wiki:MindSeer_Package_Guide

Version 2 (modified by ebmoore, 11 years ago) (diff)

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Package Overview

While there are many packages in MindSeer, there is a method to the madness. To begin with, a good deal of the structure is designed to eliminate circular dependencies. Also things are split up so that some packages could be broken off with relatively little work for use in other projects.

edu.washington.biostr.sig

Packages in this hierarchy are owned by the University of Washington and the long name follows Java guidelines. This also includes 3 classes. These classes handle creating and managing objects with unique ids across communicating platforms. This is also where the base class for SynchronizationObserver? lives.

brainj3d

These files are what make up MindSeer.

colors

Colors contain classes related to color schemes (which assign colors to intensity values) and some utilties (class Colors) for converting strings to colors and back again.

controls

These are custom SwingHTMLObjects and collections. They are in a separate package because they are compiled into the Client version.

core

The core comprises the central classes for ensuring that MindSeer works. These include most communication links, the client UI, the Viewport, MindSeer specific Data Set classes (the generic classes are in the vault package) and the security protocol.

client

This includes the Client Manager (which manages communication and acts as a central hub), the callback mechanism, and the client UI (the menus and the base class for Layout Managers).

guicomponents

These are client specific user interface items like the Splash Screen during login and the popup to save data.

layout

Concrete implementations of Layout Managers and helper files live here.

display

These classes extract user displayable names for objects in trees and lists.

files

Files contain the MindSeer specific data set details. These refer to the Data Set as a Workspace and include details on creating a tree for the data set.

security

The security files contain the details on establishing and enforcing permissions for users and groups. This delves heavily into the Java security model. Most of these are package private for security purposes.

vault

The vault classes were originally conceived as a library for metadata about files. It is not known if this library could be used externally from MindSeer. It contains most of the MindSeer independent logic for displaying, querying and building a data set. The original design was a little ambitious and so users can create alternate backing stores using databases or basic maps.

core

These are the central classes for creating nodes, associating meta data and creating collections (DataVault?) of files with metadata. It also contains classes to execute queries.

display

This includes classes for displaying and rearranging trees in Swing.

files

These classe include filters for file types and utilities for files.

remote

These classes were supposed to handle synchronization of the vault. They are not used or tested.

xml

The xml package contains classes to convert a Data Vault to or from XML.

nifti

Generic NIFTI classes live here. They can be used as an external library for reading NIFTI files. Because it also handles SPM's transform, this library depends on matfile.

matfile

These classes are responsible for reading a Matlab version 4 or 5 file and converting it into Java objects. They are a separate library from MindSeer.

org.eiderman

Packages in this hierarchy are copyrighted by Eider Moore. They were from his personal library and released under the LGPL.