out of date content - available for reference purposes only

View Modes

under construction 

IGB will have the ability to display features using different methods called View Modes.
Each View Mode will only be appropriate to certain feature types. (@ indicates an existing mode)

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-Ann
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Michael and I had a long talk about this yesterday (the various ways that the user
can view/modify the data) and we thought we should go over this with the group at
some point.

Some points to consider:

• the view modes can do two things, one is just redisplay the track differently, the
  other is to show the new view mode in a new track, like the
  Make Annotation Depth Graph menu item.
• the user can make some pretty complicated operations on the data. We could have
  a panel the graphically displays how the track was created. The user could even
  click on one of the intermediate steps to see that data in a new track. For example:

abc.bed
\
(merge) - * - (not) - * - (depth) - *
/ \
def.bed \
(ratio) - mygraph.wig
uvw.bedgraph /
\ /
(median) - * -
/
xyz.wig

where * is an intermediate file (yes, no one would do this in real life).

• we want them to be able to be efficient, that is, to operate on a small zoomed in region
  (if possible) rather than have to process the entire chromosome every time.

Lance
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Thinking about this some more, the current approach makes sense for now. A view mode is at some level at "template" for a plot. The template will include things like: the geometric primitive that is drawn, and the scales from the data to the visual attributes of those primitives. Plots also often have a "statistical computation" associated with them, e.g., with histograms.

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