Package org.openbel.framework.core.compiler.expansion

Examples of org.openbel.framework.core.compiler.expansion.ModificationExpansionRule.expand()

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        List<Statement> stmts;

        // valid substitution
        term = BELParser.parseTerm("p(HGNC:TNF,sub(V,599,E))");
        assertThat(rule.match(term), is(true));
        stmts = rule.expand(term);
        assertThat(stmts.size(), is(1));
        assertThat(stmts.get(0).toBELShortForm(),
                is("p(HGNC:TNF) hasVariant p(HGNC:TNF,sub(V,599,E))"));

        // valid truncation
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                is("p(HGNC:TNF) hasVariant p(HGNC:TNF,sub(V,599,E))"));

        // valid truncation
        term = BELParser.parseTerm("p(HGNC:TNF,trunc(S,1099))");
        assertThat(rule.match(term), is(true));
        stmts = rule.expand(term);
        assertThat(stmts.size(), is(1));
        assertThat(stmts.get(0).toBELShortForm(),
                is("p(HGNC:TNF) hasVariant p(HGNC:TNF,trunc(S,1099))"));

        // valid protein modification
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                is("p(HGNC:TNF) hasVariant p(HGNC:TNF,trunc(S,1099))"));

        // valid protein modification
        term = BELParser.parseTerm("p(HGNC:TNF,pmod(P,Y))");
        assertThat(rule.match(term), is(true));
        stmts = rule.expand(term);
        assertThat(stmts.size(), is(1));
        assertThat(stmts.get(0).toBELShortForm(),
                is("p(HGNC:TNF) hasModification p(HGNC:TNF,pmod(P,Y))"));

        // valid fusion
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                is("p(HGNC:TNF) hasModification p(HGNC:TNF,pmod(P,Y))"));

        // valid fusion
        term = BELParser.parseTerm("p(HGNC:TNF,fus(HGNC:ABL1))");
        assertThat(rule.match(term), is(true));
        stmts = rule.expand(term);
        assertThat(stmts.size(), is(1));
        assertThat(stmts.get(0).toBELShortForm(),
                is("p(HGNC:TNF) hasVariant p(HGNC:TNF,fus(HGNC:ABL1))"));

        // invalid based on outer function
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