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Add feature threshold indicator to zoom widget #1196

Merged
merged 4 commits into from
Jan 21, 2023
Merged

Add feature threshold indicator to zoom widget #1196

merged 4 commits into from
Jan 21, 2023

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lbergelson
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@jrobinso
This is a minor feature that I have wanted in the past so I figured I would try implementing it. Good learning project to play with some of the stuff I haven't touched yet.

  • implementing getVisibilityWindow() on coverage and alignment tracks
  • Adding an indicator to the Zoom control to show which zoom levels will display reads / features

This is what it looks like when there are 2 different thresholds set (variants AND reads) notice the two shades to indicate the separate thresholds.

Screen Shot 2022-08-16 at 3 33 45 PM

I implemented it in a kind of hacky way so I'd really like to hear feedback about better ways to get the threshold from the tracks into the widget without poling through them each time you redraw. It's probably not that expensive so it may not be worth doing anything smarter.

Also happy to change the look of it.

@jrobinso
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This is a neat feature, however we can have many tracks loaded each with a unique visibility window. Think of 10 or 20, a combination of VCF, bigBed, and indexed annotations. This is not uncommon as you might think.

@lbergelson
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@jrobinso If they all implement getVisibilityWindow() then it should pick up all the thresholds and display them all, although the color will probably saturate and be hard to see if you have too many.

jrobinso
jrobinso reviewed Jan 10, 2023
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src/main/java/org/broad/igv/ui/panel/ZoomSliderPanel.java

transGraphics.setColor(TRANSPARENT_BLUE);
Rectangle maxZoom = zoomLevelRects[zoomLevelRects.length - 1];
for (Integer window : visibilityThresholds) {
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There's a bug here somewhere, array index can be negative. I'll drop more details in the "conversation" widget

@jrobinso
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@lbergelson Looks good overall, but there is a bug. I'm not sure how I got in this state, but here are the previous steps

(1) load the session test/sessions/base_mods/HiFi_basemodfications.xml from the repository (File > Load Session...)
(2) From "Load from server" loaded Common Snps 1.4.2 from "Annotations - Variations and Repeats", and "Gencode v4.0" from "Annotations - Genes".
(3) Set the visibility window of the Snps track to 1, visibility window of Gencode track to -1.
(4) Tried to remove the alignment & coverage tracks to see effect on zoom bar, at this point I noticed it was frozen and stack trace. I'm not sure when the stack trace was created, it could have been prior to (4)

SEVERE [Jan 10,2023 09:53] [DefaultExceptionHandler] java.lang.ArrayIndexOutOfBoundsException: Index -3 out of bounds for length 22
	at org.broad.igv.ui.panel.ZoomSliderPanel.paintVisibilityThresholds(ZoomSliderPanel.java:222)
	at org.broad.igv.ui.panel.ZoomSliderPanel.paintHorizontal(ZoomSliderPanel.java:204)
	at org.broad.igv.ui.panel.ZoomSliderPanel.paintComponent(ZoomSliderPanel.java:122)

@lbergelson
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@jrobinso Good catch. I'll look into that.

@lbergelson lbergelson self-assigned this Jan 11, 2023
lbergelson and others added 4 commits January 20, 2023 11:05
@lbergelson
implementing getVisibilityWindow()
dc1454b
@lbergelson
Add feature threshold indicator to zoom widget
0da82e6 
* Add an indicator to show which zoom level will start dispalying features/reads
* closes #1192
@jrobinso @lbergelson
Reduce transparency value for zoom slider viz window indicator to "25".
349347e 
Update text session xml
@lbergelson
fix exception when feature window size was larger than the contig length
82813f4 
* extracted a log2 function instead of using a wierd static log2 constant everywhere
@lbergelson
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@jrobinso I believe I have fixed the issue. It seemed to occur when the feature window was larger than the current chromosome length causing it to produce a negative log value. I capped the window length when calculating the zoom now so there shouldn't be anymore negative numbers there.

@jrobinso jrobinso merged commit 0e41fbf into master Jan 21, 2023
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Looks good now

@jrobinso jrobinso deleted the lb_add_zoom_indicator branch January 21, 2023 05:37
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