MesquiteButtons are objects that draw on-screen images and have an on and off state, and when touched they call a MesquiteCommand that is associated with each. Currently these are used for the tools in the tool palettes.
Tools in the sense of selectable cursors are MesquiteTool objects. These include the TreeTools, which have associated MesquiteCommands for touching branches, dropping branches, and touching taxon names. If the tool is touched or dropped, the appropriate MesquiteCommand is called with branch numbers passed as parameters. There are also TableTools for the editors of Character Data.
Tools currently are shown in ToolPalettes, which each MesquiteWindow can show on its left side if its setPalette(ToolPalette palette) method is called.