uberlibsbgn

API goal

// simplest building possible
Macromolecule m = new Macromolecule("PROT") // don't care about id
  .position(10,10)                          // don't care about sizes
  .addUnitOfInfo("receptor", TOP)           // don't care about computing auxiliary bboxes              
  .multimer();                              // don't care about class name management
  
// simple checks
m.hasUnitOfInfo(regexp);
m.isIn(complexOrCompartment);
m.getOutgoingArcs();
m.getDirectNeighbors();

// simple composite management
complex.include(m);
complex.getSubunits();
compartment.getIncluded();

// easy and efficient indexing
map.getAll("macromolecule");
map.getTopLevelGlyphs();

// easy traversing
map.visitRecursive();
map.visitEPNs();
map.visitTopLevel();

TODO

• finish index manager rework
• ports
• get rid of fluent glyph setters, impossible to keep it consistent
• start notes and extension
• style management (find good lib for color and gradient management, javafx should do)
• RDF (with rdf4j probably)
• interface with some graph lib (jgraphT probably)
• use jsoup for notes management and possibly extensions
• refactor glyph factory/builder
• more complete id management allow ids from sbgnml for arcs and aux units, maybe other entities
• and so much more...

Ideas

• canonicalize sbgnml with org.apache.xml.security from santuario then diff possible with diff libs
• possible to convert whole xml to rdf directly using rdf mapper (carml)
• possible to mine pathway informations directly from any rdf, so building sbgn from any detailed enough knowledgebase should be feasible