SunnyXu / SBMLDiagrams

MIT License
5 stars 1 forks source link

Version 2: Convert Anna Deckard's Autolayout to python or reuse libSBNW #71

Open hsauro opened 2 years ago

hsauro commented 2 years ago

Anna Deckard wrote quite a good autolayout algorithm for biochemical networks. The original code is in C# but there is also a C translation written by Medley.

It would be useful to have access to this algorithm in SBMLDiagrams V2. Two possibilities, translate the C# code to Python and develop a cross-platform package that can be used from Python. It might be easiest however to use the Medley code, libSBNW but you'll have to create cross-platform versions which might be a problem. However, that might already be solved in the GitHub SBNW repository

If you convert Anna's C# code to python this eliminates the cross-platform issues but it would take longer to do. Decide which approach you want to use.

The C# code can be found here:

https://sourceforge.net/p/jdesigner/code/HEAD/tree/trunk/csharp/SBWautolayout/DrawNetwork/AutoLayout/

The C/C++ code can be found here:

https://libsbml-draw.readthedocs.io/en/latest/_downloads/libsbml_draw.pdf

https://github.com/sys-bio/libsbml-draw