Package org.openbel.framework.common.protonetwork.model

Examples of org.openbel.framework.common.protonetwork.model.StatementTable

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     * {@inheritDoc}
     */
    @Override
    public void expandTerms(final Document doc, final ProtoNetwork pn) {
        final ProtoNetworkBuilder pnb = new ProtoNetworkBuilder(doc);
        final StatementTable st = pn.getStatementTable();
        final List<TableStatement> stmts = st.getStatements();
        final Map<Integer, Statement> si = st.getIndexedStatements();

        final List<Statement> expansions = new ArrayList<Statement>();
        for (int i = 0, n = stmts.size(); i < n; i++) {
            final Statement stmt = si.get(i);

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        } else {
            rules.add(extractRule);
        }
        rules.add(reciprocalRule);

        final StatementTable st = pn.getStatementTable();
        final List<TableStatement> ts = st.getStatements();
        final Map<Integer, Statement> index = st.getIndexedStatements();

        for (int i = 0, n = ts.size(); i < n; i++) {
            final Statement stmt = index.get(i);

            if (stmt == null) {
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                protoNetwork1.getAnnotationValueTable().addAnnotationValue(
                        newDefinitionId, av.getAnnotationValue());
            }

            // union statements
            StatementTable statementTable = protoNetwork2.getStatementTable();
            List<TableStatement> statements = statementTable.getStatements();
            List<String> terms = protoNetwork2.getTermTable().getTermValues();
            Map<Integer, Integer> termMap = new HashMap<Integer, Integer>(
                    terms.size());
            for (int j = 0; j < statements.size(); j++) {
                mergeStatement(j, statements.get(j), protoNetwork1,
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                new TableParameter(new TableNamespace(hgncNs), "AIFM1")));
        assertTrue(termTable.getTermValues().contains("proteinAbundance(#)"));
        assertTrue(termTable.getTermValues().contains("geneAbundance(#)"));

        //Test extracted statements
        StatementTable statementTable = protoNetwork.getStatementTable();

        assertEquals(6, statementTable.getStatements().size());
    }
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Related Classes of org.openbel.framework.common.protonetwork.model.StatementTable

  • org.openbel.framework.common.enums.FunctionEnum
  • org.openbel.framework.common.enums.RelationshipType
  • org.openbel.framework.common.InvalidArgument
  • org.openbel.framework.common.model.AnnotationGroup
  • org.openbel.framework.common.model.Namespace
  • org.openbel.framework.common.model.Parameter
  • org.openbel.framework.common.model.Statement
  • org.openbel.framework.common.model.Term
  • org.openbel.framework.core.compiler.expansion.ExpansionServiceImpl
  • org.openbel.framework.core.protonetwork.ProtoNetworkBuilderTest
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