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cmdcolin / mafviewer

A JBrowse plugin to view multiple alignment format (MAF) files
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alter color scheme for adjacent alignment blocks #11

Open rdhayes opened 7 years ago

rdhayes commented 7 years ago

With plant data, we are seeing a good number of alignments blocks that are contiguous, but contain different query fragments. These render and look like a single block.

Options we are considering: 1) color start and end residues differently 2) alter hue of the color scheme for alternating blocks (unclear how easy that would be with lineToFeature Parser calls happening asynchronously.

Possibly related, is it also possible that the mouseover image map for contiguous blocks overlaps itself? We are seeing some of the segments in a group like this not respond to a click event.

Again, this might be more clear once I have a public test browser available...

cmdcolin commented 6 years ago

Are there any updates for this?

cmdcolin commented 6 years ago

I would suggest that this is basically outside the scope of this plugin. If you feel differently I guess I am open to suggestions though.

My reasoning: The concept of different parts of the query sequence being assembled into a contiguous chain seems essential to just what the "chaining and maffing" algorithms do. If you need more nuanced detection of boundaries I think we need a special "chain" type track that shows such things. The MAF track already has a lot of things going on, and perhaps a specialized "chain" track that illustrates boundaries and such is useful.

cmdcolin commented 6 years ago

On another note, mouseover/clicking were very glitchy and are disabled for now. Will re-enable if it can be made better.