General Modularity Example Module Projects & Files Commands & Scripting Windows Menus Charts Tables Buttons & tools Trees and Taxa Characters & Models Documentation General Utilities Table of Contents Overview To Do: issues and problems Home page of user's manual User's introduction to how Mesquite works Classes and Interfaces (javadoc output)

Source code now available at http://mesquiteproject.org/mesquite/download/source.html

Mesquite documentation for developers

W. Maddison (updated April 2000)

The developer's documentation for the Mesquite system is incomplete, and is considerably out of date in places.

Table of Contents

• General
  • Overview of developer's documentation
  • Home page of user's manual
  • User's introduction to how Mesquite works
  • Classes and Interfaces (javadoc output)
• Modular architecture
  • Developer's introduction to modularity
  • User's introduction to modularity
  • Modules: subclasses of MesquiteModule
  • Modules employing other modules
  • Duty Classes
  • Writing modules
  • Documentation for particular modules
  • Packages of Modules
  • Also: class MesquiteModule
• An example module: a simple tree window
  • Introduction to the Baby Tree Window module
  • The module's source code
  • Employing other modules
  • Menus
  • Commands & snapshots
  • Automatic documentation generation
  • Windows
• Projects and files
  • Introduction -- 1999
  • Reading and Writing NEXUS files -- 1999
  • An example module that reads a NEXUS block
  • Preferences -- 1999
  • Also: Saving the current state of calculations and windows
  • Also: User's introduction to projects and files
  • Also: class MesquiteProject
  • Also: class MesquiteFile
• Commands & Scripting
  • Commands -- 1999
  • Scripting
  • Snapshots -- 2000
  • Macros
  • Cloning windows
  • Also: User's guide to scripting language
  • Also: class MesquiteCommand
  • Also: interface Commandable
  • Also: class CommandChecker
  • Also: class Snapshot
  • Also: class Puppeteer
• Windows & display units
  • Windows -- 1999
  • Special subclasses of windows
  • The window information bar -- 1999
  • Tool palettes
  • Panels, labels
  • Clocks
  • Also: Windows in an example module
• Menus
  • Menus -- 1999
  • How to add menus and menu items
  • Where menus get added
  • Also: Menus in an example module
• Charts
  • Charts -- skeletal
  • ChartWindow
  • Charts in an example module
• Tables
  • Tables -- 1999
  • TableWindow
  • Tables in an example module
• Buttons and Tools
  • Buttons and tools -- 1999
  • Tool palettes
  • Tools in an example module
• Trees and terminal taxa
  • Taxa
  • Managing taxa blocks
  • Trees
  • Tree blocks and managing tree blocks
  • Tree Drawing
• Characters and models
  • Character data
  • Example module using character data
  • Character models
• Documentation
  • Mesquite's automatic documentation system
  • Command explanations
  • Menu and control explanations
• General utilities
  • Special objects for handling numbers
  • String manipulation
  • Utilities & interfaces