Add new menu items for show/hide feature labels, set max height, and set compact display mode

[cmdcolin]

This adds

• Track menu item to show/hide feature labels
• Set compact setting on the features
• Also adds a maxDisplayedBpPerPx default, which is otherwise unset on normal BasicTrack, allowing it to not try to render gigantic regions when too far zoomed out (we instead get a prompt where you can force render)

I think these things are helpful add ons to the BasicTrack concept
Since this track type actually works in tandem with the SvgFeatureRenderer closely, it is in the plugins/svg

Possibly we could imagine de-emphasizing the svg'ness, so I just call this a FeatureTrack

[codecov]

Codecov Report

Merging #1394 (aa7b852) into master (d4bd417) will decrease coverage by 0.05%.
The diff coverage is 51.51%.

@@            Coverage Diff             @@
##           master    #1394      +/-   ##
==========================================
- Coverage   58.83%   58.78%   -0.06%     
==========================================
  Files         450      452       +2     
  Lines       20845    20847       +2     
  Branches     4941     4942       +1     
==========================================
- Hits        12265    12255      -10     
- Misses       8272     8283      +11     
- Partials      308      309       +1     

Impacted Files	Coverage Δ
plugins/filtering/src/index.ts	100.00% <ø> (ø)
plugins/lollipop/src/index.ts	100.00% <ø> (ø)
...g/src/SvgFeatureRenderer/components/Subfeatures.js	11.11% <0.00%> (-1.39%)	⬇️
...rc/LinearPileupDisplay/components/SetMaxHeight.tsx	7.69% <7.69%> (ø)
...c/LinearFeatureDisplay/components/SetMaxHeight.tsx	7.69% <7.69%> (ø)
...lugins/alignments/src/LinearPileupDisplay/model.ts	73.25% <54.54%> (+3.76%)	⬆️
...near-genome-view/src/LinearFeatureDisplay/model.ts	67.39% <67.39%> (ø)
...nome-view/src/LinearFeatureDisplay/configSchema.ts	100.00% <100.00%> (ø)
plugins/linear-genome-view/src/index.ts	91.66% <100.00%> (+2.77%)	⬆️
...gFeatureRenderer/components/SvgFeatureRendering.js	55.55% <100.00%> (+0.35%)	⬆️
... and 28 more

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[rbuels]

with the merger of #1398, seems like this needs to be updated?

[cmdcolin]

I could update but technically the displaymode took the name FeatureTrack. Should it be renamed back to BasicTrack and then this stays being FeatureTrack?

[garrettjstevens]

I think this would fit best being converted to a new display of FeatureTrack

[cmdcolin]

Started trying out the conversion to a so called "LinearFeatureDisplay"

Gives an error on opening the track though

[cmdcolin]

index.js:1 Warning: React.createElement: type is invalid -- expected a string (for built-in components) or a class/function (for composite components) but got: undefined. You likely forgot to export your component from the file it's defined in, or you might have mixed up default and named imports.

Check your code at BaseLinearDisplay.tsx:91.
    in wrappedComponent (at TrackContainer.tsx:128)
    in div (at TrackContainer.tsx:123)
    in div (created by ForwardRef(Paper))
    in ForwardRef(Paper) (created by WithStyles(ForwardRef(Paper)))
    in WithStyles(ForwardRef(Paper)) (at TrackContainer.tsx:111)
    in div (at TrackContainer.tsx:98)
    in TrackContainer (at LinearGenomeView.tsx:83)
    in div (at TracksContainer.tsx:169)
    in TracksContainer (at LinearGenomeView.tsx:69)
    in div (at LinearGenomeView.tsx:46)

[cmdcolin]

Works now...very cool...

Is there a way to make LinearFeatureDisplay the default of FeatureTrack? It seems to be already the default but is there a way to ensure that?

[garrettjstevens]

By default it goes off the order the displays are registered. If you want to make a display that's registered later the default or want to be extra sure a display is default, you can see an example of how the AlignmentsTrack prioritizes the LinearAlignmentsDisplay in plugins/alignments/src/index.ts (comments in the code).

[cmdcolin]

I think I dont have a handle on the track type whereas the alignments track says track.addDisplayType

[cmdcolin]

Regarding #1398 I mentioned that being able to toggle for example a gene track into a lollipop track was somewhat weird to me

One possibility is that this PR replaces the existing FeatureTrack concept, and then the other things turn back into other track types or display types that are unrelated to featuretrack

[cmdcolin]

This is not implemented yet but could be an option

[cmdcolin]

Note that #1398 had a discuss in meeting tag maybe related to this

[garrettjstevens]

A few comments:

• If this only works with the SvgFeatureRenderer, maybe it should limit it to that renderer only in the config schema instead of all renderers
• Having "Display mode" and "Display types" in the track menu seems confusing. Maybe call it "feature display mode"?
• Having the feature display mode and show/hide labels in both the model and in the config seems to make it so that in some cases, changing them in the config doesn't do anything anymore.

[cmdcolin]

Might end up that we change this from being a new display mode for FeatureTrack to maybe a new track type like GeneTrack, which can implement more specialized logic that helps gene features (e.g. custom widget, maybe other things)

[cmdcolin]

I refreshed this branch.

It makes it so FeatureTrack by default only has one displaymode registered to it, so that a gene track for example cannot be toggled into a lollipop via the track menu

[cmdcolin]

Some cases, the max height indicator is not displayed on, for example, the GFF3Tabix volvox track if I use "Set max height" dialog to make it 20. At 40 it does work. Unclear what the reason is, but it does work for the purpose of increasing max height if you hit the limit