Hierarchy For All Packages

Package Hierarchies:

net.sf.octet.builder, net.sf.octet.collection, net.sf.octet.error, net.sf.octet.model, net.sf.octet.query, net.sf.octet.task, net.sf.octet.test, net.sf.octet.traversal, net.sf.octet.util, net.sf.octet.xml

Class Hierarchy

• class java.lang.Object
  • class net.sf.octet.builder.AbstractRepresentationBuilder (implements net.sf.octet.builder.RepresentationBuilder)
    • class net.sf.octet.builder.AbstractMoleculeBuilder (implements net.sf.octet.builder.RepresentationBuilder)
  • class net.sf.octet.builder.AbstractRepresentationBuilder.AtomTemplate (implements net.sf.octet.builder.AtomProxy)
  • class net.sf.octet.builder.AbstractRepresentationBuilder.BondingSystemTemplate (implements net.sf.octet.builder.BondingSystemProxy)
  • class net.sf.octet.builder.AbstractRepresentationBuilder.ConfigurationTemplate (implements net.sf.octet.builder.ConfigurationProxy)
  • class net.sf.octet.builder.AbstractRepresentationBuilder.ConformationTemplate
  • class net.sf.octet.builder.AbstractRepresentationBuilder.GammaSequenceTemplate (implements net.sf.octet.builder.GammaSequenceProxy)
  • class net.sf.octet.builder.AbstractRepresentationBuilder.HalfPlaneTemplate (implements net.sf.octet.builder.HalfPlaneProxy)
  • class net.sf.octet.builder.AbstractRepresentationBuilder.OrbitalTemplate (implements net.sf.octet.builder.OrbitalProxy)
  • class net.sf.octet.builder.AbstractRepresentationBuilder.PaddleWheelTemplate
  • class net.sf.octet.query.AllCyclesMoleculeQuery (implements net.sf.octet.query.MoleculeQuery)
  • class net.sf.octet.util.ArrayKit
  • class net.sf.octet.util.ArraySequence (implements net.sf.octet.util.Sequence)
  • class junit.framework.Assert
    • class junit.framework.TestCase (implements junit.framework.Test)
      • class net.sf.octet.test.OctetTestCase
        • class net.sf.octet.test.AllCyclesQueryTest
        • class net.sf.octet.test.AntibondingElectronsTest
        • class net.sf.octet.test.AtomGraphTest
        • class net.sf.octet.test.AtomicSystemTest
        • class net.sf.octet.test.AtomPairTest
        • class net.sf.octet.test.BreadthTraverserTest
        • class net.sf.octet.test.CollectionsTest
        • class net.sf.octet.test.ConfigurationTest
        • class net.sf.octet.test.ConformationTest
        • class net.sf.octet.test.CycleSystemTraverserTest
        • class net.sf.octet.test.CycleTraverserTest
        • class net.sf.octet.test.DepthTraverserTest
        • class net.sf.octet.test.FlexMolHandlerTest
        • class net.sf.octet.test.FlexMolRoundTripTest
        • class net.sf.octet.test.ImplicitHydrogenTest
        • class net.sf.octet.test.IsomorphismTest
        • class net.sf.octet.test.MolecularMassTest
        • class net.sf.octet.test.MoleculeBuilderTest
        • class net.sf.octet.test.MoleculeConvertorTest
        • class net.sf.octet.test.MoleculeQueryBuilderTest
        • class net.sf.octet.test.MoleculeTest
        • class net.sf.octet.test.NonbondingValenceElectronsTest
        • class net.sf.octet.test.OrderedSetTest
        • class net.sf.octet.test.QueryTest
        • class net.sf.octet.test.SequenceTest
        • class net.sf.octet.test.StereoTest
  • class net.sf.octet.model.AtomGraphDecorator (implements net.sf.octet.model.AtomGraph)
    • class net.sf.octet.model.BasicBondingSystem (implements net.sf.octet.model.BondingSystem)
    • class net.sf.octet.model.BasicGammaSequence (implements net.sf.octet.model.GammaSequence)
  • class net.sf.octet.collection.BasicAtomCollection (implements net.sf.octet.collection.AtomCollection)
  • class net.sf.octet.model.BasicAtomGraph (implements net.sf.octet.model.AtomGraph)
  • class net.sf.octet.collection.BasicAtomGraphCollection (implements net.sf.octet.collection.AtomGraphCollection)
  • class net.sf.octet.collection.BasicAtomicSymbolCollection (implements net.sf.octet.collection.AtomicSymbolCollection)
  • class net.sf.octet.model.BasicAtomicSystem (implements net.sf.octet.model.AtomicSystem)
  • class net.sf.octet.collection.BasicAtomMap (implements net.sf.octet.collection.AtomMap)
  • class net.sf.octet.model.BasicAtomPair (implements net.sf.octet.model.AtomPair)
  • class net.sf.octet.collection.BasicAtomPairCollection (implements net.sf.octet.collection.AtomPairCollection)
  • class net.sf.octet.collection.BasicBondingSystemCollection (implements net.sf.octet.collection.BondingSystemCollection)
  • class net.sf.octet.traversal.BasicBreadthTraverser (implements net.sf.octet.traversal.BreadthTraverser)
  • class net.sf.octet.model.BasicConfiguration (implements net.sf.octet.model.Configuration)
  • class net.sf.octet.query.BasicConfigurationComparator (implements net.sf.octet.query.ConfigurationComparator)
  • class net.sf.octet.model.BasicConformation (implements net.sf.octet.model.Conformation)
  • class net.sf.octet.query.BasicConformationComparator (implements net.sf.octet.query.ConformationComparator)
  • class net.sf.octet.traversal.BasicCycleSystemTraverser (implements net.sf.octet.traversal.CycleSystemTraverser)
  • class net.sf.octet.traversal.BasicDepthTraverser (implements net.sf.octet.traversal.DepthTraverser)
  • class net.sf.octet.model.BasicElectron (implements net.sf.octet.model.Electron)
  • class net.sf.octet.collection.BasicElectronCollection (implements net.sf.octet.collection.ElectronCollection)
    • class net.sf.octet.model.BasicOrbital (implements net.sf.octet.model.Orbital)
  • class net.sf.octet.xml.BasicFlexMolHandler (implements net.sf.octet.xml.FlexMolHandler)
  • class net.sf.octet.xml.BasicFlexMolWriter (implements net.sf.octet.xml.FlexMolWriter)
  • class net.sf.octet.collection.BasicGammaSequenceCollection (implements net.sf.octet.collection.GammaSequenceCollection)
  • class net.sf.octet.model.BasicHalfPlane (implements net.sf.octet.model.HalfPlane)
  • class net.sf.octet.collection.BasicHalfPlaneCollection (implements net.sf.octet.collection.HalfPlaneCollection)
  • class net.sf.octet.util.BasicMeasurement (implements net.sf.octet.util.Measurement)
  • class net.sf.octet.builder.BasicMoleculeBuilder (implements net.sf.octet.builder.MoleculeBuilder)
  • class net.sf.octet.model.BasicMoleculeConvertor (implements net.sf.octet.model.MoleculeConvertor)
  • class net.sf.octet.query.BasicMoleculeQueryBuilder (implements net.sf.octet.query.MoleculeQueryBuilder)
  • class net.sf.octet.model.BasicNonbondingShell (implements net.sf.octet.model.NonbondingShell)
  • class net.sf.octet.collection.BasicNucleusCollection (implements net.sf.octet.collection.NucleusCollection)
  • class net.sf.octet.collection.BasicOrbitalCollection (implements net.sf.octet.collection.OrbitalCollection)
  • class net.sf.octet.model.BasicPaddleWheel (implements net.sf.octet.model.PaddleWheel)
  • class net.sf.octet.collection.BasicPaddleWheelCollection (implements net.sf.octet.collection.PaddleWheelCollection)
  • class net.sf.octet.query.BasicPaddleWheelComparator (implements net.sf.octet.query.PaddleWheelComparator)
  • class net.sf.octet.traversal.BasicTraversalHandler (implements net.sf.octet.traversal.TraversalHandler)
  • class net.sf.octet.query.BilateralQueryStrategy (implements net.sf.octet.query.MoleculeQueryStrategy)
  • class net.sf.octet.util.BuilderKit
  • class net.sf.octet.query.CachedMoleculeQuery (implements net.sf.octet.query.MoleculeQuery)
  • class net.sf.octet.util.CollectionKit
  • class net.sf.octet.test.CompleteTest
  • class net.sf.octet.traversal.HanserCycleTraverser (implements net.sf.octet.traversal.CycleTraverser)
  • class net.sf.octet.model.MoleculeDecorator (implements net.sf.octet.model.Molecule)
  • class net.sf.octet.util.MoleculeKit
  • class net.sf.octet.util.MoleculePrinter
  • class net.sf.octet.util.OrderedSet (implements java.util.List, java.util.Set)
  • class net.sf.octet.query.PaddleWheelInvertor (implements net.sf.octet.model.PaddleWheel)
  • class net.sf.octet.traversal.PrintingHandler (implements net.sf.octet.traversal.TraversalHandler)
  • class org.apache.tools.ant.ProjectComponent
    • class org.apache.tools.ant.Task
      • class net.sf.octet.task.WriteFlexMolExamples
  • class net.sf.octet.util.RepresentationKit
  • class net.sf.octet.model.SimpleBondingSystem (implements net.sf.octet.model.BondingSystem)
  • class net.sf.octet.model.SimpleHalfPlane (implements net.sf.octet.model.HalfPlane)
  • class net.sf.octet.util.StringFragmenter
  • class net.sf.octet.util.StringKit
  • class net.sf.octet.query.TemplateAtomQuery (implements net.sf.octet.query.AtomQuery)
  • class net.sf.octet.query.TemplateMoleculeQuery (implements net.sf.octet.query.MoleculeQuery)
  • class java.lang.Throwable (implements java.io.Serializable)
    • class java.lang.Exception
      • class java.lang.RuntimeException
        • class net.sf.octet.error.IllegalRepresentationException
        • class net.sf.octet.error.InvalidAtomMapException
        • class net.sf.octet.error.NoSuchAtomException
        • class net.sf.octet.error.NoSuchAtomicSymbolException
        • class net.sf.octet.error.NoSuchAtomPairException
        • class net.sf.octet.error.NoSuchBondingSystemException
        • class net.sf.octet.error.NoSuchGammaSequenceException
        • class net.sf.octet.error.NoSuchNucleusException
        • class net.sf.octet.error.NoSuchPaddleWheelException
        • class net.sf.octet.error.NoSuchProxyException
  • class net.sf.octet.traversal.UllmanIsomorphismTraverser (implements net.sf.octet.traversal.IsomorphismTraverser)
  • class net.sf.octet.query.UnilateralQueryStrategy (implements net.sf.octet.query.MoleculeQueryStrategy)
  • class net.sf.octet.query.WildcardAtomQuery (implements net.sf.octet.query.AtomQuery)
  • class org.xml.sax.helpers.XMLFilterImpl (implements org.xml.sax.ContentHandler, org.xml.sax.DTDHandler, org.xml.sax.EntityResolver, org.xml.sax.ErrorHandler, org.xml.sax.XMLFilter)
    • class net.sf.octet.xml.XMLWriter
      • class net.sf.octet.xml.DataWriter

Interface Hierarchy

• interface net.sf.octet.model.Atom
• interface net.sf.octet.collection.AtomCollection
  • interface net.sf.octet.model.AtomGraph (also extends net.sf.octet.collection.AtomPairCollection)
    • interface net.sf.octet.model.BondingSystem
    • interface net.sf.octet.model.GammaSequence
    • interface net.sf.octet.model.Molecule (also extends net.sf.octet.collection.BondingSystemCollection)
• interface net.sf.octet.collection.AtomGraphCollection
• interface net.sf.octet.collection.AtomGraphIterator
• interface net.sf.octet.model.AtomicSymbol
• interface net.sf.octet.collection.AtomicSymbolCollection
  • interface net.sf.octet.model.AtomicSystem
• interface net.sf.octet.collection.AtomicSymbolIterator
• interface net.sf.octet.collection.AtomIterator
• interface net.sf.octet.collection.AtomMap
• interface net.sf.octet.model.AtomPair
• interface net.sf.octet.collection.AtomPairCollection
  • interface net.sf.octet.model.AtomGraph (also extends net.sf.octet.collection.AtomCollection)
    • interface net.sf.octet.model.BondingSystem
    • interface net.sf.octet.model.GammaSequence
    • interface net.sf.octet.model.Molecule (also extends net.sf.octet.collection.BondingSystemCollection)
• interface net.sf.octet.collection.AtomPairIterator
• interface net.sf.octet.builder.AtomProxy
• interface net.sf.octet.query.AtomQuery
• interface net.sf.octet.collection.BondingSystemCollection
  • interface net.sf.octet.model.Molecule (also extends net.sf.octet.model.AtomGraph)
• interface net.sf.octet.collection.BondingSystemIterator
• interface net.sf.octet.builder.BondingSystemProxy
• interface net.sf.octet.traversal.BreadthTraverser
• interface net.sf.octet.query.ConfigurationComparator
  • interface net.sf.octet.query.MoleculeQueryStrategy (also extends net.sf.octet.query.ConformationComparator, net.sf.octet.traversal.IsomorphismTraverser)
• interface net.sf.octet.builder.ConfigurationProxy
• interface net.sf.octet.query.ConformationComparator
  • interface net.sf.octet.query.MoleculeQueryStrategy (also extends net.sf.octet.query.ConfigurationComparator, net.sf.octet.traversal.IsomorphismTraverser)
• interface org.xml.sax.ContentHandler
  • interface net.sf.octet.xml.FlexMolHandler
• interface net.sf.octet.traversal.CycleSystemTraverser
• interface net.sf.octet.traversal.CycleTraverser
• interface net.sf.octet.traversal.DepthTraverser
• interface net.sf.octet.model.Electron
• interface net.sf.octet.collection.ElectronCollection
  • interface net.sf.octet.model.NonbondingShell (also extends net.sf.octet.collection.OrbitalCollection)
  • interface net.sf.octet.model.Orbital
• interface net.sf.octet.collection.ElectronIterator
• interface net.sf.octet.xml.ForeignContent
• interface net.sf.octet.collection.GammaSequenceCollection
  • interface net.sf.octet.model.Conformation (also extends net.sf.octet.collection.PaddleWheelCollection)
• interface net.sf.octet.collection.GammaSequenceIterator
• interface net.sf.octet.builder.GammaSequenceProxy
• interface net.sf.octet.model.HalfPlane
• interface net.sf.octet.collection.HalfPlaneCollection
  • interface net.sf.octet.model.PaddleWheel
• interface net.sf.octet.collection.HalfPlaneIterator
• interface net.sf.octet.builder.HalfPlaneProxy
• interface net.sf.octet.traversal.IsomorphismTraverser
  • interface net.sf.octet.query.MoleculeQueryStrategy (also extends net.sf.octet.query.ConfigurationComparator, net.sf.octet.query.ConformationComparator)
• interface net.sf.octet.util.Measurement
• interface net.sf.octet.model.MoleculeConvertor
• interface net.sf.octet.query.MoleculeQuery
• interface net.sf.octet.model.Nucleus
• interface net.sf.octet.collection.NucleusCollection
  • interface net.sf.octet.model.IsotopicDistribution
• interface net.sf.octet.collection.NucleusIterator
• interface net.sf.octet.collection.OrbitalCollection
  • interface net.sf.octet.model.NonbondingShell (also extends net.sf.octet.collection.ElectronCollection)
• interface net.sf.octet.collection.OrbitalIterator
• interface net.sf.octet.builder.OrbitalProxy
• interface net.sf.octet.collection.PaddleWheelCollection
  • interface net.sf.octet.model.Configuration
  • interface net.sf.octet.model.Conformation (also extends net.sf.octet.collection.GammaSequenceCollection)
• interface net.sf.octet.query.PaddleWheelComparator
• interface net.sf.octet.collection.PaddleWheelIterator
• interface net.sf.octet.builder.RepresentationBuilder
  • interface net.sf.octet.xml.FlexMolWriter
  • interface net.sf.octet.builder.MoleculeBuilder
  • interface net.sf.octet.query.MoleculeQueryBuilder
• interface net.sf.octet.util.Sequence
• interface net.sf.octet.traversal.TraversalHandler
  • interface net.sf.octet.traversal.BreadthTraverser.Handler
  • interface net.sf.octet.traversal.CycleSystemTraverser.Handler
  • interface net.sf.octet.traversal.CycleTraverser.Handler
  • interface net.sf.octet.traversal.DepthTraverser.Handler
  • interface net.sf.octet.traversal.IsomorphismTraverser.Handler