SBGN brick: Post-translational modification

[ugurdogrusoz]

Let's implement this set now according to the guidelines, reusing as much code as possible where it makes sense.

[ugurdogrusoz]

I don't see the dropbox to determine the subtype (phosphorylation, etc.)?!

[msalihaltun]

I can see them right now. Yours looks like yesterday's version somehow.

[ugurdogrusoz]

Based on the feedback from Alexander & Adrien, let's allow the user to:

• [x] Add multiple modifications (row with dropdown box containing different types of modifications and the Residue field could be increased to be 1 or more), each having a possibly different modification (e.g. 2 phosphorylations and 1 methylation).
• [x] We should get rid of the square brackets we have when there is a residue provided.
• [x] I suggest we get rid of the checkbox for Residue and assume there is no residue when nothing is input to simply UI.
• [x] Add a checkbox for Multimer to describe the input and output macromolecules (put this after Input & Output as checkbox in the middle of the row?).
• [x] When Multimer is checked (both Regulator and Input/Output pair), we should enable the count (2 by default) next to "Multimer" and allow it to be an integer that is 2 or more. This will be reflected in the the macromolecule as a Unit of Information with label "N:2", "N:3", etc.
• [x] Turns out a catalysis arc cannot be connected to Nucleic acid feature, Perturbing agent, and Source and sink. So, let's remove these from the associated dropdown box.

[ugurdogrusoz]

• [x] Let's please change the tooltip for multimer count to "Integer value of at least 2"
• [x] This count should be grayed out unless Multimer is checked.
• [x] Multimer checkbox should be succeeded with a count (just like in Regulator).

[ugurdogrusoz]

• [x] change multimer count infobox to "unit of information" (not "state variable")
• [x] let's experiment with the idea to perform an auto-resize to input and output macromolecules as new units of information are added or deleted (resize node to content for both input and output)

[msalihaltun]

Auto resize does a couple things that may be an issue. First is, at first macromolecules are smaller in width because of the resize. And when many units of information are added, since position was determined before node creation, they get very close to, or even overlap with, the process node.

[msalihaltun]

I will make another small change to dynamically change position after resize.

[msalihaltun]

I made the change now, it should be okay.

[ugurdogrusoz]

It'd be nice if auto-resize took the node label into account as well.

[msalihaltun]

Should be okay with https://github.com/iVis-at-Bilkent/chise.js/commit/148442f3e623c03201dc0456aa146b37767550e0

[ugurdogrusoz]

Thanks auto-resizing is working nicely now but as that happens we lose the vertical alignment (top-to-bottom layout):

[msalihaltun]

Seems I overlooked the fact that I need to consider orientation as I reposition the nodes getting larger.