Package org.openbel.bel.model

Examples of org.openbel.bel.model.BELStatement

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        final Set<BELNamespaceDefinition> nsset = constrainedHashSet(2);
        nsset.add(new BELNamespaceDefinition("HGNC", DEFAULT_NS, true));
        nsset.add(new BELNamespaceDefinition("EGID", NS, false));
        final List<BELStatementGroup> sglist = sizedArrayList(1);
        final BELStatementGroup sg = new BELStatementGroup("Example");
        sg.getStatements().add(new BELStatement("p(AKT1) => g(EGID:1024)"));
        sglist.add(sg);
        final BELDocument beldoc = new BELDocument(dh, null, nsset, sglist);

        // convert to common model
        final BELDocumentConverter converter = new BELDocumentConverter();
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        List<BELStatementGroup> groups = doc.getBelStatementGroups();
        BELStatementGroup group = groups.get(0);
        List<BELStatement> stmts = group.getStatements();
        assertTrue(stmts.size() == 1);

        BELStatement stmt = stmts.get(0);
        List<BELAnnotation> annos = stmt.getAnnotations();
        assertTrue(annos.size() == 1);

        BELAnnotation anno = annos.get(0);
        assertTrue(anno.getValues().size() == 1);
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        List<BELStatementGroup> groups = doc.getBelStatementGroups();
        BELStatementGroup group = groups.get(0);
        List<BELStatement> stmts = group.getStatements();
        assertTrue(stmts.size() == 1);

        BELStatement stmt = stmts.get(0);

        BELEvidence evidence = stmt.getEvidence();
        assertNotNull(evidence);

        BELCitation citation = stmt.getCitation();
        assertNotNull(citation);

        assertEquals("Evidence\nneeded", evidence.getEvidenceLine());
        assertEquals("PubMed", citation.getType());
        assertEquals("X", citation.getName());
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                    }

                    final List<BELAnnotation> annotations = new ArrayList<BELAnnotation>(effectiveAnnotations.values());

                    // build statement and keep track of it for validation purposes
                    final BELStatement stmt = new BELStatement(stmtBuilder.toString(), annotations, citationContext, evidenceContext, commentText);
                    stmtlist.add(stmt);

                    // add statement to scoped statement group
                    if (activeStatementGroup != null) {
                        activeStatementGroup.getStatements().add(stmt);
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Related Classes of org.openbel.bel.model.BELStatement

  • org.openbel.framework.common.bel.converters.BELDocumentConverterTest
  • org.openbel.framework.common.bel.parser.BELScriptParserTest
  • org.openbel.framework.common.bel.parser.BELScriptWalker
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