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<h1 class="epydoc">Source Code for <a href="Bio.config.SeqDBRegistry-module.html">Module Bio.config.SeqDBRegistry</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.  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-docstring">"""This module handles seqdatabase.INI file.</tt> </tt>
<a name="L7"></a><tt class="py-lineno">  7</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L8"></a><tt class="py-lineno">  8</tt>  <tt class="py-line"><tt class="py-docstring">Classes:</tt> </tt>
<a name="L9"></a><tt class="py-lineno">  9</tt>  <tt class="py-line"><tt class="py-docstring">SeqDBRegistry   Holds databases from seqdatabase.INI.</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt>  <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">os</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt>  <tt class="py-line"> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</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-keyword">import</tt> <tt id="link-2" class="py-name" targets="Module Bio.config.DBRegistry=Bio.config.DBRegistry-module.html,Class Bio.config.DBRegistry.DBRegistry=Bio.config.DBRegistry.DBRegistry-class.html"><a title="Bio.config.DBRegistry
Bio.config.DBRegistry.DBRegistry" class="py-name" href="#" onclick="return doclink('link-2', 'DBRegistry', 'link-2');">DBRegistry</a></tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt>  <tt class="py-line"> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt>  <tt class="py-line"><tt class="py-comment"># 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"># _list_ini_paths    Return a list of standard places for INI files.</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"># _list_ini_files    Return a list of INI files that exist.</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"># </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_ini_file     Load an INI file into a set of RegisterableObjects.</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"># _make_flat_db</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"># _make_biofetch_db</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># _make_biosql_db</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># _openfu            Open a file or URL.</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># _warn              Register a warning message.</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt>  <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="SeqDBRegistry"></a><div id="SeqDBRegistry-def"><a name="L28"></a><tt class="py-lineno"> 28</tt> <a class="py-toggle" href="#" id="SeqDBRegistry-toggle" onclick="return toggle('SeqDBRegistry');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.config.SeqDBRegistry.SeqDBRegistry-class.html">SeqDBRegistry</a><tt class="py-op">(</tt><tt class="py-base-class">DBRegistry</tt><tt class="py-op">.</tt><tt class="py-base-class">DBRegistry</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SeqDBRegistry-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="SeqDBRegistry-expanded"><a name="L29"></a><tt class="py-lineno"> 29</tt>  <tt class="py-line">    <tt class="py-docstring">"""This object implements a dictionary-like interface to sequence</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt>  <tt class="py-line"><tt class="py-docstring">    databases.  To get a list of the databases available, do:</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt>  <tt class="py-line"><tt class="py-docstring">    Bio.seqdb.keys()</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">    Then, you can access the database using:</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt>  <tt class="py-line"><tt class="py-docstring">    Bio.seqdb[DATABASE_NAME][SEQUENCE_ID]</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="SeqDBRegistry.__init__"></a><div id="SeqDBRegistry.__init__-def"><a name="L37"></a><tt class="py-lineno"> 37</tt> <a class="py-toggle" href="#" id="SeqDBRegistry.__init__-toggle" onclick="return toggle('SeqDBRegistry.__init__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.config.SeqDBRegistry.SeqDBRegistry-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-op">:</tt> </tt>
</div><div id="SeqDBRegistry.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SeqDBRegistry.__init__-expanded"><a name="L38"></a><tt class="py-lineno"> 38</tt>  <tt class="py-line">        <tt id="link-3" class="py-name"><a title="Bio.config.DBRegistry
Bio.config.DBRegistry.DBRegistry" class="py-name" href="#" onclick="return doclink('link-3', 'DBRegistry', 'link-2');">DBRegistry</a></tt><tt class="py-op">.</tt><tt id="link-4" class="py-name"><a title="Bio.config.DBRegistry
Bio.config.DBRegistry.DBRegistry" class="py-name" href="#" onclick="return doclink('link-4', 'DBRegistry', 'link-2');">DBRegistry</a></tt><tt class="py-op">.</tt><tt id="link-5" class="py-name" targets="Method Bio.Affy.CelFile.CelConsumer.__init__()=Bio.Affy.CelFile.CelConsumer-class.html#__init__,Method Bio.Affy.CelFile.CelParser.__init__()=Bio.Affy.CelFile.CelParser-class.html#__init__,Method Bio.Affy.CelFile.CelRecord.__init__()=Bio.Affy.CelFile.CelRecord-class.html#__init__,Method Bio.Ais.Immune.__init__()=Bio.Ais.Immune-class.html#__init__,Method Bio.Ais.Lymphocyte.__init__()=Bio.Ais.Lymphocyte-class.html#__init__,Method Bio.Align.AlignInfo.PSSM.__init__()=Bio.Align.AlignInfo.PSSM-class.html#__init__,Method Bio.Align.AlignInfo.SummaryInfo.__init__()=Bio.Align.AlignInfo.SummaryInfo-class.html#__init__,Method Bio.Align.FormatConvert.FormatConverter.__init__()=Bio.Align.FormatConvert.FormatConverter-class.html#__init__,Method 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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__
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Martel.Expression.Assert.__init__
Martel.Expression.Debug.__init__
Martel.Expression.FastFeature.__init__
Martel.Expression.Group.__init__
Martel.Expression.GroupRef.__init__
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Martel.Expression.Literal.__init__
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Martel.Expression.NullOp.__init__
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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-5', '__init__', 'link-5');">__init__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt id="link-6" 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-6', 'name', 'link-6');">name</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L39"></a><tt class="py-lineno"> 39</tt>  <tt class="py-line">         </tt>
<a name="SeqDBRegistry._load"></a><div id="SeqDBRegistry._load-def"><a name="L40"></a><tt class="py-lineno"> 40</tt> <a class="py-toggle" href="#" id="SeqDBRegistry._load-toggle" onclick="return toggle('SeqDBRegistry._load');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.config.SeqDBRegistry.SeqDBRegistry-class.html#_load">_load</a><tt class="py-op">(</tt><tt class="py-param">self</tt><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="SeqDBRegistry._load-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SeqDBRegistry._load-expanded"><a name="L41"></a><tt class="py-lineno"> 41</tt>  <tt class="py-line">        <tt class="py-comment"># path is always None here</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-name">sources</tt> <tt class="py-op">=</tt> <tt id="link-7" class="py-name" targets="Function Bio.config.SeqDBRegistry._list_ini_files()=Bio.config.SeqDBRegistry-module.html#_list_ini_files"><a title="Bio.config.SeqDBRegistry._list_ini_files" class="py-name" href="#" onclick="return doclink('link-7', '_list_ini_files', 'link-7');">_list_ini_files</a></tt><tt class="py-op">(</tt><tt class="py-string">"seqdatabase.ini"</tt><tt class="py-op">)</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">file</tt> <tt class="py-keyword">in</tt> <tt class="py-name">sources</tt><tt class="py-op">:</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt>  <tt class="py-line">            <tt class="py-name">objects</tt> <tt class="py-op">=</tt> <tt id="link-8" class="py-name" targets="Function Bio.config.SeqDBRegistry._load_registry_objects()=Bio.config.SeqDBRegistry-module.html#_load_registry_objects"><a title="Bio.config.SeqDBRegistry._load_registry_objects" class="py-name" href="#" onclick="return doclink('link-8', '_load_registry_objects', 'link-8');">_load_registry_objects</a></tt><tt class="py-op">(</tt><tt class="py-name">file</tt><tt class="py-op">)</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">objects</tt><tt class="py-op">:</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt>  <tt class="py-line">                <tt class="py-keyword">for</tt> <tt id="link-9" 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-9', 'obj', 'link-9');">obj</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">objects</tt><tt class="py-op">:</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt>  <tt class="py-line">                    <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-10" class="py-name" targets="Method Bio.config.Registry.Registry.register()=Bio.config.Registry.Registry-class.html#register"><a title="Bio.config.Registry.Registry.register" class="py-name" href="#" onclick="return doclink('link-10', 'register', 'link-10');">register</a></tt><tt class="py-op">(</tt><tt id="link-11" class="py-name"><a title="Bio.Encodings.IUPACEncoding.obj" class="py-name" href="#" onclick="return doclink('link-11', 'obj', 'link-9');">obj</a></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">break</tt>   <tt class="py-comment"># Use the first one that exists.</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt>  <tt class="py-line">            <tt id="link-12" class="py-name" targets="Function Bio.config.SeqDBRegistry._warn()=Bio.config.SeqDBRegistry-module.html#_warn"><a title="Bio.config.SeqDBRegistry._warn" class="py-name" href="#" onclick="return doclink('link-12', '_warn', 'link-12');">_warn</a></tt><tt class="py-op">(</tt><tt class="py-string">"I could not load any seqdatabase files."</tt><tt class="py-op">)</tt> </tt>
</div><a name="L51"></a><tt class="py-lineno"> 51</tt>  <tt class="py-line"> </tt>
<a name="SeqDBRegistry.__getitem__"></a><div id="SeqDBRegistry.__getitem__-def"><a name="L52"></a><tt class="py-lineno"> 52</tt> <a class="py-toggle" href="#" id="SeqDBRegistry.__getitem__-toggle" onclick="return toggle('SeqDBRegistry.__getitem__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.config.SeqDBRegistry.SeqDBRegistry-class.html#__getitem__">__getitem__</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-op">:</tt> </tt>
</div><div id="SeqDBRegistry.__getitem__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SeqDBRegistry.__getitem__-expanded"><a name="L53"></a><tt class="py-lineno"> 53</tt>  <tt class="py-line">        <tt class="py-keyword">try</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 id="link-13" class="py-name"><a title="Bio.config.DBRegistry
Bio.config.DBRegistry.DBRegistry" class="py-name" href="#" onclick="return doclink('link-13', 'DBRegistry', 'link-2');">DBRegistry</a></tt><tt class="py-op">.</tt><tt id="link-14" class="py-name"><a title="Bio.config.DBRegistry
Bio.config.DBRegistry.DBRegistry" class="py-name" href="#" onclick="return doclink('link-14', 'DBRegistry', 'link-2');">DBRegistry</a></tt><tt class="py-op">.</tt><tt id="link-15" class="py-name" targets="Method Bio.Align.AlignInfo.PSSM.__getitem__()=Bio.Align.AlignInfo.PSSM-class.html#__getitem__,Method Bio.Crystal.Chain.__getitem__()=Bio.Crystal.Chain-class.html#__getitem__,Method Bio.Crystal.Crystal.__getitem__()=Bio.Crystal.Crystal-class.html#__getitem__,Method Bio.DBXRef.BioformatDBName.__getitem__()=Bio.DBXRef.BioformatDBName-class.html#__getitem__,Method Bio.DBXRef.UnknownDBName.__getitem__()=Bio.DBXRef.UnknownDBName-class.html#__getitem__,Method Bio.Data.CodonTable.AmbiguousForwardTable.__getitem__()=Bio.Data.CodonTable.AmbiguousForwardTable-class.html#__getitem__,Method Bio.EUtils.DBIdsClient.BaseDBIdsRecordSet.__getitem__()=Bio.EUtils.DBIdsClient.BaseDBIdsRecordSet-class.html#__getitem__,Method Bio.EUtils.Datatypes.DBIds.__getitem__()=Bio.EUtils.Datatypes.DBIds-class.html#__getitem__,Method Bio.EUtils.HistoryClient.BaseHistoryRecordSet.__getitem__()=Bio.EUtils.HistoryClient.BaseHistoryRecordSet-class.html#__getitem__,Method Bio.EUtils.MultiDict._BaseMultiDict.__getitem__()=Bio.EUtils.MultiDict._BaseMultiDict-class.html#__getitem__,Method Bio.EUtils.POM.ElementNode.__getitem__()=Bio.EUtils.POM.ElementNode-class.html#__getitem__,Method Bio.FSSP.fssp_rec.fff_rec.__getitem__()=Bio.FSSP.fssp_rec.fff_rec-class.html#__getitem__,Method Bio.GFF.GenericTools.ForgivingDictionary.__getitem__()=Bio.GFF.GenericTools.ForgivingDictionary-class.html#__getitem__,Method Bio.GFF.easy.FeatureDict.__getitem__()=Bio.GFF.easy.FeatureDict-class.html#__getitem__,Method Bio.GenBank.NCBIDictionary.__getitem__()=Bio.GenBank.NCBIDictionary-class.html#__getitem__,Method Bio.Gobase.Dictionary.__getitem__()=Bio.Gobase.Dictionary-class.html#__getitem__,Method Bio.Mindy.BaseDB.DictLookup.__getitem__()=Bio.Mindy.BaseDB.DictLookup-class.html#__getitem__,Method Bio.Mindy.BaseDB.OpenDB.__getitem__()=Bio.Mindy.BaseDB.OpenDB-class.html#__getitem__,Method Bio.Mindy.BerkeleyDB.BerkeleyDB.__getitem__()=Bio.Mindy.BerkeleyDB.BerkeleyDB-class.html#__getitem__,Method Bio.Mindy.BerkeleyDB.PrimaryNamespace.__getitem__()=Bio.Mindy.BerkeleyDB.PrimaryNamespace-class.html#__getitem__,Method Bio.Mindy.BerkeleyDB.SecondaryNamespace.__getitem__()=Bio.Mindy.BerkeleyDB.SecondaryNamespace-class.html#__getitem__,Method Bio.Mindy.FlatDB.BisectFile.__getitem__()=Bio.Mindy.FlatDB.BisectFile-class.html#__getitem__,Method Bio.Mindy.FlatDB.DiskFlatDB.__getitem__()=Bio.Mindy.FlatDB.DiskFlatDB-class.html#__getitem__,Method Bio.Mindy.FlatDB.MemoryFlatDB.__getitem__()=Bio.Mindy.FlatDB.MemoryFlatDB-class.html#__getitem__,Method Bio.Mindy.FlatDB.PrimaryNamespace.__getitem__()=Bio.Mindy.FlatDB.PrimaryNamespace-class.html#__getitem__,Method Bio.Mindy.FlatDB.PrimaryTable.__getitem__()=Bio.Mindy.FlatDB.PrimaryTable-class.html#__getitem__,Method Bio.Mindy.FlatDB.SecondaryNamespace.__getitem__()=Bio.Mindy.FlatDB.SecondaryNamespace-class.html#__getitem__,Method Bio.Mindy.FlatDB.SecondaryTable.__getitem__()=Bio.Mindy.FlatDB.SecondaryTable-class.html#__getitem__,Method Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.__getitem__()=Bio.PDB.AbstractPropertyMap.AbstractPropertyMap-class.html#__getitem__,Method Bio.PDB.Chain.Chain.__getitem__()=Bio.PDB.Chain.Chain-class.html#__getitem__,Method Bio.PDB.Entity.Entity.__getitem__()=Bio.PDB.Entity.Entity-class.html#__getitem__,Method Bio.PDB.FragmentMapper'.FragmentMapper.__getitem__()=Bio.PDB.FragmentMapper%27.FragmentMapper-class.html#__getitem__,Method Bio.PDB.MMCIF2Dict.MMCIF2Dict.__getitem__()=Bio.PDB.MMCIF2Dict.MMCIF2Dict-class.html#__getitem__,Method Bio.PDB.Vector'.Vector.__getitem__()=Bio.PDB.Vector%27.Vector-class.html#__getitem__,Method Bio.PropertyManager.CreateDict.__getitem__()=Bio.PropertyManager.CreateDict-class.html#__getitem__,Method Bio.Prosite.Dictionary.__getitem__()=Bio.Prosite.Dictionary-class.html#__getitem__,Method Bio.Prosite.ExPASyDictionary.__getitem__()=Bio.Prosite.ExPASyDictionary-class.html#__getitem__,Method Bio.Prosite.Pattern.Prosite.__getitem__()=Bio.Prosite.Pattern.Prosite-class.html#__getitem__,Method Bio.Prosite.Pattern.PrositeMatch.__getitem__()=Bio.Prosite.Pattern.PrositeMatch-class.html#__getitem__,Method Bio.Prosite.Prodoc.Dictionary.__getitem__()=Bio.Prosite.Prodoc.Dictionary-class.html#__getitem__,Method Bio.Prosite.Prodoc.ExPASyDictionary.__getitem__()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#__getitem__,Method Bio.PubMed.Dictionary.__getitem__()=Bio.PubMed.Dictionary-class.html#__getitem__,Method Bio.Rebase.Dictionary.__getitem__()=Bio.Rebase.Dictionary-class.html#__getitem__,Method Bio.Restriction.Restriction.FormattedSeq.__getitem__()=Bio.Restriction.Restriction.FormattedSeq-class.html#__getitem__,Method Bio.SCOP.Cla.Index.__getitem__()=Bio.SCOP.Cla.Index-class.html#__getitem__,Method Bio.SCOP.FileIndex.FileIndex.__getitem__()=Bio.SCOP.FileIndex.FileIndex-class.html#__getitem__,Method Bio.SCOP.FileIndex.defaultdict.__getitem__()=Bio.SCOP.FileIndex.defaultdict-class.html#__getitem__,Method Bio.SCOP.Raf.SeqMapIndex.__getitem__()=Bio.SCOP.Raf.SeqMapIndex-class.html#__getitem__,Method Bio.Seq.MutableSeq.__getitem__()=Bio.Seq.MutableSeq-class.html#__getitem__,Method Bio.Seq.Seq.__getitem__()=Bio.Seq.Seq-class.html#__getitem__,Method Bio.SeqIO.Interfaces.InterlacedSequenceIterator.__getitem__()=Bio.SeqIO.Interfaces.InterlacedSequenceIterator-class.html#__getitem__,Method Bio.SeqIO.StockholmIO.StockholmIterator.__getitem__()=Bio.SeqIO.StockholmIO.StockholmIterator-class.html#__getitem__,Method Bio.SwissProt.SProt.Dictionary.__getitem__()=Bio.SwissProt.SProt.Dictionary-class.html#__getitem__,Method Bio.SwissProt.SProt.ExPASyDictionary.__getitem__()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#__getitem__,Method Bio.config.DBRegistry.DBGroup.__getitem__()=Bio.config.DBRegistry.DBGroup-class.html#__getitem__,Method Bio.config.DBRegistry.DBObject.__getitem__()=Bio.config.DBRegistry.DBObject-class.html#__getitem__,Method Bio.config.Registry.Registry.__getitem__()=Bio.config.Registry.Registry-class.html#__getitem__,Method Bio.config.SeqDBRegistry.SeqDBRegistry.__getitem__()=Bio.config.SeqDBRegistry.SeqDBRegistry-class.html#__getitem__,Method BioSQL.BioSeq.DBSeq.__getitem__()=BioSQL.BioSeq.DBSeq-class.html#__getitem__,Method BioSQL.BioSeqDatabase.BioSeqDatabase.__getitem__()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#__getitem__,Method BioSQL.BioSeqDatabase.DBServer.__getitem__()=BioSQL.BioSeqDatabase.DBServer-class.html#__getitem__,Method Martel.Iterator.Iterate.__getitem__()=Martel.Iterator.Iterate-class.html#__getitem__,Method Martel.Parser.MartelAttributeList.__getitem__()=Martel.Parser.MartelAttributeList-class.html#__getitem__,Method Martel.msre_parse.SubPattern.__getitem__()=Martel.msre_parse.SubPattern-class.html#__getitem__,Method Martel.test.support.Storage.__getitem__()=Martel.test.support.Storage-class.html#__getitem__"><a title="Bio.Align.AlignInfo.PSSM.__getitem__
Bio.Crystal.Chain.__getitem__
Bio.Crystal.Crystal.__getitem__
Bio.DBXRef.BioformatDBName.__getitem__
Bio.DBXRef.UnknownDBName.__getitem__
Bio.Data.CodonTable.AmbiguousForwardTable.__getitem__
Bio.EUtils.DBIdsClient.BaseDBIdsRecordSet.__getitem__
Bio.EUtils.Datatypes.DBIds.__getitem__
Bio.EUtils.HistoryClient.BaseHistoryRecordSet.__getitem__
Bio.EUtils.MultiDict._BaseMultiDict.__getitem__
Bio.EUtils.POM.ElementNode.__getitem__
Bio.FSSP.fssp_rec.fff_rec.__getitem__
Bio.GFF.GenericTools.ForgivingDictionary.__getitem__
Bio.GFF.easy.FeatureDict.__getitem__
Bio.GenBank.NCBIDictionary.__getitem__
Bio.Gobase.Dictionary.__getitem__
Bio.Mindy.BaseDB.DictLookup.__getitem__
Bio.Mindy.BaseDB.OpenDB.__getitem__
Bio.Mindy.BerkeleyDB.BerkeleyDB.__getitem__
Bio.Mindy.BerkeleyDB.PrimaryNamespace.__getitem__
Bio.Mindy.BerkeleyDB.SecondaryNamespace.__getitem__
Bio.Mindy.FlatDB.BisectFile.__getitem__
Bio.Mindy.FlatDB.DiskFlatDB.__getitem__
Bio.Mindy.FlatDB.MemoryFlatDB.__getitem__
Bio.Mindy.FlatDB.PrimaryNamespace.__getitem__
Bio.Mindy.FlatDB.PrimaryTable.__getitem__
Bio.Mindy.FlatDB.SecondaryNamespace.__getitem__
Bio.Mindy.FlatDB.SecondaryTable.__getitem__
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.__getitem__
Bio.PDB.Chain.Chain.__getitem__
Bio.PDB.Entity.Entity.__getitem__
Bio.PDB.FragmentMapper'.FragmentMapper.__getitem__
Bio.PDB.MMCIF2Dict.MMCIF2Dict.__getitem__
Bio.PDB.Vector'.Vector.__getitem__
Bio.PropertyManager.CreateDict.__getitem__
Bio.Prosite.Dictionary.__getitem__
Bio.Prosite.ExPASyDictionary.__getitem__
Bio.Prosite.Pattern.Prosite.__getitem__
Bio.Prosite.Pattern.PrositeMatch.__getitem__
Bio.Prosite.Prodoc.Dictionary.__getitem__
Bio.Prosite.Prodoc.ExPASyDictionary.__getitem__
Bio.PubMed.Dictionary.__getitem__
Bio.Rebase.Dictionary.__getitem__
Bio.Restriction.Restriction.FormattedSeq.__getitem__
Bio.SCOP.Cla.Index.__getitem__
Bio.SCOP.FileIndex.FileIndex.__getitem__
Bio.SCOP.FileIndex.defaultdict.__getitem__
Bio.SCOP.Raf.SeqMapIndex.__getitem__
Bio.Seq.MutableSeq.__getitem__
Bio.Seq.Seq.__getitem__
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.__getitem__
Bio.SeqIO.StockholmIO.StockholmIterator.__getitem__
Bio.SwissProt.SProt.Dictionary.__getitem__
Bio.SwissProt.SProt.ExPASyDictionary.__getitem__
Bio.config.DBRegistry.DBGroup.__getitem__
Bio.config.DBRegistry.DBObject.__getitem__
Bio.config.Registry.Registry.__getitem__
Bio.config.SeqDBRegistry.SeqDBRegistry.__getitem__
BioSQL.BioSeq.DBSeq.__getitem__
BioSQL.BioSeqDatabase.BioSeqDatabase.__getitem__
BioSQL.BioSeqDatabase.DBServer.__getitem__
Martel.Iterator.Iterate.__getitem__
Martel.Parser.MartelAttributeList.__getitem__
Martel.msre_parse.SubPattern.__getitem__
Martel.test.support.Storage.__getitem__" class="py-name" href="#" onclick="return doclink('link-15', '__getitem__', 'link-15');">__getitem__</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"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-16', 'name', 'link-6');">name</a></tt><tt class="py-op">)</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt>  <tt class="py-line">        <tt class="py-keyword">except</tt> <tt class="py-name">KeyError</tt><tt class="py-op">,</tt> <tt id="link-17" 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-17', 'x', 'link-17');">x</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">raise</tt> <tt class="py-name">KeyError</tt><tt class="py-op">,</tt> <tt class="py-string">"Unknown database: %s"</tt> <tt class="py-op">%</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt id="link-18" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-18', 'x', 'link-17');">x</a></tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L57"></a><tt class="py-lineno"> 57</tt>  <tt class="py-line">         </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt>  <tt class="py-line"> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt>  <tt class="py-line"><tt id="link-19" class="py-name" targets="Variable Bio.config.SeqDBRegistry.seqdb=Bio.config.SeqDBRegistry-module.html#seqdb"><a title="Bio.config.SeqDBRegistry.seqdb" class="py-name" href="#" onclick="return doclink('link-19', 'seqdb', 'link-19');">seqdb</a></tt> <tt class="py-op">=</tt> <tt id="link-20" class="py-name" targets="Module Bio.config.SeqDBRegistry=Bio.config.SeqDBRegistry-module.html,Class Bio.config.SeqDBRegistry.SeqDBRegistry=Bio.config.SeqDBRegistry.SeqDBRegistry-class.html"><a title="Bio.config.SeqDBRegistry
Bio.config.SeqDBRegistry.SeqDBRegistry" class="py-name" href="#" onclick="return doclink('link-20', 'SeqDBRegistry', 'link-20');">SeqDBRegistry</a></tt><tt class="py-op">(</tt><tt class="py-string">"seqdb"</tt><tt class="py-op">)</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt>  <tt class="py-line"> </tt>
<a name="_warn"></a><div id="_warn-def"><a name="L61"></a><tt class="py-lineno"> 61</tt> <a class="py-toggle" href="#" id="_warn-toggle" onclick="return toggle('_warn');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.config.SeqDBRegistry-module.html#_warn">_warn</a><tt class="py-op">(</tt><tt class="py-param">message</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_warn-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_warn-expanded"><a name="L62"></a><tt class="py-lineno"> 62</tt>  <tt class="py-line">    <tt class="py-keyword">import</tt> <tt class="py-name">warnings</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt>  <tt class="py-line">    <tt class="py-name">warnings</tt><tt class="py-op">.</tt><tt class="py-name">warn</tt><tt class="py-op">(</tt><tt id="link-21" class="py-name" targets="Variable Bio.DocSQL.Query.message=Bio.DocSQL.Query-class.html#message"><a title="Bio.DocSQL.Query.message" class="py-name" href="#" onclick="return doclink('link-21', 'message', 'link-21');">message</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L64"></a><tt class="py-lineno"> 64</tt>  <tt class="py-line">     </tt>
<a name="_load_registry_objects"></a><div id="_load_registry_objects-def"><a name="L65"></a><tt class="py-lineno"> 65</tt> <a class="py-toggle" href="#" id="_load_registry_objects-toggle" onclick="return toggle('_load_registry_objects');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.config.SeqDBRegistry-module.html#_load_registry_objects">_load_registry_objects</a><tt class="py-op">(</tt><tt class="py-param">ini_file</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_load_registry_objects-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_load_registry_objects-expanded"><a name="L66"></a><tt class="py-lineno"> 66</tt>  <tt class="py-line">    <tt class="py-comment"># Return a list of RegisterableObjects.</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-keyword">import</tt> <tt id="link-22" class="py-name" targets="Module Bio.config._stanzaformat=Bio.config._stanzaformat-module.html"><a title="Bio.config._stanzaformat" class="py-name" href="#" onclick="return doclink('link-22', '_stanzaformat', 'link-22');">_stanzaformat</a></tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt>  <tt class="py-line"> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt>  <tt class="py-line">    <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt>  <tt class="py-line">        <tt class="py-name">stanzas</tt> <tt class="py-op">=</tt> <tt id="link-23" class="py-name"><a title="Bio.config._stanzaformat" class="py-name" href="#" onclick="return doclink('link-23', '_stanzaformat', 'link-22');">_stanzaformat</a></tt><tt class="py-op">.</tt><tt id="link-24" class="py-name" targets="Function Bio.MarkovModel.load()=Bio.MarkovModel-module.html#load,Method Bio.Mindy.BaseDB.WriteDB.load()=Bio.Mindy.BaseDB.WriteDB-class.html#load,Function Bio.config._stanzaformat.load()=Bio.config._stanzaformat-module.html#load,Method BioSQL.BioSeqDatabase.BioSeqDatabase.load()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#load"><a title="Bio.MarkovModel.load
Bio.Mindy.BaseDB.WriteDB.load
Bio.config._stanzaformat.load
BioSQL.BioSeqDatabase.BioSeqDatabase.load" class="py-name" href="#" onclick="return doclink('link-24', 'load', 'link-24');">load</a></tt><tt class="py-op">(</tt><tt id="link-25" class="py-name" targets="Function Bio.config.SeqDBRegistry._openfu()=Bio.config.SeqDBRegistry-module.html#_openfu"><a title="Bio.config.SeqDBRegistry._openfu" class="py-name" href="#" onclick="return doclink('link-25', '_openfu', 'link-25');">_openfu</a></tt><tt class="py-op">(</tt><tt class="py-name">ini_file</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt>  <tt class="py-line">    <tt class="py-keyword">except</tt> <tt class="py-name">ValueError</tt><tt class="py-op">,</tt> <tt id="link-26" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-26', 'x', 'link-17');">x</a></tt><tt class="py-op">:</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt>  <tt class="py-line">        <tt id="link-27" class="py-name"><a title="Bio.config.SeqDBRegistry._warn" class="py-name" href="#" onclick="return doclink('link-27', '_warn', 'link-12');">_warn</a></tt><tt class="py-op">(</tt><tt class="py-string">"Can't load seqdb.  Syntax error in %s: %s"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">ini_file</tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt id="link-28" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-28', 'x', 'link-17');">x</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">None</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"># Make sure the file is the right version.</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-keyword">if</tt> <tt class="py-name">stanzas</tt><tt class="py-op">.</tt><tt id="link-29" class="py-name" targets="Method Bio.AlignAce.Parser.AlignAceConsumer.version()=Bio.AlignAce.Parser.AlignAceConsumer-class.html#version,Method Bio.Blast.NCBIStandalone._HeaderConsumer.version()=Bio.Blast.NCBIStandalone._HeaderConsumer-class.html#version,Method Bio.GenBank._FeatureConsumer.version()=Bio.GenBank._FeatureConsumer-class.html#version,Method Bio.GenBank._RecordConsumer.version()=Bio.GenBank._RecordConsumer-class.html#version,Variable Bio.MetaTool.metatool_format.version=Bio.MetaTool.metatool_format-module.html#version,Variable Bio.expressions.genbank.version=Bio.expressions.genbank-module.html#version"><a title="Bio.AlignAce.Parser.AlignAceConsumer.version
Bio.Blast.NCBIStandalone._HeaderConsumer.version
Bio.GenBank._FeatureConsumer.version
Bio.GenBank._RecordConsumer.version
Bio.MetaTool.metatool_format.version
Bio.expressions.genbank.version" class="py-name" href="#" onclick="return doclink('link-29', 'version', 'link-29');">version</a></tt> <tt class="py-op">&gt;</tt> <tt class="py-string">"1.00"</tt><tt class="py-op">:</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt>  <tt class="py-line">        <tt id="link-30" class="py-name"><a title="Bio.config.SeqDBRegistry._warn" class="py-name" href="#" onclick="return doclink('link-30', '_warn', 'link-12');">_warn</a></tt><tt class="py-op">(</tt><tt class="py-string">"I can't handle stanza files with version %s"</tt> <tt class="py-op">%</tt> <tt class="py-name">stanzas</tt><tt class="py-op">.</tt><tt id="link-31" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.version
Bio.Blast.NCBIStandalone._HeaderConsumer.version
Bio.GenBank._FeatureConsumer.version
Bio.GenBank._RecordConsumer.version
Bio.MetaTool.metatool_format.version
Bio.expressions.genbank.version" class="py-name" href="#" onclick="return doclink('link-31', 'version', 'link-29');">version</a></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">return</tt> <tt class="py-name">None</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt>  <tt class="py-line"> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt>  <tt class="py-line">    <tt class="py-name">protocol2handler</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt>  <tt class="py-line">        <tt class="py-string">'flat'</tt> <tt class="py-op">:</tt> <tt id="link-32" class="py-name" targets="Function Bio.config.SeqDBRegistry._make_flat_db()=Bio.config.SeqDBRegistry-module.html#_make_flat_db"><a title="Bio.config.SeqDBRegistry._make_flat_db" class="py-name" href="#" onclick="return doclink('link-32', '_make_flat_db', 'link-32');">_make_flat_db</a></tt><tt class="py-op">,</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt>  <tt class="py-line">        <tt class="py-string">'biofetch'</tt> <tt class="py-op">:</tt> <tt id="link-33" class="py-name" targets="Function Bio.config.SeqDBRegistry._make_biofetch_db()=Bio.config.SeqDBRegistry-module.html#_make_biofetch_db"><a title="Bio.config.SeqDBRegistry._make_biofetch_db" class="py-name" href="#" onclick="return doclink('link-33', '_make_biofetch_db', 'link-33');">_make_biofetch_db</a></tt><tt class="py-op">,</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt>  <tt class="py-line">        <tt class="py-string">'biosql'</tt> <tt class="py-op">:</tt> <tt id="link-34" class="py-name" targets="Function Bio.config.SeqDBRegistry._make_biosql_db()=Bio.config.SeqDBRegistry-module.html#_make_biosql_db"><a title="Bio.config.SeqDBRegistry._make_biosql_db" class="py-name" href="#" onclick="return doclink('link-34', '_make_biosql_db', 'link-34');">_make_biosql_db</a></tt><tt class="py-op">,</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt>  <tt class="py-line">        <tt class="py-op">}</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt>  <tt class="py-line"> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt>  <tt class="py-line">    <tt class="py-name">inidata</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt>  <tt class="py-comment"># list of (section name, section key, dict of tag-&gt;value)</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">stanza</tt> <tt class="py-keyword">in</tt> <tt class="py-name">stanzas</tt><tt class="py-op">.</tt><tt class="py-name">stanzas</tt><tt class="py-op">:</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt>  <tt class="py-line">        <tt class="py-name">section_name</tt><tt class="py-op">,</tt> <tt class="py-name">tagvalue_dict</tt> <tt class="py-op">=</tt> <tt class="py-name">stanza</tt><tt class="py-op">.</tt><tt id="link-35" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-35', 'name', 'link-6');">name</a></tt><tt class="py-op">,</tt> <tt class="py-name">stanza</tt><tt class="py-op">.</tt><tt class="py-name">tag_value_dict</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt>  <tt class="py-line">        <tt class="py-name">section_key</tt> <tt class="py-op">=</tt> <tt class="py-name">section_name</tt><tt class="py-op">.</tt><tt class="py-name">lower</tt><tt class="py-op">(</tt><tt class="py-op">)</tt>   <tt class="py-comment"># case insensitive</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt>  <tt class="py-line">        <tt class="py-name">inidata</tt><tt class="py-op">.</tt><tt id="link-36" 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-36', 'append', 'link-36');">append</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">section_name</tt><tt class="py-op">,</tt> <tt class="py-name">section_key</tt><tt class="py-op">,</tt> <tt class="py-name">tagvalue_dict</tt><tt class="py-op">)</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"># Do some checking on each of the stanzas.  If there are errors,</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"># then ignore them.</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">seen</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt>  <tt class="py-comment"># Which sections we have already seen.</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt>  <tt class="py-line">    <tt id="link-37" class="py-name" targets="Variable Bio.PDB.Polypeptide.i=Bio.PDB.Polypeptide-module.html#i"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-37', 'i', 'link-37');">i</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt>  <tt class="py-line">    <tt class="py-keyword">while</tt> <tt id="link-38" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-38', 'i', 'link-37');">i</a></tt> <tt class="py-op">&lt;</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">inidata</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt>  <tt class="py-line">        <tt class="py-name">section_name</tt><tt class="py-op">,</tt> <tt class="py-name">section_key</tt><tt class="py-op">,</tt> <tt class="py-name">tagvalue_dict</tt> <tt class="py-op">=</tt> <tt class="py-name">inidata</tt><tt class="py-op">[</tt><tt id="link-39" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-39', 'i', 'link-37');">i</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-comment"># Make sure the stanza has a "protocol".</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-keyword">if</tt> <tt class="py-string">"protocol"</tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-name">tagvalue_dict</tt><tt class="py-op">:</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt>  <tt class="py-line">            <tt id="link-40" class="py-name"><a title="Bio.config.SeqDBRegistry._warn" class="py-name" href="#" onclick="return doclink('link-40', '_warn', 'link-12');">_warn</a></tt><tt class="py-op">(</tt><tt class="py-string">"%s stanza missing 'protocol'.  Skipping"</tt> <tt class="py-op">%</tt> <tt class="py-name">section_name</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">del</tt> <tt class="py-name">inidata</tt><tt class="py-op">[</tt><tt id="link-41" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-41', 'i', 'link-37');">i</a></tt><tt class="py-op">]</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt>  <tt class="py-line">        <tt class="py-comment"># Make sure the stanza has a "location".</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-keyword">elif</tt> <tt class="py-string">"location"</tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-name">tagvalue_dict</tt><tt class="py-op">:</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt>  <tt class="py-line">            <tt id="link-42" class="py-name"><a title="Bio.config.SeqDBRegistry._warn" class="py-name" href="#" onclick="return doclink('link-42', '_warn', 'link-12');">_warn</a></tt><tt class="py-op">(</tt><tt class="py-string">"%s stanza missing 'location'.  Skipping"</tt> <tt class="py-op">%</tt> <tt class="py-name">section_name</tt><tt class="py-op">)</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt>  <tt class="py-line">            <tt class="py-keyword">del</tt> <tt class="py-name">inidata</tt><tt class="py-op">[</tt><tt id="link-43" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-43', 'i', 'link-37');">i</a></tt><tt class="py-op">]</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt>  <tt class="py-line">        <tt class="py-comment"># Make sure we can handle the "protocol".</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-keyword">elif</tt> <tt class="py-name">tagvalue_dict</tt><tt class="py-op">[</tt><tt class="py-string">'protocol'</tt><tt class="py-op">]</tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-name">protocol2handler</tt><tt class="py-op">:</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt>  <tt class="py-line">            <tt id="link-44" class="py-name"><a title="Bio.config.SeqDBRegistry._warn" class="py-name" href="#" onclick="return doclink('link-44', '_warn', 'link-12');">_warn</a></tt><tt class="py-op">(</tt><tt class="py-string">"%s protocol not handled.  Skipping"</tt> <tt class="py-op">%</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt>  <tt class="py-line">                  <tt class="py-name">tagvalue_dict</tt><tt class="py-op">[</tt><tt class="py-string">'protocol'</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt>  <tt class="py-line">            <tt class="py-keyword">del</tt> <tt class="py-name">inidata</tt><tt class="py-op">[</tt><tt id="link-45" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-45', 'i', 'link-37');">i</a></tt><tt class="py-op">]</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt>  <tt class="py-line">        <tt class="py-comment"># Make sure this stanza has not already been defined.</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-keyword">elif</tt> <tt class="py-name">section_key</tt> <tt class="py-keyword">in</tt> <tt class="py-name">seen</tt><tt class="py-op">:</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt>  <tt class="py-line">            <tt id="link-46" class="py-name"><a title="Bio.config.SeqDBRegistry._warn" class="py-name" href="#" onclick="return doclink('link-46', '_warn', 'link-12');">_warn</a></tt><tt class="py-op">(</tt><tt class="py-string">"%s stanza already exists.  Skipping"</tt> <tt class="py-op">%</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt>  <tt class="py-line">                  <tt class="py-name">section_key</tt><tt class="py-op">)</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt>  <tt class="py-line">            <tt class="py-keyword">del</tt> <tt class="py-name">inidata</tt><tt class="py-op">[</tt><tt id="link-47" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-47', 'i', 'link-37');">i</a></tt><tt class="py-op">]</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt>  <tt class="py-line">            <tt class="py-name">seen</tt><tt class="py-op">[</tt><tt class="py-name">section_key</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt>  <tt class="py-line">            <tt id="link-48" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-48', 'i', 'link-37');">i</a></tt> <tt class="py-op">+=</tt> <tt class="py-number">1</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt>  <tt class="py-line"> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt>  <tt class="py-line">    <tt class="py-comment"># serial_groups is a list of fallback groups.  This is an</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-comment"># undocumented feature unsupported in the OBDA spec 1.00!</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-name">registry_objects</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt>  <tt class="py-comment"># list of RegisterableObjects</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt>  <tt class="py-line">    <tt class="py-name">serial_groups</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt>     <tt class="py-comment"># list of group_name, obj in group</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">section_name</tt><tt class="py-op">,</tt> <tt class="py-name">section_key</tt><tt class="py-op">,</tt> <tt class="py-name">tagvalue_dict</tt> <tt class="py-keyword">in</tt> <tt class="py-name">inidata</tt><tt class="py-op">:</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt>  <tt class="py-line">        <tt class="py-name">handler</tt> <tt class="py-op">=</tt> <tt class="py-name">protocol2handler</tt><tt class="py-op">.</tt><tt id="link-49" class="py-name" targets="Method Bio.Crystal.Crystal.get()=Bio.Crystal.Crystal-class.html#get,Method Bio.Data.CodonTable.AmbiguousForwardTable.get()=Bio.Data.CodonTable.AmbiguousForwardTable-class.html#get,Method Bio.EUtils.MultiDict._BaseMultiDict.get()=Bio.EUtils.MultiDict._BaseMultiDict-class.html#get,Method Bio.EUtils.POM.ElementNode.get()=Bio.EUtils.POM.ElementNode-class.html#get,Method Bio.GenBank.NCBIDictionary.get()=Bio.GenBank.NCBIDictionary-class.html#get,Method Bio.Mindy.BaseDB.DictLookup.get()=Bio.Mindy.BaseDB.DictLookup-class.html#get,Method Bio.Prosite.ExPASyDictionary.get()=Bio.Prosite.ExPASyDictionary-class.html#get,Method Bio.Prosite.Prodoc.ExPASyDictionary.get()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#get,Method Bio.PubMed.Dictionary.get()=Bio.PubMed.Dictionary-class.html#get,Method Bio.Restriction.Restriction.RestrictionBatch.get()=Bio.Restriction.Restriction.RestrictionBatch-class.html#get,Method Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get()=Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder-class.html#get,Method Bio.SeqUtils.MissingTable.get()=Bio.SeqUtils.MissingTable-class.html#get,Method Bio.SwissProt.SProt.ExPASyDictionary.get()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#get,Method Bio.config.DBRegistry.DBGroup.get()=Bio.config.DBRegistry.DBGroup-class.html#get,Method Bio.config.DBRegistry.DBObject.get()=Bio.config.DBRegistry.DBObject-class.html#get,Method Bio.config.Registry.Registry.get()=Bio.config.Registry.Registry-class.html#get,Method Martel.Parser.MartelAttributeList.get()=Martel.Parser.MartelAttributeList-class.html#get,Method Martel.msre_parse.Tokenizer.get()=Martel.msre_parse.Tokenizer-class.html#get"><a title="Bio.Crystal.Crystal.get
Bio.Data.CodonTable.AmbiguousForwardTable.get
Bio.EUtils.MultiDict._BaseMultiDict.get
Bio.EUtils.POM.ElementNode.get
Bio.GenBank.NCBIDictionary.get
Bio.Mindy.BaseDB.DictLookup.get
Bio.Prosite.ExPASyDictionary.get
Bio.Prosite.Prodoc.ExPASyDictionary.get
Bio.PubMed.Dictionary.get
Bio.Restriction.Restriction.RestrictionBatch.get
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get
Bio.SeqUtils.MissingTable.get
Bio.SwissProt.SProt.ExPASyDictionary.get
Bio.config.DBRegistry.DBGroup.get
Bio.config.DBRegistry.DBObject.get
Bio.config.Registry.Registry.get
Martel.Parser.MartelAttributeList.get
Martel.msre_parse.Tokenizer.get" class="py-name" href="#" onclick="return doclink('link-49', 'get', 'link-49');">get</a></tt><tt class="py-op">(</tt><tt class="py-name">tagvalue_dict</tt><tt class="py-op">[</tt><tt class="py-string">'protocol'</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt>  <tt class="py-line">        <tt id="link-50" class="py-name"><a title="Bio.Encodings.IUPACEncoding.obj" class="py-name" href="#" onclick="return doclink('link-50', 'obj', 'link-9');">obj</a></tt> <tt class="py-op">=</tt> <tt class="py-name">handler</tt><tt class="py-op">(</tt><tt class="py-name">section_name</tt><tt class="py-op">,</tt> <tt class="py-name">tagvalue_dict</tt><tt class="py-op">)</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt>  <tt class="py-line">        <tt class="py-name">registry_objects</tt><tt class="py-op">.</tt><tt id="link-51" class="py-name"><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-51', 'append', 'link-36');">append</a></tt><tt class="py-op">(</tt><tt id="link-52" class="py-name"><a title="Bio.Encodings.IUPACEncoding.obj" class="py-name" href="#" onclick="return doclink('link-52', 'obj', 'link-9');">obj</a></tt><tt class="py-op">)</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt>  <tt class="py-line"> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">tagvalue_dict</tt><tt class="py-op">.</tt><tt id="link-53" 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-53', 'has_key', 'link-53');">has_key</a></tt><tt class="py-op">(</tt><tt class="py-string">"fallback_group"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt>  <tt class="py-line">            <tt class="py-name">group_name</tt> <tt class="py-op">=</tt> <tt class="py-name">tagvalue_dict</tt><tt class="py-op">[</tt><tt class="py-string">'fallback_group'</tt><tt class="py-op">]</tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt>  <tt class="py-line">            <tt class="py-name">serial_groups</tt><tt class="py-op">.</tt><tt id="link-54" class="py-name"><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-54', 'append', 'link-36');">append</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">group_name</tt><tt class="py-op">,</tt> <tt id="link-55" class="py-name"><a title="Bio.Encodings.IUPACEncoding.obj" class="py-name" href="#" onclick="return doclink('link-55', 'obj', 'link-9');">obj</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt>  <tt class="py-line"> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt>  <tt class="py-line">    <tt class="py-comment"># Now make the group objects.</tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt id="link-56" class="py-name" targets="Method Bio.Prosite.Pattern.PrositeMatch.groups()=Bio.Prosite.Pattern.PrositeMatch-class.html#groups"><a title="Bio.Prosite.Pattern.PrositeMatch.groups" class="py-name" href="#" onclick="return doclink('link-56', 'groups', 'link-56');">groups</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt>  <tt class="py-comment"># name -&gt; DBGroup object</tt> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">group_name</tt><tt class="py-op">,</tt> <tt id="link-57" class="py-name"><a title="Bio.Encodings.IUPACEncoding.obj" class="py-name" href="#" onclick="return doclink('link-57', 'obj', 'link-9');">obj</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">serial_groups</tt><tt class="py-op">:</tt> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt id="link-58" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.groups" class="py-name" href="#" onclick="return doclink('link-58', 'groups', 'link-56');">groups</a></tt><tt class="py-op">.</tt><tt id="link-59" 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-59', 'has_key', 'link-53');">has_key</a></tt><tt class="py-op">(</tt><tt class="py-name">group_name</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt>  <tt class="py-line">            <tt id="link-60" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.groups" class="py-name" href="#" onclick="return doclink('link-60', 'groups', 'link-56');">groups</a></tt><tt class="py-op">[</tt><tt class="py-name">group_name</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-61" class="py-name"><a title="Bio.config.DBRegistry
Bio.config.DBRegistry.DBRegistry" class="py-name" href="#" onclick="return doclink('link-61', 'DBRegistry', 'link-2');">DBRegistry</a></tt><tt class="py-op">.</tt><tt id="link-62" class="py-name" targets="Class Bio.config.DBRegistry.DBGroup=Bio.config.DBRegistry.DBGroup-class.html"><a title="Bio.config.DBRegistry.DBGroup" class="py-name" href="#" onclick="return doclink('link-62', 'DBGroup', 'link-62');">DBGroup</a></tt><tt class="py-op">(</tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt>  <tt class="py-line">                <tt class="py-name">group_name</tt><tt class="py-op">,</tt> <tt class="py-name">behavior</tt><tt class="py-op">=</tt><tt class="py-string">"serial"</tt><tt class="py-op">)</tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt>  <tt class="py-line">        <tt id="link-63" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.groups" class="py-name" href="#" onclick="return doclink('link-63', 'groups', 'link-56');">groups</a></tt><tt class="py-op">[</tt><tt class="py-name">group_name</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-64" 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-64', 'add', 'link-64');">add</a></tt><tt class="py-op">(</tt><tt id="link-65" class="py-name"><a title="Bio.Encodings.IUPACEncoding.obj" class="py-name" href="#" onclick="return doclink('link-65', 'obj', 'link-9');">obj</a></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">registry_objects</tt><tt class="py-op">.</tt><tt id="link-66" 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-66', 'extend', 'link-66');">extend</a></tt><tt class="py-op">(</tt><tt id="link-67" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.groups" class="py-name" href="#" onclick="return doclink('link-67', 'groups', 'link-56');">groups</a></tt><tt class="py-op">.</tt><tt id="link-68" class="py-name" targets="Method Bio.Crystal.Crystal.values()=Bio.Crystal.Crystal-class.html#values,Method Bio.EUtils.MultiDict._BaseMultiDict.values()=Bio.EUtils.MultiDict._BaseMultiDict-class.html#values,Method Bio.GenBank.NCBIDictionary.values()=Bio.GenBank.NCBIDictionary-class.html#values,Method Bio.Mindy.BaseDB.DictLookup.values()=Bio.Mindy.BaseDB.DictLookup-class.html#values,Method Bio.Prosite.ExPASyDictionary.values()=Bio.Prosite.ExPASyDictionary-class.html#values,Method Bio.Prosite.Prodoc.ExPASyDictionary.values()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#values,Method Bio.PubMed.Dictionary.values()=Bio.PubMed.Dictionary-class.html#values,Method Bio.SwissProt.SProt.ExPASyDictionary.values()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#values,Method Bio.config.Registry.Registry.values()=Bio.config.Registry.Registry-class.html#values,Method BioSQL.BioSeqDatabase.BioSeqDatabase.values()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#values,Method BioSQL.BioSeqDatabase.DBServer.values()=BioSQL.BioSeqDatabase.DBServer-class.html#values,Method Martel.Parser.MartelAttributeList.values()=Martel.Parser.MartelAttributeList-class.html#values"><a title="Bio.Crystal.Crystal.values
Bio.EUtils.MultiDict._BaseMultiDict.values
Bio.GenBank.NCBIDictionary.values
Bio.Mindy.BaseDB.DictLookup.values
Bio.Prosite.ExPASyDictionary.values
Bio.Prosite.Prodoc.ExPASyDictionary.values
Bio.PubMed.Dictionary.values
Bio.SwissProt.SProt.ExPASyDictionary.values
Bio.config.Registry.Registry.values
BioSQL.BioSeqDatabase.BioSeqDatabase.values
BioSQL.BioSeqDatabase.DBServer.values
Martel.Parser.MartelAttributeList.values" class="py-name" href="#" onclick="return doclink('link-68', 'values', 'link-68');">values</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">registry_objects</tt> </tt>
</div><a name="L142"></a><tt class="py-lineno">142</tt>  <tt class="py-line"> </tt>
<a name="_make_biofetch_db"></a><div id="_make_biofetch_db-def"><a name="L143"></a><tt class="py-lineno">143</tt> <a class="py-toggle" href="#" id="_make_biofetch_db-toggle" onclick="return toggle('_make_biofetch_db');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.config.SeqDBRegistry-module.html#_make_biofetch_db">_make_biofetch_db</a><tt class="py-op">(</tt><tt class="py-param">name</tt><tt class="py-op">,</tt> <tt class="py-param">tagvalue_dict</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_make_biofetch_db-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_make_biofetch_db-expanded"><a name="L144"></a><tt class="py-lineno">144</tt>  <tt class="py-line">    <tt class="py-keyword">from</tt> <tt id="link-69" class="py-name" targets="Package Martel=Martel-module.html"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-69', 'Martel', 'link-69');">Martel</a></tt> <tt class="py-keyword">import</tt> <tt id="link-70" class="py-name" targets="Class Martel.Expression.Str=Martel.Expression.Str-class.html,Function Martel.Str()=Martel-module.html#Str"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-70', 'Str', 'link-70');">Str</a></tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt>  <tt class="py-line">    <tt class="py-comment"># Make the CGIDB object for the registry.</tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-name">params</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt>  <tt class="py-line">    <tt class="py-name">params</tt><tt class="py-op">[</tt><tt class="py-string">'name'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-71" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-71', 'name', 'link-6');">name</a></tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt>  <tt class="py-line">    <tt class="py-name">params</tt><tt class="py-op">[</tt><tt class="py-string">'cgi'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">tagvalue_dict</tt><tt class="py-op">[</tt><tt class="py-string">'location'</tt><tt class="py-op">]</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt>  <tt class="py-line">    <tt class="py-name">dbname</tt> <tt class="py-op">=</tt> <tt class="py-name">tagvalue_dict</tt><tt class="py-op">.</tt><tt id="link-72" class="py-name"><a title="Bio.Crystal.Crystal.get
Bio.Data.CodonTable.AmbiguousForwardTable.get
Bio.EUtils.MultiDict._BaseMultiDict.get
Bio.EUtils.POM.ElementNode.get
Bio.GenBank.NCBIDictionary.get
Bio.Mindy.BaseDB.DictLookup.get
Bio.Prosite.ExPASyDictionary.get
Bio.Prosite.Prodoc.ExPASyDictionary.get
Bio.PubMed.Dictionary.get
Bio.Restriction.Restriction.RestrictionBatch.get
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get
Bio.SeqUtils.MissingTable.get
Bio.SwissProt.SProt.ExPASyDictionary.get
Bio.config.DBRegistry.DBGroup.get
Bio.config.DBRegistry.DBObject.get
Bio.config.Registry.Registry.get
Martel.Parser.MartelAttributeList.get
Martel.msre_parse.Tokenizer.get" class="py-name" href="#" onclick="return doclink('link-72', 'get', 'link-49');">get</a></tt><tt class="py-op">(</tt><tt class="py-string">"dbname"</tt><tt class="py-op">,</tt> <tt class="py-string">"embl"</tt><tt class="py-op">)</tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt>  <tt class="py-line">    <tt class="py-name">params</tt><tt class="py-op">[</tt><tt class="py-string">'params'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-string">'style'</tt><tt class="py-op">,</tt> <tt class="py-string">'raw'</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt>  <tt class="py-line">                        <tt class="py-op">(</tt><tt class="py-string">'db'</tt><tt class="py-op">,</tt> <tt class="py-name">dbname</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt>  <tt class="py-line">                        <tt class="py-op">]</tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt>  <tt class="py-line">    <tt class="py-name">params</tt><tt class="py-op">[</tt><tt class="py-string">'key'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-string">'id'</tt> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt>  <tt class="py-line">    <tt class="py-name">params</tt><tt class="py-op">[</tt><tt class="py-string">'doc'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-string">"Retrieve sequences from the %s database."</tt> <tt class="py-op">%</tt> <tt class="py-name">dbname</tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt>  <tt class="py-line"> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt>  <tt class="py-line">    <tt class="py-name">params</tt><tt class="py-op">[</tt><tt class="py-string">'failure_cases'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt>  <tt class="py-line">        <tt class="py-op">(</tt><tt id="link-73" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-73', 'Str', 'link-70');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"ERROR 1"</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-string">"Unknown database."</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt>  <tt class="py-line">        <tt class="py-op">(</tt><tt id="link-74" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-74', 'Str', 'link-70');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"ERROR 2"</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-string">"Unknown style."</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt>  <tt class="py-line">        <tt class="py-op">(</tt><tt id="link-75" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-75', 'Str', 'link-70');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"ERROR 3"</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-string">"Format not known for database."</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt>  <tt class="py-line">        <tt class="py-op">(</tt><tt id="link-76" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-76', 'Str', 'link-70');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"ERROR 4"</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-string">"ID not found in database."</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt>  <tt class="py-line">        <tt class="py-op">(</tt><tt id="link-77" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-77', 'Str', 'link-70');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"ERROR 5"</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-string">"Too many IDs."</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt>  <tt class="py-line">        <tt class="py-op">]</tt> </tt>
<a name="L163"></a><tt class="py-lineno">163</tt>  <tt class="py-line">     </tt>
<a name="L164"></a><tt class="py-lineno">164</tt>  <tt class="py-line">    <tt class="py-comment"># All other params are ignored silently.</tt> </tt>
<a name="L165"></a><tt class="py-lineno">165</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-keyword">return</tt> <tt id="link-78" class="py-name"><a title="Bio.config.DBRegistry
Bio.config.DBRegistry.DBRegistry" class="py-name" href="#" onclick="return doclink('link-78', 'DBRegistry', 'link-2');">DBRegistry</a></tt><tt class="py-op">.</tt><tt id="link-79" class="py-name" targets="Class Bio.config.DBRegistry.CGIDB=Bio.config.DBRegistry.CGIDB-class.html"><a title="Bio.config.DBRegistry.CGIDB" class="py-name" href="#" onclick="return doclink('link-79', 'CGIDB', 'link-79');">CGIDB</a></tt><tt class="py-op">(</tt><tt class="py-op">**</tt><tt class="py-name">params</tt><tt class="py-op">)</tt> </tt>
</div><a name="L166"></a><tt class="py-lineno">166</tt>  <tt class="py-line"> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt>  <tt class="py-line"><tt class="py-comment">##def _make_biocorba_db(name, tagvalue_dict):</tt> </tt>
<a name="L168"></a><tt class="py-lineno">168</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">##    """Register a BioCorba style database defined in the registry."""</tt> </tt>
<a name="L169"></a><tt class="py-lineno">169</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">##    params = {}</tt> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">##    params['name'] = name</tt> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">##    params['ior_ref'] = tagvalue_dict['location']</tt> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">##    return DBRegistry.BioCorbaDB(**params)</tt> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt>  <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="_make_biosql_db"></a><div id="_make_biosql_db-def"><a name="L174"></a><tt class="py-lineno">174</tt> <a class="py-toggle" href="#" id="_make_biosql_db-toggle" onclick="return toggle('_make_biosql_db');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.config.SeqDBRegistry-module.html#_make_biosql_db">_make_biosql_db</a><tt class="py-op">(</tt><tt class="py-param">name</tt><tt class="py-op">,</tt> <tt class="py-param">tagvalue_dict</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_make_biosql_db-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_make_biosql_db-expanded"><a name="L175"></a><tt class="py-lineno">175</tt>  <tt class="py-line">    <tt class="py-docstring">"""Register a BioSQL database defined in the registry."""</tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt>  <tt class="py-line">    <tt class="py-keyword">import</tt> <tt class="py-name">re</tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt>  <tt class="py-line">    <tt class="py-name">params</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt>  <tt class="py-line">    <tt class="py-name">params</tt><tt class="py-op">[</tt><tt class="py-string">'name'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-80" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-80', 'name', 'link-6');">name</a></tt> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt>  <tt class="py-line"> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt>  <tt class="py-line">    <tt class="py-comment"># Make sure the location has the right format.</tt> </tt>
<a name="L181"></a><tt class="py-lineno">181</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt id="link-81" class="py-name" targets="Method Bio.Parsers.spark.GenericASTMatcher.match()=Bio.Parsers.spark.GenericASTMatcher-class.html#match,Method Bio.Prosite.Pattern.Prosite.match()=Bio.Prosite.Pattern.Prosite-class.html#match,Function Bio.triefind.match()=Bio.triefind-module.html#match,Method Martel.msre_parse.Tokenizer.match()=Martel.msre_parse.Tokenizer-class.html#match"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-81', 'match', 'link-81');">match</a></tt><tt class="py-op">(</tt><tt class="py-string">r"[a-zA-Z0-9_]+:\d+$"</tt><tt class="py-op">,</tt> <tt class="py-name">tagvalue_dict</tt><tt class="py-op">[</tt><tt class="py-string">'location'</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L182"></a><tt class="py-lineno">182</tt>  <tt class="py-line">        <tt id="link-82" class="py-name"><a title="Bio.config.SeqDBRegistry._warn" class="py-name" href="#" onclick="return doclink('link-82', '_warn', 'link-12');">_warn</a></tt><tt class="py-op">(</tt><tt class="py-string">"Invalid location string: %s.  I want &lt;host:port&gt;.  Skipping"</tt> <tt class="py-op">%</tt> </tt>
<a name="L183"></a><tt class="py-lineno">183</tt>  <tt class="py-line">              <tt class="py-name">tagvalue_dict</tt><tt class="py-op">[</tt><tt class="py-string">'location'</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L184"></a><tt class="py-lineno">184</tt>  <tt class="py-line">    <tt class="py-name">host</tt><tt class="py-op">,</tt> <tt class="py-name">port</tt> <tt class="py-op">=</tt> <tt class="py-name">tagvalue_dict</tt><tt class="py-op">[</tt><tt class="py-string">'location'</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-83" 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-83', 'split', 'link-83');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">":"</tt><tt class="py-op">)</tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt>  <tt class="py-line">    <tt class="py-name">params</tt><tt class="py-op">[</tt><tt class="py-string">'db_host'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">host</tt> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt>  <tt class="py-line">    <tt class="py-name">params</tt><tt class="py-op">[</tt><tt class="py-string">'db_port'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">port</tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt>  <tt class="py-line">     </tt>
<a name="L188"></a><tt class="py-lineno">188</tt>  <tt class="py-line">    <tt class="py-name">params</tt><tt class="py-op">[</tt><tt class="py-string">'sql_db'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">tagvalue_dict</tt><tt class="py-op">[</tt><tt class="py-string">'biodbname'</tt><tt class="py-op">]</tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt>  <tt class="py-line">    <tt class="py-name">params</tt><tt class="py-op">[</tt><tt class="py-string">'db_type'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">tagvalue_dict</tt><tt class="py-op">.</tt><tt id="link-84" class="py-name"><a title="Bio.Crystal.Crystal.get
Bio.Data.CodonTable.AmbiguousForwardTable.get
Bio.EUtils.MultiDict._BaseMultiDict.get
Bio.EUtils.POM.ElementNode.get
Bio.GenBank.NCBIDictionary.get
Bio.Mindy.BaseDB.DictLookup.get
Bio.Prosite.ExPASyDictionary.get
Bio.Prosite.Prodoc.ExPASyDictionary.get
Bio.PubMed.Dictionary.get
Bio.Restriction.Restriction.RestrictionBatch.get
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get
Bio.SeqUtils.MissingTable.get
Bio.SwissProt.SProt.ExPASyDictionary.get
Bio.config.DBRegistry.DBGroup.get
Bio.config.DBRegistry.DBObject.get
Bio.config.Registry.Registry.get
Martel.Parser.MartelAttributeList.get
Martel.msre_parse.Tokenizer.get" class="py-name" href="#" onclick="return doclink('link-84', 'get', 'link-49');">get</a></tt><tt class="py-op">(</tt><tt class="py-string">'driver'</tt><tt class="py-op">,</tt> <tt class="py-string">'mysql'</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">lower</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt>  <tt class="py-line">    <tt class="py-name">params</tt><tt class="py-op">[</tt><tt class="py-string">'db_user'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">tagvalue_dict</tt><tt class="py-op">.</tt><tt id="link-85" class="py-name"><a title="Bio.Crystal.Crystal.get
Bio.Data.CodonTable.AmbiguousForwardTable.get
Bio.EUtils.MultiDict._BaseMultiDict.get
Bio.EUtils.POM.ElementNode.get
Bio.GenBank.NCBIDictionary.get
Bio.Mindy.BaseDB.DictLookup.get
Bio.Prosite.ExPASyDictionary.get
Bio.Prosite.Prodoc.ExPASyDictionary.get
Bio.PubMed.Dictionary.get
Bio.Restriction.Restriction.RestrictionBatch.get
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get
Bio.SeqUtils.MissingTable.get
Bio.SwissProt.SProt.ExPASyDictionary.get
Bio.config.DBRegistry.DBGroup.get
Bio.config.DBRegistry.DBObject.get
Bio.config.Registry.Registry.get
Martel.Parser.MartelAttributeList.get
Martel.msre_parse.Tokenizer.get" class="py-name" href="#" onclick="return doclink('link-85', 'get', 'link-49');">get</a></tt><tt class="py-op">(</tt><tt class="py-string">'user'</tt><tt class="py-op">,</tt> <tt class="py-string">'root'</tt><tt class="py-op">)</tt> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt>  <tt class="py-line">    <tt class="py-name">params</tt><tt class="py-op">[</tt><tt class="py-string">'db_passwd'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">tagvalue_dict</tt><tt class="py-op">.</tt><tt id="link-86" class="py-name"><a title="Bio.Crystal.Crystal.get
Bio.Data.CodonTable.AmbiguousForwardTable.get
Bio.EUtils.MultiDict._BaseMultiDict.get
Bio.EUtils.POM.ElementNode.get
Bio.GenBank.NCBIDictionary.get
Bio.Mindy.BaseDB.DictLookup.get
Bio.Prosite.ExPASyDictionary.get
Bio.Prosite.Prodoc.ExPASyDictionary.get
Bio.PubMed.Dictionary.get
Bio.Restriction.Restriction.RestrictionBatch.get
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get
Bio.SeqUtils.MissingTable.get
Bio.SwissProt.SProt.ExPASyDictionary.get
Bio.config.DBRegistry.DBGroup.get
Bio.config.DBRegistry.DBObject.get
Bio.config.Registry.Registry.get
Martel.Parser.MartelAttributeList.get
Martel.msre_parse.Tokenizer.get" class="py-name" href="#" onclick="return doclink('link-86', 'get', 'link-49');">get</a></tt><tt class="py-op">(</tt><tt class="py-string">'passwd'</tt><tt class="py-op">,</tt> <tt class="py-string">''</tt><tt class="py-op">)</tt> </tt>
<a name="L192"></a><tt class="py-lineno">192</tt>  <tt class="py-line">    <tt class="py-name">params</tt><tt class="py-op">[</tt><tt class="py-string">'namespace_db'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">tagvalue_dict</tt><tt class="py-op">[</tt><tt class="py-string">'dbname'</tt><tt class="py-op">]</tt> </tt>
<a name="L193"></a><tt class="py-lineno">193</tt>  <tt class="py-line"> </tt>
<a name="L194"></a><tt class="py-lineno">194</tt>  <tt class="py-line">    <tt class="py-name">params</tt><tt class="py-op">[</tt><tt class="py-string">"doc"</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-string">"Retrieve %s sequences from BioSQL hosted at %s"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt>  <tt class="py-line">        <tt class="py-name">tagvalue_dict</tt><tt class="py-op">[</tt><tt class="py-string">'dbname'</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">host</tt><tt class="py-op">)</tt> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt>  <tt class="py-line"> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt id="link-87" class="py-name"><a title="Bio.config.DBRegistry
Bio.config.DBRegistry.DBRegistry" class="py-name" href="#" onclick="return doclink('link-87', 'DBRegistry', 'link-2');">DBRegistry</a></tt><tt class="py-op">.</tt><tt id="link-88" class="py-name" targets="Class Bio.config.DBRegistry.BioSQLDB=Bio.config.DBRegistry.BioSQLDB-class.html"><a title="Bio.config.DBRegistry.BioSQLDB" class="py-name" href="#" onclick="return doclink('link-88', 'BioSQLDB', 'link-88');">BioSQLDB</a></tt><tt class="py-op">(</tt><tt class="py-op">**</tt><tt class="py-name">params</tt><tt class="py-op">)</tt> </tt>
</div><a name="L198"></a><tt class="py-lineno">198</tt>  <tt class="py-line"> </tt>
<a name="_make_flat_db"></a><div id="_make_flat_db-def"><a name="L199"></a><tt class="py-lineno">199</tt> <a class="py-toggle" href="#" id="_make_flat_db-toggle" onclick="return toggle('_make_flat_db');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.config.SeqDBRegistry-module.html#_make_flat_db">_make_flat_db</a><tt class="py-op">(</tt><tt class="py-param">name</tt><tt class="py-op">,</tt> <tt class="py-param">tagvalue_dict</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_make_flat_db-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_make_flat_db-expanded"><a name="L200"></a><tt class="py-lineno">200</tt>  <tt class="py-line">    <tt class="py-docstring">"""Register a Berkeley or Flat indexed file defined in the registry."""</tt> </tt>
<a name="L201"></a><tt class="py-lineno">201</tt>  <tt class="py-line">    <tt class="py-name">params</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt>  <tt class="py-line">    <tt class="py-name">params</tt><tt class="py-op">[</tt><tt class="py-string">'name'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-89" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-89', 'name', 'link-6');">name</a></tt> </tt>
<a name="L203"></a><tt class="py-lineno">203</tt>  <tt class="py-line">    <tt class="py-name">params</tt><tt class="py-op">[</tt><tt class="py-string">'dbname'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">tagvalue_dict</tt><tt class="py-op">[</tt><tt class="py-string">"dbname"</tt><tt class="py-op">]</tt> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt>  <tt class="py-line">    <tt class="py-name">params</tt><tt class="py-op">[</tt><tt class="py-string">'doc'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-string">"Retrieve %s sequences from a local database."</tt> <tt class="py-op">%</tt> \ </tt>
<a name="L205"></a><tt class="py-lineno">205</tt>  <tt class="py-line">                    <tt class="py-name">tagvalue_dict</tt><tt class="py-op">[</tt><tt class="py-string">"dbname"</tt><tt class="py-op">]</tt> </tt>
<a name="L206"></a><tt class="py-lineno">206</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt id="link-90" class="py-name"><a title="Bio.config.DBRegistry
Bio.config.DBRegistry.DBRegistry" class="py-name" href="#" onclick="return doclink('link-90', 'DBRegistry', 'link-2');">DBRegistry</a></tt><tt class="py-op">.</tt><tt id="link-91" class="py-name" targets="Class Bio.config.DBRegistry.IndexedFileDB=Bio.config.DBRegistry.IndexedFileDB-class.html"><a title="Bio.config.DBRegistry.IndexedFileDB" class="py-name" href="#" onclick="return doclink('link-91', 'IndexedFileDB', 'link-91');">IndexedFileDB</a></tt><tt class="py-op">(</tt><tt class="py-op">**</tt><tt class="py-name">params</tt><tt class="py-op">)</tt> </tt>
</div><a name="L207"></a><tt class="py-lineno">207</tt>  <tt class="py-line">         </tt>
<a name="_openfu"></a><div id="_openfu-def"><a name="L208"></a><tt class="py-lineno">208</tt> <a class="py-toggle" href="#" id="_openfu-toggle" onclick="return toggle('_openfu');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.config.SeqDBRegistry-module.html#_openfu">_openfu</a><tt class="py-op">(</tt><tt class="py-param">file_or_url</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_openfu-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_openfu-expanded"><a name="L209"></a><tt class="py-lineno">209</tt>  <tt class="py-line">    <tt class="py-docstring">"""Guess whether this is a file or url and open it."""</tt> </tt>
<a name="L210"></a><tt class="py-lineno">210</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">file_or_url</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">4</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">lower</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-string">'http'</tt><tt class="py-op">:</tt> </tt>
<a name="L211"></a><tt class="py-lineno">211</tt>  <tt class="py-line">        <tt class="py-keyword">import</tt> <tt class="py-name">urllib</tt> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">urllib</tt><tt class="py-op">.</tt><tt class="py-name">urlopen</tt><tt class="py-op">(</tt><tt class="py-name">file_or_url</tt><tt class="py-op">)</tt> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt>  <tt class="py-line">    <tt class="py-comment"># doesn't look like a URL, guess it's a file.</tt> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-keyword">return</tt> <tt id="link-92" class="py-name" targets="Function Bio.Mindy.FlatDB.open()=Bio.Mindy.FlatDB-module.html#open,Function Bio.Mindy.open()=Bio.Mindy-module.html#open"><a title="Bio.Mindy.FlatDB.open
Bio.Mindy.open" class="py-name" href="#" onclick="return doclink('link-92', 'open', 'link-92');">open</a></tt><tt class="py-op">(</tt><tt class="py-name">file_or_url</tt><tt class="py-op">)</tt> </tt>
</div><a name="L215"></a><tt class="py-lineno">215</tt>  <tt class="py-line"> </tt>
<a name="_list_ini_paths"></a><div id="_list_ini_paths-def"><a name="L216"></a><tt class="py-lineno">216</tt> <a class="py-toggle" href="#" id="_list_ini_paths-toggle" onclick="return toggle('_list_ini_paths');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.config.SeqDBRegistry-module.html#_list_ini_paths">_list_ini_paths</a><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_list_ini_paths-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_list_ini_paths-expanded"><a name="L217"></a><tt class="py-lineno">217</tt>  <tt class="py-line">    <tt class="py-docstring">"""_list_ini_paths() -&gt; list of URL's or paths to search for files.</tt> </tt>
<a name="L218"></a><tt class="py-lineno">218</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L219"></a><tt class="py-lineno">219</tt>  <tt class="py-line"><tt class="py-docstring">    The default places to look for registry files are:</tt> </tt>
<a name="L220"></a><tt class="py-lineno">220</tt>  <tt class="py-line"><tt class="py-docstring">    - ${HOME}/.bioinformatics</tt> </tt>
<a name="L221"></a><tt class="py-lineno">221</tt>  <tt class="py-line"><tt class="py-docstring">    - /etc/bioinformatics</tt> </tt>
<a name="L222"></a><tt class="py-lineno">222</tt>  <tt class="py-line"><tt class="py-docstring">    - http://www.open-bio.org/registry</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 class="py-docstring">    The OBDA_SEARCH_PATH environment variable, if specified, overrides</tt> </tt>
<a name="L225"></a><tt class="py-lineno">225</tt>  <tt class="py-line"><tt class="py-docstring">    the default.  This should be a "+" separated list of paths or</tt> </tt>
<a name="L226"></a><tt class="py-lineno">226</tt>  <tt class="py-line"><tt class="py-docstring">    URL's.</tt> </tt>
<a name="L227"></a><tt class="py-lineno">227</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L228"></a><tt class="py-lineno">228</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L229"></a><tt class="py-lineno">229</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">environ</tt><tt class="py-op">.</tt><tt id="link-93" 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-93', 'has_key', 'link-53');">has_key</a></tt><tt class="py-op">(</tt><tt class="py-string">"OBDA_SEARCH_PATH"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L230"></a><tt class="py-lineno">230</tt>  <tt class="py-line">        <tt class="py-name">paths</tt> <tt class="py-op">=</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">environ</tt><tt class="py-op">[</tt><tt class="py-string">"OBDA_SEARCH_PATH"</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-94" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-94', 'split', 'link-83');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">"+"</tt><tt class="py-op">)</tt> </tt>
<a name="L231"></a><tt class="py-lineno">231</tt>  <tt class="py-line">    <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L232"></a><tt class="py-lineno">232</tt>  <tt class="py-line">        <tt class="py-name">paths</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt> </tt>
<a name="L233"></a><tt class="py-lineno">233</tt>  <tt class="py-line">            <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">sep</tt><tt class="py-op">,</tt> <tt class="py-string">"etc"</tt><tt class="py-op">,</tt> <tt class="py-string">"bioinformatics"</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-comment">#/etc/bioinformatics</tt> </tt>
<a name="L234"></a><tt class="py-lineno">234</tt>  <tt class="py-line">            <tt class="py-string">"http://www.open-bio.org/registry"</tt><tt class="py-op">,</tt> </tt>
<a name="L235"></a><tt class="py-lineno">235</tt>  <tt class="py-line">            <tt class="py-op">]</tt> </tt>
<a name="L236"></a><tt class="py-lineno">236</tt>  <tt class="py-line">        <tt class="py-comment"># $HOME/.bioinformatics</tt> </tt>
<a name="L237"></a><tt class="py-lineno">237</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-keyword">if</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">environ</tt><tt class="py-op">.</tt><tt id="link-95" 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-95', 'has_key', 'link-53');">has_key</a></tt><tt class="py-op">(</tt><tt class="py-string">"HOME"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L238"></a><tt class="py-lineno">238</tt>  <tt class="py-line">            <tt class="py-name">p</tt> <tt class="py-op">=</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">environ</tt><tt class="py-op">[</tt><tt class="py-string">"HOME"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-string">".bioinformatics"</tt><tt class="py-op">)</tt> </tt>
<a name="L239"></a><tt class="py-lineno">239</tt>  <tt class="py-line">            <tt class="py-name">paths</tt><tt class="py-op">.</tt><tt id="link-96" class="py-name" targets="Method Bio.Crystal.Chain.insert()=Bio.Crystal.Chain-class.html#insert,Method Bio.EUtils.POM.Comment.insert()=Bio.EUtils.POM.Comment-class.html#insert,Method Bio.EUtils.POM.ElementNode.insert()=Bio.EUtils.POM.ElementNode-class.html#insert,Method Bio.EUtils.POM.IndentedText.insert()=Bio.EUtils.POM.IndentedText-class.html#insert,Method Bio.Seq.MutableSeq.insert()=Bio.Seq.MutableSeq-class.html#insert,Method Martel.msre_parse.SubPattern.insert()=Martel.msre_parse.SubPattern-class.html#insert"><a title="Bio.Crystal.Chain.insert
Bio.EUtils.POM.Comment.insert
Bio.EUtils.POM.ElementNode.insert
Bio.EUtils.POM.IndentedText.insert
Bio.Seq.MutableSeq.insert
Martel.msre_parse.SubPattern.insert" class="py-name" href="#" onclick="return doclink('link-96', 'insert', 'link-96');">insert</a></tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">p</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 class="py-name">paths</tt> </tt>
</div><a name="L241"></a><tt class="py-lineno">241</tt>  <tt class="py-line"> </tt>
<a name="_list_ini_files"></a><div id="_list_ini_files-def"><a name="L242"></a><tt class="py-lineno">242</tt> <a class="py-toggle" href="#" id="_list_ini_files-toggle" onclick="return toggle('_list_ini_files');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.config.SeqDBRegistry-module.html#_list_ini_files">_list_ini_files</a><tt class="py-op">(</tt><tt class="py-param">filename</tt><tt class="py-op">,</tt> <tt class="py-param">also_search</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>
</div><div id="_list_ini_files-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_list_ini_files-expanded"><a name="L243"></a><tt class="py-lineno">243</tt>  <tt class="py-line">    <tt class="py-docstring">"""_list_ini_files(filename) -&gt; list of files to search (in order)"""</tt> </tt>
<a name="L244"></a><tt class="py-lineno">244</tt>  <tt class="py-line">    <tt id="link-97" class="py-name" targets="Variable Bio.expressions.hmmpfam.files=Bio.expressions.hmmpfam-module.html#files"><a title="Bio.expressions.hmmpfam.files" class="py-name" href="#" onclick="return doclink('link-97', 'files', 'link-97');">files</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L245"></a><tt class="py-lineno">245</tt>  <tt class="py-line">    <tt class="py-name">searchpath</tt> <tt class="py-op">=</tt> <tt id="link-98" class="py-name" targets="Function Bio.config.SeqDBRegistry._list_ini_paths()=Bio.config.SeqDBRegistry-module.html#_list_ini_paths"><a title="Bio.config.SeqDBRegistry._list_ini_paths" class="py-name" href="#" onclick="return doclink('link-98', '_list_ini_paths', 'link-98');">_list_ini_paths</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-name">also_search</tt> </tt>
<a name="L246"></a><tt class="py-lineno">246</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">path</tt> <tt class="py-keyword">in</tt> <tt class="py-name">searchpath</tt><tt class="py-op">:</tt> </tt>
<a name="L247"></a><tt class="py-lineno">247</tt>  <tt class="py-line">        <tt class="py-comment"># works for files and urls</tt> </tt>
<a name="L248"></a><tt class="py-lineno">248</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-name">fullname</tt> <tt class="py-op">=</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">path</tt><tt class="py-op">,</tt> <tt class="py-name">filename</tt><tt class="py-op">)</tt> </tt>
<a name="L249"></a><tt class="py-lineno">249</tt>  <tt class="py-line">        <tt class="py-comment"># Check to see if this name works.  If so, add it to the list.</tt> </tt>
<a name="L250"></a><tt class="py-lineno">250</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L251"></a><tt class="py-lineno">251</tt>  <tt class="py-line">            <tt id="link-99" class="py-name"><a title="Bio.config.SeqDBRegistry._openfu" class="py-name" href="#" onclick="return doclink('link-99', '_openfu', 'link-25');">_openfu</a></tt><tt class="py-op">(</tt><tt class="py-name">fullname</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">except</tt> <tt class="py-name">IOError</tt><tt class="py-op">:</tt> </tt>
<a name="L253"></a><tt class="py-lineno">253</tt>  <tt class="py-line">            <tt class="py-keyword">pass</tt> </tt>
<a name="L254"></a><tt class="py-lineno">254</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L255"></a><tt class="py-lineno">255</tt>  <tt class="py-line">            <tt id="link-100" class="py-name"><a title="Bio.expressions.hmmpfam.files" class="py-name" href="#" onclick="return doclink('link-100', 'files', 'link-97');">files</a></tt><tt class="py-op">.</tt><tt id="link-101" class="py-name"><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-101', 'append', 'link-36');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">fullname</tt><tt class="py-op">)</tt> </tt>
<a name="L256"></a><tt class="py-lineno">256</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt id="link-102" class="py-name"><a title="Bio.expressions.hmmpfam.files" class="py-name" href="#" onclick="return doclink('link-102', 'files', 'link-97');">files</a></tt> </tt>
</div><a name="L257"></a><tt class="py-lineno">257</tt>  <tt class="py-line"> </tt>
<a name="L258"></a><tt class="py-lineno">258</tt>  <tt class="py-line"><tt class="py-comment">##def _urlparamdecode(string):</tt> </tt>
<a name="L259"></a><tt class="py-lineno">259</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">##    """Return a list of (tag, value) from a URL's GET string"""</tt> </tt>
<a name="L260"></a><tt class="py-lineno">260</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">##    params = []</tt> </tt>
<a name="L261"></a><tt class="py-lineno">261</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">##    pairs = string.split("&amp;")</tt> </tt>
<a name="L262"></a><tt class="py-lineno">262</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">##    for tagvalue in pairs:</tt> </tt>
<a name="L263"></a><tt class="py-lineno">263</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">##        i = tagvalue.find("=")</tt> </tt>
<a name="L264"></a><tt class="py-lineno">264</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">##        if i &gt;= 0:</tt> </tt>
<a name="L265"></a><tt class="py-lineno">265</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">##            tag, value = tagvalue[:i], tagvalue[i+1:]</tt> </tt>
<a name="L266"></a><tt class="py-lineno">266</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">##        else:</tt> </tt>
<a name="L267"></a><tt class="py-lineno">267</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">##            tag, value = "", tagvalue</tt> </tt>
<a name="L268"></a><tt class="py-lineno">268</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">##        tag, value = urllib.unquote(tag), urllib.unquote(value)</tt> </tt>
<a name="L269"></a><tt class="py-lineno">269</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">##        params.append((tag, value))</tt> </tt>
<a name="L270"></a><tt class="py-lineno">270</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">##    return params</tt> </tt>
<a name="L271"></a><tt class="py-lineno">271</tt>  <tt class="py-line"><tt class="py-comment"></tt> </tt><script type="text/javascript">
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