/** Setup - Set up a test BEL {@link Document}. */
@Before
public void setupTest() {
NamespaceGroup namespaceGroup = new NamespaceGroup();
Namespace entrezGeneNs = new Namespace("EG", "http://www.belscript.org/ns/entrez-gene");
Namespace hgncNs = new Namespace("HGNC", "http://www.belscript.org/ns/hgnc");
namespaceGroup.setNamespaces(asList(entrezGeneNs, hgncNs));
StatementGroup statementGroup = new StatementGroup();
AnnotationDefinition speciesDefinition =
new AnnotationDefinition("species", "Description", "Usage", asList("9606"));
AnnotationDefinition tissueDefinition =
new AnnotationDefinition("tissue", "Description", "Usage", asList("TH1", "TH2", "AB3"));
AnnotationGroup annotationGroup = new AnnotationGroup();
annotationGroup.setAnnotations(
asList(
CommonModelFactory.getInstance().createAnnotation("9606", speciesDefinition),
CommonModelFactory.getInstance().createAnnotation("TH1", tissueDefinition)));
annotationGroup.setEvidence(
CommonModelFactory.getInstance()
.createEvidence(
"the elevation of intracellular cAMP concentration that results from increased glucagon production also plays a role in the down-regulation process"));
statementGroup.setAnnotationGroup(annotationGroup);
FunctionEnum p = FunctionEnum.PROTEIN_ABUNDANCE;
List<BELObject> args = new ArrayList<BELObject>();
args.add(CommonModelFactory.getInstance().createParameter(hgncNs, "NFKB"));
Term t = new Term(p, args);
FunctionEnum r = FunctionEnum.RNA_ABUNDANCE;
args = new ArrayList<BELObject>();
args.add(CommonModelFactory.getInstance().createParameter(hgncNs, "FAS"));
Term t2 = new Term(r, args);
Statement simpleIncrease =
new Statement(
t,
"",
annotationGroup,
new org.openbel.framework.common.model.Statement.Object(t2),
RelationshipType.INCREASES);
statementGroup.setStatements(asList(simpleIncrease));
Header header = new Header("", asList("Unladen"), asList("Swallow"), "", "", "", "", "");
Document document = new Document(header, statementGroup);
document.setDefinitions(asList(speciesDefinition, tissueDefinition));
document.setNamespaceGroup(namespaceGroup);
protoNetwork = new ProtoNetworkBuilder(document).buildProtoNetwork();
}
@Override
public Token parse() {
funcName = first.getNext();
if (!funcName.isIdentifier())
throw new RuntimeException("Expected identifier for function name, found: " + funcName);
GluonFunction.registerFunction(funcName.getValue());
Token test = funcName.getNext();
if (!test.isOperator(Operator.BRACKET_LEFT))
throw new RuntimeException("Expected '(' for function parmater list, found: " + test);
test = test.getNext();
while (test.isIdentifier()) {
Variable param = new Variable(test, scope, true);
parameters.add(param);
test = param.parse(true);
if (test.isOperator(Operator.COMMA)) test = test.getNext();
}
if (!test.isOperator(Operator.BRACKET_RIGHT))
throw new RuntimeException("Expected ')' for function parmater list, found: " + test);
test = test.getNext();
if (!test.isOperator(Operator.COLON) && !test.isOperator(Operator.BRACE_LEFT))
throw new RuntimeException("Expected ':' or '{' in function def, found: " + test);
if (test.isOperator(Operator.COLON)) {
test = funcName.getNext();
if (!test.isOperator(Operator.BRACKET_LEFT))
throw new RuntimeException("Expected '(' for function return list, found: " + test);
test = test.getNext();
while (test.isIdentifier()) {
returns.add(test);
test = test.getNext();
if (test.isOperator(Operator.COMMA)) test = test.getNext();
}
if (!test.isOperator(Operator.BRACKET_RIGHT))
throw new RuntimeException("Expected ')' for function return list, found: " + test);
}
if (!test.isOperator(Operator.BRACE_LEFT))
throw new RuntimeException("Expected opening brace for function logic, found: " + test);
test = test.getNext();
if (!test.isNewline())
throw new RuntimeException("Expected newline before function logic, found: " + test);
test = test.getNext();
Operator[] targets = {Operator.BRACE_RIGHT};
logic = new StatementGroup(test, targets, scope);
test = logic.parse();
if (!test.isOperator(Operator.BRACE_RIGHT))
throw new RuntimeException("Expected closing brace for function logic, found: " + test);
return test.getNext();
}
@Override
public Token parse() {
Token next = first.getNext();
if (!next.isOperator(Operator.BRACKET_LEFT))
throw new RuntimeException("Expected '(' after WHILE, found: " + next);
next = next.getNext();
testExp = new BooleanExpression(next, scope);
next = testExp.parse();
if (!next.isOperator(Operator.BRACKET_RIGHT))
throw new RuntimeException("Expected ')' after WHILE condition, found: " + next);
next = next.getNext();
if (!next.isNewline()) throw new RuntimeException("Expected newline, found: " + next);
next = next.getNext();
Keyword[] target = {Keyword.END};
statements = new StatementGroup(next, target, scope);
next = statements.parse();
return next.getNext();
}
@Override
public void print(int level) {
printLevel(level);
printLn("WHILE");
testExp.print(level + 1);
printLevel(level);
printLn("DO");
statements.print(level + 1);
}
@Override
public void emitCode(GluonOutput code) {
code.comment("Function: " + funcName.getValue());
String funcLabel = GluonFunction.getLabel(funcName.getValue());
// Setup variables passed in on stack for use
int offset = 4; // + 4 * parameters.size();
int used = 4;
for (Variable parameter : parameters) {
int stackOffset = offset + used;
used += 4;
code.code(parameter.getLabel() + " EQU EBP + " + stackOffset);
}
// Function
code.label(funcLabel);
// Push BP
code.code("PUSH EBP");
// Mov BP, SP
code.code("MOV EBP, ESP");
// Local variables
scope.emitCreateScope(code);
// Push all reg
code.code("PUSH EAX");
code.code("PUSH EBX");
code.code("PUSH ECX");
code.code("PUSH EDX");
// Actual function logic
code.comment("Function code start");
logic.emitCode(code);
code.comment("Function code end");
// Pop all reg
code.code("POP EDX");
code.code("POP ECX");
code.code("POP EBX");
code.code("POP EAX");
// Local variables
scope.emitDistroyScope(code);
// Pop BP
code.code("POP EBP");
// Ret paramaters
code.code("RET");
scope.buildRestore(code, parameters, true);
code.comment("Function end: " + funcName.getValue());
}
@Override
public void emitCode(GluonOutput code) {
// Creae labels
String labelStart = GluonLabels.createLabel(first, "start");
String labelEnd = GluonLabels.createLabel(first, "end");
GluonLabels.addEndLabel(labelEnd);
code.comment("While Statement");
code.label(labelStart);
testExp.emitCode(code);
code.code("TEST AL, AL ;EAX, EAX");
code.code("JZ " + labelEnd);
statements.emitCode(code);
code.code("JMP " + labelStart);
code.label(labelEnd);
code.comment("End While");
GluonLabels.removeEndLabel(labelEnd);
}
