Closed ozgunbabur closed 6 years ago
The relevant part of the code to change this is below.
There is some bug in the implementation. Try loading below sif (remove the .txt extension, github does not let me load .sif directly).
You will see that compound members are mostly ordered alphabetically. Mostly! Look at the end of them.
@ozgunbabur getWith()
in https://github.com/PathwayCommons/chibe/blob/master/src/main/java/org/gvt/layout/BiPaLayout.java#L287 is calling shiftToLastRow()
. It seems that this call is the reason of the bug. Shall I remove that call and the method itself as well if it has no other usage?
Yes, I don't see any reason a getter method should modify the organization. Please try removing it.
On Fri, Jan 5, 2018 at 11:00 AM, metincansiper notifications@github.com wrote:
@ozgunbabur https://github.com/ozgunbabur getWith() in https://github.com/PathwayCommons/chibe/blob/master/src/main/java/org/gvt/ layout/BiPaLayout.java#L287 is calling shiftToLastRow(). It seems that this call is the reason of the bug. Shall I remove that call and the method itself as well if it has no other usage?
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/PathwayCommons/chibe/issues/69#issuecomment-355636943, or mute the thread https://github.com/notifications/unsubscribe-auth/ABUCCx06b_o7-Chqtj4BMrNj-ljKMLqQks5tHnFqgaJpZM4RIsFo .
I removed it in PR #71
ChiBE tiles the members of a Complex in mechanistic view, similarly when rendering a SIF network, ChiBE groups the nodes with the same topology, which helps for complexity management. However, when the compound node has too many members, it becomes difficult to find a member because they are not sorted alphabetically.
The current design of the tiling algorithm does not allow for sorting members because the tiling is not performed first left-to-right then up-to-bottom. Current algorithm always try to maintain a square while the compound grows with new members, hence it grows from topleft-to-bottomright. We may consider changing this design to favor member sorting.