A place to start listing and ranking features for the large tree viewer

Major features

• Lookup table with names for internal nodes (default or custom)
• Change both height and width of 'blue rectangle'
• Clade based focus (select a clade and that defines window) - snap to clade (default & optional)
  • both on left and right windows
• Saving views, bookmarks
• Mouse over detail on triangles - show names, numer of species, subtrees
• Display branch lengths & scale bar
• Scroll through labels in a collapsed triangle
• Highlighting one or more labels as landmarks
• Not show species names unless displaying a tip (if lookup table available)
• Split screen on main viewer area, i.e. to compare depth / timing between clades
• User configuration of tools (add tools to toolbar) for select, zoom, collapse, annotate, etc
• Input / output NeXML & PhyloWS
• Support presentation: Export as svg, pdf, jpeg, etc
• Find most recent common ancestor of two nodes, highlight path
• Get info on clades (number species, depth, newick string, subtree length, time)

Long term features

• Other layouts - rectangular, circular, unrooted, etc. This is the highest priority item for round 2
• Autopruning - of branches and labels
• Ability to edit tree (and output saved tree)
• Select a label for 'guaranteed visibility' - this is likely out of scope
• Merging & assembling trees

Necessary but (hopefully) small

Search for labels
Re-root
Ability to ladderize
Rotate clades
Rotate whole tree so that labels are across top rather than down side
Manually collapse clades
Ability to change fonts
Even up the triangles (i.e. isoceles)

Notes from telecon with Tamara

Adam, Mike, Karen and Tamara met via webex on March 2 to discuss the prototype. Here are the notes from that conversation:

• think about how the application would behave not only as the main focus window, but also as a 'helper' application to something else. What would the view look like?
• the current view has three vertical panes: overview, detail of branching and names. The user should be able to adjust the width of each one.
• should be able to get 80% of the functionality of Guaranteed Visibility with a fairly small amount of work. Have a small set of interesting nodes / landmarks, but don't try and deal with the sub-pixel issues.
• for very large trees, perhaps there should be one or more intermediate views (right now, we have two). There is lots of available screen real estate in the main viewer.
• investigate having a few labels / landmarks on the overview tree (small, perhaps at an angle to reduce space).
• Top 10 list of landmarks, or some sort of importance measure for landmarks (could this be learned from the users in the various views of the DE?)
• Use search results as landmarks for Poor Man's Guaranteed Visibility (overwriting what landmarks might already be there)
• if we implement manual collapse of nodes, how do we incorporate this into the automated expand & collapse. Collapsed nodes have a different icon and user would have to manually un-collapse. Should be an Un-collapse All option.
• Path highlighting in both windows
• Triangle "height". In the current version, sister clades that are collapsed can be at different depths. This is a function of the layout algorithm and the structure of the subtree, but implies something about the relative age / height of the clades. This is probably a more important issue in Presentation mode than in Browsing mode, and fixing it might make the zooming jumpy. So, perhaps an Equal Height for Sister Clades option that the user can turn off / on and would be off by default