Package toxTree.core

This packages contains only interface definitions, defining essential classes in toxTree application.

See: Description

Interface Summary

Interface	Description
IDecisionCategories	A list of IDecisionCategory instances
IDecisionCategory	An interface definition to represent a chemical category The application of a decision tree IDecisionMethod results in assigning a category to the query chemical.
IDecisionCategoryEditor
IDecisionInteractive	An interface for rules, requiring user interaction (e.g.
IDecisionMethod	An interface to represent a decision tree.
IDecisionMethodEditor
IDecisionMethodPrority
IDecisionMethodsList	A list of IDecisionMethod instances
IDecisionResult	An interface definition to represent the result of applying a IDecisionMethod.
IDecisionRule	An interface definition to represent a rule, that will be used in a IDecisionMethod.
IDecisionRuleEditor	Each rule IDecisionRule should provides an editor, which is a class, implementing this interface.
IDecisionRuleList	A list of IDecisionRule
IDecisionTransition	An interface representing a transition between decision rules IDecisionRule in a decision tree IDecisionMethod.
IDescriptorBased
IFilteredMolecules
IImplementationDetails
IMetaboliteGenerator
IMoleculesIterator
IProcessRule
IProgressStatus
IRuleRange
IRuleSubstructures	An interface to support substructure rules
IRuleValue
IToxTreeEditor	Parent interface for all editors in ToxTree.
XMLSerializable

Class Summary

Class	Description
ConnectionMatrix
Introspection	A singleton class with static method to provide some sort of introspection :) Used in decision tree editor to provide a list of available decision trees, available rules, available categories.
SmartElementsList	Same as HashSet, but understands "X" as halogen elements.
ToxTreeClassLoader
ToxTreeDescriptor
ToxTreeObjectInputStream	Loading non-default serialized classes is tricky ...
ToxTreePackageEntries	a List of ToxTreePackageEntry
ToxTreePackageEntry	A class, containing information about className, its package and a toString() output

Enum Summary

Enum	Description
IDecisionInteractive.UserOptions

Package toxTree.core Description

This packages contains only interface definitions, defining essential classes in toxTree application.

• A decision tree should implement interface IDecisionMethod
• A decision rule should implement interface IDecisionRule
• The application of a decision tree on a query molecule assigns it to a category IDecisionCategory
• The path followed through the decision tree should be provided by IDecisionResult

The existence of these interfaces allows various implementation of decision rules, trees and categories, which can nevertheless be used interdependently.

A set of classes implementing these interfaces can be found in package toxTree.tree

Plugins

Plugins are .jar files, containing any one or all of the following:

• Decision tree(s), i.e. classes implementing IDecisionMethod
• Rule(s), i.e. classes implementing IDecisionRule
• Categories, i.e. classes implementing IDecisionCategory

Plugins are searched at run-time in the following directories:

• The directory where toxTree.jar resides (current directory).
• The directory "ext" below the current directory.

Plugins containing decision trees are searched when presenting a list of available trees. Plugins containing rules are searched when presenting a list of available rules. Plugins containing categories are searched when presenting a list of available categories.
The Cramer tree CramerRules is used by default, but relies on the same mechanism. It is distributed in toxCramer.jar. A demo decision tree is available at SubstructureTree and distributed in toxDemo.jar.