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)

Annotations/Alignments

• MaxExpanded @
• Collapsed @
• ScrollExpanded - like MaxExpanded, but with a vertical scroll, and no max stack depth
• Depth @
• Tabular - show the data in a table like the Selection Info tab (rows/columns reversed)
• Gaps removed @ (this is in the Sliced View)

Alignments

• Mismatch @
• Mismatch Pileup @

Graphs

• Bar @
• Line @
• Dot @
• Min/Max/Avg @
• Heat Map @
• StairStep @
• Histogram
• these can be combined with the graph collapse/expand option

Operations

View Modes can be the result of an operation or series of operations on the SeqSymmetry data
e.g the not annotation operation, or the log graph operation. The view mode is on the output
SeqSymmetry of the operation.

Varying

View Modes can be varying, depending on the view state, for example for a zoomed out annotation,
the depth view mode is shown, but when zoomed in, the MaxExpanded annotation view mode is shown.

Notes

• some of the view modes can be options, like collapsed/expanded graphs, or
  Gaps Removed for annotations, or histogram bin width for graphs.
• The different View Modes can have parameters, like the user options in the track preferences.
  These same options can be instead linked to the data.

discussion

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Hi,

For Operation View Mode,
I have added a popup menu called "Transform". It holds all transformation that applies to current file type category. Once a transform is applied, it starts with a default view mode based on output.

This view mode can be changed from popup menu called "View Mode".

Are you ok with this? Or would like to change these behavior?

–
Hiral
=======
I liked your other idea to put Transform (Operation?) in a top-level menu.

But this can work too.

I think that at this moment, we can't be sure what the best UI solution will be. For this, we'll need to try it with users. The important thing is to be flexible so that we can quickly iterate the design as we learn more about how users (apart from ourselves) will work with it.

-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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