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

Mesquite Development Reference

W. Maddison (updated August 2005)

The best way to learn how to program for Mesquite is to look at example source files, e.g. at mesquite.examples. We are building some tutorials with examples. This reference documentation is incomplete, and it may be out of date in places.

Table of Contents

• General
  • Overview of developer's documentation
  • Home page of user's manual — see Mesquite_Folder/docs/mesquite/manual.html or the current version online.
  • User's introduction to how Mesquite works — see Mesquite_Folder/docs/mesquite/howMesquiteWorks.html or the current version online.
  • Classes and Interfaces (javadoc output) See especially the package mesquite.lib.
• 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
• Package of example modules
  • directory of mesquite.examples
  • Downloading and compiling example modules with eclipse
• 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
  • Reading and Writing NEXUS files
  • Preferences
  • 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
  • Scripting
  • Snapshots
  • 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
  • Special subclasses of windows
  • The window information bar
  • Tool palettes
  • Panels, labels
  • Clocks
  • Also: Windows in an example module
• Menus
  • Menus
  • How to add menus and menu items
  • Where menus get added
  • Also: Menus in an example module
• Charts
  • Charts
  • ChartWindow
  • Charts in an example module
• Tables
  • Tables
  • TableWindow
  • Tables in an example module
• Buttons and Tools
  • Buttons and tools
  • 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