A Visual Language for Browsing, Undoing, and Redoing Graphical Interface Commands

We present the concept of an editable graphical history that allows the user to review and modify the actions performed with a graphical user interface. Using a pictorial metaphor borrowed from comic strips, an editable graphical history consists of a series of panels that depict in chronological order the important events in the history of a user's session. We discuss the visual language used in editable graphical histories, and describe Chimera, a graphical editor that generates these histories automatically. The user may scroll through the sequence of panels, reviewing actions at different levels of detail, and selectively undoing, modifying, and redoing previous actions. Chimera's editable graphical histories are constructed from parts of the editor window, the editor control panel, and the editor's pop up menus. Panels indicate both the objects that are modified and the actions performed on them. We describe the heuristics used to determine the objects depicted in each panel, the style in which they are drawn, and how actions are distributed among panels

TreeDyn: towards dynamic graphics and annotations for analyses of trees

BACKGROUND: Analyses of biomolecules for biodiversity, phylogeny or structure/function studies often use graphical tree representations. Many powerful tree editors are now available, but existing tree visualization tools make little use of meta-information related to the entities under study such as taxonomic descriptions or gene functions that can hardly be encoded within the tree itself (if using popular tree formats). Consequently, a tedious manual analysis and post-processing of the tree graphics are required if one needs to use external information for displaying or investigating trees. RESULTS: We have developed TreeDyn, a tool using annotations and dynamic graphical methods for editing and analyzing multiple trees. The main features of TreeDyn are 1) the management of multiple windows and multiple trees per window, 2) the export of graphics to several standard file formats with or without HTML encapsulation and a new format called TGF, which enables saving and restoring graphical analysis, 3) the projection of texts or symbols facing leaf labels or linked to nodes, through manual pasting or by using annotation files, 4) the highlight of graphical elements after querying leaf labels (or annotations) or by selection of graphical elements and information extraction, 5) the highlight of targeted trees according to a source tree browsed by the user, 6) powerful scripts for automating repetitive graphical tasks, 7) a command line interpreter enabling the use of TreeDyn through CGI scripts for online building of trees, 8) the inclusion of a library of packages dedicated to specific research fields involving trees. CONCLUSION: TreeDyn is a tree visualization and annotation tool which includes tools for tree manipulation and annotation and uses meta-information through dynamic graphical operators or scripting to help analyses and annotations of single trees or tree collections