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Progress reports, produced roughly every two months, about the toolbox interactive wiki diagrams code.
See: PR1, PR2 and PR3

Progress Report 3

For start of June 2020

Parallels: Biochemistry and Code

Two more of the diagram types are now used for both biochemistry (left) and source code (right). 760px

Here are the biology related demos.

New Features

  • Zoomable-images: Audacity's ruler zooms in steps, whereas this one and the image it gives a scale for can be smoothly zoomed and panned.
    • This is part of a 'slippy-maps'/'google-maps' style of image navigation that can be applied to generated images to reveal more detail as you zoom in. That navigation will get used for large biochemical pathways charts.


  • Chronogram
    • This is a variation on a bar chart. The chronogram is the start of unifying bar charts, spindle charts and cladograms.


  • Cell-wall diagrams
    • This 'cell wall' component repeats an object along a (Catmull-Rom spline) path. In the demo a schematic representation of a lipid is repeated to make a lipid bilayer.
  • Image transforms.
    • We can rotate and reflect any component-object. This was first needed to make zoomable rulers work in both vertical and horizontal orientation.

Incremental Improvements

  • KWIC displays
    • Now have 'zebra' striping to make it easier for the eye to follow a line.
    • Text shorter than the line is now gapped rather than being repeated to use the space.
  • Tiles Display
    • Now highlights the tile on hover
  • Fixes
    • The 'i' icon no longer flickers on a click.
    • Clicked detail panel no longer stays around longer than intended.
    • On Safari on Catalina the 'globes' plots now use the size Safari gives, rather than the size requested. This works around a bug in Safari that led to weird/distorted maps.
    • Fixed: Spurious selection when dragging on canvas.
    • Fixed: Dragging stops when we drag off screen and then return.

Recap of 'Combinatorial Features'

Combinatorial features that work with multiple or all diagram types are central:

  • The master-detail 'large tooltips' to annotate a diagram
  • The slippy-map navigation to support navigation of diagrams
  • Rotations and reflections to allow charts/diagrams in different orientations.
  • Packing into layouts (Horizontal Stack, Vertical Stack and Overlay)
  • Chooser to choose one from several choices of diagram
  • Repeating a simple diagram along a path

Lessons / Insights

  • Chronograms suggest a way to unify tree based diagrams and chart based diagrams.
  • Code keeps 'escaping' into special case methods. I need a more powerful mechanism than 'fixing it by hand' to keep the code general.