This API provides documentation for the packages and classes making up the Omegahat software distribution.

See:
Description

Packages

org.omegahat.DataStructures.Data
org.omegahat.DataStructures.Data.Viewers
org.omegahat.DataStructures.Matrix
org.omegahat.DataStructures.Trees
org.omegahat.Environment.Compile	Generic code underlying the dynamic compilation of classes.
org.omegahat.Environment.Console	Basic shell/command-line interpreter front end for interactive language.
org.omegahat.Environment.Databases	Variety of containers for Omegahat objects providing database facilities (storage and retrieval by keys).
org.omegahat.Environment.DataStructures	Interfaces used by the language to implement extensible operator overloading, etc.
org.omegahat.Environment.Debugger	Early work on providing debugging facilities.
org.omegahat.Environment.Debugger.ParserViewer	Simple GUI viewer of the sub-expressions in a top-level task expression.
org.omegahat.Environment.GUI	Incomplete Swing-based GUI front-end to the interactive interpreter.
org.omegahat.Environment.GUITools	Collection of classes that allow Omega functions to be used as event callbacks.
org.omegahat.Environment.GUITools.MethodViewer	Display of fields, methods, constructors of class(es).
org.omegahat.Environment.Interpreter	The different evaluators, evaluator group managers and interfaces controlling the interactive language.
org.omegahat.Environment.IO	Filters for processing directories, filenames, zip and Jar files.
org.omegahat.Environment.Language	Basic language-level objects such as functions, closures, lazy evaluation classes, etc.
org.omegahat.Environment.Language.UserClasses	Interpreted/user-level class facility in interactive language.
org.omegahat.Environment.lib.Language	Collection of interpreted and compiled utility functions that can be dynamically added and removed to and from an evaluator to provide convenience facilities such as sequence functions, subset operations, Switch, time and Quote functions, etc.
org.omegahat.Environment.ObjectDataStructures	S-like vector and list classes implemented succinctly in terms of Java objects rather than primitives.
org.omegahat.Environment.Parser.AntlrParser	The ANTLR grammar for the current interactive language.
org.omegahat.Environment.Parser.Parse	Data structures used by the parser to create expression trees.
org.omegahat.Environment.System	Class controlling the interactive environment (class loaders, etc.)
org.omegahat.Environment.TaskManagement	Classes to manage tasks, by manipulating queues of objects that implement the Task interface.
org.omegahat.Environment.Tools.ClassHierarchy	GUI viewer for class relationships.
org.omegahat.Environment.Tools.ClassList	Facilities for resolving and loading classes (given partially qualified class names) from URLs, regular directories, archives (zip and jar files), whether the entries be in the system classpath or not.
org.omegahat.Environment.Tools.DataScanner	Quite general filters/tools to read data from streams.
org.omegahat.Environment.Tools.Factory	Generic factory mechanism to be extended where a factory is needed.
org.omegahat.Environment.Tools.FileLocator	Facilities for locating files from a collection of directories, archives, remote servers, etc.
org.omegahat.Environment.Tools.VariableExpansion	Mechanism to expand shell-like variable references from a supplied table.
org.omegahat.Environment.Utils	Convenient data structure classes that don't really belong anywhere else.
org.omegahat.Graphics.Devices	The interfaces and classes defining output devices (including Components) and also graphics parameters.
org.omegahat.Graphics.Layouts	Classes defining the region allocation, that is the layout facilities at the level of a single device (Component).
org.omegahat.Graphics.lib.Language	Methods providing operator overloading (specificall [ and [[) in the interpreted Omegahat language for GraphicalContainerInt.
org.omegahat.Graphics.Plots	High-level plotting classes that use the different org.omegahat.Graphics.Primitives, org.omegahat.Graphics.Layouts and org.omegahat.Graphics.Devices.
org.omegahat.Graphics.Plots.DataStructures	Classes describing data contents used in particular plot types.
org.omegahat.Graphics.Plots.Examples	Example applications and classes for using the Graphics.Plots classes.
org.omegahat.Graphics.Plots.Examples.Events
org.omegahat.Graphics.Primitives	Classes defining graphical objects in general, plus particular primitive objects, and related drawing primitives.
org.omegahat.Graphics.Utils	Color utilities (parser factory) for graphics used by some GUI tools.
org.omegahat.Graphics.Viewers	Classes for displaying not the plot, but the data structures which define the plot, that is, the graph hierarchy.
org.omegahat.Interfaces.Converters	Basic interfaces for converting objects between systems.
org.omegahat.Interfaces.CORBA	CORBA facilities for Java and interactive Omegahat languages.
org.omegahat.Interfaces.CORBA.Parser	Extensions to basic parser to support CORBA method invocation with same syntax as local method calls.
org.omegahat.Interfaces.CORBA.TaskManagement	Classes for managing distributed tasks through CORBA, dispatching tasks from an Omega TaskQueue.
org.omegahat.Interfaces.CORBA.Tools.InterfaceRepository	Interface Repository contents viewer GUI.
org.omegahat.Interfaces.CORBA.Tools.NameServer	Naming Service GUI viewer.
org.omegahat.Interfaces.CORBA.Tools.Support	GUI Classes supporting CORBA tools in parallel packages.
org.omegahat.Interfaces.Managers	Manager facility for conversion between objects in different systems.
org.omegahat.Models.Formulae.Expressions	Data structures associated with model language parser.
org.omegahat.Models.Formulae.Parser	Very early start on model language parser.
org.omegahat.Numerics.GeneticAlgorithms	Interfaces and classes to perform operations using the Genetic Algorithm approach to combinatorial optimization and exploration.
org.omegahat.Numerics.LinearAlgebra	Access to algorithms for common operations in linear algebra, and to classes for the inputs and outputs of these operations.
org.omegahat.Numerics.Optimizers	A collection of interfaces and some basic classes to perform iterations in the context of optimization.
org.omegahat.Probability.Distributions	Basic classes for parametric probability distributions, and specifically the Student T.
org.omegahat.Probability.Distributions.Native	Implementation of the Student T distribution via JNI and the R source, if it is available on your machine.
org.omegahat.S.InterfaceManager.Converters	Interfaces and classes used to generate converters that know how to convert objects to S; these allow users to define such conversion methods.
org.omegahat.S.InterfaceManager.Managers	Specialization of the Interfaces.Managers class to S.
org.omegahat.XML.DataStructures	Package defining data structures connecting XML information with classes used in other packages.
org.omegahat.XML.lib.Language	Methods providing operator overloading (specificall [ and [[) in the interpreted Omegahat language for XML classes - Node, NodeList, attribute NodeMaps.
org.omegahat.XML.Readers	Some readers for dataframes stored in XML dataframes, supporting both row and column oriented XML DTDs.
org.omegahat.XML.Validation	Tools to validate an XML document using a non-terminating error handler so that all errors are displayed for the document rather than a single one and exit.

This API provides documentation for the packages and classes making up the Omegahat software distribution. The software is provided as part of the Omega project for statistical software. The initial distribution is intended to suggest the spirit of the project, point out some interesting directions, and perhaps provide tools that will be useful for those who want to explore these directions, particularly in the context of Java and the Web. We cordially invite anyone interested to try things out, look at the code, and if possible contribute to our work.

At the same time, we should make it clear that this is in no way a finished system for statistical computing, still less a competitor for the existing languages and systems. There are many exciting new things that can be done with the approaches explored here, but the details required to make it all a ``real'' system are only sketched. In the spirit of open-source software, we want to publicize the ideas early to get the maximum feedback and contributions from anyone interested.

Omegahat currently consists of three main parts:

1. the Java classes and interfaces described in this API;
2. an interactive language, accessible through the shell script omegahat, included with this distribution;
3. inter-system interfaces, currently from S and R to CORBA and Java.

The Java classes are suitable building-blocks for others interested in statistical software based on Java. In particular, there are a number of interfaces and classes in which we have taken first steps at recasting familiar statistical computing concepts (e.g. data frames, graphics objects) into the new context. Here we especially need lots of feedback and suggestions for improvements, because the implementation of these concepts will be crucial for future work.

The interactive language can largely be seen at this stage as a way to develop Java-based software interactively. It provides convenient access to Java classes, both within Omegahat and generally, along with some features for defining global functions and data structures that are convenient for interactive computing. An introduction is available in a Postscript document.

The main packages described in this API are:

• the Environment packages, which together provide support for the interactive language, but individually also provide useful tools for things such as data structures, databases and IO;
• the Graphics packages, which illustrate an approach to graphics combining a general form of graphics object with the Java facilities such as Swing and 2D graphics;
• the Interfaces packages which provide different inter-system interfaces including the CORBA inter-application facilities for Java, SPlus and R; inter-language interfaces between SPlus/R for each of Java, Perl, Python, etc.
• basic data-related classes in DataStructures/Data for data frames, data lists and different types of variables and a data-grid display and editor;
• XML facilities for reading and validating arbitrary documents, syntactic facilities for manipulating XML trees, and readers for data sets with specific DTDs and also facilities for parsing XML in both R and SPlus.
• a preliminary approach to expressing statistical models in Omegahat, included almost entirely to get feedback on some early approaches to defining models in Omegahat;
• a generic optimization interface in Numerics;
• Java classes that can be used with C/C++ code to provide Java access from S and R via a .Java() function.