Examples with ModuleDefinition org.sbolstandard.core2.ModuleDefinition used on opensource projects

Example 21 with ModuleDefinition

use of org.sbolstandard.core2.ModuleDefinition in project libSBOLj by SynBioDex.

the class ModuleDefModuleTree method createModuleMDGraph.

public void createModuleMDGraph(SBOLDocument doc, int depth, ArrayList<String> mdNames, ArrayList<Integer> address, ModuleDefinition parentMd) throws SBOLValidationException {
    // System.out.println("depth = " + depth);
    if (depth > 0) {
        for (int i = 1; i <= numOfModules; i++) {
            address.add(i);
            System.out.println("address = " + intArrayListToString(address));
            System.out.println("addrSelfRef = " + intArrayListToString(addrCirfRef));
            String mdId = "md_" + intArrayListToString(address);
            String mId = "m_" + intArrayListToString(address);
            System.out.println("mdId = " + mdId);
            // System.out.println("mId = " + mId);
            if (intArrayListToString(address).equals(intArrayListToString(addrCirfRef))) {
                int circularRefIndex = randInt(0, mdNames.size() - 1);
                // int circleRefIndex = mdNames.size()-1; // Force 10704 to occur.
                System.out.println("circleRefIndex = " + circularRefIndex);
                System.out.println("address = " + intArrayListToString(address));
                System.out.println("addrCirRef = " + intArrayListToString(addrCirfRef));
                System.out.println("mdNames = " + mdNames);
                if (circularRefIndex == mdNames.size() - 1) {
                    System.out.println("Expect 11704");
                    expectedError = "11704";
                } else {
                    System.out.println("Expect 11705");
                    expectedError = "11705";
                }
                System.out.println("Last module displayId (mId) = " + mId);
                System.out.println("parentMd displayId = " + parentMd.getDisplayId());
                System.out.println("mdName = " + mdNames.get(circularRefIndex));
                // create the circular reference from module with mId to module definition selected by mdNames.get(circularRefIndex).
                parentMd.createModule(mId, mdNames.get(circularRefIndex));
            } else {
                ModuleDefinition childMd = doc.createModuleDefinition(mdId);
                parentMd.createModule(mId, mdId);
                mdNames.add(mdId);
                // System.out.println(mdId);
                // System.out.println("Interm. Module displayId = " + m.getDisplayId());
                System.out.println("mdNames = " + mdNames);
                createModuleMDGraph(doc, depth - 1, mdNames, address, childMd);
                mdNames.remove(mdId);
            }
            address.remove(address.size() - 1);
        }
    }
}