List of addFunctionArgument() Examples

Examples of addFunctionArgument()

org.openbel.framework.common.model.Term.addFunctionArgument()
Adds a function argument to the end of the function argument list.
The argument will be additionally added to the terms or parameters, depending on its type.
@param arg BEL object function argument @throws InvalidArgument Thrown if {@code arg} is null @throws UnsupportedOperationException Thrown if {@code arg} is not a{@link Term} or {@link Parameter}

Examples of org.openbel.framework.common.model.Term.addFunctionArgument()

     * @return
     */
    protected Term convert(Term orig, Parameter speciesParam) {
        Term t = new Term(orig.getFunctionEnum());
        for (BELObject o : orig.getFunctionArguments()) {
            t.addFunctionArgument(convert(o, speciesParam));
        }
        return t;
    }


    /**

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Examples of org.openbel.framework.common.model.Term.addFunctionArgument()

        Term mt = (Term) modArgument;


        FunctionEnum fx = mt.getFunctionEnum();


        Term proteinTrm = new Term(PROTEIN_ABUNDANCE);
        proteinTrm.addFunctionArgument(pp);


        Statement stmt = null;
        final Object obj = new Object(term);
        if (isMutation(fx)) {
            // mutation

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Examples of org.openbel.framework.common.model.Term.addFunctionArgument()

     * @return
     */
    protected Term convert(Term orig) {
        Term t = new Term(orig.getFunctionEnum());
        for (BELObject o : orig.getFunctionArguments()) {
            t.addFunctionArgument(convert(o));
        }
        return t;
    }


    /**

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Examples of org.openbel.framework.common.model.Term.addFunctionArgument()

                  arg=argument();


                  state._fsp--;


                  adaptor.addChild(root_0, arg.getTree());
                   outerTerm.addFunctionArgument((arg!=null?arg.r:null)); 


                  }
                  break;


              default :

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Examples of org.openbel.framework.common.model.Term.addFunctionArgument()


                          state._fsp--;


                          adaptor.addChild(root_0, it.getTree());


                                      parentTerm.addFunctionArgument((it!=null?it.r:null));
                                  


                          }
                          break;
                      case 2 :

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Examples of org.openbel.framework.common.model.Term.addFunctionArgument()

                          pp=param();


                          state._fsp--;


                          adaptor.addChild(root_0, pp.getTree());
                           parentTerm.addFunctionArgument((pp!=null?pp.r:null)); 


                          }
                          break;


                  }

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Examples of org.openbel.framework.common.model.Term.addFunctionArgument()

                    // protein family parameter
                    entry = new TableEntry(val, rl);
                    if (entries.contains(entry)) {
                        // construct family term once, in case we find matches
                        final Term fpt = new Term(PROTEIN_ABUNDANCE);
                        fpt.addFunctionArgument(new Parameter(ns, val));
                        final Term fat = new Term(f);
                        fat.addFunctionArgument(fpt);


                        // since we found a molecular activity function for a
                        // protein family look up UUIDs for all entries

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Examples of org.openbel.framework.common.model.Term.addFunctionArgument()

                    if (entries.contains(entry)) {
                        // construct family term once, in case we find matches
                        final Term fpt = new Term(PROTEIN_ABUNDANCE);
                        fpt.addFunctionArgument(new Parameter(ns, val));
                        final Term fat = new Term(f);
                        fat.addFunctionArgument(fpt);


                        // since we found a molecular activity function for a
                        // protein family look up UUIDs for all entries
                        // ... loading uuids on demand to save resources
                        if (eu == null) {

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Examples of org.openbel.framework.common.model.Term.addFunctionArgument()

                            // do we have protein family member parameter uuid
                            // in molecular activity function entries?
                            if (eu.contains(uuid)) {
                                // construct member term
                                final Term mpt = new Term(PROTEIN_ABUNDANCE);
                                mpt.addFunctionArgument(new Parameter(mns, mval));
                                final Term mat = new Term(f);
                                mat.addFunctionArgument(mpt);


                                // construct isA statement between member and family
                                isaStmts.add(new Statement(mat, null,

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Examples of org.openbel.framework.common.model.Term.addFunctionArgument()

                            if (eu.contains(uuid)) {
                                // construct member term
                                final Term mpt = new Term(PROTEIN_ABUNDANCE);
                                mpt.addFunctionArgument(new Parameter(mns, mval));
                                final Term mat = new Term(f);
                                mat.addFunctionArgument(mpt);


                                // construct isA statement between member and family
                                isaStmts.add(new Statement(mat, null,
                                        null, new Object(fat), IS_A));
                                inferred++;

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