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LegumeFederation / cmap-js

Display and compare biological maps (genetic, physical, cytogenetic, genomic, linkage groups, chromosomes, scaffolds).
GNU General Public License v3.0
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manually adding a second track just alters both new and old track #92

Closed bradfordcondon closed 6 years ago

bradfordcondon commented 6 years ago

I have SNP and microsatellite markers. I press + on the right site, add microsat in red to the right.

screen shot 2018-05-11 at 10 44 50 am

OK, great. I then press the + on the left side of the map. I add the SNP markers, in green.

screen shot 2018-05-11 at 10 45 06 am

Now I have two snp marker tracks on the left in red.

awilkey commented 6 years ago

Is this the fulll steps to reproduce? I can't think offhand what would lead to this behavior, but I will take a look into it.

bradfordcondon commented 6 years ago

I actually cant reproduce with your default configuration. so maybe something about my input or configuration?

Here is mine... https://gist.github.com/bradfordcondon/f6e8210672e737ef9823c943333d7b96

awilkey commented 6 years ago

Out of curiosity, can you replicate the behavior on the default configuration on the "gm_genome glyma.Chr01" track (track 3)?

bradfordcondon commented 6 years ago

yes! exactly as described above.

awilkey commented 6 years ago

Ok, I think I know exactly what's breaking. I should have a patch ready this afternoon.

bradfordcondon commented 6 years ago

Great, thank you!

Semi related question, how can these tracks (marker tracks) be pre-defined in the configuration json? The documentation says track types are only for QTL and manhattan but clearly marker works too?

awilkey commented 6 years ago

QTL is a bit of a minsomer from early development. Markers are drawn as a QTL track, but the format is set with a minimum height to account for markers and other one-dimensional data points that may need to be displayed off the map backbone.

awilkey commented 6 years ago

Could you pull the bugfix/trackdup branch and check to see if the behavior persists? I think it should be fixed, but would like a second set of eyes.

bradfordcondon commented 6 years ago

This is the results of first adding snp tracks on left as red, and then adding synteny tracks on right as blue

screen shot 2018-05-11 at 2 41 38 pm
awilkey commented 6 years ago

I just tried the exact same thing, and didn't have an issue off the same branch (though there are some definite issues with the really long labels I need to look into...)

screen shot 2018-05-11 at 13 48 05

bradfordcondon commented 6 years ago

are you scrolling to the right to get to the third map or removing? I'm having complicating issues with scrolling and the brown linking lines that may be contributing to the problem...

awilkey commented 6 years ago

Scrolling, there is some work being done at the moment to make scrolling easier, but right now the most responsive way is to actually click and drag in alpha warning box. (Hit detection if you allow the default window scrollbars to populate tends to get hijacked by the feature canvases before it reaches the scrollbar.)

bradfordcondon commented 6 years ago

yes scrollign in the alpha warning box does help a lot.

OK I also was not hitting "apply" in the color change box.

screen shot 2018-05-11 at 2 59 18 pm

So I guess the issue is resolved, thank you

awilkey commented 6 years ago

Good! I'll merge the patch directly into both master and develop and close, as it is a simple enough fix.