Hierarchy For All Packages

Package Hierarchies:

ambit2.core.config, ambit2.core.data, ambit2.core.data.distances, ambit2.core.data.experiment, ambit2.core.data.model, ambit2.core.external, ambit2.core.groups, ambit2.core.io, ambit2.core.io.bcf, ambit2.core.processors, ambit2.core.processors.batch, ambit2.core.processors.quality, ambit2.core.processors.structure, ambit2.core.processors.structure.key, ambit2.core.smiles

Class Hierarchy

• java.lang.Object
  • java.util.AbstractCollection<E> (implements java.util.Collection<E>)
    • java.util.AbstractList<E> (implements java.util.List<E>)
      • java.util.ArrayList<E> (implements java.lang.Cloneable, java.util.List<E>, java.util.RandomAccess, java.io.Serializable)
        • ambit2.core.data.experiment.StudyList
        • ambit2.core.data.experiment.StudyTemplate
  • ambit2.core.groups.AbstractGroup.EmptyIterator<T> (implements java.util.Iterator<E>)
  • ambit2.core.groups.AbstractGroup.SelfIterable<T> (implements java.lang.Iterable<T>)
  • ambit2.core.config.AmbitCONSTANTS
  • ambit2.core.data.ArrayResult<T> (implements org.openscience.cdk.qsar.result.IDescriptorResult)
    • ambit2.core.data.IntArrayResult
  • ambit2.core.data.distances.AtomDistance
  • org.openscience.cdk.ChemObject (implements java.lang.Cloneable, org.openscience.cdk.interfaces.IChemObject, java.io.Serializable)
    • org.openscience.cdk.Element (implements java.lang.Cloneable, org.openscience.cdk.interfaces.IElement, java.io.Serializable)
      • org.openscience.cdk.Isotope (implements java.lang.Cloneable, org.openscience.cdk.interfaces.IIsotope, java.io.Serializable)
        • org.openscience.cdk.AtomType (implements java.lang.Cloneable, org.openscience.cdk.interfaces.IAtomType, java.io.Serializable)
          • org.openscience.cdk.Atom (implements java.lang.Cloneable, org.openscience.cdk.interfaces.IAtom, java.io.Serializable)
            • org.openscience.cdk.PseudoAtom (implements java.lang.Cloneable, org.openscience.cdk.interfaces.IPseudoAtom, java.io.Serializable)
              • ambit2.core.groups.AbstractGroup (implements ambit2.core.groups.ISGroup)
                • ambit2.core.groups.ComponentGroup
                • ambit2.core.groups.ContainerGroup
                • ambit2.core.groups.DataGroup
                • ambit2.core.groups.GenericGroup
                • ambit2.core.groups.MonomerGroup
                • ambit2.core.groups.MultipleGroup (implements ambit2.core.groups.IExpandable)
                • ambit2.core.groups.StructureRepeatingUnit
                • ambit2.core.groups.SuperAtom (implements ambit2.core.groups.IExpandable)
    • ambit2.core.groups.SuppleAtomContainer (implements java.lang.Cloneable, org.openscience.cdk.interfaces.IChemObjectListener, ambit2.core.groups.IFiltered<T>, org.openscience.cdk.interfaces.IMolecule, java.io.Serializable)
  • ambit2.base.external.CommandShell<INPUT,OUTPUT> (implements ambit2.base.interfaces.IProcessor<Target,Result>)
    • ambit2.core.external.ShellSDFoutput<INPUT>
      • ambit2.core.smiles.OpenBabelShell
  • ambit2.core.io.CompoundImageTools
  • ambit2.core.smiles.DeduceBondSystemTool
  • ambit2.base.processors.DefaultAmbitProcessor<Target,Result> (implements ambit2.base.interfaces.IProcessor<Target,Result>)
    • ambit2.core.processors.structure.AbstractPropertyGenerator<P>
    • ambit2.core.processors.AbstractRepresentationConvertor<Item,Content,Output,R,Media,ItemReporter>
    • ambit2.core.processors.structure.AtomConfigurator
      • ambit2.core.processors.structure.HydrogenAdderProcessor
    • ambit2.core.data.distances.AtomDistanceProcessor
    • ambit2.core.processors.quality.ChemicalStructureQualityCheck
    • ambit2.core.processors.structure.CloneProcessor
    • ambit2.core.processors.structure.key.EmptyKey (implements ambit2.core.processors.structure.key.IStructureKey<Target,Result>)
    • ambit2.core.processors.structure.FingerprintGenerator
    • ambit2.core.processors.structure.key.InchiKey (implements ambit2.core.processors.structure.key.IStructureKey<Target,Result>)
    • ambit2.core.processors.structure.InchiProcessor
    • ambit2.core.processors.structure.MoleculeReader
    • ambit2.core.processors.structure.MoleculeWriter
    • ambit2.core.processors.ProcessorFileExport<Content> (implements ambit2.base.processors.Reporter<Content,Output>)
    • ambit2.core.processors.structure.key.PropertyKey<Result> (implements ambit2.core.processors.structure.key.IStructureKey<Target,Result>)
      • ambit2.core.processors.structure.key.CASKey
      • ambit2.core.processors.structure.key.DSSToxCID
      • ambit2.core.processors.structure.key.DSSToxRID
      • ambit2.core.processors.structure.key.EINECSKey
      • ambit2.core.processors.structure.key.InchiPropertyKey
      • ambit2.core.processors.structure.key.PubchemCID
    • ambit2.core.processors.structure.key.SmilesKey (implements ambit2.core.processors.structure.key.IStructureKey<Target,Result>)
    • ambit2.core.processors.structure.StructureTypeProcessor
  • org.openscience.cdk.io.DefaultChemObjectReader (implements org.openscience.cdk.io.IChemObjectReader)
    • ambit2.core.io.DelimitedFileReader (implements org.openscience.cdk.io.IChemObjectReader)
    • ambit2.core.io.MDLReader
    • org.openscience.cdk.io.MDLReader
      • ambit2.core.io.FilteredMDLReader
    • ambit2.core.io.MDLV2000ReaderExtended
  • org.openscience.cdk.io.DefaultChemObjectWriter (implements org.openscience.cdk.io.IChemObjectWriter)
    • ambit2.core.io.FilesWithHeaderWriter
      • ambit2.core.io.DelimitedFileWriter
      • ambit2.core.io.PDFWriter
    • ambit2.core.io.FileWithHeaderWriter
      • ambit2.core.io.XLSFileWriter
    • ambit2.core.io.MDLWriter
  • ambit2.core.processors.batch.DefaultIOState (implements ambit2.base.interfaces.IInputOutputState)
    • ambit2.core.processors.batch.DefaultInputState (implements ambit2.core.io.IInputState)
  • org.openscience.cdk.io.iterator.DefaultIteratingChemObjectReader (implements org.openscience.cdk.io.iterator.IIteratingChemObjectReader)
    • ambit2.core.io.IteratingChemObjectReaderWrapper
    • ambit2.core.io.IteratingFilesWithHeaderReader
      • ambit2.core.io.IteratingDelimitedFileReader (implements org.openscience.cdk.io.iterator.IIteratingChemObjectReader)
      • ambit2.core.io.IteratingXLSReader
        • ambit2.core.io.bcf.EurasBCFReader
    • ambit2.core.io.IteratingFolderReader<T,ItemReader>
      • ambit2.core.io.IteratingMolFolderReader
      • ambit2.core.io.RawIteratingFolderReader (implements ambit2.core.io.IRawReader<T>)
    • org.openscience.cdk.io.iterator.IteratingMDLReader
      • ambit2.core.io.InteractiveIteratingMDLReader
    • ambit2.core.io.MyIteratingMDLReader
    • ambit2.core.io.RandomAccessReader (implements ambit2.base.interfaces.IRandomAccessChemObjectReader, java.lang.Runnable)
      • ambit2.core.io.RandomAccessSDFReader
    • ambit2.core.io.RawIteratingReader<T> (implements ambit2.core.io.IRawReader<T>)
      • ambit2.core.io.RawIteratingMOLReader
      • ambit2.core.io.RawIteratingSDFReader
  • ambit2.core.io.DelimitedFileFormat (implements org.openscience.cdk.io.formats.IChemFormatMatcher)
  • ambit2.core.data.EINECS
  • ambit2.core.groups.FilteredList<T> (implements ambit2.core.groups.IFiltered<T>, java.util.List<E>)
  • org.openscience.cdk.io.setting.IOSetting
    • ambit2.core.io.MolPropertiesIOSetting
  • ambit2.core.io.IteratingFileReader (implements org.openscience.cdk.io.iterator.IIteratingChemObjectReader)
  • com.jgoodies.binding.beans.Model (implements com.jgoodies.binding.beans.Observable, java.io.Serializable)
    • ambit2.base.data.AmbitBean
      • ambit2.core.data.experiment.Study
        • ambit2.core.data.experiment.AQUIREStudy
      • ambit2.core.data.experiment.TemplateField
    • ambit2.core.io.FileState (implements ambit2.base.interfaces.IInputOutputState)
      • ambit2.core.io.FileInputState (implements ambit2.core.io.IInputState)
      • ambit2.core.io.FileOutputState (implements ambit2.core.io.IOutputState)
  • ambit2.core.data.model.ModelWrapper<T,TrainingInstances,TestInstances,Content>
  • ambit2.core.data.MoleculeTools
  • ambit2.base.data.Profile<P>
    • ambit2.base.data.Template
      • ambit2.core.data.experiment.AquireTemplate
      • ambit2.core.data.experiment.DefaultTemplate
      • ambit2.core.data.experiment.DSSToxLC50Template
        • ambit2.core.data.experiment.DSSToxCarcinogenicityTemplate
        • ambit2.core.data.experiment.DSSToxERBindingTemplate
      • ambit2.core.data.experiment.LLNATemplate
  • ambit2.core.io.RawIteratingWrapper<R> (implements ambit2.core.io.IRawReader<T>)
  • java.io.Reader (implements java.io.Closeable, java.lang.Readable)
    • java.io.FilterReader
      • ambit2.core.io.MultiNewlineFilterReader
  • org.openscience.cdk.io.ReaderFactory
    • ambit2.core.io.ReaderFactoryExtended
  • ambit2.core.config.Resources
  • ambit2.core.io.SDFBrokenLineTerminationConverter
  • ambit2.core.io.SGroupMDL2000Helper
  • ambit2.core.io.SimpleIOListener (implements org.openscience.cdk.io.listener.IReaderListener, org.openscience.cdk.io.listener.IWriterListener)
  • ambit2.core.smiles.SmilesParserWrapper (implements java.beans.PropertyChangeListener)
  • ambit2.core.data.StringDescriptorResultType (implements org.openscience.cdk.qsar.result.IDescriptorResult)
  • java.lang.Throwable (implements java.io.Serializable)
    • java.lang.Exception
      • ambit2.core.groups.GroupException
        • ambit2.core.groups.GroupNotFoundException
        • ambit2.core.groups.UnsupportedGroupOperation
  • ambit2.core.io.XLSFileFormat (implements org.openscience.cdk.io.formats.IChemFormatMatcher)

Interface Hierarchy

• java.lang.Cloneable
  • org.openscience.cdk.interfaces.IChemObject
    • org.openscience.cdk.interfaces.IElement
      • org.openscience.cdk.interfaces.IIsotope
        • org.openscience.cdk.interfaces.IAtomType
          • org.openscience.cdk.interfaces.IAtom
            • ambit2.core.groups.ISGroup (also extends java.lang.Comparable<T>)
• java.lang.Comparable<T>
  • ambit2.core.groups.ISGroup (also extends org.openscience.cdk.interfaces.IAtom)
• org.openscience.cdk.io.IChemObjectIO
  • org.openscience.cdk.io.iterator.IIteratingChemObjectReader (also extends java.util.Iterator<E>)
    • ambit2.core.io.IRawReader<T>
• ambit2.core.groups.IExpandable
• ambit2.core.groups.IFiltered<T>
• java.util.Iterator<E>
  • org.openscience.cdk.io.iterator.IIteratingChemObjectReader (also extends org.openscience.cdk.io.IChemObjectIO)
    • ambit2.core.io.IRawReader<T>
• java.io.Serializable
  • ambit2.base.interfaces.IInputOutputState
    • ambit2.core.io.IInputState
    • ambit2.core.io.IOutputState
  • ambit2.base.interfaces.IProcessor<Target,Result>
    • ambit2.core.processors.structure.key.IStructureKey<Target,Result>

Enum Hierarchy

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    • ambit2.core.config.AmbitCONSTANTS.STRUC_TYPE
    • ambit2.core.groups.DataGroup.DGROUP_DISPLAY
    • ambit2.core.groups.DataGroup.SGROUP_FIELD
    • ambit2.core.groups.ContainerGroup.SGROUP_MIXTURE
    • ambit2.core.io.SGroupMDL2000Helper.SGROUP_LINE
    • ambit2.core.io.SGroupMDL2000Helper.SGROUP_TYPE
    • ambit2.core.io.SGroupMDL2000Helper.SGROUP_POLYMER_TYPE
    • ambit2.core.io.SGroupMDL2000Helper.SGROUP_CONNECTIVITY
    • ambit2.core.smiles.SmilesParserWrapper.SMILES_PARSER