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<h1 class="epydoc">Source Code for <a href="Bio.config.FormatRegistry-module.html">Module Bio.config.FormatRegistry</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno">  1</tt>  <tt class="py-line"><tt class="py-comment"># Copyright 2002 by Jeffrey Chang, Andrew Dalke.  All rights reserved.</tt> </tt>
<a name="L2"></a><tt class="py-lineno">  2</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># This code is part of the Biopython distribution and governed by its</tt> </tt>
<a name="L3"></a><tt class="py-lineno">  3</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># license.  Please see the LICENSE file that should have been included</tt> </tt>
<a name="L4"></a><tt class="py-lineno">  4</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># as part of this package.</tt> </tt>
<a name="L5"></a><tt class="py-lineno">  5</tt>  <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L6"></a><tt class="py-lineno">  6</tt>  <tt class="py-line"><tt class="py-comment"># This is based on some older code by Andrew Dalke.</tt> </tt>
<a name="L7"></a><tt class="py-lineno">  7</tt>  <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L8"></a><tt class="py-lineno">  8</tt>  <tt class="py-line"><tt class="py-docstring">"""Implements a Registry to store Martel-type format expressions.</tt> </tt>
<a name="L9"></a><tt class="py-lineno">  9</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt>  <tt class="py-line"><tt class="py-docstring">Classes:</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt>  <tt class="py-line"><tt class="py-docstring">FormatRegistry   Holds Biopython formats in a dictionary-like interface.</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt>  <tt class="py-line"><tt class="py-docstring">FormatObject     Describes a Biopython file format.</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt>  <tt class="py-line"><tt class="py-docstring">FormatGroup      Describes a group of Biopython file formats.</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt>  <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt>  <tt class="py-line"><tt class="py-comment"># Private Functions:</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># _parses_file     Return whether an expression can parse a file.</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># _parses_string   Return whether an expression can parse a string.</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># _normalize_expression   Turn an expression or path into an expression.</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># _load_first_existing    Return the first format that loads successfully.</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># _load_expression        Load a Martel expression.</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># _load_object            Load a Python object.</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt>  <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-0', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-1" class="py-name" targets="Package Bio.config=Bio.config-module.html"><a title="Bio.config" class="py-name" href="#" onclick="return doclink('link-1', 'config', 'link-1');">config</a></tt><tt class="py-op">.</tt><tt id="link-2" class="py-name" targets="Module Bio.config.Registry=Bio.config.Registry-module.html,Class Bio.config.Registry.Registry=Bio.config.Registry.Registry-class.html"><a title="Bio.config.Registry
Bio.config.Registry.Registry" class="py-name" href="#" onclick="return doclink('link-2', 'Registry', 'link-2');">Registry</a></tt> <tt class="py-keyword">import</tt> <tt class="py-op">*</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt>  <tt class="py-line"> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-3" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-3', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-4" class="py-name"><a title="Bio.config" class="py-name" href="#" onclick="return doclink('link-4', 'config', 'link-1');">config</a></tt> <tt class="py-keyword">import</tt> <tt id="link-5" class="py-name" targets="Module Bio.config._support=Bio.config._support-module.html,Module Bio.dbdefs._support=Bio.dbdefs._support-module.html"><a title="Bio.config._support
Bio.dbdefs._support" class="py-name" href="#" onclick="return doclink('link-5', '_support', 'link-5');">_support</a></tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt>  <tt class="py-line"> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt>  <tt class="py-line"> </tt>
<a name="FormatRegistry"></a><div id="FormatRegistry-def"><a name="L29"></a><tt class="py-lineno"> 29</tt> <a class="py-toggle" href="#" id="FormatRegistry-toggle" onclick="return toggle('FormatRegistry');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.config.FormatRegistry.FormatRegistry-class.html">FormatRegistry</a><tt class="py-op">(</tt><tt class="py-base-class">Registry</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FormatRegistry-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="FormatRegistry-expanded"><a name="L30"></a><tt class="py-lineno"> 30</tt>  <tt class="py-line">    <tt class="py-docstring">"""This implements a dictionary-like interface to Biopython file</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt>  <tt class="py-line"><tt class="py-docstring">    formats.</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt>  <tt class="py-line"><tt class="py-docstring">    Methods:</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt>  <tt class="py-line"><tt class="py-docstring">    find_builder  Find a builder that converts from a format to an object.</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt>  <tt class="py-line"><tt class="py-docstring">    find_writer   Find a writer that can write an object to a format.</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="FormatRegistry.__init__"></a><div id="FormatRegistry.__init__-def"><a name="L38"></a><tt class="py-lineno"> 38</tt> <a class="py-toggle" href="#" id="FormatRegistry.__init__-toggle" onclick="return toggle('FormatRegistry.__init__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.config.FormatRegistry.FormatRegistry-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">name</tt><tt class="py-op">,</tt> <tt class="py-param">load_path</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt>  <tt class="py-line">                 <tt class="py-param">builder_path</tt><tt class="py-op">=</tt><tt class="py-string">"Bio.builders"</tt><tt class="py-op">,</tt> <tt class="py-param">writer_path</tt><tt class="py-op">=</tt><tt class="py-string">"Bio.writers"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FormatRegistry.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="FormatRegistry.__init__-expanded"><a name="L40"></a><tt class="py-lineno"> 40</tt>  <tt class="py-line">        <tt id="link-6" class="py-name"><a title="Bio.config.Registry
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Bio.EUtils.Datatypes.Problem.__init__
Bio.EUtils.Datatypes.Provider.__init__
Bio.EUtils.Datatypes.Range.__init__
Bio.EUtils.Datatypes.SearchResult.__init__
Bio.EUtils.Datatypes.Summary.__init__
Bio.EUtils.Datatypes.Term.__init__
Bio.EUtils.Datatypes.WithinNDays.__init__
Bio.EUtils.HistoryClient.BaseHistoryRecordSet.__init__
Bio.EUtils.HistoryClient.HistoryClient.__init__
Bio.EUtils.HistoryClient.HistoryCookie.__init__
Bio.EUtils.HistoryClient.HistoryLookup.__init__
Bio.EUtils.HistoryClient.HistoryRecord.__init__
Bio.EUtils.MultiDict.OrderedMultiDict.__init__
Bio.EUtils.MultiDict.UnorderedMultiDict.__init__
Bio.EUtils.POM.Comment.__init__
Bio.EUtils.POM.ContentModel.__init__
Bio.EUtils.POM.DTDConsumerForSourceGeneration.__init__
Bio.EUtils.POM.ElementNode.__init__
Bio.EUtils.POM.IndentedText.__init__
Bio.EUtils.POM.ObjectParserHandler.__init__
Bio.EUtils.POM.POMDocument.__init__
Bio.EUtils.POM.XMLAttribute.__init__
Bio.EUtils.POM._ContentModelGenerator.__init__
Bio.EUtils.ReseekFile.ReseekFile.__init__
Bio.EUtils.ThinClient.ThinClient.__init__
Bio.EUtils.parse.UsePOMParser.__init__
Bio.EUtils.sourcegen.ClassHolder.__init__
Bio.EUtils.sourcegen.FunctionHolder.__init__
Bio.EUtils.sourcegen.MethodHolder.__init__
Bio.EUtils.sourcegen.SourceFile.__init__
Bio.EUtils.sourcegen.SourceGen.__init__
Bio.Emboss.Applications.EConsenseCommandline.__init__
Bio.Emboss.Applications.EInvertedCommandline.__init__
Bio.Emboss.Applications.ENeighborCommandline.__init__
Bio.Emboss.Applications.EProtDistCommandline.__init__
Bio.Emboss.Applications.EProtParsCommandline.__init__
Bio.Emboss.Applications.ESeqBootCommandline.__init__
Bio.Emboss.Applications.ETandemCommandline.__init__
Bio.Emboss.Applications.Est2GenomeCommandline.__init__
Bio.Emboss.Applications.FuzznucCommandline.__init__
Bio.Emboss.Applications.PalindromeCommandline.__init__
Bio.Emboss.Applications.Primer3Commandline.__init__
Bio.Emboss.Applications.PrimerSearchCommandline.__init__
Bio.Emboss.Applications.TranalignCommandline.__init__
Bio.Emboss.Applications.WaterCommandline.__init__
Bio.Emboss.Primer.Primer3Parser.__init__
Bio.Emboss.Primer.Primer3Primers.__init__
Bio.Emboss.Primer.Primer3Record.__init__
Bio.Emboss.Primer.PrimerSearchAmplifier.__init__
Bio.Emboss.Primer.PrimerSearchInputRecord.__init__
Bio.Emboss.Primer.PrimerSearchOutputRecord.__init__
Bio.Emboss.Primer.PrimerSearchParser.__init__
Bio.Emboss.Primer._Primer3RecordConsumer.__init__
Bio.Emboss.Primer._Primer3Scanner.__init__
Bio.Emboss.Primer._PrimerSearchRecordConsumer.__init__
Bio.Emboss.Primer._PrimerSearchScanner.__init__
Bio.Entrez.Parser.DataHandler.__init__
Bio.Entrez.Parser.StructureElement.__init__
Bio.Enzyme.DataRecord.__init__
Bio.Enzyme.EnzymeRecord.__init__
Bio.Enzyme.Iterator.__init__
Bio.Enzyme.RecordParser.__init__
Bio.Enzyme._RecordConsumer.__init__
Bio.FSSP.FSSPAlignDict.__init__
Bio.FSSP.FSSPAlignRec.__init__
Bio.FSSP.FSSPHeader.__init__
Bio.FSSP.FSSPSumRec.__init__
Bio.FSSP.FSSPTools.FSSPMultAlign.__init__
Bio.FSSP.PosAlign.__init__
Bio.FSSP.fssp_rec.fff_rec.__init__
Bio.Fasta.FastaAlign.FastaAlignment.__init__
Bio.Fasta.Iterator.__init__
Bio.Fasta.Record.__init__
Bio.Fasta.RecordParser.__init__
Bio.Fasta.SequenceParser.__init__
Bio.File.SGMLHandle.__init__
Bio.File.SGMLStripper.MyParser.__init__
Bio.File.SGMLStripper.__init__
Bio.File.UndoHandle.__init__
Bio.FilteredReader.FilteredReader.__init__
Bio.GA.Crossover.General.SafeFitnessCrossover.__init__
Bio.GA.Crossover.GeneralPoint.GeneralPointCrossover.__init__
Bio.GA.Crossover.GeneralPoint.InterleaveCrossover.__init__
Bio.GA.Crossover.Point.SinglePointCrossover.__init__
Bio.GA.Crossover.TwoPoint.TwoPointCrossover.__init__
Bio.GA.Crossover.Uniform.UniformCrossover.__init__
Bio.GA.Evolver.GenerationEvolver.__init__
Bio.GA.Evolver.SteadyStateEvolver.__init__
Bio.GA.Mutation.General.SafeFitnessMutation.__init__
Bio.GA.Mutation.Simple.ConversionMutation.__init__
Bio.GA.Mutation.Simple.SinglePositionMutation.__init__
Bio.GA.Organism.Organism.__init__
Bio.GA.Repair.Stabilizing.AmbiguousRepair.__init__
Bio.GA.Selection.Abstract.AbstractSelection.__init__
Bio.GA.Selection.Diversity.DiversitySelection.__init__
Bio.GA.Selection.RouletteWheel.RouletteWheelSelection.__init__
Bio.GA.Selection.Tournament.TournamentSelection.__init__
Bio.GFF.Connection.__init__
Bio.GFF.Feature.__init__
Bio.GFF.FeatureAggregate.__init__
Bio.GFF.FeatureQuery.__init__
Bio.GFF.FeatureQueryRow.__init__
Bio.GFF.GenericTools.ArgsParser.__init__
Bio.GFF.GenericTools.Surrogate.__init__
Bio.GFF.GenericTools.TempFile.__init__
Bio.GFF.RetrieveSeqname.__init__
Bio.GFF.Segment.__init__
Bio.GFF.easy.FeatureDict.__init__
Bio.GFF.easy.Location.__init__
Bio.GFF.easy.LocationFromCoords.__init__
Bio.GFF.easy.LocationFromString.__init__
Bio.GFF.easy.LocationJoin.__init__
Bio.GenBank.FeatureParser.__init__
Bio.GenBank.Iterator.__init__
Bio.GenBank.LocationParser.AbsoluteLocation.__init__
Bio.GenBank.LocationParser.Between.__init__
Bio.GenBank.LocationParser.FeatureName.__init__
Bio.GenBank.LocationParser.Function.__init__
Bio.GenBank.LocationParser.HighBound.__init__
Bio.GenBank.LocationParser.Integer.__init__
Bio.GenBank.LocationParser.LocationParser.__init__
Bio.GenBank.LocationParser.LocationScanner.__init__
Bio.GenBank.LocationParser.LowBound.__init__
Bio.GenBank.LocationParser.Path.__init__
Bio.GenBank.LocationParser.Range.__init__
Bio.GenBank.LocationParser.Symbol.__init__
Bio.GenBank.LocationParser.Token.__init__
Bio.GenBank.LocationParser.TwoBound.__init__
Bio.GenBank.NCBIDictionary.__init__
Bio.GenBank.Record.Feature.__init__
Bio.GenBank.Record.Qualifier.__init__
Bio.GenBank.Record.Record.__init__
Bio.GenBank.Record.Reference.__init__
Bio.GenBank.RecordParser.__init__
Bio.GenBank.Scanner.InsdcScanner.__init__
Bio.GenBank._BaseGenBankConsumer.__init__
Bio.GenBank._FeatureConsumer.__init__
Bio.GenBank._RecordConsumer.__init__
Bio.GenBank.utils.FeatureValueCleaner.__init__
Bio.Geo.Record.Record.__init__
Bio.Gobase.Dictionary.__init__
Bio.Gobase.GeneRecord.__init__
Bio.Gobase.Iterator.__init__
Bio.Gobase.ProteinRecord.__init__
Bio.Gobase.Record.__init__
Bio.Gobase.RecordParser.__init__
Bio.Gobase.SequenceRecord.__init__
Bio.Gobase._RecordConsumer.__init__
Bio.Graphics.BasicChromosome.Chromosome.__init__
Bio.Graphics.BasicChromosome.ChromosomeSegment.__init__
Bio.Graphics.BasicChromosome.Organism.__init__
Bio.Graphics.BasicChromosome.TelomereSegment.__init__
Bio.Graphics.BasicChromosome._ChromosomeComponent.__init__
Bio.Graphics.Comparative.ComparativeScatterPlot.__init__
Bio.Graphics.DisplayRepresentation.ChromosomeCounts.__init__
Bio.Graphics.Distribution.BarChartDistribution.__init__
Bio.Graphics.Distribution.DistributionPage.__init__
Bio.Graphics.Distribution.LineDistribution.__init__
Bio.HMM.DynamicProgramming.AbstractDPAlgorithms.__init__
Bio.HMM.DynamicProgramming.LogDPAlgorithms.__init__
Bio.HMM.DynamicProgramming.ScaledDPAlgorithms.__init__
Bio.HMM.MarkovModel.HiddenMarkovModel.__init__
Bio.HMM.MarkovModel.MarkovModelBuilder.__init__
Bio.HMM.Trainer.AbstractTrainer.__init__
Bio.HMM.Trainer.BaumWelchTrainer.__init__
Bio.HMM.Trainer.KnownStateTrainer.__init__
Bio.HMM.Trainer.TrainingSequence.__init__
Bio.HotRand.HotCache.__init__
Bio.HotRand.HotRandom.__init__
Bio.Index._InMemoryIndex.__init__
Bio.Index._ShelveIndex.__init__
Bio.IntelliGenetics.IntelliGeneticsReader.__init__
Bio.IntelliGenetics.Iterator.__init__
Bio.IntelliGenetics.Record.Record.__init__
Bio.IntelliGenetics.RecordParser.__init__
Bio.IntelliGenetics._RecordConsumer.__init__
Bio.IntelliGenetics._Scanner.__init__
Bio.KDTree.CKDTree.KDTree.__init__
Bio.KDTree.CKDTree.KDTreePtr.__init__
Bio.KDTree.KDTree.KDTree.__init__
Bio.KEGG.Compound.Record.__init__
Bio.KEGG.Enzyme.Record.__init__
Bio.LocusLink.Iterator.__init__
Bio.LocusLink.Record.__init__
Bio.LocusLink.RecordParser.__init__
Bio.LocusLink._RecordConsumer.__init__
Bio.LocusLink._Scanner.__init__
Bio.LocusLink.web_parse.Record.__init__
Bio.LocusLink.web_parse.Token.__init__
Bio.LocusLink.web_parse.Url.__init__
Bio.LogisticRegression.LogisticRegression.__init__
Bio.MEME.Motif.Instance.__init__
Bio.MEME.Motif.MEMEMotif.__init__
Bio.MEME.Motif.Motif.__init__
Bio.MEME.Parser.MASTParser.__init__
Bio.MEME.Parser.MASTRecord.__init__
Bio.MEME.Parser.MEMEParser.__init__
Bio.MEME.Parser.MEMERecord.__init__
Bio.MEME.Parser._MASTConsumer.__init__
Bio.MEME.Parser._MEMEConsumer.__init__
Bio.MarkovModel.MarkovModel.__init__
Bio.MaxEntropy.MaxEntropy.__init__
Bio.Medline.Iterator.__init__
Bio.Medline.Record.__init__
Bio.Medline.RecordParser.__init__
Bio.Medline._RecordConsumer.__init__
Bio.MetaTool.Iterator.__init__
Bio.MetaTool.Record.Metabolite.__init__
Bio.MetaTool.Record.MetaboliteRole.__init__
Bio.MetaTool.Record.PathwayTransform.__init__
Bio.MetaTool.Record.Record.__init__
Bio.MetaTool.RecordParser.__init__
Bio.MetaTool._RecordConsumer.__init__
Bio.MetaTool._Scanner.__init__
Bio.Mindy.BaseDB.OpenDB.__init__
Bio.Mindy.BerkeleyDB.BerkeleyDB.__init__
Bio.Mindy.BerkeleyDB.PrimaryNamespace.__init__
Bio.Mindy.BerkeleyDB.SecondaryNamespace.__init__
Bio.Mindy.FlatDB.BaseFlatDB.__init__
Bio.Mindy.FlatDB.BisectFile.__init__
Bio.Mindy.FlatDB.DiskFlatDB.__init__
Bio.Mindy.FlatDB.MemoryFlatDB.__init__
Bio.Mindy.FlatDB.PrimaryNamespace.__init__
Bio.Mindy.FlatDB.PrimaryTable.__init__
Bio.Mindy.FlatDB.SecondaryNamespace.__init__
Bio.Mindy.FlatDB.SecondaryTable.__init__
Bio.Mindy.Location.Location.__init__
Bio.Mindy.SimpleSeqRecord.BaseSeqRecordIndexer.__init__
Bio.Mindy.SimpleSeqRecord.FixDocumentBuilder.__init__
Bio.Mindy.SimpleSeqRecord.FunctionIndexer.__init__
Bio.Mindy.SimpleSeqRecord.SimpleIndexer.__init__
Bio.Mindy.XPath.GrabXPathNodes.__init__
Bio.NBRF.Iterator.__init__
Bio.NBRF.Record.Record.__init__
Bio.NBRF.RecordParser.__init__
Bio.NBRF._RecordConsumer.__init__
Bio.NBRF._Scanner.__init__
Bio.NMR.xpktools.Peaklist.__init__
Bio.NMR.xpktools.XpkEntry.__init__
Bio.NaiveBayes.NaiveBayes.__init__
Bio.Ndb.Record.__init__
Bio.NetCatch.ExtractUrls.__init__
Bio.NetCatch.NetCatch.__init__
Bio.NetCatch.Url.__init__
Bio.NeuralNetwork.BackPropagation.Layer.AbstractLayer.__init__
Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer.__init__
Bio.NeuralNetwork.BackPropagation.Layer.InputLayer.__init__
Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer.__init__
Bio.NeuralNetwork.BackPropagation.Network.BasicNetwork.__init__
Bio.NeuralNetwork.Gene.Motif.MotifCoder.__init__
Bio.NeuralNetwork.Gene.Motif.MotifFinder.__init__
Bio.NeuralNetwork.Gene.Pattern.PatternIO.__init__
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.__init__
Bio.NeuralNetwork.Gene.Schema.DifferentialSchemaFitness.__init__
Bio.NeuralNetwork.Gene.Schema.GeneticAlgorithmFinder.__init__
Bio.NeuralNetwork.Gene.Schema.MostCountSchemaFitness.__init__
Bio.NeuralNetwork.Gene.Schema.RandomMotifGenerator.__init__
Bio.NeuralNetwork.Gene.Schema.Schema.__init__
Bio.NeuralNetwork.Gene.Schema.SchemaCoder.__init__
Bio.NeuralNetwork.Gene.Schema.SchemaFactory.__init__
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.__init__
Bio.NeuralNetwork.Gene.Schema.SimpleFinisher.__init__
Bio.NeuralNetwork.Gene.Signature.SignatureCoder.__init__
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.__init__
Bio.NeuralNetwork.StopTraining.ValidationIncreaseStop.__init__
Bio.NeuralNetwork.Training.ExampleManager.__init__
Bio.NeuralNetwork.Training.TrainingExample.__init__
Bio.Nexus.Nexus.Block.__init__
Bio.Nexus.Nexus.CharBuffer.__init__
Bio.Nexus.Nexus.Commandline.__init__
Bio.Nexus.Nexus.Nexus.__init__
Bio.Nexus.Nexus.StepMatrix.__init__
Bio.Nexus.Nodes.Chain.__init__
Bio.Nexus.Nodes.Node.__init__
Bio.Nexus.Trees.NodeData.__init__
Bio.Nexus.Trees.Tree.__init__
Bio.PDB.AbstractPropertyMap.AbstractAtomPropertyMap.__init__
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.__init__
Bio.PDB.AbstractPropertyMap.AbstractResiduePropertyMap.__init__
Bio.PDB.Atom.Atom.__init__
Bio.PDB.Atom.DisorderedAtom.__init__
Bio.PDB.Chain.Chain.__init__
Bio.PDB.DSSP'.DSSP.__init__
Bio.PDB.Dice.ChainSelector.__init__
Bio.PDB.Entity.DisorderedEntityWrapper.__init__
Bio.PDB.Entity.Entity.__init__
Bio.PDB.FragmentMapper'.Fragment.__init__
Bio.PDB.FragmentMapper'.FragmentMapper.__init__
Bio.PDB.HSExposure.ExposureCN.__init__
Bio.PDB.HSExposure.HSExposureCA.__init__
Bio.PDB.HSExposure.HSExposureCB.__init__
Bio.PDB.HSExposure._AbstractHSExposure.__init__
Bio.PDB.MMCIF2Dict.MMCIF2Dict.__init__
Bio.PDB.Model.Model.__init__
Bio.PDB.NACCESS.NACCESS.__init__
Bio.PDB.NACCESS.NACCESS_atomic.__init__
Bio.PDB.NeighborSearch.NeighborSearch.__init__
Bio.PDB.PDBIO'.PDBIO.__init__
Bio.PDB.PDBList'.PDBList.__init__
Bio.PDB.PDBParser'.PDBParser.__init__
Bio.PDB.PSEA.PSEA.__init__
Bio.PDB.Polypeptide.CaPPBuilder.__init__
Bio.PDB.Polypeptide.PPBuilder.__init__
Bio.PDB.Polypeptide._PPBuilder.__init__
Bio.PDB.Residue.DisorderedResidue.__init__
Bio.PDB.Residue.Residue.__init__
Bio.PDB.ResidueDepth'.ResidueDepth.__init__
Bio.PDB.Structure.Structure.__init__
Bio.PDB.StructureAlignment'.StructureAlignment.__init__
Bio.PDB.StructureBuilder.StructureBuilder.__init__
Bio.PDB.Superimposer'.Superimposer.__init__
Bio.PDB.Vector'.Vector.__init__
Bio.ParserSupport.EventGenerator.__init__
Bio.ParserSupport.SGMLStrippingConsumer.__init__
Bio.ParserSupport.TaggingConsumer.__init__
Bio.Parsers.spark.GenericASTBuilder.__init__
Bio.Parsers.spark.GenericASTMatcher.__init__
Bio.Parsers.spark.GenericASTTraversal.__init__
Bio.Parsers.spark.GenericParser.__init__
Bio.Parsers.spark.GenericScanner.__init__
Bio.Pathway.Network.__init__
Bio.Pathway.Reaction.__init__
Bio.Pathway.Rep.Graph.Graph.__init__
Bio.Pathway.Rep.HashSet.HashSet.__init__
Bio.Pathway.Rep.MultiGraph.MultiGraph.__init__
Bio.Pathway.System.__init__
Bio.PopGen.Async.Async.__init__
Bio.PopGen.Async.DirectoryRetriever.__init__
Bio.PopGen.Async.FileRetriever.__init__
Bio.PopGen.Async.Local.Local.__init__
Bio.PopGen.FDist.Async.FDistAsync.__init__
Bio.PopGen.FDist.Async.SplitFDist.__init__
Bio.PopGen.FDist.Controller.FDistController.__init__
Bio.PopGen.FDist.Record.__init__
Bio.PopGen.FDist.RecordParser.__init__
Bio.PopGen.FDist._RecordConsumer.__init__
Bio.PopGen.GenePop.Record.__init__
Bio.PopGen.GenePop.RecordParser.__init__
Bio.PopGen.GenePop._RecordConsumer.__init__
Bio.PopGen.SimCoal.Async.SimCoalCache.__init__
Bio.PopGen.SimCoal.Cache.SimCoalCache.__init__
Bio.PopGen.SimCoal.Controller.SimCoalController.__init__
Bio.PropertyManager.PropertyManager.__init__
Bio.Prosite.Dictionary.__init__
Bio.Prosite.ExPASyDictionary.__init__
Bio.Prosite.Iterator.__init__
Bio.Prosite.Pattern.Prosite.__init__
Bio.Prosite.Pattern.PrositeMatch.__init__
Bio.Prosite.Pattern.PrositeTerm.__init__
Bio.Prosite.PatternHit.__init__
Bio.Prosite.Prodoc.Dictionary.__init__
Bio.Prosite.Prodoc.ExPASyDictionary.__init__
Bio.Prosite.Prodoc.Iterator.__init__
Bio.Prosite.Prodoc.Record.__init__
Bio.Prosite.Prodoc.RecordParser.__init__
Bio.Prosite.Prodoc.Reference.__init__
Bio.Prosite.Prodoc._RecordConsumer.__init__
Bio.Prosite.Record.__init__
Bio.Prosite.RecordParser.__init__
Bio.Prosite._RecordConsumer.__init__
Bio.PubMed.Dictionary.__init__
Bio.Rebase.Dictionary.__init__
Bio.Rebase.Iterator.__init__
Bio.Rebase.Record.__init__
Bio.Rebase.RecordParser.__init__
Bio.Rebase._RecordConsumer.__init__
Bio.Restriction.PrintFormat.PrintFormat.__init__
Bio.Restriction.Restriction.Analysis.__init__
Bio.Restriction.Restriction.FormattedSeq.__init__
Bio.Restriction.Restriction.RestrictionBatch.__init__
Bio.Restriction.Restriction.RestrictionType.__init__
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.__init__
Bio.Restriction._Update.RestrictionCompiler.TypeCompiler.__init__
Bio.Restriction._Update.RestrictionCompiler.newenzyme.__init__
Bio.Restriction._Update.Update.ConnectionError.__init__
Bio.Restriction._Update.Update.FtpNameError.__init__
Bio.Restriction._Update.Update.FtpPasswordError.__init__
Bio.Restriction._Update.Update.RebaseUpdate.__init__
Bio.SCOP.Astral.__init__
Bio.SCOP.Cla.Index.__init__
Bio.SCOP.Cla.Iterator.__init__
Bio.SCOP.Cla.Parser.__init__
Bio.SCOP.Cla.Record.__init__
Bio.SCOP.Des.Iterator.__init__
Bio.SCOP.Des.Parser.__init__
Bio.SCOP.Des.Record.__init__
Bio.SCOP.Dom.Iterator.__init__
Bio.SCOP.Dom.Record.__init__
Bio.SCOP.Domain.__init__
Bio.SCOP.FileIndex.FileIndex.__init__
Bio.SCOP.FileIndex.defaultdict.__init__
Bio.SCOP.Hie.Iterator.__init__
Bio.SCOP.Hie.Parser.__init__
Bio.SCOP.Hie.Record.__init__
Bio.SCOP.Node.__init__
Bio.SCOP.Raf.Iterator.__init__
Bio.SCOP.Raf.Parser.__init__
Bio.SCOP.Raf.Res.__init__
Bio.SCOP.Raf.SeqMap.__init__
Bio.SCOP.Raf.SeqMapIndex.__init__
Bio.SCOP.Residues'.Residues.__init__
Bio.SCOP.Scop.__init__
Bio.SGMLExtractor.SGMLExtractor.LocalParser.__init__
Bio.SGMLExtractor.SGMLExtractor.__init__
Bio.SGMLExtractor.SGMLExtractorHandle.__init__
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.__init__
Bio.Saf.Iterator.__init__
Bio.Saf.Record.Record.__init__
Bio.Saf.RecordParser.__init__
Bio.Saf._RecordConsumer.__init__
Bio.Saf._Scanner.__init__
Bio.Search.Algorithm.__init__
Bio.Search.Database.__init__
Bio.Search.HSP.__init__
Bio.Search.HSPSeq.__init__
Bio.Search.Hit.__init__
Bio.Search.HomologySeq.__init__
Bio.Search.Query.__init__
Bio.Search.Search.__init__
Bio.Search.TableInfo.__init__
Bio.Search._SeqLength.__init__
Bio.Seq.MutableSeq.__init__
Bio.Seq.Seq.__init__
Bio.SeqFeature.AbstractPosition.__init__
Bio.SeqFeature.AfterPosition.__init__
Bio.SeqFeature.BeforePosition.__init__
Bio.SeqFeature.BetweenPosition.__init__
Bio.SeqFeature.ExactPosition.__init__
Bio.SeqFeature.FeatureLocation.__init__
Bio.SeqFeature.OneOfPosition.__init__
Bio.SeqFeature.PositionGap.__init__
Bio.SeqFeature.Reference.__init__
Bio.SeqFeature.SeqFeature.__init__
Bio.SeqFeature.WithinPosition.__init__
Bio.SeqIO.ClustalIO.ClustalWriter.__init__
Bio.SeqIO.FastaIO.FastaWriter.__init__
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.__init__
Bio.SeqIO.Interfaces.SequenceIterator.__init__
Bio.SeqIO.Interfaces.SequenceWriter.__init__
Bio.SeqIO.Interfaces.SequentialSequenceWriter.__init__
Bio.SeqIO.PhylipIO.PhylipWriter.__init__
Bio.SeqIO.StockholmIO.StockholmIterator.__init__
Bio.SeqIO.StockholmIO.StockholmWriter.__init__
Bio.SeqRecord.SeqRecord.__init__
Bio.SeqUtils.CodonUsage.CodonAdaptationIndex.__init__
Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint.__init__
Bio.SeqUtils.MissingTable.__init__
Bio.SeqUtils.ProtParam.ProteinAnalysis.__init__
Bio.Sequencing.Ace.ACEFileRecord.__init__
Bio.Sequencing.Ace.ACEParser.__init__
Bio.Sequencing.Ace.Contig.__init__
Bio.Sequencing.Ace.Iterator.__init__
Bio.Sequencing.Ace.Reads.__init__
Bio.Sequencing.Ace.RecordParser.__init__
Bio.Sequencing.Ace._RecordConsumer.__init__
Bio.Sequencing.Ace.af.__init__
Bio.Sequencing.Ace.bs.__init__
Bio.Sequencing.Ace.ct.__init__
Bio.Sequencing.Ace.ds.__init__
Bio.Sequencing.Ace.qa.__init__
Bio.Sequencing.Ace.rd.__init__
Bio.Sequencing.Ace.rt.__init__
Bio.Sequencing.Ace.wa.__init__
Bio.Sequencing.Ace.wr.__init__
Bio.Sequencing.Phd.Iterator.__init__
Bio.Sequencing.Phd.Record.__init__
Bio.Sequencing.Phd.RecordParser.__init__
Bio.Sequencing.Phd._RecordConsumer.__init__
Bio.Std.StdTerm.__init__
Bio.StdHandler.ConvertDispatchHandler.__init__
Bio.StdHandler.ConvertHandler.__init__
Bio.StdHandler.Feature.__init__
Bio.StdHandler.Handle_dbxref.__init__
Bio.StdHandler.Handle_feature_location.__init__
Bio.StdHandler.Handle_feature_qualifier.__init__
Bio.StdHandler.Handle_features.__init__
Bio.StdHandler.Handle_hsp.__init__
Bio.StdHandler.RecognizeHandler.__init__
Bio.SubsMat.FreqTable.FreqTable.__init__
Bio.SubsMat.SeqMat.__init__
Bio.SwissProt.KeyWList.ListParser.__init__
Bio.SwissProt.KeyWList.Record.__init__
Bio.SwissProt.KeyWList._ListConsumer.__init__
Bio.SwissProt.KeyWList._Scanner.__init__
Bio.SwissProt.SProt.Dictionary.__init__
Bio.SwissProt.SProt.ExPASyDictionary.__init__
Bio.SwissProt.SProt.Iterator.__init__
Bio.SwissProt.SProt.Record.__init__
Bio.SwissProt.SProt.RecordParser.__init__
Bio.SwissProt.SProt.Reference.__init__
Bio.SwissProt.SProt.SequenceParser.__init__
Bio.SwissProt.SProt._RecordConsumer.__init__
Bio.SwissProt.SProt._SequenceConsumer.__init__
Bio.Transcribe.Transcribe.__init__
Bio.Translate.Translator.__init__
Bio.UniGene.Iterator.__init__
Bio.UniGene.RecordParser.__init__
Bio.UniGene.UnigeneProtsimRecord.__init__
Bio.UniGene.UnigeneRecord.__init__
Bio.UniGene.UnigeneSTSRecord.__init__
Bio.UniGene.UnigeneSequenceRecord.__init__
Bio.UniGene._RecordConsumer.__init__
Bio.WWW.RequestLimiter.__init__
Bio.Wise.dnal.Statistics.__init__
Bio.Wise.psw.AlignmentColumn.__init__
Bio.Wise.psw.ColumnUnit.__init__
Bio.Writer.Writer.__init__
Bio.biblio.Biblio.__init__
Bio.biblio.BiblioCollection.__init__
Bio.builders.Search.search.BuildSearch.__init__
Bio.builders.SeqRecord.sequence.BuildSeqRecord.__init__
Bio.config.DBRegistry.BioCorbaDB.__init__
Bio.config.DBRegistry.BioSQLDB.__init__
Bio.config.DBRegistry.CGIDB.__init__
Bio.config.DBRegistry.DBGroup.__init__
Bio.config.DBRegistry.DBObject.__init__
Bio.config.DBRegistry.DBRegistry.__init__
Bio.config.DBRegistry.EUtilsDB.__init__
Bio.config.DBRegistry.IndexedFileDB.__init__
Bio.config.FormatRegistry.FormatGroup.__init__
Bio.config.FormatRegistry.FormatObject.__init__
Bio.config.FormatRegistry.FormatRegistry.__init__
Bio.config.Registry.RegisterableGroup.__init__
Bio.config.Registry.RegisterableObject.__init__
Bio.config.Registry.Registry.__init__
Bio.config.SeqDBRegistry.SeqDBRegistry.__init__
Bio.config._stanzaformat.Stanza.__init__
Bio.config._stanzaformat.StanzaFormat.__init__
Bio.config._support.make_cached_expression.__init__
Bio.config._support.make_rate_limited_function.__init__
Bio.kNN.kNN.__init__
Bio.pairwise2.affine_penalty.__init__
Bio.pairwise2.dictionary_match.__init__
Bio.pairwise2.identity_match.__init__
Bio.writers.SeqRecord.embl.WriteEmbl.__init__
Bio.writers.SeqRecord.fasta.WriteFasta.__init__
BioSQL.BioSeq.DBSeq.__init__
BioSQL.BioSeq.DBSeqRecord.__init__
BioSQL.BioSeqDatabase.Adaptor.__init__
BioSQL.BioSeqDatabase.BioSeqDatabase.__init__
BioSQL.BioSeqDatabase.DBServer.__init__
BioSQL.DBUtils.Generic_dbutils.__init__
BioSQL.Loader.DatabaseLoader.__init__
BioSQL.Loader.DatabaseRemover.__init__
Martel.Dispatch.Callback.__init__
Martel.Dispatch.DispatchHandler.__init__
Martel.Dispatch.Dispatcher.__init__
Martel.Dispatch.Multicall.__init__
Martel.Dispatch.RemapEnd.__init__
Martel.Dispatch.RemapStart.__init__
Martel.Expression.Alt.__init__
Martel.Expression.Any.__init__
Martel.Expression.Assert.__init__
Martel.Expression.Debug.__init__
Martel.Expression.FastFeature.__init__
Martel.Expression.Group.__init__
Martel.Expression.GroupRef.__init__
Martel.Expression.HeaderFooter.__init__
Martel.Expression.Literal.__init__
Martel.Expression.MaxRepeat.__init__
Martel.Expression.NullOp.__init__
Martel.Expression.ParseRecords.__init__
Martel.Expression.PassThrough.__init__
Martel.Expression.Seq.__init__
Martel.Expression.Str.__init__
Martel.Generate.CheckAssert.__init__
Martel.Generate.CheckAssertNot.__init__
Martel.Generate.CheckGroupRef.__init__
Martel.Generate.GeneratorState.__init__
Martel.Generate.HandleRepeatCount.__init__
Martel.Generate.SetGroupValue.__init__
Martel.Generate._call_call.__init__
Martel.Generate._call_calltag.__init__
Martel.Generate.print_debug.__init__
Martel.Generate.print_info.__init__
Martel.IterParser.IterHeaderFooter.__init__
Martel.IterParser.IterRecords.__init__
Martel.Iterator.EventStream.__init__
Martel.Iterator.HeaderFooterEventStream.__init__
Martel.Iterator.Iterate.__init__
Martel.Iterator.Iterator.__init__
Martel.Iterator.IteratorHeaderFooter.__init__
Martel.Iterator.IteratorRecords.__init__
Martel.Iterator.RecordEventStream.__init__
Martel.Iterator.StoreEvents.__init__
Martel.LAX.ElementInfo.__init__
Martel.LAX.LAX.__init__
Martel.Parser.HeaderFooterParser.__init__
Martel.Parser.Parser.__init__
Martel.Parser.ParserIncompleteException.__init__
Martel.Parser.ParserPositionException.__init__
Martel.Parser.RecordParser.__init__
Martel.RecordReader.CountLines.__init__
Martel.RecordReader.EndsWith.__init__
Martel.RecordReader.Everything.__init__
Martel.RecordReader.Nothing.__init__
Martel.RecordReader.RecordReader.__init__
Martel.RecordReader.StartsWith.__init__
Martel.RecordReader.Until.__init__
Martel.convert_re.GroupNames.__init__
Martel.msre_parse.Pattern.__init__
Martel.msre_parse.SubPattern.__init__
Martel.msre_parse.Tokenizer.__init__
Martel.test.support.CheckGood.__init__
Martel.test.support.Dump.__init__
Martel.test.support.Storage.__init__
Martel.test.test_Parser.CountErrors.__init__
Martel.test.test_Parser.CountRecords.__init__
Martel.test.test_delimiter.CatchFields.__init__
Martel.test.test_optimize.GetErrorPos.__init__" class="py-name" href="#" onclick="return doclink('link-7', '__init__', 'link-7');">__init__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt id="link-8" class="py-name" targets="Variable Bio.Encodings.IUPACEncoding.name=Bio.Encodings.IUPACEncoding-module.html#name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-8', 'name', 'link-8');">name</a></tt><tt class="py-op">,</tt> <tt class="py-name">load_path</tt><tt class="py-op">=</tt><tt class="py-name">load_path</tt><tt class="py-op">)</tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_builder_path</tt> <tt class="py-op">=</tt> <tt class="py-name">builder_path</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_writer_path</tt> <tt class="py-op">=</tt> <tt class="py-name">writer_path</tt> </tt>
</div><a name="L43"></a><tt class="py-lineno"> 43</tt>  <tt class="py-line">         </tt>
<a name="FormatRegistry.normalize"></a><div id="FormatRegistry.normalize-def"><a name="L44"></a><tt class="py-lineno"> 44</tt> <a class="py-toggle" href="#" id="FormatRegistry.normalize-toggle" onclick="return toggle('FormatRegistry.normalize');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.config.FormatRegistry.FormatRegistry-class.html#normalize">normalize</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">name_or_format</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> <tt class="py-comment"># XXX appropriate?</tt> </tt>
</div><a name="L45"></a><tt class="py-lineno"> 45</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">name_or_format</tt><tt class="py-op">,</tt> <tt id="link-9" class="py-name" targets="Variable Bio.GenBank.LocationParser.Integer.type=Bio.GenBank.LocationParser.Integer-class.html#type,Variable Bio.GenBank.LocationParser.Symbol.type=Bio.GenBank.LocationParser.Symbol-class.html#type,Variable Bio.GenBank.LocationParser.UnsignedInteger.type=Bio.GenBank.LocationParser.UnsignedInteger-class.html#type"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-9', 'type', 'link-9');">type</a></tt><tt class="py-op">(</tt><tt class="py-string">""</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt>  <tt class="py-line">            <tt class="py-comment"># It's a name</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt>  <tt class="py-line"><tt class="py-comment"></tt>            <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">[</tt><tt class="py-name">name_or_format</tt><tt class="py-op">]</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">name_or_format</tt> </tt>
</div><a name="L49"></a><tt class="py-lineno"> 49</tt>  <tt class="py-line"> </tt>
<a name="FormatRegistry._build_parent_path"></a><div id="FormatRegistry._build_parent_path-def"><a name="L50"></a><tt class="py-lineno"> 50</tt> <a class="py-toggle" href="#" id="FormatRegistry._build_parent_path-toggle" onclick="return toggle('FormatRegistry._build_parent_path');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.config.FormatRegistry.FormatRegistry-class.html#_build_parent_path">_build_parent_path</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">format</tt><tt class="py-op">,</tt> <tt class="py-param">visited</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FormatRegistry._build_parent_path-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="FormatRegistry._build_parent_path-expanded"><a name="L51"></a><tt class="py-lineno"> 51</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">visited</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt>  <tt class="py-line">            <tt class="py-name">visited</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">visited</tt><tt class="py-op">.</tt><tt id="link-10" class="py-name" targets="Method Bio.Crystal.Crystal.has_key()=Bio.Crystal.Crystal-class.html#has_key,Method Bio.EUtils.POM.ElementNode.has_key()=Bio.EUtils.POM.ElementNode-class.html#has_key,Method Bio.GenBank.NCBIDictionary.has_key()=Bio.GenBank.NCBIDictionary-class.html#has_key,Method Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key()=Bio.PDB.AbstractPropertyMap.AbstractPropertyMap-class.html#has_key,Method Bio.PDB.FragmentMapper'.FragmentMapper.has_key()=Bio.PDB.FragmentMapper%27.FragmentMapper-class.html#has_key,Method Bio.Prosite.ExPASyDictionary.has_key()=Bio.Prosite.ExPASyDictionary-class.html#has_key,Method Bio.Prosite.Prodoc.ExPASyDictionary.has_key()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#has_key,Method Bio.PubMed.Dictionary.has_key()=Bio.PubMed.Dictionary-class.html#has_key,Method Bio.SwissProt.SProt.ExPASyDictionary.has_key()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#has_key,Method Martel.Parser.MartelAttributeList.has_key()=Martel.Parser.MartelAttributeList-class.html#has_key"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-10', 'has_key', 'link-10');">has_key</a></tt><tt class="py-op">(</tt><tt id="link-11" class="py-name" targets="Method Bio.Restriction.Restriction.RestrictionBatch.format()=Bio.Restriction.Restriction.RestrictionBatch-class.html#format,Variable Bio.expressions.blast.ncbiblast.format=Bio.expressions.blast.ncbiblast-module.html#format,Variable Bio.expressions.blast.wublast.format=Bio.expressions.blast.wublast-module.html#format,Variable Bio.expressions.blocks.format=Bio.expressions.blocks-module.html#format,Variable Bio.expressions.embl.embl65.format=Bio.expressions.embl.embl65-module.html#format,Variable Bio.expressions.fasta.format=Bio.expressions.fasta-module.html#format,Variable Bio.expressions.genbank.format=Bio.expressions.genbank-module.html#format,Variable Bio.expressions.hmmpfam.format=Bio.expressions.hmmpfam-module.html#format,Variable Bio.expressions.swissprot.ipi.format=Bio.expressions.swissprot.ipi-module.html#format,Variable Bio.expressions.swissprot.speclist.format=Bio.expressions.swissprot.speclist-module.html#format,Variable Bio.expressions.swissprot.sprot38.format=Bio.expressions.swissprot.sprot38-module.html#format,Variable Bio.expressions.swissprot.sprot40.format=Bio.expressions.swissprot.sprot40-module.html#format,Variable Bio.expressions.transfac.format=Bio.expressions.transfac-module.html#format,Variable Martel.test.test_swissprot38.format=Martel.test.test_swissprot38-module.html#format,Variable Martel.test.testformats.swissprot38.format=Martel.test.testformats.swissprot38-module.html#format"><a title="Bio.Restriction.Restriction.RestrictionBatch.format
Bio.expressions.blast.ncbiblast.format
Bio.expressions.blast.wublast.format
Bio.expressions.blocks.format
Bio.expressions.embl.embl65.format
Bio.expressions.fasta.format
Bio.expressions.genbank.format
Bio.expressions.hmmpfam.format
Bio.expressions.swissprot.ipi.format
Bio.expressions.swissprot.speclist.format
Bio.expressions.swissprot.sprot38.format
Bio.expressions.swissprot.sprot40.format
Bio.expressions.transfac.format
Martel.test.test_swissprot38.format
Martel.test.testformats.swissprot38.format" class="py-name" href="#" onclick="return doclink('link-11', 'format', 'link-11');">format</a></tt><tt class="py-op">.</tt><tt id="link-12" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-12', 'name', 'link-8');">name</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt>  <tt class="py-line">        <tt class="py-name">format_list</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt id="link-13" class="py-name"><a title="Bio.Restriction.Restriction.RestrictionBatch.format
Bio.expressions.blast.ncbiblast.format
Bio.expressions.blast.wublast.format
Bio.expressions.blocks.format
Bio.expressions.embl.embl65.format
Bio.expressions.fasta.format
Bio.expressions.genbank.format
Bio.expressions.hmmpfam.format
Bio.expressions.swissprot.ipi.format
Bio.expressions.swissprot.speclist.format
Bio.expressions.swissprot.sprot38.format
Bio.expressions.swissprot.sprot40.format
Bio.expressions.transfac.format
Martel.test.test_swissprot38.format
Martel.test.testformats.swissprot38.format" class="py-name" href="#" onclick="return doclink('link-13', 'format', 'link-11');">format</a></tt><tt class="py-op">]</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">parent</tt> <tt class="py-keyword">in</tt> <tt id="link-14" class="py-name"><a title="Bio.Restriction.Restriction.RestrictionBatch.format
Bio.expressions.blast.ncbiblast.format
Bio.expressions.blast.wublast.format
Bio.expressions.blocks.format
Bio.expressions.embl.embl65.format
Bio.expressions.fasta.format
Bio.expressions.genbank.format
Bio.expressions.hmmpfam.format
Bio.expressions.swissprot.ipi.format
Bio.expressions.swissprot.speclist.format
Bio.expressions.swissprot.sprot38.format
Bio.expressions.swissprot.sprot40.format
Bio.expressions.transfac.format
Martel.test.test_swissprot38.format
Martel.test.testformats.swissprot38.format" class="py-name" href="#" onclick="return doclink('link-14', 'format', 'link-11');">format</a></tt><tt class="py-op">.</tt><tt class="py-name">_parents</tt><tt class="py-op">:</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt>  <tt class="py-line">            <tt class="py-name">format_list</tt><tt class="py-op">.</tt><tt id="link-15" class="py-name" targets="Method Bio.EUtils.POM.ElementNode.extend()=Bio.EUtils.POM.ElementNode-class.html#extend,Method Bio.SCOP.Raf.SeqMap.extend()=Bio.SCOP.Raf.SeqMap-class.html#extend,Method Bio.Seq.MutableSeq.extend()=Bio.Seq.MutableSeq-class.html#extend"><a title="Bio.EUtils.POM.ElementNode.extend
Bio.SCOP.Raf.SeqMap.extend
Bio.Seq.MutableSeq.extend" class="py-name" href="#" onclick="return doclink('link-15', 'extend', 'link-15');">extend</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-16" class="py-name" targets="Method Bio.config.FormatRegistry.FormatRegistry._build_parent_path()=Bio.config.FormatRegistry.FormatRegistry-class.html#_build_parent_path"><a title="Bio.config.FormatRegistry.FormatRegistry._build_parent_path" class="py-name" href="#" onclick="return doclink('link-16', '_build_parent_path', 'link-16');">_build_parent_path</a></tt><tt class="py-op">(</tt><tt class="py-name">parent</tt><tt class="py-op">,</tt> <tt class="py-name">visited</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">format_list</tt> </tt>
</div><a name="L59"></a><tt class="py-lineno"> 59</tt>  <tt class="py-line"> </tt>
<a name="FormatRegistry._build_child_path"></a><div id="FormatRegistry._build_child_path-def"><a name="L60"></a><tt class="py-lineno"> 60</tt> <a class="py-toggle" href="#" id="FormatRegistry._build_child_path-toggle" onclick="return toggle('FormatRegistry._build_child_path');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.config.FormatRegistry.FormatRegistry-class.html#_build_child_path">_build_child_path</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">format</tt><tt class="py-op">,</tt> <tt class="py-param">visited</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FormatRegistry._build_child_path-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="FormatRegistry._build_child_path-expanded"><a name="L61"></a><tt class="py-lineno"> 61</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">visited</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt>  <tt class="py-line">            <tt class="py-name">visited</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">visited</tt><tt class="py-op">.</tt><tt id="link-17" class="py-name"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-17', 'has_key', 'link-10');">has_key</a></tt><tt class="py-op">(</tt><tt id="link-18" class="py-name"><a title="Bio.Restriction.Restriction.RestrictionBatch.format
Bio.expressions.blast.ncbiblast.format
Bio.expressions.blast.wublast.format
Bio.expressions.blocks.format
Bio.expressions.embl.embl65.format
Bio.expressions.fasta.format
Bio.expressions.genbank.format
Bio.expressions.hmmpfam.format
Bio.expressions.swissprot.ipi.format
Bio.expressions.swissprot.speclist.format
Bio.expressions.swissprot.sprot38.format
Bio.expressions.swissprot.sprot40.format
Bio.expressions.transfac.format
Martel.test.test_swissprot38.format
Martel.test.testformats.swissprot38.format" class="py-name" href="#" onclick="return doclink('link-18', 'format', 'link-11');">format</a></tt><tt class="py-op">.</tt><tt id="link-19" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-19', 'name', 'link-8');">name</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt>  <tt class="py-line">        <tt class="py-name">format_list</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt id="link-20" class="py-name"><a title="Bio.Restriction.Restriction.RestrictionBatch.format
Bio.expressions.blast.ncbiblast.format
Bio.expressions.blast.wublast.format
Bio.expressions.blocks.format
Bio.expressions.embl.embl65.format
Bio.expressions.fasta.format
Bio.expressions.genbank.format
Bio.expressions.hmmpfam.format
Bio.expressions.swissprot.ipi.format
Bio.expressions.swissprot.speclist.format
Bio.expressions.swissprot.sprot38.format
Bio.expressions.swissprot.sprot40.format
Bio.expressions.transfac.format
Martel.test.test_swissprot38.format
Martel.test.testformats.swissprot38.format" class="py-name" href="#" onclick="return doclink('link-20', 'format', 'link-11');">format</a></tt><tt class="py-op">]</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">child</tt> <tt class="py-keyword">in</tt> <tt class="py-name">getattr</tt><tt class="py-op">(</tt><tt id="link-21" class="py-name"><a title="Bio.Restriction.Restriction.RestrictionBatch.format
Bio.expressions.blast.ncbiblast.format
Bio.expressions.blast.wublast.format
Bio.expressions.blocks.format
Bio.expressions.embl.embl65.format
Bio.expressions.fasta.format
Bio.expressions.genbank.format
Bio.expressions.hmmpfam.format
Bio.expressions.swissprot.ipi.format
Bio.expressions.swissprot.speclist.format
Bio.expressions.swissprot.sprot38.format
Bio.expressions.swissprot.sprot40.format
Bio.expressions.transfac.format
Martel.test.test_swissprot38.format
Martel.test.testformats.swissprot38.format" class="py-name" href="#" onclick="return doclink('link-21', 'format', 'link-11');">format</a></tt><tt class="py-op">,</tt> <tt class="py-string">'objs'</tt><tt class="py-op">,</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt>  <tt class="py-line">            <tt class="py-name">format_list</tt><tt class="py-op">.</tt><tt id="link-22" class="py-name"><a title="Bio.EUtils.POM.ElementNode.extend
Bio.SCOP.Raf.SeqMap.extend
Bio.Seq.MutableSeq.extend" class="py-name" href="#" onclick="return doclink('link-22', 'extend', 'link-15');">extend</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-23" class="py-name" targets="Method Bio.config.FormatRegistry.FormatRegistry._build_child_path()=Bio.config.FormatRegistry.FormatRegistry-class.html#_build_child_path"><a title="Bio.config.FormatRegistry.FormatRegistry._build_child_path" class="py-name" href="#" onclick="return doclink('link-23', '_build_child_path', 'link-23');">_build_child_path</a></tt><tt class="py-op">(</tt><tt class="py-name">child</tt><tt class="py-op">,</tt> <tt class="py-name">visited</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">format_list</tt> </tt>
</div><a name="L69"></a><tt class="py-lineno"> 69</tt>  <tt class="py-line">         </tt>
<a name="FormatRegistry.find_builder"></a><div id="FormatRegistry.find_builder-def"><a name="L70"></a><tt class="py-lineno"> 70</tt> <a class="py-toggle" href="#" id="FormatRegistry.find_builder-toggle" onclick="return toggle('FormatRegistry.find_builder');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.config.FormatRegistry.FormatRegistry-class.html#find_builder">find_builder</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">from_format</tt><tt class="py-op">,</tt> <tt class="py-param">to_io</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FormatRegistry.find_builder-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="FormatRegistry.find_builder-expanded"><a name="L71"></a><tt class="py-lineno"> 71</tt>  <tt class="py-line">        <tt class="py-comment"># The directory of the builders is organized according to:</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-comment"># builders/io/format</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-name">basemodulename</tt> <tt class="py-op">=</tt> <tt class="py-string">"%s.%s"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_builder_path</tt><tt class="py-op">,</tt> <tt class="py-name">to_io</tt><tt class="py-op">.</tt><tt class="py-name">abbrev</tt><tt class="py-op">)</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt>  <tt class="py-line"> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt>  <tt class="py-line">        <tt class="py-comment"># Search through the formats in the order of most specific to</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-comment"># most general.</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-name">all_formats</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-24" class="py-name"><a title="Bio.config.FormatRegistry.FormatRegistry._build_parent_path" class="py-name" href="#" onclick="return doclink('link-24', '_build_parent_path', 'link-16');">_build_parent_path</a></tt><tt class="py-op">(</tt><tt class="py-name">from_format</tt><tt class="py-op">)</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt id="link-25" class="py-name"><a title="Bio.Restriction.Restriction.RestrictionBatch.format
Bio.expressions.blast.ncbiblast.format
Bio.expressions.blast.wublast.format
Bio.expressions.blocks.format
Bio.expressions.embl.embl65.format
Bio.expressions.fasta.format
Bio.expressions.genbank.format
Bio.expressions.hmmpfam.format
Bio.expressions.swissprot.ipi.format
Bio.expressions.swissprot.speclist.format
Bio.expressions.swissprot.sprot38.format
Bio.expressions.swissprot.sprot40.format
Bio.expressions.transfac.format
Martel.test.test_swissprot38.format
Martel.test.testformats.swissprot38.format" class="py-name" href="#" onclick="return doclink('link-25', 'format', 'link-11');">format</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">all_formats</tt><tt class="py-op">:</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt>  <tt class="py-line">            <tt id="link-26" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-26', 'name', 'link-8');">name</a></tt> <tt class="py-op">=</tt> <tt class="py-name">basemodulename</tt> <tt class="py-op">+</tt> <tt class="py-string">"."</tt> <tt class="py-op">+</tt> <tt id="link-27" class="py-name"><a title="Bio.Restriction.Restriction.RestrictionBatch.format
Bio.expressions.blast.ncbiblast.format
Bio.expressions.blast.wublast.format
Bio.expressions.blocks.format
Bio.expressions.embl.embl65.format
Bio.expressions.fasta.format
Bio.expressions.genbank.format
Bio.expressions.hmmpfam.format
Bio.expressions.swissprot.ipi.format
Bio.expressions.swissprot.speclist.format
Bio.expressions.swissprot.sprot38.format
Bio.expressions.swissprot.sprot40.format
Bio.expressions.transfac.format
Martel.test.test_swissprot38.format
Martel.test.testformats.swissprot38.format" class="py-name" href="#" onclick="return doclink('link-27', 'format', 'link-11');">format</a></tt><tt class="py-op">.</tt><tt class="py-name">abbrev</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt>  <tt class="py-line">            <tt class="py-name">module</tt> <tt class="py-op">=</tt> <tt id="link-28" class="py-name"><a title="Bio.config._support
Bio.dbdefs._support" class="py-name" href="#" onclick="return doclink('link-28', '_support', 'link-5');">_support</a></tt><tt class="py-op">.</tt><tt id="link-29" class="py-name" targets="Function Bio.config._support.safe_load_module()=Bio.config._support-module.html#safe_load_module"><a title="Bio.config._support.safe_load_module" class="py-name" href="#" onclick="return doclink('link-29', 'safe_load_module', 'link-29');">safe_load_module</a></tt><tt class="py-op">(</tt><tt id="link-30" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-30', 'name', 'link-8');">name</a></tt><tt class="py-op">)</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">module</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt>  <tt class="py-line">                <tt class="py-keyword">break</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt>  <tt class="py-line">            <tt class="py-keyword">raise</tt> <tt class="py-name">TypeError</tt><tt class="py-op">(</tt><tt class="py-string">"Cannot find builder for %r"</tt> <tt class="py-op">%</tt> <tt class="py-name">to_io</tt><tt class="py-op">.</tt><tt class="py-name">abbrev</tt><tt class="py-op">)</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">module</tt><tt class="py-op">.</tt><tt class="py-name">make_builder</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L86"></a><tt class="py-lineno"> 86</tt>  <tt class="py-line"> </tt>
<a name="FormatRegistry.find_writer"></a><div id="FormatRegistry.find_writer-def"><a name="L87"></a><tt class="py-lineno"> 87</tt> <a class="py-toggle" href="#" id="FormatRegistry.find_writer-toggle" onclick="return toggle('FormatRegistry.find_writer');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.config.FormatRegistry.FormatRegistry-class.html#find_writer">find_writer</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">from_io</tt><tt class="py-op">,</tt> <tt class="py-param">to_format</tt><tt class="py-op">,</tt> <tt class="py-param">outfile</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FormatRegistry.find_writer-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="FormatRegistry.find_writer-expanded"><a name="L88"></a><tt class="py-lineno"> 88</tt>  <tt class="py-line">        <tt class="py-comment"># The directory of the writers is organized according to:</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-comment"># writers/io/format</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-name">basemodulename</tt> <tt class="py-op">=</tt> <tt class="py-string">"%s.%s"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_writer_path</tt><tt class="py-op">,</tt> <tt class="py-name">from_io</tt><tt class="py-op">.</tt><tt class="py-name">abbrev</tt><tt class="py-op">)</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt>  <tt class="py-line">         </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt>  <tt class="py-line">        <tt class="py-comment"># Search through the formats in the order of most general to</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-comment"># most specific.</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-name">all_formats</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-31" class="py-name"><a title="Bio.config.FormatRegistry.FormatRegistry._build_child_path" class="py-name" href="#" onclick="return doclink('link-31', '_build_child_path', 'link-23');">_build_child_path</a></tt><tt class="py-op">(</tt><tt class="py-name">to_format</tt><tt class="py-op">)</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt id="link-32" class="py-name"><a title="Bio.Restriction.Restriction.RestrictionBatch.format
Bio.expressions.blast.ncbiblast.format
Bio.expressions.blast.wublast.format
Bio.expressions.blocks.format
Bio.expressions.embl.embl65.format
Bio.expressions.fasta.format
Bio.expressions.genbank.format
Bio.expressions.hmmpfam.format
Bio.expressions.swissprot.ipi.format
Bio.expressions.swissprot.speclist.format
Bio.expressions.swissprot.sprot38.format
Bio.expressions.swissprot.sprot40.format
Bio.expressions.transfac.format
Martel.test.test_swissprot38.format
Martel.test.testformats.swissprot38.format" class="py-name" href="#" onclick="return doclink('link-32', 'format', 'link-11');">format</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">all_formats</tt><tt class="py-op">:</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt>  <tt class="py-line">            <tt id="link-33" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-33', 'name', 'link-8');">name</a></tt> <tt class="py-op">=</tt> <tt class="py-name">basemodulename</tt> <tt class="py-op">+</tt> <tt class="py-string">"."</tt> <tt class="py-op">+</tt> <tt id="link-34" class="py-name"><a title="Bio.Restriction.Restriction.RestrictionBatch.format
Bio.expressions.blast.ncbiblast.format
Bio.expressions.blast.wublast.format
Bio.expressions.blocks.format
Bio.expressions.embl.embl65.format
Bio.expressions.fasta.format
Bio.expressions.genbank.format
Bio.expressions.hmmpfam.format
Bio.expressions.swissprot.ipi.format
Bio.expressions.swissprot.speclist.format
Bio.expressions.swissprot.sprot38.format
Bio.expressions.swissprot.sprot40.format
Bio.expressions.transfac.format
Martel.test.test_swissprot38.format
Martel.test.testformats.swissprot38.format" class="py-name" href="#" onclick="return doclink('link-34', 'format', 'link-11');">format</a></tt><tt class="py-op">.</tt><tt class="py-name">abbrev</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt>  <tt class="py-line">            <tt class="py-name">module</tt> <tt class="py-op">=</tt> <tt id="link-35" class="py-name"><a title="Bio.config._support
Bio.dbdefs._support" class="py-name" href="#" onclick="return doclink('link-35', '_support', 'link-5');">_support</a></tt><tt class="py-op">.</tt><tt id="link-36" class="py-name"><a title="Bio.config._support.safe_load_module" class="py-name" href="#" onclick="return doclink('link-36', 'safe_load_module', 'link-29');">safe_load_module</a></tt><tt class="py-op">(</tt><tt id="link-37" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-37', 'name', 'link-8');">name</a></tt><tt class="py-op">)</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">module</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt>  <tt class="py-line">                <tt class="py-keyword">break</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt>  <tt class="py-line">            <tt class="py-keyword">raise</tt> <tt class="py-name">TypeError</tt><tt class="py-op">(</tt><tt class="py-string">"Cannot find writer for %r"</tt> <tt class="py-op">%</tt> <tt class="py-name">from_io</tt><tt class="py-op">.</tt><tt class="py-name">abbrev</tt><tt class="py-op">)</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">module</tt><tt class="py-op">.</tt><tt class="py-name">make_writer</tt><tt class="py-op">(</tt><tt class="py-name">outfile</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L103"></a><tt class="py-lineno">103</tt>  <tt class="py-line"> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt>  <tt class="py-line"><tt id="link-38" class="py-name" targets="Variable Bio.config.FormatRegistry.formats=Bio.config.FormatRegistry-module.html#formats,Package Martel.formats=Martel.formats-module.html"><a title="Bio.config.FormatRegistry.formats
Martel.formats" class="py-name" href="#" onclick="return doclink('link-38', 'formats', 'link-38');">formats</a></tt> <tt class="py-op">=</tt> <tt id="link-39" class="py-name" targets="Module Bio.config.FormatRegistry=Bio.config.FormatRegistry-module.html,Class Bio.config.FormatRegistry.FormatRegistry=Bio.config.FormatRegistry.FormatRegistry-class.html"><a title="Bio.config.FormatRegistry
Bio.config.FormatRegistry.FormatRegistry" class="py-name" href="#" onclick="return doclink('link-39', 'FormatRegistry', 'link-39');">FormatRegistry</a></tt><tt class="py-op">(</tt><tt class="py-string">"formats"</tt><tt class="py-op">,</tt> <tt class="py-string">"Bio.formatdefs"</tt><tt class="py-op">)</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt>  <tt class="py-line"> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt>  <tt class="py-line"> </tt>
<a name="FormatObject"></a><div id="FormatObject-def"><a name="L107"></a><tt class="py-lineno">107</tt> <a class="py-toggle" href="#" id="FormatObject-toggle" onclick="return toggle('FormatObject');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.config.FormatRegistry.FormatObject-class.html">FormatObject</a><tt class="py-op">(</tt><tt class="py-base-class">RegisterableObject</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FormatObject-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="FormatObject-expanded"><a name="L108"></a><tt class="py-lineno">108</tt>  <tt class="py-line">    <tt class="py-docstring">"""This object stores Biopython file formats and provides methods</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt>  <tt class="py-line"><tt class="py-docstring">    to work on them.</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt>  <tt class="py-line"><tt class="py-docstring">    Methods:</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt>  <tt class="py-line"><tt class="py-docstring">    identify        Identify the format at a URL.</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt>  <tt class="py-line"><tt class="py-docstring">    identifyFile    Identify the format of a file.</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt>  <tt class="py-line"><tt class="py-docstring">    identifyString  Identify the format of a string.</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt>  <tt class="py-line"><tt class="py-docstring">    make_parser     Make a parser that can parse the format.</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt>  <tt class="py-line"><tt class="py-docstring">    make_iterator   Make an iterator over files of this format.</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="FormatObject.__init__"></a><div id="FormatObject.__init__-def"><a name="L120"></a><tt class="py-lineno">120</tt> <a class="py-toggle" href="#" id="FormatObject.__init__-toggle" onclick="return toggle('FormatObject.__init__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.config.FormatRegistry.FormatObject-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">name</tt><tt class="py-op">,</tt> <tt class="py-param">expression</tt><tt class="py-op">,</tt> <tt class="py-param">abbrev</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">doc</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt>  <tt class="py-line">                 <tt class="py-param">filter</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">multirecord</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FormatObject.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="FormatObject.__init__-expanded"><a name="L122"></a><tt class="py-lineno">122</tt>  <tt class="py-line">        <tt class="py-docstring">"""FormatObject(name, expression[, abbrev][, doc]</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt>  <tt class="py-line"><tt class="py-docstring">        [, filter][, multirecord])</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt>  <tt class="py-line"><tt class="py-docstring">        name is the name of the object, abbrev is an abbreviation for</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt>  <tt class="py-line"><tt class="py-docstring">        the name, and doc is some documentation describing the object.</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt>  <tt class="py-line"><tt class="py-docstring">        expression is a Martel.Expression that can parse this format.</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt>  <tt class="py-line"><tt class="py-docstring">        filter is an optional Martel.Expression that can be used to</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt>  <tt class="py-line"><tt class="py-docstring">        quickly determine whether some input is parseable by this</tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt>  <tt class="py-line"><tt class="py-docstring">        format.</tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt>  <tt class="py-line"><tt class="py-docstring">        multirecord is either 0/1 indicating whether this format can</tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt>  <tt class="py-line"><tt class="py-docstring">        be used to parse multiple records.  By default, it is 1.</tt> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt>  <tt class="py-line">        <tt class="py-keyword">import</tt> <tt class="py-name">operator</tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt>  <tt class="py-line">        <tt id="link-40" class="py-name" targets="Class Bio.config.Registry.RegisterableObject=Bio.config.Registry.RegisterableObject-class.html"><a title="Bio.config.Registry.RegisterableObject" class="py-name" href="#" onclick="return doclink('link-40', 'RegisterableObject', 'link-40');">RegisterableObject</a></tt><tt class="py-op">.</tt><tt id="link-41" class="py-name"><a title="Bio.Affy.CelFile.CelConsumer.__init__
Bio.Affy.CelFile.CelParser.__init__
Bio.Affy.CelFile.CelRecord.__init__
Bio.Ais.Immune.__init__
Bio.Ais.Lymphocyte.__init__
Bio.Align.AlignInfo.PSSM.__init__
Bio.Align.AlignInfo.SummaryInfo.__init__
Bio.Align.FormatConvert.FormatConverter.__init__
Bio.Align.Generic.Alignment.__init__
Bio.AlignAce.Applications.AlignAceCommandline.__init__
Bio.AlignAce.Applications.CompareAceCommandline.__init__
Bio.AlignAce.Motif.Motif.__init__
Bio.AlignAce.Parser.AlignAceConsumer.__init__
Bio.AlignAce.Parser.AlignAceParser.__init__
Bio.AlignAce.Parser.CompareAceConsumer.__init__
Bio.AlignAce.Parser.CompareAceParser.__init__
Bio.AlignIO.Interfaces.AlignmentIterator.__init__
Bio.AlignIO.Interfaces.AlignmentWriter.__init__
Bio.AlignIO.Interfaces.SequentialAlignmentWriter.__init__
Bio.Alphabet.AlphabetEncoder.__init__
Bio.Alphabet.Gapped.__init__
Bio.Alphabet.HasStopCodon.__init__
Bio.Application.AbstractCommandline.__init__
Bio.Application.ApplicationResult.__init__
Bio.Application._AbstractParameter.__init__
Bio.Blast.Applications.BlastallCommandline.__init__
Bio.Blast.Applications.FastacmdCommandline.__init__
Bio.Blast.NCBIStandalone.BlastErrorParser.__init__
Bio.Blast.NCBIStandalone.BlastParser.__init__
Bio.Blast.NCBIStandalone.Iterator.__init__
Bio.Blast.NCBIStandalone.PSIBlastParser.__init__
Bio.Blast.NCBIStandalone._BlastConsumer.__init__
Bio.Blast.NCBIStandalone._BlastErrorConsumer.__init__
Bio.Blast.NCBIStandalone._PSIBlastConsumer.__init__
Bio.Blast.NCBIWWW.BlastParser.__init__
Bio.Blast.NCBIXML.BlastParser.__init__
Bio.Blast.NCBIXML._XMLparser.__init__
Bio.Blast.ParseBlastTable.BlastTableEntry.__init__
Bio.Blast.ParseBlastTable.BlastTableReader.__init__
Bio.Blast.ParseBlastTable.BlastTableRec.__init__
Bio.Blast.Record.Alignment.__init__
Bio.Blast.Record.Blast.__init__
Bio.Blast.Record.DatabaseReport.__init__
Bio.Blast.Record.Description.__init__
Bio.Blast.Record.HSP.__init__
Bio.Blast.Record.Header.__init__
Bio.Blast.Record.MultipleAlignment.__init__
Bio.Blast.Record.PSIBlast.__init__
Bio.Blast.Record.Parameters.__init__
Bio.Blast.Record.Round.__init__
Bio.CAPS.CAPSMap.__init__
Bio.CAPS.DifferentialCutsite.__init__
Bio.CDD.Iterator.__init__
Bio.CDD.Record.Record.__init__
Bio.CDD.RecordParser.__init__
Bio.CDD._RecordConsumer.__init__
Bio.CDD._Scanner.__init__
Bio.Clustalw.ClustalAlignment.__init__
Bio.Clustalw.MultipleAlignCL.__init__
Bio.Cluster.DataFile.__init__
Bio.Cluster.Record.__init__
Bio.Compass.Iterator.__init__
Bio.Compass.Record.__init__
Bio.Compass.RecordParser.__init__
Bio.Compass._Consumer.__init__
Bio.Crystal.Chain.__init__
Bio.Crystal.Crystal.__init__
Bio.Crystal.CrystalError.__init__
Bio.Crystal.Error.__init__
Bio.Crystal.Hetero.__init__
Bio.DBXRef.DBXRef.__init__
Bio.Data.CodonTable.AmbiguousCodonTable.__init__
Bio.Data.CodonTable.AmbiguousForwardTable.__init__
Bio.Data.CodonTable.CodonTable.__init__
Bio.Data.CodonTable.NCBICodonTable.__init__
Bio.Decode.DecodeParser.__init__
Bio.Decode.DecodeScanner.__init__
Bio.Decode.Float.__init__
Bio.Decode.Function.__init__
Bio.Decode.FunctionCall.__init__
Bio.Decode.FunctionCallChain.__init__
Bio.Decode.FunctionName.__init__
Bio.Decode.Integer.__init__
Bio.Decode.String.__init__
Bio.Decode.Token.__init__
Bio.Decode.ValueToken.__init__
Bio.DocSQL.Create.__init__
Bio.DocSQL.Insert.__init__
Bio.DocSQL.IterationCursor.__init__
Bio.DocSQL.Query.__init__
Bio.DocSQL.QueryAll.__init__
Bio.DocSQL.QueryGeneric.__init__
Bio.DocSQL.QueryRow.__init__
Bio.DocSQL.QuerySingle.__init__
Bio.ECell.ECellError.__init__
Bio.ECell.Error.__init__
Bio.ECell.Iterator.__init__
Bio.ECell.Record.Record.__init__
Bio.ECell.RecordParser.__init__
Bio.ECell._RecordConsumer.__init__
Bio.ECell._Scanner.__init__
Bio.EUtils.Config.DatabaseInfo.__init__
Bio.EUtils.DBIdsClient.BaseDBIdsRecordSet.__init__
Bio.EUtils.DBIdsClient.DBIdsClient.__init__
Bio.EUtils.DBIdsClient.DBIdsLookup.__init__
Bio.EUtils.Datatypes.BinaryOp.__init__
Bio.EUtils.Datatypes.CheckLinkSet.__init__
Bio.EUtils.Datatypes.DBIds.__init__
Bio.EUtils.Datatypes.Date.__init__
Bio.EUtils.Datatypes.DateRange.__init__
Bio.EUtils.Datatypes.EUtilsSearchError.__init__
Bio.EUtils.Datatypes.IdCheck.__init__
Bio.EUtils.Datatypes.IdUrlSet.__init__
Bio.EUtils.Datatypes.Link.__init__
Bio.EUtils.Datatypes.LinkSetDb.__init__
Bio.EUtils.Datatypes.LinksLinkSet.__init__
Bio.EUtils.Datatypes.NeighborLinkSet.__init__
Bio.EUtils.Datatypes.ObjUrl.__init__
Bio.EUtils.Datatypes.PostResult.__init__
Bio.EUtils.Datatypes.Problem.__init__
Bio.EUtils.Datatypes.Provider.__init__
Bio.EUtils.Datatypes.Range.__init__
Bio.EUtils.Datatypes.SearchResult.__init__
Bio.EUtils.Datatypes.Summary.__init__
Bio.EUtils.Datatypes.Term.__init__
Bio.EUtils.Datatypes.WithinNDays.__init__
Bio.EUtils.HistoryClient.BaseHistoryRecordSet.__init__
Bio.EUtils.HistoryClient.HistoryClient.__init__
Bio.EUtils.HistoryClient.HistoryCookie.__init__
Bio.EUtils.HistoryClient.HistoryLookup.__init__
Bio.EUtils.HistoryClient.HistoryRecord.__init__
Bio.EUtils.MultiDict.OrderedMultiDict.__init__
Bio.EUtils.MultiDict.UnorderedMultiDict.__init__
Bio.EUtils.POM.Comment.__init__
Bio.EUtils.POM.ContentModel.__init__
Bio.EUtils.POM.DTDConsumerForSourceGeneration.__init__
Bio.EUtils.POM.ElementNode.__init__
Bio.EUtils.POM.IndentedText.__init__
Bio.EUtils.POM.ObjectParserHandler.__init__
Bio.EUtils.POM.POMDocument.__init__
Bio.EUtils.POM.XMLAttribute.__init__
Bio.EUtils.POM._ContentModelGenerator.__init__
Bio.EUtils.ReseekFile.ReseekFile.__init__
Bio.EUtils.ThinClient.ThinClient.__init__
Bio.EUtils.parse.UsePOMParser.__init__
Bio.EUtils.sourcegen.ClassHolder.__init__
Bio.EUtils.sourcegen.FunctionHolder.__init__
Bio.EUtils.sourcegen.MethodHolder.__init__
Bio.EUtils.sourcegen.SourceFile.__init__
Bio.EUtils.sourcegen.SourceGen.__init__
Bio.Emboss.Applications.EConsenseCommandline.__init__
Bio.Emboss.Applications.EInvertedCommandline.__init__
Bio.Emboss.Applications.ENeighborCommandline.__init__
Bio.Emboss.Applications.EProtDistCommandline.__init__
Bio.Emboss.Applications.EProtParsCommandline.__init__
Bio.Emboss.Applications.ESeqBootCommandline.__init__
Bio.Emboss.Applications.ETandemCommandline.__init__
Bio.Emboss.Applications.Est2GenomeCommandline.__init__
Bio.Emboss.Applications.FuzznucCommandline.__init__
Bio.Emboss.Applications.PalindromeCommandline.__init__
Bio.Emboss.Applications.Primer3Commandline.__init__
Bio.Emboss.Applications.PrimerSearchCommandline.__init__
Bio.Emboss.Applications.TranalignCommandline.__init__
Bio.Emboss.Applications.WaterCommandline.__init__
Bio.Emboss.Primer.Primer3Parser.__init__
Bio.Emboss.Primer.Primer3Primers.__init__
Bio.Emboss.Primer.Primer3Record.__init__
Bio.Emboss.Primer.PrimerSearchAmplifier.__init__
Bio.Emboss.Primer.PrimerSearchInputRecord.__init__
Bio.Emboss.Primer.PrimerSearchOutputRecord.__init__
Bio.Emboss.Primer.PrimerSearchParser.__init__
Bio.Emboss.Primer._Primer3RecordConsumer.__init__
Bio.Emboss.Primer._Primer3Scanner.__init__
Bio.Emboss.Primer._PrimerSearchRecordConsumer.__init__
Bio.Emboss.Primer._PrimerSearchScanner.__init__
Bio.Entrez.Parser.DataHandler.__init__
Bio.Entrez.Parser.StructureElement.__init__
Bio.Enzyme.DataRecord.__init__
Bio.Enzyme.EnzymeRecord.__init__
Bio.Enzyme.Iterator.__init__
Bio.Enzyme.RecordParser.__init__
Bio.Enzyme._RecordConsumer.__init__
Bio.FSSP.FSSPAlignDict.__init__
Bio.FSSP.FSSPAlignRec.__init__
Bio.FSSP.FSSPHeader.__init__
Bio.FSSP.FSSPSumRec.__init__
Bio.FSSP.FSSPTools.FSSPMultAlign.__init__
Bio.FSSP.PosAlign.__init__
Bio.FSSP.fssp_rec.fff_rec.__init__
Bio.Fasta.FastaAlign.FastaAlignment.__init__
Bio.Fasta.Iterator.__init__
Bio.Fasta.Record.__init__
Bio.Fasta.RecordParser.__init__
Bio.Fasta.SequenceParser.__init__
Bio.File.SGMLHandle.__init__
Bio.File.SGMLStripper.MyParser.__init__
Bio.File.SGMLStripper.__init__
Bio.File.UndoHandle.__init__
Bio.FilteredReader.FilteredReader.__init__
Bio.GA.Crossover.General.SafeFitnessCrossover.__init__
Bio.GA.Crossover.GeneralPoint.GeneralPointCrossover.__init__
Bio.GA.Crossover.GeneralPoint.InterleaveCrossover.__init__
Bio.GA.Crossover.Point.SinglePointCrossover.__init__
Bio.GA.Crossover.TwoPoint.TwoPointCrossover.__init__
Bio.GA.Crossover.Uniform.UniformCrossover.__init__
Bio.GA.Evolver.GenerationEvolver.__init__
Bio.GA.Evolver.SteadyStateEvolver.__init__
Bio.GA.Mutation.General.SafeFitnessMutation.__init__
Bio.GA.Mutation.Simple.ConversionMutation.__init__
Bio.GA.Mutation.Simple.SinglePositionMutation.__init__
Bio.GA.Organism.Organism.__init__
Bio.GA.Repair.Stabilizing.AmbiguousRepair.__init__
Bio.GA.Selection.Abstract.AbstractSelection.__init__
Bio.GA.Selection.Diversity.DiversitySelection.__init__
Bio.GA.Selection.RouletteWheel.RouletteWheelSelection.__init__
Bio.GA.Selection.Tournament.TournamentSelection.__init__
Bio.GFF.Connection.__init__
Bio.GFF.Feature.__init__
Bio.GFF.FeatureAggregate.__init__
Bio.GFF.FeatureQuery.__init__
Bio.GFF.FeatureQueryRow.__init__
Bio.GFF.GenericTools.ArgsParser.__init__
Bio.GFF.GenericTools.Surrogate.__init__
Bio.GFF.GenericTools.TempFile.__init__
Bio.GFF.RetrieveSeqname.__init__
Bio.GFF.Segment.__init__
Bio.GFF.easy.FeatureDict.__init__
Bio.GFF.easy.Location.__init__
Bio.GFF.easy.LocationFromCoords.__init__
Bio.GFF.easy.LocationFromString.__init__
Bio.GFF.easy.LocationJoin.__init__
Bio.GenBank.FeatureParser.__init__
Bio.GenBank.Iterator.__init__
Bio.GenBank.LocationParser.AbsoluteLocation.__init__
Bio.GenBank.LocationParser.Between.__init__
Bio.GenBank.LocationParser.FeatureName.__init__
Bio.GenBank.LocationParser.Function.__init__
Bio.GenBank.LocationParser.HighBound.__init__
Bio.GenBank.LocationParser.Integer.__init__
Bio.GenBank.LocationParser.LocationParser.__init__
Bio.GenBank.LocationParser.LocationScanner.__init__
Bio.GenBank.LocationParser.LowBound.__init__
Bio.GenBank.LocationParser.Path.__init__
Bio.GenBank.LocationParser.Range.__init__
Bio.GenBank.LocationParser.Symbol.__init__
Bio.GenBank.LocationParser.Token.__init__
Bio.GenBank.LocationParser.TwoBound.__init__
Bio.GenBank.NCBIDictionary.__init__
Bio.GenBank.Record.Feature.__init__
Bio.GenBank.Record.Qualifier.__init__
Bio.GenBank.Record.Record.__init__
Bio.GenBank.Record.Reference.__init__
Bio.GenBank.RecordParser.__init__
Bio.GenBank.Scanner.InsdcScanner.__init__
Bio.GenBank._BaseGenBankConsumer.__init__
Bio.GenBank._FeatureConsumer.__init__
Bio.GenBank._RecordConsumer.__init__
Bio.GenBank.utils.FeatureValueCleaner.__init__
Bio.Geo.Record.Record.__init__
Bio.Gobase.Dictionary.__init__
Bio.Gobase.GeneRecord.__init__
Bio.Gobase.Iterator.__init__
Bio.Gobase.ProteinRecord.__init__
Bio.Gobase.Record.__init__
Bio.Gobase.RecordParser.__init__
Bio.Gobase.SequenceRecord.__init__
Bio.Gobase._RecordConsumer.__init__
Bio.Graphics.BasicChromosome.Chromosome.__init__
Bio.Graphics.BasicChromosome.ChromosomeSegment.__init__
Bio.Graphics.BasicChromosome.Organism.__init__
Bio.Graphics.BasicChromosome.TelomereSegment.__init__
Bio.Graphics.BasicChromosome._ChromosomeComponent.__init__
Bio.Graphics.Comparative.ComparativeScatterPlot.__init__
Bio.Graphics.DisplayRepresentation.ChromosomeCounts.__init__
Bio.Graphics.Distribution.BarChartDistribution.__init__
Bio.Graphics.Distribution.DistributionPage.__init__
Bio.Graphics.Distribution.LineDistribution.__init__
Bio.HMM.DynamicProgramming.AbstractDPAlgorithms.__init__
Bio.HMM.DynamicProgramming.LogDPAlgorithms.__init__
Bio.HMM.DynamicProgramming.ScaledDPAlgorithms.__init__
Bio.HMM.MarkovModel.HiddenMarkovModel.__init__
Bio.HMM.MarkovModel.MarkovModelBuilder.__init__
Bio.HMM.Trainer.AbstractTrainer.__init__
Bio.HMM.Trainer.BaumWelchTrainer.__init__
Bio.HMM.Trainer.KnownStateTrainer.__init__
Bio.HMM.Trainer.TrainingSequence.__init__
Bio.HotRand.HotCache.__init__
Bio.HotRand.HotRandom.__init__
Bio.Index._InMemoryIndex.__init__
Bio.Index._ShelveIndex.__init__
Bio.IntelliGenetics.IntelliGeneticsReader.__init__
Bio.IntelliGenetics.Iterator.__init__
Bio.IntelliGenetics.Record.Record.__init__
Bio.IntelliGenetics.RecordParser.__init__
Bio.IntelliGenetics._RecordConsumer.__init__
Bio.IntelliGenetics._Scanner.__init__
Bio.KDTree.CKDTree.KDTree.__init__
Bio.KDTree.CKDTree.KDTreePtr.__init__
Bio.KDTree.KDTree.KDTree.__init__
Bio.KEGG.Compound.Record.__init__
Bio.KEGG.Enzyme.Record.__init__
Bio.LocusLink.Iterator.__init__
Bio.LocusLink.Record.__init__
Bio.LocusLink.RecordParser.__init__
Bio.LocusLink._RecordConsumer.__init__
Bio.LocusLink._Scanner.__init__
Bio.LocusLink.web_parse.Record.__init__
Bio.LocusLink.web_parse.Token.__init__
Bio.LocusLink.web_parse.Url.__init__
Bio.LogisticRegression.LogisticRegression.__init__
Bio.MEME.Motif.Instance.__init__
Bio.MEME.Motif.MEMEMotif.__init__
Bio.MEME.Motif.Motif.__init__
Bio.MEME.Parser.MASTParser.__init__
Bio.MEME.Parser.MASTRecord.__init__
Bio.MEME.Parser.MEMEParser.__init__
Bio.MEME.Parser.MEMERecord.__init__
Bio.MEME.Parser._MASTConsumer.__init__
Bio.MEME.Parser._MEMEConsumer.__init__
Bio.MarkovModel.MarkovModel.__init__
Bio.MaxEntropy.MaxEntropy.__init__
Bio.Medline.Iterator.__init__
Bio.Medline.Record.__init__
Bio.Medline.RecordParser.__init__
Bio.Medline._RecordConsumer.__init__
Bio.MetaTool.Iterator.__init__
Bio.MetaTool.Record.Metabolite.__init__
Bio.MetaTool.Record.MetaboliteRole.__init__
Bio.MetaTool.Record.PathwayTransform.__init__
Bio.MetaTool.Record.Record.__init__
Bio.MetaTool.RecordParser.__init__
Bio.MetaTool._RecordConsumer.__init__
Bio.MetaTool._Scanner.__init__
Bio.Mindy.BaseDB.OpenDB.__init__
Bio.Mindy.BerkeleyDB.BerkeleyDB.__init__
Bio.Mindy.BerkeleyDB.PrimaryNamespace.__init__
Bio.Mindy.BerkeleyDB.SecondaryNamespace.__init__
Bio.Mindy.FlatDB.BaseFlatDB.__init__
Bio.Mindy.FlatDB.BisectFile.__init__
Bio.Mindy.FlatDB.DiskFlatDB.__init__
Bio.Mindy.FlatDB.MemoryFlatDB.__init__
Bio.Mindy.FlatDB.PrimaryNamespace.__init__
Bio.Mindy.FlatDB.PrimaryTable.__init__
Bio.Mindy.FlatDB.SecondaryNamespace.__init__
Bio.Mindy.FlatDB.SecondaryTable.__init__
Bio.Mindy.Location.Location.__init__
Bio.Mindy.SimpleSeqRecord.BaseSeqRecordIndexer.__init__
Bio.Mindy.SimpleSeqRecord.FixDocumentBuilder.__init__
Bio.Mindy.SimpleSeqRecord.FunctionIndexer.__init__
Bio.Mindy.SimpleSeqRecord.SimpleIndexer.__init__
Bio.Mindy.XPath.GrabXPathNodes.__init__
Bio.NBRF.Iterator.__init__
Bio.NBRF.Record.Record.__init__
Bio.NBRF.RecordParser.__init__
Bio.NBRF._RecordConsumer.__init__
Bio.NBRF._Scanner.__init__
Bio.NMR.xpktools.Peaklist.__init__
Bio.NMR.xpktools.XpkEntry.__init__
Bio.NaiveBayes.NaiveBayes.__init__
Bio.Ndb.Record.__init__
Bio.NetCatch.ExtractUrls.__init__
Bio.NetCatch.NetCatch.__init__
Bio.NetCatch.Url.__init__
Bio.NeuralNetwork.BackPropagation.Layer.AbstractLayer.__init__
Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer.__init__
Bio.NeuralNetwork.BackPropagation.Layer.InputLayer.__init__
Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer.__init__
Bio.NeuralNetwork.BackPropagation.Network.BasicNetwork.__init__
Bio.NeuralNetwork.Gene.Motif.MotifCoder.__init__
Bio.NeuralNetwork.Gene.Motif.MotifFinder.__init__
Bio.NeuralNetwork.Gene.Pattern.PatternIO.__init__
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.__init__
Bio.NeuralNetwork.Gene.Schema.DifferentialSchemaFitness.__init__
Bio.NeuralNetwork.Gene.Schema.GeneticAlgorithmFinder.__init__
Bio.NeuralNetwork.Gene.Schema.MostCountSchemaFitness.__init__
Bio.NeuralNetwork.Gene.Schema.RandomMotifGenerator.__init__
Bio.NeuralNetwork.Gene.Schema.Schema.__init__
Bio.NeuralNetwork.Gene.Schema.SchemaCoder.__init__
Bio.NeuralNetwork.Gene.Schema.SchemaFactory.__init__
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.__init__
Bio.NeuralNetwork.Gene.Schema.SimpleFinisher.__init__
Bio.NeuralNetwork.Gene.Signature.SignatureCoder.__init__
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.__init__
Bio.NeuralNetwork.StopTraining.ValidationIncreaseStop.__init__
Bio.NeuralNetwork.Training.ExampleManager.__init__
Bio.NeuralNetwork.Training.TrainingExample.__init__
Bio.Nexus.Nexus.Block.__init__
Bio.Nexus.Nexus.CharBuffer.__init__
Bio.Nexus.Nexus.Commandline.__init__
Bio.Nexus.Nexus.Nexus.__init__
Bio.Nexus.Nexus.StepMatrix.__init__
Bio.Nexus.Nodes.Chain.__init__
Bio.Nexus.Nodes.Node.__init__
Bio.Nexus.Trees.NodeData.__init__
Bio.Nexus.Trees.Tree.__init__
Bio.PDB.AbstractPropertyMap.AbstractAtomPropertyMap.__init__
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.__init__
Bio.PDB.AbstractPropertyMap.AbstractResiduePropertyMap.__init__
Bio.PDB.Atom.Atom.__init__
Bio.PDB.Atom.DisorderedAtom.__init__
Bio.PDB.Chain.Chain.__init__
Bio.PDB.DSSP'.DSSP.__init__
Bio.PDB.Dice.ChainSelector.__init__
Bio.PDB.Entity.DisorderedEntityWrapper.__init__
Bio.PDB.Entity.Entity.__init__
Bio.PDB.FragmentMapper'.Fragment.__init__
Bio.PDB.FragmentMapper'.FragmentMapper.__init__
Bio.PDB.HSExposure.ExposureCN.__init__
Bio.PDB.HSExposure.HSExposureCA.__init__
Bio.PDB.HSExposure.HSExposureCB.__init__
Bio.PDB.HSExposure._AbstractHSExposure.__init__
Bio.PDB.MMCIF2Dict.MMCIF2Dict.__init__
Bio.PDB.Model.Model.__init__
Bio.PDB.NACCESS.NACCESS.__init__
Bio.PDB.NACCESS.NACCESS_atomic.__init__
Bio.PDB.NeighborSearch.NeighborSearch.__init__
Bio.PDB.PDBIO'.PDBIO.__init__
Bio.PDB.PDBList'.PDBList.__init__
Bio.PDB.PDBParser'.PDBParser.__init__
Bio.PDB.PSEA.PSEA.__init__
Bio.PDB.Polypeptide.CaPPBuilder.__init__
Bio.PDB.Polypeptide.PPBuilder.__init__
Bio.PDB.Polypeptide._PPBuilder.__init__
Bio.PDB.Residue.DisorderedResidue.__init__
Bio.PDB.Residue.Residue.__init__
Bio.PDB.ResidueDepth'.ResidueDepth.__init__
Bio.PDB.Structure.Structure.__init__
Bio.PDB.StructureAlignment'.StructureAlignment.__init__
Bio.PDB.StructureBuilder.StructureBuilder.__init__
Bio.PDB.Superimposer'.Superimposer.__init__
Bio.PDB.Vector'.Vector.__init__
Bio.ParserSupport.EventGenerator.__init__
Bio.ParserSupport.SGMLStrippingConsumer.__init__
Bio.ParserSupport.TaggingConsumer.__init__
Bio.Parsers.spark.GenericASTBuilder.__init__
Bio.Parsers.spark.GenericASTMatcher.__init__
Bio.Parsers.spark.GenericASTTraversal.__init__
Bio.Parsers.spark.GenericParser.__init__
Bio.Parsers.spark.GenericScanner.__init__
Bio.Pathway.Network.__init__
Bio.Pathway.Reaction.__init__
Bio.Pathway.Rep.Graph.Graph.__init__
Bio.Pathway.Rep.HashSet.HashSet.__init__
Bio.Pathway.Rep.MultiGraph.MultiGraph.__init__
Bio.Pathway.System.__init__
Bio.PopGen.Async.Async.__init__
Bio.PopGen.Async.DirectoryRetriever.__init__
Bio.PopGen.Async.FileRetriever.__init__
Bio.PopGen.Async.Local.Local.__init__
Bio.PopGen.FDist.Async.FDistAsync.__init__
Bio.PopGen.FDist.Async.SplitFDist.__init__
Bio.PopGen.FDist.Controller.FDistController.__init__
Bio.PopGen.FDist.Record.__init__
Bio.PopGen.FDist.RecordParser.__init__
Bio.PopGen.FDist._RecordConsumer.__init__
Bio.PopGen.GenePop.Record.__init__
Bio.PopGen.GenePop.RecordParser.__init__
Bio.PopGen.GenePop._RecordConsumer.__init__
Bio.PopGen.SimCoal.Async.SimCoalCache.__init__
Bio.PopGen.SimCoal.Cache.SimCoalCache.__init__
Bio.PopGen.SimCoal.Controller.SimCoalController.__init__
Bio.PropertyManager.PropertyManager.__init__
Bio.Prosite.Dictionary.__init__
Bio.Prosite.ExPASyDictionary.__init__
Bio.Prosite.Iterator.__init__
Bio.Prosite.Pattern.Prosite.__init__
Bio.Prosite.Pattern.PrositeMatch.__init__
Bio.Prosite.Pattern.PrositeTerm.__init__
Bio.Prosite.PatternHit.__init__
Bio.Prosite.Prodoc.Dictionary.__init__
Bio.Prosite.Prodoc.ExPASyDictionary.__init__
Bio.Prosite.Prodoc.Iterator.__init__
Bio.Prosite.Prodoc.Record.__init__
Bio.Prosite.Prodoc.RecordParser.__init__
Bio.Prosite.Prodoc.Reference.__init__
Bio.Prosite.Prodoc._RecordConsumer.__init__
Bio.Prosite.Record.__init__
Bio.Prosite.RecordParser.__init__
Bio.Prosite._RecordConsumer.__init__
Bio.PubMed.Dictionary.__init__
Bio.Rebase.Dictionary.__init__
Bio.Rebase.Iterator.__init__
Bio.Rebase.Record.__init__
Bio.Rebase.RecordParser.__init__
Bio.Rebase._RecordConsumer.__init__
Bio.Restriction.PrintFormat.PrintFormat.__init__
Bio.Restriction.Restriction.Analysis.__init__
Bio.Restriction.Restriction.FormattedSeq.__init__
Bio.Restriction.Restriction.RestrictionBatch.__init__
Bio.Restriction.Restriction.RestrictionType.__init__
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.__init__
Bio.Restriction._Update.RestrictionCompiler.TypeCompiler.__init__
Bio.Restriction._Update.RestrictionCompiler.newenzyme.__init__
Bio.Restriction._Update.Update.ConnectionError.__init__
Bio.Restriction._Update.Update.FtpNameError.__init__
Bio.Restriction._Update.Update.FtpPasswordError.__init__
Bio.Restriction._Update.Update.RebaseUpdate.__init__
Bio.SCOP.Astral.__init__
Bio.SCOP.Cla.Index.__init__
Bio.SCOP.Cla.Iterator.__init__
Bio.SCOP.Cla.Parser.__init__
Bio.SCOP.Cla.Record.__init__
Bio.SCOP.Des.Iterator.__init__
Bio.SCOP.Des.Parser.__init__
Bio.SCOP.Des.Record.__init__
Bio.SCOP.Dom.Iterator.__init__
Bio.SCOP.Dom.Record.__init__
Bio.SCOP.Domain.__init__
Bio.SCOP.FileIndex.FileIndex.__init__
Bio.SCOP.FileIndex.defaultdict.__init__
Bio.SCOP.Hie.Iterator.__init__
Bio.SCOP.Hie.Parser.__init__
Bio.SCOP.Hie.Record.__init__
Bio.SCOP.Node.__init__
Bio.SCOP.Raf.Iterator.__init__
Bio.SCOP.Raf.Parser.__init__
Bio.SCOP.Raf.Res.__init__
Bio.SCOP.Raf.SeqMap.__init__
Bio.SCOP.Raf.SeqMapIndex.__init__
Bio.SCOP.Residues'.Residues.__init__
Bio.SCOP.Scop.__init__
Bio.SGMLExtractor.SGMLExtractor.LocalParser.__init__
Bio.SGMLExtractor.SGMLExtractor.__init__
Bio.SGMLExtractor.SGMLExtractorHandle.__init__
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.__init__
Bio.Saf.Iterator.__init__
Bio.Saf.Record.Record.__init__
Bio.Saf.RecordParser.__init__
Bio.Saf._RecordConsumer.__init__
Bio.Saf._Scanner.__init__
Bio.Search.Algorithm.__init__
Bio.Search.Database.__init__
Bio.Search.HSP.__init__
Bio.Search.HSPSeq.__init__
Bio.Search.Hit.__init__
Bio.Search.HomologySeq.__init__
Bio.Search.Query.__init__
Bio.Search.Search.__init__
Bio.Search.TableInfo.__init__
Bio.Search._SeqLength.__init__
Bio.Seq.MutableSeq.__init__
Bio.Seq.Seq.__init__
Bio.SeqFeature.AbstractPosition.__init__
Bio.SeqFeature.AfterPosition.__init__
Bio.SeqFeature.BeforePosition.__init__
Bio.SeqFeature.BetweenPosition.__init__
Bio.SeqFeature.ExactPosition.__init__
Bio.SeqFeature.FeatureLocation.__init__
Bio.SeqFeature.OneOfPosition.__init__
Bio.SeqFeature.PositionGap.__init__
Bio.SeqFeature.Reference.__init__
Bio.SeqFeature.SeqFeature.__init__
Bio.SeqFeature.WithinPosition.__init__
Bio.SeqIO.ClustalIO.ClustalWriter.__init__
Bio.SeqIO.FastaIO.FastaWriter.__init__
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.__init__
Bio.SeqIO.Interfaces.SequenceIterator.__init__
Bio.SeqIO.Interfaces.SequenceWriter.__init__
Bio.SeqIO.Interfaces.SequentialSequenceWriter.__init__
Bio.SeqIO.PhylipIO.PhylipWriter.__init__
Bio.SeqIO.StockholmIO.StockholmIterator.__init__
Bio.SeqIO.StockholmIO.StockholmWriter.__init__
Bio.SeqRecord.SeqRecord.__init__
Bio.SeqUtils.CodonUsage.CodonAdaptationIndex.__init__
Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint.__init__
Bio.SeqUtils.MissingTable.__init__
Bio.SeqUtils.ProtParam.ProteinAnalysis.__init__
Bio.Sequencing.Ace.ACEFileRecord.__init__
Bio.Sequencing.Ace.ACEParser.__init__
Bio.Sequencing.Ace.Contig.__init__
Bio.Sequencing.Ace.Iterator.__init__
Bio.Sequencing.Ace.Reads.__init__
Bio.Sequencing.Ace.RecordParser.__init__
Bio.Sequencing.Ace._RecordConsumer.__init__
Bio.Sequencing.Ace.af.__init__
Bio.Sequencing.Ace.bs.__init__
Bio.Sequencing.Ace.ct.__init__
Bio.Sequencing.Ace.ds.__init__
Bio.Sequencing.Ace.qa.__init__
Bio.Sequencing.Ace.rd.__init__
Bio.Sequencing.Ace.rt.__init__
Bio.Sequencing.Ace.wa.__init__
Bio.Sequencing.Ace.wr.__init__
Bio.Sequencing.Phd.Iterator.__init__
Bio.Sequencing.Phd.Record.__init__
Bio.Sequencing.Phd.RecordParser.__init__
Bio.Sequencing.Phd._RecordConsumer.__init__
Bio.Std.StdTerm.__init__
Bio.StdHandler.ConvertDispatchHandler.__init__
Bio.StdHandler.ConvertHandler.__init__
Bio.StdHandler.Feature.__init__
Bio.StdHandler.Handle_dbxref.__init__
Bio.StdHandler.Handle_feature_location.__init__
Bio.StdHandler.Handle_feature_qualifier.__init__
Bio.StdHandler.Handle_features.__init__
Bio.StdHandler.Handle_hsp.__init__
Bio.StdHandler.RecognizeHandler.__init__
Bio.SubsMat.FreqTable.FreqTable.__init__
Bio.SubsMat.SeqMat.__init__
Bio.SwissProt.KeyWList.ListParser.__init__
Bio.SwissProt.KeyWList.Record.__init__
Bio.SwissProt.KeyWList._ListConsumer.__init__
Bio.SwissProt.KeyWList._Scanner.__init__
Bio.SwissProt.SProt.Dictionary.__init__
Bio.SwissProt.SProt.ExPASyDictionary.__init__
Bio.SwissProt.SProt.Iterator.__init__
Bio.SwissProt.SProt.Record.__init__
Bio.SwissProt.SProt.RecordParser.__init__
Bio.SwissProt.SProt.Reference.__init__
Bio.SwissProt.SProt.SequenceParser.__init__
Bio.SwissProt.SProt._RecordConsumer.__init__
Bio.SwissProt.SProt._SequenceConsumer.__init__
Bio.Transcribe.Transcribe.__init__
Bio.Translate.Translator.__init__
Bio.UniGene.Iterator.__init__
Bio.UniGene.RecordParser.__init__
Bio.UniGene.UnigeneProtsimRecord.__init__
Bio.UniGene.UnigeneRecord.__init__
Bio.UniGene.UnigeneSTSRecord.__init__
Bio.UniGene.UnigeneSequenceRecord.__init__
Bio.UniGene._RecordConsumer.__init__
Bio.WWW.RequestLimiter.__init__
Bio.Wise.dnal.Statistics.__init__
Bio.Wise.psw.AlignmentColumn.__init__
Bio.Wise.psw.ColumnUnit.__init__
Bio.Writer.Writer.__init__
Bio.biblio.Biblio.__init__
Bio.biblio.BiblioCollection.__init__
Bio.builders.Search.search.BuildSearch.__init__
Bio.builders.SeqRecord.sequence.BuildSeqRecord.__init__
Bio.config.DBRegistry.BioCorbaDB.__init__
Bio.config.DBRegistry.BioSQLDB.__init__
Bio.config.DBRegistry.CGIDB.__init__
Bio.config.DBRegistry.DBGroup.__init__
Bio.config.DBRegistry.DBObject.__init__
Bio.config.DBRegistry.DBRegistry.__init__
Bio.config.DBRegistry.EUtilsDB.__init__
Bio.config.DBRegistry.IndexedFileDB.__init__
Bio.config.FormatRegistry.FormatGroup.__init__
Bio.config.FormatRegistry.FormatObject.__init__
Bio.config.FormatRegistry.FormatRegistry.__init__
Bio.config.Registry.RegisterableGroup.__init__
Bio.config.Registry.RegisterableObject.__init__
Bio.config.Registry.Registry.__init__
Bio.config.SeqDBRegistry.SeqDBRegistry.__init__
Bio.config._stanzaformat.Stanza.__init__
Bio.config._stanzaformat.StanzaFormat.__init__
Bio.config._support.make_cached_expression.__init__
Bio.config._support.make_rate_limited_function.__init__
Bio.kNN.kNN.__init__
Bio.pairwise2.affine_penalty.__init__
Bio.pairwise2.dictionary_match.__init__
Bio.pairwise2.identity_match.__init__
Bio.writers.SeqRecord.embl.WriteEmbl.__init__
Bio.writers.SeqRecord.fasta.WriteFasta.__init__
BioSQL.BioSeq.DBSeq.__init__
BioSQL.BioSeq.DBSeqRecord.__init__
BioSQL.BioSeqDatabase.Adaptor.__init__
BioSQL.BioSeqDatabase.BioSeqDatabase.__init__
BioSQL.BioSeqDatabase.DBServer.__init__
BioSQL.DBUtils.Generic_dbutils.__init__
BioSQL.Loader.DatabaseLoader.__init__
BioSQL.Loader.DatabaseRemover.__init__
Martel.Dispatch.Callback.__init__
Martel.Dispatch.DispatchHandler.__init__
Martel.Dispatch.Dispatcher.__init__
Martel.Dispatch.Multicall.__init__
Martel.Dispatch.RemapEnd.__init__
Martel.Dispatch.RemapStart.__init__
Martel.Expression.Alt.__init__
Martel.Expression.Any.__init__
Martel.Expression.Assert.__init__
Martel.Expression.Debug.__init__
Martel.Expression.FastFeature.__init__
Martel.Expression.Group.__init__
Martel.Expression.GroupRef.__init__
Martel.Expression.HeaderFooter.__init__
Martel.Expression.Literal.__init__
Martel.Expression.MaxRepeat.__init__
Martel.Expression.NullOp.__init__
Martel.Expression.ParseRecords.__init__
Martel.Expression.PassThrough.__init__
Martel.Expression.Seq.__init__
Martel.Expression.Str.__init__
Martel.Generate.CheckAssert.__init__
Martel.Generate.CheckAssertNot.__init__
Martel.Generate.CheckGroupRef.__init__
Martel.Generate.GeneratorState.__init__
Martel.Generate.HandleRepeatCount.__init__
Martel.Generate.SetGroupValue.__init__
Martel.Generate._call_call.__init__
Martel.Generate._call_calltag.__init__
Martel.Generate.print_debug.__init__
Martel.Generate.print_info.__init__
Martel.IterParser.IterHeaderFooter.__init__
Martel.IterParser.IterRecords.__init__
Martel.Iterator.EventStream.__init__
Martel.Iterator.HeaderFooterEventStream.__init__
Martel.Iterator.Iterate.__init__
Martel.Iterator.Iterator.__init__
Martel.Iterator.IteratorHeaderFooter.__init__
Martel.Iterator.IteratorRecords.__init__
Martel.Iterator.RecordEventStream.__init__
Martel.Iterator.StoreEvents.__init__
Martel.LAX.ElementInfo.__init__
Martel.LAX.LAX.__init__
Martel.Parser.HeaderFooterParser.__init__
Martel.Parser.Parser.__init__
Martel.Parser.ParserIncompleteException.__init__
Martel.Parser.ParserPositionException.__init__
Martel.Parser.RecordParser.__init__
Martel.RecordReader.CountLines.__init__
Martel.RecordReader.EndsWith.__init__
Martel.RecordReader.Everything.__init__
Martel.RecordReader.Nothing.__init__
Martel.RecordReader.RecordReader.__init__
Martel.RecordReader.StartsWith.__init__
Martel.RecordReader.Until.__init__
Martel.convert_re.GroupNames.__init__
Martel.msre_parse.Pattern.__init__
Martel.msre_parse.SubPattern.__init__
Martel.msre_parse.Tokenizer.__init__
Martel.test.support.CheckGood.__init__
Martel.test.support.Dump.__init__
Martel.test.support.Storage.__init__
Martel.test.test_Parser.CountErrors.__init__
Martel.test.test_Parser.CountRecords.__init__
Martel.test.test_delimiter.CatchFields.__init__
Martel.test.test_optimize.GetErrorPos.__init__" class="py-name" href="#" onclick="return doclink('link-41', '__init__', 'link-7');">__init__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt id="link-42" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-42', 'name', 'link-8');">name</a></tt><tt class="py-op">,</tt> <tt class="py-name">abbrev</tt><tt class="py-op">,</tt> <tt class="py-name">doc</tt><tt class="py-op">)</tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">expression</tt> <tt class="py-op">=</tt> <tt id="link-43" class="py-name" targets="Function Bio.config.FormatRegistry._normalize_expression()=Bio.config.FormatRegistry-module.html#_normalize_expression"><a title="Bio.config.FormatRegistry._normalize_expression" class="py-name" href="#" onclick="return doclink('link-43', '_normalize_expression', 'link-43');">_normalize_expression</a></tt><tt class="py-op">(</tt><tt class="py-name">expression</tt><tt class="py-op">)</tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-44" class="py-name" targets="Function Bio.FSSP.FSSPTools.filter()=Bio.FSSP.FSSPTools-module.html#filter,Method Bio.FilteredReader.FilteredReader.filter()=Bio.FilteredReader.FilteredReader-class.html#filter,Variable Bio.expressions.swissprot.filter=Bio.expressions.swissprot-module.html#filter"><a title="Bio.FSSP.FSSPTools.filter
Bio.FilteredReader.FilteredReader.filter
Bio.expressions.swissprot.filter" class="py-name" href="#" onclick="return doclink('link-44', 'filter', 'link-44');">filter</a></tt> <tt class="py-op">=</tt> <tt id="link-45" class="py-name"><a title="Bio.config.FormatRegistry._normalize_expression" class="py-name" href="#" onclick="return doclink('link-45', '_normalize_expression', 'link-43');">_normalize_expression</a></tt><tt class="py-op">(</tt><tt id="link-46" class="py-name"><a title="Bio.FSSP.FSSPTools.filter
Bio.FilteredReader.FilteredReader.filter
Bio.expressions.swissprot.filter" class="py-name" href="#" onclick="return doclink('link-46', 'filter', 'link-44');">filter</a></tt><tt class="py-op">)</tt> <tt class="py-keyword">or</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">expression</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-47" class="py-name"><a title="Bio.FSSP.FSSPTools.filter
Bio.FilteredReader.FilteredReader.filter
Bio.expressions.swissprot.filter" class="py-name" href="#" onclick="return doclink('link-47', 'filter', 'link-44');">filter</a></tt> <tt class="py-op">=</tt> <tt id="link-48" class="py-name"><a title="Bio.config._support
Bio.dbdefs._support" class="py-name" href="#" onclick="return doclink('link-48', '_support', 'link-5');">_support</a></tt><tt class="py-op">.</tt><tt id="link-49" class="py-name" targets="Class Bio.config._support.make_cached_expression=Bio.config._support.make_cached_expression-class.html"><a title="Bio.config._support.make_cached_expression" class="py-name" href="#" onclick="return doclink('link-49', 'make_cached_expression', 'link-49');">make_cached_expression</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-50" class="py-name"><a title="Bio.FSSP.FSSPTools.filter
Bio.FilteredReader.FilteredReader.filter
Bio.expressions.swissprot.filter" class="py-name" href="#" onclick="return doclink('link-50', 'filter', 'link-44');">filter</a></tt><tt class="py-op">)</tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">multirecord</tt> <tt class="py-op">=</tt> <tt class="py-name">operator</tt><tt class="py-op">.</tt><tt class="py-name">truth</tt><tt class="py-op">(</tt><tt class="py-name">multirecord</tt><tt class="py-op">)</tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_parser_cache</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L144"></a><tt class="py-lineno">144</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_iterator_cache</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_parents</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
</div><a name="L146"></a><tt class="py-lineno">146</tt>  <tt class="py-line">         </tt>
<a name="FormatObject.identifyFile"></a><div id="FormatObject.identifyFile-def"><a name="L147"></a><tt class="py-lineno">147</tt> <a class="py-toggle" href="#" id="FormatObject.identifyFile-toggle" onclick="return toggle('FormatObject.identifyFile');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.config.FormatRegistry.FormatObject-class.html#identifyFile">identifyFile</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">infile</tt><tt class="py-op">,</tt> <tt class="py-param">debug_level</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FormatObject.identifyFile-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="FormatObject.identifyFile-expanded"><a name="L148"></a><tt class="py-lineno">148</tt>  <tt class="py-line">        <tt class="py-docstring">"""S.identifyFile(infile[, debug_level]) -&gt; FormatObject or None"""</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt id="link-51" class="py-name" targets="Function Bio.config.FormatRegistry._parses_file()=Bio.config.FormatRegistry-module.html#_parses_file"><a title="Bio.config.FormatRegistry._parses_file" class="py-name" href="#" onclick="return doclink('link-51', '_parses_file', 'link-51');">_parses_file</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-52" class="py-name"><a title="Bio.FSSP.FSSPTools.filter
Bio.FilteredReader.FilteredReader.filter
Bio.expressions.swissprot.filter" class="py-name" href="#" onclick="return doclink('link-52', 'filter', 'link-44');">filter</a></tt><tt class="py-op">,</tt> <tt class="py-name">infile</tt><tt class="py-op">,</tt> <tt class="py-name">debug_level</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> <tt class="py-name">self</tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">None</tt> </tt>
</div><a name="L152"></a><tt class="py-lineno">152</tt>  <tt class="py-line">     </tt>
<a name="FormatObject.identifyString"></a><div id="FormatObject.identifyString-def"><a name="L153"></a><tt class="py-lineno">153</tt> <a class="py-toggle" href="#" id="FormatObject.identifyString-toggle" onclick="return toggle('FormatObject.identifyString');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.config.FormatRegistry.FormatObject-class.html#identifyString">identifyString</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">s</tt><tt class="py-op">,</tt> <tt class="py-param">debug_level</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FormatObject.identifyString-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="FormatObject.identifyString-expanded"><a name="L154"></a><tt class="py-lineno">154</tt>  <tt class="py-line">        <tt class="py-docstring">"""S.identifyString(s[, debug_level]) -&gt; FormatObject or None"""</tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt id="link-53" class="py-name" targets="Function Bio.config.FormatRegistry._parses_string()=Bio.config.FormatRegistry-module.html#_parses_string"><a title="Bio.config.FormatRegistry._parses_string" class="py-name" href="#" onclick="return doclink('link-53', '_parses_string', 'link-53');">_parses_string</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-54" class="py-name"><a title="Bio.FSSP.FSSPTools.filter
Bio.FilteredReader.FilteredReader.filter
Bio.expressions.swissprot.filter" class="py-name" href="#" onclick="return doclink('link-54', 'filter', 'link-44');">filter</a></tt><tt class="py-op">,</tt> <tt id="link-55" class="py-name" targets="Variable Martel.test.test_swissprot38.s=Martel.test.test_swissprot38-module.html#s"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-55', 's', 'link-55');">s</a></tt><tt class="py-op">,</tt> <tt class="py-name">debug_level</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> <tt class="py-name">self</tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">None</tt> </tt>
</div><a name="L158"></a><tt class="py-lineno">158</tt>  <tt class="py-line">     </tt>
<a name="FormatObject.identify"></a><div id="FormatObject.identify-def"><a name="L159"></a><tt class="py-lineno">159</tt> <a class="py-toggle" href="#" id="FormatObject.identify-toggle" onclick="return toggle('FormatObject.identify');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.config.FormatRegistry.FormatObject-class.html#identify">identify</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">source</tt><tt class="py-op">,</tt> <tt class="py-param">debug_level</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FormatObject.identify-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="FormatObject.identify-expanded"><a name="L160"></a><tt class="py-lineno">160</tt>  <tt class="py-line">        <tt class="py-docstring">"""S.identify(source[, debug_level]) -&gt; FormatObject or None"""</tt> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt>  <tt class="py-line">        <tt id="link-56" class="py-name" targets="Method Bio.GenBank._FeatureConsumer.source()=Bio.GenBank._FeatureConsumer-class.html#source,Method Bio.GenBank._RecordConsumer.source()=Bio.GenBank._RecordConsumer-class.html#source,Method Bio.Medline._RecordConsumer.source()=Bio.Medline._RecordConsumer-class.html#source,Method Bio.Pathway.Network.source()=Bio.Pathway.Network-class.html#source,Method Bio.Rebase._RecordConsumer.source()=Bio.Rebase._RecordConsumer-class.html#source"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-56', 'source', 'link-56');">source</a></tt> <tt class="py-op">=</tt> <tt id="link-57" class="py-name" targets="Module Bio.EUtils.ReseekFile=Bio.EUtils.ReseekFile-module.html,Class Bio.EUtils.ReseekFile.ReseekFile=Bio.EUtils.ReseekFile.ReseekFile-class.html"><a title="Bio.EUtils.ReseekFile
Bio.EUtils.ReseekFile.ReseekFile" class="py-name" href="#" onclick="return doclink('link-57', 'ReseekFile', 'link-57');">ReseekFile</a></tt><tt class="py-op">.</tt><tt id="link-58" class="py-name" targets="Function Bio.EUtils.ReseekFile.prepare_input_source()=Bio.EUtils.ReseekFile-module.html#prepare_input_source"><a title="Bio.EUtils.ReseekFile.prepare_input_source" class="py-name" href="#" onclick="return doclink('link-58', 'prepare_input_source', 'link-58');">prepare_input_source</a></tt><tt class="py-op">(</tt><tt id="link-59" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-59', 'source', 'link-56');">source</a></tt><tt class="py-op">)</tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt>  <tt class="py-line">        <tt class="py-name">f</tt> <tt class="py-op">=</tt> <tt id="link-60" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-60', 'source', 'link-56');">source</a></tt><tt class="py-op">.</tt><tt class="py-name">getCharacterStream</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-keyword">or</tt> <tt id="link-61" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-61', 'source', 'link-56');">source</a></tt><tt class="py-op">.</tt><tt class="py-name">getByteStream</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L163"></a><tt class="py-lineno">163</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-62" class="py-name" targets="Method Bio.config.FormatRegistry.FormatGroup.identifyFile()=Bio.config.FormatRegistry.FormatGroup-class.html#identifyFile,Method Bio.config.FormatRegistry.FormatObject.identifyFile()=Bio.config.FormatRegistry.FormatObject-class.html#identifyFile"><a title="Bio.config.FormatRegistry.FormatGroup.identifyFile
Bio.config.FormatRegistry.FormatObject.identifyFile" class="py-name" href="#" onclick="return doclink('link-62', 'identifyFile', 'link-62');">identifyFile</a></tt><tt class="py-op">(</tt><tt class="py-name">f</tt><tt class="py-op">,</tt> <tt class="py-name">debug_level</tt><tt class="py-op">)</tt> </tt>
</div><a name="L164"></a><tt class="py-lineno">164</tt>  <tt class="py-line"> </tt>
<a name="FormatObject.make_parser"></a><div id="FormatObject.make_parser-def"><a name="L165"></a><tt class="py-lineno">165</tt> <a class="py-toggle" href="#" id="FormatObject.make_parser-toggle" onclick="return toggle('FormatObject.make_parser');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.config.FormatRegistry.FormatObject-class.html#make_parser">make_parser</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">select_names</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">debug_level</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FormatObject.make_parser-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="FormatObject.make_parser-expanded"><a name="L166"></a><tt class="py-lineno">166</tt>  <tt class="py-line">        <tt class="py-docstring">"""S.make_parser([select_names][, debug_level]) -&gt; parser"""</tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt id="link-63" class="py-name" targets="Function Martel.select_names()=Martel-module.html#select_names"><a title="Martel.select_names" class="py-name" href="#" onclick="return doclink('link-63', 'select_names', 'link-63');">select_names</a></tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L168"></a><tt class="py-lineno">168</tt>  <tt class="py-line">            <tt id="link-64" class="py-name"><a title="Martel.select_names" class="py-name" href="#" onclick="return doclink('link-64', 'select_names', 'link-63');">select_names</a></tt> <tt class="py-op">=</tt> <tt id="link-65" class="py-name" targets="Method Bio.Pathway.Rep.HashSet.HashSet.list()=Bio.Pathway.Rep.HashSet.HashSet-class.html#list"><a title="Bio.Pathway.Rep.HashSet.HashSet.list" class="py-name" href="#" onclick="return doclink('link-65', 'list', 'link-65');">list</a></tt><tt class="py-op">(</tt><tt id="link-66" class="py-name"><a title="Martel.select_names" class="py-name" href="#" onclick="return doclink('link-66', 'select_names', 'link-63');">select_names</a></tt><tt class="py-op">)</tt> </tt>
<a name="L169"></a><tt class="py-lineno">169</tt>  <tt class="py-line">            <tt id="link-67" class="py-name"><a title="Martel.select_names" class="py-name" href="#" onclick="return doclink('link-67', 'select_names', 'link-63');">select_names</a></tt><tt class="py-op">.</tt><tt id="link-68" class="py-name" targets="Method Bio.PDB.Residue.DisorderedResidue.sort()=Bio.PDB.Residue.DisorderedResidue-class.html#sort,Method Bio.PDB.Residue.Residue.sort()=Bio.PDB.Residue.Residue-class.html#sort,Method Bio.Sequencing.Ace.ACEFileRecord.sort()=Bio.Sequencing.Ace.ACEFileRecord-class.html#sort"><a title="Bio.PDB.Residue.DisorderedResidue.sort
Bio.PDB.Residue.Residue.sort
Bio.Sequencing.Ace.ACEFileRecord.sort" class="py-name" href="#" onclick="return doclink('link-68', 'sort', 'link-68');">sort</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt>  <tt class="py-line">            <tt id="link-69" class="py-name" targets="Variable Bio.Translate.key=Bio.Translate-module.html#key"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-69', 'key', 'link-69');">key</a></tt> <tt class="py-op">=</tt> <tt class="py-name">tuple</tt><tt class="py-op">(</tt><tt id="link-70" class="py-name"><a title="Martel.select_names" class="py-name" href="#" onclick="return doclink('link-70', 'select_names', 'link-63');">select_names</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">debug_level</tt> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt>  <tt class="py-line">            <tt id="link-71" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-71', 'key', 'link-69');">key</a></tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-name">debug_level</tt> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt>  <tt class="py-line"> </tt>
<a name="L174"></a><tt class="py-lineno">174</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_parser_cache</tt><tt class="py-op">.</tt><tt id="link-72" class="py-name"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-72', 'has_key', 'link-10');">has_key</a></tt><tt class="py-op">(</tt><tt id="link-73" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-73', 'key', 'link-69');">key</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt>  <tt class="py-line">            <tt class="py-keyword">import</tt> <tt id="link-74" class="py-name" targets="Package Martel=Martel-module.html"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-74', 'Martel', 'link-74');">Martel</a></tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt>  <tt class="py-line">            <tt id="link-75" class="py-name" targets="Variable Bio.Affy.CelFile.exp=Bio.Affy.CelFile-module.html#exp,Variable Bio.LogisticRegression.exp=Bio.LogisticRegression-module.html#exp,Variable Bio.MarkovModel.exp=Bio.MarkovModel-module.html#exp,Variable Bio.MaxEntropy.exp=Bio.MaxEntropy-module.html#exp,Variable Bio.NaiveBayes.exp=Bio.NaiveBayes-module.html#exp,Variable Bio.Statistics.lowess.exp=Bio.Statistics.lowess-module.html#exp,Variable Bio.distance.exp=Bio.distance-module.html#exp,Variable Bio.kNN.exp=Bio.kNN-module.html#exp"><a title="Bio.Affy.CelFile.exp
Bio.LogisticRegression.exp
Bio.MarkovModel.exp
Bio.MaxEntropy.exp
Bio.NaiveBayes.exp
Bio.Statistics.lowess.exp
Bio.distance.exp
Bio.kNN.exp" class="py-name" href="#" onclick="return doclink('link-75', 'exp', 'link-75');">exp</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">expression</tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt id="link-76" class="py-name"><a title="Martel.select_names" class="py-name" href="#" onclick="return doclink('link-76', 'select_names', 'link-63');">select_names</a></tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt>  <tt class="py-line">                <tt id="link-77" class="py-name"><a title="Bio.Affy.CelFile.exp
Bio.LogisticRegression.exp
Bio.MarkovModel.exp
Bio.MaxEntropy.exp
Bio.NaiveBayes.exp
Bio.Statistics.lowess.exp
Bio.distance.exp
Bio.kNN.exp" class="py-name" href="#" onclick="return doclink('link-77', 'exp', 'link-75');">exp</a></tt> <tt class="py-op">=</tt> <tt id="link-78" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-78', 'Martel', 'link-74');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-79" class="py-name"><a title="Martel.select_names" class="py-name" href="#" onclick="return doclink('link-79', 'select_names', 'link-63');">select_names</a></tt><tt class="py-op">(</tt><tt id="link-80" class="py-name"><a title="Bio.Affy.CelFile.exp
Bio.LogisticRegression.exp
Bio.MarkovModel.exp
Bio.MaxEntropy.exp
Bio.NaiveBayes.exp
Bio.Statistics.lowess.exp
Bio.distance.exp
Bio.kNN.exp" class="py-name" href="#" onclick="return doclink('link-80', 'exp', 'link-75');">exp</a></tt><tt class="py-op">,</tt> <tt id="link-81" class="py-name"><a title="Martel.select_names" class="py-name" href="#" onclick="return doclink('link-81', 'select_names', 'link-63');">select_names</a></tt><tt class="py-op">)</tt> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt>  <tt class="py-line">            <tt class="py-name">p</tt> <tt class="py-op">=</tt> <tt id="link-82" class="py-name"><a title="Bio.Affy.CelFile.exp
Bio.LogisticRegression.exp
Bio.MarkovModel.exp
Bio.MaxEntropy.exp
Bio.NaiveBayes.exp
Bio.Statistics.lowess.exp
Bio.distance.exp
Bio.kNN.exp" class="py-name" href="#" onclick="return doclink('link-82', 'exp', 'link-75');">exp</a></tt><tt class="py-op">.</tt><tt id="link-83" class="py-name" targets="Method Bio.config.FormatRegistry.FormatObject.make_parser()=Bio.config.FormatRegistry.FormatObject-class.html#make_parser,Method Bio.config._support.make_cached_expression.make_parser()=Bio.config._support.make_cached_expression-class.html#make_parser,Method Martel.Expression.Expression.make_parser()=Martel.Expression.Expression-class.html#make_parser,Method Martel.Expression.HeaderFooter.make_parser()=Martel.Expression.HeaderFooter-class.html#make_parser,Method Martel.Expression.ParseRecords.make_parser()=Martel.Expression.ParseRecords-class.html#make_parser"><a title="Bio.config.FormatRegistry.FormatObject.make_parser
Bio.config._support.make_cached_expression.make_parser
Martel.Expression.Expression.make_parser
Martel.Expression.HeaderFooter.make_parser
Martel.Expression.ParseRecords.make_parser" class="py-name" href="#" onclick="return doclink('link-83', 'make_parser', 'link-83');">make_parser</a></tt><tt class="py-op">(</tt><tt class="py-name">debug_level</tt> <tt class="py-op">=</tt> <tt class="py-name">debug_level</tt><tt class="py-op">)</tt> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_parser_cache</tt><tt class="py-op">[</tt><tt id="link-84" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-84', 'key', 'link-69');">key</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">p</tt> </tt>
<a name="L181"></a><tt class="py-lineno">181</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_parser_cache</tt><tt class="py-op">[</tt><tt id="link-85" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-85', 'key', 'link-69');">key</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-86" class="py-name" targets="Method Bio.Crystal.Crystal.copy()=Bio.Crystal.Crystal-class.html#copy,Method Bio.GA.Organism.Organism.copy()=Bio.GA.Organism.Organism-class.html#copy,Method Bio.GenBank.NCBIDictionary.copy()=Bio.GenBank.NCBIDictionary-class.html#copy,Method Bio.PDB.Vector'.Vector.copy()=Bio.PDB.Vector%27.Vector-class.html#copy,Method Bio.Prosite.ExPASyDictionary.copy()=Bio.Prosite.ExPASyDictionary-class.html#copy,Method Bio.Prosite.Pattern.PrositeTerm.copy()=Bio.Prosite.Pattern.PrositeTerm-class.html#copy,Method Bio.Prosite.Prodoc.ExPASyDictionary.copy()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#copy,Method Bio.PubMed.Dictionary.copy()=Bio.PubMed.Dictionary-class.html#copy,Method Bio.SwissProt.SProt.ExPASyDictionary.copy()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#copy,Method Martel.Expression.Any.copy()=Martel.Expression.Any-class.html#copy,Method Martel.Expression.AnyEol.copy()=Martel.Expression.AnyEol-class.html#copy,Method Martel.Expression.Assert.copy()=Martel.Expression.Assert-class.html#copy,Method Martel.Expression.AtBeginning.copy()=Martel.Expression.AtBeginning-class.html#copy,Method Martel.Expression.AtEnd.copy()=Martel.Expression.AtEnd-class.html#copy,Method Martel.Expression.Debug.copy()=Martel.Expression.Debug-class.html#copy,Method Martel.Expression.Dot.copy()=Martel.Expression.Dot-class.html#copy,Method Martel.Expression.Expression.copy()=Martel.Expression.Expression-class.html#copy,Method Martel.Expression.ExpressionList.copy()=Martel.Expression.ExpressionList-class.html#copy,Method Martel.Expression.FastFeature.copy()=Martel.Expression.FastFeature-class.html#copy,Method Martel.Expression.Group.copy()=Martel.Expression.Group-class.html#copy,Method Martel.Expression.GroupRef.copy()=Martel.Expression.GroupRef-class.html#copy,Method Martel.Expression.HeaderFooter.copy()=Martel.Expression.HeaderFooter-class.html#copy,Method Martel.Expression.Literal.copy()=Martel.Expression.Literal-class.html#copy,Method Martel.Expression.MaxRepeat.copy()=Martel.Expression.MaxRepeat-class.html#copy,Method Martel.Expression.NullOp.copy()=Martel.Expression.NullOp-class.html#copy,Method Martel.Expression.ParseRecords.copy()=Martel.Expression.ParseRecords-class.html#copy,Method Martel.Expression.PassThrough.copy()=Martel.Expression.PassThrough-class.html#copy,Method Martel.Expression.Str.copy()=Martel.Expression.Str-class.html#copy,Method Martel.IterParser.IterHeaderFooter.copy()=Martel.IterParser.IterHeaderFooter-class.html#copy,Method Martel.IterParser.IterRecords.copy()=Martel.IterParser.IterRecords-class.html#copy,Method Martel.Iterator.IteratorRecords.copy()=Martel.Iterator.IteratorRecords-class.html#copy,Method Martel.Parser.HeaderFooterParser.copy()=Martel.Parser.HeaderFooterParser-class.html#copy,Method Martel.Parser.Parser.copy()=Martel.Parser.Parser-class.html#copy,Method Martel.Parser.RecordParser.copy()=Martel.Parser.RecordParser-class.html#copy"><a title="Bio.Crystal.Crystal.copy
Bio.GA.Organism.Organism.copy
Bio.GenBank.NCBIDictionary.copy
Bio.PDB.Vector'.Vector.copy
Bio.Prosite.ExPASyDictionary.copy
Bio.Prosite.Pattern.PrositeTerm.copy
Bio.Prosite.Prodoc.ExPASyDictionary.copy
Bio.PubMed.Dictionary.copy
Bio.SwissProt.SProt.ExPASyDictionary.copy
Martel.Expression.Any.copy
Martel.Expression.AnyEol.copy
Martel.Expression.Assert.copy
Martel.Expression.AtBeginning.copy
Martel.Expression.AtEnd.copy
Martel.Expression.Debug.copy
Martel.Expression.Dot.copy
Martel.Expression.Expression.copy
Martel.Expression.ExpressionList.copy
Martel.Expression.FastFeature.copy
Martel.Expression.Group.copy
Martel.Expression.GroupRef.copy
Martel.Expression.HeaderFooter.copy
Martel.Expression.Literal.copy
Martel.Expression.MaxRepeat.copy
Martel.Expression.NullOp.copy
Martel.Expression.ParseRecords.copy
Martel.Expression.PassThrough.copy
Martel.Expression.Str.copy
Martel.IterParser.IterHeaderFooter.copy
Martel.IterParser.IterRecords.copy
Martel.Iterator.IteratorRecords.copy
Martel.Parser.HeaderFooterParser.copy
Martel.Parser.Parser.copy
Martel.Parser.RecordParser.copy" class="py-name" href="#" onclick="return doclink('link-86', 'copy', 'link-86');">copy</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L182"></a><tt class="py-lineno">182</tt>  <tt class="py-line">     </tt>
<a name="FormatObject.make_iterator"></a><div id="FormatObject.make_iterator-def"><a name="L183"></a><tt class="py-lineno">183</tt> <a class="py-toggle" href="#" id="FormatObject.make_iterator-toggle" onclick="return toggle('FormatObject.make_iterator');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.config.FormatRegistry.FormatObject-class.html#make_iterator">make_iterator</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">tag</tt><tt class="py-op">=</tt><tt class="py-string">"record"</tt><tt class="py-op">,</tt> <tt class="py-param">select_names</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">debug_level</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FormatObject.make_iterator-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="FormatObject.make_iterator-expanded"><a name="L184"></a><tt class="py-lineno">184</tt>  <tt class="py-line">        <tt class="py-docstring">"""S.make_iterator([tag][, select_names][, debug_level]) -&gt; iterator"""</tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt id="link-87" class="py-name"><a title="Martel.select_names" class="py-name" href="#" onclick="return doclink('link-87', 'select_names', 'link-63');">select_names</a></tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt>  <tt class="py-line">            <tt id="link-88" class="py-name"><a title="Martel.select_names" class="py-name" href="#" onclick="return doclink('link-88', 'select_names', 'link-63');">select_names</a></tt> <tt class="py-op">=</tt> <tt id="link-89" class="py-name"><a title="Bio.Pathway.Rep.HashSet.HashSet.list" class="py-name" href="#" onclick="return doclink('link-89', 'list', 'link-65');">list</a></tt><tt class="py-op">(</tt><tt id="link-90" class="py-name"><a title="Martel.select_names" class="py-name" href="#" onclick="return doclink('link-90', 'select_names', 'link-63');">select_names</a></tt><tt class="py-op">)</tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt>  <tt class="py-line">            <tt id="link-91" class="py-name"><a title="Martel.select_names" class="py-name" href="#" onclick="return doclink('link-91', 'select_names', 'link-63');">select_names</a></tt><tt class="py-op">.</tt><tt id="link-92" class="py-name"><a title="Bio.PDB.Residue.DisorderedResidue.sort
Bio.PDB.Residue.Residue.sort
Bio.Sequencing.Ace.ACEFileRecord.sort" class="py-name" href="#" onclick="return doclink('link-92', 'sort', 'link-68');">sort</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt>  <tt class="py-line">            <tt id="link-93" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-93', 'key', 'link-69');">key</a></tt> <tt class="py-op">=</tt> <tt class="py-name">tuple</tt><tt class="py-op">(</tt><tt id="link-94" class="py-name"><a title="Martel.select_names" class="py-name" href="#" onclick="return doclink('link-94', 'select_names', 'link-63');">select_names</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">debug_level</tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt>  <tt class="py-line">            <tt id="link-95" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-95', 'key', 'link-69');">key</a></tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-name">debug_level</tt> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt>  <tt class="py-line"> </tt>
<a name="L192"></a><tt class="py-lineno">192</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_iterator_cache</tt><tt class="py-op">.</tt><tt id="link-96" class="py-name"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-96', 'has_key', 'link-10');">has_key</a></tt><tt class="py-op">(</tt><tt id="link-97" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-97', 'key', 'link-69');">key</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L193"></a><tt class="py-lineno">193</tt>  <tt class="py-line">            <tt class="py-keyword">import</tt> <tt id="link-98" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-98', 'Martel', 'link-74');">Martel</a></tt> </tt>
<a name="L194"></a><tt class="py-lineno">194</tt>  <tt class="py-line">            <tt id="link-99" class="py-name"><a title="Bio.Affy.CelFile.exp
Bio.LogisticRegression.exp
Bio.MarkovModel.exp
Bio.MaxEntropy.exp
Bio.NaiveBayes.exp
Bio.Statistics.lowess.exp
Bio.distance.exp
Bio.kNN.exp" class="py-name" href="#" onclick="return doclink('link-99', 'exp', 'link-75');">exp</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">expression</tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt id="link-100" class="py-name"><a title="Martel.select_names" class="py-name" href="#" onclick="return doclink('link-100', 'select_names', 'link-63');">select_names</a></tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt>  <tt class="py-line">                <tt id="link-101" class="py-name"><a title="Bio.Affy.CelFile.exp
Bio.LogisticRegression.exp
Bio.MarkovModel.exp
Bio.MaxEntropy.exp
Bio.NaiveBayes.exp
Bio.Statistics.lowess.exp
Bio.distance.exp
Bio.kNN.exp" class="py-name" href="#" onclick="return doclink('link-101', 'exp', 'link-75');">exp</a></tt> <tt class="py-op">=</tt> <tt id="link-102" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-102', 'Martel', 'link-74');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-103" class="py-name"><a title="Martel.select_names" class="py-name" href="#" onclick="return doclink('link-103', 'select_names', 'link-63');">select_names</a></tt><tt class="py-op">(</tt><tt id="link-104" class="py-name"><a title="Bio.Affy.CelFile.exp
Bio.LogisticRegression.exp
Bio.MarkovModel.exp
Bio.MaxEntropy.exp
Bio.NaiveBayes.exp
Bio.Statistics.lowess.exp
Bio.distance.exp
Bio.kNN.exp" class="py-name" href="#" onclick="return doclink('link-104', 'exp', 'link-75');">exp</a></tt><tt class="py-op">,</tt> <tt id="link-105" class="py-name"><a title="Martel.select_names" class="py-name" href="#" onclick="return doclink('link-105', 'select_names', 'link-63');">select_names</a></tt><tt class="py-op">)</tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt>  <tt class="py-line">            <tt class="py-name">p</tt> <tt class="py-op">=</tt> <tt id="link-106" class="py-name"><a title="Bio.Affy.CelFile.exp
Bio.LogisticRegression.exp
Bio.MarkovModel.exp
Bio.MaxEntropy.exp
Bio.NaiveBayes.exp
Bio.Statistics.lowess.exp
Bio.distance.exp
Bio.kNN.exp" class="py-name" href="#" onclick="return doclink('link-106', 'exp', 'link-75');">exp</a></tt><tt class="py-op">.</tt><tt id="link-107" class="py-name" targets="Method Bio.config.FormatRegistry.FormatObject.make_iterator()=Bio.config.FormatRegistry.FormatObject-class.html#make_iterator,Method Martel.Expression.Expression.make_iterator()=Martel.Expression.Expression-class.html#make_iterator,Method Martel.Expression.HeaderFooter.make_iterator()=Martel.Expression.HeaderFooter-class.html#make_iterator,Method Martel.Expression.ParseRecords.make_iterator()=Martel.Expression.ParseRecords-class.html#make_iterator"><a title="Bio.config.FormatRegistry.FormatObject.make_iterator
Martel.Expression.Expression.make_iterator
Martel.Expression.HeaderFooter.make_iterator
Martel.Expression.ParseRecords.make_iterator" class="py-name" href="#" onclick="return doclink('link-107', 'make_iterator', 'link-107');">make_iterator</a></tt><tt class="py-op">(</tt><tt id="link-108" class="py-name" targets="Variable Martel.Time.tag=Martel.Time-module.html#tag"><a title="Martel.Time.tag" class="py-name" href="#" onclick="return doclink('link-108', 'tag', 'link-108');">tag</a></tt><tt class="py-op">,</tt> <tt class="py-name">debug_level</tt> <tt class="py-op">=</tt> <tt class="py-name">debug_level</tt><tt class="py-op">)</tt> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_iterator_cache</tt><tt class="py-op">[</tt><tt id="link-109" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-109', 'key', 'link-69');">key</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">p</tt> </tt>
<a name="L199"></a><tt class="py-lineno">199</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_iterator_cache</tt><tt class="py-op">[</tt><tt id="link-110" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-110', 'key', 'link-69');">key</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-111" class="py-name"><a title="Bio.Crystal.Crystal.copy
Bio.GA.Organism.Organism.copy
Bio.GenBank.NCBIDictionary.copy
Bio.PDB.Vector'.Vector.copy
Bio.Prosite.ExPASyDictionary.copy
Bio.Prosite.Pattern.PrositeTerm.copy
Bio.Prosite.Prodoc.ExPASyDictionary.copy
Bio.PubMed.Dictionary.copy
Bio.SwissProt.SProt.ExPASyDictionary.copy
Martel.Expression.Any.copy
Martel.Expression.AnyEol.copy
Martel.Expression.Assert.copy
Martel.Expression.AtBeginning.copy
Martel.Expression.AtEnd.copy
Martel.Expression.Debug.copy
Martel.Expression.Dot.copy
Martel.Expression.Expression.copy
Martel.Expression.ExpressionList.copy
Martel.Expression.FastFeature.copy
Martel.Expression.Group.copy
Martel.Expression.GroupRef.copy
Martel.Expression.HeaderFooter.copy
Martel.Expression.Literal.copy
Martel.Expression.MaxRepeat.copy
Martel.Expression.NullOp.copy
Martel.Expression.ParseRecords.copy
Martel.Expression.PassThrough.copy
Martel.Expression.Str.copy
Martel.IterParser.IterHeaderFooter.copy
Martel.IterParser.IterRecords.copy
Martel.Iterator.IteratorRecords.copy
Martel.Parser.HeaderFooterParser.copy
Martel.Parser.Parser.copy
Martel.Parser.RecordParser.copy" class="py-name" href="#" onclick="return doclink('link-111', 'copy', 'link-86');">copy</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L200"></a><tt class="py-lineno">200</tt>  <tt class="py-line">     </tt>
<a name="FormatGroup"></a><div id="FormatGroup-def"><a name="L201"></a><tt class="py-lineno">201</tt> <a class="py-toggle" href="#" id="FormatGroup-toggle" onclick="return toggle('FormatGroup');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.config.FormatRegistry.FormatGroup-class.html">FormatGroup</a><tt class="py-op">(</tt><tt class="py-base-class">RegisterableGroup</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FormatGroup-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="FormatGroup-expanded"><a name="L202"></a><tt class="py-lineno">202</tt>  <tt class="py-line">    <tt class="py-docstring">"""This object holds a group of FormatObjects.</tt> </tt>
<a name="L203"></a><tt class="py-lineno">203</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt>  <tt class="py-line"><tt class="py-docstring">    Methods:</tt> </tt>
<a name="L205"></a><tt class="py-lineno">205</tt>  <tt class="py-line"><tt class="py-docstring">    identify        Identify the format at a URL.</tt> </tt>
<a name="L206"></a><tt class="py-lineno">206</tt>  <tt class="py-line"><tt class="py-docstring">    identifyFile    Identify the format of a file.</tt> </tt>
<a name="L207"></a><tt class="py-lineno">207</tt>  <tt class="py-line"><tt class="py-docstring">    identifyString  Identify the format of a string.</tt> </tt>
<a name="L208"></a><tt class="py-lineno">208</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L209"></a><tt class="py-lineno">209</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="FormatGroup.__init__"></a><div id="FormatGroup.__init__-def"><a name="L210"></a><tt class="py-lineno">210</tt> <a class="py-toggle" href="#" id="FormatGroup.__init__-toggle" onclick="return toggle('FormatGroup.__init__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.config.FormatRegistry.FormatGroup-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">name</tt><tt class="py-op">,</tt> <tt class="py-param">abbrev</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">filter</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">multirecord</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FormatGroup.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="FormatGroup.__init__-expanded"><a name="L211"></a><tt class="py-lineno">211</tt>  <tt class="py-line">        <tt class="py-docstring">"""FormatGroup(name[, abbrev][, filter][, multirecord])</tt> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt>  <tt class="py-line"><tt class="py-docstring">        name is the name of the object, abbrev is an abbreviation for</tt> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt>  <tt class="py-line"><tt class="py-docstring">        the name.</tt> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L216"></a><tt class="py-lineno">216</tt>  <tt class="py-line"><tt class="py-docstring">        filter is an optional Martel.Expression that can be used to</tt> </tt>
<a name="L217"></a><tt class="py-lineno">217</tt>  <tt class="py-line"><tt class="py-docstring">        quickly determine whether some input is parseable by this</tt> </tt>
<a name="L218"></a><tt class="py-lineno">218</tt>  <tt class="py-line"><tt class="py-docstring">        group.</tt> </tt>
<a name="L219"></a><tt class="py-lineno">219</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L220"></a><tt class="py-lineno">220</tt>  <tt class="py-line"><tt class="py-docstring">        multirecord is either 0/1 indicating whether this format can</tt> </tt>
<a name="L221"></a><tt class="py-lineno">221</tt>  <tt class="py-line"><tt class="py-docstring">        be used to parse multiple records.  By default, it is 1.</tt> </tt>
<a name="L222"></a><tt class="py-lineno">222</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L223"></a><tt class="py-lineno">223</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L224"></a><tt class="py-lineno">224</tt>  <tt class="py-line">        <tt id="link-112" class="py-name" targets="Class Bio.config.Registry.RegisterableGroup=Bio.config.Registry.RegisterableGroup-class.html"><a title="Bio.config.Registry.RegisterableGroup" class="py-name" href="#" onclick="return doclink('link-112', 'RegisterableGroup', 'link-112');">RegisterableGroup</a></tt><tt class="py-op">.</tt><tt id="link-113" class="py-name"><a title="Bio.Affy.CelFile.CelConsumer.__init__
Bio.Affy.CelFile.CelParser.__init__
Bio.Affy.CelFile.CelRecord.__init__
Bio.Ais.Immune.__init__
Bio.Ais.Lymphocyte.__init__
Bio.Align.AlignInfo.PSSM.__init__
Bio.Align.AlignInfo.SummaryInfo.__init__
Bio.Align.FormatConvert.FormatConverter.__init__
Bio.Align.Generic.Alignment.__init__
Bio.AlignAce.Applications.AlignAceCommandline.__init__
Bio.AlignAce.Applications.CompareAceCommandline.__init__
Bio.AlignAce.Motif.Motif.__init__
Bio.AlignAce.Parser.AlignAceConsumer.__init__
Bio.AlignAce.Parser.AlignAceParser.__init__
Bio.AlignAce.Parser.CompareAceConsumer.__init__
Bio.AlignAce.Parser.CompareAceParser.__init__
Bio.AlignIO.Interfaces.AlignmentIterator.__init__
Bio.AlignIO.Interfaces.AlignmentWriter.__init__
Bio.AlignIO.Interfaces.SequentialAlignmentWriter.__init__
Bio.Alphabet.AlphabetEncoder.__init__
Bio.Alphabet.Gapped.__init__
Bio.Alphabet.HasStopCodon.__init__
Bio.Application.AbstractCommandline.__init__
Bio.Application.ApplicationResult.__init__
Bio.Application._AbstractParameter.__init__
Bio.Blast.Applications.BlastallCommandline.__init__
Bio.Blast.Applications.FastacmdCommandline.__init__
Bio.Blast.NCBIStandalone.BlastErrorParser.__init__
Bio.Blast.NCBIStandalone.BlastParser.__init__
Bio.Blast.NCBIStandalone.Iterator.__init__
Bio.Blast.NCBIStandalone.PSIBlastParser.__init__
Bio.Blast.NCBIStandalone._BlastConsumer.__init__
Bio.Blast.NCBIStandalone._BlastErrorConsumer.__init__
Bio.Blast.NCBIStandalone._PSIBlastConsumer.__init__
Bio.Blast.NCBIWWW.BlastParser.__init__
Bio.Blast.NCBIXML.BlastParser.__init__
Bio.Blast.NCBIXML._XMLparser.__init__
Bio.Blast.ParseBlastTable.BlastTableEntry.__init__
Bio.Blast.ParseBlastTable.BlastTableReader.__init__
Bio.Blast.ParseBlastTable.BlastTableRec.__init__
Bio.Blast.Record.Alignment.__init__
Bio.Blast.Record.Blast.__init__
Bio.Blast.Record.DatabaseReport.__init__
Bio.Blast.Record.Description.__init__
Bio.Blast.Record.HSP.__init__
Bio.Blast.Record.Header.__init__
Bio.Blast.Record.MultipleAlignment.__init__
Bio.Blast.Record.PSIBlast.__init__
Bio.Blast.Record.Parameters.__init__
Bio.Blast.Record.Round.__init__
Bio.CAPS.CAPSMap.__init__
Bio.CAPS.DifferentialCutsite.__init__
Bio.CDD.Iterator.__init__
Bio.CDD.Record.Record.__init__
Bio.CDD.RecordParser.__init__
Bio.CDD._RecordConsumer.__init__
Bio.CDD._Scanner.__init__
Bio.Clustalw.ClustalAlignment.__init__
Bio.Clustalw.MultipleAlignCL.__init__
Bio.Cluster.DataFile.__init__
Bio.Cluster.Record.__init__
Bio.Compass.Iterator.__init__
Bio.Compass.Record.__init__
Bio.Compass.RecordParser.__init__
Bio.Compass._Consumer.__init__
Bio.Crystal.Chain.__init__
Bio.Crystal.Crystal.__init__
Bio.Crystal.CrystalError.__init__
Bio.Crystal.Error.__init__
Bio.Crystal.Hetero.__init__
Bio.DBXRef.DBXRef.__init__
Bio.Data.CodonTable.AmbiguousCodonTable.__init__
Bio.Data.CodonTable.AmbiguousForwardTable.__init__
Bio.Data.CodonTable.CodonTable.__init__
Bio.Data.CodonTable.NCBICodonTable.__init__
Bio.Decode.DecodeParser.__init__
Bio.Decode.DecodeScanner.__init__
Bio.Decode.Float.__init__
Bio.Decode.Function.__init__
Bio.Decode.FunctionCall.__init__
Bio.Decode.FunctionCallChain.__init__
Bio.Decode.FunctionName.__init__
Bio.Decode.Integer.__init__
Bio.Decode.String.__init__
Bio.Decode.Token.__init__
Bio.Decode.ValueToken.__init__
Bio.DocSQL.Create.__init__
Bio.DocSQL.Insert.__init__
Bio.DocSQL.IterationCursor.__init__
Bio.DocSQL.Query.__init__
Bio.DocSQL.QueryAll.__init__
Bio.DocSQL.QueryGeneric.__init__
Bio.DocSQL.QueryRow.__init__
Bio.DocSQL.QuerySingle.__init__
Bio.ECell.ECellError.__init__
Bio.ECell.Error.__init__
Bio.ECell.Iterator.__init__
Bio.ECell.Record.Record.__init__
Bio.ECell.RecordParser.__init__
Bio.ECell._RecordConsumer.__init__
Bio.ECell._Scanner.__init__
Bio.EUtils.Config.DatabaseInfo.__init__
Bio.EUtils.DBIdsClient.BaseDBIdsRecordSet.__init__
Bio.EUtils.DBIdsClient.DBIdsClient.__init__
Bio.EUtils.DBIdsClient.DBIdsLookup.__init__
Bio.EUtils.Datatypes.BinaryOp.__init__
Bio.EUtils.Datatypes.CheckLinkSet.__init__
Bio.EUtils.Datatypes.DBIds.__init__
Bio.EUtils.Datatypes.Date.__init__
Bio.EUtils.Datatypes.DateRange.__init__
Bio.EUtils.Datatypes.EUtilsSearchError.__init__
Bio.EUtils.Datatypes.IdCheck.__init__
Bio.EUtils.Datatypes.IdUrlSet.__init__
Bio.EUtils.Datatypes.Link.__init__
Bio.EUtils.Datatypes.LinkSetDb.__init__
Bio.EUtils.Datatypes.LinksLinkSet.__init__
Bio.EUtils.Datatypes.NeighborLinkSet.__init__
Bio.EUtils.Datatypes.ObjUrl.__init__
Bio.EUtils.Datatypes.PostResult.__init__
Bio.EUtils.Datatypes.Problem.__init__
Bio.EUtils.Datatypes.Provider.__init__
Bio.EUtils.Datatypes.Range.__init__
Bio.EUtils.Datatypes.SearchResult.__init__
Bio.EUtils.Datatypes.Summary.__init__
Bio.EUtils.Datatypes.Term.__init__
Bio.EUtils.Datatypes.WithinNDays.__init__
Bio.EUtils.HistoryClient.BaseHistoryRecordSet.__init__
Bio.EUtils.HistoryClient.HistoryClient.__init__
Bio.EUtils.HistoryClient.HistoryCookie.__init__
Bio.EUtils.HistoryClient.HistoryLookup.__init__
Bio.EUtils.HistoryClient.HistoryRecord.__init__
Bio.EUtils.MultiDict.OrderedMultiDict.__init__
Bio.EUtils.MultiDict.UnorderedMultiDict.__init__
Bio.EUtils.POM.Comment.__init__
Bio.EUtils.POM.ContentModel.__init__
Bio.EUtils.POM.DTDConsumerForSourceGeneration.__init__
Bio.EUtils.POM.ElementNode.__init__
Bio.EUtils.POM.IndentedText.__init__
Bio.EUtils.POM.ObjectParserHandler.__init__
Bio.EUtils.POM.POMDocument.__init__
Bio.EUtils.POM.XMLAttribute.__init__
Bio.EUtils.POM._ContentModelGenerator.__init__
Bio.EUtils.ReseekFile.ReseekFile.__init__
Bio.EUtils.ThinClient.ThinClient.__init__
Bio.EUtils.parse.UsePOMParser.__init__
Bio.EUtils.sourcegen.ClassHolder.__init__
Bio.EUtils.sourcegen.FunctionHolder.__init__
Bio.EUtils.sourcegen.MethodHolder.__init__
Bio.EUtils.sourcegen.SourceFile.__init__
Bio.EUtils.sourcegen.SourceGen.__init__
Bio.Emboss.Applications.EConsenseCommandline.__init__
Bio.Emboss.Applications.EInvertedCommandline.__init__
Bio.Emboss.Applications.ENeighborCommandline.__init__
Bio.Emboss.Applications.EProtDistCommandline.__init__
Bio.Emboss.Applications.EProtParsCommandline.__init__
Bio.Emboss.Applications.ESeqBootCommandline.__init__
Bio.Emboss.Applications.ETandemCommandline.__init__
Bio.Emboss.Applications.Est2GenomeCommandline.__init__
Bio.Emboss.Applications.FuzznucCommandline.__init__
Bio.Emboss.Applications.PalindromeCommandline.__init__
Bio.Emboss.Applications.Primer3Commandline.__init__
Bio.Emboss.Applications.PrimerSearchCommandline.__init__
Bio.Emboss.Applications.TranalignCommandline.__init__
Bio.Emboss.Applications.WaterCommandline.__init__
Bio.Emboss.Primer.Primer3Parser.__init__
Bio.Emboss.Primer.Primer3Primers.__init__
Bio.Emboss.Primer.Primer3Record.__init__
Bio.Emboss.Primer.PrimerSearchAmplifier.__init__
Bio.Emboss.Primer.PrimerSearchInputRecord.__init__
Bio.Emboss.Primer.PrimerSearchOutputRecord.__init__
Bio.Emboss.Primer.PrimerSearchParser.__init__
Bio.Emboss.Primer._Primer3RecordConsumer.__init__
Bio.Emboss.Primer._Primer3Scanner.__init__
Bio.Emboss.Primer._PrimerSearchRecordConsumer.__init__
Bio.Emboss.Primer._PrimerSearchScanner.__init__
Bio.Entrez.Parser.DataHandler.__init__
Bio.Entrez.Parser.StructureElement.__init__
Bio.Enzyme.DataRecord.__init__
Bio.Enzyme.EnzymeRecord.__init__
Bio.Enzyme.Iterator.__init__
Bio.Enzyme.RecordParser.__init__
Bio.Enzyme._RecordConsumer.__init__
Bio.FSSP.FSSPAlignDict.__init__
Bio.FSSP.FSSPAlignRec.__init__
Bio.FSSP.FSSPHeader.__init__
Bio.FSSP.FSSPSumRec.__init__
Bio.FSSP.FSSPTools.FSSPMultAlign.__init__
Bio.FSSP.PosAlign.__init__
Bio.FSSP.fssp_rec.fff_rec.__init__
Bio.Fasta.FastaAlign.FastaAlignment.__init__
Bio.Fasta.Iterator.__init__
Bio.Fasta.Record.__init__
Bio.Fasta.RecordParser.__init__
Bio.Fasta.SequenceParser.__init__
Bio.File.SGMLHandle.__init__
Bio.File.SGMLStripper.MyParser.__init__
Bio.File.SGMLStripper.__init__
Bio.File.UndoHandle.__init__
Bio.FilteredReader.FilteredReader.__init__
Bio.GA.Crossover.General.SafeFitnessCrossover.__init__
Bio.GA.Crossover.GeneralPoint.GeneralPointCrossover.__init__
Bio.GA.Crossover.GeneralPoint.InterleaveCrossover.__init__
Bio.GA.Crossover.Point.SinglePointCrossover.__init__
Bio.GA.Crossover.TwoPoint.TwoPointCrossover.__init__
Bio.GA.Crossover.Uniform.UniformCrossover.__init__
Bio.GA.Evolver.GenerationEvolver.__init__
Bio.GA.Evolver.SteadyStateEvolver.__init__
Bio.GA.Mutation.General.SafeFitnessMutation.__init__
Bio.GA.Mutation.Simple.ConversionMutation.__init__
Bio.GA.Mutation.Simple.SinglePositionMutation.__init__
Bio.GA.Organism.Organism.__init__
Bio.GA.Repair.Stabilizing.AmbiguousRepair.__init__
Bio.GA.Selection.Abstract.AbstractSelection.__init__
Bio.GA.Selection.Diversity.DiversitySelection.__init__
Bio.GA.Selection.RouletteWheel.RouletteWheelSelection.__init__
Bio.GA.Selection.Tournament.TournamentSelection.__init__
Bio.GFF.Connection.__init__
Bio.GFF.Feature.__init__
Bio.GFF.FeatureAggregate.__init__
Bio.GFF.FeatureQuery.__init__
Bio.GFF.FeatureQueryRow.__init__
Bio.GFF.GenericTools.ArgsParser.__init__
Bio.GFF.GenericTools.Surrogate.__init__
Bio.GFF.GenericTools.TempFile.__init__
Bio.GFF.RetrieveSeqname.__init__
Bio.GFF.Segment.__init__
Bio.GFF.easy.FeatureDict.__init__
Bio.GFF.easy.Location.__init__
Bio.GFF.easy.LocationFromCoords.__init__
Bio.GFF.easy.LocationFromString.__init__
Bio.GFF.easy.LocationJoin.__init__
Bio.GenBank.FeatureParser.__init__
Bio.GenBank.Iterator.__init__
Bio.GenBank.LocationParser.AbsoluteLocation.__init__
Bio.GenBank.LocationParser.Between.__init__
Bio.GenBank.LocationParser.FeatureName.__init__
Bio.GenBank.LocationParser.Function.__init__
Bio.GenBank.LocationParser.HighBound.__init__
Bio.GenBank.LocationParser.Integer.__init__
Bio.GenBank.LocationParser.LocationParser.__init__
Bio.GenBank.LocationParser.LocationScanner.__init__
Bio.GenBank.LocationParser.LowBound.__init__
Bio.GenBank.LocationParser.Path.__init__
Bio.GenBank.LocationParser.Range.__init__
Bio.GenBank.LocationParser.Symbol.__init__
Bio.GenBank.LocationParser.Token.__init__
Bio.GenBank.LocationParser.TwoBound.__init__
Bio.GenBank.NCBIDictionary.__init__
Bio.GenBank.Record.Feature.__init__
Bio.GenBank.Record.Qualifier.__init__
Bio.GenBank.Record.Record.__init__
Bio.GenBank.Record.Reference.__init__
Bio.GenBank.RecordParser.__init__
Bio.GenBank.Scanner.InsdcScanner.__init__
Bio.GenBank._BaseGenBankConsumer.__init__
Bio.GenBank._FeatureConsumer.__init__
Bio.GenBank._RecordConsumer.__init__
Bio.GenBank.utils.FeatureValueCleaner.__init__
Bio.Geo.Record.Record.__init__
Bio.Gobase.Dictionary.__init__
Bio.Gobase.GeneRecord.__init__
Bio.Gobase.Iterator.__init__
Bio.Gobase.ProteinRecord.__init__
Bio.Gobase.Record.__init__
Bio.Gobase.RecordParser.__init__
Bio.Gobase.SequenceRecord.__init__
Bio.Gobase._RecordConsumer.__init__
Bio.Graphics.BasicChromosome.Chromosome.__init__
Bio.Graphics.BasicChromosome.ChromosomeSegment.__init__
Bio.Graphics.BasicChromosome.Organism.__init__
Bio.Graphics.BasicChromosome.TelomereSegment.__init__
Bio.Graphics.BasicChromosome._ChromosomeComponent.__init__
Bio.Graphics.Comparative.ComparativeScatterPlot.__init__
Bio.Graphics.DisplayRepresentation.ChromosomeCounts.__init__
Bio.Graphics.Distribution.BarChartDistribution.__init__
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Bio.LocusLink.web_parse.Url.__init__
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Bio.MEME.Motif.MEMEMotif.__init__
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Bio.MEME.Parser.MEMERecord.__init__
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Bio.Medline._RecordConsumer.__init__
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Bio.Mindy.BerkeleyDB.BerkeleyDB.__init__
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Bio.NMR.xpktools.Peaklist.__init__
Bio.NMR.xpktools.XpkEntry.__init__
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Bio.NetCatch.Url.__init__
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Bio.PDB.MMCIF2Dict.MMCIF2Dict.__init__
Bio.PDB.Model.Model.__init__
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Bio.PropertyManager.PropertyManager.__init__
Bio.Prosite.Dictionary.__init__
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Bio.Prosite.Pattern.Prosite.__init__
Bio.Prosite.Pattern.PrositeMatch.__init__
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Bio.Prosite.Prodoc.Dictionary.__init__
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Bio.Restriction.Restriction.Analysis.__init__
Bio.Restriction.Restriction.FormattedSeq.__init__
Bio.Restriction.Restriction.RestrictionBatch.__init__
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Bio.Restriction._Update.RestrictionCompiler.newenzyme.__init__
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Bio.Restriction._Update.Update.FtpNameError.__init__
Bio.Restriction._Update.Update.FtpPasswordError.__init__
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Bio.SCOP.Cla.Index.__init__
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Bio.SCOP.Dom.Iterator.__init__
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Bio.SCOP.Domain.__init__
Bio.SCOP.FileIndex.FileIndex.__init__
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Bio.SCOP.Hie.Iterator.__init__
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Bio.SCOP.Hie.Record.__init__
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Bio.SCOP.Raf.Iterator.__init__
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Bio.SCOP.Raf.Res.__init__
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Bio.SGMLExtractor.SGMLExtractor.LocalParser.__init__
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Bio.SGMLExtractor.SGMLExtractorHandle.__init__
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.__init__
Bio.Saf.Iterator.__init__
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Bio.Saf._RecordConsumer.__init__
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Bio.Search.Algorithm.__init__
Bio.Search.Database.__init__
Bio.Search.HSP.__init__
Bio.Search.HSPSeq.__init__
Bio.Search.Hit.__init__
Bio.Search.HomologySeq.__init__
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Bio.Search.TableInfo.__init__
Bio.Search._SeqLength.__init__
Bio.Seq.MutableSeq.__init__
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Bio.SeqFeature.AbstractPosition.__init__
Bio.SeqFeature.AfterPosition.__init__
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Bio.SeqFeature.BetweenPosition.__init__
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Bio.SeqFeature.FeatureLocation.__init__
Bio.SeqFeature.OneOfPosition.__init__
Bio.SeqFeature.PositionGap.__init__
Bio.SeqFeature.Reference.__init__
Bio.SeqFeature.SeqFeature.__init__
Bio.SeqFeature.WithinPosition.__init__
Bio.SeqIO.ClustalIO.ClustalWriter.__init__
Bio.SeqIO.FastaIO.FastaWriter.__init__
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.__init__
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Bio.SeqIO.Interfaces.SequenceWriter.__init__
Bio.SeqIO.Interfaces.SequentialSequenceWriter.__init__
Bio.SeqIO.PhylipIO.PhylipWriter.__init__
Bio.SeqIO.StockholmIO.StockholmIterator.__init__
Bio.SeqIO.StockholmIO.StockholmWriter.__init__
Bio.SeqRecord.SeqRecord.__init__
Bio.SeqUtils.CodonUsage.CodonAdaptationIndex.__init__
Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint.__init__
Bio.SeqUtils.MissingTable.__init__
Bio.SeqUtils.ProtParam.ProteinAnalysis.__init__
Bio.Sequencing.Ace.ACEFileRecord.__init__
Bio.Sequencing.Ace.ACEParser.__init__
Bio.Sequencing.Ace.Contig.__init__
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Bio.Sequencing.Ace.Reads.__init__
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Bio.Sequencing.Ace.af.__init__
Bio.Sequencing.Ace.bs.__init__
Bio.Sequencing.Ace.ct.__init__
Bio.Sequencing.Ace.ds.__init__
Bio.Sequencing.Ace.qa.__init__
Bio.Sequencing.Ace.rd.__init__
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Bio.Sequencing.Ace.wa.__init__
Bio.Sequencing.Ace.wr.__init__
Bio.Sequencing.Phd.Iterator.__init__
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Bio.Sequencing.Phd._RecordConsumer.__init__
Bio.Std.StdTerm.__init__
Bio.StdHandler.ConvertDispatchHandler.__init__
Bio.StdHandler.ConvertHandler.__init__
Bio.StdHandler.Feature.__init__
Bio.StdHandler.Handle_dbxref.__init__
Bio.StdHandler.Handle_feature_location.__init__
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Bio.SubsMat.FreqTable.FreqTable.__init__
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Bio.SwissProt.KeyWList.ListParser.__init__
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Bio.SwissProt.SProt._RecordConsumer.__init__
Bio.SwissProt.SProt._SequenceConsumer.__init__
Bio.Transcribe.Transcribe.__init__
Bio.Translate.Translator.__init__
Bio.UniGene.Iterator.__init__
Bio.UniGene.RecordParser.__init__
Bio.UniGene.UnigeneProtsimRecord.__init__
Bio.UniGene.UnigeneRecord.__init__
Bio.UniGene.UnigeneSTSRecord.__init__
Bio.UniGene.UnigeneSequenceRecord.__init__
Bio.UniGene._RecordConsumer.__init__
Bio.WWW.RequestLimiter.__init__
Bio.Wise.dnal.Statistics.__init__
Bio.Wise.psw.AlignmentColumn.__init__
Bio.Wise.psw.ColumnUnit.__init__
Bio.Writer.Writer.__init__
Bio.biblio.Biblio.__init__
Bio.biblio.BiblioCollection.__init__
Bio.builders.Search.search.BuildSearch.__init__
Bio.builders.SeqRecord.sequence.BuildSeqRecord.__init__
Bio.config.DBRegistry.BioCorbaDB.__init__
Bio.config.DBRegistry.BioSQLDB.__init__
Bio.config.DBRegistry.CGIDB.__init__
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Bio.config.DBRegistry.EUtilsDB.__init__
Bio.config.DBRegistry.IndexedFileDB.__init__
Bio.config.FormatRegistry.FormatGroup.__init__
Bio.config.FormatRegistry.FormatObject.__init__
Bio.config.FormatRegistry.FormatRegistry.__init__
Bio.config.Registry.RegisterableGroup.__init__
Bio.config.Registry.RegisterableObject.__init__
Bio.config.Registry.Registry.__init__
Bio.config.SeqDBRegistry.SeqDBRegistry.__init__
Bio.config._stanzaformat.Stanza.__init__
Bio.config._stanzaformat.StanzaFormat.__init__
Bio.config._support.make_cached_expression.__init__
Bio.config._support.make_rate_limited_function.__init__
Bio.kNN.kNN.__init__
Bio.pairwise2.affine_penalty.__init__
Bio.pairwise2.dictionary_match.__init__
Bio.pairwise2.identity_match.__init__
Bio.writers.SeqRecord.embl.WriteEmbl.__init__
Bio.writers.SeqRecord.fasta.WriteFasta.__init__
BioSQL.BioSeq.DBSeq.__init__
BioSQL.BioSeq.DBSeqRecord.__init__
BioSQL.BioSeqDatabase.Adaptor.__init__
BioSQL.BioSeqDatabase.BioSeqDatabase.__init__
BioSQL.BioSeqDatabase.DBServer.__init__
BioSQL.DBUtils.Generic_dbutils.__init__
BioSQL.Loader.DatabaseLoader.__init__
BioSQL.Loader.DatabaseRemover.__init__
Martel.Dispatch.Callback.__init__
Martel.Dispatch.DispatchHandler.__init__
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Martel.Dispatch.RemapEnd.__init__
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Martel.Expression.NullOp.__init__
Martel.Expression.ParseRecords.__init__
Martel.Expression.PassThrough.__init__
Martel.Expression.Seq.__init__
Martel.Expression.Str.__init__
Martel.Generate.CheckAssert.__init__
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Martel.Generate.GeneratorState.__init__
Martel.Generate.HandleRepeatCount.__init__
Martel.Generate.SetGroupValue.__init__
Martel.Generate._call_call.__init__
Martel.Generate._call_calltag.__init__
Martel.Generate.print_debug.__init__
Martel.Generate.print_info.__init__
Martel.IterParser.IterHeaderFooter.__init__
Martel.IterParser.IterRecords.__init__
Martel.Iterator.EventStream.__init__
Martel.Iterator.HeaderFooterEventStream.__init__
Martel.Iterator.Iterate.__init__
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Martel.Iterator.IteratorHeaderFooter.__init__
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Martel.Iterator.StoreEvents.__init__
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Martel.test.support.CheckGood.__init__
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<a name="L227"></a><tt class="py-lineno">227</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-119" class="py-name"><a title="Bio.FSSP.FSSPTools.filter
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<a name="L228"></a><tt class="py-lineno">228</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">multirecord</tt> <tt class="py-op">=</tt> <tt class="py-name">multirecord</tt> </tt>
<a name="L229"></a><tt class="py-lineno">229</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_parents</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
</div><a name="L230"></a><tt class="py-lineno">230</tt>  <tt class="py-line">         </tt>
<a name="FormatGroup.identifyFile"></a><div id="FormatGroup.identifyFile-def"><a name="L231"></a><tt class="py-lineno">231</tt> <a class="py-toggle" href="#" id="FormatGroup.identifyFile-toggle" onclick="return toggle('FormatGroup.identifyFile');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.config.FormatRegistry.FormatGroup-class.html#identifyFile">identifyFile</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">infile</tt><tt class="py-op">,</tt> <tt class="py-param">debug_level</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FormatGroup.identifyFile-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="FormatGroup.identifyFile-expanded"><a name="L232"></a><tt class="py-lineno">232</tt>  <tt class="py-line">        <tt class="py-docstring">"""S.identifyFile(infile[, debug_level]) -&gt; FormatObject or None"""</tt> </tt>
<a name="L233"></a><tt class="py-lineno">233</tt>  <tt class="py-line">        <tt class="py-comment"># See if the filter test weeds things out</tt> </tt>
<a name="L234"></a><tt class="py-lineno">234</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-123" class="py-name"><a title="Bio.FSSP.FSSPTools.filter
Bio.FilteredReader.FilteredReader.filter
Bio.expressions.swissprot.filter" class="py-name" href="#" onclick="return doclink('link-123', 'filter', 'link-44');">filter</a></tt><tt class="py-op">:</tt> </tt>
<a name="L235"></a><tt class="py-lineno">235</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt id="link-124" class="py-name"><a title="Bio.config.FormatRegistry._parses_file" class="py-name" href="#" onclick="return doclink('link-124', '_parses_file', 'link-51');">_parses_file</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-125" class="py-name"><a title="Bio.FSSP.FSSPTools.filter
Bio.FilteredReader.FilteredReader.filter
Bio.expressions.swissprot.filter" class="py-name" href="#" onclick="return doclink('link-125', 'filter', 'link-44');">filter</a></tt><tt class="py-op">,</tt> <tt class="py-name">infile</tt><tt class="py-op">,</tt> <tt class="py-name">debug_level</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L236"></a><tt class="py-lineno">236</tt>  <tt class="py-line">                <tt class="py-keyword">return</tt> <tt class="py-name">None</tt> </tt>
<a name="L237"></a><tt class="py-lineno">237</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt id="link-126" class="py-name" targets="Variable Bio.Encodings.IUPACEncoding.obj=Bio.Encodings.IUPACEncoding-module.html#obj"><a title="Bio.Encodings.IUPACEncoding.obj" class="py-name" href="#" onclick="return doclink('link-126', 'obj', 'link-126');">obj</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">objs</tt><tt class="py-op">:</tt> </tt>
<a name="L238"></a><tt class="py-lineno">238</tt>  <tt class="py-line">            <tt id="link-127" class="py-name"><a title="Bio.Restriction.Restriction.RestrictionBatch.format
Bio.expressions.blast.ncbiblast.format
Bio.expressions.blast.wublast.format
Bio.expressions.blocks.format
Bio.expressions.embl.embl65.format
Bio.expressions.fasta.format
Bio.expressions.genbank.format
Bio.expressions.hmmpfam.format
Bio.expressions.swissprot.ipi.format
Bio.expressions.swissprot.speclist.format
Bio.expressions.swissprot.sprot38.format
Bio.expressions.swissprot.sprot40.format
Bio.expressions.transfac.format
Martel.test.test_swissprot38.format
Martel.test.testformats.swissprot38.format" class="py-name" href="#" onclick="return doclink('link-127', 'format', 'link-11');">format</a></tt> <tt class="py-op">=</tt> <tt id="link-128" class="py-name"><a title="Bio.Encodings.IUPACEncoding.obj" class="py-name" href="#" onclick="return doclink('link-128', 'obj', 'link-126');">obj</a></tt><tt class="py-op">.</tt><tt id="link-129" class="py-name"><a title="Bio.config.FormatRegistry.FormatGroup.identifyFile
Bio.config.FormatRegistry.FormatObject.identifyFile" class="py-name" href="#" onclick="return doclink('link-129', 'identifyFile', 'link-62');">identifyFile</a></tt><tt class="py-op">(</tt><tt class="py-name">infile</tt><tt class="py-op">,</tt> <tt class="py-name">debug_level</tt><tt class="py-op">=</tt><tt class="py-name">debug_level</tt><tt class="py-op">)</tt> </tt>
<a name="L239"></a><tt class="py-lineno">239</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt id="link-130" class="py-name"><a title="Bio.Restriction.Restriction.RestrictionBatch.format
Bio.expressions.blast.ncbiblast.format
Bio.expressions.blast.wublast.format
Bio.expressions.blocks.format
Bio.expressions.embl.embl65.format
Bio.expressions.fasta.format
Bio.expressions.genbank.format
Bio.expressions.hmmpfam.format
Bio.expressions.swissprot.ipi.format
Bio.expressions.swissprot.speclist.format
Bio.expressions.swissprot.sprot38.format
Bio.expressions.swissprot.sprot40.format
Bio.expressions.transfac.format
Martel.test.test_swissprot38.format
Martel.test.testformats.swissprot38.format" class="py-name" href="#" onclick="return doclink('link-130', 'format', 'link-11');">format</a></tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L240"></a><tt class="py-lineno">240</tt>  <tt class="py-line">                <tt class="py-keyword">return</tt> <tt id="link-131" class="py-name"><a title="Bio.Restriction.Restriction.RestrictionBatch.format
Bio.expressions.blast.ncbiblast.format
Bio.expressions.blast.wublast.format
Bio.expressions.blocks.format
Bio.expressions.embl.embl65.format
Bio.expressions.fasta.format
Bio.expressions.genbank.format
Bio.expressions.hmmpfam.format
Bio.expressions.swissprot.ipi.format
Bio.expressions.swissprot.speclist.format
Bio.expressions.swissprot.sprot38.format
Bio.expressions.swissprot.sprot40.format
Bio.expressions.transfac.format
Martel.test.test_swissprot38.format
Martel.test.testformats.swissprot38.format" class="py-name" href="#" onclick="return doclink('link-131', 'format', 'link-11');">format</a></tt> </tt>
<a name="L241"></a><tt class="py-lineno">241</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">None</tt> </tt>
</div><a name="L242"></a><tt class="py-lineno">242</tt>  <tt class="py-line"> </tt>
<a name="FormatGroup.identifyString"></a><div id="FormatGroup.identifyString-def"><a name="L243"></a><tt class="py-lineno">243</tt> <a class="py-toggle" href="#" id="FormatGroup.identifyString-toggle" onclick="return toggle('FormatGroup.identifyString');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.config.FormatRegistry.FormatGroup-class.html#identifyString">identifyString</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">s</tt><tt class="py-op">,</tt> <tt class="py-param">debug_level</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FormatGroup.identifyString-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="FormatGroup.identifyString-expanded"><a name="L244"></a><tt class="py-lineno">244</tt>  <tt class="py-line">        <tt class="py-docstring">"""S.identifyString(s[, debug_level]) -&gt; FormatObject or None"""</tt> </tt>
<a name="L245"></a><tt class="py-lineno">245</tt>  <tt class="py-line">        <tt class="py-keyword">from</tt> <tt class="py-name">StringIO</tt> <tt class="py-keyword">import</tt> <tt class="py-name">StringIO</tt> </tt>
<a name="L246"></a><tt class="py-lineno">246</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-132" class="py-name"><a title="Bio.config.FormatRegistry.FormatGroup.identifyFile
Bio.config.FormatRegistry.FormatObject.identifyFile" class="py-name" href="#" onclick="return doclink('link-132', 'identifyFile', 'link-62');">identifyFile</a></tt><tt class="py-op">(</tt><tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt id="link-133" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-133', 's', 'link-55');">s</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">debug_level</tt><tt class="py-op">)</tt> </tt>
</div><a name="L247"></a><tt class="py-lineno">247</tt>  <tt class="py-line"> </tt>
<a name="FormatGroup.identify"></a><div id="FormatGroup.identify-def"><a name="L248"></a><tt class="py-lineno">248</tt> <a class="py-toggle" href="#" id="FormatGroup.identify-toggle" onclick="return toggle('FormatGroup.identify');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.config.FormatRegistry.FormatGroup-class.html#identify">identify</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">source</tt><tt class="py-op">,</tt> <tt class="py-param">debug_level</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FormatGroup.identify-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="FormatGroup.identify-expanded"><a name="L249"></a><tt class="py-lineno">249</tt>  <tt class="py-line">        <tt class="py-docstring">"""S.identify(source[, debug_level]) -&gt; FormatObject or None"""</tt> </tt>
<a name="L250"></a><tt class="py-lineno">250</tt>  <tt class="py-line">        <tt id="link-134" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-134', 'source', 'link-56');">source</a></tt> <tt class="py-op">=</tt> <tt id="link-135" class="py-name"><a title="Bio.EUtils.ReseekFile
Bio.EUtils.ReseekFile.ReseekFile" class="py-name" href="#" onclick="return doclink('link-135', 'ReseekFile', 'link-57');">ReseekFile</a></tt><tt class="py-op">.</tt><tt id="link-136" class="py-name"><a title="Bio.EUtils.ReseekFile.prepare_input_source" class="py-name" href="#" onclick="return doclink('link-136', 'prepare_input_source', 'link-58');">prepare_input_source</a></tt><tt class="py-op">(</tt><tt id="link-137" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-137', 'source', 'link-56');">source</a></tt><tt class="py-op">)</tt> </tt>
<a name="L251"></a><tt class="py-lineno">251</tt>  <tt class="py-line">        <tt class="py-name">f</tt> <tt class="py-op">=</tt> <tt id="link-138" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-138', 'source', 'link-56');">source</a></tt><tt class="py-op">.</tt><tt class="py-name">getCharacterStream</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-keyword">or</tt> <tt id="link-139" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-139', 'source', 'link-56');">source</a></tt><tt class="py-op">.</tt><tt class="py-name">getByteStream</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L252"></a><tt class="py-lineno">252</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-140" class="py-name"><a title="Bio.config.FormatRegistry.FormatGroup.identifyFile
Bio.config.FormatRegistry.FormatObject.identifyFile" class="py-name" href="#" onclick="return doclink('link-140', 'identifyFile', 'link-62');">identifyFile</a></tt><tt class="py-op">(</tt><tt class="py-name">f</tt><tt class="py-op">,</tt> <tt class="py-name">debug_level</tt><tt class="py-op">)</tt> </tt>
</div><a name="L253"></a><tt class="py-lineno">253</tt>  <tt class="py-line"> </tt>
<a name="FormatGroup.add"></a><div id="FormatGroup.add-def"><a name="L254"></a><tt class="py-lineno">254</tt> <a class="py-toggle" href="#" id="FormatGroup.add-toggle" onclick="return toggle('FormatGroup.add');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.config.FormatRegistry.FormatGroup-class.html#add">add</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">obj</tt><tt class="py-op">,</tt> <tt class="py-op">*</tt><tt class="py-param">args</tt><tt class="py-op">,</tt> <tt class="py-op">**</tt><tt class="py-param">keywds</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FormatGroup.add-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="FormatGroup.add-expanded"><a name="L255"></a><tt class="py-lineno">255</tt>  <tt class="py-line">        <tt class="py-keyword">import</tt> <tt class="py-name">weakref</tt> </tt>
<a name="L256"></a><tt class="py-lineno">256</tt>  <tt class="py-line">        <tt id="link-141" class="py-name"><a title="Bio.config.Registry.RegisterableGroup" class="py-name" href="#" onclick="return doclink('link-141', 'RegisterableGroup', 'link-112');">RegisterableGroup</a></tt><tt class="py-op">.</tt><tt id="link-142" class="py-name" targets="Variable Bio.Affy.CelFile.add=Bio.Affy.CelFile-module.html#add,Method Bio.EUtils.POM.ElementNode.add()=Bio.EUtils.POM.ElementNode-class.html#add,Method Bio.GFF.easy.Location.add()=Bio.GFF.easy.Location-class.html#add,Method Bio.Graphics.BasicChromosome._ChromosomeComponent.add()=Bio.Graphics.BasicChromosome._ChromosomeComponent-class.html#add,Variable Bio.LogisticRegression.add=Bio.LogisticRegression-module.html#add,Variable Bio.MarkovModel.add=Bio.MarkovModel-module.html#add,Variable Bio.MaxEntropy.add=Bio.MaxEntropy-module.html#add,Variable Bio.NaiveBayes.add=Bio.NaiveBayes-module.html#add,Method Bio.Nexus.Nexus.StepMatrix.add()=Bio.Nexus.Nexus.StepMatrix-class.html#add,Method Bio.Nexus.Nodes.Chain.add()=Bio.Nexus.Nodes.Chain-class.html#add,Method Bio.PDB.Entity.Entity.add()=Bio.PDB.Entity.Entity-class.html#add,Method Bio.PDB.Residue.DisorderedResidue.add()=Bio.PDB.Residue.DisorderedResidue-class.html#add,Method Bio.PDB.Residue.Residue.add()=Bio.PDB.Residue.Residue-class.html#add,Method Bio.Pathway.Rep.HashSet.HashSet.add()=Bio.Pathway.Rep.HashSet.HashSet-class.html#add,Method Bio.Restriction.Restriction.RestrictionBatch.add()=Bio.Restriction.Restriction.RestrictionBatch-class.html#add,Variable Bio.Statistics.lowess.add=Bio.Statistics.lowess-module.html#add,Method Bio.config.FormatRegistry.FormatGroup.add()=Bio.config.FormatRegistry.FormatGroup-class.html#add,Method Bio.config.Registry.RegisterableGroup.add()=Bio.config.Registry.RegisterableGroup-class.html#add,Variable Bio.distance.add=Bio.distance-module.html#add,Variable Bio.kNN.add=Bio.kNN-module.html#add,Method Martel.Dispatch.MulticallEnd.add()=Martel.Dispatch.MulticallEnd-class.html#add,Method Martel.Dispatch.MulticallStart.add()=Martel.Dispatch.MulticallStart-class.html#add"><a title="Bio.Affy.CelFile.add
Bio.EUtils.POM.ElementNode.add
Bio.GFF.easy.Location.add
Bio.Graphics.BasicChromosome._ChromosomeComponent.add
Bio.LogisticRegression.add
Bio.MarkovModel.add
Bio.MaxEntropy.add
Bio.NaiveBayes.add
Bio.Nexus.Nexus.StepMatrix.add
Bio.Nexus.Nodes.Chain.add
Bio.PDB.Entity.Entity.add
Bio.PDB.Residue.DisorderedResidue.add
Bio.PDB.Residue.Residue.add
Bio.Pathway.Rep.HashSet.HashSet.add
Bio.Restriction.Restriction.RestrictionBatch.add
Bio.Statistics.lowess.add
Bio.config.FormatRegistry.FormatGroup.add
Bio.config.Registry.RegisterableGroup.add
Bio.distance.add
Bio.kNN.add
Martel.Dispatch.MulticallEnd.add
Martel.Dispatch.MulticallStart.add" class="py-name" href="#" onclick="return doclink('link-142', 'add', 'link-142');">add</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt id="link-143" class="py-name"><a title="Bio.Encodings.IUPACEncoding.obj" class="py-name" href="#" onclick="return doclink('link-143', 'obj', 'link-126');">obj</a></tt><tt class="py-op">,</tt> <tt class="py-op">*</tt><tt class="py-name">args</tt><tt class="py-op">,</tt> <tt class="py-op">**</tt><tt class="py-name">keywds</tt><tt class="py-op">)</tt> </tt>
<a name="L257"></a><tt class="py-lineno">257</tt>  <tt class="py-line">        <tt id="link-144" class="py-name"><a title="Bio.Encodings.IUPACEncoding.obj" class="py-name" href="#" onclick="return doclink('link-144', 'obj', 'link-126');">obj</a></tt><tt class="py-op">.</tt><tt class="py-name">_parents</tt><tt class="py-op">.</tt><tt id="link-145" class="py-name" targets="Method Bio.Crystal.Chain.append()=Bio.Crystal.Chain-class.html#append,Method Bio.EUtils.POM.ElementNode.append()=Bio.EUtils.POM.ElementNode-class.html#append,Method Bio.EUtils.sourcegen.SourceFile.append()=Bio.EUtils.sourcegen.SourceFile-class.html#append,Method Bio.SCOP.Raf.SeqMap.append()=Bio.SCOP.Raf.SeqMap-class.html#append,Method Bio.Seq.MutableSeq.append()=Bio.Seq.MutableSeq-class.html#append,Method Bio.Wise.psw.Alignment.append()=Bio.Wise.psw.Alignment-class.html#append,Method Bio.Wise.psw.AlignmentColumn.append()=Bio.Wise.psw.AlignmentColumn-class.html#append,Method Martel.msre_parse.SubPattern.append()=Martel.msre_parse.SubPattern-class.html#append"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-145', 'append', 'link-145');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">weakref</tt><tt class="py-op">.</tt><tt class="py-name">proxy</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L258"></a><tt class="py-lineno">258</tt>  <tt class="py-line">         </tt>
<a name="L259"></a><tt class="py-lineno">259</tt>  <tt class="py-line"> </tt>
<a name="_parses_file"></a><div id="_parses_file-def"><a name="L260"></a><tt class="py-lineno">260</tt> <a class="py-toggle" href="#" id="_parses_file-toggle" onclick="return toggle('_parses_file');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.config.FormatRegistry-module.html#_parses_file">_parses_file</a><tt class="py-op">(</tt><tt class="py-param">expression</tt><tt class="py-op">,</tt> <tt class="py-param">infile</tt><tt class="py-op">,</tt> <tt class="py-param">debug_level</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_parses_file-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_parses_file-expanded"><a name="L261"></a><tt class="py-lineno">261</tt>  <tt class="py-line">    <tt class="py-comment"># Return a boolean indicating whether expression can parse infile.</tt> </tt>
<a name="L262"></a><tt class="py-lineno">262</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-keyword">from</tt> <tt id="link-146" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-146', 'Bio', 'link-0');">Bio</a></tt> <tt class="py-keyword">import</tt> <tt id="link-147" class="py-name" targets="Module Bio.StdHandler=Bio.StdHandler-module.html"><a title="Bio.StdHandler" class="py-name" href="#" onclick="return doclink('link-147', 'StdHandler', 'link-147');">StdHandler</a></tt> </tt>
<a name="L263"></a><tt class="py-lineno">263</tt>  <tt class="py-line">    <tt class="py-keyword">from</tt> <tt id="link-148" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-148', 'Martel', 'link-74');">Martel</a></tt> <tt class="py-keyword">import</tt> <tt id="link-149" class="py-name" targets="Module Bio.AlignAce.Parser=Bio.AlignAce.Parser-module.html,Module Bio.Entrez.Parser=Bio.Entrez.Parser-module.html,Module Bio.MEME.Parser=Bio.MEME.Parser-module.html,Class Bio.SCOP.Cla.Parser=Bio.SCOP.Cla.Parser-class.html,Class Bio.SCOP.Des.Parser=Bio.SCOP.Des.Parser-class.html,Class Bio.SCOP.Dom.Parser=Bio.SCOP.Dom.Parser-class.html,Class Bio.SCOP.Hie.Parser=Bio.SCOP.Hie.Parser-class.html,Class Bio.SCOP.Raf.Parser=Bio.SCOP.Raf.Parser-class.html,Module Martel.Parser=Martel.Parser-module.html,Class Martel.Parser.Parser=Martel.Parser.Parser-class.html"><a title="Bio.AlignAce.Parser
Bio.Entrez.Parser
Bio.MEME.Parser
Bio.SCOP.Cla.Parser
Bio.SCOP.Des.Parser
Bio.SCOP.Dom.Parser
Bio.SCOP.Hie.Parser
Bio.SCOP.Raf.Parser
Martel.Parser
Martel.Parser.Parser" class="py-name" href="#" onclick="return doclink('link-149', 'Parser', 'link-149');">Parser</a></tt> </tt>
<a name="L264"></a><tt class="py-lineno">264</tt>  <tt class="py-line">     </tt>
<a name="L265"></a><tt class="py-lineno">265</tt>  <tt class="py-line">    <tt class="py-name">parser</tt> <tt class="py-op">=</tt> <tt class="py-name">expression</tt><tt class="py-op">.</tt><tt id="link-150" class="py-name"><a title="Bio.config.FormatRegistry.FormatObject.make_parser
Bio.config._support.make_cached_expression.make_parser
Martel.Expression.Expression.make_parser
Martel.Expression.HeaderFooter.make_parser
Martel.Expression.ParseRecords.make_parser" class="py-name" href="#" onclick="return doclink('link-150', 'make_parser', 'link-83');">make_parser</a></tt><tt class="py-op">(</tt><tt class="py-name">debug_level</tt><tt class="py-op">)</tt> </tt>
<a name="L266"></a><tt class="py-lineno">266</tt>  <tt class="py-line">    <tt class="py-name">handler</tt> <tt class="py-op">=</tt> <tt id="link-151" class="py-name"><a title="Bio.StdHandler" class="py-name" href="#" onclick="return doclink('link-151', 'StdHandler', 'link-147');">StdHandler</a></tt><tt class="py-op">.</tt><tt id="link-152" class="py-name" targets="Class Bio.StdHandler.RecognizeHandler=Bio.StdHandler.RecognizeHandler-class.html"><a title="Bio.StdHandler.RecognizeHandler" class="py-name" href="#" onclick="return doclink('link-152', 'RecognizeHandler', 'link-152');">RecognizeHandler</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L267"></a><tt class="py-lineno">267</tt>  <tt class="py-line">    <tt class="py-name">parser</tt><tt class="py-op">.</tt><tt class="py-name">setErrorHandler</tt><tt class="py-op">(</tt><tt class="py-name">handler</tt><tt class="py-op">)</tt> </tt>
<a name="L268"></a><tt class="py-lineno">268</tt>  <tt class="py-line">    <tt class="py-name">parser</tt><tt class="py-op">.</tt><tt class="py-name">setContentHandler</tt><tt class="py-op">(</tt><tt class="py-name">handler</tt><tt class="py-op">)</tt> </tt>
<a name="L269"></a><tt class="py-lineno">269</tt>  <tt class="py-line">    <tt class="py-name">pos</tt> <tt class="py-op">=</tt> <tt class="py-name">infile</tt><tt class="py-op">.</tt><tt id="link-153" class="py-name" targets="Method Bio.EUtils.ReseekFile.ReseekFile.tell()=Bio.EUtils.ReseekFile.ReseekFile-class.html#tell,Method Bio.File.UndoHandle.tell()=Bio.File.UndoHandle-class.html#tell,Method Martel.msre_parse.Tokenizer.tell()=Martel.msre_parse.Tokenizer-class.html#tell"><a title="Bio.EUtils.ReseekFile.ReseekFile.tell
Bio.File.UndoHandle.tell
Martel.msre_parse.Tokenizer.tell" class="py-name" href="#" onclick="return doclink('link-153', 'tell', 'link-153');">tell</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L270"></a><tt class="py-lineno">270</tt>  <tt class="py-line">    <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L271"></a><tt class="py-lineno">271</tt>  <tt class="py-line">        <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L272"></a><tt class="py-lineno">272</tt>  <tt class="py-line">            <tt class="py-name">parser</tt><tt class="py-op">.</tt><tt id="link-154" class="py-name" targets="Method Bio.EUtils.POM.POMDocument.parseFile()=Bio.EUtils.POM.POMDocument-class.html#parseFile,Method Martel.Parser.HeaderFooterParser.parseFile()=Martel.Parser.HeaderFooterParser-class.html#parseFile,Method Martel.Parser.Parser.parseFile()=Martel.Parser.Parser-class.html#parseFile,Method Martel.Parser.RecordParser.parseFile()=Martel.Parser.RecordParser-class.html#parseFile"><a title="Bio.EUtils.POM.POMDocument.parseFile
Martel.Parser.HeaderFooterParser.parseFile
Martel.Parser.Parser.parseFile
Martel.Parser.RecordParser.parseFile" class="py-name" href="#" onclick="return doclink('link-154', 'parseFile', 'link-154');">parseFile</a></tt><tt class="py-op">(</tt><tt class="py-name">infile</tt><tt class="py-op">)</tt> </tt>
<a name="L273"></a><tt class="py-lineno">273</tt>  <tt class="py-line">        <tt class="py-keyword">except</tt> <tt id="link-155" class="py-name"><a title="Bio.AlignAce.Parser
Bio.Entrez.Parser
Bio.MEME.Parser
Bio.SCOP.Cla.Parser
Bio.SCOP.Des.Parser
Bio.SCOP.Dom.Parser
Bio.SCOP.Hie.Parser
Bio.SCOP.Raf.Parser
Martel.Parser
Martel.Parser.Parser" class="py-name" href="#" onclick="return doclink('link-155', 'Parser', 'link-149');">Parser</a></tt><tt class="py-op">.</tt><tt id="link-156" class="py-name" targets="Class Martel.Parser.ParserException=Martel.Parser.ParserException-class.html"><a title="Martel.Parser.ParserException" class="py-name" href="#" onclick="return doclink('link-156', 'ParserException', 'link-156');">ParserException</a></tt><tt class="py-op">:</tt> </tt>
<a name="L274"></a><tt class="py-lineno">274</tt>  <tt class="py-line">            <tt class="py-keyword">pass</tt> </tt>
<a name="L275"></a><tt class="py-lineno">275</tt>  <tt class="py-line">    <tt class="py-keyword">finally</tt><tt class="py-op">:</tt> </tt>
<a name="L276"></a><tt class="py-lineno">276</tt>  <tt class="py-line">        <tt class="py-name">infile</tt><tt class="py-op">.</tt><tt id="link-157" class="py-name" targets="Method Bio.EUtils.ReseekFile.ReseekFile.seek()=Bio.EUtils.ReseekFile.ReseekFile-class.html#seek,Method Bio.File.UndoHandle.seek()=Bio.File.UndoHandle-class.html#seek,Method Martel.msre_parse.Tokenizer.seek()=Martel.msre_parse.Tokenizer-class.html#seek"><a title="Bio.EUtils.ReseekFile.ReseekFile.seek
Bio.File.UndoHandle.seek
Martel.msre_parse.Tokenizer.seek" class="py-name" href="#" onclick="return doclink('link-157', 'seek', 'link-157');">seek</a></tt><tt class="py-op">(</tt><tt class="py-name">pos</tt><tt class="py-op">)</tt> </tt>
<a name="L277"></a><tt class="py-lineno">277</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">handler</tt><tt class="py-op">.</tt><tt class="py-name">recognized</tt> </tt>
</div><a name="L278"></a><tt class="py-lineno">278</tt>  <tt class="py-line">  </tt>
<a name="_parses_string"></a><div id="_parses_string-def"><a name="L279"></a><tt class="py-lineno">279</tt> <a class="py-toggle" href="#" id="_parses_string-toggle" onclick="return toggle('_parses_string');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.config.FormatRegistry-module.html#_parses_string">_parses_string</a><tt class="py-op">(</tt><tt class="py-param">expression</tt><tt class="py-op">,</tt> <tt class="py-param">s</tt><tt class="py-op">,</tt> <tt class="py-param">debug_level</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_parses_string-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_parses_string-expanded"><a name="L280"></a><tt class="py-lineno">280</tt>  <tt class="py-line">    <tt class="py-keyword">from</tt> <tt class="py-name">StringIO</tt> <tt class="py-keyword">import</tt> <tt class="py-name">StringIO</tt> </tt>
<a name="L281"></a><tt class="py-lineno">281</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt id="link-158" class="py-name"><a title="Bio.config.FormatRegistry._parses_string" class="py-name" href="#" onclick="return doclink('link-158', '_parses_string', 'link-53');">_parses_string</a></tt><tt class="py-op">(</tt><tt class="py-name">expression</tt><tt class="py-op">,</tt> <tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt id="link-159" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-159', 's', 'link-55');">s</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">debug_level</tt><tt class="py-op">)</tt> </tt>
</div><a name="L282"></a><tt class="py-lineno">282</tt>  <tt class="py-line"> </tt>
<a name="_normalize_expression"></a><div id="_normalize_expression-def"><a name="L283"></a><tt class="py-lineno">283</tt> <a class="py-toggle" href="#" id="_normalize_expression-toggle" onclick="return toggle('_normalize_expression');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.config.FormatRegistry-module.html#_normalize_expression">_normalize_expression</a><tt class="py-op">(</tt><tt class="py-param">expression_or_path</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_normalize_expression-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_normalize_expression-expanded"><a name="L284"></a><tt class="py-lineno">284</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">expression_or_path</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L285"></a><tt class="py-lineno">285</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">None</tt> </tt>
<a name="L286"></a><tt class="py-lineno">286</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt id="link-160" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-160', 'type', 'link-9');">type</a></tt><tt class="py-op">(</tt><tt class="py-name">expression_or_path</tt><tt class="py-op">)</tt> <tt class="py-op">!=</tt> <tt id="link-161" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-161', 'type', 'link-9');">type</a></tt><tt class="py-op">(</tt><tt class="py-string">""</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L287"></a><tt class="py-lineno">287</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">expression_or_path</tt> </tt>
<a name="L288"></a><tt class="py-lineno">288</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt id="link-162" class="py-name" targets="Function Bio.config.FormatRegistry._load_expression()=Bio.config.FormatRegistry-module.html#_load_expression"><a title="Bio.config.FormatRegistry._load_expression" class="py-name" href="#" onclick="return doclink('link-162', '_load_expression', 'link-162');">_load_expression</a></tt><tt class="py-op">(</tt><tt class="py-name">expression_or_path</tt><tt class="py-op">)</tt> </tt>
</div><a name="L289"></a><tt class="py-lineno">289</tt>  <tt class="py-line"> </tt>
<a name="_load_expression"></a><div id="_load_expression-def"><a name="L290"></a><tt class="py-lineno">290</tt> <a class="py-toggle" href="#" id="_load_expression-toggle" onclick="return toggle('_load_expression');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.config.FormatRegistry-module.html#_load_expression">_load_expression</a><tt class="py-op">(</tt><tt class="py-param">path</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_load_expression-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_load_expression-expanded"><a name="L291"></a><tt class="py-lineno">291</tt>  <tt class="py-line">    <tt class="py-keyword">from</tt> <tt id="link-163" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-163', 'Martel', 'link-74');">Martel</a></tt> <tt class="py-keyword">import</tt> <tt id="link-164" class="py-name" targets="Class Bio.EUtils.Datatypes.Expression=Bio.EUtils.Datatypes.Expression-class.html,Module Martel.Expression=Martel.Expression-module.html,Class Martel.Expression.Expression=Martel.Expression.Expression-class.html"><a title="Bio.EUtils.Datatypes.Expression
Martel.Expression
Martel.Expression.Expression" class="py-name" href="#" onclick="return doclink('link-164', 'Expression', 'link-164');">Expression</a></tt> </tt>
<a name="L292"></a><tt class="py-lineno">292</tt>  <tt class="py-line">    <tt id="link-165" class="py-name" targets="Variable Bio.MarkovModel.x=Bio.MarkovModel-module.html#x,Variable Bio.Statistics.lowess.x=Bio.Statistics.lowess-module.html#x"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-165', 'x', 'link-165');">x</a></tt> <tt class="py-op">=</tt> <tt id="link-166" class="py-name" targets="Function Bio.config.FormatRegistry._load_object()=Bio.config.FormatRegistry-module.html#_load_object"><a title="Bio.config.FormatRegistry._load_object" class="py-name" href="#" onclick="return doclink('link-166', '_load_object', 'link-166');">_load_object</a></tt><tt class="py-op">(</tt><tt class="py-name">path</tt><tt class="py-op">)</tt> </tt>
<a name="L293"></a><tt class="py-lineno">293</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt id="link-167" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-167', 'x', 'link-165');">x</a></tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L294"></a><tt class="py-lineno">294</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-168" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-168', 'x', 'link-165');">x</a></tt><tt class="py-op">,</tt> <tt id="link-169" class="py-name"><a title="Bio.EUtils.Datatypes.Expression
Martel.Expression
Martel.Expression.Expression" class="py-name" href="#" onclick="return doclink('link-169', 'Expression', 'link-164');">Expression</a></tt><tt class="py-op">.</tt><tt id="link-170" class="py-name"><a title="Bio.EUtils.Datatypes.Expression
Martel.Expression
Martel.Expression.Expression" class="py-name" href="#" onclick="return doclink('link-170', 'Expression', 'link-164');">Expression</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L295"></a><tt class="py-lineno">295</tt>  <tt class="py-line">            <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L296"></a><tt class="py-lineno">296</tt>  <tt class="py-line">                <tt class="py-name">klass</tt> <tt class="py-op">=</tt> <tt id="link-171" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-171', 'x', 'link-165');">x</a></tt><tt class="py-op">.</tt><tt class="py-name">__class__</tt><tt class="py-op">.</tt><tt class="py-name">__name__</tt> </tt>
<a name="L297"></a><tt class="py-lineno">297</tt>  <tt class="py-line">            <tt class="py-keyword">except</tt> <tt class="py-name">AttributeError</tt><tt class="py-op">:</tt> </tt>
<a name="L298"></a><tt class="py-lineno">298</tt>  <tt class="py-line">                <tt class="py-name">klass</tt> <tt class="py-op">=</tt> <tt id="link-172" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-172', 'type', 'link-9');">type</a></tt><tt class="py-op">(</tt><tt id="link-173" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-173', 'x', 'link-165');">x</a></tt><tt class="py-op">)</tt> </tt>
<a name="L299"></a><tt class="py-lineno">299</tt>  <tt class="py-line">                <tt class="py-keyword">raise</tt> <tt class="py-name">TypeError</tt><tt class="py-op">(</tt><tt class="py-string">"%r should be a Martel Expression but "</tt> \ </tt>
<a name="L300"></a><tt class="py-lineno">300</tt>  <tt class="py-line">                                <tt class="py-string">"is a %r"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">path</tt><tt class="py-op">,</tt> <tt class="py-name">klass</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L301"></a><tt class="py-lineno">301</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt id="link-174" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-174', 'x', 'link-165');">x</a></tt> </tt>
<a name="L302"></a><tt class="py-lineno">302</tt>  <tt class="py-line">  </tt>
<a name="L303"></a><tt class="py-lineno">303</tt>  <tt class="py-line">    <tt class="py-comment"># Expression not found; make a useful error message</tt> </tt>
<a name="L304"></a><tt class="py-lineno">304</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-name">msg</tt> <tt class="py-op">=</tt> <tt class="py-string">"Could not find %r\n"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">path</tt><tt class="py-op">,</tt><tt class="py-op">)</tt> </tt>
<a name="L305"></a><tt class="py-lineno">305</tt>  <tt class="py-line">    <tt class="py-name">msg</tt> <tt class="py-op">=</tt> <tt class="py-name">msg</tt> <tt class="py-op">+</tt> <tt class="py-string">"(You may need to add the top-level module to the PYTHONPATH)"</tt> </tt>
<a name="L306"></a><tt class="py-lineno">306</tt>  <tt class="py-line">    <tt class="py-keyword">raise</tt> <tt class="py-name">TypeError</tt><tt class="py-op">(</tt><tt class="py-name">msg</tt><tt class="py-op">)</tt> </tt>
</div><a name="L307"></a><tt class="py-lineno">307</tt>  <tt class="py-line"> </tt>
<a name="_load_object"></a><div id="_load_object-def"><a name="L308"></a><tt class="py-lineno">308</tt> <a class="py-toggle" href="#" id="_load_object-toggle" onclick="return toggle('_load_object');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.config.FormatRegistry-module.html#_load_object">_load_object</a><tt class="py-op">(</tt><tt class="py-param">path</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_load_object-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_load_object-expanded"><a name="L309"></a><tt class="py-lineno">309</tt>  <tt class="py-line">    <tt class="py-name">terms</tt> <tt class="py-op">=</tt> <tt class="py-name">path</tt><tt class="py-op">.</tt><tt id="link-175" class="py-name" targets="Method Bio.Nexus.Trees.Tree.split()=Bio.Nexus.Trees.Tree-class.html#split,Method Bio.Restriction.Restriction.RestrictionBatch.split()=Bio.Restriction.Restriction.RestrictionBatch-class.html#split"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-175', 'split', 'link-175');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">"."</tt><tt class="py-op">)</tt> </tt>
<a name="L310"></a><tt class="py-lineno">310</tt>  <tt class="py-line">    <tt id="link-176" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-176', 's', 'link-55');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-name">terms</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L311"></a><tt class="py-lineno">311</tt>  <tt class="py-line">    <tt class="py-comment"># Import all the needed modules</tt> </tt>
<a name="L312"></a><tt class="py-lineno">312</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-comment"># (Don't know which are modules and which are classes, so simply</tt> </tt>
<a name="L313"></a><tt class="py-lineno">313</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-comment"># stop when imports fail.)</tt> </tt>
<a name="L314"></a><tt class="py-lineno">314</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-comment"># The order of appends is correct, since the last element cannot</tt> </tt>
<a name="L315"></a><tt class="py-lineno">315</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-comment"># be a module.</tt> </tt>
<a name="L316"></a><tt class="py-lineno">316</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt id="link-177" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-177', 'x', 'link-165');">x</a></tt> <tt class="py-op">=</tt> <tt class="py-name">__import__</tt><tt class="py-op">(</tt><tt id="link-178" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-178', 's', 'link-55');">s</a></tt><tt class="py-op">)</tt> </tt>
<a name="L317"></a><tt class="py-lineno">317</tt>  <tt class="py-line">    <tt class="py-name">prev_term</tt> <tt class="py-op">=</tt> <tt id="link-179" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-179', 's', 'link-55');">s</a></tt> </tt>
<a name="L318"></a><tt class="py-lineno">318</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">term</tt> <tt class="py-keyword">in</tt> <tt class="py-name">terms</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L319"></a><tt class="py-lineno">319</tt>  <tt class="py-line">        <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L320"></a><tt class="py-lineno">320</tt>  <tt class="py-line">            <tt class="py-name">__import__</tt><tt class="py-op">(</tt><tt id="link-180" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-180', 's', 'link-55');">s</a></tt><tt class="py-op">)</tt> </tt>
<a name="L321"></a><tt class="py-lineno">321</tt>  <tt class="py-line">        <tt class="py-keyword">except</tt> <tt class="py-name">SyntaxError</tt><tt class="py-op">,</tt> <tt class="py-name">exc</tt><tt class="py-op">:</tt> </tt>
<a name="L322"></a><tt class="py-lineno">322</tt>  <tt class="py-line"><tt class="py-comment">##            raise SyntaxError("%s during import of %r" % (exc, s)), \</tt> </tt>
<a name="L323"></a><tt class="py-lineno">323</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">##                  None, sys.exc_info()[2]</tt> </tt>
<a name="L324"></a><tt class="py-lineno">324</tt>  <tt class="py-line"><tt class="py-comment"></tt>            <tt class="py-keyword">raise</tt> </tt>
<a name="L325"></a><tt class="py-lineno">325</tt>  <tt class="py-line">        <tt class="py-keyword">except</tt> <tt class="py-name">ImportError</tt><tt class="py-op">,</tt> <tt class="py-name">exc</tt><tt class="py-op">:</tt> </tt>
<a name="L326"></a><tt class="py-lineno">326</tt>  <tt class="py-line">            <tt class="py-comment"># This is the only way I know to tell if the module</tt> </tt>
<a name="L327"></a><tt class="py-lineno">327</tt>  <tt class="py-line"><tt class="py-comment"></tt>            <tt class="py-comment"># could not be loaded because it doesn't exist.</tt> </tt>
<a name="L328"></a><tt class="py-lineno">328</tt>  <tt class="py-line"><tt class="py-comment"></tt>            <tt class="py-name">error_text</tt> <tt class="py-op">=</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">exc</tt><tt class="py-op">)</tt> </tt>
<a name="L329"></a><tt class="py-lineno">329</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">error_text</tt><tt class="py-op">.</tt><tt id="link-181" class="py-name" targets="Method Bio.EUtils.POM.ElementNode.find()=Bio.EUtils.POM.ElementNode-class.html#find,Method Bio.NeuralNetwork.Gene.Motif.MotifFinder.find()=Bio.NeuralNetwork.Gene.Motif.MotifFinder-class.html#find,Method Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find()=Bio.NeuralNetwork.Gene.Schema.SchemaFinder-class.html#find,Method Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find()=Bio.NeuralNetwork.Gene.Signature.SignatureFinder-class.html#find,Method Bio.biblio.Biblio.find()=Bio.biblio.Biblio-class.html#find,Function Bio.triefind.find()=Bio.triefind-module.html#find"><a title="Bio.EUtils.POM.ElementNode.find
Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.biblio.Biblio.find
Bio.triefind.find" class="py-name" href="#" onclick="return doclink('link-181', 'find', 'link-181');">find</a></tt><tt class="py-op">(</tt><tt class="py-string">"No module named %s"</tt> <tt class="py-op">%</tt> <tt class="py-name">prev_term</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L330"></a><tt class="py-lineno">330</tt>  <tt class="py-line">                <tt class="py-keyword">raise</tt> </tt>
<a name="L331"></a><tt class="py-lineno">331</tt>  <tt class="py-line">            <tt class="py-keyword">break</tt> </tt>
<a name="L332"></a><tt class="py-lineno">332</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">term</tt><tt class="py-op">:</tt> </tt>
<a name="L333"></a><tt class="py-lineno">333</tt>  <tt class="py-line">            <tt class="py-keyword">raise</tt> <tt class="py-name">TypeError</tt><tt class="py-op">(</tt><tt class="py-string">"There's a '.' in the wrong place: %r"</tt> <tt class="py-op">%</tt> \ </tt>
<a name="L334"></a><tt class="py-lineno">334</tt>  <tt class="py-line">                            <tt class="py-op">(</tt><tt class="py-name">path</tt><tt class="py-op">,</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L335"></a><tt class="py-lineno">335</tt>  <tt class="py-line">        <tt id="link-182" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-182', 's', 'link-55');">s</a></tt> <tt class="py-op">=</tt> <tt id="link-183" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-183', 's', 'link-55');">s</a></tt> <tt class="py-op">+</tt> <tt class="py-string">"."</tt> <tt class="py-op">+</tt> <tt class="py-name">term</tt> </tt>
<a name="L336"></a><tt class="py-lineno">336</tt>  <tt class="py-line">        <tt class="py-name">prev_term</tt> <tt class="py-op">=</tt> <tt class="py-name">term</tt> </tt>
<a name="L337"></a><tt class="py-lineno">337</tt>  <tt class="py-line"> </tt>
<a name="L338"></a><tt class="py-lineno">338</tt>  <tt class="py-line">    <tt class="py-comment"># Get the requested object</tt> </tt>
<a name="L339"></a><tt class="py-lineno">339</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt id="link-184" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-184', 's', 'link-55');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-name">terms</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L340"></a><tt class="py-lineno">340</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">term</tt> <tt class="py-keyword">in</tt> <tt class="py-name">terms</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L341"></a><tt class="py-lineno">341</tt>  <tt class="py-line">        <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L342"></a><tt class="py-lineno">342</tt>  <tt class="py-line">            <tt id="link-185" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-185', 'x', 'link-165');">x</a></tt> <tt class="py-op">=</tt> <tt class="py-name">getattr</tt><tt class="py-op">(</tt><tt id="link-186" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-186', 'x', 'link-165');">x</a></tt><tt class="py-op">,</tt> <tt class="py-name">term</tt><tt class="py-op">)</tt> </tt>
<a name="L343"></a><tt class="py-lineno">343</tt>  <tt class="py-line">        <tt class="py-keyword">except</tt> <tt class="py-name">AttributeError</tt><tt class="py-op">:</tt> </tt>
<a name="L344"></a><tt class="py-lineno">344</tt>  <tt class="py-line">            <tt class="py-keyword">raise</tt> <tt class="py-name">AttributeError</tt><tt class="py-op">(</tt><tt class="py-string">"%s object (%r) has no attribute %r"</tt> <tt class="py-op">%</tt> \ </tt>
<a name="L345"></a><tt class="py-lineno">345</tt>  <tt class="py-line">                                 <tt class="py-op">(</tt><tt id="link-187" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-187', 'type', 'link-9');">type</a></tt><tt class="py-op">(</tt><tt id="link-188" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-188', 'x', 'link-165');">x</a></tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">__name__</tt><tt class="py-op">,</tt> <tt id="link-189" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-189', 's', 'link-55');">s</a></tt><tt class="py-op">,</tt> <tt class="py-name">term</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L346"></a><tt class="py-lineno">346</tt>  <tt class="py-line">        <tt id="link-190" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-190', 's', 'link-55');">s</a></tt> <tt class="py-op">=</tt> <tt id="link-191" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-191', 's', 'link-55');">s</a></tt> <tt class="py-op">+</tt> <tt class="py-string">"."</tt> <tt class="py-op">+</tt> <tt class="py-name">term</tt> </tt>
<a name="L347"></a><tt class="py-lineno">347</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt id="link-192" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-192', 'x', 'link-165');">x</a></tt> </tt>
</div><a name="L348"></a><tt class="py-lineno">348</tt>  <tt class="py-line"> </tt>
<a name="_load_first_existing"></a><div id="_load_first_existing-def"><a name="L349"></a><tt class="py-lineno">349</tt> <a class="py-toggle" href="#" id="_load_first_existing-toggle" onclick="return toggle('_load_first_existing');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.config.FormatRegistry-module.html#_load_first_existing">_load_first_existing</a><tt class="py-op">(</tt><tt class="py-param">basemodulename</tt><tt class="py-op">,</tt> <tt class="py-param">possible_formats</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_load_first_existing-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_load_first_existing-expanded"><a name="L350"></a><tt class="py-lineno">350</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt id="link-193" class="py-name"><a title="Bio.Restriction.Restriction.RestrictionBatch.format
Bio.expressions.blast.ncbiblast.format
Bio.expressions.blast.wublast.format
Bio.expressions.blocks.format
Bio.expressions.embl.embl65.format
Bio.expressions.fasta.format
Bio.expressions.genbank.format
Bio.expressions.hmmpfam.format
Bio.expressions.swissprot.ipi.format
Bio.expressions.swissprot.speclist.format
Bio.expressions.swissprot.sprot38.format
Bio.expressions.swissprot.sprot40.format
Bio.expressions.transfac.format
Martel.test.test_swissprot38.format
Martel.test.testformats.swissprot38.format" class="py-name" href="#" onclick="return doclink('link-193', 'format', 'link-11');">format</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">possible_formats</tt><tt class="py-op">:</tt> </tt>
<a name="L351"></a><tt class="py-lineno">351</tt>  <tt class="py-line">        <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L352"></a><tt class="py-lineno">352</tt>  <tt class="py-line">            <tt class="py-name">module</tt> <tt class="py-op">=</tt> <tt id="link-194" class="py-name"><a title="Bio.config._support
Bio.dbdefs._support" class="py-name" href="#" onclick="return doclink('link-194', '_support', 'link-5');">_support</a></tt><tt class="py-op">.</tt><tt id="link-195" class="py-name" targets="Function Bio.config._support.load_module()=Bio.config._support-module.html#load_module"><a title="Bio.config._support.load_module" class="py-name" href="#" onclick="return doclink('link-195', 'load_module', 'link-195');">load_module</a></tt><tt class="py-op">(</tt><tt class="py-name">basemodulename</tt> <tt class="py-op">+</tt> <tt class="py-string">"."</tt> <tt class="py-op">+</tt> <tt id="link-196" class="py-name"><a title="Bio.Restriction.Restriction.RestrictionBatch.format
Bio.expressions.blast.ncbiblast.format
Bio.expressions.blast.wublast.format
Bio.expressions.blocks.format
Bio.expressions.embl.embl65.format
Bio.expressions.fasta.format
Bio.expressions.genbank.format
Bio.expressions.hmmpfam.format
Bio.expressions.swissprot.ipi.format
Bio.expressions.swissprot.speclist.format
Bio.expressions.swissprot.sprot38.format
Bio.expressions.swissprot.sprot40.format
Bio.expressions.transfac.format
Martel.test.test_swissprot38.format
Martel.test.testformats.swissprot38.format" class="py-name" href="#" onclick="return doclink('link-196', 'format', 'link-11');">format</a></tt><tt class="py-op">.</tt><tt class="py-name">abbrev</tt><tt class="py-op">)</tt> </tt>
<a name="L353"></a><tt class="py-lineno">353</tt>  <tt class="py-line">        <tt class="py-keyword">except</tt> <tt class="py-name">ImportError</tt><tt class="py-op">,</tt> <tt class="py-name">exc</tt><tt class="py-op">:</tt> </tt>
<a name="L354"></a><tt class="py-lineno">354</tt>  <tt class="py-line">            <tt class="py-comment"># This is the only way I know to tell if the module</tt> </tt>
<a name="L355"></a><tt class="py-lineno">355</tt>  <tt class="py-line"><tt class="py-comment"></tt>            <tt class="py-comment"># could not be loaded because it doesn't exist.</tt> </tt>
<a name="L356"></a><tt class="py-lineno">356</tt>  <tt class="py-line"><tt class="py-comment"></tt>            <tt class="py-name">error_text</tt> <tt class="py-op">=</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">exc</tt><tt class="py-op">)</tt> </tt>
<a name="L357"></a><tt class="py-lineno">357</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">error_text</tt><tt class="py-op">.</tt><tt id="link-197" class="py-name"><a title="Bio.EUtils.POM.ElementNode.find
Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.biblio.Biblio.find
Bio.triefind.find" class="py-name" href="#" onclick="return doclink('link-197', 'find', 'link-181');">find</a></tt><tt class="py-op">(</tt><tt class="py-string">"No module named %s"</tt> <tt class="py-op">%</tt> <tt id="link-198" class="py-name"><a title="Bio.Restriction.Restriction.RestrictionBatch.format
Bio.expressions.blast.ncbiblast.format
Bio.expressions.blast.wublast.format
Bio.expressions.blocks.format
Bio.expressions.embl.embl65.format
Bio.expressions.fasta.format
Bio.expressions.genbank.format
Bio.expressions.hmmpfam.format
Bio.expressions.swissprot.ipi.format
Bio.expressions.swissprot.speclist.format
Bio.expressions.swissprot.sprot38.format
Bio.expressions.swissprot.sprot40.format
Bio.expressions.transfac.format
Martel.test.test_swissprot38.format
Martel.test.testformats.swissprot38.format" class="py-name" href="#" onclick="return doclink('link-198', 'format', 'link-11');">format</a></tt><tt class="py-op">.</tt><tt class="py-name">abbrev</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L358"></a><tt class="py-lineno">358</tt>  <tt class="py-line">                <tt class="py-keyword">raise</tt> </tt>
<a name="L359"></a><tt class="py-lineno">359</tt>  <tt class="py-line">            <tt class="py-keyword">continue</tt> </tt>
<a name="L360"></a><tt class="py-lineno">360</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">module</tt> </tt>
<a name="L361"></a><tt class="py-lineno">361</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">None</tt> </tt>
</div><a name="L362"></a><tt class="py-lineno">362</tt>  <tt class="py-line"> </tt><script type="text/javascript">
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