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## Hierarchy For All Packages

Package Hierarchies:
  calhoun.analysis.crf, calhoun.analysis.crf.executables.viewer, calhoun.analysis.crf.features.generic, calhoun.analysis.crf.features.interval13, calhoun.analysis.crf.features.interval29, calhoun.analysis.crf.features.supporting, calhoun.analysis.crf.features.supporting.phylogenetic, calhoun.analysis.crf.features.tricycle13, calhoun.analysis.crf.io, calhoun.analysis.crf.scoring, calhoun.analysis.crf.solver, calhoun.analysis.crf.solver.semimarkov, calhoun.analysis.crf.statistics, calhoun.analysis.crf.test, calhoun.analysis.crf.test.slow, calhoun.seq, calhoun.seq.test, calhoun.util

## Class Hierarchy

- java.lang.Object
  - calhoun.analysis.crf.AbstractFeatureManager<InputType> (implements calhoun.analysis.crf.FeatureManager<InputType>)
    - calhoun.analysis.crf.features.interval13.BlastInterval13 (implements calhoun.analysis.crf.FeatureManagerNode<InputType>)
    - calhoun.analysis.crf.features.tricycle13.CodingStopFeature (implements calhoun.analysis.crf.FeatureManagerEdge<InputType>)
    - calhoun.analysis.crf.CompositeFeatureManager (implements calhoun.analysis.crf.FeatureManagerEdge<InputType>, calhoun.analysis.crf.FeatureManagerEdgeExplicitLength<InputType>, calhoun.analysis.crf.FeatureManagerNode<InputType>, calhoun.analysis.crf.FeatureManagerNodeExplicitLength<InputType>)
      - calhoun.analysis.crf.BeanModel (implements calhoun.analysis.crf.ModelManager)
        - calhoun.analysis.crf.features.interval13.Interval13Model
        - calhoun.analysis.crf.features.interval29.Interval29Model
        - calhoun.analysis.crf.test.ZeroOrderModel
          - calhoun.analysis.crf.test.ZeroOrderManager
      - calhoun.analysis.crf.ConstrainedFeatureManager
    - calhoun.analysis.crf.test.ConstraintTest.FixedEdges (implements calhoun.analysis.crf.FeatureManagerEdge<InputType>)
    - calhoun.analysis.crf.features.tricycle13.EmissionMarkovFeature (implements calhoun.analysis.crf.FeatureManagerNode<InputType>)
    - calhoun.analysis.crf.features.generic.EndFeatures (implements calhoun.analysis.crf.FeatureManagerNode<InputType>)
    - calhoun.analysis.crf.features.tricycle13.ESTEdge (implements calhoun.analysis.crf.FeatureManagerEdge<InputType>, calhoun.analysis.crf.FeatureManagerNode<InputType>)
    - calhoun.analysis.crf.features.tricycle13.ESTExon (implements calhoun.analysis.crf.FeatureManagerNode<InputType>)
    - calhoun.analysis.crf.features.interval13.ESTInterval13 (implements calhoun.analysis.crf.FeatureManagerEdge<InputType>, calhoun.analysis.crf.FeatureManagerNode<InputType>)
    - calhoun.analysis.crf.features.interval29.ESTInterval29 (implements calhoun.analysis.crf.FeatureManagerEdge<InputType>, calhoun.analysis.crf.FeatureManagerNode<InputType>)
    - calhoun.analysis.crf.features.tricycle13.ESTIntron (implements calhoun.analysis.crf.FeatureManagerNode<InputType>)
    - calhoun.analysis.crf.features.tricycle13.FelsensteinFeatures (implements calhoun.analysis.crf.FeatureManagerNode<InputType>)
    - calhoun.analysis.crf.features.interval13.FootprintsInterval13 (implements calhoun.analysis.crf.FeatureManagerNode<InputType>)
    - calhoun.analysis.crf.features.interval29.FootprintsInterval29 (implements calhoun.analysis.crf.FeatureManagerNode<InputType>)
    - calhoun.analysis.crf.features.tricycle13.GapConjunctionFeatures (implements calhoun.analysis.crf.FeatureManagerNode<InputType>)
    - calhoun.analysis.crf.features.interval13.GapFeaturesInterval13 (implements calhoun.analysis.crf.FeatureManagerNode<InputType>)
    - calhoun.analysis.crf.features.interval29.GapFeaturesInterval29 (implements calhoun.analysis.crf.FeatureManagerNode<InputType>)
    - calhoun.analysis.crf.features.tricycle13.GeneConstraints (implements calhoun.analysis.crf.FeatureManagerEdge<InputType>)
    - calhoun.analysis.crf.features.interval13.GeneConstraintsInterval13 (implements calhoun.analysis.crf.FeatureManagerEdge<InputType>, calhoun.analysis.crf.FeatureManagerNode<InputType>)
    - calhoun.analysis.crf.features.interval29.GeneConstraintsInterval29 (implements calhoun.analysis.crf.FeatureManagerEdge<InputType>, calhoun.analysis.crf.FeatureManagerNode<InputType>)
    - calhoun.analysis.crf.test.GeneConstraintsToy (implements calhoun.analysis.crf.FeatureManagerEdge<InputType>)
    - calhoun.analysis.crf.features.generic.IndicatorEdges (implements calhoun.analysis.crf.FeatureManagerEdge<InputType>)
    - calhoun.analysis.crf.features.tricycle13.IntervalPresenceFeatures (implements calhoun.analysis.crf.FeatureManagerNode<InputType>)
    - calhoun.analysis.crf.features.tricycle13.IntronLengthFeature (implements calhoun.analysis.crf.FeatureManagerNodeExplicitLength<InputType>)
    - calhoun.analysis.crf.features.tricycle13.KmerFeatures (implements calhoun.analysis.crf.FeatureManagerNode<InputType>)
    - calhoun.analysis.crf.features.tricycle13.MaxentMotifFeatures (implements calhoun.analysis.crf.FeatureManagerEdge<InputType>)
    - calhoun.analysis.crf.features.tricycle13.PfamGenic (implements calhoun.analysis.crf.FeatureManagerNode<InputType>)
    - calhoun.analysis.crf.features.tricycle13.PfamPhase (implements calhoun.analysis.crf.FeatureManagerNode<InputType>)
    - calhoun.analysis.crf.features.interval13.PhylogeneticLogprobInterval13 (implements calhoun.analysis.crf.FeatureManagerNode<InputType>)
    - calhoun.analysis.crf.features.tricycle13.PositionWeightMatrixFeatures (implements calhoun.analysis.crf.FeatureManagerEdge<InputType>)
    - calhoun.analysis.crf.features.tricycle13.PWM_evolution (implements calhoun.analysis.crf.FeatureManagerEdge<InputType>)
    - calhoun.analysis.crf.features.interval13.PWMInterval13 (implements calhoun.analysis.crf.FeatureManagerEdge<InputType>)
    - calhoun.analysis.crf.features.interval29.PWMInterval29 (implements calhoun.analysis.crf.FeatureManagerEdge<InputType>)
    - calhoun.analysis.crf.features.interval13.ReferenceBasePredictorInterval13Base
      - calhoun.analysis.crf.features.interval13.ReferenceBasePredictorInterval13 (implements calhoun.analysis.crf.FeatureManagerNodeBoundaries<InputType>)
      - calhoun.analysis.crf.features.interval13.ReferenceBasePredictorNodeOnlyInterval13 (implements calhoun.analysis.crf.FeatureManagerNode<InputType>)
      - calhoun.analysis.crf.features.interval13.ReferenceBasePredictorZeroPadInterval13 (implements calhoun.analysis.crf.FeatureManagerNodeBoundaries<InputType>)
    - calhoun.analysis.crf.features.interval29.ReferenceBasePredictorInterval29Base
      - calhoun.analysis.crf.features.interval29.ReferenceBasePredictorInterval29 (implements calhoun.analysis.crf.FeatureManagerNodeBoundaries<InputType>)
      - calhoun.analysis.crf.features.interval29.ReferenceBasePredictorNodeOnlyInterval29 (implements calhoun.analysis.crf.FeatureManagerNode<InputType>)
      - calhoun.analysis.crf.features.interval29.ReferenceBasePredictorZeroPadInterval29 (implements calhoun.analysis.crf.FeatureManagerNodeBoundaries<InputType>)
    - calhoun.analysis.crf.features.generic.StartFeatures (implements calhoun.analysis.crf.FeatureManagerNode<InputType>)
    - calhoun.analysis.crf.features.interval13.StateTransitionsInterval13 (implements calhoun.analysis.crf.FeatureManagerEdge<InputType>)
    - calhoun.analysis.crf.features.interval29.StateTransitionsInterval29 (implements calhoun.analysis.crf.FeatureManagerEdge<InputType>)
    - calhoun.analysis.crf.test.TestFeatures.TestFeature (implements calhoun.analysis.crf.FeatureManager<InputType>)
      - calhoun.analysis.crf.test.TestFeatures.EmissionFeature (implements calhoun.analysis.crf.FeatureManagerNode<InputType>)
      - calhoun.analysis.crf.test.TestFeatures.ExplicitHalfExponentialLengthFeature (implements calhoun.analysis.crf.FeatureManagerEdge<InputType>, calhoun.analysis.crf.FeatureManagerNodeExplicitLength<InputType>)
      - calhoun.analysis.crf.test.TestFeatures.ExponentialLengthFeature (implements calhoun.analysis.crf.FeatureManagerEdge<InputType>)
      - calhoun.analysis.crf.test.TestFeatures.GaussianLengthFeature (implements calhoun.analysis.crf.FeatureManagerNodeExplicitLength<InputType>)
      - calhoun.analysis.crf.test.TestFeatures.HalfExponentialLengthFeature (implements calhoun.analysis.crf.FeatureManagerEdge<InputType>)
    - calhoun.analysis.crf.features.generic.WeightedEdges (implements calhoun.analysis.crf.FeatureManagerEdge<InputType>)
    - calhoun.analysis.crf.features.generic.WeightedStateChanges (implements calhoun.analysis.crf.FeatureManagerEdge<InputType>)
  - javax.swing.table.AbstractTableModel (implements java.io.Serializable, javax.swing.table.TableModel)
    - calhoun.analysis.crf.executables.viewer.ViterbiTableModel
  - calhoun.analysis.crf.io.AlignmentTree (implements calhoun.analysis.crf.io.InputComponentIO)
  - calhoun.analysis.crf.io.AllIntergenicHiddenStateReader (implements calhoun.analysis.crf.io.TrainingSequenceIO)
  - junit.framework.Assert
    - junit.framework.TestCase (implements junit.framework.Test)
      - calhoun.util.AbstractTestCase
        - calhoun.analysis.crf.test.BasicStatsTest
        - calhoun.analysis.crf.test.CacheProcessorTest
        - calhoun.analysis.crf.test.CacheProcessorTestRealShort
        - calhoun.analysis.crf.test.CacheTest
        - calhoun.analysis.crf.test.ConstraintTest
        - calhoun.analysis.crf.test.CRFIOTest
        - calhoun.analysis.crf.test.CRFTest
        - calhoun.analysis.crf.test.FeatureTest
        - calhoun.analysis.crf.test.FileInputHandlerTest
        - calhoun.analysis.crf.test.FunctionEvalTest
        - calhoun.analysis.crf.test.GammaDistributionsTest
        - calhoun.analysis.crf.test.GapConjunctionFeaturesTest
        - calhoun.analysis.crf.test.GeneConstraintsInterval13Test
        - calhoun.analysis.crf.test.GTFWriterTest
        - calhoun.analysis.crf.test.Interval13BaselineTest
        - calhoun.analysis.crf.test.Interval29BaselineTest
        - calhoun.seq.test.KmerHasherTest
        - calhoun.analysis.crf.test.LBFGSTest
        - calhoun.analysis.crf.test.LogprobLookupTest
        - calhoun.analysis.crf.test.MatrixOperationsTest
        - calhoun.analysis.crf.test.MaxentMotifModelTest
        - calhoun.analysis.crf.test.MaximumExpectedAccuracyTest
        - calhoun.analysis.crf.test.MultipleSequenceTest
        - calhoun.analysis.crf.test.NewickTreeManipulationTest
        - calhoun.analysis.crf.test.NonGradientTest
        - calhoun.analysis.crf.test.PredictedActualBinaryContingencyTableTest
        - calhoun.analysis.crf.test.RangeMapExamples
        - calhoun.analysis.crf.test.RealIOTest
        - calhoun.analysis.crf.test.RecyclingBufferTest
        - calhoun.analysis.crf.test.ReferenceBasePredictorTest
        - calhoun.seq.test.RepeatedSubsequenceTest
        - calhoun.analysis.crf.test.SemiMarkovTest
        - calhoun.analysis.crf.test.SequenceConverterTest
        - calhoun.analysis.crf.test.slow.SlowTestMaxentMotifModel
        - calhoun.analysis.crf.test.ValidPathsTest
      - calhoun.analysis.crf.test.Interval13FeatureTest
      - calhoun.analysis.crf.test.Interval29FeatureTest
  - calhoun.util.Assert
  - calhoun.analysis.crf.statistics.BasicStats
  - calhoun.analysis.crf.BeanModel.Edge (implements java.io.Serializable)
  - calhoun.analysis.crf.BeanModel.Node (implements java.io.Serializable)
  - calhoun.analysis.crf.features.supporting.phylogenetic.BinaryTreeNode (implements java.io.Serializable)
  - calhoun.analysis.crf.solver.CacheProcessor.FeatureEvaluation
  - calhoun.analysis.crf.solver.CacheProcessor.LengthFeatureEvaluation
  - calhoun.analysis.crf.solver.CacheProcessor.SolverSetup
  - calhoun.analysis.crf.solver.CacheProcessor.StatePotentials
  - calhoun.analysis.crf.solver.CacheProcessorBasic (implements calhoun.analysis.crf.solver.CacheProcessor)
    - calhoun.analysis.crf.solver.CacheProcessorDeluxe
    - calhoun.analysis.crf.solver.NoCachingCacheProcessor
  - calhoun.analysis.crf.CacheStrategySpec
  - calhoun.analysis.crf.CacheStrategySpec.DenseBoundaryCachingDetails
  - calhoun.analysis.crf.CacheStrategySpec.DenseBoundaryEntry
  - calhoun.analysis.crf.CacheStrategySpec.DenseCachingDetails
  - calhoun.analysis.crf.solver.semimarkov.CleanMaximumLikelihoodSemiMarkovGradient (implements calhoun.analysis.crf.CRFObjectiveFunctionGradient)
    - calhoun.analysis.crf.solver.semimarkov.CleanLocalScoreSemiMarkovGradient
      - calhoun.analysis.crf.solver.MaximumExpectedAccuracySemiMarkovGradient
  - calhoun.util.ColtUtil
  - calhoun.analysis.crf.features.supporting.phylogenetic.ColumnConditionalLogProbability (implements java.io.Serializable)
  - java.awt.Component (implements java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable)
    - java.awt.Container
      - javax.swing.JComponent (implements java.io.Serializable)
        - javax.swing.JLabel (implements javax.accessibility.Accessible, javax.swing.SwingConstants)
          - javax.swing.table.DefaultTableCellRenderer (implements java.io.Serializable, javax.swing.table.TableCellRenderer)
            - calhoun.analysis.crf.executables.viewer.ViterbiTableModel.ViterbiCellRenderer
      - java.awt.Window (implements javax.accessibility.Accessible)
        - java.awt.Frame (implements java.awt.MenuContainer)
          - javax.swing.JFrame (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants)
            - calhoun.analysis.crf.executables.viewer.ViterbiViewerApp
  - calhoun.analysis.crf.io.CompositeInput (implements java.io.Serializable)
  - calhoun.analysis.crf.io.CompositeInput.InputComponent (implements java.io.Serializable)
  - calhoun.analysis.crf.io.CompositeInput.LegacyInputHandler (implements calhoun.analysis.crf.io.InputHandler)
  - calhoun.analysis.crf.Conrad (implements java.io.Serializable)
  - calhoun.analysis.crf.CRFInference.InferenceResult
  - calhoun.util.DenseBooleanMatrix2D (implements java.io.Serializable)
  - calhoun.util.DenseIntMatrix2D (implements java.io.Serializable)
  - java.util.Dictionary<K,V>
    - java.util.Hashtable<K,V> (implements java.lang.Cloneable, java.util.Map<K,V>, java.io.Serializable)
      - java.util.Properties
        - calhoun.util.TypedProperties
  - calhoun.analysis.crf.features.tricycle13.EmissionMarkovFeature.MarkovHistory (implements java.io.Serializable)
  - calhoun.analysis.crf.features.supporting.phylogenetic.EvolutionaryModel (implements java.io.Serializable)
  - calhoun.analysis.crf.test.ExampleTrees
  - calhoun.analysis.crf.io.ExtensionMapper (implements calhoun.analysis.crf.io.FilenameMapper)
  - calhoun.analysis.crf.io.FastaAlignmentInput (implements calhoun.analysis.crf.io.InputComponentIO)
  - calhoun.analysis.crf.io.FastaInput (implements calhoun.analysis.crf.io.InputComponentIO)
  - calhoun.seq.FastaIterator (implements java.util.Iterator<E>)
  - calhoun.seq.FastaWriter
  - calhoun.util.FileDiff
  - calhoun.util.FileUtil
  - calhoun.util.FilterIterator<A> (implements java.util.Iterator<E>)
  - calhoun.analysis.crf.solver.FixedWeightOptimizer (implements calhoun.analysis.crf.CRFTraining)
  - java.util.logging.Formatter
    - calhoun.util.SimplerFormatter
  - calhoun.analysis.crf.statistics.GammaDistribution
  - calhoun.analysis.crf.io.GTFInputInterval13 (implements calhoun.analysis.crf.io.TrainingSequenceIO)
    - calhoun.analysis.crf.io.GTFInputInterval29
  - calhoun.analysis.crf.io.InputHandlerBase (implements calhoun.analysis.crf.io.InputHandler)
    - calhoun.analysis.crf.io.InputHandlerDirectory
    - calhoun.analysis.crf.io.InputHandlerFile
  - calhoun.analysis.crf.io.InputHandlerInterleaved (implements calhoun.analysis.crf.io.InputHandler)
  - calhoun.analysis.crf.io.InputSequenceBoolean (implements calhoun.analysis.crf.io.InputSequence<A>)
  - calhoun.analysis.crf.io.InputSequenceCharacter (implements calhoun.analysis.crf.io.InputSequence<A>)
  - calhoun.analysis.crf.io.InputSequenceComposite (implements calhoun.analysis.crf.io.InputSequence<A>)
  - calhoun.analysis.crf.io.InputSequenceInt (implements calhoun.analysis.crf.io.InputSequence<A>)
  - calhoun.analysis.crf.io.InputSequenceObject<T> (implements calhoun.analysis.crf.io.InputSequence<A>)
  - calhoun.analysis.crf.io.InterleavedInputComponentBase (implements calhoun.analysis.crf.io.InterleavedInputComponent)
    - calhoun.analysis.crf.io.BooleanInput
    - calhoun.analysis.crf.io.IntervalInput
    - calhoun.analysis.crf.io.IntInput (implements calhoun.analysis.crf.io.TrainingSequenceIO)
      - calhoun.analysis.crf.io.Interval21HiddenSequenceTranslator
      - calhoun.analysis.crf.io.IntInputInterval29
    - calhoun.analysis.crf.io.MultipleAlignmentInput
    - calhoun.analysis.crf.io.NameInput
    - calhoun.analysis.crf.io.StringInput
  - calhoun.analysis.crf.features.interval13.Interval13Tools
  - calhoun.analysis.crf.features.interval29.Interval29Tools
  - calhoun.analysis.crf.io.IntervalInputSequence (implements calhoun.analysis.crf.io.InputSequence<A>)
  - calhoun.analysis.crf.io.IntervalInputSequence.IntervalPosition
  - calhoun.analysis.crf.io.IntervalInputSequence.IntervalRangeMapValue
  - calhoun.analysis.crf.io.IteratorAdapterInputComponent (implements java.util.Iterator<E>)
  - calhoun.analysis.crf.io.IteratorAdapterTrainingSequenceInput<T> (implements java.util.Iterator<E>)
  - calhoun.seq.KmerHasher (implements java.io.Serializable)
  - calhoun.analysis.crf.solver.LogFiles
  - calhoun.analysis.crf.features.supporting.LogProbLookup (implements java.io.Serializable)
  - calhoun.analysis.crf.solver.LookbackBuffer
  - calhoun.analysis.crf.features.supporting.MarkovPredictorLogprob (implements java.io.Serializable)
  - calhoun.analysis.crf.features.supporting.MaxentMotifModel
  - calhoun.analysis.crf.solver.MaximumLikelihoodGradient (implements calhoun.analysis.crf.CRFObjectiveFunctionGradient)
  - calhoun.analysis.crf.solver.MaximumLikelihoodSemiMarkovGradient (implements calhoun.analysis.crf.CRFObjectiveFunctionGradient)
  - calhoun.analysis.crf.statistics.MixtureOfGammas (implements java.io.Serializable)
  - calhoun.analysis.crf.io.MultipleAlignmentInputSequence (implements calhoun.analysis.crf.io.InputSequence<A>)
  - calhoun.analysis.crf.io.MultipleAlignmentInputSequence.MultipleAlignmentColumn
  - calhoun.analysis.crf.io.NameInputSequence (implements calhoun.analysis.crf.io.InputSequence<A>)
  - calhoun.analysis.crf.features.supporting.phylogenetic.NucleotideSubstitutionModel (implements java.io.Serializable)
    - calhoun.analysis.crf.features.supporting.phylogenetic.HKY85Model
    - calhoun.analysis.crf.features.supporting.phylogenetic.Kimura80Model
  - calhoun.analysis.crf.features.supporting.phylogenetic.NucleotideSubstitutionModelTest
  - calhoun.analysis.crf.io.OutputHandlerComposite (implements calhoun.analysis.crf.io.OutputHandler)
  - calhoun.analysis.crf.io.OutputHandlerGeneCallPredict (implements calhoun.analysis.crf.io.OutputHandler)
  - calhoun.analysis.crf.io.OutputHandlerGeneCallPredict.Results (implements java.io.Serializable)
  - calhoun.analysis.crf.io.OutputHandlerGeneCallStats (implements calhoun.analysis.crf.io.OutputHandler)
    - calhoun.analysis.crf.io.OutputHandlerGeneCallStatsInterval29
  - calhoun.analysis.crf.io.OutputHandlerGeneCallStats.Results (implements java.io.Serializable)
  - calhoun.analysis.crf.io.OutputHandlerWriter (implements calhoun.analysis.crf.io.OutputHandler)
  - calhoun.analysis.crf.features.supporting.phylogenetic.PhylogeneticTreeFelsensteinOrder (implements java.io.Serializable)
  - calhoun.analysis.crf.features.tricycle13.PositionWeightMatrixFeatures.Geometry (implements java.io.Serializable)
  - calhoun.analysis.crf.statistics.PredictedActualBinaryContingencyTable (implements java.io.Serializable)
  - calhoun.util.PrimeUtil
  - calhoun.analysis.crf.features.supporting.PWMLookup (implements java.io.Serializable)
  - calhoun.seq.QualityIterator (implements java.util.Iterator<E>)
  - calhoun.util.RangeMap (implements java.io.Serializable)
  - calhoun.util.RangeMap.Interval
  - calhoun.analysis.crf.solver.RecyclingBuffer<T>
  - calhoun.seq.RepeatedSubsequence
  - calhoun.util.ResourceLoader
  - calhoun.analysis.crf.features.supporting.phylogenetic.RootedBinaryPhylogeneticTree (implements java.io.Serializable)
  - calhoun.analysis.crf.solver.SeededOptimizer (implements calhoun.analysis.crf.CRFTraining)
  - calhoun.analysis.crf.SemiMarkovSetup
  - calhoun.analysis.crf.solver.SemiMarkovViterbi (implements calhoun.analysis.crf.CRFInference)
  - calhoun.analysis.crf.solver.SemiMarkovViterbiNoCache (implements calhoun.analysis.crf.CRFInference)
  - calhoun.analysis.crf.io.SequenceConverter
  - calhoun.seq.SimpleFastaSequence (implements calhoun.seq.FastaSequence, java.io.Serializable)
    - calhoun.seq.FastaIterator.ReaderSequence
  - calhoun.analysis.crf.solver.SimplexOptimizer (implements calhoun.analysis.crf.CRFTraining)
  - calhoun.analysis.crf.scoring.SimScoreMaxStateAgreement (implements calhoun.analysis.crf.LocalPathSimilarityScore)
  - calhoun.analysis.crf.scoring.SimScoreMinCodingMiscallsSV13 (implements calhoun.analysis.crf.LocalPathSimilarityScore)
  - calhoun.analysis.crf.scoring.SimScoreMinExonBoundaryMiscallsSV13 (implements calhoun.analysis.crf.LocalPathSimilarityScore)
  - calhoun.analysis.crf.scoring.SimScoreStateAndExonBoundariesInt13 (implements calhoun.analysis.crf.LocalPathSimilarityScore)
  - calhoun.analysis.crf.solver.StandardOptimizer (implements calhoun.analysis.crf.CRFTraining)
  - calhoun.analysis.crf.features.interval13.StateLengthLogprobInterval13 (implements calhoun.analysis.crf.FeatureManagerNodeExplicitLength<InputType>)
  - calhoun.analysis.crf.features.interval29.StateLengthLogprobInterval29 (implements calhoun.analysis.crf.FeatureManagerNodeExplicitLength<InputType>)
  - calhoun.analysis.crf.test.TestFeatures
  - java.lang.Throwable (implements java.io.Serializable)
    - java.lang.Exception
      - java.lang.RuntimeException
        - calhoun.util.CheckException
        - calhoun.util.ConfigException
          - calhoun.util.DataException
        - calhoun.util.ErrorException
  - calhoun.analysis.crf.io.TrainingSequence<A> (implements calhoun.analysis.crf.io.InputSequence<A>)
  - calhoun.analysis.crf.solver.TwoPassOptimizer (implements calhoun.analysis.crf.CRFTraining)
  - calhoun.util.Util
  - calhoun.analysis.crf.solver.Viterbi (implements calhoun.analysis.crf.CRFInference)
  - calhoun.util.XmlDiff
  - calhoun.util.XmlUtil

## Interface Hierarchy

- calhoun.analysis.crf.solver.CacheProcessor
- calhoun.analysis.crf.CRFInference
- calhoun.analysis.crf.CRFObjectiveFunctionGradient
- calhoun.analysis.crf.CRFTraining
- calhoun.seq.FastaSequence
- calhoun.analysis.crf.FeatureList
- calhoun.analysis.crf.io.FilenameMapper
- calhoun.analysis.crf.io.InputSequence<A>
- calhoun.analysis.crf.LocalPathSimilarityScore
- calhoun.util.ResourceLoader.ResourceFinder
- java.io.Serializable
  - calhoun.analysis.crf.FeatureManager<InputType>
    - calhoun.analysis.crf.FeatureManagerEdge<InputType>
      - calhoun.analysis.crf.ModelManager (also extends calhoun.analysis.crf.FeatureManagerEdgeExplicitLength<InputType>, calhoun.analysis.crf.FeatureManagerNode<InputType>, calhoun.analysis.crf.FeatureManagerNodeExplicitLength<InputType>)
    - calhoun.analysis.crf.FeatureManagerEdgeExplicitLength<InputType>
      - calhoun.analysis.crf.ModelManager (also extends calhoun.analysis.crf.FeatureManagerEdge<InputType>, calhoun.analysis.crf.FeatureManagerNode<InputType>, calhoun.analysis.crf.FeatureManagerNodeExplicitLength<InputType>)
    - calhoun.analysis.crf.FeatureManagerNode<InputType>
      - calhoun.analysis.crf.FeatureManagerNodeBoundaries<InputType>
      - calhoun.analysis.crf.ModelManager (also extends calhoun.analysis.crf.FeatureManagerEdge<InputType>, calhoun.analysis.crf.FeatureManagerEdgeExplicitLength<InputType>, calhoun.analysis.crf.FeatureManagerNodeExplicitLength<InputType>)
    - calhoun.analysis.crf.FeatureManagerNodeBoundaries<InputType>
    - calhoun.analysis.crf.FeatureManagerNodeExplicitLength<InputType>
      - calhoun.analysis.crf.ModelManager (also extends calhoun.analysis.crf.FeatureManagerEdge<InputType>, calhoun.analysis.crf.FeatureManagerEdgeExplicitLength<InputType>, calhoun.analysis.crf.FeatureManagerNode<InputType>)
    - calhoun.analysis.crf.ModelManager (also extends calhoun.analysis.crf.FeatureManagerEdge<InputType>, calhoun.analysis.crf.FeatureManagerEdgeExplicitLength<InputType>, calhoun.analysis.crf.FeatureManagerNode<InputType>, calhoun.analysis.crf.FeatureManagerNodeExplicitLength<InputType>)
  - calhoun.analysis.crf.FeatureManagerEdge<InputType>
    - calhoun.analysis.crf.ModelManager (also extends calhoun.analysis.crf.FeatureManagerEdgeExplicitLength<InputType>, calhoun.analysis.crf.FeatureManagerNode<InputType>, calhoun.analysis.crf.FeatureManagerNodeExplicitLength<InputType>)
  - calhoun.analysis.crf.FeatureManagerEdgeExplicitLength<InputType>
    - calhoun.analysis.crf.ModelManager (also extends calhoun.analysis.crf.FeatureManagerEdge<InputType>, calhoun.analysis.crf.FeatureManagerNode<InputType>, calhoun.analysis.crf.FeatureManagerNodeExplicitLength<InputType>)
  - calhoun.analysis.crf.FeatureManagerNode<InputType>
    - calhoun.analysis.crf.FeatureManagerNodeBoundaries<InputType>
    - calhoun.analysis.crf.ModelManager (also extends calhoun.analysis.crf.FeatureManagerEdge<InputType>, calhoun.analysis.crf.FeatureManagerEdgeExplicitLength<InputType>, calhoun.analysis.crf.FeatureManagerNodeExplicitLength<InputType>)
  - calhoun.analysis.crf.FeatureManagerNodeBoundaries<InputType>
  - calhoun.analysis.crf.FeatureManagerNodeExplicitLength<InputType>
    - calhoun.analysis.crf.ModelManager (also extends calhoun.analysis.crf.FeatureManagerEdge<InputType>, calhoun.analysis.crf.FeatureManagerEdgeExplicitLength<InputType>, calhoun.analysis.crf.FeatureManagerNode<InputType>)
  - calhoun.analysis.crf.io.InputComponentIO
    - calhoun.analysis.crf.io.InterleavedInputComponent
  - calhoun.analysis.crf.io.InputHandler
  - calhoun.analysis.crf.io.InterleavedInputComponent
  - calhoun.seq.KmerHasher.CharacterHash
  - calhoun.analysis.crf.ModelManager (also extends calhoun.analysis.crf.FeatureManagerEdge<InputType>, calhoun.analysis.crf.FeatureManagerEdgeExplicitLength<InputType>, calhoun.analysis.crf.FeatureManagerNode<InputType>, calhoun.analysis.crf.FeatureManagerNodeExplicitLength<InputType>)
  - calhoun.analysis.crf.io.OutputHandler
  - calhoun.analysis.crf.io.TrainingSequenceIO

## Enum Hierarchy

- java.lang.Object
  - java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    - calhoun.analysis.crf.CacheStrategySpec.CacheStrategy
    - calhoun.analysis.crf.features.tricycle13.KmerFeatures.Cardinality

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