sync zoom resolution in synteny; support more than 3 genome coordinate windows

[alpapan]

it would be really nice if there was a button or function to set all the genomes to be the same scale/bp resolution in the synteny browser.
at the moment i have to do it manually using a calculator and setting the end coordinates:

one other thing i noticed is that the panel to provide coordinates for each scaffold is only available when up to 3 genomes are selected for synteny view. if a fourth one is entered, the panel disappears (presumably lack of estate space on the horizontal axis?)

finally, this may or may not be an intentional bug but when you provide multiple rows (more than 2 genomes) in the genome synteny selection view:

then you must make sure you click on the second arrow (circled red in screenshot). One issue is that the arrows have no background so it wasn't immediately obvious (yes i know, i'm dumb!), but also from a productivity PoV, it would be great if the default was populated for all pairs. The default is populated for the first pair and pressing launch is allowed even if you haven't selected anything for the other pairs. the result is a broken viewer (due to missing synteny track) with no error on why. I think the easiest solution would be to populate the first option for a synteny track for all rows/pairs of genomes (often only one is configured) just like it is done with the first pair of genomes.

hope that makes sense!

[cmdcolin]

it would be really nice if there was a button or function to set all the genomes to be the same scale/bp resolution in the synteny browser.

this exists, it is called "square view"

one other thing i noticed is that the panel to provide coordinates for each scaffold is only available when up to 3 genomes are selected for synteny view. if a fourth one is entered, the panel disappears (presumably lack of estate space on the horizontal axis?)

yes, it hides itself automatically at >3. you can show them though with search icon->Show search boxes

then you must make sure you click on the second arrow (circled red in screenshot)....it would be great if the default was populated for all pairs

yes this is the expected workflow to manually click the arrows. it might be better to make them more obvious somehow. it could also prevent you from submitting if you haven't chosen. I don't know if "autopopulating with the first item from 'existing tracks'" is the best default behavior though. maybe it is....it could just be somewhat random what syntny track you get depending on your instance

[alpapan]

yes preventing the form submittion without a track selected for each could just give a warning and solve the issue