTENTMODEL Variable in class Bio.EUtils.DTDs.eLink_020511.NameAbbr
CONTENTMODEL Variable in class Bio.EUtils.DTDs.eLink_020511.ObjUrl
CONTENTMODEL Variable in class Bio.EUtils.DTDs.eLink_020511.Provider
CONTENTMODEL Variable in class Bio.EUtils.DTDs.eLink_020511.Score
CONTENTMODEL Variable in class Bio.EUtils.DTDs.eLink_020511.SubjectType
CONTENTMODEL Variable in class Bio.EUtils.DTDs.eLink_020511.Url
CONTENTMODEL Variable in class Bio.EUtils.DTDs.eLink_020511.eLinkResult
CONTENTMODEL Variable in class Bio.EUtils.DTDs.ePost_020511.ERROR
CONTENTMODEL Variable in class Bio.EUtils.DTDs.ePost_020511.Id
CONTENTMODEL Variable in class Bio.EUtils.DTDs.ePost_020511.InvalidIdList
CONTENTMODEL Variable in class Bio.EUtils.DTDs.ePost_020511.QueryKey
CONTENTMODEL Variable in class Bio.EUtils.DTDs.ePost_020511.WebEnv
CONTENTMODEL Variable in class Bio.EUtils.DTDs.ePost_020511.ePostResult
CONTENTMODEL Variable in class Bio.EUtils.DTDs.eSearch_020511.Count
CONTENTMODEL Variable in class Bio.EUtils.DTDs.eSearch_020511.ERROR
CONTENTMODEL Variable in class Bio.EUtils.DTDs.eSearch_020511.ErrorList
CONTENTMODEL Variable in class Bio.EUtils.DTDs.eSearch_020511.Explode
CONTENTMODEL Variable in class Bio.EUtils.DTDs.eSearch_020511.Field
CONTENTMODEL Variable in class Bio.EUtils.DTDs.eSearch_020511.FieldNotFound
CONTENTMODEL Variable in class Bio.EUtils.DTDs.eSearch_020511.From
CONTENTMODEL Variable in class Bio.EUtils.DTDs.eSearch_020511.Id
CONTENTMODEL Variable in class Bio.EUtils.DTDs.eSearch_020511.IdList
CONTENTMODEL Variable in class Bio.EUtils.DTDs.eSearch_020511.OP
CONTENTMODEL Variable in class Bio.EUtils.DTDs.eSearch_020511.OutputMessage
CONTENTMODEL Variable in class Bio.EUtils.DTDs.eSearch_020511.PhraseIgnored
CONTENTMODEL Variable in class Bio.EUtils.DTDs.eSearch_020511.PhraseNotFound
CONTENTMODEL Variable in class Bio.EUtils.DTDs.eSearch_020511.QueryKey
CONTENTMODEL Variable in class Bio.EUtils.DTDs.eSearch_020511.QueryTranslation
CONTENTMODEL Variable in class Bio.EUtils.DTDs.eSearch_020511.QuotedPhraseNotFound
CONTENTMODEL Variable in class Bio.EUtils.DTDs.eSearch_020511.RetMax
CONTENTMODEL Variable in class Bio.EUtils.DTDs.eSearch_020511.RetStart
CONTENTMODEL Variable in class Bio.EUtils.DTDs.eSearch_020511.Term
CONTENTMODEL Variable in class Bio.EUtils.DTDs.eSearch_020511.TermSet
CONTENTMODEL Variable in class Bio.EUtils.DTDs.eSearch_020511.To
CONTENTMODEL Variable in class Bio.EUtils.DTDs.eSearch_020511.Translation
CONTENTMODEL Variable in class Bio.EUtils.DTDs.eSearch_020511.TranslationSet
CONTENTMODEL Variable in class Bio.EUtils.DTDs.eSearch_020511.TranslationStack
CONTENTMODEL Variable in class Bio.EUtils.DTDs.eSearch_020511.WarningList
CONTENTMODEL Variable in class Bio.EUtils.DTDs.eSearch_020511.WebEnv
CONTENTMODEL Variable in class Bio.EUtils.DTDs.eSearch_020511.eSearchResult
CONTENTMODEL Variable in class Bio.EUtils.DTDs.eSummary_020511.DocSum
CONTENTMODEL Variable in class Bio.EUtils.DTDs.eSummary_020511.ERROR
CONTENTMODEL Variable in class Bio.EUtils.DTDs.eSummary_020511.Id
CONTENTMODEL Variable in class Bio.EUtils.DTDs.eSummary_020511.Item
CONTENTMODEL Variable in class Bio.EUtils.DTDs.eSummary_020511.eSummaryResult
ContentModel Class in module Bio.EUtils.POM
CONTENTMODEL Variable in class Bio.EUtils.POM.ElementNode
CONTENTMODEL Variable in class Bio.EUtils.POM.ElementNode
contents Function in module Bio.listfns
Contig Class in module Bio.Sequencing.Ace
converged Method in class Bio.Blast.NCBIStandalone._DescriptionConsumer
ConversionMutation Class in module Bio.GA.Mutation.Simple
convert Method in class Bio.FormatIO.FormatIO
convert_absolute_support Method in class Bio.Nexus.Trees.Tree
convert_any Function in module Martel.convert_re
convert_assert Function in module Martel.convert_re
convert_assert_not Function in module Martel.convert_re
convert_at Function in module Martel.convert_re
convert_branch Function in module Martel.convert_re
convert_charref Method in class sgmllib.SGMLParser
convert_codepoint Method in class sgmllib.SGMLParser
convert_entityref Method in class sgmllib.SGMLParser
convert_groupref Function in module Martel.convert_re
convert_in Function in module Martel.convert_re
convert_list Function in module Martel.convert_re
convert_literal Function in module Martel.convert_re
convert_max_repeat Function in module Martel.convert_re
convert_newline Function in module Martel.convert_re
convert_not_literal Function in module Martel.convert_re
convert_re Module in package Martel
convert_std_feature Function in module Bio.builders.SeqRecord.sequence
convert_subpattern Function in module Martel.convert_re
convert_summary_Date Function in module Bio.EUtils.parse
convert_summary_Date_string Function in module Bio.EUtils.parse
convert_summary_Integer Function in module Bio.EUtils.parse
convert_summary_Items Function in module Bio.EUtils.parse
convert_summary_List Function in module Bio.EUtils.parse
convert_summary_String Function in module Bio.EUtils.parse
convert_summary_Unknown Function in module Bio.EUtils.parse
ConvertDispatchHandler Class in module Bio.StdHandler
ConvertHandler Class in module Bio.StdHandler
copen Module in package Bio.MultiProc
copen_fn Function in module Bio.MultiProc.copen
copen_sys Function in module Bio.MultiProc.copen
copy Method in class Bio.Crystal.Crystal
copy Method in class Bio.GA.Organism.Organism
copy Method in class Bio.Prosite.ExPASyDictionary
copy Method in class Bio.Prosite.Pattern.PrositeTerm
copy Method in class Bio.Prosite.Prodoc.ExPASyDictionary
copy Method in class Bio.PubMed.Dictionary
copy Method in class Bio.SwissProt.SProt.ExPASyDictionary
copy Method in class Martel.Expression.Any
copy Method in class Martel.Expression.AnyEol
copy Method in class Martel.Expression.Assert
copy Method in class Martel.Expression.AtBeginning
copy Method in class Martel.Expression.AtEnd
copy Method in class Martel.Expression.Debug
copy Method in class Martel.Expression.Dot
copy Method in class Martel.Expression.Expression
copy Method in class Martel.Expression.ExpressionList
copy Method in class Martel.Expression.FastFeature
copy Method in class Martel.Expression.Group
copy Method in class Martel.Expression.GroupRef
copy Method in class Martel.Expression.HeaderFooter
copy Method in class Martel.Expression.Literal
copy Method in class Martel.Expression.MaxRepeat
copy Method in class Martel.Expression.NullOp
copy Method in class Martel.Expression.ParseRecords
copy Method in class Martel.Expression.PassThrough
copy Method in class Martel.Expression.Str
copy Method in class Martel.IterParser.IterHeaderFooter
copy Method in class Martel.IterParser.IterRecords
copy Method in class Martel.Iterator.IteratorRecords
copy Method in class Martel.Parser.HeaderFooterParser
copy Method in class Martel.Parser.Parser
copy Method in class Martel.Parser.RecordParser
copy Method in class __builtin__.dict
copy Method in class xml.sax.xmlreader.AttributesImpl
count Method in class Bio.Crystal.Chain
Count Class in module Bio.EUtils.DTDs.eInfo_020511
Count Class in module Bio.EUtils.DTDs.eSearch_020511
count Method in class Bio.NeuralNetwork.Gene.Pattern.PatternRepository
count Method in class Bio.Seq.MutableSeq
count Method in class Bio.Seq.Seq
count Function in module Bio.listfns
count Method in class __builtin__.list
count Method in class __builtin__.str
count_monomers Function in module Bio.utils
count_records Function in module Martel.test.test_RecordReader2
CountErrors Class in module Martel.test.test_Parser
CountLines Class in module Martel.RecordReader
CountRecords Class in module Martel.test.test_Parser
country Method in class Bio.Medline._RecordConsumer
crc Module in package Bio
crc64 Function in module Bio.crc
create Function in module Bio.Mindy.FlatDB
create_berkeleydb Function in module Bio.Mindy.SimpleSeqRecord
create_flatdb Function in module Bio.Mindy.SimpleSeqRecord
create_lymphocyte Method in class Bio.Ais.Immune
CreateDict Class in module Bio.PropertyManager
crop_matrix Method in class Bio.Nexus.Nexus.Nexus
Crossover Package in package Bio.GA
Crystal Package in package Bio
Crystal Class in package Bio.Crystal
CrystalError Class in package Bio.Crystal
cstatus Method in class Bio.Nexus.Nexus.Nexus
ct Class in module Bio.Sequencing.Ace
ct_data Method in class Bio.Sequencing.Ace._RecordConsumer
ct_start Method in class Bio.Sequencing.Ace._RecordConsumer
Data Package in package Bio
data Package in package Bio in class BioSQL.BioSeq.DBSeq
data_entered Method in class Bio.Rebase._RecordConsumer
data_modified Method in class Bio.Rebase._RecordConsumer
data_table Function in module Bio.NMR.xpktools
databank_reference Method in class Bio.Enzyme._RecordConsumer
database Method in class Bio.Blast.NCBIStandalone._DatabaseReportConsumer
Database Class in module Bio.EUtils.DTDs.LinkOut
Database Class in module Bio.Search
database_cross_reference Method in class Bio.SwissProt.SProt._RecordConsumer
database_info Method in class Bio.Blast.NCBIStandalone._HeaderConsumer
database_length Method in class Bio.Blast.NCBIStandalone._ParametersConsumer
database_name Function in module Bio.Std
database_num_letters Function in module Bio.Std
database_num_sequences Function in module Bio.Std
database_reference Method in class Bio.Prosite._RecordConsumer
DatabaseDict Class in module Bio.EUtils.Config
DatabaseInfo Class in module Bio.EUtils.Config
DatabaseLoader Class in module BioSQL.Loader
DatabaseRemover Class in module BioSQL.Loader
DatabaseReport Class in module Bio.Blast.Record
DataRecord Class in package Bio.Enzyme
Datatypes Module in package Bio.EUtils
Date Class in module Bio.EUtils.Datatypes
date Method in class Bio.Prosite._RecordConsumer
date Method in class Bio.SwissProt.SProt._RecordConsumer
date_field Method in class Bio.Gobase._RecordConsumer
DateRange Class in module Bio.EUtils.Datatypes
dbdefs Package in package Bio
DbFrom Class in module Bio.EUtils.DTDs.eLink_020511
DBGroup Class in module Bio.config.DBRegistry
dbid Function in module Bio.Std
DBIds Function in package Bio.EUtils
dbids Function in package Bio.EUtils in class Bio.EUtils.DBIdsClient.DBIdsLookup
dbids Function in package Bio.EUtils in class Bio.EUtils.DBIdsClient.DBIdsLookup in class Bio.EUtils.Datatypes.CheckLinkSet
DBIds Class in module Bio.EUtils.Datatypes
dbids Class in module Bio.EUtils.Datatypes in class Bio.EUtils.Datatypes.LinkSetDb
dbids Class in module Bio.EUtils.Datatypes in class Bio.EUtils.Datatypes.LinkSetDb in class Bio.EUtils.HistoryClient.HistoryLookup
DBIdsClient Module in package Bio.EUtils
DBIdsClient Class in module Bio.EUtils.DBIdsClient
DBIdsLookup Class in module Bio.EUtils.DBIdsClient
DBIdsRecord Class in module Bio.EUtils.DBIdsClient
DbInfo Class in module Bio.EUtils.DTDs.eInfo_020511
DbList Class in module Bio.EUtils.DTDs.eInfo_020511
DbName Class in module Bio.EUtils.DTDs.eInfo_020511
DBObject Class in module Bio.config.DBRegistry
DBRegistry Module in package Bio.config
DBRegistry Class in module Bio.config.DBRegistry
DBSeq Class in module BioSQL.BioSeq
DBSeqRecord Class in module BioSQL.BioSeq
DBServer Class in module BioSQL.BioSeqDatabase
DbTo Class in module Bio.EUtils.DTDs.eInfo_020511
DbTo Class in module Bio.EUtils.DTDs.eLink_020511
DBUtils Module in package BioSQL
DBXRef Module in package Bio
DBXRef Class in module Bio.DBXRef
dbxref Function in module Bio.Std
dbxref_dbid Function in module Bio.Std
dbxref_dbname Function in module Bio.Std
dbxref_negate Function in module Bio.Std
dbxrefs Function in module Bio.Std in class BioSQL.BioSeq.DBSeqRecord
Debug Class in module Martel.Expression
Decode Module in package Bio
decode Method in class __builtin__.str
DecodeParser Class in module Bio.Decode
DecodeScanner Class in module Bio.Decode
default Method in class Bio.Parsers.spark.GenericASTTraversal
DEFAULT_PSEUDO Variable in class Bio.HMM.MarkovModel.MarkovModelBuilder
define_block Function in module Bio.expressions.genbank
del_attribute Method in class Bio.EUtils.sourcegen.ClassHolder
del_attribute Method in class Bio.EUtils.sourcegen.FunctionHolder
del_parser Method in class Bio.EUtils.POM.POMDocument
DelimitedFields Function in package Martel
delimiter Module in package Martel.test.testformats
delimiter Function in module Martel.test.testformats.delimiter
delnode Method in class Bio.EUtils.POM.POMDocument
demo Method in class reportlab.graphics.widgetbase.Widget
description Method in class Bio.Blast.NCBIStandalone._DescriptionConsumer
Description Class in module Bio.Blast.Record
description Method in class Bio.Enzyme._RecordConsumer
description Method in class Bio.Prosite._RecordConsumer
description Function in module Bio.Std
description Method in class Bio.SwissProt.SProt._RecordConsumer
description Method in class Bio.SwissProt.SProt._SequenceConsumer
description_block Function in module Bio.Std
description_header Method in class Bio.Blast.NCBIStandalone._DescriptionConsumer
description_line Function in module Bio.Std
Descriptor Class in module Bio.EUtils.DTDs.eInfo_020511
destroy Method in class Bio.EUtils.POM.ElementNode
destroy Method in class Bio.EUtils.POM.IndentedText
destroy_transition Method in class Bio.HMM.MarkovModel.MarkovModelBuilder
detach Method in class Bio.EUtils.POM.ElementNode
df_search Function in module Bio.Pathway.Rep.MultiGraph
dict Class in module __builtin__
Dictionary Class in package Bio.Gobase
Dictionary Class in package Bio.Prosite
Dictionary Class in module Bio.Prosite.Prodoc
Dictionary Class in module Bio.PubMed
Dictionary Class in package Bio.Rebase
Dictionary Class in module Bio.SwissProt.SProt
dictionary_match Class in module Bio.pairwise2
DictLookup Class in module Bio.Mindy.BaseDB
difference Method in class Bio.Pathway.Rep.HashSet.HashSet
difference Function in module Bio.listfns
DifferentialCutsite Class in package Bio.CAPS
DifferentialSchemaFitness Class in module Bio.NeuralNetwork.Gene.Schema
Digits Function in package Martel
disease Method in class Bio.Enzyme._RecordConsumer
DiskFlatDB Class in module Bio.Mindy.FlatDB
Dispatch Module in package Martel
Dispatcher Class in module Martel.Dispatch
DispatchHandler Class in module Martel.Dispatch
display Method in class Bio.Nexus.Trees.Tree
DisplayRepresentation Module in package Bio.Graphics
distance Method in class Bio.Nexus.Trees.Tree
distance Module in package Bio
Distribution Module in package Bio.Graphics
DistributionPage Class in module Bio.Graphics.Distribution
Diversity Module in package Bio.GA.Selection
DiversitySelection Class in module Bio.GA.Selection.Diversity
DNAAlphabet Class in package Bio.Alphabet
do_br Method in class Bio.InterPro.InterProParser
do_br Method in class Bio.Ndb.NdbParser
do_crossover Method in class Bio.GA.Crossover.General.SafeFitnessCrossover
do_crossover Method in class Bio.GA.Crossover.GeneralPoint.GeneralPointCrossover
do_crossover Method in class Bio.GA.Crossover.Uniform.UniformCrossover
do_input Method in class Bio.Blast.NCBIWWW._FormParser
do_it Function in module Bio.EUtils.dtd2py
do_test Function in module Martel.test.test_delimiter
DocSum Class in module Bio.EUtils.DTDs.eSummary_020511
documentation Method in class Bio.Prosite._RecordConsumer
Dot Class in module Martel.Expression
download_many Function in module Bio.PubMed
draw Method in class Bio.Graphics.BasicChromosome.Chromosome
draw Method in class Bio.Graphics.BasicChromosome.ChromosomeSegment
draw Method in class Bio.Graphics.BasicChromosome.Organism
draw Method in class Bio.Graphics.BasicChromosome._ChromosomeComponent
draw Method in class Bio.Graphics.Distribution.BarChartDistribution
draw Method in class Bio.Graphics.Distribution.DistributionPage
draw Method in class Bio.Graphics.Distribution.LineDistribution
draw Method in class reportlab.graphics.widgetbase.Widget
draw_to_file Method in class Bio.Graphics.Comparative.ComparativeScatterPlot
dropoff_1st_pass Method in class Bio.Blast.NCBIStandalone._ParametersConsumer
ds Method in class Bio.Sequencing.Ace._RecordConsumer
ds Class in module Bio.Sequencing.Ace
dtd2py Module in package Bio.EUtils
dtd_end Method in class Bio.EUtils.POM.DTDConsumerForSourceGeneration
dtd_start Method in class Bio.EUtils.POM.DTDConsumerForSourceGeneration
DTDConsumerForSourceGeneration Class in module Bio.EUtils.POM
DTDs Package in package Bio.EUtils
dumb_consensus Method in class Bio.Align.AlignInfo.SummaryInfo
dump Method in class Martel.msre_parse.SubPattern
Dump Class in module Martel.test.support
dump Method in class Martel.test.support.Storage
dump Function in module Martel.test.test_swissprot38
dump_saved Function in module Bio.FilteredReader
dumpProperties Method in class reportlab.graphics.widgetbase.PropHolder
dye Method in class Bio.Sequencing.Phd._RecordConsumer
DynamicProgramming Module in package Bio.HMM
EConsenseCommandline Class in module Bio.Emboss.Applications
edges Method in class Bio.Pathway.Rep.Graph.Graph
edges Method in class Bio.Pathway.Rep.MultiGraph.MultiGraph
efetch Method in class Bio.EUtils.DBIdsClient.PublicationDBIdsFetchMixin
efetch Method in class Bio.EUtils.DBIdsClient.SequenceDBIdsFetchMixin
efetch Method in class Bio.EUtils.HistoryClient.PublicationHistoryFetchMixin
efetch Method in class Bio.EUtils.HistoryClient.SequenceHistoryFetchMixin
efetch Function in module Bio.WWW.NCBI
efetch_using_dbids Method in class Bio.EUtils.ThinClient.ThinClient
efetch_using_history Method in class Bio.EUtils.ThinClient.ThinClient
effective_database_length Method in class Bio.Blast.NCBIStandalone._ParametersConsumer
effective_hsp_length Method in class Bio.Blast.NCBIStandalone._ParametersConsumer
effective_query_length Method in class Bio.Blast.NCBIStandalone._ParametersConsumer
effective_search_space Method in class Bio.Blast.NCBIStandalone._ParametersConsumer
effective_search_space_used Method in class Bio.Blast.NCBIStandalone._ParametersConsumer
eInfo_020511 Module in package Bio.EUtils.DTDs
eInfoResult Class in module Bio.EUtils.DTDs.eInfo_020511
EInvertedCommandline Class in module Bio.Emboss.Applications
elapsed Method in class Bio.MultiProc.copen._ProcHandle
element Method in class Martel.LAX.LAX
element Method in class Martel.LAX.LAXAttrs
element Method in class Martel.LAX.LAXPositions
ElementInfo Class in module Martel.LAX
ElementNode Class in module Bio.EUtils.POM
elink Method in class Bio.EUtils.DBIdsClient.DBIdsLookup
elink Method in class Bio.EUtils.HistoryClient.HistoryLookup
elink Function in module Bio.WWW.NCBI
eLink_020511 Module in package Bio.EUtils.DTDs
elink_using_dbids Method in class Bio.EUtils.ThinClient.ThinClient
elink_using_history Method in class Bio.EUtils.ThinClient.ThinClient
eLinkResult Class in module Bio.EUtils.DTDs.eLink_020511
embl Module in package Bio.dbdefs
embl Package in package Bio.expressions
embl Module in package Bio.formatdefs
embl Module in package Bio.writers.SeqRecord
embl65 Module in package Bio.expressions.embl
Emboss Package in package Bio
empty Method in class Bio.Pathway.Rep.HashSet.HashSet
empty Module in package Bio.writers.SeqRecord
Empty Function in package Martel
encode Method in class __builtin__.str
encode_motif Method in class Bio.NeuralNetwork.Gene.Schema.Schema
Encodings Package in package Bio
end Method in class Bio.Prosite.Pattern.PrositeMatch
end Method in class Bio.StdHandler.Handle_feature_location
end Method in class Bio.StdHandler.Handle_feature_location
end Method in class Bio.StdHandler.Handle_feature_qualifier
end Method in class Bio.StdHandler.Handle_features
end Method in class Bio.StdHandler.Handle_hsp_seqalign
end Method in class Bio.StdHandler.Handle_hsp_seqalign
end Method in class Bio.StdHandler.Handle_hsp_seqalign
end Method in class Bio.StdHandler.Handle_hsp_seqalign
end Method in class Bio.StdHandler.Handle_hsp_seqalign
end Method in class Bio.StdHandler.Handle_hsp_seqalign
end Method in class Bio.StdHandler.Handle_search_header
end Method in class Bio.StdHandler.Handle_search_header
end Method in class Bio.StdHandler.Handle_search_header
end Method in class Bio.StdHandler.Handle_search_header
end Method in class Bio.StdHandler.Handle_search_header
end Method in class Bio.StdHandler.Handle_search_header
end Method in class Bio.StdHandler.Handle_search_header
end Method in class Bio.StdHandler.Handle_search_info
end Method in class Bio.StdHandler.Handle_search_info
end Method in class Bio.StdHandler.Handle_search_table
end Method in class Bio.builders.Search.search.BuildSearch
end Method in class Bio.builders.Search.search.BuildSearch
end Method in class Martel.LAX.LAX
end_ Method in class Bio.StdHandler.Handle_search_info
end_ Method in class Bio.builders.Search.search.BuildSearch
end_a Method in class Bio.InterPro.InterProParser
end_a Method in class Bio.NetCatch.ExtractUrls
end_alignment Method in class Bio.Blast.NCBIStandalone._AlignmentConsumer
end_alignment Method in class Bio.Blast.NCBIStandalone._BlastConsumer
end_alignment Method in class Bio.Blast.NCBIStandalone._PSIBlastConsumer
end_block Method in class Bio.StdHandler.Handle_search_header
end_block Method in class Bio.builders.Search.search.BuildSearch
end_contig Method in class Bio.Sequencing.Ace._RecordConsumer
end_database_report Method in class Bio.Blast.NCBIStandalone._BlastConsumer
end_database_report Method in class Bio.Blast.NCBIStandalone._DatabaseReportConsumer
end_database_report Method in class Bio.Blast.NCBIStandalone._PSIBlastConsumer
end_dbid Method in class Bio.StdHandler.Handle_dbid
end_dbxref Method in class Bio.StdHandler.Handle_dbxref
end_dbxref_dbid Method in class Bio.StdHandler.Handle_dbxref
end_dbxref_dbname Method in class Bio.StdHandler.Handle_dbxref
end_description Method in class Bio.StdHandler.Handle_description
end_description_block Method in class Bio.StdHandler.Handle_description
end_descriptions Method in class Bio.Blast.NCBIStandalone._BlastConsumer
end_descriptions Method in class Bio.Blast.NCBIStandalone._DescriptionConsumer
end_descriptions Method in class Bio.Blast.NCBIStandalone._PSIBlastConsumer
end_fast_dbxref Method in class Bio.StdHandler.Handle_dbxref
end_feature Method in class Bio.StdHandler.Handle_feature_location
end_feature Method in class Bio.StdHandler.Handle_features
end_feature_block Method in class Bio.StdHandler.Handle_features
end_feature_description Method in class Bio.StdHandler.Handle_features
end_feature_location Method in class Bio.StdHandler.Handle_feature_location
end_feature_qualifier Method in class Bio.StdHandler.Handle_feature_qualifier
end_feature_qualifier_description Method in class Bio.StdHandler.Handle_feature_qualifier
end_form Method in class Bio.Blast.NCBIWWW._FormParser
end_h1 Method in class Bio.Ndb.NdbParser
end_h2 Method in class Bio.InterPro.InterProParser
end_h2 Method in class Bio.Ndb.NdbParser
end_header Method in class Bio.Blast.NCBIStandalone._BlastConsumer
end_header Method in class Bio.Blast.NCBIStandalone._HeaderConsumer
end_header Method in class Bio.Blast.NCBIStandalone._PSIBlastConsumer
end_hit Method in class Bio.builders.Search.search.BuildSearch
end_hsp Method in class Bio.Blast.NCBIStandalone._BlastConsumer
end_hsp Method in class Bio.Blast.NCBIStandalone._HSPConsumer
end_hsp Method in class Bio.Blast.NCBIStandalone._PSIBlastConsumer
end_hsp Method in class Bio.StdHandler.Handle_hsp
end_hsp Method in class Bio.StdHandler.Handle_hsp_seqalign
end_hsp_frame Method in class Bio.StdHandler.Handle_hsp
end_hsp_seqalign_homology_seq Method in class Bio.StdHandler.Handle_hsp_seqalign
end_hsp_seqalign_query_leader Method in class Bio.StdHandler.Handle_hsp_seqalign
end_hsp_seqalign_query_seq Method in class Bio.StdHandler.Handle_hsp_seqalign
end_hsp_seqalign_subject_seq Method in class Bio.StdHandler.Handle_hsp_seqalign
end_hsp_value Method in class Bio.StdHandler.Handle_hsp
end_i Method in class Bio.InterPro.InterProParser
end_i Method in class Bio.Ndb.NdbParser
end_li Method in class Bio.InterPro.InterProParser
end_li Method in class Bio.Ndb.NdbParser
end_ol Method in class Bio.InterPro.InterProParser
end_parameters Method in class Bio.Blast.NCBIStandalone._BlastConsumer
end_parameters Method in class Bio.Blast.NCBIStandalone._PSIBlastConsumer
end_parameters Method in class Bio.Blast.NCBIStandalone._ParametersConsumer
end_record Method in class Bio.Emboss.Primer._Primer3RecordConsumer
end_record Method in class Bio.Emboss.Primer._PrimerSearchRecordConsumer
end_record Method in class Bio.Medline._RecordConsumer
end_record Method in class Bio.Mindy.SimpleSeqRecord.FixDocumentBuilder
end_record Method in class Bio.Prosite.Prodoc._RecordConsumer
end_record Method in class Bio.Prosite._RecordConsumer
end_record Method in class Bio.SwissProt.SProt._RecordConsumer
end_record Method in class Bio.SwissProt.SProt._SequenceConsumer
end_record Method in class Bio.builders.SeqRecord.sequence.BuildSeqRecord
end_search_header Method in class Bio.StdHandler.Handle_search_header
end_search_table Method in class Bio.StdHandler.Handle_search_table
end_search_table_entry Method in class Bio.StdHandler.Handle_search_table
end_search_table_value Method in class Bio.StdHandler.Handle_search_table
end_sequence Method in class Bio.Gobase._RecordConsumer
end_sequence Method in class Bio.Rebase._RecordConsumer
end_sequence Method in class Bio.Sequencing.Phd._RecordConsumer
end_sequence Method in class Bio.StdHandler.Handle_sequence
end_sequence_block Method in class Bio.StdHandler.Handle_sequence
end_sub Method in class Bio.Ndb.NdbParser
end_td Method in class Bio.InterPro.InterProParser
end_ul Method in class Bio.InterPro.InterProParser
end_ul Method in class Bio.Ndb.NdbParser
endDocument Method in class Bio.EUtils.POM.ObjectParserHandler
endDocument Method in class Bio.ParserSupport.EventGenerator
endDocument Method in class Martel.Dispatch.Dispatcher
endDocument Method in class Martel.Iterator.StoreEvents
endDocument Method in class Martel.LAX.LAX
endDocument Method in class Martel.test.support.CheckGood
endDocument Method in class Martel.test.support.Dump
endDocument Method in class xml.sax.handler.ContentHandler
endElement Method in class Bio.Blast.NCBIXML._XMLparser
endElement Method in class Bio.EUtils.POM.ObjectParserHandler
endElement Method in class Bio.Medline.NLMMedlineXML._IndexerHandler
endElement Method in class Bio.Mindy.XPath.GrabXPathNodes
endElement Method in class Bio.ParserSupport.EventGenerator
endElement Method in class Bio.StdHandler.ConvertHandler
endElement Method in class Bio.StdHandler.RecognizeHandler
endElement Method in class Martel.Dispatch.Dispatcher
endElement Method in class Martel.Iterator.StoreEvents
endElement Method in class Martel.LAX.LAX
endElement Method in class Martel.test.support.Dump
endElement Method in class Martel.test.test_delimiter.CatchFields
endElement Method in class Martel.test.test_macros.Capture
endElement Method in class xml.sax.handler.ContentHandler
endElementNS Method in class xml.sax.handler.ContentHandler
endPrefixMapping Method in class xml.sax.handler.ContentHandler
EndsWith Class in module Martel.RecordReader
endswith Method in class __builtin__.str
ENeighborCommandline Class in module Bio.Emboss.Applications
english_abstract Method in class Bio.Medline._RecordConsumer
ENTITIES Class in module Bio.EUtils.POM
ENTITY Class in module Bio.EUtils.POM
entity_or_charref Variable in class sgmllib.SGMLParser
entity_or_charref Variable in class sgmllib.SGMLParser
entity_or_charref Variable in class sgmllib.SGMLParser
entity_or_charref Variable in class sgmllib.SGMLParser
entity_or_charref Variable in class sgmllib.SGMLParser
entity_or_charref Variable in class sgmllib.SGMLParser
entity_or_charref Variable in class sgmllib.SGMLParser
entitydefs Variable in class sgmllib.SGMLParser
entitydefs Variable in class sgmllib.SGMLParser
entitydefs Variable in class sgmllib.SGMLParser
entitydefs Variable in class sgmllib.SGMLParser
entitydefs Variable in class sgmllib.SGMLParser
entitydefs Variable in class sgmllib.SGMLParser
entitydefs Variable in class sgmllib.SGMLParser
entry_date Method in class Bio.Medline._RecordConsumer
entry_month Method in class Bio.Medline._RecordConsumer
Enumeration Class in module Bio.EUtils.POM
Enzyme Package in package Bio
enzyme_num Method in class Bio.Rebase._RecordConsumer
EnzymeRecord Class in package Bio.Enzyme
Eof Function in package Martel
Eol Function in package Martel
epost Method in class Bio.EUtils.ThinClient.ThinClient
epost Function in module Bio.WWW.NCBI
ePost_020511 Module in package Bio.EUtils.DTDs
ePostResult Class in module Bio.EUtils.DTDs.ePost_020511
EProtDistCommandline Class in module Bio.Emboss.Applications
EProtParsCommandline Class in module Bio.Emboss.Applications
equal_weight Function in module Bio.kNN
Error Class in package Bio.Crystal
ERROR Class in module Bio.EUtils.DTDs.eInfo_020511
ERROR Class in module Bio.EUtils.DTDs.eLink_020511
ERROR Class in module Bio.EUtils.DTDs.ePost_020511
ERROR Class in module Bio.EUtils.DTDs.eSearch_020511
ERROR Class in module Bio.EUtils.DTDs.eSummary_020511
ERROR Variable in class Bio.EUtils.Datatypes.Problem
ERROR Variable in class Bio.EUtils.Datatypes.Problem
ERROR Variable in class Bio.EUtils.Datatypes.Problem
ERROR Variable in class Bio.EUtils.Datatypes.Problem
ERROR Variable in class Bio.EUtils.Datatypes.Problem
ERROR Variable in class Bio.EUtils.Datatypes.Problem
ERROR Variable in class Bio.EUtils.Datatypes.Problem
ERROR Variable in class Bio.EUtils.Datatypes.Problem
error Method in class Bio.Parsers.spark.GenericParser
error Method in class Bio.Parsers.spark.GenericScanner
error Method in class Martel.Iterator.StoreEvents
error Class in module Martel.msre_constants
error Method in class Martel.test.support.Dump
error Method in class Martel.test.test_Parser.CountErrors
error Method in class Martel.test.test_optimize.GetErrorPos
error Method in class markupbase.ParserBase
error Method in class sgmllib.SGMLParser
error Method in class xml.sax.handler.ErrorHandler
ErrorHandler Class in module xml.sax.handler
ErrorList Class in module Bio.EUtils.DTDs.eSearch_020511
ErrorProblem Class in module Bio.EUtils.Datatypes
escape Function in module Bio.EUtils.POM
escape Function in module Martel.Dispatch
escape Function in module Martel.Expression
esearch Method in class Bio.EUtils.ThinClient.ThinClient
esearch Function in module Bio.WWW.NCBI
eSearch_020511 Module in package Bio.EUtils.DTDs
eSearchResult Class in module Bio.EUtils.DTDs.eSearch_020511
ESeqBootCommandline Class in module Bio.Emboss.Applications
Est2GenomeCommandline Class in module Bio.Emboss.Applications
estimate_params Method in class Bio.HMM.Trainer.AbstractTrainer
esummary Method in class Bio.EUtils.DBIdsClient.DBIdsLookup
esummary Method in class Bio.EUtils.HistoryClient.HistoryLookup
eSummary_020511 Module in package Bio.EUtils.DTDs
esummary_using_dbids Method in class Bio.EUtils.ThinClient.ThinClient
esummary_using_history Method in class Bio.EUtils.ThinClient.ThinClient
eSummaryResult Class in module Bio.EUtils.DTDs.eSummary_020511
ETandemCommandline Class in module Bio.Emboss.Applications
euclidean Function in module Bio.distance
euclidean_py Function in module Bio.distance
EUtils Package in package Bio
EUtilsDB Class in module Bio.config.DBRegistry
EUtilsError Class in module Bio.EUtils.Datatypes
EUtilsSearchError Class in module Bio.EUtils.Datatypes
EventGenerator Class in module Bio.ParserSupport
EventStream Class in module Martel.Iterator
Everything Class in module Martel.RecordReader
evolve Method in class Bio.GA.Evolver.GenerationEvolver
Evolver Module in package Bio.GA
ExactPosition Class in module Bio.SeqFeature
ExampleManager Class in module Bio.NeuralNetwork.Training
Exception Class in module exceptions
ExclQuery Class in module Bio.EUtils.DTDs.LinkOut
execute Method in class BioSQL.BioSeqDatabase.Adaptor
execute_and_fetch_col0 Method in class BioSQL.BioSeqDatabase.Adaptor
execute_and_fetchall Method in class BioSQL.BioSeqDatabase.Adaptor
execute_one Method in class BioSQL.BioSeqDatabase.Adaptor
expand_template Function in module Martel.msre_parse
expandtabs Method in class __builtin__.str
ExPASy Module in package Bio.WWW
ExPASyDictionary Class in package Bio.Prosite
ExPASyDictionary Class in module Bio.Prosite.Prodoc
ExPASyDictionary Class in module Bio.SwissProt.SProt
Explode Class in module Bio.EUtils.DTDs.eSearch_020511
export_fasta Method in class Bio.Nexus.Nexus.Nexus
EXPRESS Method in class Bio.UniGene._RecordConsumer
Expression Class in module Bio.EUtils.Datatypes
Expression Module in package Martel
Expression Class in module Martel.Expression
ExpressionList Class in module Martel.Expression
expressions Package in package Bio
extend Method in class Bio.EUtils.POM.ElementNode
extend Method in class Bio.Seq.MutableSeq
extend Method in class __builtin__.list
ExtendedIUPACDNA Class in module Bio.Alphabet.IUPAC
ExtendedIUPACProtein Class in module Bio.Alphabet.IUPAC
extract_keywords Function in module Bio.SwissProt.KeyWList
extract_urls Method in class Bio.NetCatch.ExtractUrls
ExtractUrls Class in module Bio.NetCatch
EZRetrieve Module in package Bio
fast_dbxref Function in module Bio.Std
fasta Module in package Bio.dbdefs
fasta Module in package Bio.expressions
fasta Module in package Bio.writers.SeqRecord
fasta_mult_align Method in class Bio.FSSP.FSSPAlignDict
FastacmdCommandline Class in module Bio.Blast.Applications
FastFeature Class in module Martel.Expression
fatalError Method in class Bio.StdHandler.RecognizeHandler
fatalError Method in class Martel.Iterator.StoreEvents
fatalError Method in class Martel.test.support.Dump
fatalError Method in class Martel.test.test_Parser.CountErrors
fatalError Method in class xml.sax.handler.ErrorHandler
fcmp Function in module Bio.mathfns
feature Function in module Bio.Std
Feature Class in module Bio.StdHandler
feature_block Function in module Bio.Std
feature_description Function in module Bio.Std
feature_location Function in module Bio.Std
feature_location_end Function in module Bio.Std
feature_location_start Function in module Bio.Std
feature_name Function in module Bio.Std
feature_qualifier Function in module Bio.Std
feature_qualifier_description Function in module Bio.Std
feature_qualifier_name Function in module Bio.Std
feature_table Method in class Bio.SwissProt.SProt._RecordConsumer
FeatureLocation Class in module Bio.SeqFeature
features Class in module Bio.SeqFeature in class BioSQL.BioSeq.DBSeqRecord
features Method in class Martel.Expression.Expression
features Method in class Martel.Expression.ExpressionList
features Method in class Martel.Expression.FastFeature
features Method in class Martel.Expression.Group
features Method in class Martel.Expression.HeaderFooter
features Method in class Martel.Expression.MaxRepeat
features Method in class Martel.Expression.ParseRecords
features Method in class Martel.Expression.PassThrough
feed Method in class Bio.Affy.CelFile.CelScanner
feed Method in class Bio.AlignAce.Scanner.AlignAceScanner
feed Method in class Bio.AlignAce.Scanner.CompareAceScanner
feed Method in class Bio.Blast.NCBIStandalone._Scanner
feed Method in class Bio.Blast.NCBIWWW._Scanner
feed Method in class Bio.Compass._Scanner
feed Method in class Bio.Emboss.Primer._Primer3Scanner
feed Method in class Bio.Emboss.Primer._PrimerSearchScanner
feed Method in class Bio.Enzyme._Scanner
feed Method in class Bio.Gobase._Scanner
feed Method in class Bio.InterPro.InterProParser
feed Method in class Bio.MEME.Parser._MASTScanner
feed Method in class Bio.MEME.Parser._MEMEScanner
feed Method in class Bio.Medline._Scanner
feed Method in class Bio.Ndb.NdbParser
feed Method in class Bio.NetCatch.ExtractUrls
feed Method in class Bio.Prosite.Prodoc._Scanner
feed Method in class Bio.Prosite._Scanner
feed Method in class Bio.Rebase._Scanner
feed Method in class Bio.Sequencing.Ace._Scanner
feed Method in class Bio.Sequencing.Phd._Scanner
feed Method in class Bio.SwissProt.KeyWList._Scanner
feed Method in class Bio.SwissProt.SProt._Scanner
feed Method in class Bio.UniGene._Scanner
feed Method in class sgmllib.SGMLParser
fetch Method in class Bio.EUtils.Mixins.PublicationFetchMixin
fetch_dbid_by_dbname Method in class BioSQL.BioSeqDatabase.Adaptor
fetch_seqid_by_accession Method in class BioSQL.BioSeqDatabase.Adaptor
fetch_seqid_by_display_id Method in class BioSQL.BioSeqDatabase.Adaptor
fetch_seqid_by_identifier Method in class BioSQL.BioSeqDatabase.Adaptor
fetch_seqid_by_version Method in class BioSQL.BioSeqDatabase.Adaptor
fetch_seqids_by_accession Method in class BioSQL.BioSeqDatabase.Adaptor
fff_rec Class in module Bio.FSSP.fssp_rec
Field Class in module Bio.EUtils.DTDs.eInfo_020511
Field Class in module Bio.EUtils.DTDs.eSearch_020511
FieldNotFound Class in module Bio.EUtils.DTDs.eSearch_020511
FieldNotFound Class in module Bio.EUtils.Datatypes
File Module in package Bio
FiledList Class in module Bio.EUtils.DTDs.eInfo_020511
fileno Method in class Bio.MultiProc.copen._ProcHandle
fill_chromosome Method in class Bio.Graphics.DisplayRepresentation.ChromosomeCounts
fill_header Method in class Bio.FSSP.FSSPHeader
fill_hot_cache Method in class Bio.HotRand.HotCache
filter Function in module Bio.FSSP.FSSPTools
filter Method in class Bio.FilteredReader.FilteredReader
FilteredReader Module in package Bio
FilteredReader Class in module Bio.FilteredReader
find Method in class Bio.EUtils.POM.ElementNode
find Method in class Bio.NeuralNetwork.Gene.Motif.MotifFinder
find Method in class Bio.NeuralNetwork.Gene.Schema.SchemaFinder
find Method in class Bio.NeuralNetwork.Gene.Signature.SignatureFinder
find Function in module Bio.triefind
find Method in class __builtin__.str
find_ambiguous Method in class Bio.NeuralNetwork.Gene.Schema.Schema
find_anychar Function in module Bio.stringfns
find_builder Method in class Bio.config.FormatRegistry.FormatRegistry
find_differences Method in class Bio.NeuralNetwork.Gene.Motif.MotifFinder
find_differences Method in class Bio.NeuralNetwork.Gene.Schema.SchemaFinder
find_elements Method in class Bio.EUtils.POM.ElementNode
find_matches Method in class Bio.NeuralNetwork.Gene.Schema.Schema
find_related Function in module Bio.PubMed
find_schemas Method in class Bio.NeuralNetwork.Gene.Schema.GeneticAlgorithmFinder
find_states Function in module Bio.MarkovModel
find_submodules Function in module Bio.config._support
find_terms Function in module Bio.Prosite.Pattern
find_words Function in module Bio.triefind
find_writer Method in class Bio.config.FormatRegistry.FormatRegistry
finish_endtag Method in class sgmllib.SGMLParser
finish_shorttag Method in class sgmllib.SGMLParser
finish_starttag Method in class sgmllib.SGMLParser
fix Method in class Bio.Crystal.Crystal
fix_punctuation Function in module Bio.FilteredReader
FixDocumentBuilder Class in module Bio.Mindy.SimpleSeqRecord
fixspaces Function in module Bio.Decode
FlatDB Module in package Bio.Mindy
flatten Method in class Martel.Dispatch.Multicall
Float Class in module Bio.Decode
Float Function in package Martel
float_param Function in module Bio.expressions.blast.ncbiblast
float_stat Function in module Bio.expressions.blast.ncbiblast
flush Method in class Bio.Mindy.FlatDB.MemoryFlatDB
format_alignment Function in module Bio.pairwise2
FormatConvert Module in package Bio.Align
FormatConverter Class in module Bio.Align.FormatConvert
formatdefs Package in package Bio
FormatGroup Class in module Bio.config.FormatRegistry
FormatIO Module in package Bio
FormatIO Class in module Bio.FormatIO
FormatIOIterator Class in module Bio.FormatIO
FormatObject Class in module Bio.config.FormatRegistry
FormatRegistry Module in package Bio.config
FormatRegistry Class in module Bio.config.FormatRegistry
formats Package in package Martel
forward_algorithm Method in class Bio.HMM.DynamicProgramming.AbstractDPAlgorithms
forward_gc Method in class Bio.Emboss.Primer._Primer3RecordConsumer
forward_length Method in class Bio.Emboss.Primer._Primer3RecordConsumer
forward_seq Method in class Bio.Emboss.Primer._Primer3RecordConsumer
forward_start Method in class Bio.Emboss.Primer._Primer3RecordConsumer
forward_table Variable in class Bio.Data.CodonTable.CodonTable
forward_table Variable in class Bio.Data.CodonTable.CodonTable
forward_table Variable in class Bio.Data.CodonTable.CodonTable
forward_table Variable in class Bio.Data.CodonTable.CodonTable
forward_table Variable in class Bio.Data.CodonTable.CodonTable
forward_tm Method in class Bio.Emboss.Primer._Primer3RecordConsumer
found_antigen Method in class Bio.Ais.Immune
foundMatch Method in class Bio.Parsers.spark.GenericASTMatcher
Fragments Class in module Bio.EUtils.POM
frame Method in class Bio.Blast.NCBIStandalone._HSPConsumer
frameshift Method in class Bio.Blast.NCBIStandalone._ParametersConsumer
FreqTable Module in package Bio.SubsMat
FreqTable Class in module Bio.SubsMat.FreqTable
From Class in module Bio.EUtils.DTDs.eSearch_020511
from_dbids Method in class Bio.EUtils.DBIdsClient.DBIdsClient
from_dbids Function in module Bio.EUtils.DBIdsClient
from_motifs Method in class Bio.NeuralNetwork.Gene.Schema.SchemaFactory
from_parser Function in module Bio.DBXRef
from_signatures Method in class Bio.NeuralNetwork.Gene.Schema.SchemaFactory
fromkeys Method in class __builtin__.type
fromkeys Method in class __builtin__.type
fromkeys Method in class __builtin__.type
fromkeys Method in class __builtin__.type
fromkeys Method in class __builtin__.type
fromkeys Method in class __builtin__.type
fromkeys Method in class __builtin__.type
fromkeys Method in class __builtin__.type
fromkeys Method in class __builtin__.type
fromkeys Method in class __builtin__.type
fromkeys Method in class __builtin__.type
fromkeys Method in class __builtin__.type
fromkeys Method in class __builtin__.type
fromkeys Method in class __builtin__.type
fromkeys Method in class __builtin__.type
FSSP Package in package Bio
fssp_rec Module in package Bio.FSSP
FSSPAlign Class in module Bio.FSSP.FSSPTools
FSSPAlignDict Class in package Bio.FSSP
FSSPAlignRec Class in package Bio.FSSP
FSSPHeader Class in package Bio.FSSP
FSSPMultAlign Class in module Bio.FSSP.FSSPTools
FSSPSumDict Class in package Bio.FSSP
FSSPSumRec Class in package Bio.FSSP
FSSPTools Module in package Bio.FSSP
full_repr Method in class Bio.EUtils.POM.ElementNode
full_repr Method in class Bio.EUtils.POM.IndentedText
fullpath Method in class Bio.EUtils.POM.ElementNode
fullpath Method in class Bio.EUtils.POM.IndentedText
Function Class in module Bio.Decode
function_population Function in module Bio.GA.Organism
FunctionCall Class in module Bio.Decode
FunctionCallChain Class in module Bio.Decode
FunctionHolder Class in module Bio.EUtils.sourcegen
FunctionIndexer Class in module Bio.Mindy.SimpleSeqRecord
FunctionName Class in module Bio.Decode
FuzznucCommandline Class in module Bio.Emboss.Applications
GA Package in package Bio
gap_char Variable in class Bio.Alphabet.Gapped
gap_consensus Method in class Bio.Align.AlignInfo.SummaryInfo
gap_penalties Method in class Bio.Blast.NCBIStandalone._ParametersConsumer
gap_trigger Method in class Bio.Blast.NCBIStandalone._ParametersConsumer
gap_x_dropoff Method in class Bio.Blast.NCBIStandalone._ParametersConsumer
gap_x_dropoff_final Method in class Bio.Blast.NCBIStandalone._ParametersConsumer
gaponly Method in class Bio.Nexus.Nexus.Nexus
Gapped Class in package Bio.Alphabet
gapped Method in class Bio.Blast.NCBIStandalone._DatabaseReportConsumer
gen_iterator Function in module Martel.test.test_IterParser
genbank Module in package Bio.dbdefs
genbank Module in package Bio.expressions
genbank Module in package Bio.formatdefs
genBlank Method in class Bio.EUtils.sourcegen.SourceGen
genClass Method in class Bio.EUtils.sourcegen.SourceGen
genClass Function in module Bio.EUtils.sourcegen
genComment Method in class Bio.EUtils.sourcegen.SourceGen
genComment Function in module Bio.EUtils.sourcegen
Gene Package in package Bio.NeuralNetwork
GENE Method in class Bio.UniGene._RecordConsumer
GENE_ID Method in class Bio.UniGene._RecordConsumer
gene_name Method in class Bio.SwissProt.SProt._RecordConsumer
gene_symbol Method in class Bio.Medline._RecordConsumer
General Module in package Bio.GA.Crossover
General Module in package Bio.GA.Mutation
GeneralPoint Module in package Bio.GA.Crossover
GeneralPointCrossover Class in module Bio.GA.Crossover.GeneralPoint
Generate Module in package Martel
generate Function in module Martel.Generate
generate_alt Function in module Martel.Generate
generate_any Function in module Martel.Generate
generate_assert Function in module Martel.Generate
generate_at_beginning Function in module Martel.Generate
generate_at_end Function in module Martel.Generate
generate_debug Function in module Martel.Generate
generate_dot Function in module Martel.Generate
generate_eol Function in module Martel.Generate
generate_group Function in module Martel.Generate
generate_groupref Function in module Martel.Generate
generate_literal Function in module Martel.Generate
generate_max_repeat Function in module Martel.Generate
generate_named_max_repeat Function in module Martel.Generate
generate_null_op Function in module Martel.Generate
generate_parser Function in module Martel.Generate
generate_pass_through Function in module Martel.Generate
generate_seq Function in module Martel.Generate
generate_str Function in module Martel.Generate
GenerationEvolver Class in module Bio.GA.Evolver
GeneratorState Class in module Martel.Generate
GeneRecord Class in package Bio.Gobase
Generic Module in package Bio.Align
Generic_dbutils Class in module BioSQL.DBUtils
generic_run Function in package Bio.Application
GenericASTBuilder Class in module Bio.Parsers.spark
GenericASTMatcher Class in module Bio.Parsers.spark
GenericASTTraversal Class in module Bio.Parsers.spark
GenericASTTraversalPruningException Class in module Bio.Parsers.spark
GenericParser Class in module Bio.Parsers.spark
GenericScanner Class in module Bio.Parsers.spark
GeneticAlgorithmFinder Class in module Bio.NeuralNetwork.Gene.Schema
genFunc Method in class Bio.EUtils.sourcegen.SourceGen
genFunc Function in module Bio.EUtils.sourcegen
genImport Method in class Bio.EUtils.sourcegen.SourceGen
genImport Function in module Bio.EUtils.sourcegen
genMethod Method in class Bio.EUtils.sourcegen.SourceGen
genMethod Function in module Bio.EUtils.sourcegen
get Method in class Bio.Crystal.Crystal
get Method in class Bio.Data.CodonTable.AmbiguousForwardTable
get Method in class Bio.EUtils.MultiDict._BaseMultiDict
get Method in class Bio.EUtils.POM.ElementNode
get Method in class Bio.Mindy.BaseDB.DictLookup
get Method in class Bio.Prosite.ExPASyDictionary
get Method in class Bio.Prosite.Prodoc.ExPASyDictionary
get Method in class Bio.PubMed.Dictionary
get Method in class Bio.SwissProt.SProt.ExPASyDictionary
get Method in class Bio.config.DBRegistry.DBGroup
get Method in class Bio.config.DBRegistry.DBObject
get Method in class Bio.config.Registry.Registry
get Method in class Martel.Parser.MartelAttributeList
get Method in class Martel.msre_parse.Tokenizer
get Method in class __builtin__.dict
get Method in class xml.sax.xmlreader.AttributesImpl
get_alignment_length Method in class Bio.Align.Generic.Alignment
get_all Method in class Bio.NeuralNetwork.Gene.Pattern.PatternRepository
get_all_primary_ids Method in class BioSQL.BioSeqDatabase.BioSeqDatabase
get_all_seqs Method in class Bio.Align.Generic.Alignment
get_all_urls Method in class Bio.NetCatch.NetCatch
get_as Method in class Bio.config.DBRegistry.DBGroup
get_as Method in class Bio.config.DBRegistry.DBObject
get_attribute Method in class Bio.EUtils.POM.ElementNode
get_attribute Method in class Bio.EUtils.sourcegen.ClassHolder
get_attribute Method in class Bio.EUtils.sourcegen.FunctionHolder
get_blank_emissions Method in class Bio.HMM.MarkovModel.HiddenMarkovModel
get_blank_transitions Method in class Bio.HMM.MarkovModel.HiddenMarkovModel
get_builder Method in class Bio.Mindy.SimpleSeqRecord.BaseSeqRecordIndexer
get_characters Method in class Martel.Dispatch.DispatchHandler
get_characters Method in class Martel.Dispatch.Dispatcher
get_children Method in class Bio.EUtils.POM.ElementNode
get_column Method in class Bio.Align.AlignInfo.SummaryInfo
get_column Method in class Bio.Align.Generic.Alignment
get_data Method in class Bio.Nexus.Nodes.Node
get_dbutils Function in module BioSQL.DBUtils
get_differing Method in class Bio.NeuralNetwork.Gene.Pattern.PatternRepository
get_document Method in class Bio.EUtils.POM.POMDocument
get_dtd_compiler Function in module Bio.EUtils.POM
get_element Method in class Bio.EUtils.POM.ElementNode
get_element Function in module Martel.test.test_attrs
get_entry Method in class Bio.Mindy.FlatDB.BisectFile
get_error Method in class Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer
get_escape_length Method in class Bio.EUtils.POM.IndentedText
get_generator Function in module Bio.EUtils.sourcegen
get_id Method in class Bio.Nexus.Nodes.Node
get_id_dictionary Method in class Bio.Mindy.SimpleSeqRecord.BaseSeqRecordIndexer
get_id_dictionary Method in class Bio.Mindy.SimpleSeqRecord.FunctionIndexer
get_id_dictionary Method in class Bio.Mindy.SimpleSeqRecord.SimpleIndexer
get_info Method in class Bio.Mindy.XPath.GrabXPathNodes
get_init_rms Method in class Bio.SVDSuperimposer.SVDSuperimposer.SVDSuperimposer
get_instance_by_name Method in class Bio.MEME.Motif.Motif
get_interpro_entry Function in module Bio.WWW.InterPro
get_markov_model Method in class Bio.HMM.MarkovModel.MarkovModelBuilder
get_merge_text Function in module Martel.optimize
get_mod_file Function in module Bio.EUtils.POM
get_motif_by_name Method in class Bio.MEME.Parser.MASTRecord
get_motif_by_name Method in class Bio.MEME.Parser.MEMERecord
get_motif_matches Method in class Bio.MEME.Parser.MASTRecord
get_motif_matches_for_sequence Method in class Bio.MEME.Parser.MASTRecord
get_original_taxon_order Method in class Bio.Nexus.Nexus.Nexus
get_parent Method in class Bio.EUtils.POM.ElementNode
get_parser Method in class Bio.EUtils.POM.POMDocument
get_parser Function in module Bio.EUtils.POM
get_prev Method in class Bio.Nexus.Nodes.Node
get_PrimarySeq_stream Method in class BioSQL.BioSeqDatabase.BioSeqDatabase
get_prodoc_entry Function in module Bio.WWW.ExPASy
get_prosite_entry Function in module Bio.WWW.ExPASy
get_query_params Method in class Bio.EUtils.Datatypes.DateRange
get_query_params Method in class Bio.EUtils.Datatypes.WithinNDays
get_random Method in class Bio.NeuralNetwork.Gene.Pattern.PatternRepository
get_residue Method in class Bio.Align.AlignInfo.PSSM
get_result Method in class Bio.Application.ApplicationResult
get_rms Method in class Bio.SVDSuperimposer.SVDSuperimposer.SVDSuperimposer
get_rotran Method in class Bio.SVDSuperimposer.SVDSuperimposer.SVDSuperimposer
get_segment_info Method in class Bio.Graphics.DisplayRepresentation.ChromosomeCounts
get_Seq_by_acc Method in class BioSQL.BioSeqDatabase.BioSeqDatabase
get_Seq_by_id Method in class BioSQL.BioSeqDatabase.BioSeqDatabase
get_seq_by_num Method in class Bio.Align.Generic.Alignment
get_Seq_by_primary_id Method in class BioSQL.BioSeqDatabase.BioSeqDatabase
get_Seq_by_ver Method in class BioSQL.BioSeqDatabase.BioSeqDatabase
get_Seqs_by_acc Method in class BioSQL.BioSeqDatabase.BioSeqDatabase
get_sourcefile Function in module Bio.EUtils.sourcegen
get_sprot_raw Function in module Bio.WWW.ExPASy
get_start_end Function in module Bio.Nexus.Nexus
get_starttag_text Method in class sgmllib.SGMLParser
get_subseq_as_string Method in class BioSQL.BioSeqDatabase.Adaptor
get_succ Method in class Bio.Nexus.Nodes.Node
get_supported_features Method in class Martel.Dispatch.DispatchHandler
get_taxa Method in class Bio.Nexus.Trees.Tree
get_terminals Method in class Bio.Nexus.Trees.Tree
get_text Method in class Bio.EUtils.POM.Comment
get_text Method in class Bio.EUtils.POM.IndentedText
get_top Method in class Bio.NeuralNetwork.Gene.Pattern.PatternRepository
get_top_percentage Method in class Bio.NeuralNetwork.Gene.Pattern.PatternRepository
get_transformed Method in class Bio.SVDSuperimposer.SVDSuperimposer.SVDSuperimposer
get_urls_by_index Method in class Bio.NetCatch.NetCatch
get_urls_by_label Method in class Bio.NetCatch.NetCatch
get_urls_by_range Method in class Bio.NetCatch.NetCatch
getall Method in class Bio.EUtils.MultiDict._BaseMultiDict
getall Method in class Bio.EUtils.POM.ElementNode
getBounds Method in class reportlab.graphics.widgetbase.Widget
getContentHandler Method in class xml.sax.xmlreader.XMLReader
getDTDHandler Method in class xml.sax.xmlreader.XMLReader
getEntityResolver Method in class xml.sax.xmlreader.XMLReader
getErrorHandler Method in class xml.sax.xmlreader.XMLReader
GetErrorPos Class in module Martel.test.test_optimize
getException Method in class xml.sax._exceptions.SAXException
getFeature Method in class xml.sax.xmlreader.XMLReader
getLength Method in class Martel.Parser.MartelAttributeList
getLength Method in class xml.sax.xmlreader.AttributesImpl
getMessage Method in class xml.sax._exceptions.SAXException
getName Method in class Bio.MultiProc.Task.Task
getName Method in class Martel.Parser.MartelAttributeList
getNameByQName Method in class xml.sax.xmlreader.AttributesImpl
getNames Method in class xml.sax.xmlreader.AttributesImpl
getnode Method in class Bio.EUtils.POM.POMDocument
GetObject Class in module Bio.EUtils.parse
getpos Method in class markupbase.ParserBase
getProperties Method in class reportlab.graphics.widgetbase.PropHolder
getProperty Method in class xml.sax.xmlreader.XMLReader
getQNameByName Method in class xml.sax.xmlreader.AttributesImpl
getQNames Method in class xml.sax.xmlreader.AttributesImpl
gettype Method in class Bio.EUtils.Config.DatabaseDict
getType Method in class Martel.Parser.MartelAttributeList
getType Method in class xml.sax.xmlreader.AttributesImpl
getValue Method in class Martel.Parser.MartelAttributeList
getValue Method in class xml.sax.xmlreader.AttributesImpl
getValueByQName Method in class xml.sax.xmlreader.AttributesImpl
getwidth Method in class Martel.msre_parse.SubPattern
global_alphabet Variable in class Bio.StdHandler.Handle_sequence
goahead Method in class sgmllib.SGMLParser
Gobase Package in package Bio
GrabElements Class in module Martel.test.test_attrs
GrabXPathNodes Class in module Bio.Mindy.XPath
Graph Module in package Bio.Pathway.Rep
Graph Class in module Bio.Pathway.Rep.Graph
Graphics Package in package Bio
group Method in class Bio.Prosite.Pattern.PrositeMatch
Group Class in module Martel.Expression
Group Function in package Martel
group_elem Function in module Bio.Medline.nlmmedline_001211_format
group_elem Function in module Bio.Medline.nlmmedline_010319_format
group_elem Function in module Bio.Medline.nlmmedline_011101_format
group_elem Function in module Bio.Medline.nlmmedline_031101_format
group_names Method in class Martel.Expression.Expression
group_names Method in class Martel.Expression.ExpressionList
group_names Method in class Martel.Expression.Group
group_names Method in class Martel.Expression.HeaderFooter
group_names Method in class Martel.Expression.MaxRepeat
group_names Method in class Martel.Expression.ParseRecords
group_names Method in class Martel.Expression.PassThrough
GroupNames Class in module Martel.convert_re
GroupRef Class in module Martel.Expression
groups Method in class Bio.Prosite.Pattern.PrositeMatch
guess_gaps Method in class Bio.Ais.Immune
handle_charref Method in class sgmllib.SGMLParser
handle_comment Method in class Bio.EUtils.POM.DTDConsumerForSourceGeneration
handle_comment Method in class sgmllib.SGMLParser
handle_data Method in class Bio.File.MyParser
handle_data Method in class Bio.InterPro.InterProParser
handle_data Method in class Bio.Ndb.NdbParser
handle_data Method in class Bio.NetCatch.ExtractUrls
handle_data Method in class Bio.SGMLExtractor.LocalParser
handle_data Method in class sgmllib.SGMLParser
Handle_dbid Class in module Bio.StdHandler
Handle_dbxref Class in module Bio.StdHandler
handle_decl Method in class sgmllib.SGMLParser
Handle_description Class in module Bio.StdHandler
handle_endtag Method in class sgmllib.SGMLParser
handle_entityref Method in class sgmllib.SGMLParser
Handle_feature_location Class in module Bio.StdHandler
Handle_feature_qualifier Class in module Bio.StdHandler
Handle_features Class in module Bio.StdHandler
Handle_hsp Class in module Bio.StdHandler
Handle_hsp_seqalign Class in module Bio.StdHandler
handle_pi Method in class Bio.EUtils.POM.DTDConsumerForSourceGeneration
handle_pi Method in class sgmllib.SGMLParser
Handle_search_header Class in module Bio.StdHandler
Handle_search_info Class in module Bio.StdHandler
Handle_search_table Class in module Bio.StdHandler
Handle_sequence Class in module Bio.StdHandler
handle_starttag Method in class Bio.InterPro.InterProParser
handle_starttag Method in class sgmllib.SGMLParser
HandleRepeatCount Class in module Martel.Generate
has_attribute Method in class Bio.EUtils.POM.ElementNode
has_attributes Method in class Bio.EUtils.POM.IndentedText
has_children Method in class Bio.EUtils.POM.ElementNode
has_children Method in class Bio.EUtils.POM.IndentedText
has_expr Function in module Bio.dbdefs._support
has_group Function in module Martel.test.test_macros
has_key Method in class Bio.Crystal.Crystal
has_key Method in class Bio.EUtils.POM.ElementNode
has_key Method in class Bio.Prosite.ExPASyDictionary
has_key Method in class Bio.Prosite.Prodoc.ExPASyDictionary
has_key Method in class Bio.PubMed.Dictionary
has_key Method in class Bio.SwissProt.SProt.ExPASyDictionary
has_key Method in class Martel.Parser.MartelAttributeList
has_key Method in class __builtin__.dict
has_key Method in class xml.sax.xmlreader.AttributesImpl
has_no_group Function in module Martel.test.test_macros
has_str Function in module Bio.dbdefs._support
has_trailing_linefeed Function in module Bio.FilteredReader
hasAttributes Method in class Bio.EUtils.POM.ElementNode
HashSet Module in package Bio.Pathway.Rep
HashSet Class in module Bio.Pathway.Rep.HashSet
HasStopCodon Class in package Bio.Alphabet
Header Class in module Bio.Blast.Record
HEADER Variable in class Bio.EUtils.POM.POMDocument
HeaderFooter Class in module Martel.Expression
HeaderFooterEventStream Class in module Martel.Iterator
HeaderFooterParser Class in module Martel.Parser
Hetero Class in package Bio.Crystal
hex_convert Function in module Bio.HotRand
HiddenLayer Class in module Bio.NeuralNetwork.BackPropagation.Layer
HiddenMarkovModel Class in module Bio.HMM.MarkovModel
Hierarchy Class in module Bio.EUtils.DTDs.eInfo_020511
HistoryClient Module in package Bio.EUtils
HistoryClient Class in module Bio.EUtils.HistoryClient
HistoryCookie Class in module Bio.EUtils.HistoryClient
HistoryLookup Class in module Bio.EUtils.HistoryClient
HistoryRecord Class in module Bio.EUtils.HistoryClient
Hit Class in module Bio.Search
hit Function in module Bio.Std
hit_alignment Method in class Bio.Compass._Consumer
hit_coverage Method in class Bio.Compass.Record
hit_description Function in module Bio.Std
hit_length Function in module Bio.Std
HMM Package in package Bio
hmmpfam Module in package Bio.expressions
HomologySeq Class in module Bio.Search
hot_rand Method in class Bio.HotRand.HotRandom
HotCache Class in module Bio.HotRand
HotRand Module in package Bio
HotRandom Class in module Bio.HotRand
HPModel Class in module Bio.Alphabet.Reduced
HSP Class in module Bio.Blast.Record
HSP Class in module Bio.Search
hsp Function in module Bio.Std
hsp_frame Function in module Bio.Std
hsp_seqalign Function in module Bio.Std
hsp_seqalign_homology_seq Function in module Bio.Std
hsp_seqalign_query_end Function in module Bio.Std
hsp_seqalign_query_leader Function in module Bio.Std
hsp_seqalign_query_name Function in module Bio.Std
hsp_seqalign_query_seq Function in module Bio.Std
hsp_seqalign_query_start Function in module Bio.Std
hsp_seqalign_subject_end Function in module Bio.Std
hsp_seqalign_subject_name Function in module Bio.Std
hsp_seqalign_subject_seq Function in module Bio.Std
hsp_seqalign_subject_start Function in module Bio.Std
hsp_strand Function in module Bio.Std
hsp_value Function in module Bio.Std
hsps_gapped Method in class Bio.Blast.NCBIStandalone._ParametersConsumer
hsps_no_gap Method in class Bio.Blast.NCBIStandalone._ParametersConsumer
hsps_prelim_gapped Method in class Bio.Blast.NCBIStandalone._ParametersConsumer
hsps_prelim_gapped_attempted Method in class Bio.Blast.NCBIStandalone._ParametersConsumer
HSPSeq Class in module Bio.Search
IconUrl Class in module Bio.EUtils.DTDs.LinkOut
IconUrl Class in module Bio.EUtils.DTDs.eLink_020511
Id Class in module Bio.EUtils.DTDs.eLink_020511
Id Class in module Bio.EUtils.DTDs.ePost_020511
Id Class in module Bio.EUtils.DTDs.eSearch_020511
Id Class in module Bio.EUtils.DTDs.eSummary_020511
ID Class in module Bio.EUtils.POM
ID Method in class Bio.UniGene._RecordConsumer
IdCheck Class in module Bio.EUtils.Datatypes
IdCheckList Class in module Bio.EUtils.DTDs.eLink_020511
identification Method in class Bio.Enzyme._RecordConsumer
identification Method in class Bio.Medline._RecordConsumer
identification Method in class Bio.Prosite._RecordConsumer
identification Method in class Bio.SwissProt.SProt._RecordConsumer
identification Method in class Bio.SwissProt.SProt._SequenceConsumer
identify Method in class Bio.config.FormatRegistry.FormatGroup
identify Method in class Bio.config.FormatRegistry.FormatObject
identifyFile Method in class Bio.config.FormatRegistry.FormatGroup
identifyFile Method in class Bio.config.FormatRegistry.FormatObject
identifyString Method in class Bio.config.FormatRegistry.FormatGroup
identifyString Method in class Bio.config.FormatRegistry.FormatObject
identities Method in class Bio.Blast.NCBIStandalone._HSPConsumer
identity_match Class in module Bio.pairwise2
IdList Class in module Bio.EUtils.DTDs.eLink_020511
IdList Class in module Bio.EUtils.DTDs.eSearch_020511
IDREF Class in module Bio.EUtils.POM
IDREFS Class in module Bio.EUtils.POM
IdUrlList Class in module Bio.EUtils.DTDs.eLink_020511
IdUrlSet Class in module Bio.EUtils.DTDs.eLink_020511
IdUrlSet Class in module Bio.EUtils.Datatypes
IF Function in module Bio.EUtils.POM
ignorableWhitespace Method in class Bio.EUtils.POM.ObjectParserHandler
ignorableWhitespace Method in class xml.sax.handler.ContentHandler
ignore_characters Method in class Bio.StdHandler.ConvertHandler
Immune Class in package Bio.Ais
import_dict Method in class Bio.NetCatch.NetCatch
InclQuery Class in module Bio.EUtils.DTDs.LinkOut
IndentedText Class in module Bio.EUtils.POM
index Method in class Bio.Crystal.Chain
index Method in class Bio.EUtils.POM.ElementNode
Index Module in package Bio
index Function in module Bio.Medline.NLMMedlineXML
index Method in class Bio.Seq.MutableSeq
index Method in class __builtin__.list
index Method in class __builtin__.str
index_file Function in package Bio.Gobase
index_file Function in module Bio.Prosite.Prodoc
index_file Function in package Bio.Prosite
index_file Function in package Bio.Rebase
index_file Function in module Bio.SwissProt.SProt
index_many Function in module Bio.Medline.NLMMedlineXML
IndexedFileDB Class in module Bio.config.DBRegistry
indexesof Function in module Bio.listfns
Info Class in module Bio.EUtils.DTDs.eLink_020511
information_content Method in class Bio.Align.AlignInfo.SummaryInfo
inherit_indent Method in class Bio.EUtils.POM.ElementNode
InputLayer Class in module Bio.NeuralNetwork.BackPropagation.Layer
insert Method in class Bio.Crystal.Chain
insert Method in class Bio.EUtils.POM.Comment
insert Method in class Bio.EUtils.POM.ElementNode
insert Method in class Bio.EUtils.POM.IndentedText
insert Method in class Bio.Seq.MutableSeq
insert Method in class Martel.msre_parse.SubPattern
insert Method in class __builtin__.list
insert_element Method in class Bio.MarkupEditor.MarkupEditor
insert_gap Method in class Bio.Nexus.Nexus.Nexus
insert_raw_text Method in class Bio.MarkupEditor.MarkupEditor
insert_singleton Method in class Bio.MarkupEditor.MarkupEditor
insert_text Method in class Bio.MarkupEditor.MarkupEditor
Instance Class in module Bio.MEME.Motif
int_field Method in class Bio.Gobase._RecordConsumer
int_param Function in module Bio.expressions.blast.ncbiblast
int_stat Function in module Bio.expressions.blast.ncbiblast
intd Function in module Bio.mathfns
Integer Class in module Bio.Decode
Integer Function in package Martel
intensities Method in class Bio.Affy.CelFile.CelRecord
Interaction Class in package Bio.Pathway
interactions Method in class Bio.Pathway.Network
InterleaveCrossover Class in module Bio.GA.Crossover.GeneralPoint
internal_gc Method in class Bio.Emboss.Primer._Primer3RecordConsumer
internal_length Method in class Bio.Emboss.Primer._Primer3RecordConsumer
internal_seq Method in class Bio.Emboss.Primer._Primer3RecordConsumer
internal_start Method in class Bio.Emboss.Primer._Primer3RecordConsumer
internal_tm Method in class Bio.Emboss.Primer._Primer3RecordConsumer
InterPro Package in package Bio
InterPro Module in package Bio.WWW
interpro Module in package Bio.dbdefs
InterProParser Class in package Bio.InterPro
intersection Method in class Bio.Pathway.Rep.HashSet.HashSet
intersection Function in module Bio.listfns
InvalidIdList Class in module Bio.EUtils.DTDs.ePost_020511
invert Method in class Bio.Nexus.Nexus.Nexus
invert Function in module Martel.convert_re
is_absolute_url Function in module Bio.NetCatch
is_bifurcating Method in class Bio.Nexus.Trees.Tree
is_blank_line Function in module Bio.ParserSupport
is_char Function in module Martel.msre_parse
is_compatible Method in class Bio.Nexus.Trees.Tree
is_empty Method in class Bio.EUtils.POM.ContentModel
is_empty Function in module Bio.SGMLExtractor
is_finished Method in class Bio.NeuralNetwork.Gene.Schema.SimpleFinisher
is_firstchar Function in module Martel.msre_parse
is_identical Method in class Bio.Nexus.Trees.Tree
is_mergeable Function in module Martel.optimize
is_monophyletic Method in class Bio.Nexus.Trees.Tree
is_parent_of Method in class Bio.Nexus.Nodes.Chain
isAlive Method in class Bio.MultiProc.Task.Task
isalnum Method in class __builtin__.str
isalpha Method in class __builtin__.str
IsDate Class in module Bio.EUtils.DTDs.eInfo_020511
isdigit Method in class __builtin__.str
islower Method in class __builtin__.str
isname Function in module Martel.msre_parse
isname_with_attrs Function in module Martel.msre_parse
IsNumerical Class in module Bio.EUtils.DTDs.eInfo_020511
issn Method in class Bio.Medline._RecordConsumer
isspace Method in class __builtin__.str
issue_part_supplement Method in class Bio.Medline._RecordConsumer
istitle Method in class __builtin__.str
isupper Method in class __builtin__.str
Item Class in module Bio.EUtils.DTDs.eSummary_020511
item Method in class Bio.EUtils.Datatypes.DBIds
itemindex Function in module Bio.listfns
items Method in class Bio.Crystal.Crystal
items Method in class Bio.EUtils.MultiDict._BaseMultiDict
items Method in class Bio.Mindy.BaseDB.DictLookup
items Method in class Bio.Prosite.ExPASyDictionary
items Method in class Bio.Prosite.Prodoc.ExPASyDictionary
items Method in class Bio.PubMed.Dictionary
items Method in class Bio.SwissProt.SProt.ExPASyDictionary
items Method in class Bio.config.Registry.Registry
items Function in module Bio.listfns
items Method in class BioSQL.BioSeqDatabase.BioSeqDatabase
items Method in class BioSQL.BioSeqDatabase.DBServer
items Method in class Martel.Parser.MartelAttributeList
items Method in class __builtin__.dict
items Method in class xml.sax.xmlreader.AttributesImpl
iterate Method in class Martel.IterParser.IterHeaderFooter
iterate Method in class Martel.IterParser.IterRecords
Iterate Class in module Martel.Iterator
iterate Method in class Martel.Iterator.Iterator
iterate Method in class Martel.Iterator.IteratorHeaderFooter
iterate Method in class Martel.Iterator.IteratorRecords
iterateFile Method in class Martel.IterParser.IterHeaderFooter
iterateFile Method in class Martel.IterParser.IterRecords
iterateFile Method in class Martel.Iterator.Iterator
iterateFile Method in class Martel.Iterator.IteratorHeaderFooter
iterateFile Method in class Martel.Iterator.IteratorRecords
iterateString Method in class Martel.IterParser.IterHeaderFooter
iterateString Method in class Martel.IterParser.IterRecords
iterateString Method in class Martel.Iterator.Iterator
iterateString Method in class Martel.Iterator.IteratorHeaderFooter
iterateString Method in class Martel.Iterator.IteratorRecords
Iterator Class in module Bio.Blast.NCBIStandalone
Iterator Class in package Bio.Compass
Iterator Class in package Bio.Enzyme
Iterator Class in package Bio.Gobase
Iterator Class in package Bio.Medline
Iterator Class in package Bio.Prosite
Iterator Class in module Bio.Prosite.Prodoc
Iterator Class in package Bio.Rebase
Iterator Class in module Bio.Sequencing.Ace
Iterator Class in module Bio.Sequencing.Phd
Iterator Class in module Bio.SwissProt.SProt
Iterator Class in package Bio.UniGene
Iterator Module in package Martel
Iterator Class in module Martel.Iterator
IteratorHeaderFooter Class in module Martel.Iterator
IteratorRecords Class in module Martel.Iterator
IterHeaderFooter Class in module Martel.IterParser
iteritems Method in class __builtin__.dict
iterkeys Method in class __builtin__.dict
IterParser Module in package Martel
IterRecords Class in module Martel.IterParser
itervalues Method in class __builtin__.dict
IUPAC Module in package Bio.Alphabet
IUPACAmbiguousDNA Class in module Bio.Alphabet.IUPAC
IUPACAmbiguousRNA Class in module Bio.Alphabet.IUPAC
IUPACData Module in package Bio.Data
IUPACEncoding Module in package Bio.Encodings
IUPACProtein Class in module Bio.Alphabet.IUPAC
IUPACUnambiguousDNA Class in module Bio.Alphabet.IUPAC
IUPACUnambiguousRNA Class in module Bio.Alphabet.IUPAC
join Method in class __builtin__.str
join_english Function in module Bio.Decode
join_fixspaces Function in module Bio.Decode
journal_subset Method in class Bio.Medline._RecordConsumer
journal_title_code Method in class Bio.Medline._RecordConsumer
ka_params Method in class Bio.Blast.NCBIStandalone._DatabaseReportConsumer
ka_params_gap Method in class Bio.Blast.NCBIStandalone._DatabaseReportConsumer
KEGG Package in package Bio
keys Method in class Bio.Crystal.Crystal
keys Method in class Bio.EUtils.MultiDict._BaseMultiDict
keys Method in class Bio.Mindy.BaseDB.DictLookup
keys Method in class Bio.Mindy.BaseDB.OpenDB
keys Method in class Bio.Mindy.FlatDB.PrimaryNamespace
keys Method in class Bio.Mindy.FlatDB.PrimaryTable
keys Method in class Bio.Mindy.FlatDB.SecondaryNamespace
keys Method in class Bio.Mindy.FlatDB.SecondaryTable
keys Method in class Bio.Prosite.ExPASyDictionary
keys Method in class Bio.Prosite.Prodoc.ExPASyDictionary
keys Method in class Bio.PubMed.Dictionary
keys Method in class Bio.SwissProt.SProt.Dictionary
keys Method in class Bio.SwissProt.SProt.ExPASyDictionary
keys Method in class Bio.config.Registry.Registry
keys Method in class BioSQL.BioSeqDatabase.BioSeqDatabase
keys Method in class BioSQL.BioSeqDatabase.DBServer
keys Method in class Martel.Parser.MartelAttributeList
keys Method in class __builtin__.dict
keys Method in class xml.sax.xmlreader.AttributesImpl
KeyWList Module in package Bio.SwissProt
keyword Method in class Bio.SwissProt.KeyWList._ListConsumer
keyword Method in class Bio.SwissProt.SProt._RecordConsumer
kill Method in class Bio.Nexus.Nodes.Chain
kNN Module in package Bio
kNN Class in module Bio.kNN
KnownStateTrainer Class in module Bio.HMM.Trainer
labels Method in class Bio.Pathway.Rep.Graph.Graph
labels Method in class Bio.Pathway.Rep.MultiGraph.MultiGraph
language Method in class Bio.Medline._RecordConsumer
last_id Method in class BioSQL.BioSeqDatabase.Adaptor
last_id Method in class BioSQL.DBUtils.Generic_dbutils
last_id Method in class BioSQL.DBUtils.Mysql_dbutils
last_id Method in class BioSQL.DBUtils.Pgdb_dbutils
last_id Method in class BioSQL.DBUtils.Psycopg_dbutils
last_revision_date Method in class Bio.Medline._RecordConsumer
LAX Module in package Martel
LAX Class in module Martel.LAX
LAXAttrs Class in module Martel.LAX
LAXPositions Class in module Martel.LAX
Layer Module in package Bio.NeuralNetwork.BackPropagation
lazy_auto_immune_check Method in class Bio.Ais.Immune
lcc Module in package Bio
lcc_mult Function in module Bio.lcc
lcc_simp Function in module Bio.lcc
lcheck Method in class Bio.EUtils.Mixins.LinkMixin
lchomp Function in module Bio.Decode
length Method in class Bio.Blast.NCBIStandalone._AlignmentConsumer
lengths Method in class Bio.Compass._Consumer
letter_sum Method in class Bio.SubsMat.SeqMat
letters Variable in class Bio.Alphabet.Alphabet
letters Variable in class Bio.Alphabet.Alphabet
letters Variable in class Bio.Alphabet.IUPAC.ExtendedIUPACDNA
letters Variable in class Bio.Alphabet.IUPAC.ExtendedIUPACProtein
letters Variable in class Bio.Alphabet.IUPAC.IUPACAmbiguousDNA
letters Variable in class Bio.Alphabet.IUPAC.IUPACAmbiguousRNA
letters Variable in class Bio.Alphabet.IUPAC.IUPACProtein
letters Variable in class Bio.Alphabet.IUPAC.IUPACUnambiguousDNA
letters Variable in class Bio.Alphabet.IUPAC.IUPACUnambiguousRNA
letters Variable in class Bio.Alphabet.Reduced.HPModel
letters Variable in class Bio.Alphabet.Reduced.Murphy10
letters Variable in class Bio.Alphabet.Reduced.Murphy15
letters Variable in class Bio.Alphabet.Reduced.Murphy4
letters Variable in class Bio.Alphabet.Reduced.Murphy8
letters Variable in class Bio.Alphabet.Reduced.PC5
letters Variable in class Bio.Alphabet.SecondaryStructure
letters Variable in class Bio.Alphabet.SingleLetterAlphabet
letters Variable in class Bio.Alphabet.SingleLetterAlphabet
letters Variable in class Bio.Alphabet.SingleLetterAlphabet
letters Variable in class Bio.Alphabet.SingleLetterAlphabet
letters Variable in class Bio.Alphabet.SingleLetterAlphabet
letters Variable in class Bio.Alphabet.ThreeLetterProtein
letters Variable in class Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet
LineDistribution Class in module Bio.Graphics.Distribution
Link Class in module Bio.EUtils.DTDs.LinkOut
Link Class in module Bio.EUtils.DTDs.eInfo_020511
Link Class in module Bio.EUtils.DTDs.eLink_020511
Link Class in module Bio.EUtils.Datatypes
link Method in class Bio.Nexus.Nodes.Chain
LinkId Class in module Bio.EUtils.DTDs.LinkOut
LinkList Class in module Bio.EUtils.DTDs.eInfo_020511
LinkMixin Class in module Bio.EUtils.Mixins
LinkName Class in module Bio.EUtils.DTDs.eLink_020511
LinkOut Module in package Bio.EUtils.DTDs
LinkSet Class in module Bio.EUtils.DTDs.LinkOut
LinkSet Class in module Bio.EUtils.DTDs.eLink_020511
LinkSetDb Class in module Bio.EUtils.DTDs.eLink_020511
LinkSetDb Class in module Bio.EUtils.Datatypes
LinksLinkSet Class in module Bio.EUtils.Datatypes
list Method in class Bio.Pathway.Rep.HashSet.HashSet
list Class in module __builtin__
list_ambiguous_codons Function in module Bio.Data.CodonTable
list_any_ids Method in class BioSQL.BioSeqDatabase.Adaptor
list_biodatabase_names Method in class BioSQL.BioSeqDatabase.Adaptor
list_bioentry_display_ids Method in class BioSQL.BioSeqDatabase.Adaptor
list_bioentry_ids Method in class BioSQL.BioSeqDatabase.Adaptor
list_possible_proteins Function in module Bio.Data.CodonTable
listfns Module in package Bio
ListParser Class in module Bio.SwissProt.KeyWList
Literal Class in module Martel.Expression
ljust Method in class __builtin__.str
llinks Method in class Bio.EUtils.Mixins.LinkMixin
load Function in module Bio.MarkovModel
load Method in class Bio.Mindy.BaseDB.WriteDB
load Function in module Bio.config._stanzaformat
load Method in class BioSQL.BioSeqDatabase.BioSeqDatabase
load_database_sql Method in class BioSQL.BioSeqDatabase.DBServer
load_module Function in module Bio.config._support
load_seqrecord Method in class BioSQL.Loader.DatabaseLoader
Loader Module in package BioSQL
local_test_main Function in module Martel.test.run_tests
LocalParser Class in module Bio.SGMLExtractor
LocalParser Class in module Bio.SGMLExtractor
Location Module in package Bio.Mindy
Location Class in module Bio.Mindy.Location
log_likelihood Method in class Bio.HMM.Trainer.AbstractTrainer
LogDPAlgorithms Class in module Bio.HMM.DynamicProgramming
logistic_function Function in module Bio.NeuralNetwork.BackPropagation.Layer
LogisticRegression Module in package Bio
LogisticRegression Class in module Bio.LogisticRegression
lookup Method in class Bio.Mindy.BaseDB.OpenDB
lookup Method in class BioSQL.BioSeqDatabase.BioSeqDatabase
lower Method in class __builtin__.str
lowess Module in package Bio.Statistics
lowess Function in module Bio.Statistics.lowess
LowQualityBlastError Class in module Bio.Blast.NCBIStandalone
lstrip Method in class __builtin__.str
Lymphocyte Class in package Bio.Ais
lymphocyte_factory Method in class Bio.Ais.Immune
main Function in module Bio.EUtils.dtd2py
main Function in package Bio.Mindy
main Function in module Bio.expressions.blast.wublast
main Function in module Martel.test.run_tests
major_revision_date Method in class Bio.Medline._RecordConsumer
make_1id Function in module Bio.expressions.fasta
make_2id Function in module Bio.expressions.fasta
make_back_table Function in module Bio.Data.CodonTable
make_cached_expression Class in module Bio.config._support
make_consensus Method in class Bio.MEME.Motif.Motif
make_decoder Function in module Bio.Decode
make_entropy Method in class Bio.SubsMat.SeqMat
make_expression Function in module Martel.Time
make_expression Function in module Martel.convert_re
make_iterator Method in class Bio.config.FormatRegistry.FormatObject
make_iterator Method in class Martel.Expression.Expression
make_iterator Method in class Martel.Expression.HeaderFooter
make_iterator Method in class Martel.Expression.ParseRecords
make_log_odds_matrix Function in package Bio.SubsMat
make_node Function in module Bio.EUtils.POM
make_parser Method in class Bio.config.FormatRegistry.FormatObject
make_parser Method in class Bio.config._support.make_cached_expression
make_parser Method in class Martel.Expression.Expression
make_parser Method in class Martel.Expression.HeaderFooter
make_parser Method in class Martel.Expression.ParseRecords
make_pattern Function in module Martel.Time
make_pssm Method in class Bio.MEME.Motif.Motif
make_rate_limited_function Class in module Bio.config._support
make_relative_entropy Method in class Bio.SubsMat.SeqMat
make_timed_function Class in module Bio.config._support
make_typechecked_decoder Function in module Bio.Decode
make_writer Method in class Bio.FormatIO.FormatIO
makedict Function in module Martel.msre_constants
makeFIRST Method in class Bio.Parsers.spark.GenericParser
makeRE Method in class Bio.Parsers.spark.GenericScanner
mapped_pattern Method in class Bio.Prosite.Pattern.PrositeMatch
mapping Method in class Bio.Prosite.Pattern.PrositeMatch
MarkovModel Module in package Bio.HMM
MarkovModel Module in package Bio
MarkovModel Class in module Bio.MarkovModel
MarkovModelBuilder Class in module Bio.HMM.MarkovModel
MarkupEditor Module in package Bio
MarkupEditor Class in module Bio.MarkupEditor
Martel Package
MartelAttributeList Class in module Martel.Parser
MASTParser Class in module Bio.MEME.Parser
MASTRecord Class in module Bio.MEME.Parser
match Method in class Bio.Parsers.spark.GenericASTMatcher
match Method in class Bio.Prosite.Pattern.Prosite
match Function in module Bio.triefind
match Method in class Martel.msre_parse.Tokenizer
match_all Function in module Bio.triefind
match_r Method in class Bio.Parsers.spark.GenericASTMatcher
match_sequence Function in package Bio.Ais
matches_schema Function in module Bio.NeuralNetwork.Gene.Schema
matchpath Method in class Bio.EUtils.POM.ElementNode
matchpath Method in class Bio.EUtils.POM.IndentedText
mathfns Module in package Bio
matrix Method in class Bio.Blast.NCBIStandalone._ParametersConsumer
matrix Method in class Bio.Prosite._RecordConsumer
MatrixInfo Module in package Bio.SubsMat
MaxEntropy Module in package Bio
MaxEntropy Class in module Bio.MaxEntropy
MaxRepeat Class in module Martel.Expression
MaxRepeat Function in package Martel
Medline Package in package Bio
medline Module in package Bio.dbdefs
MEME Package in package Bio
MEMEMotif Class in module Bio.MEME.Motif
MEMEParser Class in module Bio.MEME.Parser
MEMERecord Class in module Bio.MEME.Parser
MemoryFlatDB Class in module Bio.Mindy.FlatDB
Menu Class in module Bio.EUtils.DTDs.eInfo_020511
MenuName Class in module Bio.EUtils.DTDs.eInfo_020511
merge_strings Function in module Martel.optimize
mesh_heading Method in class Bio.Medline._RecordConsumer
mesh_tree_number Method in class Bio.Medline._RecordConsumer
message Variable in class exceptions.BaseException
message Variable in class exceptions.BaseException
message Variable in class exceptions.BaseException
message Variable in class exceptions.BaseException
message Variable in class exceptions.BaseException
message Variable in class exceptions.BaseException
message Variable in class exceptions.BaseException
message Variable in class exceptions.BaseException
message Variable in class exceptions.BaseException
message Variable in class exceptions.BaseException
message Variable in class exceptions.BaseException
message Variable in class exceptions.BaseException
message Variable in class exceptions.BaseException
message Variable in class exceptions.BaseException
message Variable in class exceptions.BaseException
message Variable in class exceptions.BaseException
message Variable in class exceptions.BaseException
message Variable in class exceptions.BaseException
message Variable in class exceptions.BaseException
message Variable in class exceptions.BaseException
message Variable in class exceptions.BaseException
message Variable in class exceptions.BaseException
message Variable in class exceptions.BaseException
message Variable in class exceptions.BaseException
message Variable in class exceptions.BaseException
message Variable in class exceptions.BaseException
MethodHolder Class in module Bio.EUtils.sourcegen
methylation Method in class Bio.Rebase._RecordConsumer
microorganism Method in class Bio.Rebase._RecordConsumer
MidPoint Class in module Bio.MarkupEditor
Mindy Package in package Bio
Mixins Module in package Bio.EUtils
ml_estimator Method in class Bio.HMM.Trainer.AbstractTrainer
model_sequences Method in class Bio.Blast.NCBIStandalone._DescriptionConsumer
MostCountSchemaFitness Class in module Bio.NeuralNetwork.Gene.Schema
Motif Module in package Bio.AlignAce
Motif Class in module Bio.AlignAce.Motif
motif Method in class Bio.AlignAce.Parser.AlignAceConsumer
Motif Module in package Bio.MEME
Motif Class in module Bio.MEME.Motif
Motif Module in package Bio.NeuralNetwork.Gene
motif_hit Method in class Bio.AlignAce.Parser.AlignAceConsumer
motif_mask Method in class Bio.AlignAce.Parser.AlignAceConsumer
motif_name Method in class Bio.MEME.Parser._MEMEConsumer
motif_score Method in class Bio.AlignAce.Parser.AlignAceConsumer
motif_score Method in class Bio.AlignAce.Parser.CompareAceConsumer
MotifCoder Class in module Bio.NeuralNetwork.Gene.Motif
MotifFinder Class in module Bio.NeuralNetwork.Gene.Motif
mro Method in class __builtin__.type
msre_constants Module in package Martel
msre_parse Module in package Martel
mult_align Function in module Bio.FSSP.FSSPTools
multalign Method in class Bio.Blast.NCBIStandalone._AlignmentConsumer
Multicall Class in module Martel.Dispatch
MulticallEnd Class in module Martel.Dispatch
MulticallStart Class in module Martel.Dispatch
MultiDict Module in package Bio.EUtils
MultiGraph Module in package Bio.Pathway.Rep
MultiGraph Class in module Bio.Pathway.Rep.MultiGraph
MultipleAlignment Class in module Bio.Blast.Record
MultiProc Package in package Bio
Murphy10 Class in module Bio.Alphabet.Reduced
Murphy15 Class in module Bio.Alphabet.Reduced
Murphy4 Class in module Bio.Alphabet.Reduced
Murphy8 Class in module Bio.Alphabet.Reduced
must_not_parse Function in module Martel.test.test_macros
must_parse Function in module Martel.test.test_macros
MutableSeq Class in module Bio.Seq
mutate Method in class Bio.GA.Mutation.General.SafeFitnessMutation
mutate Method in class Bio.GA.Mutation.Simple.ConversionMutation
mutate Method in class Bio.GA.Mutation.Simple.SinglePositionMutation
mutate_and_crossover Method in class Bio.GA.Selection.Abstract.AbstractSelection
Mutation Package in package Bio.GA
MyParser Class in module Bio.File
MyParser Class in module Bio.File
Mysql_dbutils Class in module BioSQL.DBUtils
NaiveBayes Module in package Bio
NaiveBayes Class in module Bio.NaiveBayes
Name Class in module Bio.EUtils.DTDs.LinkOut
Name Class in module Bio.EUtils.DTDs.eInfo_020511
Name Class in module Bio.EUtils.DTDs.eLink_020511
name_filter Function in module Bio.FSSP.FSSPTools
NameAbbr Class in module Bio.EUtils.DTDs.LinkOut
NameAbbr Class in module Bio.EUtils.DTDs.eLink_020511
names Method in class Bio.Compass._Consumer
NCBI Module in package Bio.WWW
ncbiblast Module in package Bio.expressions.blast
NCBICodonTable Class in module Bio.Data.CodonTable
NCBICodonTableDNA Class in module Bio.Data.CodonTable
NCBICodonTableRNA Class in module Bio.Data.CodonTable
NCBIStandalone Module in package Bio.Blast
NCBIWWW Module in package Bio.Blast
NCBIXML Module in package Bio.Blast
ncheck Method in class Bio.EUtils.Mixins.LinkMixin
ncols Method in class Bio.Affy.CelFile.CelRecord
Ndb Package in package Bio
NdbParser Class in package Bio.Ndb
neighbor_links Method in class Bio.EUtils.Mixins.LinkMixin
NeighborLinkSet Class in module Bio.EUtils.Datatypes
NetCatch Module in package Bio
NetCatch Class in module Bio.NetCatch
Network Module in package Bio.NeuralNetwork.BackPropagation
Network Class in package Bio.Pathway
NeuralNetwork Package in package Bio
new_attribute Method in class Bio.EUtils.POM.DTDConsumerForSourceGeneration
new_database Method in class BioSQL.BioSeqDatabase.DBServer
new_element_type Method in class Bio.EUtils.POM.DTDConsumerForSourceGeneration
new_external_entity Method in class Bio.EUtils.POM.DTDConsumerForSourceGeneration
new_external_pe Method in class Bio.EUtils.POM.DTDConsumerForSourceGeneration
new_general_entity Method in class Bio.EUtils.POM.DTDConsumerForSourceGeneration
new_group_tag Method in class Martel.Generate.GeneratorState
new_notation Method in class Bio.EUtils.POM.DTDConsumerForSourceGeneration
new_parameter_entity Method in class Bio.EUtils.POM.DTDConsumerForSourceGeneration
next Method in class Bio.Blast.NCBIStandalone.Iterator
next Method in class Bio.Blast.ParseBlastTable.BlastTableReader
next Method in class Bio.Compass.Iterator
next Method in class Bio.Enzyme.Iterator
next Method in class Bio.FormatIO.FormatIOIterator
next Method in class Bio.Gobase.Iterator
next Method in class Bio.Medline.Iterator
next Method in class Bio.Nexus.Nexus.CharBuffer
next Method in class Bio.Prosite.Iterator
next Method in class Bio.Prosite.Prodoc.Iterator
next Method in class Bio.Rebase.Iterator
next Method in class Bio.Sequencing.Ace.Iterator
next Method in class Bio.Sequencing.Phd.Iterator
next Method in class Bio.SwissProt.SProt.Iterator
next Method in class Bio.UniGene.Iterator
next Method in class Martel.Iterator.EventStream
next Method in class Martel.Iterator.HeaderFooterEventStream
next Method in class Martel.Iterator.Iterate
next Method in class Martel.Iterator.RecordEventStream
next Method in class Martel.RecordReader.CountLines
next Method in class Martel.RecordReader.EndsWith
next Method in class Martel.RecordReader.Everything
next Method in class Martel.RecordReader.Nothing
next Method in class Martel.RecordReader.RecordReader
next Method in class Martel.RecordReader.StartsWith
next Method in class Martel.RecordReader.Until
next_id Method in class BioSQL.DBUtils.Pgdb_dbutils
next_id Method in class BioSQL.DBUtils.Psycopg_dbutils
next_nonwhitespace Method in class Bio.Nexus.Nexus.CharBuffer
next_num Method in class Bio.HotRand.HotCache
next_until Method in class Bio.Nexus.Nexus.CharBuffer
next_word Method in class Bio.Nexus.Nexus.CharBuffer
Nexus Package in package Bio
Nexus Module in package Bio.Nexus
Nexus Class in module Bio.Nexus.Nexus
NexusError Class in module Bio.Nexus.Nexus
nlmmedline_001211_format Module in package Bio.Medline
nlmmedline_010319_format Module in package Bio.Medline
nlmmedline_011101_format Module in package Bio.Medline
nlmmedline_031101_format Module in package Bio.Medline
NLMMedlineXML Module in package Bio.Medline
NMR Package in package Bio
NMTOKEN Class in module Bio.EUtils.POM
NMTOKENS Class in module Bio.EUtils.POM
no_author Method in class Bio.Medline._RecordConsumer
no_hits Method in class Bio.Blast.NCBIStandalone._DescriptionConsumer
nobuffer Method in class Bio.EUtils.ReseekFile.ReseekFile
NoCase Function in module Martel.Expression
node Method in class Bio.EUtils.POM.ElementNode
Node Class in module Bio.Nexus.Nodes
node Method in class Bio.Nexus.Trees.Tree
NodeData Class in module Bio.Nexus.Trees
NodeException Class in module Bio.Nexus.Nodes
Nodes Module in package Bio.Nexus
nodes Method in class Bio.Pathway.Rep.Graph.Graph
nodes Method in class Bio.Pathway.Rep.MultiGraph.MultiGraph
NOEtools Module in package Bio.NMR
noevent Method in class Bio.AlignAce.Parser.AlignAceConsumer
noevent Method in class Bio.Blast.NCBIStandalone._BlastErrorConsumer
noevent Method in class Bio.MEME.Parser._MASTConsumer
noevent Method in class Bio.MEME.Parser._MEMEConsumer
nonmodel_sequences Method in class Bio.Blast.NCBIStandalone._DescriptionConsumer
nonterminal Method in class Bio.Parsers.spark.GenericASTBuilder
normalize Class in module Bio.EUtils.DTDs.LinkOut
normalize Method in class Bio.config.FormatRegistry.FormatRegistry
normalize Function in module Martel.test.test_RecordReader2
Not Class in module Bio.EUtils.Datatypes
Nothing Class in module Martel.RecordReader
npix Method in class Bio.Affy.CelFile.CelRecord
nrows Method in class Bio.Affy.CelFile.CelRecord
nucleotide_alphabet Variable in class Bio.Data.CodonTable.CodonTable
nucleotide_alphabet Variable in class Bio.Data.CodonTable.CodonTable
nucleotide_alphabet Variable in class Bio.Data.CodonTable.NCBICodonTable
nucleotide_alphabet Variable in class Bio.Data.CodonTable.NCBICodonTableDNA
nucleotide_alphabet Variable in class Bio.Data.CodonTable.NCBICodonTableRNA
NucleotideAlphabet Class in package Bio.Alphabet
NullOp Class in module Martel.Expression
num_Adeno2 Method in class Bio.Rebase._RecordConsumer
num_ambiguous Method in class Bio.NeuralNetwork.Gene.Schema.Schema
num_extends Method in class Bio.Blast.NCBIStandalone._ParametersConsumer
num_good_extends Method in class Bio.Blast.NCBIStandalone._ParametersConsumer
num_hits Method in class Bio.Blast.NCBIStandalone._ParametersConsumer
num_Lambda Method in class Bio.Rebase._RecordConsumer
num_left Method in class Bio.MultiProc.Scheduler.Scheduler
num_letters_in_database Method in class Bio.Blast.NCBIStandalone._DatabaseReportConsumer
num_matches Method in class Bio.NeuralNetwork.Gene.Schema.Schema
num_pBR322 Method in class Bio.Rebase._RecordConsumer
num_PhiX174 Method in class Bio.Rebase._RecordConsumer
num_running Method in class Bio.MultiProc.Scheduler.Scheduler
num_seqs_better_e Method in class Bio.Blast.NCBIStandalone._ParametersConsumer
num_sequences Method in class Bio.Blast.NCBIStandalone._ParametersConsumer
num_sequences_in_database Method in class Bio.Blast.NCBIStandalone._DatabaseReportConsumer
num_SV40 Method in class Bio.Rebase._RecordConsumer
Number Function in module Bio.expressions.blast.ncbiblast
number_of_references Method in class Bio.Medline._RecordConsumer
numerical_results Method in class Bio.Prosite._RecordConsumer
object Class in module __builtin__
ObjectList Class in module Bio.EUtils.DTDs.LinkOut
ObjectParserHandler Class in module Bio.EUtils.POM
ObjectSelector Class in module Bio.EUtils.DTDs.LinkOut
ObjectUrl Class in module Bio.EUtils.DTDs.LinkOut
ObjId Class in module Bio.EUtils.DTDs.LinkOut
ObjUrl Class in module Bio.EUtils.DTDs.eLink_020511
ObjUrl Class in module Bio.EUtils.Datatypes
observed_frequency_to_substitution_matrix Function in package Bio.SubsMat
OneOfPosition Class in module Bio.SeqFeature
OP Class in module Bio.EUtils.DTDs.eSearch_020511
open Function in module Bio.Mindy.FlatDB
open Function in package Bio.Mindy
open_database Function in module BioSQL.BioSeqDatabase
open_file Function in module Bio.Mindy.compression
OpenDB Class in module Bio.Mindy.BaseDB
opengroup Method in class Martel.convert_re.GroupNames
opengroup Method in class Martel.msre_parse.Pattern
Opt Function in package Martel
optimize Module in package Martel
optimize Function in module Martel.optimize
optimize_unnamed_groups Function in module Martel.optimize
optimize_unnamed_groups_recursive Function in module Martel.optimize
Or Class in module Bio.EUtils.Datatypes
OrderedMultiDict Class in module Bio.EUtils.MultiDict
organelle Method in class Bio.SwissProt.SProt._RecordConsumer
Organism Module in package Bio.GA
Organism Class in module Bio.GA.Organism
Organism Class in module Bio.Graphics.BasicChromosome
organism_classification Method in class Bio.SwissProt.SProt._RecordConsumer
organism_host Method in class Bio.SwissProt.SProt._RecordConsumer
organism_species Method in class Bio.SwissProt.SProt._RecordConsumer
original_taxon_order Method in class Bio.SwissProt.SProt._RecordConsumer in class Bio.Nexus.Nexus.Nexus
OutputLayer Class in module Bio.NeuralNetwork.BackPropagation.Layer
OutputMessage Class in module Bio.EUtils.DTDs.eSearch_020511
OutputMessage Class in module Bio.EUtils.Datatypes
p_arg Method in class Bio.Decode.DecodeParser
p_args Method in class Bio.Decode.DecodeParser
p_expression Method in class Bio.Decode.DecodeParser
p_term Method in class Bio.Decode.DecodeParser
pad Class in module Bio.EUtils.DTDs.LinkOut
pagination Method in class Bio.Medline._RecordConsumer
pairlist_to_dict Function in package Bio.InterPro
pairwise2 Module in package Bio
PalindromeCommandline Class in module Bio.Emboss.Applications
parameter Method in class Bio.AlignAce.Parser.AlignAceConsumer
parameters Method in class Bio.AlignAce.Parser.AlignAceConsumer
Parameters Class in module Bio.Blast.Record
parent_edges Method in class Bio.Pathway.Rep.Graph.Graph
parent_edges Method in class Bio.Pathway.Rep.MultiGraph.MultiGraph
parents Method in class Bio.Pathway.Rep.Graph.Graph
parents Method in class Bio.Pathway.Rep.MultiGraph.MultiGraph
parse Method in class Bio.Affy.CelFile.CelParser
parse Method in class Bio.AlignAce.Parser.AlignAceParser
parse Method in class Bio.AlignAce.Parser.CompareAceParser
parse Method in class Bio.Blast.NCBIStandalone.BlastErrorParser
parse Method in class Bio.Blast.NCBIStandalone.BlastParser
parse Method in class Bio.Blast.NCBIStandalone.PSIBlastParser
parse Method in class Bio.Blast.NCBIWWW.BlastParser
parse Method in class Bio.Blast.NCBIXML.BlastParser
parse Function in module Bio.Blast.NCBIXML
parse Method in class Bio.Compass.RecordParser
parse Function in module Bio.Decode
parse Method in class Bio.EUtils.POM.POMDocument
parse Module in package Bio.EUtils
parse Method in class Bio.Emboss.Primer.Primer3Parser
parse Method in class Bio.Emboss.Primer.PrimerSearchParser
parse Method in class Bio.Enzyme.RecordParser
parse Method in class Bio.Gobase.RecordParser
parse Method in class Bio.InterPro.InterProParser
parse Method in class Bio.MEME.Parser.MASTParser
parse Method in class Bio.MEME.Parser.MEMEParser
parse Method in class Bio.Medline.RecordParser
parse Method in class Bio.Ndb.NdbParser
parse Method in class Bio.ParserSupport.AbstractParser
parse Method in class Bio.Parsers.spark.GenericParser
parse Method in class Bio.Prosite.Prodoc.RecordParser
parse Method in class Bio.Prosite.RecordParser
parse Method in class Bio.Rebase.RecordParser
parse Method in class Bio.Sequencing.Ace.ACEParser
parse Method in class Bio.Sequencing.Ace.RecordParser
parse Method in class Bio.Sequencing.Phd.RecordParser
parse Method in class Bio.SwissProt.KeyWList.ListParser
parse Method in class Bio.SwissProt.SProt.RecordParser
parse Method in class Bio.SwissProt.SProt.SequenceParser
parse Method in class Bio.UniGene.RecordParser
parse Method in class Martel.Parser.HeaderFooterParser
parse Method in class Martel.Parser.Parser
parse Method in class Martel.Parser.RecordParser
parse Function in module Martel.msre_parse
parse Method in class xml.sax.xmlreader.XMLReader
parse_comment Method in class markupbase.ParserBase
parse_declaration Method in class markupbase.ParserBase
parse_endtag Method in class sgmllib.SGMLParser
parse_fetch_identifiers Function in module Bio.EUtils.parse
parse_fetch_publication_xml Function in module Bio.EUtils.parse
parse_fetch_sequence_xml Function in module Bio.EUtils.parse
parse_file Method in class Bio.ParserSupport.AbstractParser
parse_lcheck Function in module Bio.EUtils.parse
parse_link_xml Function in module Bio.EUtils.parse
parse_llinks Function in module Bio.EUtils.parse
parse_marked_section Method in class markupbase.ParserBase
parse_neighbor_links Function in module Bio.EUtils.parse
parse_pi Method in class sgmllib.SGMLParser
parse_post Function in module Bio.EUtils.parse
parse_search Function in module Bio.EUtils.parse
parse_simple_xpath Function in module Bio.Mindy.XPath
parse_single Function in module Bio.EZRetrieve
parse_starttag Method in class sgmllib.SGMLParser
parse_str Method in class Bio.ParserSupport.AbstractParser
parse_summary_xml Function in module Bio.EUtils.parse
parse_template Function in module Martel.msre_parse
parse_using_dtd Method in class Bio.EUtils.parse.UsePOMParser
ParseBlastTable Module in package Bio.Blast
parseFile Method in class Bio.EUtils.POM.POMDocument
parseFile Method in class Martel.Parser.HeaderFooterParser
parseFile Method in class Martel.Parser.Parser
parseFile Method in class Martel.Parser.RecordParser
Parser Module in package Bio.AlignAce
Parser Module in package Bio.MEME
Parser Module in package Martel
Parser Class in module Martel.Parser
ParserBase Class in module markupbase
ParseRecords Class in module Martel.Expression
ParserException Class in module Martel.Parser
ParserIncompleteException Class in module Martel.Parser
ParserPositionException Class in module Martel.Parser
ParserRecordException Class in module Martel.Parser
Parsers Package in package Bio
ParserSupport Module in package Bio
parseString Method in class Martel.Parser.HeaderFooterParser
parseString Method in class Martel.Parser.Parser
parseString Method in class Martel.Parser.RecordParser
partition Method in class __builtin__.str
PassThrough Class in module Martel.Expression
pathname Method in class Bio.EUtils.POM.ElementNode
Pathway Package in package Bio
Pattern Module in package Bio.NeuralNetwork.Gene
Pattern Module in package Bio.Prosite
pattern Method in class Bio.Prosite._RecordConsumer
Pattern Class in module Martel.msre_parse
pattern_mapping Function in module Bio.Prosite.Pattern
PatternHit Class in package Bio.Prosite
PatternIO Class in module Bio.NeuralNetwork.Gene.Pattern
PatternRepository Class in module Bio.NeuralNetwork.Gene.Pattern
PC5 Class in module Bio.Alphabet.Reduced
pdb Method in class Bio.FSSP.FSSPAlignDict
pdb Module in package Bio.dbdefs
pdb_reference Method in class Bio.Prosite._RecordConsumer
pdb_res_num Variable in class Bio.FSSP.fssp_rec.align
Peaklist Class in module Bio.NMR.xpktools
peek Method in class Bio.Nexus.Nexus.CharBuffer
peek_nonwhitespace Method in class Bio.Nexus.Nexus.CharBuffer
peek_word Method in class Bio.Nexus.Nexus.CharBuffer
peekline Method in class Bio.File.UndoHandle
percent_monomers Function in module Bio.utils
personal_name_as_subject Method in class Bio.Medline._RecordConsumer
Pgdb_dbutils Class in module BioSQL.DBUtils
Phd Module in package Bio.Sequencing
PhraseIgnored Class in module Bio.EUtils.DTDs.eSearch_020511
PhraseIgnored Class in module Bio.EUtils.Datatypes
PhraseNotFound Class in module Bio.EUtils.DTDs.eSearch_020511
PhraseNotFound Class in module Bio.EUtils.Datatypes
phred_version Method in class Bio.Sequencing.Phd._RecordConsumer
pick_a_lymphocyte Method in class Bio.Ais.Immune
pmfetch Function in module Bio.WWW.NCBI
pmneighbor Function in module Bio.WWW.NCBI
pmqty Function in module Bio.WWW.NCBI
Point Module in package Bio.GA.Crossover
poll Method in class Bio.MultiProc.copen._ProcHandle
POM Module in package Bio.EUtils
POMDocument Class in module Bio.EUtils.POM
pop Method in class Bio.Seq.MutableSeq
pop Method in class __builtin__.dict
pop Method in class __builtin__.list
popitem Method in class Bio.Crystal.Crystal
popitem Method in class __builtin__.dict
pos_align_list2dict Method in class Bio.FSSP.FSSPAlignRec
pos_specific_score_matrix Method in class Bio.Align.AlignInfo.SummaryInfo
PosAlign Class in package Bio.FSSP
PositionGap Class in module Bio.SeqFeature
positive_alignment Method in class Bio.Compass._Consumer
post Method in class Bio.EUtils.HistoryClient.HistoryClient
posted_date Method in class Bio.Blast.NCBIStandalone._DatabaseReportConsumer
postorder Method in class Bio.Parsers.spark.GenericASTTraversal
PostResult Class in module Bio.EUtils.Datatypes
predict Method in class Bio.NeuralNetwork.BackPropagation.Network.BasicNetwork
predictNOE Function in module Bio.NMR.NOEtools
preorder Method in class Bio.Parsers.spark.GenericASTTraversal
prepare_input_source Function in module Bio.EUtils.ReseekFile
preprocess Method in class Bio.Parsers.spark.GenericASTBuilder
preprocess Method in class Bio.Parsers.spark.GenericASTMatcher
preprocess Method in class Bio.Parsers.spark.GenericParser
pretty_print_prediction Function in module Bio.HMM.Utilities
primary_key_name Method in class Bio.Mindy.SimpleSeqRecord.BaseSeqRecordIndexer
primary_key_name Method in class Bio.Mindy.SimpleSeqRecord.FunctionIndexer
primary_key_name Method in class Bio.Mindy.SimpleSeqRecord.SimpleIndexer
PrimaryNamespace Class in module Bio.Mindy.FlatDB
PrimaryTable Class in module Bio.Mindy.FlatDB
Primer Module in package Bio.Emboss
primer3_format Module in package Bio.Emboss
Primer3Commandline Class in module Bio.Emboss.Applications
Primer3Parser Class in module Bio.Emboss.Primer
Primer3Primers Class in module Bio.Emboss.Primer
Primer3Record Class in module Bio.Emboss.Primer
primer_name Method in class Bio.Emboss.Primer._PrimerSearchRecordConsumer
primersearch_format Module in package Bio.Emboss
PrimerSearchAmplifier Class in module Bio.Emboss.Primer
PrimerSearchCommandline Class in module Bio.Emboss.Applications
PrimerSearchInputRecord Class in module Bio.Emboss.Primer
PrimerSearchOutputRecord Class in module Bio.Emboss.Primer
PrimerSearchParser Class in module Bio.Emboss.Primer
print_debug Class in module Martel.Generate
print_full_mat Method in class Bio.SubsMat.SeqMat
print_info Class in module Martel.Generate
print_info_content Function in module Bio.Align.AlignInfo
print_mat Method in class Bio.SubsMat.SeqMat
print_matrix Function in module Bio.pairwise2
prlinks Method in class Bio.EUtils.Mixins.LinkMixin
Problem Class in module Bio.EUtils.Datatypes
processing_instruction Method in class Bio.EUtils.POM.ElementNode
processingInstruction Method in class Bio.EUtils.POM.ObjectParserHandler
processingInstruction Method in class xml.sax.handler.ContentHandler
Prodoc Module in package Bio.Prosite
prodoc Module in package Bio.dbdefs
product_size Method in class Bio.Emboss.Primer._Primer3RecordConsumer
profilewidth Method in class Bio.Compass._Consumer
PropertyManager Module in package Bio
PropertyManager Class in module Bio.PropertyManager
PropHolder Class in module reportlab.graphics.widgetbase
Prosite Package in package Bio
Prosite Class in module Bio.Prosite.Pattern
prosite Module in package Bio.dbdefs
prosite_reference Method in class Bio.Enzyme._RecordConsumer
prosite_reference Method in class Bio.Prosite.Prodoc._RecordConsumer
prosite_to_grouped_re Function in module Bio.Prosite.Pattern
prosite_to_re Function in module Bio.Prosite.Pattern
PrositeAlphabet Class in module Bio.Prosite.Pattern
PrositeMatch Class in module Bio.Prosite.Pattern
PrositeTerm Class in module Bio.Prosite.Pattern
protein_alphabet Variable in class Bio.Data.CodonTable.CodonTable
protein_alphabet Variable in class Bio.Data.CodonTable.CodonTable
protein_alphabet Variable in class Bio.Data.CodonTable.NCBICodonTable
protein_alphabet Variable in class Bio.Data.CodonTable.NCBICodonTable
protein_alphabet Variable in class Bio.Data.CodonTable.NCBICodonTable
ProteinAlphabet Class in package Bio.Alphabet
ProteinRecord Class in package Bio.Gobase
prototype Method in class Bio.Rebase._RecordConsumer
PROTSIM Method in class Bio.UniGene._RecordConsumer
provideNode Method in class reportlab.graphics.shapes.UserNode
provideNode Method in class reportlab.graphics.widgetbase.Widget
Provider Class in module Bio.EUtils.DTDs.LinkOut
Provider Class in module Bio.EUtils.DTDs.eLink_020511
Provider Class in module Bio.EUtils.Datatypes
ProviderId Class in module Bio.EUtils.DTDs.LinkOut
prune Method in class Bio.Nexus.Trees.Tree
prune Method in class Bio.Parsers.spark.GenericASTTraversal
PSIBlast Class in module Bio.Blast.Record
PSIBlastParser Class in module Bio.Blast.NCBIStandalone
PSSM Class in module Bio.Align.AlignInfo
Psycopg_dbutils Class in module BioSQL.DBUtils
publication_date Method in class Bio.Medline._RecordConsumer
publication_type Method in class Bio.Medline._RecordConsumer
PublicationDBIdsFetchMixin Class in module Bio.EUtils.DBIdsClient
PublicationDBIdsRecord Class in module Bio.EUtils.DBIdsClient
PublicationDBIdsRecordSet Class in module Bio.EUtils.DBIdsClient
PublicationFetchMixin Class in module Bio.EUtils.Mixins
PublicationHistoryFetchMixin Class in module Bio.EUtils.HistoryClient
PublicationHistoryRecord Class in module Bio.EUtils.HistoryClient
PublicationHistoryRecordSet Class in module Bio.EUtils.HistoryClient
PubMed Module in package Bio
pubmed_id Method in class Bio.Medline._RecordConsumer
Punctuation Function in package Martel
pwm Method in class Bio.AlignAce.Motif.Motif
qa Method in class Bio.Sequencing.Ace._RecordConsumer
qa Class in module Bio.Sequencing.Ace
qblast Function in module Bio.Blast.NCBIWWW
quality_levels Method in class Bio.Sequencing.Phd._RecordConsumer
query Method in class Bio.Blast.NCBIStandalone._HSPConsumer
Query Class in module Bio.EUtils.DTDs.LinkOut
Query Class in module Bio.Search
query Function in module Bio.WWW.NCBI
query_alignment Method in class Bio.Compass._Consumer
query_coverage Method in class Bio.Compass.Record
query_description Function in module Bio.Std
query_description_block Function in module Bio.Std
query_info Method in class Bio.Blast.NCBIStandalone._HeaderConsumer
query_length Method in class Bio.Blast.NCBIStandalone._ParametersConsumer
query_size Function in module Bio.Std
QueryKey Class in module Bio.EUtils.DTDs.ePost_020511
QueryKey Class in module Bio.EUtils.DTDs.eSearch_020511
QueryTranslation Class in module Bio.EUtils.DTDs.eSearch_020511
QuotedPhraseNotFound Class in module Bio.EUtils.DTDs.eSearch_020511
QuotedPhraseNotFound Class in module Bio.EUtils.Datatypes
quotestrip Function in module Bio.Nexus.Nexus
random_motif Method in class Bio.NeuralNetwork.Gene.Schema.RandomMotifGenerator
random_population Function in module Bio.GA.Organism
random_test Method in class Bio.Ais.Immune
randomize Method in class Bio.Nexus.Trees.Tree
RandomMotifGenerator Class in module Bio.NeuralNetwork.Gene.Schema
Range Class in module Bio.EUtils.Datatypes
rd Class in module Bio.Sequencing.Ace
rd_data Method in class Bio.Sequencing.Ace._RecordConsumer
rd_header Method in class Bio.Sequencing.Ace._RecordConsumer
Re Function in package Martel
Reaction Class in package Bio.Pathway
reactions Method in class Bio.Pathway.System
read Method in class Bio.AlignAce.Motif.Motif
read Method in class Bio.EUtils.ReseekFile.ReseekFile
read Method in class Bio.File.SGMLHandle
read Method in class Bio.File.UndoHandle
read Method in class Bio.FilteredReader.FilteredReader
read Method in class Bio.FormatIO.FormatIO
read Method in class Bio.Medline.NLMMedlineXML._SavedDataHandle
read Method in class Bio.MultiProc.copen._PickleHandle
read Method in class Bio.MultiProc.copen._ProcHandle
read Method in class Bio.NeuralNetwork.Gene.Pattern.PatternIO
read Method in class Bio.Nexus.Nexus.Nexus
read Method in class Bio.SGMLExtractor.SGMLExtractorHandle
read_and_call Function in module Bio.ParserSupport
read_and_call_until Function in module Bio.ParserSupport
read_and_call_while Function in module Bio.ParserSupport
read_block Method in class Bio.FilteredReader.FilteredReader
read_config Function in module Bio.Mindy.BaseDB
read_count Function in module Bio.SubsMat.FreqTable
read_dna Method in class Bio.Sequencing.Phd._RecordConsumer
read_freq Function in module Bio.SubsMat.FreqTable
read_fssp Function in package Bio.FSSP
read_repr Method in class Bio.EUtils.POM.POMDocument
read_text_matrix Function in package Bio.SubsMat
read_to_end Method in class Bio.FilteredReader.FilteredReader
ReaderError Class in module Martel.RecordReader
readFile Method in class Bio.FormatIO.FormatIO
ReadIntensity Method in class Bio.Affy.CelFile.CelConsumer
readline Method in class Bio.EUtils.ReseekFile.ReseekFile
readline Method in class Bio.File.SGMLHandle
readline Method in class Bio.File.UndoHandle
readline Method in class Bio.MultiProc.copen._ProcHandle
readline Method in class Bio.SGMLExtractor.SGMLExtractorHandle
readlines Method in class Bio.EUtils.ReseekFile.ReseekFile
readlines Method in class Bio.File.SGMLHandle
readlines Method in class Bio.File.UndoHandle
readlines Method in class Bio.MultiProc.copen._ProcHandle
readlines Method in class Bio.SGMLExtractor.SGMLExtractorHandle
Reads Class in module Bio.Sequencing.Ace
readString Method in class Bio.FormatIO.FormatIO
Rebase Package in package Bio
recalculate_fitness Method in class Bio.GA.Organism.Organism
RecognizeHandler Class in module Bio.StdHandler
Record Module in package Bio.Blast
Record Class in package Bio.Compass
Record Class in package Bio.Gobase
Record Class in package Bio.InterPro
Record Class in package Bio.Medline
Record Class in package Bio.Ndb
Record Class in module Bio.Prosite.Prodoc
Record Class in package Bio.Prosite
Record Class in package Bio.Rebase
Record Class in module Bio.Sequencing.Phd
record Function in module Bio.Std
Record Class in module Bio.SwissProt.SProt
record_originator Method in class Bio.Medline._RecordConsumer
RecordEventStream Class in module Martel.Iterator
RecordParser Class in package Bio.Compass
RecordParser Class in package Bio.Enzyme
RecordParser Class in package Bio.Gobase
RecordParser Class in package Bio.Medline
RecordParser Class in module Bio.Prosite.Prodoc
RecordParser Class in package Bio.Prosite
RecordParser Class in package Bio.Rebase
RecordParser Class in module Bio.Sequencing.Ace
RecordParser Class in module Bio.Sequencing.Phd
RecordParser Class in module Bio.SwissProt.SProt
RecordParser Class in package Bio.UniGene
RecordParser Class in module Martel.Parser
RecordReader Module in package Martel
RecordReader Class in module Martel.RecordReader
reduce_sequence Function in module Bio.utils
Reduced Module in package Bio.Alphabet
reference Method in class Bio.Blast.NCBIStandalone._HeaderConsumer
Reference Class in module Bio.Prosite.Prodoc
reference Method in class Bio.Prosite.Prodoc._RecordConsumer
Reference Class in module Bio.SeqFeature
Reference Class in module Bio.SwissProt.SProt
reference_author Method in class Bio.SwissProt.SProt._RecordConsumer
reference_comment Method in class Bio.SwissProt.SProt._RecordConsumer
reference_cross_reference Method in class Bio.SwissProt.SProt._RecordConsumer
reference_location Method in class Bio.SwissProt.SProt._RecordConsumer
reference_number Method in class Bio.SwissProt.SProt._RecordConsumer
reference_position Method in class Bio.SwissProt.SProt._RecordConsumer
reference_title Method in class Bio.SwissProt.SProt._RecordConsumer
reflect Method in class Bio.Parsers.spark.GenericScanner
register Method in class Bio.config.Registry.Registry
register_ncbi_table Function in module Bio.Data.CodonTable
RegisterableGroup Class in module Bio.config.Registry
RegisterableObject Class in module Bio.config.Registry
Registry Module in package Bio.config
Registry Class in module Bio.config.Registry
remainder Method in class Martel.RecordReader.CountLines
remainder Method in class Martel.RecordReader.EndsWith
remainder Method in class Martel.RecordReader.Everything
remainder Method in class Martel.RecordReader.Nothing
remainder Method in class Martel.RecordReader.RecordReader
remainder Method in class Martel.RecordReader.StartsWith
remainder Method in class Martel.RecordReader.Until
RemapEnd Class in module Martel.Dispatch
RemapStart Class in module Martel.Dispatch
remove Method in class Bio.Crystal.Chain
remove Method in class Bio.Graphics.BasicChromosome._ChromosomeComponent
remove Method in class Bio.Pathway.Rep.HashSet.HashSet
remove Method in class Bio.Seq.MutableSeq
remove Method in class BioSQL.Loader.DatabaseRemover
remove Method in class __builtin__.list
remove_database Method in class BioSQL.BioSeqDatabase.DBServer
remove_edge Method in class Bio.Pathway.Rep.Graph.Graph
remove_edge Method in class Bio.Pathway.Rep.MultiGraph.MultiGraph
remove_empty_line Function in module Bio.FilteredReader
remove_leading_whitespace Function in module Bio.FilteredReader
remove_node Method in class Bio.Pathway.Rep.Graph.Graph
remove_node Method in class Bio.Pathway.Rep.MultiGraph.MultiGraph
remove_polyA Method in class Bio.NeuralNetwork.Gene.Pattern.PatternRepository
remove_reaction Method in class Bio.Pathway.System
remove_succ Method in class Bio.Nexus.Nodes.Node
remove_useless_dot Function in module Bio.FilteredReader
Rep Package in package Bio.Pathway
Rep Function in package Martel
Rep1 Function in package Martel
Repair Package in package Bio.GA
repair Method in class Bio.GA.Repair.Stabilizing.AmbiguousRepair
reparent Method in class Bio.EUtils.POM.ElementNode
replace Method in class __builtin__.str
replace_entry Function in module Bio.NMR.xpktools
replace_groups Function in package Martel
replace_text Method in class Bio.EUtils.POM.ElementNode
replacement_dictionary Method in class Bio.Align.AlignInfo.SummaryInfo
RepN Function in package Martel
report_unbalanced Method in class sgmllib.SGMLParser
representation Method in class Bio.NeuralNetwork.Gene.Motif.MotifCoder
representation Method in class Bio.NeuralNetwork.Gene.Schema.SchemaCoder
representation Method in class Bio.NeuralNetwork.Gene.Signature.SignatureCoder
RequestLimiter Class in package Bio.WWW
res_name Variable in class Bio.FSSP.fssp_rec.align
ReseekFile Module in package Bio.EUtils
ReseekFile Class in module Bio.EUtils.ReseekFile
reset Method in class Bio.Blast.NCBIXML.BlastParser
reset Method in class Bio.InterPro.InterProParser
reset Method in class Bio.Ndb.NdbParser
reset Method in class Bio.NetCatch.ExtractUrls
reset Method in class markupbase.ParserBase
reset Method in class sgmllib.SGMLParser
residue_dict Method in class Bio.NMR.xpktools.Peaklist
resolve Method in class Bio.Parsers.spark.GenericASTMatcher
resolve Method in class Bio.Parsers.spark.GenericParser
resolve Method in class Bio.PropertyManager.PropertyManager
resolve_class Method in class Bio.PropertyManager.PropertyManager
rest Method in class Bio.Nexus.Nexus.CharBuffer
RESTR_EXPR Method in class Bio.UniGene._RecordConsumer
RetMax Class in module Bio.EUtils.DTDs.eSearch_020511
retrieve_single Function in module Bio.EZRetrieve
RetStart Class in module Bio.EUtils.DTDs.eSearch_020511
reverse Method in class Bio.Pathway.Reaction
reverse Method in class Bio.Seq.MutableSeq
reverse Method in class __builtin__.list
reverse_complement Method in class Bio.Seq.MutableSeq
reverse_complement Method in class Bio.Seq.Seq
reverse_complement Function in module Bio.Seq
reverse_gc Method in class Bio.Emboss.Primer._Primer3RecordConsumer
reverse_length Method in class Bio.Emboss.Primer._Primer3RecordConsumer
reverse_name Method in class Martel.convert_re.GroupNames
reverse_seq Method in class Bio.Emboss.Primer._Primer3RecordConsumer
reverse_start Method in class Bio.Emboss.Primer._Primer3RecordConsumer
reverse_tm Method in class Bio.Emboss.Primer._Primer3RecordConsumer
rfind Method in class __builtin__.str
rfind_anychar Function in module Bio.stringfns
rindex Method in class __builtin__.str
rint Function in module Bio.pairwise2
rjust Method in class __builtin__.str
RNAAlphabet Class in package Bio.Alphabet
rollback Method in class BioSQL.BioSeqDatabase.Adaptor
root_with_outgroup Method in class Bio.Nexus.Trees.Tree
RouletteWheel Module in package Bio.GA.Selection
RouletteWheelSelection Class in module Bio.GA.Selection.RouletteWheel
round Method in class Bio.Blast.NCBIStandalone._BlastConsumer
round Method in class Bio.Blast.NCBIStandalone._DescriptionConsumer
Round Class in module Bio.Blast.Record
Rows Method in class Bio.Affy.CelFile.CelConsumer
rpartition Method in class __builtin__.str
rpsblast Function in module Bio.Blast.NCBIStandalone
rsplit Method in class __builtin__.str
rstrip Method in class __builtin__.str
rt Class in module Bio.Sequencing.Ace
rt_data Method in class Bio.Sequencing.Ace._RecordConsumer
rt_start Method in class Bio.Sequencing.Ace._RecordConsumer
Rule Class in module Bio.EUtils.DTDs.LinkOut
rule Method in class Bio.Prosite._RecordConsumer
RuleToMany Class in module Bio.EUtils.DTDs.LinkOut
run Method in class Bio.AlignAce.Applications.AlignAceCommandline
run Method in class Bio.AlignAce.Applications.CompareAceCommandline
run Method in class Bio.MultiProc.Scheduler.Scheduler
run Method in class Bio.MultiProc.Task.Task
run Function in package Bio.MultiProc
run Method in class Bio.SVDSuperimposer.SVDSuperimposer.SVDSuperimposer
run_tests Module in package Martel.test
safe_exp Function in module Bio.mathfns
safe_int Function in module Bio.Decode
safe_load_module Function in module Bio.config._support
safe_log Function in module Bio.mathfns
safe_log2 Function in module Bio.mathfns
safe_peekline Function in module Bio.ParserSupport
safe_readline Function in module Bio.ParserSupport
SafeFitnessCrossover Class in module Bio.GA.Crossover.General
SafeFitnessMutation Class in module Bio.GA.Mutation.General
safename Function in module Bio.Nexus.Nexus
save Function in module Bio.MarkovModel
save_characters Method in class Martel.Dispatch.DispatchHandler
save_characters Method in class Martel.Dispatch.Dispatcher
save_info Method in class Bio.Mindy.XPath.GrabXPathNodes
saveline Method in class Bio.File.UndoHandle
SAXException Class in module xml.sax._exceptions
sbjct Method in class Bio.Blast.NCBIStandalone._HSPConsumer
scale_segment_value Method in class Bio.Graphics.DisplayRepresentation.ChromosomeCounts
ScaledDPAlgorithms Class in module Bio.HMM.DynamicProgramming
scan Function in module Bio.Decode
scan_sequence_expasy Function in package Bio.Prosite
Scanner Module in package Bio.AlignAce
scanprosite1 Function in module Bio.WWW.ExPASy
Scheduler Module in package Bio.MultiProc
Scheduler Class in module Bio.MultiProc.Scheduler
Schema Module in package Bio.NeuralNetwork.Gene
Schema Class in module Bio.NeuralNetwork.Gene.Schema
SchemaCoder Class in module Bio.NeuralNetwork.Gene.Schema
SchemaDNAAlphabet Class in module Bio.NeuralNetwork.Gene.Schema
SchemaFactory Class in module Bio.NeuralNetwork.Gene.Schema
SchemaFinder Class in module Bio.NeuralNetwork.Gene.Schema
SCOP Module in package Bio.WWW
score Method in class Bio.Blast.NCBIStandalone._HSPConsumer
Score Class in module Bio.EUtils.DTDs.eLink_020511
score_hit Method in class Bio.AlignAce.Motif.Motif
scores Method in class Bio.Compass._Consumer
scramble Method in class Bio.Ais.Immune
search Method in class Bio.EUtils.DBIdsClient.DBIdsClient
search Method in class Bio.EUtils.HistoryClient.HistoryClient
search Method in class Bio.Prosite.Pattern.Prosite
Search Module in package Bio
Search Class in module Bio.Search
search Function in module Bio.WWW.SCOP
Search Package in package Bio.builders
search Module in package Bio.builders.Search
search Module in package Bio.formatdefs
search_accum_weight Method in class Bio.Ais.Immune
search_for Function in module Bio.PubMed
search_header Function in module Bio.Std
search_instances Method in class Bio.AlignAce.Motif.Motif
search_parameter Function in module Bio.Std
search_pwm Method in class Bio.AlignAce.Motif.Motif
search_statistic Function in module Bio.Std
search_table Function in module Bio.Std
search_table_description Function in module Bio.Std
search_table_entry Function in module Bio.Std
search_table_value Function in module Bio.Std
search_taxon Method in class Bio.Nexus.Trees.Tree
SearchResult Class in module Bio.EUtils.Datatypes
secondary_key_names Method in class Bio.Mindy.SimpleSeqRecord.BaseSeqRecordIndexer
secondary_key_names Method in class Bio.Mindy.SimpleSeqRecord.FunctionIndexer
secondary_key_names Method in class Bio.Mindy.SimpleSeqRecord.SimpleIndexer
secondary_source_id Method in class Bio.Medline._RecordConsumer
SecondaryNamespace Class in module Bio.Mindy.FlatDB
SecondaryStructure Class in package Bio.Alphabet
SecondaryTable Class in module Bio.Mindy.FlatDB
seek Method in class Bio.EUtils.ReseekFile.ReseekFile
seek Method in class Bio.File.UndoHandle
seek Method in class Martel.msre_parse.Tokenizer
select Method in class Bio.GA.Selection.Abstract.AbstractSelection
select Method in class Bio.GA.Selection.Diversity.DiversitySelection
select Method in class Bio.GA.Selection.RouletteWheel.RouletteWheelSelection
select Method in class Bio.GA.Selection.Tournament.TournamentSelection
select_at_random Method in class Bio.Ais.Immune
select_names Function in package Martel
Selection Package in package Bio.GA
Separator Class in module Bio.EUtils.DTDs.LinkOut
Seq Module in package Bio
Seq Class in module Bio.Seq
seq Class in module Bio.Seq in class BioSQL.BioSeq.DBSeqRecord
Seq Class in module Martel.Expression
Seq Function in package Martel
SeqDBRegistry Module in package Bio.config
SeqDBRegistry Class in module Bio.config.SeqDBRegistry
SeqFeature Module in package Bio
SeqFeature Class in module Bio.SeqFeature
SeqMat Class in package Bio.SubsMat
SeqRecord Module in package Bio
SeqRecord Class in module Bio.SeqRecord
SeqRecord Package in package Bio.builders
SeqRecord Package in package Bio.writers
sequence Method in class Bio.AlignAce.Parser.AlignAceConsumer
sequence Method in class Bio.FSSP.FSSPAlignDict
sequence Method in class Bio.Rebase._RecordConsumer
sequence Function in module Bio.Std
SEQUENCE Method in class Bio.UniGene._RecordConsumer
sequence Module in package Bio.builders.SeqRecord
sequence Module in package Bio.formatdefs
sequence_block Function in module Bio.Std
sequence_data Method in class Bio.SwissProt.SProt._RecordConsumer
sequence_data Method in class Bio.SwissProt.SProt._SequenceConsumer
sequence_header Method in class Bio.SwissProt.SProt._RecordConsumer
SequenceDBIdsFetchMixin Class in module Bio.EUtils.DBIdsClient
SequenceDBIdsRecord Class in module Bio.EUtils.DBIdsClient
SequenceDBIdsRecordSet Class in module Bio.EUtils.DBIdsClient
SequenceFetchMixin Class in module Bio.EUtils.Mixins
SequenceHistoryFetchMixin Class in module Bio.EUtils.HistoryClient
SequenceHistoryRecord Class in module Bio.EUtils.HistoryClient
SequenceHistoryRecordSet Class in module Bio.EUtils.HistoryClient
SequenceParser Class in module Bio.SwissProt.SProt
SequenceRecord Class in package Bio.Gobase
sequences Method in class Bio.AlignAce.Parser.AlignAceConsumer
Sequencing Package in package Bio
set Method in class Bio.Nexus.Nexus.StepMatrix
set Method in class Bio.SVDSuperimposer.SVDSuperimposer.SVDSuperimposer
set Method in class Bio.config.DBRegistry.DBObject
set_attribute Method in class Bio.EUtils.POM.ElementNode
set_data Method in class Bio.Nexus.Nodes.Node
set_defaults Method in class Bio.Ais.Immune
set_dirty Method in class Bio.EUtils.POM.POMDocument
set_emission_pseudocount Method in class Bio.HMM.MarkovModel.MarkovModelBuilder
set_emission_score Method in class Bio.HMM.MarkovModel.MarkovModelBuilder
set_equal_probabilities Method in class Bio.HMM.MarkovModel.MarkovModelBuilder
set_id Method in class Bio.Nexus.Nodes.Node
set_indented Method in class Bio.EUtils.POM.ElementNode
set_inline Method in class Bio.EUtils.POM.ElementNode
set_level Method in class Bio.EUtils.POM.ElementNode
set_level Method in class Bio.EUtils.POM.IndentedText
set_mask Method in class Bio.AlignAce.Motif.Motif
set_namespace Method in class Bio.EUtils.POM.ElementNode
set_original_taxon_order Method in class Bio.Nexus.Nexus.Nexus
set_parameter Method in class Bio.Application.AbstractCommandline
set_prev Method in class Bio.Nexus.Nodes.Node
set_random_probabilities Method in class Bio.HMM.MarkovModel.MarkovModelBuilder
set_scale Method in class Bio.Graphics.DisplayRepresentation.ChromosomeCounts
set_subtree Method in class Bio.Nexus.Trees.Tree
set_succ Method in class Bio.Nexus.Nodes.Node
set_text Method in class Bio.EUtils.POM.Comment
set_text Method in class Bio.EUtils.POM.IndentedText
set_transition_pseudocount Method in class Bio.HMM.MarkovModel.MarkovModelBuilder
set_transition_score Method in class Bio.HMM.MarkovModel.MarkovModelBuilder
set_weight Method in class Bio.NeuralNetwork.BackPropagation.Layer.AbstractLayer
set_weight Method in class Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer
setCharacterSaver Method in class Martel.Dispatch.DispatchHandler
setContentHandler Method in class xml.sax.xmlreader.XMLReader
setdefault Method in class Bio.Crystal.Crystal
setdefault Method in class __builtin__.dict
setDocumentLocator Method in class Bio.EUtils.POM.ObjectParserHandler
setDocumentLocator Method in class xml.sax.handler.ContentHandler
setDTDHandler Method in class xml.sax.xmlreader.XMLReader
setEntityResolver Method in class xml.sax.xmlreader.XMLReader
setErrorHandler Method in class xml.sax.xmlreader.XMLReader
setFeature Method in class xml.sax.xmlreader.XMLReader
SetGroupValue Class in module Martel.Generate
setliteral Method in class sgmllib.SGMLParser
setLocale Method in class xml.sax.xmlreader.XMLReader
setLocation Method in class Martel.Parser.ParserException
setName Method in class Bio.MultiProc.Task.Task
setnode Method in class Bio.EUtils.POM.POMDocument
setnomoretags Method in class sgmllib.SGMLParser
setProperties Method in class reportlab.graphics.widgetbase.PropHolder
setProperty Method in class xml.sax.xmlreader.XMLReader
setup Module in package Bio.EUtils
severity Variable in class Bio.EUtils.Datatypes.ErrorProblem
severity Variable in class Bio.EUtils.Datatypes.ErrorProblem
severity Variable in class Bio.EUtils.Datatypes.FieldNotFound
severity Variable in class Bio.EUtils.Datatypes.WarningProblem
severity Variable in class Bio.EUtils.Datatypes.WarningProblem
severity Variable in class Bio.EUtils.Datatypes.WarningProblem
severity Variable in class Bio.EUtils.Datatypes.WarningProblem
SGMLExtractor Module in package Bio
SGMLExtractor Class in module Bio.SGMLExtractor
SGMLExtractorHandle Class in module Bio.SGMLExtractor
SGMLHandle Class in module Bio.File
SGMLParser Class in module sgmllib
SGMLStripper Class in module Bio.File
SGMLStrippingConsumer Class in module Bio.ParserSupport
ShortQueryBlastError Class in module Bio.Blast.NCBIStandalone
Signature Module in package Bio.NeuralNetwork.Gene
SignatureCoder Class in module Bio.NeuralNetwork.Gene.Signature
SignatureFinder Class in module Bio.NeuralNetwork.Gene.Signature
sim Method in class Bio.AlignAce.Motif.Motif
Simple Module in package Bio.GA.Mutation
Simple Function in module Martel.test.testformats.swissprot38
simple_elem Function in module Bio.Medline.nlmmedline_001211_format
simple_elem Function in module Bio.Medline.nlmmedline_010319_format
simple_elem Function in module Bio.Medline.nlmmedline_011101_format
simple_elem Function in module Bio.Medline.nlmmedline_031101_format
SimpleFinisher Class in module Bio.NeuralNetwork.Gene.Schema
SimpleIndexer Class in module Bio.Mindy.SimpleSeqRecord
SimpleRecordFilter Function in package Martel
SimpleSeqRecord Module in package Bio.Mindy
simplify Method in class Martel.Dispatch.Multicall
single_primer_line Method in class Bio.Emboss.Primer._Primer3RecordConsumer
SingleLetterAlphabet Class in package Bio.Alphabet
SinglePointCrossover Class in module Bio.GA.Crossover.Point
SinglePositionMutation Class in module Bio.GA.Mutation.Simple
SingleToken Class in module Bio.EUtils.DTDs.eInfo_020511
sink Method in class Bio.Pathway.Network
sink_interactions Method in class Bio.Pathway.Network
size Method in class Bio.Affy.CelFile.CelRecord
size Variable in class Bio.Alphabet.Alphabet
size Variable in class Bio.Alphabet.Alphabet
size Variable in class Bio.Alphabet.Alphabet
size Variable in class Bio.Alphabet.Reduced.HPModel
size Variable in class Bio.Alphabet.Reduced.Murphy10
size Variable in class Bio.Alphabet.Reduced.Murphy15
size Variable in class Bio.Alphabet.Reduced.Murphy4
size Variable in class Bio.Alphabet.Reduced.Murphy8
size Variable in class Bio.Alphabet.Reduced.PC5
size Variable in class Bio.Alphabet.SingleLetterAlphabet
size Variable in class Bio.Alphabet.SingleLetterAlphabet
size Variable in class Bio.Alphabet.SingleLetterAlphabet
size Variable in class Bio.Alphabet.SingleLetterAlphabet
size Variable in class Bio.Alphabet.SingleLetterAlphabet
size Variable in class Bio.Alphabet.SingleLetterAlphabet
size Variable in class Bio.Alphabet.SingleLetterAlphabet
size Variable in class Bio.Alphabet.SingleLetterAlphabet
size Variable in class Bio.Alphabet.SingleLetterAlphabet
size Variable in class Bio.Alphabet.SingleLetterAlphabet
size Variable in class Bio.Alphabet.SingleLetterAlphabet
size Variable in class Bio.Alphabet.SingleLetterAlphabet
size Variable in class Bio.Alphabet.SingleLetterAlphabet
size Variable in class Bio.Alphabet.ThreeLetterProtein
skip_empty_group Function in module Martel.optimize
skip_whitespace Method in class Bio.Nexus.Nexus.CharBuffer
SkipLinesTo Function in package Martel
SkipLinesUntil Function in package Martel
skippedEntity Method in class xml.sax.handler.ContentHandler
smprint Method in class Bio.Nexus.Nexus.StepMatrix
sort Method in class Bio.Sequencing.Ace.ACEFileRecord
sort Method in class __builtin__.list
source Method in class Bio.Medline._RecordConsumer
source Method in class Bio.Pathway.Network
source Method in class Bio.Rebase._RecordConsumer
source_interactions Method in class Bio.Pathway.Network
SourceFile Class in module Bio.EUtils.sourcegen
sourcegen Module in package Bio.EUtils
SourceGen Class in module Bio.EUtils.sourcegen
Spaces Function in package Martel
span Method in class Bio.Prosite.Pattern.PrositeMatch
spark Module in package Bio.Parsers
special_list Method in class Bio.Medline._RecordConsumer
species Method in class Bio.Pathway.Network
species Method in class Bio.Pathway.Reaction
species Method in class Bio.Pathway.System
split Method in class Bio.Nexus.Trees.Tree
split Method in class __builtin__.str
splitany Function in module Bio.stringfns
splitlines Method in class __builtin__.str
SProt Module in package Bio.SwissProt
sprot_search_de Function in module Bio.WWW.ExPASy
sprot_search_ful Function in module Bio.WWW.ExPASy
SS Function in module Bio.expressions.transfac
ss1 Variable in class Bio.FSSP.fssp_rec.align
Stabilizing Module in package Bio.GA.Repair
StandardError Class in module exceptions
Stanza Class in module Bio.config._stanzaformat
StanzaFormat Class in module Bio.config._stanzaformat
start Method in class Bio.MultiProc.Task.Task
start Method in class Bio.Prosite.Pattern.PrositeMatch
start Method in class Bio.StdHandler.Handle_feature_location
start Method in class Bio.StdHandler.Handle_feature_location
start Method in class Bio.StdHandler.Handle_feature_qualifier
start Method in class Bio.StdHandler.Handle_features
start Method in class Bio.StdHandler.Handle_hsp_seqalign
start Method in class Bio.StdHandler.Handle_hsp_seqalign
start Method in class Bio.StdHandler.Handle_hsp_seqalign
start Method in class Bio.StdHandler.Handle_hsp_seqalign
start Method in class Bio.StdHandler.Handle_hsp_seqalign
start Method in class Bio.StdHandler.Handle_hsp_seqalign
start Method in class Bio.StdHandler.Handle_search_header
start Method in class Bio.StdHandler.Handle_search_header
start Method in class Bio.StdHandler.Handle_search_header
start Method in class Bio.StdHandler.Handle_search_header
start Method in class Bio.StdHandler.Handle_search_header
start Method in class Bio.StdHandler.Handle_search_header
start Method in class Bio.StdHandler.Handle_search_header
start Method in class Bio.StdHandler.Handle_search_info
start Method in class Bio.StdHandler.Handle_search_info
start Method in class Bio.StdHandler.Handle_search_table
start Method in class Bio.builders.Search.search.BuildSearch
start Method in class Bio.builders.Search.search.BuildSearch
start Method in class Martel.LAX.LAX
start_ Method in class Bio.StdHandler.Handle_search_header
start_ Method in class Bio.StdHandler.Handle_search_info
start_ Method in class Bio.StdHandler.Handle_sequence
start_ Method in class Bio.builders.Search.search.BuildSearch
start_a Method in class Bio.InterPro.InterProParser
start_a Method in class Bio.NetCatch.ExtractUrls
start_aa_list Variable in class Bio.FSSP.fssp_rec.align
start_alignment Method in class Bio.Blast.NCBIStandalone._AlignmentConsumer
start_alphabet Method in class Bio.StdHandler.Handle_sequence
start_block Method in class Bio.StdHandler.Handle_search_header
start_block Method in class Bio.builders.Search.search.BuildSearch
start_codons Variable in class Bio.Data.CodonTable.CodonTable
start_codons Variable in class Bio.Data.CodonTable.CodonTable
start_codons Variable in class Bio.Data.CodonTable.CodonTable
start_codons Variable in class Bio.Data.CodonTable.CodonTable
start_codons Variable in class Bio.Data.CodonTable.CodonTable
start_database_report Method in class Bio.Blast.NCBIStandalone._DatabaseReportConsumer
start_dbid Method in class Bio.StdHandler.Handle_dbid
start_dbxref Method in class Bio.StdHandler.Handle_dbxref
start_dbxref_dbid Method in class Bio.StdHandler.Handle_dbxref
start_dbxref_dbname Method in class Bio.StdHandler.Handle_dbxref
start_dbxref_negate Method in class Bio.StdHandler.Handle_dbxref
start_description Method in class Bio.StdHandler.Handle_description
start_description_block Method in class Bio.StdHandler.Handle_description
start_descriptions Method in class Bio.Blast.NCBIStandalone._DescriptionConsumer
start_descriptions Method in class Bio.Blast.NCBIStandalone._PSIBlastConsumer
start_fast_dbxref Method in class Bio.StdHandler.Handle_dbxref
start_feature Method in class Bio.StdHandler.Handle_feature_location
start_feature Method in class Bio.StdHandler.Handle_features
start_feature_block Method in class Bio.StdHandler.Handle_features
start_feature_description Method in class Bio.StdHandler.Handle_features
start_feature_location Method in class Bio.StdHandler.Handle_feature_location
start_feature_qualifier Method in class Bio.StdHandler.Handle_feature_qualifier
start_feature_qualifier_description Method in class Bio.StdHandler.Handle_feature_qualifier
start_form Method in class Bio.Blast.NCBIWWW._FormParser
start_h1 Method in class Bio.Ndb.NdbParser
start_h2 Method in class Bio.InterPro.InterProParser
start_h2 Method in class Bio.Ndb.NdbParser
start_header Method in class Bio.Blast.NCBIStandalone._BlastConsumer
start_header Method in class Bio.Blast.NCBIStandalone._HeaderConsumer
start_header Method in class Bio.Blast.NCBIStandalone._PSIBlastConsumer
start_hit Method in class Bio.builders.Search.search.BuildSearch
start_hsp Method in class Bio.Blast.NCBIStandalone._HSPConsumer
start_hsp Method in class Bio.StdHandler.Handle_hsp
start_hsp Method in class Bio.StdHandler.Handle_hsp_seqalign
start_hsp_frame Method in class Bio.StdHandler.Handle_hsp
start_hsp_seqalign Method in class Bio.StdHandler.Handle_hsp_seqalign
start_hsp_seqalign_homology_seq Method in class Bio.StdHandler.Handle_hsp_seqalign
start_hsp_seqalign_query_leader Method in class Bio.StdHandler.Handle_hsp_seqalign
start_hsp_seqalign_query_seq Method in class Bio.StdHandler.Handle_hsp_seqalign
start_hsp_seqalign_subject_seq Method in class Bio.StdHandler.Handle_hsp_seqalign
start_hsp_strand Method in class Bio.StdHandler.Handle_hsp
start_hsp_value Method in class Bio.StdHandler.Handle_hsp
start_i Method in class Bio.InterPro.InterProParser
start_i Method in class Bio.Ndb.NdbParser
start_keywords Method in class Bio.SwissProt.KeyWList._ListConsumer
start_li Method in class Bio.InterPro.InterProParser
start_li Method in class Bio.Ndb.NdbParser
start_ol Method in class Bio.InterPro.InterProParser
start_parameters Method in class Bio.Blast.NCBIStandalone._ParametersConsumer
start_primer Method in class Bio.Emboss.Primer._Primer3RecordConsumer
start_record Method in class Bio.Medline._RecordConsumer
start_record Method in class Bio.Prosite.Prodoc._RecordConsumer
start_record Method in class Bio.Prosite._RecordConsumer
start_record Method in class Bio.SwissProt.SProt._RecordConsumer
start_record Method in class Bio.SwissProt.SProt._SequenceConsumer
start_record Method in class Bio.builders.SeqRecord.sequence.BuildSeqRecord
start_search_table Method in class Bio.StdHandler.Handle_search_table
start_search_table_entry Method in class Bio.StdHandler.Handle_search_table
start_search_table_value Method in class Bio.StdHandler.Handle_search_table
start_sequence Method in class Bio.Rebase._RecordConsumer
start_sequence Method in class Bio.StdHandler.Handle_sequence
start_sequence_block Method in class Bio.StdHandler.Handle_sequence
start_sub Method in class Bio.Ndb.NdbParser
start_table Method in class Bio.InterPro.InterProParser
start_td Method in class Bio.InterPro.InterProParser
start_ul Method in class Bio.InterPro.InterProParser
start_ul Method in class Bio.Ndb.NdbParser
startDocument Method in class Bio.EUtils.POM.ObjectParserHandler
startDocument Method in class Bio.Mindy.XPath.GrabXPathNodes
startDocument Method in class Bio.StdHandler.ConvertHandler
startDocument Method in class Martel.Dispatch.Dispatcher
startDocument Method in class Martel.Iterator.StoreEvents
startDocument Method in class Martel.LAX.LAX
startDocument Method in class Martel.test.support.CheckGood
startDocument Method in class Martel.test.support.Dump
startDocument Method in class Martel.test.test_attrs.GrabElements
startDocument Method in class Martel.test.test_macros.Capture
startDocument Method in class Martel.test.test_optimize.GetErrorPos
startDocument Method in class xml.sax.handler.ContentHandler
startElement Method in class Bio.Blast.NCBIXML._XMLparser
startElement Method in class Bio.EUtils.POM.ObjectParserHandler
startElement Method in class Bio.Medline.NLMMedlineXML._IndexerHandler
startElement Method in class Bio.Mindy.XPath.GrabXPathNodes
startElement Method in class Bio.ParserSupport.EventGenerator
startElement Method in class Bio.StdHandler.ConvertHandler
startElement Method in class Martel.Dispatch.Dispatcher
startElement Method in class Martel.Iterator.StoreEvents
startElement Method in class Martel.LAX.LAX
startElement Method in class Martel.test.support.Dump
startElement Method in class Martel.test.test_Parser.CountRecords
startElement Method in class Martel.test.test_attrs.GrabElements
startElement Method in class Martel.test.test_delimiter.CatchFields
startElement Method in class Martel.test.test_macros.Capture
startElement Method in class xml.sax.handler.ContentHandler
startElementNS Method in class xml.sax.handler.ContentHandler
StartIntensity Method in class Bio.Affy.CelFile.CelConsumer
startPrefixMapping Method in class xml.sax.handler.ContentHandler
starts_with Function in module Bio.stringfns
StartsWith Class in module Martel.RecordReader
startswith Method in class __builtin__.str
Statistics Package in package Bio
Std Module in package Bio
stdevs Method in class Bio.Affy.CelFile.CelRecord
StdHandler Module in package Bio
SteadyStateEvolver Class in module Bio.GA.Evolver
StepMatrix Class in module Bio.Nexus.Nexus
stochiometry Method in class Bio.Pathway.System
stop_codons Variable in class Bio.Data.CodonTable.CodonTable
stop_codons Variable in class Bio.Data.CodonTable.CodonTable
stop_codons Variable in class Bio.Data.CodonTable.CodonTable
stop_codons Variable in class Bio.Data.CodonTable.CodonTable
stop_codons Variable in class Bio.Data.CodonTable.CodonTable
stop_symbol Variable in class Bio.Alphabet.HasStopCodon
stopping_criteria Method in class Bio.NeuralNetwork.StopTraining.ValidationIncreaseStop
StopTraining Module in package Bio.NeuralNetwork
Storage Class in module Martel.test.support
StoreEvents Class in module Martel.Iterator
Str Class in module Martel.Expression
Str Function in package Martel
str Class in module __builtin__
Str1 Function in package Martel
strand Method in class Bio.Blast.NCBIStandalone._HSPConsumer
String Class in module Bio.Decode
stringfns Module in package Bio
strip Class in module Bio.EUtils.DTDs.LinkOut
strip Method in class Bio.File.SGMLStripper
strip Method in class Bio.SGMLExtractor.SGMLExtractor
strip Method in class __builtin__.str
STS Method in class Bio.UniGene._RecordConsumer
subcomponent_size Method in class Bio.Graphics.BasicChromosome.Chromosome
subheadings Method in class Bio.Medline._RecordConsumer
SubjectType Class in module Bio.EUtils.DTDs.LinkOut
SubjectType Class in module Bio.EUtils.DTDs.eLink_020511
SubObjectSelector Class in module Bio.EUtils.DTDs.LinkOut
SubPattern Class in module Martel.msre_parse
SubProvider Class in module Bio.EUtils.DTDs.LinkOut
subs Class in module Bio.EUtils.DTDs.LinkOut
SubsMat Package in package Bio
substance_name Method in class Bio.Medline._RecordConsumer
sum Method in class Bio.Nexus.Nexus.StepMatrix
sum Function in module Bio.utils
sum_2ple Function in module Bio.utils
sum_branchlength Method in class Bio.Nexus.Trees.Tree
summary Method in class Bio.EUtils.DBIdsClient.DBIdsLookup
summary Method in class Bio.EUtils.DBIdsClient.DBIdsRecord
Summary Class in module Bio.EUtils.Datatypes
summary Method in class Bio.EUtils.HistoryClient.HistoryLookup
summary Method in class Bio.EUtils.HistoryClient.HistoryRecord
SummaryInfo Class in module Bio.Align.AlignInfo
superdir Function in module Martel.Dispatch
support Module in package Martel.test
SVDSuperimposer Package in package Bio
SVDSuperimposer Module in package Bio.SVDSuperimposer
SVDSuperimposer Class in module Bio.SVDSuperimposer.SVDSuperimposer
swapcase Method in class __builtin__.str
SwissProt Package in package Bio
swissprot Module in package Bio.dbdefs
swissprot Module in package Bio.formatdefs
swissprot38 Module in package Martel.test.testformats
System Class in package Bio.Pathway
t_close_paren Method in class Bio.Decode.DecodeScanner
t_comma Method in class Bio.Decode.DecodeScanner
t_default Method in class Bio.Parsers.spark.GenericScanner
t_float Method in class Bio.Decode.DecodeScanner
t_functionname Method in class Bio.Decode.DecodeScanner
t_open_paren Method in class Bio.Decode.DecodeScanner
t_pipe Method in class Bio.Decode.DecodeScanner
t_string Method in class Bio.Decode.DecodeScanner
t_whitespace Method in class Bio.Decode.DecodeScanner
TableInfo Class in module Bio.Search
TaggingConsumer Class in module Bio.ParserSupport
take Function in module Bio.listfns
take_byfn Function in module Bio.listfns
Task Module in package Bio.MultiProc
Task Class in module Bio.MultiProc.Task
taxonomy_id Method in class Bio.SwissProt.SProt._RecordConsumer
tell Method in class Bio.EUtils.ReseekFile.ReseekFile
tell Method in class Bio.File.UndoHandle
tell Method in class Martel.msre_parse.Tokenizer
TelomereSegment Class in module Bio.Graphics.BasicChromosome
temperature Method in class Bio.Rebase._RecordConsumer
Term Class in module Bio.EUtils.DTDs.eSearch_020511
Term Class in module Bio.EUtils.Datatypes
TermCount Class in module Bio.EUtils.DTDs.eInfo_020511
terminal Method in class Bio.Parsers.spark.GenericASTBuilder
terminal_gap_to_missing Method in class Bio.Nexus.Nexus.Nexus
terminator Method in class Bio.Prosite._RecordConsumer
terminator Method in class Bio.SwissProt.SProt._RecordConsumer
TermSet Class in module Bio.EUtils.DTDs.eSearch_020511
test Function in module Bio.Decode
test Function in module Bio.EUtils.ReseekFile
test Function in module Bio.MarkupEditor
test Package in package Martel
test Method in class Martel.test.support.Storage
test Function in package Martel.test
test Function in module Martel.test.test_Expression
test Function in module Martel.test.test_Generate
test Function in module Martel.test.test_IterParser
test Function in module Martel.test.test_Iterator
test Function in module Martel.test.test_LAX
test Function in module Martel.test.test_ParseRecords
test Function in module Martel.test.test_Parser
test Function in module Martel.test.test_RecordReader
test Function in module Martel.test.test_RecordReader2
test Function in module Martel.test.test_Time
test Function in module Martel.test.test_attrs
test Function in module Martel.test.test_convert_re
test Function in module Martel.test.test_delimiter
test Function in module Martel.test.test_macros
test Function in module Martel.test.test_optimize
test Function in module Martel.test.test_swissprot38
test1 Function in module Martel.test.test_Iterator
test1 Function in module Martel.test.test_LAX
test1 Function in module Martel.test.test_optimize
test10 Function in module Martel.test.test_optimize
test11 Function in module Martel.test.test_optimize
test12 Function in module Martel.test.test_optimize
test13 Function in module Martel.test.test_optimize
test14 Function in module Martel.test.test_optimize
test15 Function in module Martel.test.test_optimize
test16 Function in module Martel.test.test_optimize
test17 Function in module Martel.test.test_optimize
test18 Function in module Martel.test.test_optimize
test19 Function in module Martel.test.test_optimize
test2 Function in module Martel.test.test_Iterator
test2 Function in module Martel.test.test_optimize
test20 Function in module Martel.test.test_optimize
test3 Function in module Martel.test.test_Iterator
test3 Function in module Martel.test.test_optimize
test4 Function in module Martel.test.test_Iterator
test4 Function in module Martel.test.test_optimize
test5 Function in module Martel.test.test_Iterator
test5 Function in module Martel.test.test_optimize
test6 Function in module Martel.test.test_optimize
test7 Function in module Martel.test.test_optimize
test8 Function in module Martel.test.test_optimize
test9 Function in module Martel.test.test_optimize
test__add__ Function in module Martel.test.test_Expression
test__or__ Function in module Martel.test.test_Expression
test_alt Function in module Martel.test.test_Expression
test_any Function in module Martel.test.test_Expression
test_assert Function in module Martel.test.test_Expression
test_at_beginning Function in module Martel.test.test_Expression
test_at_end Function in module Martel.test.test_Expression
test_attrs Module in package Martel.test
test_convert_re Module in package Martel.test
test_count Function in module Martel.test.test_RecordReader
test_count_lines Function in module Martel.test.test_RecordReader
test_count_lines Function in module Martel.test.test_RecordReader2
test_count_lines_lines Function in module Martel.test.test_RecordReader
test_DelimitedFields Function in module Martel.test.test_macros
test_delimiter Module in package Martel.test
test_Digits Function in module Martel.test.test_macros
test_docstring Function in module Martel.test.test_Time
test_dot Function in module Martel.test.test_Expression
test_end Function in module Martel.test.test_RecordReader
test_end_lines Function in module Martel.test.test_RecordReader
test_endswith Function in module Martel.test.test_RecordReader2
test_endswith_errors Function in module Martel.test.test_RecordReader2
test_endswith_exhaustive Function in module Martel.test.test_RecordReader2
test_endswith_generic Function in module Martel.test.test_RecordReader2
test_endswith_remainder Function in module Martel.test.test_RecordReader2
test_endswith_SP Function in module Martel.test.test_RecordReader2
test_escape Function in module Martel.test.test_attrs
test_everything Function in module Martel.test.test_RecordReader
test_everything Function in module Martel.test.test_RecordReader2
test_everything_lines Function in module Martel.test.test_RecordReader
test_expand Function in module Martel.test.test_Time
test_Expression Module in package Martel.test
test_fasta Function in module Martel.test.test_RecordReader
test_file Function in module Martel.test.support
test_filter Function in module Martel.test.test_LAX
test_Float Function in module Martel.test.test_macros
test_Generate Module in package Martel.test
test_group Function in module Martel.test.test_Expression
test_group_names Function in module Martel.test.test_Expression
test_groupref Function in module Martel.test.test_Expression
test_header_footer1 Function in module Martel.test.test_Iterator
test_header_footer1 Function in module Martel.test.test_Parser
test_header_footer2 Function in module Martel.test.test_Iterator
test_header_footer2 Function in module Martel.test.test_Parser
test_header_footer3 Function in module Martel.test.test_Iterator
test_header_footer3 Function in module Martel.test.test_Parser
test_header_footer4 Function in module Martel.test.test_Iterator
test_header_footer4 Function in module Martel.test.test_Parser
test_header_footer5 Function in module Martel.test.test_Iterator
test_header_footer5 Function in module Martel.test.test_Parser
test_header_footer6 Function in module Martel.test.test_Iterator
test_header_footer6 Function in module Martel.test.test_Parser
test_header_footer7 Function in module Martel.test.test_Iterator
test_header_footer7 Function in module Martel.test.test_Parser
test_header_footer8 Function in module Martel.test.test_Parser
test_header_footer_parser Function in module Martel.test.test_attrs
test_hf1 Function in module Martel.test.test_IterParser
test_hf2 Function in module Martel.test.test_IterParser
test_hf3 Function in module Martel.test.test_IterParser
test_hf4 Function in module Martel.test.test_IterParser
test_hf5 Function in module Martel.test.test_IterParser
test_hf6 Function in module Martel.test.test_IterParser
test_hf7 Function in module Martel.test.test_IterParser
test_hf8 Function in module Martel.test.test_IterParser
test_Iterator Module in package Martel.test
test_IterParser Module in package Martel.test
test_LAX Module in package Martel.test
test_literal Function in module Martel.test.test_Expression
test_macros Module in package Martel.test
test_make_iterparsers1 Function in module Martel.test.test_IterParser
test_make_iterparsers2 Function in module Martel.test.test_IterParser
test_max_repeat Function in module Martel.test.test_Expression
test_minimize Function in module Martel.test.test_Expression
test_missing_end1 Function in module Martel.test.test_IterParser
test_missing_end2 Function in module Martel.test.test_IterParser
test_missing_end3 Function in module Martel.test.test_IterParser
test_multi Function in module Martel.test.test_attrs
test_nocase Function in module Martel.test.test_Expression
test_nodes Function in module Martel.test.test_Expression
test_none Function in module Martel.test.test_attrs
test_nothing Function in module Martel.test.test_RecordReader
test_nothing Function in module Martel.test.test_RecordReader2
test_nothing_lines Function in module Martel.test.test_RecordReader
test_null_op Function in module Martel.test.test_Expression
test_optimize Module in package Martel.test
test_Parser Module in package Martel.test
test_ParseRecords Module in package Martel.test
test_Punctuation Function in module Martel.test.test_macros
test_reader_parser Function in module Martel.test.test_Parser
test_reads Function in module Bio.EUtils.ReseekFile
test_record_parser Function in module Martel.test.test_Parser
test_record_parser Function in module Martel.test.test_attrs
test_RecordReader Module in package Martel.test
test_RecordReader2 Module in package Martel.test
test_ri1 Function in module Martel.test.test_IterParser
test_ri2 Function in module Martel.test.test_IterParser
test_ri3 Function in module Martel.test.test_IterParser
test_same_tag Function in module Martel.test.test_attrs
test_seq Function in module Martel.test.test_Expression
test_single Function in module Martel.test.test_attrs
test_Spaces Function in module Martel.test.test_macros
test_start Function in module Martel.test.test_RecordReader
test_start_lines Function in module Martel.test.test_RecordReader
test_startswith Function in module Martel.test.test_RecordReader2
test_startswith_errors Function in module Martel.test.test_RecordReader2
test_startswith_exhaustive Function in module Martel.test.test_RecordReader2
test_startswith_generic Function in module Martel.test.test_RecordReader2
test_startswith_remainder Function in module Martel.test.test_RecordReader2
test_startswith_SP Function in module Martel.test.test_RecordReader2
test_str Function in module Martel.test.test_Expression
test_string Function in module Martel.test.support
test_swissprot38 Module in package Martel.test
test_syntax Function in module Martel.test.test_Time
test_terms Function in module Martel.test.test_Time
test_Time Module in package Martel.test
test_times Function in module Martel.test.test_Time
test_ToEol Function in module Martel.test.test_macros
test_ToSep Function in module Martel.test.test_macros
test_Unprintable Function in module Martel.test.test_macros
test_until Function in module Martel.test.test_RecordReader
test_until Function in module Martel.test.test_RecordReader2
test_until_lines Function in module Martel.test.test_RecordReader
test_valid_names Function in module Martel.test.test_Expression
test_Word Function in module Martel.test.test_macros
testformats Package in package Martel.test
text Method in class Bio.EUtils.POM.ElementNode
Text Class in module Bio.EUtils.POM
text Method in class Bio.Prosite.Prodoc._RecordConsumer
text_field Method in class Bio.Gobase._RecordConsumer
TextLikeMixin Class in module Bio.config.DBRegistry
ThinClient Module in package Bio.EUtils
ThinClient Class in module Bio.EUtils.ThinClient
ThreeLetterProtein Class in package Bio.Alphabet
threshold Method in class Bio.Blast.NCBIStandalone._ParametersConsumer
threshold Method in class Bio.Compass._Consumer
time Method in class Bio.Sequencing.Phd._RecordConsumer
Time Module in package Martel
time_file Function in module Martel.test.support
timetuple Method in class Bio.EUtils.Datatypes.Date
title Method in class Bio.Blast.NCBIStandalone._AlignmentConsumer
title Method in class Bio.Medline._RecordConsumer
TITLE Method in class Bio.UniGene._RecordConsumer
title Method in class __builtin__.str
title_abbreviation Method in class Bio.Medline._RecordConsumer
tname Method in class BioSQL.DBUtils.Generic_dbutils
To Class in module Bio.EUtils.DTDs.eSearch_020511
to_clustal Method in class Bio.Align.FormatConvert.FormatConverter
to_fasta Method in class Bio.Align.FormatConvert.FormatConverter
to_file Method in class Bio.MarkupEditor.MarkupEditor
to_generic Method in class Bio.Blast.Record.MultipleAlignment
to_string Method in class Bio.Nexus.Trees.Tree
ToEol Function in package Martel
Token Class in module Bio.Decode
tokenize Method in class Bio.Decode.DecodeScanner
tokenize Method in class Bio.Parsers.spark.GenericScanner
Tokenizer Class in module Martel.msre_parse
tolower Class in module Bio.EUtils.DTDs.LinkOut
tomutable Method in class Bio.Seq.Seq
ToSep Function in package Martel
toseq Method in class Bio.Seq.MutableSeq
tostring Method in class Bio.Crystal.Crystal
tostring Method in class Bio.EUtils.POM.ElementNode
tostring Method in class Bio.Prosite.Pattern.Prosite
tostring Method in class Bio.Seq.MutableSeq
tostring Method in class Bio.Seq.Seq
tostring Method in class BioSQL.BioSeq.DBSeq
total_weight Function in module Bio.utils
total_weight_range Function in module Bio.utils
toupper Class in module Bio.EUtils.DTDs.LinkOut
Tournament Module in package Bio.GA.Selection
TournamentSelection Class in module Bio.GA.Selection.Tournament
tr Function in module Bio.Decode
trace Method in class Bio.Nexus.Nodes.Chain
trace_array_max_index Method in class Bio.Sequencing.Phd._RecordConsumer
trace_array_min_index Method in class Bio.Sequencing.Phd._RecordConsumer
trace_peak_area_ratio Method in class Bio.Sequencing.Phd._RecordConsumer
track_position Function in module Martel.Generate
train Method in class Bio.HMM.Trainer.BaumWelchTrainer
train Method in class Bio.HMM.Trainer.KnownStateTrainer
train Function in module Bio.LogisticRegression
train Function in module Bio.MaxEntropy
train Function in module Bio.NaiveBayes
train Method in class Bio.NeuralNetwork.BackPropagation.Network.BasicNetwork
train Function in module Bio.kNN
train_bw Function in module Bio.MarkovModel
train_visible Function in module Bio.MarkovModel
Trainer Module in package Bio.HMM
Training Module in package Bio.NeuralNetwork
TrainingExample Class in module Bio.NeuralNetwork.Training
TrainingSequence Class in module Bio.HMM.Trainer
TranalignCommandline Class in module Bio.Emboss.Applications
transcribe Function in module Bio.Seq
Transcribe Module in package Bio
Transcribe Class in module Bio.Transcribe
transcribe Method in class Bio.Transcribe.Transcribe
transcribe Function in module Bio.utils
transfac Module in package Bio.expressions
transformation Method in class Bio.Nexus.Nexus.StepMatrix
transitions_from Method in class Bio.HMM.MarkovModel.HiddenMarkovModel
translate Function in module Bio.Seq
Translate Module in package Bio
translate Method in class Bio.Translate.Translator
translate Function in module Bio.utils
translate Method in class __builtin__.str
translate_to_stop Method in class Bio.Translate.Translator
translate_to_stop Function in module Bio.utils
Translation Class in module Bio.EUtils.DTDs.eSearch_020511
TranslationError Class in module Bio.Data.CodonTable
TranslationSet Class in module Bio.EUtils.DTDs.eSearch_020511
TranslationStack Class in module Bio.EUtils.DTDs.eSearch_020511
Translator Class in module Bio.Translate
transliterated_title Method in class Bio.Medline._RecordConsumer
Tree Class in module Bio.Nexus.Trees
TreeError Class in module Bio.Nexus.Trees
Trees Module in package Bio.Nexus
triefind Module in package Bio
trim Method in class Bio.Sequencing.Phd._RecordConsumer
tune Method in class Bio.Ais.Immune
turn3 Variable in class Bio.FSSP.fssp_rec.align
turn4 Variable in class Bio.FSSP.fssp_rec.align
turn5 Variable in class Bio.FSSP.fssp_rec.align
two_mat_DJS Function in package Bio.SubsMat
two_mat_relative_entropy Function in package Bio.SubsMat
TwoCrossover Class in module Bio.GA.Crossover.GeneralPoint
TwoPoint Module in package Bio.GA.Crossover
TwoPointCrossover Class in module Bio.GA.Crossover.TwoPoint
type Class in module __builtin__
TypeError Class in module exceptions
typestring Method in class Bio.Parsers.spark.GenericASTTraversal
typestring Method in class Bio.Parsers.spark.GenericParser
undefined Method in class Bio.Medline._RecordConsumer
UndoHandle Class in module Bio.File
unescape Function in module Bio.EUtils.POM
unescape Function in module Martel.Dispatch
unescape_C Function in module Bio.Decode
unescape_entities Function in module Bio.EUtils.parse
ungap Function in module Bio.utils
unhandled Method in class Bio.ParserSupport.TaggingConsumer
unhandled_section Method in class Bio.ParserSupport.TaggingConsumer
Uniform Module in package Bio.GA.Crossover
UniformCrossover Class in module Bio.GA.Crossover.Uniform
UniGene Package in package Bio
UnigeneProtsimRecord Class in package Bio.UniGene
UnigeneRecord Class in package Bio.UniGene
UnigeneSequenceRecord Class in package Bio.UniGene
UnigeneSTSRecord Class in package Bio.UniGene
union Method in class Bio.Pathway.Rep.HashSet.HashSet
unique_identifier Method in class Bio.Medline._RecordConsumer
unknown-10279344 Function in package Bio.KEGG
unknown_charref Method in class sgmllib.SGMLParser
unknown_decl Method in class markupbase.ParserBase
unknown_endtag Method in class Bio.SGMLExtractor.LocalParser
unknown_endtag Method in class sgmllib.SGMLParser
unknown_entityref Method in class sgmllib.SGMLParser
unknown_starttag Method in class Bio.SGMLExtractor.LocalParser
unknown_starttag Method in class sgmllib.SGMLParser
UnknownDBName Class in module Bio.DBXRef
unlink Method in class Bio.Nexus.Nodes.Chain
UnorderedMultiDict Class in module Bio.EUtils.MultiDict
Unprintable Function in package Martel
unroot Method in class Bio.Nexus.Trees.Tree
Until Class in module Martel.RecordReader
UntilEol Function in package Martel
UntilSep Function in package Martel
update Method in class Bio.Index._InMemoryIndex
update Method in class Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer
update Method in class Bio.NeuralNetwork.BackPropagation.Layer.InputLayer
update Method in class Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer
update Method in class Bio.Prosite.ExPASyDictionary
update Method in class Bio.Prosite.Prodoc.ExPASyDictionary
update Method in class Bio.PubMed.Dictionary
update Method in class Bio.SwissProt.SProt.ExPASyDictionary
update Method in class __builtin__.dict
update_emissions Method in class Bio.HMM.Trainer.BaumWelchTrainer
update_transitions Method in class Bio.HMM.Trainer.BaumWelchTrainer
updatepos Method in class markupbase.ParserBase
upper Method in class __builtin__.str
Url Class in module Bio.EUtils.DTDs.LinkOut
Url Class in module Bio.EUtils.DTDs.eLink_020511
Url Class in module Bio.NetCatch
UrlName Class in module Bio.EUtils.DTDs.LinkOut
use_lowercase Method in class Bio.EUtils.POM.ElementNode
use_truecase Method in class Bio.EUtils.POM.ElementNode
use_uppercase Method in class Bio.EUtils.POM.ElementNode
UsePOMParser Class in module Bio.EUtils.parse
UserNode Class in module reportlab.graphics.shapes
uses_tags Method in class Bio.Mindy.XPath.GrabXPathNodes
uses_tags Method in class Martel.Dispatch.Dispatcher
uses_tags Method in class Martel.LAX.LAX
Utilities Module in package Bio.HMM
utils Module in package Bio
VALID_FORMATS Variable in class Bio.Graphics.BasicChromosome.Organism
validate Method in class Bio.Crystal.Chain
validate_element Method in class Bio.Crystal.Chain
validate_key Function in package Bio.Crystal
ValidationError Class in module Bio.EUtils.POM
ValidationIncreaseStop Class in module Bio.NeuralNetwork.StopTraining
ValueError Class in module exceptions
values Method in class Bio.Crystal.Crystal
values Method in class Bio.EUtils.MultiDict._BaseMultiDict
values Method in class Bio.Mindy.BaseDB.DictLookup
values Method in class Bio.Prosite.ExPASyDictionary
values Method in class Bio.Prosite.Prodoc.ExPASyDictionary
values Method in class Bio.PubMed.Dictionary
values Method in class Bio.SwissProt.SProt.ExPASyDictionary
values Method in class Bio.config.Registry.Registry
values Method in class BioSQL.BioSeqDatabase.BioSeqDatabase
values Method in class BioSQL.BioSeqDatabase.DBServer
values Method in class Martel.Parser.MartelAttributeList
values Method in class __builtin__.dict
values Method in class xml.sax.xmlreader.AttributesImpl
ValueToken Class in module Bio.Decode
verify Method in class Bio.EUtils.POM.XMLAttribute
verify Method in class reportlab.graphics.widgetbase.PropHolder
verify_alphabet Function in module Bio.utils
verify_pattern Function in module Bio.Prosite.Pattern
version Method in class Bio.AlignAce.Parser.AlignAceConsumer
version Method in class Bio.Blast.NCBIStandalone._HeaderConsumer
viterbi Method in class Bio.HMM.MarkovModel.HiddenMarkovModel
volume_issue Method in class Bio.Medline._RecordConsumer
wa Class in module Bio.Sequencing.Ace
wa_data Method in class Bio.Sequencing.Ace._RecordConsumer
wa_start Method in class Bio.Sequencing.Ace._RecordConsumer
wait Method in class Bio.MultiProc.copen._ProcHandle
wait Method in class Bio.WWW.RequestLimiter
WARNING Variable in class Bio.EUtils.Datatypes.Problem
WARNING Variable in class Bio.EUtils.Datatypes.Problem
WARNING Variable in class Bio.EUtils.Datatypes.Problem
WARNING Variable in class Bio.EUtils.Datatypes.Problem
WARNING Variable in class Bio.EUtils.Datatypes.Problem
WARNING Variable in class Bio.EUtils.Datatypes.Problem
WARNING Variable in class Bio.EUtils.Datatypes.Problem
WARNING Variable in class Bio.EUtils.Datatypes.Problem
warning Method in class xml.sax.handler.ErrorHandler
WarningList Class in module Bio.EUtils.DTDs.eSearch_020511
WarningProblem Class in module Bio.EUtils.Datatypes
WaterCommandline Class in module Bio.Emboss.Applications
WebEnv Class in module Bio.EUtils.DTDs.ePost_020511
WebEnv Class in module Bio.EUtils.DTDs.eSearch_020511
weighted_stepmatrix Method in class Bio.Nexus.Nexus.Nexus
weighting Method in class Bio.Nexus.Nexus.StepMatrix
Widget Class in module reportlab.graphics.widgetbase
window_size Method in class Bio.Blast.NCBIStandalone._ParametersConsumer
WithinNDays Class in module Bio.EUtils.Datatypes
WithinPosition Class in module Bio.SeqFeature
Word Function in package Martel
word_field Method in class Bio.Gobase._RecordConsumer
wr Class in module Bio.Sequencing.Ace
wr_data Method in class Bio.Sequencing.Ace._RecordConsumer
wr_start Method in class Bio.Sequencing.Ace._RecordConsumer
wrap_line Function in package Bio.Crystal
write Method in class Bio.AlignAce.Motif.Motif
write Method in class Bio.EUtils.sourcegen.SourceFile
write Method in class Bio.EUtils.sourcegen.SourceGen
write Method in class Bio.NeuralNetwork.Gene.Pattern.PatternIO
write Method in class Bio.Writer.Writer
write Method in class Bio.writers.SeqRecord.embl.WriteEmbl
write Method in class Bio.writers.SeqRecord.fasta.WriteFasta
write_config Function in module Bio.Mindy.BaseDB
write_header Method in class Bio.NMR.xpktools.Peaklist
write_nexus_data Method in class Bio.Nexus.Nexus.Nexus
write_nexus_data_partitions Method in class Bio.Nexus.Nexus.Nexus
write_paths Method in class Bio.EUtils.POM.POMDocument
write_record Method in class Bio.StdHandler.ConvertDispatchHandler
write_repr Method in class Bio.EUtils.POM.POMDocument
write_seq Method in class Bio.NeuralNetwork.Gene.Pattern.PatternIO
write_xmlfile Method in class Bio.EUtils.POM.POMDocument
WriteDB Class in module Bio.Mindy.BaseDB
WriteEmbl Class in module Bio.writers.SeqRecord.embl
WriteEmpty Class in module Bio.writers.SeqRecord.empty
WriteFasta Class in module Bio.writers.SeqRecord.fasta
writefile Method in class Bio.EUtils.sourcegen.SourceFile
writefileobject Method in class Bio.EUtils.POM.POMDocument
writeFooter Method in class Bio.Writer.Writer
writeHeader Method in class Bio.Writer.Writer
writeln Method in class Bio.EUtils.sourcegen.SourceGen
Writer Module in package Bio
Writer Class in module Bio.Writer
writers Package in package Bio
wublast Module in package Bio.expressions.blast
WWW Package in package Bio
XMLAttribute Class in module Bio.EUtils.POM
XMLReader Class in module xml.sax.xmlreader
XPath Module in package Bio.Mindy
xpath_index Function in module Bio.Mindy.XPath
XpkEntry Class in module Bio.NMR.xpktools
xpktools Module in package Bio.NMR
year Method in class Bio.Medline._RecordConsumer
zfill Method in class __builtin__.str

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