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

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

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        Term term;
        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))"));
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        assertThat(stmts.get(0).toBELShortForm(),
                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))"));
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        assertThat(stmts.get(0).toBELShortForm(),
                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))"));
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        assertThat(stmts.get(0).toBELShortForm(),
                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))"));
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        assertThat(stmts.get(0).toBELShortForm(),
                is("p(HGNC:TNF) hasVariant p(HGNC:TNF,fus(HGNC:ABL1))"));

        // invalid based on outer function
        term = BELParser.parseTerm("complex(p(HGNC:TNF),p(HGNC:MAPK1))");
        assertThat(rule.match(term), is(false));

        // invalid based on missing modification argument
        term = BELParser.parseTerm("p(HGNC:TNF)");
        assertThat(rule.match(term), is(false));
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        term = BELParser.parseTerm("complex(p(HGNC:TNF),p(HGNC:MAPK1))");
        assertThat(rule.match(term), is(false));

        // invalid based on missing modification argument
        term = BELParser.parseTerm("p(HGNC:TNF)");
        assertThat(rule.match(term), is(false));

        // invalid based on non-parameter first argument
        term = BELParser.parseTerm("p(r(HGNC:TNF),sub(V,599,E))");
        assertThat(rule.match(term), is(false));
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        term = BELParser.parseTerm("p(HGNC:TNF)");
        assertThat(rule.match(term), is(false));

        // invalid based on non-parameter first argument
        term = BELParser.parseTerm("p(r(HGNC:TNF),sub(V,599,E))");
        assertThat(rule.match(term), is(false));

        // invalid based on non-term second argument
        term = BELParser.parseTerm("p(HGNC:TNF,\"Substitution at P,Y\")");
        assertThat(rule.match(term), is(false));
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        term = BELParser.parseTerm("p(r(HGNC:TNF),sub(V,599,E))");
        assertThat(rule.match(term), is(false));

        // invalid based on non-term second argument
        term = BELParser.parseTerm("p(HGNC:TNF,\"Substitution at P,Y\")");
        assertThat(rule.match(term), is(false));

        // invalid protein decorator function for second argument
        term = BELParser.parseTerm("p(HGNC:TNF,g(HGNC:AKT1))");
        assertThat(rule.match(term), is(false));
    }
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        term = BELParser.parseTerm("p(HGNC:TNF,\"Substitution at P,Y\")");
        assertThat(rule.match(term), is(false));

        // invalid protein decorator function for second argument
        term = BELParser.parseTerm("p(HGNC:TNF,g(HGNC:AKT1))");
        assertThat(rule.match(term), is(false));
    }
}
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