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Package Hierarchies:
ooc
,
softparsmap
Class Hierarchy
class java.lang.Object
class java.util.AbstractCollection (implements java.util.Collection)
class java.util.AbstractList (implements java.util.List)
class java.util.Vector (implements java.lang.Cloneable, java.util.List, java.util.RandomAccess, java.io.Serializable)
class softparsmap.
ChildSet
(implements java.util.Set)
class ooc.
AttributeConverterAbstract
(implements ooc.
AttributeConverter
)
class ooc.
AttributeConverterList
class ooc.
AttributeConverterMethod
class ooc.
AttributeConverterNumber
class ooc.
AttributeConverterBigDecimal
class ooc.
AttributeConverterDouble
class ooc.
AttributeConverterFloat
class ooc.
AttributeConverterInteger
class ooc.
AttributeConverterLong
class ooc.
AttributeConverterShort
class ooc.
AttributeConverterString
class ooc.
AttributeConverterAttributeClass
class ooc.
AttributeConverterStringOption
class ooc.
AttributeConverterBoolean
class ooc.
AttributeConverterTagIdRef
class ooc.
AttributeConverterStringList
class ooc.
AttributeConverterTag
class ooc.
AttributeConverterInstance
class ooc.
AttributeConverterInstanceThis
class softparsmap.
ChildIterator
(implements java.util.Iterator)
class ooc.
Container
class softparsmap.
PropertyFile
class softparsmap.
DataSourceIndexXmlNcbiTaxonomy
(implements java.io.Serializable)
class org.xml.sax.helpers.DefaultHandler (implements org.xml.sax.ContentHandler, org.xml.sax.DTDHandler, org.xml.sax.EntityResolver, org.xml.sax.ErrorHandler)
class ooc.
TagParser
class java.util.Dictionary
class java.util.Hashtable (implements java.lang.Cloneable, java.util.Map, java.io.Serializable)
class ooc.
DependenciesMapped
(implements ooc.
Dependencies
)
class softparsmap.
Family
(implements java.lang.Comparable)
class softparsmap.
FilePointerPart
(implements java.io.Serializable)
class softparsmap.
InferMutation
class ooc.
InstanceConstructorAbstract
(implements ooc.
InstanceConstructor
)
class ooc.
InstanceConstructorReflection
class ooc.
InstanceConstructorInjector
class ooc.
InstanceConstructorInjectorSetup
class ooc.
InstanceHolderPrimitive
(implements ooc.
InstanceHolder
)
class ooc.
InstanceHolderSingleton
(implements ooc.
InstanceHolder
)
class ooc.
InstanceInjectorAbstract
(implements ooc.
InstanceInjector
)
class ooc.
InstanceInjectorAbstractIfNull
class ooc.
InstanceInjectorAttribute
class ooc.
InstanceInjectorAttributeAll
class ooc.
InstanceInjectorAttributeAllField
class ooc.
InstanceInjectorDependency
class ooc.
InstanceInjectorMethodAbstract
class ooc.
InstanceInjectorMethodAttributes
class ooc.
InstanceInjectorMethodInstances
class ooc.
InstanceInjectorTag
class ooc.
InstanceInjectorChildInstances
class ooc.
InstanceInjectorChildTemplates
(implements java.lang.Cloneable)
class ooc.
InstanceInjectorGroup
class ooc.
InstanceInjectorMethodChildTagsAttributes
class ooc.
InstanceInjectorParentInstance
class ooc.
InstanceSetupAttribute
(implements ooc.
InstanceSetup
)
class ooc.
InstanceSetupMethod
(implements ooc.
InstanceSetup
)
class ooc.
LinkedTagInstance
(implements ooc.
Dependencies
)
class softparsmap.
AbstractDataSource
(implements softparsmap.
DataSource
)
class softparsmap.
DataSourceXmlNcbiTaxonomy
class softparsmap.
AbstractEdgeType
(implements softparsmap.
EdgeType
)
class softparsmap.
StandardEdgeType
class softparsmap.
AbstractFamilyGroup
(implements softparsmap.
FamilyGroup
)
class softparsmap.
FamilyGroupTreesInFiles
class softparsmap.
FamilyGroupTreesInFilesInfoPerRow
class softparsmap.
AbstractInparalogous
(implements softparsmap.
Inparalogous
)
class softparsmap.
InparalogousStandard
class softparsmap.
AbstractSequenceData
(implements softparsmap.
SequenceData
)
class softparsmap.
SequenceDataXml
class softparsmap.
AbstractStringNodeConverter
(implements softparsmap.
StringNodeConverter
)
class softparsmap.
StringNodeConverterStringTemplate
class softparsmap.
StringGeneNodeConverterStringTemplate
class softparsmap.
StringGeneNodeConverterDupSpe
class softparsmap.
StringGeneNodeConverterLabel
class softparsmap.
StringGeneNodeConverterNcbiNamesColumn
class softparsmap.
StringGeneNodeConverterSchreiberLabel
class softparsmap.
StringGeneNodeConverterSequenceDataXml
class softparsmap.
StringNodeConverterMapInfo
class softparsmap.
StringGeneNodeConverterSchreiberMapLabel
class softparsmap.
AbstractTreeParser
(implements softparsmap.
TreeParser
)
class softparsmap.
TreeParserDual
class softparsmap.
TreeParserNewick
class softparsmap.
Compute
class softparsmap.
ComputeFamilyGroup
class softparsmap.
ComputeFamilyNumbers
class softparsmap.
ComputeMap
class softparsmap.
ComputeMapInfo
class softparsmap.
ComputeRoot
class softparsmap.
ComputeFamilyGroupPair
class softparsmap.
ComputeCompareGeneTrees
class softparsmap.
PreferredTree
(implements java.util.Comparator)
class softparsmap.
PreferredTreeStandard
class softparsmap.
TreeStructureParserLeafList
(implements softparsmap.
TreeStructureParser
)
class softparsmap.
TreeStructureParserSchreiber
(implements softparsmap.
TreeStructureParser
)
class softparsmap.
TreeStructureParserSchreiberInfoIn
class softparsmap.
Mutation
class softparsmap.
Node
(implements java.lang.Comparable)
class softparsmap.
GeneNode
class softparsmap.
GeneLeaf
(implements java.lang.Comparable)
class softparsmap.
MuNode
class softparsmap.
SpeciesNode
class softparsmap.
SpeciesLeaf
class ooc.
Print
class softparsmap.
PrintTree
class softparsmap.
SortedCollection
(implements java.util.Collection)
class ooc.
SourceAbstract
(implements ooc.
Source
)
class ooc.
SourceInputStream
class ooc.
SourceContextAbstract
(implements ooc.
SourceContext
)
class ooc.
SourceContextClassPath
class ooc.
SourceContextDirectory
class ooc.
SourceContextFile
class ooc.
SourceTagHolder
class ooc.
SourceTagHolderJoocDescriptor
class softparsmap.
Split
class softparsmap.
StringTemplate
class ooc.
Tag
class ooc.
TagAttribute
class ooc.
TagErrorHandler
class ooc.
TagErrorMsg
(implements ooc.
TagError
)
class ooc.
TagValidatorRestrictChildTag
(implements ooc.
TagValidator
)
class ooc.
TagValidatorRestrictChildTree
class ooc.
TagValidatorTag
(implements ooc.
TagValidator
)
class ooc.
TagValidatorInstance
class ooc.
TagValidatorReflection
class java.lang.Throwable (implements java.io.Serializable)
class java.lang.Exception
class java.lang.RuntimeException
class softparsmap.
FatalException
class ooc.
NotValidException
class ooc.
OocException
class ooc.
SourceParseException
class ooc.
TagErrorHandlerException
class ooc.
TagIdException
class ooc.
Tools
class softparsmap.
TreeTextBlock
class ooc.
Validate
class java.io.Writer
class softparsmap.
CharsetFileWriter
Interface Hierarchy
interface ooc.
AttributeConverter
interface java.lang.Cloneable
interface ooc.
Template
interface softparsmap.
DataSource
interface ooc.
Dependencies
interface softparsmap.
EdgeType
interface softparsmap.
FamilyGroup
interface softparsmap.
Inparalogous
interface ooc.
InstanceConstructor
interface ooc.
InstanceHolder
interface ooc.
InstanceInjector
interface ooc.
InstanceSetup
interface softparsmap.
SequenceData
interface ooc.
Source
interface ooc.
SourceContext
interface softparsmap.
StringNodeConverter
interface ooc.
TagError
interface ooc.
TagValidator
interface softparsmap.
TreeParser
interface softparsmap.
TreeStructureParser
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