664 lines
51 KiB
HTML
664 lines
51 KiB
HTML
<?xml version="1.0" encoding="ascii"?>
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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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"DTD/xhtml1-transitional.dtd">
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<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
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<head>
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<title>Everything</title>
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<link rel="stylesheet" href="epydoc.css" type="text/css" />
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<script type="text/javascript" src="epydoc.js"></script>
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</head>
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<body bgcolor="white" text="black" link="blue" vlink="#204080"
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alink="#204080">
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<h1 class="toc">Everything</h1>
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<hr />
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<h2 class="toc">All Classes</h2>
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<a target="mainFrame" href="exceptions.AssertionError-class.html"
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>exceptions.AssertionError</a><br /> <a target="mainFrame" href="obitools.AASequence-class.html"
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>obitools.AASequence</a><br /> <a target="mainFrame" href="obitools.BioSequence-class.html"
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>obitools.BioSequence</a><br /> <a target="mainFrame" href="obitools.NucSequence-class.html"
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>obitools.NucSequence</a><br /> <a target="mainFrame" href="obitools.WrappedBioSequence-class.html"
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>obitools.WrappedBioSequence</a><br /> <a target="mainFrame" href="obitools.WrapperSet-class.html"
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>obitools.WrapperSet</a><br /> <a target="mainFrame" href="obitools.WrapperSetIterator-class.html"
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>obitools.WrapperSetIterator</a><br /> <a target="mainFrame" href="obitools.align.Alignement-class.html"
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>obitools.align.Alignement</a><br /> <a target="mainFrame" href="obitools.align.ssearch.SsearchParser-class.html"
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>obitools.align.ssearch.SsearchParser</a><br /> <a target="mainFrame" href="obitools.blast.Blast-class.html"
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>obitools.blast.Blast</a><br /> <a target="mainFrame" href="obitools.blast.BlastCovMinFilter-class.html"
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>obitools.blast.BlastCovMinFilter</a><br /> <a target="mainFrame" href="obitools.blast.BlastMatch-class.html"
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>obitools.blast.BlastMatch</a><br /> <a target="mainFrame" href="obitools.blast.BlastResult-class.html"
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>obitools.blast.BlastResult</a><br /> <a target="mainFrame" href="obitools.blast.BlastResultIterator-class.html"
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>obitools.blast.BlastResultIterator</a><br /> <a target="mainFrame" href="obitools.blast.NetBlast-class.html"
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>obitools.blast.NetBlast</a><br /> <a target="mainFrame" href="obitools.cns.quality.QualitySequence-class.html"
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>obitools.cns.quality.QualitySequence</a><br /> <a target="mainFrame" href="obitools.distances.DistanceMatrix-class.html"
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>obitools.distances.DistanceMatrix</a><br /> <a target="mainFrame" href="obitools.distances.observed.Pairewise-class.html"
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>obitools.distances.observed.Pairewise</a><br /> <a target="mainFrame" href="obitools.distances.observed.PairewiseGapRemoval-class.html"
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>obitools.distances.observed.PairewiseGapRemoval</a><br /> <a target="mainFrame" href="obitools.ecopcr.EcoPCRDBFile-class.html"
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>obitools.ecopcr.EcoPCRDBFile</a><br /> <a target="mainFrame" href="obitools.ecopcr.EcoPCRFile-class.html"
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>obitools.ecopcr.EcoPCRFile</a><br /> <a target="mainFrame" href="obitools.ecopcr.sequence.ecoPCRDBSequenceIterator-class.html"
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>obitools.ecopcr.sequence.ecoPCRDBSequenceIterator</a><br /> <a target="mainFrame" href="obitools.ecopcr.taxonomy.Taxonomy-class.html"
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>obitools.ecopcr.taxonomy.Taxonomy</a><br /> <a target="mainFrame" href="obitools.eutils.EFetch-class.html"
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>obitools.eutils.EFetch</a><br /> <a target="mainFrame" href="obitools.eutils.EUtils-class.html"
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>obitools.eutils.EUtils</a><br /> <a target="mainFrame" href="obitools.fast.Fast-class.html"
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>obitools.fast.Fast</a><br /> <a target="mainFrame" href="obitools.format.genericparser.GenericParser-class.html"
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>obitools.format.genericparser.GenericParser</a><br /> <a target="mainFrame" href="obitools.graph.DiGraph-class.html"
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>obitools.graph.DiGraph</a><br /> <a target="mainFrame" href="obitools.graph.Edge-class.html"
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>obitools.graph.Edge</a><br /> <a target="mainFrame" href="obitools.graph.Graph-class.html"
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>obitools.graph.Graph</a><br /> <a target="mainFrame" href="obitools.graph.Indexer-class.html"
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>obitools.graph.Indexer</a><br /> <a target="mainFrame" href="obitools.graph.Node-class.html"
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>obitools.graph.Node</a><br /> <a target="mainFrame" href="obitools.graph.UndirectedGraph-class.html"
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>obitools.graph.UndirectedGraph</a><br /> <a target="mainFrame" href="obitools.graph.dag.DAG-class.html"
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>obitools.graph.dag.DAG</a><br /> <a target="mainFrame" href="obitools.graph.dag.DAGNode-class.html"
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>obitools.graph.dag.DAGNode</a><br /> <a target="mainFrame" href="obitools.graph.rootedtree.RootedTree-class.html"
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>obitools.graph.rootedtree.RootedTree</a><br /> <a target="mainFrame" href="obitools.graph.rootedtree.RootedTreeNode-class.html"
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>obitools.graph.rootedtree.RootedTreeNode</a><br /> <a target="mainFrame" href="obitools.graph.tree.Forest-class.html"
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>obitools.graph.tree.Forest</a><br /> <a target="mainFrame" href="obitools.graph.tree.TreeNode-class.html"
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>obitools.graph.tree.TreeNode</a><br /> <a target="mainFrame" href="obitools.gzip.GzipFile-class.html"
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>obitools.gzip.GzipFile</a><br /> <a target="mainFrame" href="obitools.location.ComplementLocation-class.html"
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>obitools.location.ComplementLocation</a><br /> <a target="mainFrame" href="obitools.location.CompositeLocation-class.html"
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>obitools.location.CompositeLocation</a><br /> <a target="mainFrame" href="obitools.location.Location-class.html"
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>obitools.location.Location</a><br /> <a target="mainFrame" href="obitools.location.PointLocation-class.html"
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>obitools.location.PointLocation</a><br /> <a target="mainFrame" href="obitools.location.SimpleLocation-class.html"
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>obitools.location.SimpleLocation</a><br /> <a target="mainFrame" href="obitools.location.feature.Feature-class.html"
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>obitools.location.feature.Feature</a><br /> <a target="mainFrame" href="obitools.obo.parser.DefValue-class.html"
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>obitools.obo.parser.DefValue</a><br /> <a target="mainFrame" href="obitools.obo.parser.FileFormatError-class.html"
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>obitools.obo.parser.FileFormatError</a><br /> <a target="mainFrame" href="obitools.obo.parser.NameValue-class.html"
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>obitools.obo.parser.NameValue</a><br /> <a target="mainFrame" href="obitools.obo.parser.NamespaceValue-class.html"
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>obitools.obo.parser.NamespaceValue</a><br /> <a target="mainFrame" href="obitools.obo.parser.OBOEntry-class.html"
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>obitools.obo.parser.OBOEntry</a><br /> <a target="mainFrame" href="obitools.obo.parser.OBOTerm-class.html"
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>obitools.obo.parser.OBOTerm</a><br /> <a target="mainFrame" href="obitools.obo.parser.RelationshipValue-class.html"
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>obitools.obo.parser.RelationshipValue</a><br /> <a target="mainFrame" href="obitools.obo.parser.RemarkValue-class.html"
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>obitools.obo.parser.RemarkValue</a><br /> <a target="mainFrame" href="obitools.obo.parser.SynonymValue-class.html"
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>obitools.obo.parser.SynonymValue</a><br /> <a target="mainFrame" href="obitools.obo.parser.TaggedValue-class.html"
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>obitools.obo.parser.TaggedValue</a><br /> <a target="mainFrame" href="obitools.obo.parser.TrailingModifier-class.html"
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>obitools.obo.parser.TrailingModifier</a><br /> <a target="mainFrame" href="obitools.obo.parser.Xref-class.html"
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>obitools.obo.parser.Xref</a><br /> <a target="mainFrame" href="obitools.obo.parser.XrefValue-class.html"
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>obitools.obo.parser.XrefValue</a><br /> <a target="mainFrame" href="obitools.parallel.Task-class.html"
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>obitools.parallel.Task</a><br /> <a target="mainFrame" href="obitools.parallel.TaskPool-class.html"
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>obitools.parallel.TaskPool</a><br /> <a target="mainFrame" href="obitools.parallel.jobqueue.Job-class.html"
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>obitools.parallel.jobqueue.Job</a><br /> <a target="mainFrame" href="obitools.parallel.jobqueue.JobIterator-class.html"
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>obitools.parallel.jobqueue.JobIterator</a><br /> <a target="mainFrame" href="obitools.parallel.jobqueue.JobPool-class.html"
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>obitools.parallel.jobqueue.JobPool</a><br /> <a target="mainFrame" href="obitools.phylogeny.PhylogenicEdge-class.html"
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>obitools.phylogeny.PhylogenicEdge</a><br /> <a target="mainFrame" href="obitools.phylogeny.PhylogenicNode-class.html"
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>obitools.phylogeny.PhylogenicNode</a><br /> <a target="mainFrame" href="obitools.phylogeny.PhylogenicTree-class.html"
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>obitools.phylogeny.PhylogenicTree</a><br /> <a target="mainFrame" href="obitools.seqdb.AnnotatedAASequence-class.html"
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>obitools.seqdb.AnnotatedAASequence</a><br /> <a target="mainFrame" href="obitools.seqdb.AnnotatedNucSequence-class.html"
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>obitools.seqdb.AnnotatedNucSequence</a><br /> <a target="mainFrame" href="obitools.seqdb.AnnotatedSequence-class.html"
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>obitools.seqdb.AnnotatedSequence</a><br /> <a target="mainFrame" href="obitools.seqdb.genbank.GbSequence-class.html"
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>obitools.seqdb.genbank.GbSequence</a><br /> <a target="mainFrame" href="obitools.seqdb.genbank.GpepSequence-class.html"
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>obitools.seqdb.genbank.GpepSequence</a><br /> <a target="mainFrame" href="obitools.seqdb.genbank.graph.DiGraph-class.html"
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>obitools.seqdb.genbank.graph.DiGraph</a><br /> <a target="mainFrame" href="obitools.seqdb.genbank.graph.Edge-class.html"
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>obitools.seqdb.genbank.graph.Edge</a><br /> <a target="mainFrame" href="obitools.seqdb.genbank.graph.Graph-class.html"
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>obitools.seqdb.genbank.graph.Graph</a><br /> <a target="mainFrame" href="obitools.seqdb.genbank.graph.Indexer-class.html"
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>obitools.seqdb.genbank.graph.Indexer</a><br /> <a target="mainFrame" href="obitools.seqdb.genbank.graph.Node-class.html"
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>obitools.seqdb.genbank.graph.Node</a><br /> <a target="mainFrame" href="obitools.seqdb.genbank.graph.UndirectedGraph-class.html"
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>obitools.seqdb.genbank.graph.UndirectedGraph</a><br /> <a target="mainFrame" href="obitools.seqdb.genbank.graph.dag.DAG-class.html"
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>obitools.seqdb.genbank.graph.dag.DAG</a><br /> <a target="mainFrame" href="obitools.seqdb.genbank.graph.dag.DAGNode-class.html"
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>obitools.seqdb.genbank.graph.dag.DAGNode</a><br /> <a target="mainFrame" href="obitools.seqdb.genbank.graph.rootedtree.RootedTree-class.html"
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>obitools.seqdb.genbank.graph.rootedtree.RootedTree</a><br /> <a target="mainFrame" href="obitools.seqdb.genbank.graph.rootedtree.RootedTreeNode-class.html"
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>obitools.seqdb.genbank.graph.rootedtree.RootedTreeNode</a><br /> <a target="mainFrame" href="obitools.seqdb.genbank.graph.tree.Forest-class.html"
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>obitools.seqdb.genbank.graph.tree.Forest</a><br /> <a target="mainFrame" href="obitools.seqdb.genbank.graph.tree.TreeNode-class.html"
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>obitools.seqdb.genbank.graph.tree.TreeNode</a><br /> <a target="mainFrame" href="obitools.seqdb.genbank.ncbi.NCBIAccession-class.html"
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>obitools.seqdb.genbank.ncbi.NCBIAccession</a><br /> <a target="mainFrame" href="obitools.seqdb.genbank.ncbi.NCBIGenbank-class.html"
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>obitools.seqdb.genbank.ncbi.NCBIGenbank</a><br /> <a target="mainFrame" href="obitools.seqdb.genbank.ncbi.NCBIGenpep-class.html"
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>obitools.seqdb.genbank.ncbi.NCBIGenpep</a><br /> <a target="mainFrame" href="obitools.sequenceencoder.Complement-class.html"
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>obitools.sequenceencoder.Complement</a><br /> <a target="mainFrame" href="obitools.sequenceencoder.SequenceEncoder-class.html"
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>obitools.sequenceencoder.SequenceEncoder</a><br /> <a target="mainFrame" href="obitools.solexa.SolexaFile-class.html"
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>obitools.solexa.SolexaFile</a><br /> <a target="mainFrame" href="obitools.solexa.SolexaSequence-class.html"
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>obitools.solexa.SolexaSequence</a><br /> <a target="mainFrame" href="obitools.svg.Circle-class.html"
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>obitools.svg.Circle</a><br /> <a target="mainFrame" href="obitools.svg.Line-class.html"
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>obitools.svg.Line</a><br /> <a target="mainFrame" href="obitools.svg.Rectangle-class.html"
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>obitools.svg.Rectangle</a><br /> <a target="mainFrame" href="obitools.svg.Scene-class.html"
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>obitools.svg.Scene</a><br /> <a target="mainFrame" href="obitools.svg.Text-class.html"
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>obitools.svg.Text</a><br /> <a target="mainFrame" href="obitools.table.ProjectionIterator-class.html"
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>obitools.table.ProjectionIterator</a><br /> <a target="mainFrame" href="obitools.table.SelectionIterator-class.html"
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>obitools.table.SelectionIterator</a><br /> <a target="mainFrame" href="obitools.table.Table-class.html"
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>obitools.table.Table</a><br /> <a target="mainFrame" href="obitools.table.TableIterator-class.html"
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>obitools.table.TableIterator</a><br /> <a target="mainFrame" href="obitools.table.TableIteratorAsDict-class.html"
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>obitools.table.TableIteratorAsDict</a><br /> <a target="mainFrame" href="obitools.table.TableRow-class.html"
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>obitools.table.TableRow</a><br /> <a target="mainFrame" href="obitools.table.UnionIterator-class.html"
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>obitools.table.UnionIterator</a><br /> <div class="private">
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<a target="mainFrame" href="obitools.table._Row-class.html"
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>obitools.table._Row</a><br /> </div>
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<a target="mainFrame" href="obitools.table.iTableIterator-class.html"
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>obitools.table.iTableIterator</a><br /> <a target="mainFrame" href="obitools.tree.Tree-class.html"
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>obitools.tree.Tree</a><br /> <a target="mainFrame" href="obitools.tree.TreeNode-class.html"
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>obitools.tree.TreeNode</a><br /> <a target="mainFrame" href="obitools.tree.layout.NodeLayout-class.html"
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>obitools.tree.layout.NodeLayout</a><br /> <a target="mainFrame" href="obitools.tree.layout.TreeLayout-class.html"
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>obitools.tree.layout.TreeLayout</a><br /> <a target="mainFrame" href="obitools.unit.obitools.AABioseqTest-class.html"
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>obitools.unit.obitools.AABioseqTest</a><br /> <a target="mainFrame" href="obitools.unit.obitools.BioseqTest-class.html"
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>obitools.unit.obitools.BioseqTest</a><br /> <a target="mainFrame" href="obitools.unit.obitools.NucBioseqTest-class.html"
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>obitools.unit.obitools.NucBioseqTest</a><br /> <a target="mainFrame" href="obitools.utils.CachedDB-class.html"
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>obitools.utils.CachedDB</a><br /> <a target="mainFrame" href="obitools.utils.ColumnFile-class.html"
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>obitools.utils.ColumnFile</a><br /> <a target="mainFrame" href="obitools.zipfile.BadZipfile-class.html"
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>obitools.zipfile.BadZipfile</a><br /> <a target="mainFrame" href="obitools.zipfile.LargeZipFile-class.html"
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>obitools.zipfile.LargeZipFile</a><br /> <a target="mainFrame" href="obitools.zipfile.PyZipFile-class.html"
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>obitools.zipfile.PyZipFile</a><br /> <div class="private">
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<a target="mainFrame" href="obitools.zipfile.ZipExtFile-class.html"
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>obitools.zipfile.ZipExtFile</a><br /> </div>
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<a target="mainFrame" href="obitools.zipfile.ZipFile-class.html"
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>obitools.zipfile.ZipFile</a><br /> <a target="mainFrame" href="obitools.zipfile.ZipInfo-class.html"
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>obitools.zipfile.ZipInfo</a><br /> <div class="private">
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<a target="mainFrame" href="obitools.zipfile._ZipDecrypter-class.html"
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>obitools.zipfile._ZipDecrypter</a><br /> </div>
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<h2 class="toc">All Functions</h2>
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<div class="private">
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<a target="mainFrame" href="obitools-module.html#_isNucSeq"
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>obitools._isNucSeq</a><br /> </div>
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<a target="mainFrame" href="obitools.align-module.html#alignmentReader"
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>obitools.align.alignmentReader</a><br /> <a target="mainFrame" href="obitools.align.ssearch-module.html#run"
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>obitools.align.ssearch.run</a><br /> <a target="mainFrame" href="obitools.align.ssearch-module.html#ssearchIterator"
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>obitools.align.ssearch.ssearchIterator</a><br /> <a target="mainFrame" href="obitools.alignment.ace-module.html#contigIterator"
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>obitools.alignment.ace.contigIterator</a><br /> <a target="mainFrame" href="obitools.alignment-module.html#columnIterator"
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>obitools.alignment.columnIterator</a><br /> <a target="mainFrame" href="obitools-module.html#bioSeqGenerator"
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>obitools.bioSeqGenerator</a><br /> <div class="private">
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<a target="mainFrame" href="obitools.cns.quality-module.html#_qualityJoinSeq"
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>obitools.cns.quality._qualityJoinSeq</a><br /> </div>
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<a target="mainFrame" href="obitools.cns.quality-module.html#qualityIterator"
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>obitools.cns.quality.qualityIterator</a><br /> <a target="mainFrame" href="obitools.distances.phylip-module.html#writePhylipMatrix"
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>obitools.distances.phylip.writePhylipMatrix</a><br /> <a target="mainFrame" href="obitools.distances.r-module.html#writeRMatrix"
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>obitools.distances.r.writeRMatrix</a><br /> <a target="mainFrame" href="obitools.dnahash-module.html#hashCodeIterator"
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>obitools.dnahash.hashCodeIterator</a><br /> <a target="mainFrame" href="obitools.dnahash-module.html#hashSequence"
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>obitools.dnahash.hashSequence</a><br /> <a target="mainFrame" href="obitools.dnahash-module.html#hashSequences"
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>obitools.dnahash.hashSequences</a><br /> <div class="private">
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<a target="mainFrame" href="obitools.fasta-module.html#_fastaJoinSeq"
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>obitools.fasta._fastaJoinSeq</a><br /> </div>
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<div class="private">
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<a target="mainFrame" href="obitools.fasta-module.html#_parseFasta"
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>obitools.fasta._parseFasta</a><br /> </div>
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<a target="mainFrame" href="obitools.fasta-module.html#fastaAAIterator"
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>obitools.fasta.fastaAAIterator</a><br /> <a target="mainFrame" href="obitools.fasta-module.html#fastaIterator"
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>obitools.fasta.fastaIterator</a><br /> <a target="mainFrame" href="obitools.fasta-module.html#fastaNucIterator"
|
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>obitools.fasta.fastaNucIterator</a><br /> <a target="mainFrame" href="obitools.fasta-module.html#formatFasta"
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>obitools.fasta.formatFasta</a><br /> <a target="mainFrame" href="obitools.fasta-module.html#parseFastaDescription"
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>obitools.fasta.parseFastaDescription</a><br /> <a target="mainFrame" href="obitools.format.genericparser-module.html#genericEntryIteratorGenerator"
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>obitools.format.genericparser.genericEntryIteratorGenerator</a><br /> <div class="private">
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<a target="mainFrame" href="obitools.graph.algorithms.clique-module.html#_cliqueIterator"
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>obitools.graph.algorithms.clique._cliqueIterator</a><br /> </div>
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<a target="mainFrame" href="obitools.graph.algorithms.clique-module.html#cliqueIterator"
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>obitools.graph.algorithms.clique.cliqueIterator</a><br /> <a target="mainFrame" href="obitools.graph.algorithms.component-module.html#componentCount"
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>obitools.graph.algorithms.component.componentCount</a><br /> <a target="mainFrame" href="obitools.graph.algorithms.component-module.html#componentIterator"
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>obitools.graph.algorithms.component.componentIterator</a><br /> <div class="private">
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<a target="mainFrame" href="obitools.gzip-module.html#LOWU32"
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>obitools.gzip.LOWU32</a><br /> </div>
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<div class="private">
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<a target="mainFrame" href="obitools.gzip-module.html#U32"
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>obitools.gzip.U32</a><br /> </div>
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<div class="private">
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<a target="mainFrame" href="obitools.gzip-module.html#_test"
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>obitools.gzip._test</a><br /> </div>
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<a target="mainFrame" href="obitools.gzip-module.html#open"
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>obitools.gzip.open</a><br /> <div class="private">
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<a target="mainFrame" href="obitools.gzip-module.html#read32"
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>obitools.gzip.read32</a><br /> </div>
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<div class="private">
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<a target="mainFrame" href="obitools.gzip-module.html#unpack32"
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>obitools.gzip.unpack32</a><br /> </div>
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<div class="private">
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<a target="mainFrame" href="obitools.gzip-module.html#write32"
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>obitools.gzip.write32</a><br /> </div>
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<div class="private">
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<a target="mainFrame" href="obitools.gzip-module.html#write32u"
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>obitools.gzip.write32u</a><br /> </div>
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<div class="private">
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<a target="mainFrame" href="obitools.location-module.html#__locationParser"
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>obitools.location.__locationParser</a><br /> </div>
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<div class="private">
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<a target="mainFrame" href="obitools.location-module.html#__sublocationIterator"
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>obitools.location.__sublocationIterator</a><br /> </div>
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<a target="mainFrame" href="obitools.location-module.html#extractExternalRefs"
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>obitools.location.extractExternalRefs</a><br /> <a target="mainFrame" href="obitools.location.feature-module.html#featureIterator"
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>obitools.location.feature.featureIterator</a><br /> <a target="mainFrame" href="obitools.location.feature-module.html#ftParser"
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>obitools.location.feature.ftParser</a><br /> <a target="mainFrame" href="obitools.location.feature-module.html#qualifierIterator"
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>obitools.location.feature.qualifierIterator</a><br /> <a target="mainFrame" href="obitools.location.feature-module.html#textFeatureIterator"
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>obitools.location.feature.textFeatureIterator</a><br /> <a target="mainFrame" href="obitools.location-module.html#locationGenerator"
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>obitools.location.locationGenerator</a><br /> <a target="mainFrame" href="obitools.obischemas-module.html#getConnection"
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>obitools.obischemas.getConnection</a><br /> <a target="mainFrame" href="obitools.obischemas-module.html#initConnection"
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>obitools.obischemas.initConnection</a><br /> <a target="mainFrame" href="obitools.obischemas.options-module.html#addConnectionOptions"
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>obitools.obischemas.options.addConnectionOptions</a><br /> <a target="mainFrame" href="obitools.obo.parser-module.html#OBOEntryFactory"
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>obitools.obo.parser.OBOEntryFactory</a><br /> <a target="mainFrame" href="obitools.obo.parser-module.html#OBOEntryIterator"
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>obitools.obo.parser.OBOEntryIterator</a><br /> <a target="mainFrame" href="obitools.obo.parser-module.html#stanzaIterator"
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>obitools.obo.parser.stanzaIterator</a><br /> <a target="mainFrame" href="obitools.obo.parser-module.html#taggedValueFactory"
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>obitools.obo.parser.taggedValueFactory</a><br /> <a target="mainFrame" href="obitools.obo.parser-module.html#trailingModifierFactory"
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>obitools.obo.parser.trailingModifierFactory</a><br /> <a target="mainFrame" href="obitools.obo.parser-module.html#xrefFactory"
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>obitools.obo.parser.xrefFactory</a><br /> <a target="mainFrame" href="obitools.options-module.html#allEntryIterator"
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>obitools.options.allEntryIterator</a><br /> <div class="private">
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<a target="mainFrame" href="obitools.options.bioseqcutter-module.html#_beginOptionCallback"
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>obitools.options.bioseqcutter._beginOptionCallback</a><br /> </div>
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<div class="private">
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<a target="mainFrame" href="obitools.options.bioseqcutter-module.html#_endOptionCallback"
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>obitools.options.bioseqcutter._endOptionCallback</a><br /> </div>
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<a target="mainFrame" href="obitools.options.bioseqcutter-module.html#addSequenceCuttingOptions"
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>obitools.options.bioseqcutter.addSequenceCuttingOptions</a><br /> <a target="mainFrame" href="obitools.options.bioseqcutter-module.html#cutterGenerator"
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>obitools.options.bioseqcutter.cutterGenerator</a><br /> <a target="mainFrame" href="obitools.options.bioseqcutter-module.html#cutterIteratorGenerator"
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>obitools.options.bioseqcutter.cutterIteratorGenerator</a><br /> <div class="private">
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<a target="mainFrame" href="obitools.options.bioseqfilter-module.html#_attributeOptionCallback"
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>obitools.options.bioseqfilter._attributeOptionCallback</a><br /> </div>
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<div class="private">
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<a target="mainFrame" href="obitools.options.bioseqfilter-module.html#_defintionOptionCallback"
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>obitools.options.bioseqfilter._defintionOptionCallback</a><br /> </div>
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<div class="private">
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<a target="mainFrame" href="obitools.options.bioseqfilter-module.html#_identifierOptionCallback"
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>obitools.options.bioseqfilter._identifierOptionCallback</a><br /> </div>
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<div class="private">
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<a target="mainFrame" href="obitools.options.bioseqfilter-module.html#_predicatOptionCallback"
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>obitools.options.bioseqfilter._predicatOptionCallback</a><br /> </div>
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<div class="private">
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<a target="mainFrame" href="obitools.options.bioseqfilter-module.html#_sequenceOptionCallback"
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>obitools.options.bioseqfilter._sequenceOptionCallback</a><br /> </div>
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<a target="mainFrame" href="obitools.options.bioseqfilter-module.html#addSequenceFilteringOptions"
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>obitools.options.bioseqfilter.addSequenceFilteringOptions</a><br /> <a target="mainFrame" href="obitools.options.bioseqfilter-module.html#filterGenerator"
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>obitools.options.bioseqfilter.filterGenerator</a><br /> <a target="mainFrame" href="obitools.options.bioseqfilter-module.html#sequenceFilterIteratorGenerator"
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>obitools.options.bioseqfilter.sequenceFilterIteratorGenerator</a><br /> <a target="mainFrame" href="obitools.options-module.html#currentInputFileName"
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>obitools.options.currentInputFileName</a><br /> <a target="mainFrame" href="obitools.options-module.html#getOptionManager"
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>obitools.options.getOptionManager</a><br /> <a target="mainFrame" href="obitools.phylogeny.newick-module.html#nodeParser"
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>obitools.phylogeny.newick.nodeParser</a><br /> <a target="mainFrame" href="obitools.phylogeny.newick-module.html#nodeWriter"
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>obitools.phylogeny.newick.nodeWriter</a><br /> <a target="mainFrame" href="obitools.phylogeny.newick-module.html#subNodeIterator"
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>obitools.phylogeny.newick.subNodeIterator</a><br /> <a target="mainFrame" href="obitools.phylogeny.newick-module.html#treeIterator"
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>obitools.phylogeny.newick.treeIterator</a><br /> <a target="mainFrame" href="obitools.phylogeny.newick-module.html#treeParser"
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>obitools.phylogeny.newick.treeParser</a><br /> <a target="mainFrame" href="obitools.phylogeny.newick-module.html#treeWriter"
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>obitools.phylogeny.newick.treeWriter</a><br /> <div class="private">
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<a target="mainFrame" href="obitools.seqdb.genbank.graph.algorithms.clique-module.html#_cliqueIterator"
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>obitools.seqdb.genbank.graph.algorithms.clique._cliqueIterator</a><br /> </div>
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<a target="mainFrame" href="obitools.seqdb.genbank.graph.algorithms.clique-module.html#cliqueIterator"
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>obitools.seqdb.genbank.graph.algorithms.clique.cliqueIterator</a><br /> <a target="mainFrame" href="obitools.seqdb.genbank.graph.algorithms.component-module.html#componentCount"
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>obitools.seqdb.genbank.graph.algorithms.component.componentCount</a><br /> <a target="mainFrame" href="obitools.seqdb.genbank.graph.algorithms.component-module.html#componentIterator"
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>obitools.seqdb.genbank.graph.algorithms.component.componentIterator</a><br /> <a target="mainFrame" href="obitools.seqdb.genbank.ncbi-module.html#Genbank"
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>obitools.seqdb.genbank.ncbi.Genbank</a><br /> <a target="mainFrame" href="obitools.seqdb.genbank.ncbi-module.html#Genpep"
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>obitools.seqdb.genbank.ncbi.Genpep</a><br /> <div class="private">
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<a target="mainFrame" href="obitools.seqdb.genbank.parser-module.html#__gbparser"
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>obitools.seqdb.genbank.parser.__gbparser</a><br /> </div>
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<a target="mainFrame" href="obitools.seqdb.genbank.parser-module.html#genbankIterator"
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>obitools.seqdb.genbank.parser.genbankIterator</a><br /> <a target="mainFrame" href="obitools.seqdb.genbank.parser-module.html#genbankParser"
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>obitools.seqdb.genbank.parser.genbankParser</a><br /> <a target="mainFrame" href="obitools.seqdb.genbank.parser-module.html#genpepIterator"
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>obitools.seqdb.genbank.parser.genpepIterator</a><br /> <a target="mainFrame" href="obitools.seqdb.genbank.parser-module.html#genpepParser"
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>obitools.seqdb.genbank.parser.genpepParser</a><br /> <a target="mainFrame" href="obitools.svg-module.html#colorstr"
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>obitools.svg.colorstr</a><br /> <a target="mainFrame" href="obitools.svg-module.html#test"
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>obitools.svg.test</a><br /> <a target="mainFrame" href="obitools.table-module.html#concatTables"
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>obitools.table.concatTables</a><br /> <div class="private">
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<a target="mainFrame" href="obitools.table.csv-module.html#_csvParse"
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>obitools.table.csv._csvParse</a><br /> </div>
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<a target="mainFrame" href="obitools.table.csv-module.html#csvIterator"
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>obitools.table.csv.csvIterator</a><br /> <a target="mainFrame" href="obitools.table-module.html#projectTable"
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>obitools.table.projectTable</a><br /> <a target="mainFrame" href="obitools.table-module.html#subTable"
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>obitools.table.subTable</a><br /> <a target="mainFrame" href="obitools.table-module.html#tableFactory"
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>obitools.table.tableFactory</a><br /> <a target="mainFrame" href="obitools.tree.dot-module.html#nodeWriter"
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>obitools.tree.dot.nodeWriter</a><br /> <a target="mainFrame" href="obitools.tree.dot-module.html#treeWriter"
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>obitools.tree.dot.treeWriter</a><br /> <a target="mainFrame" href="obitools.tree.layout-module.html#constantColorGenerator"
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>obitools.tree.layout.constantColorGenerator</a><br /> <a target="mainFrame" href="obitools.tree.layout-module.html#isTerminalNode"
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>obitools.tree.layout.isTerminalNode</a><br /> <a target="mainFrame" href="obitools.tree.layout-module.html#notPredicatGenerator"
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>obitools.tree.layout.notPredicatGenerator</a><br /> <a target="mainFrame" href="obitools.tree.layout-module.html#predicatGeneratorIsInfoEqual"
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>obitools.tree.layout.predicatGeneratorIsInfoEqual</a><br /> <a target="mainFrame" href="obitools.tree.newick-module.html#nodeParser"
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>obitools.tree.newick.nodeParser</a><br /> <a target="mainFrame" href="obitools.tree.newick-module.html#nodeWriter"
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>obitools.tree.newick.nodeWriter</a><br /> <a target="mainFrame" href="obitools.tree.newick-module.html#subNodeIterator"
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>obitools.tree.newick.subNodeIterator</a><br /> <a target="mainFrame" href="obitools.tree.newick-module.html#treeIterator"
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>obitools.tree.newick.treeIterator</a><br /> <a target="mainFrame" href="obitools.tree.newick-module.html#treeParser"
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>obitools.tree.newick.treeParser</a><br /> <a target="mainFrame" href="obitools.tree.newick-module.html#treeWriter"
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>obitools.tree.newick.treeWriter</a><br /> <a target="mainFrame" href="obitools.tree.svg-module.html#displayTreeLayout"
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>obitools.tree.svg.displayTreeLayout</a><br /> <a target="mainFrame" href="obitools.tree.unrooted-module.html#subtreeLayout"
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>obitools.tree.unrooted.subtreeLayout</a><br /> <a target="mainFrame" href="obitools.tree.unrooted-module.html#treeLayout"
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>obitools.tree.unrooted.treeLayout</a><br /> <div class="private">
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<a target="mainFrame" href="obitools.utils.bioseq-module.html#_cmpOnKeyGenerator"
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>obitools.utils.bioseq._cmpOnKeyGenerator</a><br /> </div>
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<a target="mainFrame" href="obitools.utils.bioseq-module.html#sortSequence"
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>obitools.utils.bioseq.sortSequence</a><br /> <a target="mainFrame" href="obitools.utils.bioseq-module.html#uniqSequence"
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>obitools.utils.bioseq.uniqSequence</a><br /> <a target="mainFrame" href="obitools.utils-module.html#endLessIterator"
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>obitools.utils.endLessIterator</a><br /> <a target="mainFrame" href="obitools.utils-module.html#fileSize"
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>obitools.utils.fileSize</a><br /> <a target="mainFrame" href="obitools.utils-module.html#multiLineWrapper"
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>obitools.utils.multiLineWrapper</a><br /> <a target="mainFrame" href="obitools.utils-module.html#progressBar"
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>obitools.utils.progressBar</a><br /> <a target="mainFrame" href="obitools.utils-module.html#skipWhiteLineIterator"
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>obitools.utils.skipWhiteLineIterator</a><br /> <a target="mainFrame" href="obitools.utils-module.html#universalOpen"
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>obitools.utils.universalOpen</a><br /> <a target="mainFrame" href="obitools.utils-module.html#universalTell"
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>obitools.utils.universalTell</a><br /> <a target="mainFrame" href="obitools.word-module.html#allWordIterator"
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>obitools.word.allWordIterator</a><br /> <div class="private">
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<a target="mainFrame" href="obitools.word.options-module.html#_acceptedOptionCallback"
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>obitools.word.options._acceptedOptionCallback</a><br /> </div>
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<div class="private">
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<a target="mainFrame" href="obitools.word.options-module.html#_rejectedOptionCallback"
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>obitools.word.options._rejectedOptionCallback</a><br /> </div>
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<a target="mainFrame" href="obitools.word.options-module.html#addOligoOptions"
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>obitools.word.options.addOligoOptions</a><br /> <a target="mainFrame" href="obitools.word.options-module.html#dnaWordIterator"
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>obitools.word.options.dnaWordIterator</a><br /> <a target="mainFrame" href="obitools.word.predicat-module.html#distMinGenerator"
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>obitools.word.predicat.distMinGenerator</a><br /> <a target="mainFrame" href="obitools.word.predicat-module.html#gcUpperBondGenerator"
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>obitools.word.predicat.gcUpperBondGenerator</a><br /> <a target="mainFrame" href="obitools.word.predicat-module.html#homoPolymerGenerator"
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>obitools.word.predicat.homoPolymerGenerator</a><br /> <a target="mainFrame" href="obitools.word.predicat-module.html#rePredicatGenerator"
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>obitools.word.predicat.rePredicatGenerator</a><br /> <a target="mainFrame" href="obitools.word-module.html#wordCount"
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>obitools.word.wordCount</a><br /> <a target="mainFrame" href="obitools.word-module.html#wordDist"
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>obitools.word.wordDist</a><br /> <a target="mainFrame" href="obitools.word-module.html#wordIterator"
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>obitools.word.wordIterator</a><br /> <a target="mainFrame" href="obitools.word-module.html#wordSelector"
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>obitools.word.wordSelector</a><br /> <div class="private">
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<a target="mainFrame" href="obitools.zipfile-module.html#_EndRecData"
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>obitools.zipfile._EndRecData</a><br /> </div>
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<div class="private">
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<a target="mainFrame" href="obitools.zipfile-module.html#_EndRecData64"
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>obitools.zipfile._EndRecData64</a><br /> </div>
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<a target="mainFrame" href="obitools.zipfile-module.html#is_zipfile"
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>obitools.zipfile.is_zipfile</a><br /> <div class="private">
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<a target="mainFrame" href="obitools.zipfile-module.html#main"
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>obitools.zipfile.main</a><br /> </div>
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<h2 class="toc">All Variables</h2>
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<div class="private">
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<a target="mainFrame" href="obitools.alignment.ace-module.html#_contigIterator"
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>obitools.alignment.ace._contigIterator</a><br /> </div>
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<a target="mainFrame" href="obitools.cns-module.html#cnsTag"
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>obitools.cns.cnsTag</a><br /> <div class="private">
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<a target="mainFrame" href="obitools.dnahash-module.html#_A"
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>obitools.dnahash._A</a><br /> </div>
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<div class="private">
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<a target="mainFrame" href="obitools.dnahash-module.html#_B"
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>obitools.dnahash._B</a><br /> </div>
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<div class="private">
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<a target="mainFrame" href="obitools.dnahash-module.html#_C"
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>obitools.dnahash._C</a><br /> </div>
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<div class="private">
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<a target="mainFrame" href="obitools.dnahash-module.html#_D"
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>obitools.dnahash._D</a><br /> </div>
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<div class="private">
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<a target="mainFrame" href="obitools.dnahash-module.html#_G"
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>obitools.dnahash._G</a><br /> </div>
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<div class="private">
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<a target="mainFrame" href="obitools.dnahash-module.html#_H"
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>obitools.dnahash._H</a><br /> </div>
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<div class="private">
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<a target="mainFrame" href="obitools.dnahash-module.html#_K"
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>obitools.dnahash._K</a><br /> </div>
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<div class="private">
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<a target="mainFrame" href="obitools.dnahash-module.html#_M"
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>obitools.dnahash._M</a><br /> </div>
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<div class="private">
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<a target="mainFrame" href="obitools.dnahash-module.html#_N"
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>obitools.dnahash._N</a><br /> </div>
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<div class="private">
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<a target="mainFrame" href="obitools.dnahash-module.html#_R"
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>obitools.dnahash._R</a><br /> </div>
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<div class="private">
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<a target="mainFrame" href="obitools.dnahash-module.html#_S"
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>obitools.dnahash._S</a><br /> </div>
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<div class="private">
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<a target="mainFrame" href="obitools.dnahash-module.html#_T"
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>obitools.dnahash._T</a><br /> </div>
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<div class="private">
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<a target="mainFrame" href="obitools.dnahash-module.html#_V"
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>obitools.dnahash._V</a><br /> </div>
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<div class="private">
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<a target="mainFrame" href="obitools.dnahash-module.html#_W"
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>obitools.dnahash._W</a><br /> </div>
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<div class="private">
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<a target="mainFrame" href="obitools.dnahash-module.html#_Y"
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>obitools.dnahash._Y</a><br /> </div>
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<div class="private">
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<a target="mainFrame" href="obitools.dnahash-module.html#_dnahash"
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>obitools.dnahash._dnahash</a><br /> </div>
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<div class="private">
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<a target="mainFrame" href="obitools.fasta-module.html#_parseFastaTag"
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>obitools.fasta._parseFastaTag</a><br /> </div>
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<div class="private">
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<a target="mainFrame" href="obitools.graph.algorithms.clique-module.html#_maxsize"
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>obitools.graph.algorithms.clique._maxsize</a><br /> </div>
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<div class="private">
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<a target="mainFrame" href="obitools.graph.algorithms.clique-module.html#_notbound"
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>obitools.graph.algorithms.clique._notbound</a><br /> </div>
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<div class="private">
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<a target="mainFrame" href="obitools.graph.algorithms.clique-module.html#_sizebound"
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>obitools.graph.algorithms.clique._sizebound</a><br /> </div>
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<div class="private">
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<a target="mainFrame" href="obitools.graph.algorithms.clique-module.html#_solution"
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>obitools.graph.algorithms.clique._solution</a><br /> </div>
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<div class="private">
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<a target="mainFrame" href="obitools.gzip-module.html#FCOMMENT"
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>obitools.gzip.FCOMMENT</a><br /> </div>
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<div class="private">
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<a target="mainFrame" href="obitools.gzip-module.html#FEXTRA"
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>obitools.gzip.FEXTRA</a><br /> </div>
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<div class="private">
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<a target="mainFrame" href="obitools.gzip-module.html#FHCRC"
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>obitools.gzip.FHCRC</a><br /> </div>
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<div class="private">
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<a target="mainFrame" href="obitools.gzip-module.html#FNAME"
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>obitools.gzip.FNAME</a><br /> </div>
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<div class="private">
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<a target="mainFrame" href="obitools.gzip-module.html#FTEXT"
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>obitools.gzip.FTEXT</a><br /> </div>
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<div class="private">
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<a target="mainFrame" href="obitools.gzip-module.html#READ"
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>obitools.gzip.READ</a><br /> </div>
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<div class="private">
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<a target="mainFrame" href="obitools.gzip-module.html#WRITE"
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>obitools.gzip.WRITE</a><br /> </div>
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<div class="private">
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<a target="mainFrame" href="obitools.location-module.html#__simplelocparser"
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>obitools.location.__simplelocparser</a><br /> </div>
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<div class="private">
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<a target="mainFrame" href="obitools.location-module.html#_matchExternalRef"
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>obitools.location._matchExternalRef</a><br /> </div>
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