Package org.openbel.framework.common.model

Examples of org.openbel.framework.common.model.Term


    /**
     * {@inheritDoc}
     */
    @Override
    public List<Statement> expand(Statement s) {
        Term sub = s.getSubject();
        Term obj = s.getObject().getTerm();
        final RelationshipType rel = s.getRelationshipType();

        final Statement stmt = new Statement(obj);
        stmt.setObject(new Object(sub));
        stmt.setRelationshipType(rel);
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            label = kamNode.getLabel();
            try {
                List<BelTerm> terms = kAMStore.getSupportingTerms(kamNode);
                if (!terms.isEmpty()) {
                    BelTerm bt = terms.get(0);
                    Term t = BELParser.parseTerm(bt.getLabel());
                    label = t.toBELShortForm();
                }
            } catch (Exception e) {
                // TODO exception
            }
            labelCache.put(kamNode.getLabel(), label);
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     */
    protected String labelNode(KamNode node) throws KAMStoreException {
        List<BelTerm> terms = kAMStore.getSupportingTerms(node);
        if (!terms.isEmpty()) {
            BelTerm bt = terms.get(0);
            Term parsed;
            try {
                parsed = BELParser.parseTerm(bt.getLabel());
            } catch (Exception e) {
                return null;
            }
            Term converted = convert(parsed);

            return displayLongForm ? converted.toBELLongForm() : converted
                    .toBELShortForm();
        }
        return null;
    }
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     *
     * @param orig
     * @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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        writeObject(out, comment);
        // 2: annotation group, may be null
        AnnotationGroup ag = stmt.getAnnotationGroup();
        writeObject(out, ag);
        // 3: subject term, never null
        Term subject = stmt.getSubject();
        writeTerm(out, subject);

        // 4: statement object, may be null
        Statement.Object object = stmt.getObject();
        if (object == null) {
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        // 1: comment
        String comment = (String) readObject(in);
        // 2: annotation group
        AnnotationGroup ag = (AnnotationGroup) readObject(in);
        // 3: subject term
        Term subject = readTerm(in);

        // 4: statement object
        Statement.Object object;
        byte obyte = in.readByte();
        if (obyte == 1) {
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                } else if (obyte == 1) {
                    fxargs.add(readTerm(in));
                }
            }
        }
        return new Term(fx, fxargs);
    }
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            state._fsp--;

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

                    final Term outerTerm = new Term((f!=null?f.r:null));
               
            OPEN_PAREN3=(Token)match(input,OPEN_PAREN,FOLLOW_OPEN_PAREN_in_outer_term330);
            OPEN_PAREN3_tree = (Object)adaptor.create(OPEN_PAREN3);
            adaptor.addChild(root_0, OPEN_PAREN3_tree);

            // BELStatement.g:103:5: ( ( ',' )? arg= argument )*
            loop4:
            do {
                int alt4=2;
                int LA4_0 = input.LA(1);

                if ( ((LA4_0>=NS_PREFIX && LA4_0<=QUOTED_VALUE)||(LA4_0>=16 && LA4_0<=75)) ) {
                    alt4=1;
                }


                switch (alt4) {
              case 1 :
                  // BELStatement.g:103:6: ( ',' )? arg= argument
                  {
                  // BELStatement.g:103:6: ( ',' )?
                  int alt3=2;
                  int LA3_0 = input.LA(1);

                  if ( (LA3_0==16) ) {
                      alt3=1;
                  }
                  switch (alt3) {
                      case 1 :
                          // BELStatement.g:103:6: ','
                          {
                          char_literal4=(Token)match(input,16,FOLLOW_16_in_outer_term337);
                          char_literal4_tree = (Object)adaptor.create(char_literal4);
                          adaptor.addChild(root_0, char_literal4_tree);


                          }
                          break;

                  }

                  pushFollow(FOLLOW_argument_in_outer_term342);
                  arg=argument();

                  state._fsp--;

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

                  }
                  break;

              default :
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            state._fsp--;

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

                    final Term parentTerm = new Term((pfv!=null?pfv.r:null));
               
            OPEN_PAREN6=(Token)match(input,OPEN_PAREN,FOLLOW_OPEN_PAREN_in_term424);
            OPEN_PAREN6_tree = (Object)adaptor.create(OPEN_PAREN6);
            adaptor.addChild(root_0, OPEN_PAREN6_tree);

            // BELStatement.g:119:5: ( ( ',' )? (it= term | pp= param ) )*
            loop8:
            do {
                int alt8=2;
                int LA8_0 = input.LA(1);

                if ( ((LA8_0>=NS_PREFIX && LA8_0<=QUOTED_VALUE)||(LA8_0>=16 && LA8_0<=75)) ) {
                    alt8=1;
                }


                switch (alt8) {
              case 1 :
                  // BELStatement.g:120:9: ( ',' )? (it= term | pp= param )
                  {
                  // BELStatement.g:120:9: ( ',' )?
                  int alt6=2;
                  int LA6_0 = input.LA(1);

                  if ( (LA6_0==16) ) {
                      alt6=1;
                  }
                  switch (alt6) {
                      case 1 :
                          // BELStatement.g:120:9: ','
                          {
                          char_literal7=(Token)match(input,16,FOLLOW_16_in_term440);
                          char_literal7_tree = (Object)adaptor.create(char_literal7);
                          adaptor.addChild(root_0, char_literal7_tree);


                          }
                          break;

                  }

                  // BELStatement.g:121:9: (it= term | pp= param )
                  int alt7=2;
                  int LA7_0 = input.LA(1);

                  if ( ((LA7_0>=17 && LA7_0<=75)) ) {
                      alt7=1;
                  }
                  else if ( ((LA7_0>=NS_PREFIX && LA7_0<=QUOTED_VALUE)) ) {
                      alt7=2;
                  }
                  else {
                      NoViableAltException nvae =
                          new NoViableAltException("", 7, 0, input);

                      throw nvae;
                  }
                  switch (alt7) {
                      case 1 :
                          // BELStatement.g:121:10: it= term
                          {
                          pushFollow(FOLLOW_term_in_term454);
                          it=term();

                          state._fsp--;

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

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

                          }
                          break;
                      case 2 :
                          // BELStatement.g:124:9: pp= param
                          {
                          pushFollow(FOLLOW_param_in_term470);
                          pp=param();

                          state._fsp--;

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

                          }
                          break;

                  }
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    public List<Statement> expand(Term translocation) {
        List<Statement> statements = new ArrayList<Statement>();

        BELObject firstArgument = translocation.getFunctionArguments().get(0);

        Term abundance = (Term) firstArgument; // first argument of a
                                               // translocation term is the
                                               // abundance
        // tranlocation connects the abundance term with TRANSLOCATES
        // relationship
        Statement statement =
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