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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
__authors__ Variable in package Bio.EUtils
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.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.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.Pathway.Rep.HashSet.HashSet
__contains__ Method in class __builtin__.dict
__contains__ Method in class __builtin__.list
__contains__ Method in class __builtin__.str
__del__ Method in class Bio.Mindy.FlatDB.MemoryFlatDB
__del__ Method in class Bio.MultiProc.Task.Task
__delattr__ Method in class Bio.EUtils.POM.ElementNode
__delattr__ Method in class __builtin__.object
__delattr__ Method in class __builtin__.type
__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.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
__getattr__ Method in class Bio.Alphabet.AlphabetEncoder
__getattr__ Method in class Bio.Data.CodonTable.AmbiguousCodonTable
__getattr__ Method in class Bio.DocSQL.QueryRow
__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.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.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
__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.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.SeqIO.FASTA.FastaReader
__getitem__ Method in class Bio.SeqIO.generic.GenericFormat
__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.Exception
__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
__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.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.NCBIWWW.BlastParser
__init__ Method in class Bio.Blast.NCBIXML.BlastParser
__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.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.DocSQL.Create
__init__ Method in class Bio.DocSQL.Insert
__init__ Method in class Bio.DocSQL.IterationCursor
__init__ Method in class Bio.DocSQL.Query
__init__ Method in class Bio.DocSQL.QueryAll
__init__ Method in class Bio.DocSQL.QueryGeneric
__init__ Method in class Bio.DocSQL.QueryRow
__init__ Method in class Bio.DocSQL.QuerySingle
__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.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.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.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.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.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.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.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.LogisticRegression.LogisticRegression
__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.Record
__init__ Method in class Bio.Medline.RecordParser
__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.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.Record
__init__ Method in class Bio.Prosite.RecordParser
__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.RecordFile.RecordFile
__init__ Method in class Bio.ReseekFile.ReseekFile
__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.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.SeqIO.FASTA.FastaReader
__init__ Method in class Bio.SeqIO.FASTA.FastaWriter
__init__ Method in class Bio.SeqIO.generic.ClustalFormat
__init__ Method in class Bio.SeqIO.generic.EMBLFormat
__init__ Method in class Bio.SeqIO.generic.FastaFormat
__init__ Method in class Bio.SeqIO.generic.GCGFormat
__init__ Method in class Bio.SeqIO.generic.GenericFormat
__init__ Method in class Bio.SeqIO.generic.LargeFastaFormat
__init__ Method in class Bio.SeqIO.generic.NexusFormat
__init__ Method in class Bio.SeqIO.generic.PirFormat
__init__ Method in class Bio.SeqIO.generic.ReadSeq
__init__ Method in class Bio.SeqIO.generic.SeqRecord
__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.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.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.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.Transcribe.Transcribe
__init__ Method in class Bio.Translate.Translator
__init__ Method in class Bio.UniGene.Record
__init__ Method in class Bio.WWW.RequestLimiter
__init__ Method in class Bio.Wise.dnal.Statistics
__init__ Method in class Bio.Wise.psw.AlignmentColumn
__init__ Method in class Bio.Wise.psw.ColumnUnit
__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.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.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.Exception
__init__ Method in class markupbase.ParserBase
__init__ Method in class sgmllib.SGMLParser
__itemsize__ Variable in class __builtin__.type
__iter__ Method in class Bio.Blast.NCBIStandalone.Iterator
__iter__ Method in class Bio.DocSQL.Query
__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.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 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.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.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
__lt__ Method in class __builtin__.dict
__lt__ Method in class __builtin__.list
__lt__ Method in class __builtin__.str
__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
__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_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.DocSQL.Query
__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.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.Wise.psw.AlignmentColumn
__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
__reversed__ Method in class __builtin__.list
__rmod__ Method in class __builtin__.str
__rmul__ Method in class __builtin__.list
__rmul__ Method in class __builtin__.str
__setattr__ Method in class Bio.DocSQL.QueryRow
__setattr__ Method in class Bio.EUtils.POM.ElementNode
__setattr__ Method in class __builtin__.object
__setattr__ Method in class __builtin__.type
__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.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
__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.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.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.SeqIO.generic.SeqRecord
__str__ Method in class Bio.StdHandler.Feature
__str__ Method in class Bio.SubsMat.BadMatrix
__str__ Method in class Bio.UniGene.Record
__str__ Method in class Bio.Wise.dnal.Statistics
__str__ Method in class Bio.Wise.psw.ColumnUnit
__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.Exception
__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
__test__ Variable in module Bio.EUtils.MultiDict
__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
__version__ Variable in module Bio.DocSQL
__version__ Variable in package Bio.EUtils
__version__ Variable in module Bio.Parsers.spark
__version__ Variable in package Bio.Wise
__version__ Variable in module Bio.Wise.dnal
__version__ Variable in module Bio.Wise.psw
__version__ Variable in package Martel
__weakrefoffset__ Variable in class __builtin__.type
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
a_info Variable in module Bio.expressions.blast.ncbiblast
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
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
AC Variable in module Bio.expressions.blocks
AC Variable in module Martel.test.testformats.swissprot38
AC_block Variable in module Bio.expressions.embl.embl65
AC_block Variable in module Martel.test.testformats.swissprot38
AC_line Variable in module Bio.expressions.embl.embl65
acc Variable in class Bio.FSSP.fssp_rec.align
accession Variable in module Bio.expressions.embl.embl65
accession Variable in module Bio.expressions.genbank
accession_block Variable in module Bio.expressions.genbank
ACCREP Variable in package Bio.SubsMat
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.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_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 Method in class Martel.test.support.Storage
add_test_lines 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_url Method in class Bio.NetCatch.NetCatch
add_value_handler Function in module Bio.StdHandler
addnode Method in class Bio.EUtils.POM.POMDocument
addRule Method in class Bio.Parsers.spark.GenericParser
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 Class in module Bio.FSSP.fssp_rec
align Function in package Bio.Wise
align Function in module Bio.Wise.dnal
align Function in module Bio.Wise.psw
align Variable in module Bio.pairwise2
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
Alignment Class in module Bio.Wise.psw
alignment Variable in module Bio.expressions.blast.ncbiblast
alignment_header Variable in module Bio.expressions.hmmpfam
AlignmentColumn Class in module Bio.Wise.psw
AlignmentColumnFullException Class in module Bio.Wise.psw
AlignmentHasDifferentLengthsError Class in package Bio.CAPS
alignments_rec Variable in package Bio.FSSP
alignments_title Variable in package Bio.FSSP
all_letters_sum Method in class Bio.SubsMat.SeqMat
all_pairs Function in package Bio.Wise
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
alphabet_table Variable in module Bio.builders.SeqRecord.sequence
AlphabetEncoder Class in package Bio.Alphabet
Alt Function in package Martel
Alt Class in module Martel.Expression
ambiguity Method in class Bio.Parsers.spark.GenericParser
ambiguous_dna Variable in module Bio.Alphabet.IUPAC
ambiguous_dna_by_id Variable in module Bio.Data.CodonTable
ambiguous_dna_by_id Variable in module Bio.Translate
ambiguous_dna_by_name Variable in module Bio.Data.CodonTable
ambiguous_dna_by_name Variable in module Bio.Translate
ambiguous_dna_complement Variable in module Bio.Data.IUPACData
ambiguous_dna_letters Variable in module Bio.Data.IUPACData
ambiguous_dna_values Variable in module Bio.Data.IUPACData
ambiguous_dna_weight_ranges Variable in module Bio.Data.IUPACData
ambiguous_rna Variable in module Bio.Alphabet.IUPAC
ambiguous_rna_by_id Variable in module Bio.Data.CodonTable
ambiguous_rna_by_id Variable in module Bio.Translate
ambiguous_rna_by_name Variable in module Bio.Data.CodonTable
ambiguous_rna_by_name Variable in module Bio.Translate
ambiguous_rna_complement Variable in module Bio.Data.IUPACData
ambiguous_rna_letters Variable in module Bio.Data.IUPACData
ambiguous_rna_values Variable in module Bio.Data.IUPACData
ambiguous_rna_weight_ranges Variable in module Bio.Data.IUPACData
ambiguous_transcriber Variable in module Bio.Transcribe
AmbiguousCodonTable Class in module Bio.Data.CodonTable
AmbiguousForwardTable Class in module Bio.Data.CodonTable
AmbiguousRepair Class in module Bio.GA.Repair.Stabilizing
amplifier Variable in module Bio.Emboss.primersearch_format
amplifier_length Variable in module Bio.Emboss.primersearch_format
amplifier_length_line Variable in module Bio.Emboss.primersearch_format
amplifier_sequence Variable in module Bio.Emboss.primersearch_format
amplifier_sequence_lines Variable in module Bio.Emboss.primersearch_format
amplimer_line Variable in module Bio.Emboss.primersearch_format
And Class in module Bio.EUtils.Datatypes
annotations Class in module Bio.EUtils.Datatypes in class BioSQL.BioSeq.DBSeqRecord
ANY Variable in module Bio.EUtils.POM
Any Function in package Martel
Any Class in module Martel.Expression
ANY Variable in module Martel.msre_constants
ANY_ALL Variable in module Martel.msre_constants
any_float Variable in module Bio.Emboss.primer3_format
any_integer Variable in module Bio.Emboss.primer3_format
any_space Variable in module Bio.Emboss.primer3_format
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 Bio.Wise.psw.Alignment
append Method in class Bio.Wise.psw.AlignmentColumn
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
asdict Function in module Bio.listfns
Assert Function in package Martel
Assert Class in module Martel.Expression
ASSERT Variable in module Martel.msre_constants
ASSERT_NOT Variable in module Martel.msre_constants
AssertNot Function in package Martel
AT Variable in module Martel.msre_constants
AT_BEGINNING Variable in module Martel.msre_constants
AT_BEGINNING_LINE Variable in module Martel.msre_constants
AT_BEGINNING_STRING Variable in module Martel.msre_constants
AT_BOUNDARY Variable in module Martel.msre_constants
AT_CDATA Variable in module Bio.EUtils.POM
AT_END Variable in module Martel.msre_constants
AT_END_LINE Variable in module Martel.msre_constants
AT_END_STRING Variable in module Martel.msre_constants
AT_ENTITIES Variable in module Bio.EUtils.POM
AT_ENTITY Variable in module Bio.EUtils.POM
AT_ID Variable in module Bio.EUtils.POM
AT_IDREF Variable in module Bio.EUtils.POM
AT_IDREFS Variable in module Bio.EUtils.POM
at_line_boundary Method in class Bio.RecordFile.RecordFile
AT_LOC_BOUNDARY Variable in module Martel.msre_constants
AT_LOC_NON_BOUNDARY Variable in module Martel.msre_constants
AT_LOCALE Variable in module Martel.msre_constants
AT_MULTILINE Variable in module Martel.msre_constants
AT_NMTOKEN Variable in module Bio.EUtils.POM
AT_NMTOKENS Variable in module Bio.EUtils.POM
AT_NON_BOUNDARY Variable in module Martel.msre_constants
AT_UNI_BOUNDARY Variable in module Martel.msre_constants
AT_UNI_NON_BOUNDARY Variable in module Martel.msre_constants
AT_UNICODE Variable in module Martel.msre_constants
AtBeginning Class in module Martel.Expression
ATCODES Variable in module Martel.msre_constants
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
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
augment Method in class Bio.Parsers.spark.GenericParser
author_name Variable in module Bio.Medline.nlmmedline_001211_format
author_name Variable in module Bio.Medline.nlmmedline_010319_format
author_name Variable in module Bio.Medline.nlmmedline_011101_format
author_name Variable in module Bio.Medline.nlmmedline_031101_format
authors_block Variable in module Bio.expressions.genbank
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_matrices Variable in module Bio.SubsMat.MatrixInfo
available_results Method in class Bio.Application.ApplicationResult
avg_ambiguous_dna_weights Variable in module Bio.Data.IUPACData
avg_ambiguous_rna_weights Variable in module Bio.Data.IUPACData
avg_extended_protein_weights Variable in module Bio.Data.IUPACData
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 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
BadMatrixError Variable in package Bio.SubsMat
BANGLINE Variable in module Bio.EUtils.sourcegen
BarChartDistribution Class in module Bio.Graphics.Distribution
Base Class in module Bio.EUtils.DTDs.LinkOut
base_count Variable in module Bio.expressions.genbank
base_count_line Variable in module Bio.expressions.genbank
base_number Variable in module Bio.expressions.genbank
base_str Method in class Bio.Prosite.Pattern.PrositeTerm
BaseDB Module in package Bio.Mindy
BaseDBIdsRecordSet Class in module Bio.EUtils.DBIdsClient
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
benner22 Variable in module Bio.SubsMat.MatrixInfo
benner6 Variable in module Bio.SubsMat.MatrixInfo
benner74 Variable in module Bio.SubsMat.MatrixInfo
BetweenPosition Class in module Bio.SeqFeature
bf_search Function in module Bio.Pathway.Rep.MultiGraph
big_indent_space Variable in module Bio.expressions.genbank
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
BL Variable in module Bio.expressions.blocks
blank_line Variable in module Bio.Emboss.primer3_format
blank_line Variable in module Bio.Emboss.primersearch_format
blank_line Variable in module Bio.expressions.transfac
blank_space Variable in module Bio.expressions.genbank
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 Variable in module Bio.formatdefs.search
blast_filter Variable in module Bio.expressions.blast.ncbiblast
blastall Function in module Bio.Blast.NCBIStandalone
BlastallCommandline Class in module Bio.Blast.Applications
BlastErrorParser Class in module Bio.Blast.NCBIStandalone
blastn Variable in module Bio.expressions.blast.ncbiblast
blastn Variable in module Bio.expressions.blast.wublast
blastn Variable in module Bio.formatdefs.search
blastn_appheader Variable in module Bio.expressions.blast.ncbiblast
blastn_appheader Variable in module Bio.expressions.blast.wublast
blastn_ending Variable in module Bio.expressions.blast.ncbiblast
blastn_ending Variable in module Bio.expressions.blast.wublast
blastn_hsp_header Variable in module Bio.expressions.blast.ncbiblast
blastn_hsp_header Variable in module Bio.expressions.blast.wublast
blastn_identical Variable in module Bio.expressions.blast.ncbiblast
blastn_identities Variable in module Bio.expressions.blast.wublast
blastn_score Variable in module Bio.expressions.blast.wublast
blastn_strand Variable in module Bio.expressions.blast.wublast
blastp Variable in module Bio.expressions.blast.ncbiblast
blastp Variable in module Bio.expressions.blast.wublast
blastp Variable in module Bio.formatdefs.search
blastp_appheader Variable in module Bio.expressions.blast.ncbiblast
blastp_appheader Variable in module Bio.expressions.blast.wublast
blastp_ending Variable in module Bio.expressions.blast.ncbiblast
blastp_ending Variable in module Bio.expressions.blast.wublast
blastp_hsp_header Variable in module Bio.expressions.blast.ncbiblast
blastp_hsp_header Variable in module Bio.expressions.blast.wublast
blastp_identical Variable in module Bio.expressions.blast.ncbiblast
blastp_score Variable in module Bio.expressions.blast.wublast
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
blastx Variable in module Bio.expressions.blast.ncbiblast
blastx Variable in module Bio.expressions.blast.wublast
blastx Variable in module Bio.formatdefs.search
blastx_appheader Variable in module Bio.expressions.blast.ncbiblast
blastx_appheader Variable in module Bio.expressions.blast.wublast
blastx_ending Variable in module Bio.expressions.blast.ncbiblast
blastx_ending Variable in module Bio.expressions.blast.wublast
blastx_hsp_header Variable in module Bio.expressions.blast.ncbiblast
blastx_hsp_header Variable in module Bio.expressions.blast.wublast
blastx_identities Variable in module Bio.expressions.blast.wublast
blastx_score Variable in module Bio.expressions.blast.wublast
blastx_strand Variable in module Bio.expressions.blast.wublast
blastx_table_entry Variable in module Bio.expressions.blast.wublast
blastx_to_database Variable in module Bio.expressions.blast.wublast
Block Class in module Bio.Nexus.Nexus
blocks Module in package Bio.expressions
blosum100 Variable in module Bio.SubsMat.MatrixInfo
blosum30 Variable in module Bio.SubsMat.MatrixInfo
blosum35 Variable in module Bio.SubsMat.MatrixInfo
blosum40 Variable in module Bio.SubsMat.MatrixInfo
blosum45 Variable in module Bio.SubsMat.MatrixInfo
blosum50 Variable in module Bio.SubsMat.MatrixInfo
blosum55 Variable in module Bio.SubsMat.MatrixInfo
blosum60 Variable in module Bio.SubsMat.MatrixInfo
blosum62 Variable in module Bio.SubsMat.MatrixInfo
blosum65 Variable in module Bio.SubsMat.MatrixInfo
blosum70 Variable in module Bio.SubsMat.MatrixInfo
blosum75 Variable in module Bio.SubsMat.MatrixInfo
blosum80 Variable in module Bio.SubsMat.MatrixInfo
blosum85 Variable in module Bio.SubsMat.MatrixInfo
blosum90 Variable in module Bio.SubsMat.MatrixInfo
blosum95 Variable in module Bio.SubsMat.MatrixInfo
bogus_DR_group Variable in module Martel.test.testformats.swissprot38
Bol Function in package Martel
bootstrap Method in class Bio.Nexus.Nexus.Nexus
BRANCH Variable in module Martel.msre_constants
branchlength2support Method in class Bio.Nexus.Trees.Tree
Brief Class in module Bio.EUtils.DTDs.LinkOut
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 Variable in module Martel.msre_constants
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
Case Function in package Martel
CatchFields Class in module Martel.test.test_delimiter
categories Variable in module Martel.convert_re
CATEGORIES Variable in module Martel.msre_parse
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
CATEGORY Variable in module Martel.msre_constants
CATEGORY_DIGIT Variable in module Martel.msre_constants
CATEGORY_LINEBREAK Variable in module Martel.msre_constants
CATEGORY_LOC_NOT_WORD Variable in module Martel.msre_constants
CATEGORY_LOC_WORD Variable in module Martel.msre_constants
CATEGORY_NOT_DIGIT Variable in module Martel.msre_constants
CATEGORY_NOT_LINEBREAK Variable in module Martel.msre_constants
CATEGORY_NOT_SPACE Variable in module Martel.msre_constants
CATEGORY_NOT_WORD Variable in module Martel.msre_constants
CATEGORY_SPACE Variable in module Martel.msre_constants
CATEGORY_UNI_DIGIT Variable in module Martel.msre_constants
CATEGORY_UNI_LINEBREAK Variable in module Martel.msre_constants
CATEGORY_UNI_NOT_DIGIT Variable in module Martel.msre_constants
CATEGORY_UNI_NOT_LINEBREAK Variable in module Martel.msre_constants
CATEGORY_UNI_NOT_SPACE Variable in module Martel.msre_constants
CATEGORY_UNI_NOT_WORD Variable in module Martel.msre_constants
CATEGORY_UNI_SPACE Variable in module Martel.msre_constants
CATEGORY_UNI_WORD Variable in module Martel.msre_constants
CATEGORY_WORD Variable in module Martel.msre_constants
CC Variable in module Martel.test.testformats.swissprot38
CC_begin Variable in module Martel.test.testformats.swissprot38
CC_block Variable in module Bio.expressions.embl.embl65
CC_copyright Variable in module Martel.test.testformats.swissprot38
CC_copyright_begin Variable in module Martel.test.testformats.swissprot38
CC_copyright_end Variable in module Martel.test.testformats.swissprot38
CC_line Variable in module Bio.expressions.embl.embl65
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
CH_LOCALE Variable in module Martel.msre_constants
CH_UNICODE Variable in module Martel.msre_constants
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.EUtils.POM.ObjectParserHandler
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
CharBuffer Class in module Bio.Nexus.Nexus
CHARSET Variable in module Bio.Nexus.Nexus
CHARSET Variable in module Martel.msre_constants
CHCODES Variable in module Martel.msre_constants
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
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
Chromosome Class in module Bio.Graphics.BasicChromosome
ChromosomeCounts Class in module Bio.Graphics.DisplayRepresentation
ChromosomeSegment Class in module Bio.Graphics.BasicChromosome
Citation Class in module Bio.Medline.NLMMedlineXML
citation_format Variable in module Bio.Medline.nlmmedline_001211_format
citation_format Variable in module Bio.Medline.nlmmedline_010319_format
citation_format Variable in module Bio.Medline.nlmmedline_011101_format
citation_format Variable in module Bio.Medline.nlmmedline_031101_format
CitationParser Class in module Bio.Medline.NLMMedlineXML
CKEYWORDS Variable in module Bio.Sequencing.Phd
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.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.RecordFile.RecordFile
close Method in class Bio.SeqIO.FASTA.FastaWriter
close Method in class Bio.SeqIO.generic.GenericFormat
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
ClustalFormat Class in module Bio.SeqIO.generic
cmp_dicts Function in module Martel.test.test_attrs
CodonTable Module in package Bio.Data
CodonTable Class in module Bio.Data.CodonTable
collapse Method in class Bio.Nexus.Nodes.Chain
collectRules Method in class Bio.Parsers.spark.GenericParser
colonformat Variable in module Martel.test.testformats.delimiter
Cols Method in class Bio.Affy.CelFile.CelConsumer
ColumnUnit Class in module Bio.Wise.psw
combine Function in module Bio.Nexus.Nexus
commaformat Variable in module Martel.test.testformats.delimiter
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 Variable in module Martel.test.testformats.swissprot38
comment_block Variable in module Bio.expressions.genbank
comment_line Variable in module Bio.Emboss.primer3_format
comment_lines Variable in module Bio.expressions.fasta
comments Variable in module Bio.Emboss.primer3_format
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
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
compone Variable in module Bio.lcc
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
connection Variable in module Bio.DocSQL
consrtm_block Variable in module Bio.expressions.genbank
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
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.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
contig_block Variable in module Bio.expressions.genbank
contig_location Variable in module Bio.expressions.genbank
ConversionMutation Class in module Bio.GA.Mutation.Simple
convert Method in class Bio.FormatIO.FormatIO
Convert Method in class Bio.SeqIO.generic.ReadSeq
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_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
converter_table Variable in module Martel.convert_re
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
copyright Variable in module Bio.expressions.hmmpfam
copyright Variable in module Martel.test.test_swissprot38
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 Variable in module Bio.SubsMat.FreqTable
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
crc Module in package Bio
crc64 Function in module Bio.crc
Create Class in module Bio.DocSQL
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
crom Variable in module Bio.lcc
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
cursor Method in class Bio.DocSQL.Query
cursor Method in class Bio.DocSQL.QuerySingle
d Variable in module Bio.EUtils.setup
Data Package in package Bio
data Package in package Bio in class BioSQL.BioSeq.DBSeq
data1 Variable in module Martel.test.test_RecordReader2
data_file_division Variable in module Bio.expressions.genbank
DATA_LINE Variable in module Bio.expressions.transfac
data_table Function in module Bio.NMR.xpktools
Database Class in module Bio.EUtils.DTDs.LinkOut
Database Class in module Bio.Search
database_name Function in module Bio.Std
database_num_letters Function in module Bio.Std
database_num_sequences Function in module Bio.Std
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
databases Variable in module Bio.EUtils.Config
DataRecord Class in package Bio.Enzyme
Datatypes Module in package Bio.EUtils
Date Class in module Bio.EUtils.Datatypes
date Variable in module Bio.expressions.embl.embl65
date Variable in module Bio.expressions.genbank
DateRange Class in module Bio.EUtils.Datatypes
db Variable in module Bio.config.DBRegistry
db_source_block Variable in module Bio.expressions.genbank
db_stats Variable in module Bio.expressions.blast.ncbiblast
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
dbname_conversions Variable in module Bio.DBXRef
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
DE Variable in module Bio.expressions.blocks
DE Variable in module Martel.test.testformats.swissprot38
DE_block Variable in module Bio.expressions.embl.embl65
DE_block Variable in module Martel.test.testformats.swissprot38
DE_line Variable in module Bio.expressions.embl.embl65
Debug Class in module Martel.Expression
Decode Module in package Bio
decode Method in class __builtin__.str
decode_functions Variable in module Bio.Decode
DecodeParser Class in module Bio.Decode
DecodeScanner Class in module Bio.Decode
DEFAULT Variable in module Bio.EUtils.POM
default Method in class Bio.Parsers.spark.GenericASTTraversal
DEFAULT_BOUNDARY_CHARS Variable in module Bio.triefind
default_manager Variable in module Bio.PropertyManager
DEFAULT_PSEUDO Variable in class Bio.HMM.MarkovModel.MarkovModelBuilder
define_block Function in module Bio.expressions.genbank
definition_block Variable 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
DeleteCitation_end Variable in module Bio.Medline.nlmmedline_001211_format
DeleteCitation_end Variable in module Bio.Medline.nlmmedline_010319_format
DeleteCitation_end Variable in module Bio.Medline.nlmmedline_011101_format
DeleteCitation_end Variable in module Bio.Medline.nlmmedline_031101_format
DeleteCitation_start Variable in module Bio.Medline.nlmmedline_001211_format
DeleteCitation_start Variable in module Bio.Medline.nlmmedline_010319_format
DeleteCitation_start Variable in module Bio.Medline.nlmmedline_011101_format
DeleteCitation_start Variable in module Bio.Medline.nlmmedline_031101_format
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 Class in module Bio.Blast.Record
description Function in module Bio.Std
description_block Function in module Bio.Std
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
diagALL Variable in package Bio.SubsMat
diagNO Variable in package Bio.SubsMat
diagnostic_error_expr Variable in module Bio.dbdefs.fasta
diagnostic_error_expr Variable in module Bio.dbdefs.genbank
diagnostic_error_expr Variable in module Bio.dbdefs.medline
diagONLY Variable in package Bio.SubsMat
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
DIGITS Variable in module Martel.msre_parse
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
divisions Variable in module Bio.expressions.embl.embl65
divisions Variable in module Bio.expressions.genbank
DNAAlphabet Class in package Bio.Alphabet
dnal Module in package Bio.Wise
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_it Function in module Bio.EUtils.dtd2py
do_test Function in module Martel.test.test_delimiter
DocSQL Module in package Bio
DocSum Class in module Bio.EUtils.DTDs.eSummary_020511
DOCTYPE Variable in module Bio.Medline.nlmmedline_001211_format
DOCTYPE Variable in module Bio.Medline.nlmmedline_010319_format
DOCTYPE Variable in module Bio.Medline.nlmmedline_011101_format
DOCTYPE Variable in module Bio.Medline.nlmmedline_031101_format
doctype Variable in module Bio.Medline.nlmmedline_031101_format
domain_align_header Variable in module Bio.expressions.hmmpfam
domain_align_middle Variable in module Bio.expressions.hmmpfam
domain_align_top Variable in module Bio.expressions.hmmpfam
domain_alignment Variable in module Bio.expressions.hmmpfam
domain_header Variable in module Bio.expressions.hmmpfam
domain_hit_line Variable in module Bio.expressions.hmmpfam
Dot Class in module Martel.Expression
download_many Function in module Bio.PubMed
DR Variable in module Martel.test.testformats.swissprot38
DR_block Variable in module Bio.expressions.embl.embl65
DR_block Variable in module Martel.test.testformats.swissprot38
DR_embl Variable in module Martel.test.testformats.swissprot38
DR_general Variable in module Martel.test.testformats.swissprot38
DR_prosite Variable in module Martel.test.testformats.swissprot38
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.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
ds Class in module Bio.Sequencing.Ace
DT_ann_update Variable in module Martel.test.testformats.swissprot38
DT_block Variable in module Bio.expressions.embl.embl65
DT_created Variable in module Martel.test.testformats.swissprot38
DT_created_line Variable in module Bio.expressions.embl.embl65
DT_seq_update Variable in module Martel.test.testformats.swissprot38
DT_updated_line Variable in module Bio.expressions.embl.embl65
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 Bio.DocSQL.Query
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_RESULT Variable in module Bio.EUtils.ThinClient
dump_saved Function in module Bio.FilteredReader
dump_saved Function in module Bio.RecordFile
DUMP_URL Variable in module Bio.EUtils.ThinClient
dumpProperties Method in class reportlab.graphics.widgetbase.PropHolder
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
eInfo_020511 Module in package Bio.EUtils.DTDs
eInfoResult Class in module Bio.EUtils.DTDs.eInfo_020511
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
elements Variable in module Bio.Medline.nlmmedline_001211_format
elements Variable in module Bio.Medline.nlmmedline_010319_format
elements Variable in module Bio.Medline.nlmmedline_011101_format
elements Variable in module Bio.Medline.nlmmedline_031101_format
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
EMAIL Variable in module Bio.EUtils.ThinClient
embl Module in package Bio.dbdefs
embl Variable in module Bio.dbdefs.embl
embl Package in package Bio.expressions
embl Module in package Bio.formatdefs
embl Variable in module Bio.formatdefs.embl
embl Module in package Bio.writers.SeqRecord
embl65 Module in package Bio.expressions.embl
embl65 Variable in module Bio.formatdefs.embl
embl_dbfetch_cgi Variable in module Bio.dbdefs.embl
embl_ebi_cgi Variable in module Bio.dbdefs.embl
embl_fast Variable in module Bio.dbdefs.embl
embl_xembl_cgi Variable in module Bio.dbdefs.embl
embl_xml Variable in module Bio.dbdefs.embl
EMBLFormat Class in module Bio.SeqIO.generic
Emboss Package in package Bio
EMPTY Variable in module Bio.EUtils.POM
empty Method in class Bio.Pathway.Rep.HashSet.HashSet
empty Variable in module Bio.formatdefs.sequence
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 Variable in module Bio.expressions.blocks
end Variable in module Bio.expressions.embl.embl65
end Method in class Martel.LAX.LAX
end Variable in module Martel.test.testformats.swissprot38
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_a Method in class Bio.UniGene.UniGeneParser
end_b Method in class Bio.UniGene.UniGeneParser
end_block Method in class Bio.StdHandler.Handle_search_header
end_block Method in class Bio.builders.Search.search.BuildSearch
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_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_h1 Method in class Bio.Ndb.NdbParser
end_h2 Method in class Bio.InterPro.InterProParser
end_h2 Method in class Bio.Ndb.NdbParser
end_hit Method in class Bio.builders.Search.search.BuildSearch
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_record Method in class Bio.Mindy.SimpleSeqRecord.FixDocumentBuilder
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.StdHandler.Handle_sequence
end_sequence_block Method in class Bio.StdHandler.Handle_sequence
end_sub Method in class Bio.Ndb.NdbParser
end_table Method in class Bio.UniGene.UniGeneParser
end_td Method in class Bio.InterPro.InterProParser
end_td Method in class Bio.UniGene.UniGeneParser
end_tr Method in class Bio.UniGene.UniGeneParser
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
endElement Method in class Bio.EUtils.POM.ObjectParserHandler
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
ending Variable in module Bio.expressions.blast.wublast
ending_start Variable in module Bio.expressions.blast.wublast
EndsWith Class in module Martel.RecordReader
endswith Method in class __builtin__.str
ENeighborCommandline Class in module Bio.Emboss.Applications
ENTITIES Class in module Bio.EUtils.POM
ENTITY Class in module Bio.EUtils.POM
entitydefs Variable in module Bio.EUtils.parse
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
entitydefs Variable in class sgmllib.SGMLParser
Enumeration Class in module Bio.EUtils.POM
Enzyme Package in package Bio
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
EPSILON Variable in package Bio.SubsMat
equal_weight Function in module Bio.kNN
equiv_title Variable in package Bio.FSSP
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_expr Variable in module Bio.dbdefs.fasta
error_expr Variable in module Bio.dbdefs.genbank
error_expr Variable in module Bio.dbdefs.medline
error_message Variable in class Bio.DocSQL.Query
error_message Variable in class Bio.DocSQL.Query
error_message Variable in class Bio.DocSQL.Query
error_message Variable in class Bio.DocSQL.Query
error_message Variable in class Bio.DocSQL.Query
error_message Variable in class Bio.DocSQL.Query
error_message Variable in class Bio.DocSQL.Query
error_message Variable in class Bio.DocSQL.Query
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
ESCAPES Variable in module Martel.msre_parse
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
expect Variable in module Bio.expressions.blast.ncbiblast
expected_records Variable in module Martel.test.test_delimiter
EXPFREQ Variable in package Bio.SubsMat
Explode Class in module Bio.EUtils.DTDs.eSearch_020511
export_fasta Method in class Bio.Nexus.Nexus.Nexus
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
extended_dna Variable in module Bio.Alphabet.IUPAC
extended_dna_letters Variable in module Bio.Data.IUPACData
extended_protein Variable in module Bio.Alphabet.IUPAC
extended_protein_letters Variable in module Bio.Data.IUPACData
extended_protein_values Variable in module Bio.Data.IUPACData
extended_protein_weight_ranges Variable in module Bio.Data.IUPACData
ExtendedIUPACDNA Class in module Bio.Alphabet.IUPAC
ExtendedIUPACProtein Class in module Bio.Alphabet.IUPAC
extract_key Method in class Bio.UniGene.UniGeneParser
extract_keywords Function in module Bio.SwissProt.KeyWList
extract_saved_line Method in class Bio.RecordFile.RecordFile
extract_urls Method in class Bio.NetCatch.ExtractUrls
ExtractUrls Class in module Bio.NetCatch
EZRetrieve Module in package Bio
FAILURE Variable in module Martel.msre_constants
family_header Variable in module Bio.expressions.hmmpfam
family_hit_line Variable in module Bio.expressions.hmmpfam
fast_dbxref Function in module Bio.Std
FASTA Module in package Bio.SeqIO
fasta Module in package Bio.dbdefs
fasta Variable in module Bio.dbdefs.fasta
fasta Module in package Bio.expressions
fasta Variable in module Bio.formatdefs.sequence
fasta Module in package Bio.writers.SeqRecord
fasta_mult_align Method in class Bio.FSSP.FSSPAlignDict
fasta_sequence_eutils Variable in module Bio.dbdefs.fasta
FastacmdCommandline Class in module Bio.Blast.Applications
FastaFormat Class in module Bio.SeqIO.generic
FastaReader Class in module Bio.SeqIO.FASTA
FastaWriter Class in module Bio.SeqIO.FASTA
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
fcmp Function in module Bio.mathfns
feature Function in module Bio.Std
Feature Class in module Bio.StdHandler
feature Variable in module Bio.expressions.embl.embl65
feature Variable in module Bio.expressions.genbank
feature_block Function in module Bio.Std
feature_block Variable in module Bio.expressions.genbank
feature_block Variable in module Martel.test.testformats.swissprot38
feature_description Function in module Bio.Std
feature_key Variable in module Bio.expressions.genbank
FEATURE_KEY_INDENT Variable in module Bio.expressions.genbank
feature_key_line Variable in module Bio.expressions.genbank
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 Variable in module Bio.expressions.embl.embl65
feature_qualifier_description Function in module Bio.Std
FEATURE_QUALIFIER_INDENT Variable in module Bio.expressions.genbank
feature_qualifier_name Function in module Bio.Std
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
features_line Variable in module Bio.expressions.genbank
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.InterPro.InterProParser
feed Method in class Bio.Ndb.NdbParser
feed Method in class Bio.NetCatch.ExtractUrls
feed Method in class Bio.UniGene.UniGeneParser
feed Method in class sgmllib.SGMLParser
feng Variable in module Bio.SubsMat.MatrixInfo
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
FH_block Variable in module Bio.expressions.embl.embl65
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
files Variable in module Bio.expressions.hmmpfam
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_delim Function in module Bio.RecordFile
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_record_boundary Method in class Bio.RecordFile.RecordFile
find_related Function in module Bio.PubMed
find_schemas Method in class Bio.NeuralNetwork.Gene.Schema.GeneticAlgorithmFinder
find_start Method in class Bio.SeqIO.generic.GenericFormat
find_states Function in module Bio.MarkovModel
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
fitch Variable in module Bio.SubsMat.MatrixInfo
fix Method in class Bio.Crystal.Crystal
fix_punctuation Function in module Bio.FilteredReader
FixDocumentBuilder Class in module Bio.Mindy.SimpleSeqRecord
FIXED Variable in module Bio.EUtils.POM
fixspaces Function in module Bio.Decode
FLAGS Variable in module Martel.msre_parse
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
flush Method in class Bio.SeqIO.FASTA.FastaWriter
flush Method in class Bio.SeqIO.generic.GenericFormat
footer_format Variable in module Bio.Medline.nlmmedline_001211_format
footer_format Variable in module Bio.Medline.nlmmedline_010319_format
footer_format Variable in module Bio.Medline.nlmmedline_011101_format
footer_format Variable in module Bio.Medline.nlmmedline_031101_format
format Variable in module Bio.Medline.nlmmedline_001211_format
format Variable in module Bio.Medline.nlmmedline_010319_format
format Variable in module Bio.Medline.nlmmedline_011101_format
format Variable in module Bio.Medline.nlmmedline_031101_format
format Variable in module Bio.expressions.blast.ncbiblast
format Variable in module Bio.expressions.blast.wublast
format Variable in module Bio.expressions.blocks
format Variable in module Bio.expressions.embl.embl65
format Variable in module Bio.expressions.fasta
format Variable in module Bio.expressions.genbank
format Variable in module Bio.expressions.hmmpfam
format Variable in module Bio.expressions.transfac
format Variable in module Martel.test.testformats.swissprot38
format_alignment Function in module Bio.pairwise2
format_expression Variable in module Bio.expressions.blocks
format_expression Variable in module Bio.expressions.embl.embl65
format_expression Variable in module Martel.test.testformats.swissprot38
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 Variable in module Bio.config.FormatRegistry
formats Package in package Martel
forward_algorithm Method in class Bio.HMM.DynamicProgramming.AbstractDPAlgorithms
forward_line Variable in module Bio.Emboss.primer3_format
forward_primer_gc Variable in module Bio.Emboss.primer3_format
forward_primer_length Variable in module Bio.Emboss.primer3_format
forward_primer_seq Variable in module Bio.Emboss.primer3_format
forward_primer_start Variable in module Bio.Emboss.primer3_format
forward_primer_tm Variable in module Bio.Emboss.primer3_format
forward_strand_info Variable in module Bio.Emboss.primersearch_format
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
found_antigen Method in class Bio.Ais.Immune
FOUND_SITES_LINE Variable in module Bio.expressions.transfac
foundMatch Method in class Bio.Parsers.spark.GenericASTMatcher
fq_dbxref Variable in module Bio.expressions.embl.embl65
fq_generic Variable in module Bio.expressions.embl.embl65
Fragments Class in module Bio.EUtils.POM
frame Variable in module Bio.expressions.blast.ncbiblast
frameshift_info Variable in module Bio.expressions.blast.ncbiblast
FREQ Variable in module Bio.SubsMat.FreqTable
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
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
FT Variable in module Martel.test.testformats.swissprot38
FT_block Variable in module Bio.expressions.embl.embl65
FT_continuation Variable in module Martel.test.testformats.swissprot38
FT_range Variable in module Martel.test.testformats.swissprot38
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_stats Variable in module Bio.expressions.blast.ncbiblast
gaponly Method in class Bio.Nexus.Nexus.Nexus
Gapped Class in package Bio.Alphabet
gapped_lambda_stats Variable in module Bio.expressions.blast.ncbiblast
gb_nucleotide Variable in module Bio.dbdefs.genbank
gb_protein Variable in module Bio.dbdefs.genbank
GCGFormat Class in module Bio.SeqIO.generic
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
genbank Variable in module Bio.formatdefs.genbank
genbank_records Variable in module Bio.formatdefs.genbank
genbank_release Variable in module Bio.formatdefs.genbank
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
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
generate_table Variable 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 Module in package Bio.SeqIO
generic_alphabet Variable in package Bio.Alphabet
Generic_dbutils Class in module BioSQL.DBUtils
generic_dna Variable in package Bio.Alphabet
generic_info1 Variable in module Bio.expressions.blast.ncbiblast
generic_info2 Variable in module Bio.expressions.blast.ncbiblast
generic_nucleotide Variable in package Bio.Alphabet
generic_protein Variable in package Bio.Alphabet
generic_rna Variable in package Bio.Alphabet
generic_run Function in package Bio.Application
generic_term Variable in module Bio.expressions.fasta
generic_transcriber Variable in module Bio.Transcribe
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
GenericFormat Class in module Bio.SeqIO.generic
GenericParser Class in module Bio.Parsers.spark
GenericScanner Class in module Bio.Parsers.spark
genetic Variable in module Bio.SubsMat.MatrixInfo
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.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_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_header Method in class Bio.SeqIO.generic.GenericFormat
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_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_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.POM.ElementNode
getBounds Method in class reportlab.graphics.widgetbase.Widget
GetErrorPos Class in module Martel.test.test_optimize
getLength Method in class Martel.Parser.MartelAttributeList
getName Method in class Bio.MultiProc.Task.Task
getName Method in class Martel.Parser.MartelAttributeList
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
gettype Method in class Bio.EUtils.Config.DatabaseDict
getType Method in class Martel.Parser.MartelAttributeList
getValue Method in class Martel.Parser.MartelAttributeList
getwidth Method in class Martel.msre_parse.SubPattern
gi Variable in module Bio.expressions.genbank
global_alphabet Variable in class Bio.StdHandler.Handle_sequence
GN Variable in module Martel.test.testformats.swissprot38
GN_block Variable in module Martel.test.testformats.swissprot38
gnl_id Variable in module Bio.expressions.fasta
goahead Method in class sgmllib.SGMLParser
Gobase Package in package Bio
gonnet Variable in module Bio.SubsMat.MatrixInfo
GrabElements Class in module Martel.test.test_attrs
GrabXPathNodes Class in module Bio.Mindy.XPath
grant Variable in module Bio.SubsMat.MatrixInfo
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
GROUPREF Variable in module Martel.msre_constants
GROUPREF_IGNORE Variable in module Martel.msre_constants
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 Bio.UniGene.UniGeneParser
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_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_no_group Function in module Martel.test.test_macros
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
header Variable in class Bio.Wise.dnal.Statistics
header Variable in module Bio.expressions.blast.ncbiblast
header Variable in module Bio.expressions.blast.wublast
header Variable in module Bio.expressions.blocks
header Variable in module Bio.expressions.genbank
header Variable in module Bio.expressions.hmmpfam
header_format Variable in module Bio.Medline.nlmmedline_001211_format
header_format Variable in module Bio.Medline.nlmmedline_010319_format
header_format Variable in module Bio.Medline.nlmmedline_011101_format
header_format Variable in module Bio.Medline.nlmmedline_031101_format
header_records Variable in package Bio.FSSP
HeaderFooter Class in module Martel.Expression
HeaderFooterEventStream Class in module Martel.Iterator
HeaderFooterParser Class in module Martel.Parser
HEADERLEN Variable in module Bio.NMR.xpktools
Hetero Class in package Bio.Crystal
hex_convert Function in module Bio.HotRand
HEXDIGITS Variable in module Martel.msre_parse
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 Variable in module Bio.expressions.blast.ncbiblast
hit_coverage Method in class Bio.Compass.Record
hit_descr Variable in module Bio.expressions.blast.ncbiblast
hit_descr Variable in module Bio.expressions.blast.wublast
hit_description Function in module Bio.Std
hit_length Function in module Bio.Std
hit_length Variable in module Bio.expressions.blast.ncbiblast
hit_length Variable in module Bio.expressions.blast.wublast
HMM Package in package Bio
hmmpfam Module in package Bio.expressions
homology_line Variable in module Bio.expressions.blast.ncbiblast
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
hp_model Variable in module Bio.Alphabet.Reduced
hp_model_tab Variable in module Bio.Alphabet.Reduced
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 Variable in module Bio.expressions.blast.ncbiblast
hsp_frame Function in module Bio.Std
hsp_info Variable in module Bio.expressions.blast.ncbiblast
hsp_length Variable in module Bio.expressions.blast.ncbiblast
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
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 Variable in module Bio.expressions.blocks
ID Variable in module Martel.test.testformats.swissprot38
ID_line Variable in module Bio.expressions.embl.embl65
id_term Variable in module Bio.expressions.fasta
IdCheck Class in module Bio.EUtils.Datatypes
IdCheckList Class in module Bio.EUtils.DTDs.eLink_020511
ident Variable in module Bio.SubsMat.MatrixInfo
identifier Variable in module Bio.expressions.blocks
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 Variable in module Bio.expressions.blast.wublast
identity_fraction Method in class Bio.Wise.dnal.Statistics
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
ids Variable in module Bio.expressions.fasta
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
ignore_characters Method in class Bio.StdHandler.ConvertHandler
ignore_warnings Variable in class Bio.DocSQL.QuerySingle
ignore_warnings Variable in class Bio.DocSQL.QuerySingle
ignore_warnings Variable in class Bio.DocSQL.QuerySingle
ignore_warnings Variable in class Bio.DocSQL.QuerySingle
Immune Class in package Bio.Ais
IMPLIED Variable in module Bio.EUtils.POM
import_dict Method in class Bio.NetCatch.NetCatch
imprint_type Variable in module Bio.Medline.nlmmedline_031101_format
IN Variable in module Martel.msre_constants
IN_IGNORE Variable in module Martel.msre_constants
InclQuery Class in module Bio.EUtils.DTDs.LinkOut
INDENT Variable in module Bio.expressions.genbank
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
INDEX_TYPE Variable in module Bio.Mindy.FlatDB
IndexedFileDB Class in module Bio.config.DBRegistry
indexesof Function in module Bio.listfns
indexing_status Variable in module Bio.Medline.nlmmedline_031101_format
Info Class in module Bio.EUtils.DTDs.eLink_020511
INFO Variable in module Martel.msre_constants
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 Class in module Bio.DocSQL
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
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
INTERLEAVE Variable in module Bio.Nexus.Nexus
InterleaveCrossover Class in module Bio.GA.Crossover.GeneralPoint
InterPro Package in package Bio
InterPro Module in package Bio.WWW
interpro Module in package Bio.dbdefs
interpro Variable in module Bio.dbdefs.interpro
interpro_ebi_cgi Variable in module Bio.dbdefs.interpro
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
io Variable in module Bio.Search
ipi Variable in module Bio.formatdefs.swissprot
is_absolute_url Function in module Bio.NetCatch
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
is_prefix_in_set Function in module Bio.RecordFile
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
isspace Method in class __builtin__.str
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.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
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
IterationCursor Class in module Bio.DocSQL
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 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
johnson Variable in module Bio.SubsMat.MatrixInfo
join Method in class __builtin__.str
join_english Function in module Bio.Decode
join_fixspaces Function in module Bio.Decode
journal_block Variable in module Bio.expressions.genbank
JUMP Variable in module Martel.msre_constants
KEGG Package in package Bio
KEGG_DATA_LENGTH Variable in package Bio.KEGG
KEGG_ITEM_LENGTH Variable in package Bio.KEGG
KEGG_LINE_LENGTH Variable in package Bio.KEGG
keys Method in class Bio.Crystal.Crystal
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
KeyWList Module in package Bio.SwissProt
keywords_block Variable in module Bio.expressions.genbank
kill Method in class Bio.Nexus.Nodes.Chain
kNN Module in package Bio
kNN Class in module Bio.kNN
KNOWN_NEXUS_BLOCKS Variable in module Bio.Nexus.Nexus
KnownStateTrainer Class in module Bio.HMM.Trainer
KW Variable in module Martel.test.testformats.swissprot38
KW_block Variable in module Bio.expressions.embl.embl65
KW_block Variable in module Martel.test.testformats.swissprot38
KW_line Variable in module Bio.expressions.embl.embl65
labels Method in class Bio.Pathway.Rep.Graph.Graph
labels Method in class Bio.Pathway.Rep.MultiGraph.MultiGraph
lambda_stats Variable in module Bio.expressions.blast.ncbiblast
LargeFastaFormat Class in module Bio.SeqIO.generic
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
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
lccsal Variable in module Bio.lcc
lcheck Method in class Bio.EUtils.Mixins.LinkMixin
lchomp Function in module Bio.Decode
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
levin Variable in module Bio.SubsMat.MatrixInfo
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
LITERAL Variable in module Martel.msre_constants
LITERAL_IGNORE Variable in module Martel.msre_constants
ljust Method in class __builtin__.str
llinks Method in class Bio.EUtils.Mixins.LinkMixin
LO Variable in package Bio.SubsMat
load Function in module Bio.MarkovModel
load Method in class Bio.Mindy.BaseDB.WriteDB
load Method in class BioSQL.BioSeqDatabase.BioSeqDatabase
load_database_sql Method in class BioSQL.BioSeqDatabase.DBServer
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
location Variable in module Bio.expressions.genbank
locus Variable in module Bio.expressions.genbank
locus_line Variable in module Bio.expressions.genbank
LOG0 Variable in module Bio.MarkovModel
LOG2 Variable in module Bio.mathfns
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
MAGIC Variable in module Martel.msre_constants
main Function in module Bio.EUtils.dtd2py
main Function in package Bio.Mindy
main Function in module Bio.Wise.dnal
main Function in package Bio.Wise
main Function in module Bio.Wise.psw
main Function in module Bio.expressions.blast.wublast
main Function in module Martel.test.run_tests
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_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 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_relative_entropy Method in class Bio.SubsMat.SeqMat
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
MARK Variable in module Martel.msre_constants
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
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
match_symbols Variable in module Bio.expressions.hmmpfam
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
MATCODE Variable in module Bio.MarkovModel
mathfns Module in package Bio
MATRIX_LINE Variable in module Bio.expressions.transfac
matrix_stats Variable in module Bio.expressions.blast.ncbiblast
MatrixInfo Module in package Bio.SubsMat
MAX_ITERATIONS Variable in module Bio.MarkovModel
MAX_REPEAT Variable in module Martel.msre_constants
MAX_UNTIL Variable in module Martel.msre_constants
MaxEntropy Module in package Bio
MaxEntropy Class in module Bio.MaxEntropy
MAXREPEAT Variable in module Martel.Expression
MaxRepeat Class in module Martel.Expression
MaxRepeat Function in package Martel
MAXREPEAT Variable in module Martel.msre_constants
mclach Variable in module Bio.SubsMat.MatrixInfo
Medline Package in package Bio
medline Module in package Bio.dbdefs
medline Variable in module Bio.dbdefs.medline
medline_eutils Variable in module Bio.dbdefs.medline
medline_line Variable in module Bio.expressions.genbank
MedlineCitationSet_end Variable in module Bio.Medline.nlmmedline_001211_format
MedlineCitationSet_end Variable in module Bio.Medline.nlmmedline_010319_format
MedlineCitationSet_end Variable in module Bio.Medline.nlmmedline_011101_format
MedlineCitationSet_end Variable in module Bio.Medline.nlmmedline_031101_format
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
message Variable in class Bio.DocSQL.Query
message Variable in class Bio.DocSQL.Query
message Variable in class Bio.DocSQL.Query
message Variable in class Bio.DocSQL.Query
message Variable in class Bio.DocSQL.Query
message Variable in class Bio.DocSQL.Query
message Variable in class Bio.DocSQL.Query
message Variable in class Bio.DocSQL.Query
MethodHolder Class in module Bio.EUtils.sourcegen
MidPoint Class in module Bio.MarkupEditor
MIN_REPEAT Variable in module Martel.msre_constants
MIN_UNTIL Variable in module Martel.msre_constants
Mindy Package in package Bio
MINUS_STRAND Variable in package Bio.EUtils
Mixins Module in package Bio.EUtils
miyata Variable in module Bio.SubsMat.MatrixInfo
ml_estimator Method in class Bio.HMM.Trainer.AbstractTrainer
model_name Variable in module Bio.expressions.hmmpfam
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.NeuralNetwork.Gene
motif_hit Method in class Bio.AlignAce.Parser.AlignAceConsumer
motif_mask Method in class Bio.AlignAce.Parser.AlignAceConsumer
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
MSG_FAILURE Variable in class Bio.DocSQL.Query
MSG_FAILURE Variable in class Bio.DocSQL.Query
MSG_FAILURE Variable in class Bio.DocSQL.Query
MSG_FAILURE Variable in class Bio.DocSQL.Query
MSG_FAILURE Variable in class Bio.DocSQL.Query
MSG_FAILURE Variable in class Bio.DocSQL.Query
MSG_FAILURE Variable in class Bio.DocSQL.Query
MSG_FAILURE Variable in class Bio.DocSQL.Query
MSG_INTEGRITY_ERROR Variable in class Bio.DocSQL.Insert
MSG_SUCCESS Variable in class Bio.DocSQL.Query
MSG_SUCCESS Variable in class Bio.DocSQL.Query
MSG_SUCCESS Variable in class Bio.DocSQL.Query
MSG_SUCCESS Variable in class Bio.DocSQL.Query
MSG_SUCCESS Variable in class Bio.DocSQL.Query
MSG_SUCCESS Variable in class Bio.DocSQL.Query
MSG_SUCCESS Variable in class Bio.DocSQL.Query
MSG_SUCCESS Variable in class Bio.DocSQL.Query
msre_constants Module in package Martel
msre_parse Module in package Martel
mult_align Function in module Bio.FSSP.FSSPTools
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
murphy_10 Variable in module Bio.Alphabet.Reduced
murphy_10_tab Variable in module Bio.Alphabet.Reduced
murphy_15 Variable in module Bio.Alphabet.Reduced
murphy_15_tab Variable in module Bio.Alphabet.Reduced
murphy_4 Variable in module Bio.Alphabet.Reduced
murphy_4_tab Variable in module Bio.Alphabet.Reduced
murphy_8 Variable in module Bio.Alphabet.Reduced
murphy_8_tab Variable 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
namespace Variable in module Bio.Std
NCBI Module in package Bio.WWW
ncbi_blastn Variable in module Bio.formatdefs.search
ncbi_blastp Variable in module Bio.formatdefs.search
ncbi_blastx Variable in module Bio.formatdefs.search
ncbi_failures Variable in module Bio.dbdefs.fasta
ncbi_failures Variable in module Bio.dbdefs.genbank
ncbi_failures Variable in module Bio.dbdefs.medline
ncbi_format Variable in module Bio.expressions.genbank
ncbi_tblastn Variable in module Bio.formatdefs.search
ncbi_tblastx Variable in module Bio.formatdefs.search
ncbi_term Variable in module Bio.expressions.fasta
ncbi_version Variable in module Bio.expressions.blast.ncbiblast
ncbi_word Variable in module Bio.expressions.fasta
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
NEGATE Variable in module Martel.msre_constants
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.DocSQL.IterationCursor
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.SeqIO.FASTA.FastaReader
next Method in class Bio.SeqIO.generic.ClustalFormat
next Method in class Bio.SeqIO.generic.EMBLFormat
next Method in class Bio.SeqIO.generic.GCGFormat
next Method in class Bio.SeqIO.generic.GenericFormat
next Method in class Bio.SeqIO.generic.LargeFastaFormat
next Method in class Bio.SeqIO.generic.NexusFormat
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 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
NexusFormat Class in module Bio.SeqIO.generic
nid Variable in module Bio.expressions.genbank
nid_line Variable in module Bio.expressions.genbank
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_hit_line Variable in module Bio.expressions.hmmpfam
nobuffer Method in class Bio.EUtils.ReseekFile.ReseekFile
nobuffer Method in class Bio.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
NoInsertionError Class in module Bio.DocSQL
nonterminal Method in class Bio.Parsers.spark.GenericASTBuilder
normal_date Variable in module Bio.Medline.nlmmedline_001211_format
normal_date Variable in module Bio.Medline.nlmmedline_010319_format
normal_date Variable in module Bio.Medline.nlmmedline_011101_format
normal_date Variable in module Bio.Medline.nlmmedline_031101_format
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
not_exist_expr Variable in module Bio.dbdefs.genbank
not_header_expr Variable in module Bio.dbdefs.pdb
NOT_LITERAL Variable in module Martel.msre_constants
NOT_LITERAL_IGNORE Variable in module Martel.msre_constants
Nothing Class in module Martel.RecordReader
NOTYPE Variable in package Bio.SubsMat
npix Method in class Bio.Affy.CelFile.CelRecord
nrows Method in class Bio.Affy.CelFile.CelRecord
NS Variable in module Bio.Std
Nucleotide4Random Variable in module Bio.Align.AlignInfo
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
nucleotide_genbank_eutils Variable in module Bio.dbdefs.genbank
NucleotideAlphabet Class in package Bio.Alphabet
NullOp Class in module Martel.Expression
num_ambiguous Method in class Bio.NeuralNetwork.Gene.Schema.Schema
num_bits Variable in module Bio.expressions.blast.ncbiblast
num_identical Variable in module Bio.expressions.blast.ncbiblast
num_left Method in class Bio.MultiProc.Scheduler.Scheduler
num_matches Method in class Bio.NeuralNetwork.Gene.Schema.Schema
num_positives Variable in module Bio.expressions.blast.ncbiblast
num_running Method in class Bio.MultiProc.Scheduler.Scheduler
Number Function in module Bio.expressions.blast.ncbiblast
nwsgappep Variable in module Bio.SubsMat.MatrixInfo
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
OBSFREQ Variable in package Bio.SubsMat
OC Variable in module Martel.test.testformats.swissprot38
OC_block Variable in module Bio.expressions.embl.embl65
OC_block Variable in module Martel.test.testformats.swissprot38
OCTDIGITS Variable in module Martel.msre_parse
OG Variable in module Martel.test.testformats.swissprot38
OG_block Variable in module Bio.expressions.embl.embl65
OG_block Variable in module Martel.test.testformats.swissprot38
OneOfPosition Class in module Bio.SeqFeature
OP Class in module Bio.EUtils.DTDs.eSearch_020511
OP_IGNORE Variable in module Martel.msre_constants
OPCODES Variable in module Martel.msre_constants
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
order Variable in class Bio.SeqIO.generic.EMBLFormat
OrderedMultiDict Class in module Bio.EUtils.MultiDict
Organism Module in package Bio.GA
Organism Class in module Bio.GA.Organism
Organism Class in module Bio.Graphics.BasicChromosome
organism Variable in module Bio.expressions.embl.embl65
organism Variable in module Bio.expressions.genbank
organism_block Variable in module Bio.expressions.genbank
origin_line Variable in module Bio.expressions.genbank
original_taxon_order Variable in module Bio.expressions.genbank in class Bio.Nexus.Nexus.Nexus
OS Variable in module Martel.test.testformats.swissprot38
OS_block Variable in module Bio.expressions.embl.embl65
OS_block Variable in module Martel.test.testformats.swissprot38
OSpaces Variable in module Bio.Medline.nlmmedline_031101_format
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
pairlist_to_dict Function in package Bio.InterPro
pairwise2 Module in package Bio
pam120 Variable in module Bio.SubsMat.MatrixInfo
pam180 Variable in module Bio.SubsMat.MatrixInfo
pam250 Variable in module Bio.SubsMat.MatrixInfo
pam30 Variable in module Bio.SubsMat.MatrixInfo
pam300 Variable in module Bio.SubsMat.MatrixInfo
pam60 Variable in module Bio.SubsMat.MatrixInfo
pam90 Variable in module Bio.SubsMat.MatrixInfo
parameter Method in class Bio.AlignAce.Parser.AlignAceConsumer
parameters Method in class Bio.AlignAce.Parser.AlignAceConsumer
Parameters Class in module Bio.Blast.Record
parameters Variable in module Bio.expressions.blast.wublast
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 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.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.UniGeneParser
parse Function in module Bio.Wise.psw
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_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_line Function in module Bio.Wise.psw
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
ParseAlignment Method in class Bio.SeqIO.generic.ClustalFormat
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
ParseNexus Method in class Bio.SeqIO.generic.NexusFormat
Parser Module in package Bio.AlignAce
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
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 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
pc_5_table Variable in module Bio.Alphabet.Reduced
pdb Method in class Bio.FSSP.FSSPAlignDict
pdb Module in package Bio.dbdefs
pdb Variable in module Bio.dbdefs.pdb
pdb_ebi_cgi Variable in module Bio.dbdefs.pdb
pdb_rcsb_cgi Variable in module Bio.dbdefs.pdb
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 Variable in module Bio.Medline.nlmmedline_001211_format
personal_name Variable in module Bio.Medline.nlmmedline_010319_format
personal_name Variable in module Bio.Medline.nlmmedline_011101_format
personal_name Variable in module Bio.Medline.nlmmedline_031101_format
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
pick_a_lymphocyte Method in class Bio.Ais.Immune
pid Variable in module Bio.expressions.genbank
pid_line Variable in module Bio.expressions.genbank
PirFormat Class in module Bio.SeqIO.generic
PLUS_STRAND Variable in package Bio.EUtils
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
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
post Method in class Bio.EUtils.HistoryClient.HistoryClient
postorder Method in class Bio.Parsers.spark.GenericASTTraversal
PostResult Class in module Bio.EUtils.Datatypes
PRECISION_BRANCHLENGTH Variable in module Bio.Nexus.Trees
PRECISION_SUPPORT Variable in module Bio.Nexus.Trees
predict Method in class Bio.NeuralNetwork.BackPropagation.Network.BasicNetwork
predictNOE Function in module Bio.NMR.NOEtools
prefix Variable in class Bio.DocSQL.Query
prefix Variable in class Bio.DocSQL.Query
prefix Variable in class Bio.DocSQL.Query
prefix Variable in class Bio.DocSQL.Query
prefix Variable in class Bio.DocSQL.Query
prefix Variable in class Bio.DocSQL.Query
prefix Variable in class Bio.DocSQL.Query
prefix Variable in class Bio.DocSQL.Query
preorder Method in class Bio.Parsers.spark.GenericASTTraversal
prepare_input_source Function in module Bio.EUtils.ReseekFile
prepare_input_source Function in module Bio.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 Variable in module Bio.expressions.genbank
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
primary_line Variable in module Bio.expressions.genbank
primary_ref_line Variable in module Bio.expressions.genbank
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 Variable in module Bio.Emboss.primersearch_format
primer_name_line Variable in module Bio.Emboss.primersearch_format
primer_space Variable in module Bio.Emboss.primer3_format
primer_start_line Variable in module Bio.Emboss.primer3_format
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_item Method in class Bio.UniGene.Record
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
problem_category_mapping Variable in module Bio.EUtils.Datatypes
process_row Method in class Bio.DocSQL.QueryAll
process_row Method in class Bio.DocSQL.QueryAllFirstItem
processing_instruction Method in class Bio.EUtils.POM.ElementNode
processingInstruction Method in class Bio.EUtils.POM.ObjectParserHandler
Prodoc Module in package Bio.Prosite
prodoc Module in package Bio.dbdefs
prodoc Variable in module Bio.dbdefs.prodoc
prodoc_expasy_cgi Variable in module Bio.dbdefs.prodoc
product_size Variable in module Bio.Emboss.primer3_format
PROFILE_LINE Variable in module Bio.expressions.transfac
program_description Variable in module Bio.expressions.hmmpfam
program_version Variable in module Bio.expressions.hmmpfam
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 Variable in module Bio.dbdefs.prosite
prosite_alphabet Variable in module Bio.Prosite.Pattern
prosite_expasy_cgi Variable in module Bio.dbdefs.prosite
prosite_re Variable in module Bio.Prosite.Pattern
prosite_term_re Variable in module Bio.Prosite.Pattern
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 Variable in module Bio.Alphabet.IUPAC
Protein20Random Variable in module Bio.Align.AlignInfo
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
protein_genbank_eutils Variable in module Bio.dbdefs.genbank
protein_letters Variable in module Bio.Data.IUPACData
protein_weight_ranges Variable in module Bio.Data.IUPACData
protein_weights Variable in module Bio.Data.IUPACData
ProteinAlphabet Class in package Bio.Alphabet
ProteinRecord Class in package Bio.Gobase
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
proxy_error_expr Variable in module Bio.dbdefs.fasta
proxy_error_expr Variable in module Bio.dbdefs.genbank
proxy_error_expr Variable in module Bio.dbdefs.medline
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
psw Module in package Bio.Wise
Psycopg_dbutils Class in module BioSQL.DBUtils
pub_date Variable in module Bio.Medline.nlmmedline_001211_format
pub_date Variable in module Bio.Medline.nlmmedline_010319_format
pub_date Variable in module Bio.Medline.nlmmedline_011101_format
pub_date Variable in module Bio.Medline.nlmmedline_031101_format
PUBLICATION_TYPE Variable in module Bio.EUtils.Config
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_line Variable in module Bio.expressions.genbank
pubmed_query_format Variable in module Bio.Medline.nlmmedline_031101_format
PUNCTUATION Variable in module Bio.Nexus.Nexus
Punctuation Function in package Martel
pwm Method in class Bio.AlignAce.Motif.Motif
qa Class in module Bio.Sequencing.Ace
qblast Function in module Bio.Blast.NCBIWWW
qualifier Variable in module Bio.expressions.genbank
qualifier_space Variable in module Bio.expressions.genbank
Query Class in module Bio.DocSQL
Query Class in module Bio.EUtils.DTDs.LinkOut
Query Class in module Bio.Search
query Function in module Bio.WWW.NCBI
query_coverage Method in class Bio.Compass.Record
query_database Variable in module Bio.expressions.blast.ncbiblast
query_database Variable in module Bio.expressions.blast.wublast
query_descr Variable in module Bio.expressions.blast.ncbiblast
query_description Function in module Bio.Std
query_description_block Function in module Bio.Std
query_letters Variable in module Bio.expressions.blast.ncbiblast
query_line Variable in module Bio.expressions.blast.ncbiblast
query_size Function in module Bio.Std
QueryAll Class in module Bio.DocSQL
QueryAllFirstItem Class in module Bio.DocSQL
QueryGeneric Class in module Bio.DocSQL
QueryKey Class in module Bio.EUtils.DTDs.ePost_020511
QueryKey Class in module Bio.EUtils.DTDs.eSearch_020511
QueryRow Class in module Bio.DocSQL
QuerySingle Class in module Bio.DocSQL
quote Variable in module Bio.expressions.genbank
quoted_chars Variable in module Bio.expressions.genbank
quoted_string Variable in module Bio.expressions.genbank
QuotedPhraseNotFound Class in module Bio.EUtils.DTDs.eSearch_020511
QuotedPhraseNotFound Class in module Bio.EUtils.Datatypes
quotestrip Function in module Bio.Nexus.Nexus
RA Variable in module Martel.test.testformats.swissprot38
RA_block Variable in module Bio.expressions.embl.embl65
RA_block Variable in module Martel.test.testformats.swissprot38
RAINBOW_COLORS Variable in module Bio.Graphics.DisplayRepresentation
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
RANGE Variable in module Martel.msre_constants
rao Variable in module Bio.SubsMat.MatrixInfo
RC Variable in module Martel.test.testformats.swissprot38
RC_block Variable in module Bio.expressions.embl.embl65
RC_block Variable in module Martel.test.testformats.swissprot38
rd Class in module Bio.Sequencing.Ace
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.NeuralNetwork.Gene.Pattern.PatternIO
read Method in class Bio.Nexus.Nexus.Nexus
read Method in class Bio.RecordFile.RecordFile
read Method in class Bio.ReseekFile.ReseekFile
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_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
reader_keywords Variable in module Bio.Blast.ParseBlastTable
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.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.SGMLExtractor.SGMLExtractorHandle
Reads Class in module Bio.Sequencing.Ace
ReadSeq Class in module Bio.SeqIO.generic
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 Variable in module Bio.Emboss.primer3_format
record Variable in module Bio.Emboss.primersearch_format
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 Class in package Bio.UniGene
record Variable in module Bio.expressions.blocks
record Variable in module Bio.expressions.embl.embl65
record Variable in module Bio.expressions.fasta
record Variable in module Bio.expressions.genbank
record Variable in module Bio.expressions.hmmpfam
record Variable in module Martel.test.testformats.swissprot38
record1 Variable in module Martel.test.test_swissprot38
record2 Variable in module Martel.test.test_swissprot38
record_end Variable in module Bio.expressions.genbank
record_end Variable in module Bio.expressions.hmmpfam
RecordEventStream Class in module Martel.Iterator
RecordFile Module in package Bio
RecordFile Class in module Bio.RecordFile
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 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
Ref_template Variable in module Bio.Medline.nlmmedline_001211_format
Ref_template Variable in module Bio.Medline.nlmmedline_010319_format
Ref_template Variable in module Bio.Medline.nlmmedline_011101_format
Ref_template Variable in module Bio.Medline.nlmmedline_031101_format
Reference Class in module Bio.Prosite.Prodoc
Reference Class in module Bio.SeqFeature
Reference Class in module Bio.SwissProt.SProt
reference Variable in module Bio.expressions.embl.embl65
reference Variable in module Bio.expressions.genbank
reference Variable in module Martel.test.testformats.swissprot38
reference_bases Variable in module Bio.expressions.genbank
reference_line Variable in module Bio.expressions.genbank
reference_num Variable in module Bio.expressions.genbank
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
remark_block Variable in module Bio.expressions.genbank
remove Method in class Bio.Crystal.Chain
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
REPEAT Variable in module Martel.msre_constants
REPEAT_CHARS Variable in module Martel.msre_parse
REPEAT_ONE Variable in module Martel.msre_constants
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
REQUIRED Variable in module Bio.EUtils.POM
res_name Variable in class Bio.FSSP.fssp_rec.align
ReseekFile Module in package Bio.EUtils
ReseekFile Class in module Bio.EUtils.ReseekFile
ReseekFile Module in package Bio
ReseekFile Class in module Bio.ReseekFile
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 Bio.UniGene.UniGeneParser
reset Method in class markupbase.ParserBase
reset Method in class sgmllib.SGMLParser
residue_dict Method in class Bio.NMR.xpktools.Peaklist
residue_prefixes Variable in module Bio.expressions.genbank
residue_type Variable in module Bio.expressions.genbank
residue_types Variable in module Bio.expressions.genbank
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
restart Method in class Bio.RecordFile.RecordFile
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_line Variable in module Bio.Emboss.primer3_format
reverse_name Method in class Martel.convert_re.GroupNames
reverse_primer_gc Variable in module Bio.Emboss.primer3_format
reverse_primer_length Variable in module Bio.Emboss.primer3_format
reverse_primer_seq Variable in module Bio.Emboss.primer3_format
reverse_primer_start Variable in module Bio.Emboss.primer3_format
reverse_primer_tm Variable in module Bio.Emboss.primer3_format
reverse_strand_info Variable in module Bio.Emboss.primersearch_format
rf_line Variable in module Bio.expressions.hmmpfam
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
risler Variable in module Bio.SubsMat.MatrixInfo
rjust Method in class __builtin__.str
RL Variable in module Martel.test.testformats.swissprot38
RL_block Variable in module Bio.expressions.embl.embl65
RL_block Variable in module Martel.test.testformats.swissprot38
RN Variable in module Martel.test.testformats.swissprot38
RN_line Variable in module Bio.expressions.embl.embl65
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 Class in module Bio.Blast.Record
QueryRow Class in module Bio.DocSQL
Rows Method in class Bio.Affy.CelFile.CelConsumer
RP Variable in module Martel.test.testformats.swissprot38
RP_line Variable in module Bio.expressions.embl.embl65
rsplit Method in class __builtin__.str
rstrip Method in class __builtin__.str
rt Class in module Bio.Sequencing.Ace
RT Variable in module Martel.test.testformats.swissprot38
RT_block Variable in module Bio.expressions.embl.embl65
RT_block Variable in module Martel.test.testformats.swissprot38
Rule Class in module Bio.EUtils.DTDs.LinkOut
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
RX Variable in module Martel.test.testformats.swissprot38
RX_block Variable in module Bio.expressions.embl.embl65
RX_line Variable in module Bio.expressions.embl.embl65
s Variable in module Martel.test.test_swissprot38
s1 Variable in module Martel.test.test_swissprot38
s1_info Variable in module Bio.expressions.blast.ncbiblast
s2 Variable in module Martel.test.test_swissprot38
s2_info Variable in module Bio.expressions.blast.ncbiblast
s3 Variable in module Martel.test.test_swissprot38
safe_exp Function in module Bio.mathfns
safe_int Function in module Bio.Decode
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
sample_dir Variable in module Martel.test.test_delimiter
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
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 Class in module Bio.EUtils.DTDs.eLink_020511
score Variable in module Bio.expressions.blast.ncbiblast
score_hit Method in class Bio.AlignAce.Motif.Motif
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 Variable in module Bio.formatdefs.search
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
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 Bio.ReseekFile.ReseekFile
seek Method in class Martel.msre_parse.Tokenizer
segment Variable in module Bio.expressions.blocks
segment Variable in module Bio.expressions.genbank
segment_block Variable in module Bio.expressions.blocks
segment_line Variable in module Bio.expressions.genbank
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
seq_indent Variable in module Bio.Emboss.primersearch_format
seqdb Variable in module Bio.config.SeqDBRegistry
SeqDBRegistry Module in package Bio.config
SeqDBRegistry Class in module Bio.config.SeqDBRegistry
SeqFeature Module in package Bio
SeqFeature Class in module Bio.SeqFeature
SeqIO Package in package Bio
seqline Variable in module Bio.expressions.fasta
seqline_nonewline Variable in module Bio.expressions.fasta
SeqMat Class in package Bio.SubsMat
SeqRecord Class in module Bio.SeqIO.generic
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 Variable in module Bio.Emboss.primer3_format
sequence Method in class Bio.FSSP.FSSPAlignDict
sequence Function in module Bio.Std
sequence Module in package Bio.builders.SeqRecord
sequence Variable in module Bio.expressions.fasta
sequence Variable in module Bio.expressions.genbank
sequence Module in package Bio.formatdefs
sequence Variable in module Bio.formatdefs.sequence
sequence Variable in module Martel.test.testformats.swissprot38
sequence_block Function in module Bio.Std
sequence_descr Variable in module Bio.Emboss.primersearch_format
sequence_entry Variable in module Bio.expressions.genbank
sequence_id Variable in module Bio.Emboss.primersearch_format
sequence_info Variable in module Bio.Emboss.primersearch_format
sequence_info Variable in module Bio.expressions.hmmpfam
sequence_line Variable in module Bio.expressions.genbank
SEQUENCE_LINE Variable in module Bio.expressions.transfac
sequence_plus_spaces Variable in module Bio.expressions.genbank
SEQUENCE_TYPE Variable in module Bio.EUtils.Config
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
SEQUENCES_LENGTH_LINE Variable in module Bio.expressions.transfac
Sequencing Package in package Bio
sequtils Module 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_prop Variable in module Bio.Encodings.IUPACEncoding
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
setdefault Method in class Bio.Crystal.Crystal
setdefault Method in class __builtin__.dict
setDocumentLocator Method in class Bio.EUtils.POM.ObjectParserHandler
SetGroupValue Class in module Martel.Generate
setliteral Method in class sgmllib.SGMLParser
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
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_comment Variable in module Martel.test.testformats.swissprot38
single_letter_alphabet Variable in package Bio.Alphabet
single_primer_line Variable in module Bio.Emboss.primer3_format
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
SITE_FREQUENCY_LINE Variable in module Bio.expressions.transfac
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
size Variable in module Bio.expressions.genbank
SIZEHINT Variable in module Martel.RecordReader
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
small_indent_space Variable in module Bio.expressions.genbank
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.Pathway.Network
source_block Variable in module Bio.expressions.genbank
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
sp_sample Variable in module Martel.test.test_RecordReader
space Variable in module Bio.Medline.nlmmedline_001211_format
space Variable in module Bio.Medline.nlmmedline_010319_format
space Variable in module Bio.Medline.nlmmedline_011101_format
space Variable in module Bio.Medline.nlmmedline_031101_format
spaceformat Variable in module Martel.test.testformats.delimiter
Spaces Function in package Martel
spaces_line Variable in module Bio.expressions.blast.ncbiblast
spaces_line Variable in module Bio.expressions.blast.wublast
span Method in class Bio.Prosite.Pattern.PrositeMatch
spark Module in package Bio.Parsers
SPECIAL_CHARS Variable in module Martel.msre_parse
SPECIAL_COMMANDS Variable in module Bio.Nexus.Nexus
SPECIALCOMMENTS Variable in module Bio.Nexus.Nexus
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
sprot38 Variable in module Bio.formatdefs.swissprot
sprot40 Variable in module Bio.formatdefs.swissprot
sprot_search_de Function in module Bio.WWW.ExPASy
sprot_search_ful Function in module Bio.WWW.ExPASy
SQ Variable in module Martel.test.testformats.swissprot38
SQ_block Variable in module Bio.expressions.embl.embl65
SQ_data Variable in module Bio.expressions.embl.embl65
SQ_data Variable in module Martel.test.testformats.swissprot38
SQ_line Variable in module Bio.expressions.embl.embl65
SS Function in module Bio.expressions.transfac
ss1 Variable in class Bio.FSSP.fssp_rec.align
Stabilizing Module in package Bio.GA.Repair
standard_dna_table Variable in module Bio.Data.CodonTable
standard_rna_table Variable in module Bio.Data.CodonTable
StandardError Class in module exceptions
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_a Method in class Bio.UniGene.UniGeneParser
start_aa_list Variable in class Bio.FSSP.fssp_rec.align
start_alphabet Method in class Bio.StdHandler.Handle_sequence
start_b Method in class Bio.UniGene.UniGeneParser
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_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_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_h1 Method in class Bio.Ndb.NdbParser
start_h2 Method in class Bio.InterPro.InterProParser
start_h2 Method in class Bio.Ndb.NdbParser
start_hit Method in class Bio.builders.Search.search.BuildSearch
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_li Method in class Bio.InterPro.InterProParser
start_li Method in class Bio.Ndb.NdbParser
start_ol Method in class Bio.InterPro.InterProParser
start_primer Variable in module Bio.Emboss.primer3_format
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.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_table Method in class Bio.UniGene.UniGeneParser
start_td Method in class Bio.InterPro.InterProParser
start_td Method in class Bio.UniGene.UniGeneParser
start_tr Method in class Bio.UniGene.UniGeneParser
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
startElement Method in class Bio.EUtils.POM.ObjectParserHandler
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
StartIntensity Method in class Bio.Affy.CelFile.CelConsumer
starts_with Function in module Bio.stringfns
StartsWith Class in module Martel.RecordReader
startswith Method in class __builtin__.str
Statistics Package in package Bio
Statistics Class in module Bio.Wise.dnal
statistics Variable in module Bio.expressions.blast.wublast
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 Variable in module Bio.expressions.blast.ncbiblast
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
structure Variable in module Bio.SubsMat.MatrixInfo
subcomponent_size Method in class Bio.Graphics.BasicChromosome.Chromosome
subject_line Variable in module Bio.expressions.blast.ncbiblast
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 Variable in module Martel.msre_constants
SubPattern Class in module Martel.msre_parse
SubProvider Class in module Bio.EUtils.DTDs.LinkOut
subs Class in module Bio.EUtils.DTDs.LinkOut
SUBS Variable in package Bio.SubsMat
SubsMat Package in package Bio
SUCCESS Variable in module Martel.msre_constants
suffix Variable in class Bio.DocSQL.Query
suffix Variable in class Bio.DocSQL.Query
suffix Variable in class Bio.DocSQL.Query
suffix Variable in class Bio.DocSQL.Query
suffix Variable in class Bio.DocSQL.Query
suffix Variable in class Bio.DocSQL.Query
suffix Variable in class Bio.DocSQL.Query
suffix Variable in class Bio.DocSQL.Query
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
summary_rec Variable in package Bio.FSSP
summary_title Variable in package Bio.FSSP
summary_type_parser_table Variable in module Bio.EUtils.parse
SummaryInfo Class in module Bio.Align.AlignInfo
superdir Function in module Martel.Dispatch
support Module in package Martel.test
supports_lookahead Variable in module Martel.Generate
SV_line Variable in module Bio.expressions.embl.embl65
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 Variable in module Bio.dbdefs.swissprot
swissprot Module in package Bio.formatdefs
swissprot Variable in module Bio.formatdefs.swissprot
swissprot38 Module in package Martel.test.testformats
swissprot_expasy_cgi Variable in module Bio.dbdefs.swissprot
swissprot_usmirror_cgi Variable in module Bio.dbdefs.swissprot
symbol_forward Variable in module Bio.expressions.hmmpfam
symbol_reverse Variable in module Bio.expressions.hmmpfam
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_info Variable in module Bio.expressions.blast.ncbiblast
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
tabformat Variable in module Martel.test.testformats.delimiter
table Variable in module Bio.expressions.blast.ncbiblast
table_entry Variable in module Bio.expressions.blast.ncbiblast
table_entry Variable in module Bio.expressions.blast.wublast
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 Variable in module Bio.expressions.genbank
TAXSET Variable in module Bio.Nexus.Nexus
tblastn Variable in module Bio.expressions.blast.ncbiblast
tblastn Variable in module Bio.expressions.blast.wublast
tblastn Variable in module Bio.formatdefs.search
tblastn_appheader Variable in module Bio.expressions.blast.ncbiblast
tblastn_appheader Variable in module Bio.expressions.blast.wublast
tblastn_ending Variable in module Bio.expressions.blast.ncbiblast
tblastn_hsp_header Variable in module Bio.expressions.blast.ncbiblast
tblastn_hsp_header Variable in module Bio.expressions.blast.wublast
tblastn_identities Variable in module Bio.expressions.blast.wublast
tblastn_score Variable in module Bio.expressions.blast.ncbiblast
tblastn_score Variable in module Bio.expressions.blast.wublast
tblastn_strand Variable in module Bio.expressions.blast.wublast
tblastx Variable in module Bio.expressions.blast.ncbiblast
tblastx Variable in module Bio.formatdefs.search
tblastx_appheader Variable in module Bio.expressions.blast.ncbiblast
tblastx_appheader Variable in module Bio.expressions.blast.wublast
tblastx_ending Variable in module Bio.expressions.blast.ncbiblast
tblastx_frame Variable in module Bio.expressions.blast.ncbiblast
tblastx_hsp_header Variable in module Bio.expressions.blast.ncbiblast
tell Method in class Bio.EUtils.ReseekFile.ReseekFile
tell Method in class Bio.File.UndoHandle
tell Method in class Bio.ReseekFile.ReseekFile
tell Method in class Martel.msre_parse.Tokenizer
TelomereSegment Class in module Bio.Graphics.BasicChromosome
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
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 Function in module Bio.ReseekFile
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_list Variable in module Martel.test.test_swissprot38
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_reads Function in module Bio.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 Variable in module Martel.test.test_Iterator
text Variable in module Martel.test.test_ParseRecords
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
Time Module in package Martel
time_file Function in module Martel.test.support
timestamp Variable in module Bio.expressions.blast.wublast
timetuple Method in class Bio.EUtils.Datatypes.Date
title Variable in module Bio.expressions.fasta
title Method in class __builtin__.str
title_block Variable in module Bio.expressions.genbank
TITLE_LINE Variable in module Bio.expressions.transfac
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
to_table Variable in module Bio.expressions.blast.ncbiblast
to_table Variable in module Bio.expressions.blast.wublast
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
TOOL Variable in module Bio.EUtils.ThinClient
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
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 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 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
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
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
unambiguous_dna Variable in module Bio.Alphabet.IUPAC
unambiguous_dna_by_id Variable in module Bio.Data.CodonTable
unambiguous_dna_by_id Variable in module Bio.Translate
unambiguous_dna_by_name Variable in module Bio.Data.CodonTable
unambiguous_dna_by_name Variable in module Bio.Translate
unambiguous_dna_letters Variable in module Bio.Data.IUPACData
unambiguous_dna_weight_ranges Variable in module Bio.Data.IUPACData
unambiguous_dna_weights Variable in module Bio.Data.IUPACData
unambiguous_rna Variable in module Bio.Alphabet.IUPAC
unambiguous_rna_by_id Variable in module Bio.Data.CodonTable
unambiguous_rna_by_id Variable in module Bio.Translate
unambiguous_rna_by_name Variable in module Bio.Data.CodonTable
unambiguous_rna_by_name Variable in module Bio.Translate
unambiguous_rna_letters Variable in module Bio.Data.IUPACData
unambiguous_rna_weight_ranges Variable in module Bio.Data.IUPACData
unambiguous_rna_weights Variable in module Bio.Data.IUPACData
unambiguous_transcriber Variable in module Bio.Transcribe
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
ungapped_lambda_stats Variable in module Bio.expressions.blast.ncbiblast
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
UniGeneParser Class in package Bio.UniGene
union Method in class Bio.Pathway.Rep.HashSet.HashSet
unknown-46912546788728 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
unquoted_string Variable in module Bio.expressions.genbank
Until Class in module Martel.RecordReader
UntilEol Function in package Martel
UntilSep Function in package Martel
Update Class in module Bio.DocSQL
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_divisions Variable in module Bio.expressions.genbank
VALID_FORMATS Variable in class Bio.Graphics.BasicChromosome.Organism
valid_residue_prefixes Variable in module Bio.expressions.genbank
valid_residue_types Variable in module Bio.expressions.genbank
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.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
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 Variable in module Bio.expressions.genbank
version_line Variable in module Bio.expressions.genbank
VERY_SMALL_NUMBER Variable in module Bio.MarkovModel
viterbi Method in class Bio.HMM.MarkovModel.HiddenMarkovModel
wa Class in module Bio.Sequencing.Ace
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
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
WHITESPACE Variable in module Bio.Nexus.Nexus
whitespace Variable in module Bio.expressions.embl.embl65
WHITESPACE Variable in module Martel.msre_parse
Widget Class in module reportlab.graphics.widgetbase
Wise Package in package Bio
WithinNDays Class in module Bio.EUtils.Datatypes
WithinPosition Class in module Bio.SeqFeature
Word Function in package Martel
wr Class in module Bio.Sequencing.Ace
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.SeqIO.FASTA.FastaWriter
write Method in class Bio.SeqIO.generic.EMBLFormat
write Method in class Bio.SeqIO.generic.FastaFormat
write Method in class Bio.SeqIO.generic.GCGFormat
write Method in class Bio.SeqIO.generic.GenericFormat
write Method in class Bio.SeqIO.generic.LargeFastaFormat
write Method in class Bio.SeqIO.generic.PirFormat
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_records Method in class Bio.SeqIO.FASTA.FastaWriter
write_records Method in class Bio.SeqIO.generic.GenericFormat
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
wu_blastn Variable in module Bio.formatdefs.search
wu_blastp Variable in module Bio.formatdefs.search
wu_blastx Variable in module Bio.formatdefs.search
wublast Module in package Bio.expressions.blast
wublast_version Variable in module Bio.expressions.blast.wublast
WWW Package in package Bio
x1_info Variable in module Bio.expressions.blast.ncbiblast
x2_info Variable in module Bio.expressions.blast.ncbiblast
x3_info Variable in module Bio.expressions.blast.ncbiblast
xml_version Variable in module Bio.Medline.nlmmedline_031101_format
XMLAttribute Class in module Bio.EUtils.POM
XMLNS Variable in module Bio.Std
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
XX Variable in module Bio.expressions.embl.embl65
zfill Method in class __builtin__.str

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