Glossary - arklumpus/TreeViewer GitHub Wiki

Action module

Module used to perform a one-time action.

Attachment

A blob of data that is included together with the tree; it can represent anything, from an image file, to node states data.

Coordinates module

Module used to compute the coordinates of the nodes of the tree in the plot.

File type module

Module used to make TreeViewer compatible with a specific file type. File type modules usually declare their ability to open a file and read the trees from it one at a time as instructed by the Load file module.

Final transformed tree

The final tree that is actually plotted, after all the Further transformation modules have acted on it.

First transformed tree

The tree produced by the Transformed module, before the action of any Further transformation modules.

Further transformation module

Module used to alter the phylogenetic tree before it is drawn.

Load file module

Module used to load trees from a file and make them available to the program, either by directly storing them in system memory, or by providing a transparent interface to other means of storage.

Loaded trees

The list of (one or more) trees that have been read from the tree file and loaded.

Menu action module

Module used to perform a one-time action that is activated by clicking on a menu item.

Open file module

Another name for a File type module.

Plot action module

Module used to draw a single plot element (e.g. branches, labels...).

Selection action module

Module used to perform a one-time action that involves the node on the tree that is currently selected.

Transformer module

Module used to transform the (possibly many) trees that have been loaded from a file into a single tree that will be plotted.