wikipathways / cytoscape-wikipathways-app

WikiPathways app for Cytoscape to open and access pathways from WikiPathways
Apache License 2.0
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split edge paths #42

Closed AlexanderPico closed 7 years ago

AlexanderPico commented 7 years ago

To be considered as a special case, I noticed that any edge with an anchor is actually translated into 2 edges into Cytoscape! This is a nifty trick, but certainly breaks any hope of reusing PathVisio code or waypoints.

Currently, for example, the lower left transport of Cholesterol out of the Enterocyte was originally a single line. In Cytoscape it is now 2 lines and each line has the SAME pair of original waypoints. This is why those lines looks so crazy.

If we are going to split lines into two segments, we'll have to devise a new way to calculate the waypoints... MIght be too difficult! Should we try drawing the original lines without splitting them?

AdamStuart commented 7 years ago

Yes, I brought this up yesterday.
But currently you can move waypoints and NOT nodes, so the fix includes unlocking node position.

On Aug 3, 2017, at 5:19 PM, Alexander Pico notifications@github.com wrote:

To be considered as a special case, I noticed that any edge with an anchor is actually translated into 2 edges into Cytoscape! This is a nifty trick, but certainly breaks any hope of reusing PathVisio code or waypoints.

Currently, for example, the lower left transport of Cholesterol out of the Enterocyte was originally a single line. In Cytoscape it is now 2 lines and each line has the SAME pair of original waypoints. This is why those lines looks so crazy.

If we are going to split lines into two segments, we'll have to devise a new way to calculate the waypoints... MIght be too difficult! Should we try drawing the original lines without splitting them?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/wikipathways/cytoscape-wikipathways-app/issues/42, or mute the thread https://github.com/notifications/unsubscribe-auth/AHSv7Qs8bzLb5RsmhX6a6NptW0_ZHNLwks5sUmObgaJpZM4OtIxE.

AlexanderPico commented 7 years ago

Much improved! Now it is really easy to make minor fixes to edges and anchor positions in Cytoscape.

But for WP430, I still an issue for the edge from Lipoprotein to HDL. It's bending is the completely wrong direction. Any guesses?

screen shot 2017-08-06 at 2 49 58 pm
AlexanderPico commented 7 years ago

It's probably time now to test with series of many possible edge paths. See test GPML from Anders...

AlexanderPico commented 7 years ago

The issue is with RelX=0.5 (or -0.5) rather than integer....

test1 gpml

AdamStuart commented 7 years ago

fixed but needs more testing

AlexanderPico commented 7 years ago

Ah, noted the new app name and tested again... It works with WP430 and other related test files.