/**
* Builds the argument invocation string for calling a constructor
*
* @param classVariables The collection of member variables as XMLElements
* @param constructorArguments The set of names for constructor arguments
* @param allocatedMemberVariables The set of member variables already allocated
* @param element The specific 'new' xml element
*/
private static String buildArguments(
Vector classVariables,
Set constructorArguments,
Set allocatedMemberVariables,
IXMLElement element)
throws IOException {
XMLUtil.checkExpectedNode("new", element);
boolean comma = false;
String arguments = "";
for (Enumeration e = element.enumerateChildren(); e.hasMoreElements(); ) {
IXMLElement argument = (IXMLElement) e.nextElement();
String argType = ModelAccessor.getValueType(argument);
String value = ModelAccessor.getValue(argument);
/* Exclude cases where we do nothing to the value */
if (!primitives.contains(argType) && !value.equals("true") && !value.equals("false")) {
// CASE 0: Translate 'this'
if (value.equalsIgnoreCase("this")) {
value = "m_id";
}
// CASE 1: It is a singleton member variable which must be mapped to the singleton
else if (allocatedMemberVariables.contains(value)) {
String singletonType = getVariableType(classVariables, value);
if (primitives.contains(singletonType)) {
value = "(" + singletonType + ") singleton(" + value + ")";
} else value = "singleton(" + value + ")";
}
// CASE 2: It is a constructor argument
else if (constructorArguments.contains(value)) { // Do nothing, just use the string as is.
}
// CASE 3: Test for error - using a member before initializing it
else if (!allocatedMemberVariables.contains(value) && isMember(classVariables, value)) {
value = "!ERROR: Cannot use " + value + " without prior initialization.";
}
// Otherwise it is a string or enumerataion
else if (argType.equals("string")
|| // It is an enumeartion of some kind
ModelAccessor.isEnumeration(argType)
|| argType.equals("symbol")) {
value = "LabelStr(\"" + XMLUtil.escapeQuotes(value) + "\")";
}
// If we fall through to here, there is an error.
else value = "!ERROR:BAD ASSIGNMENT";
}
// CASE 3: It is a true or false value
if (comma) arguments = arguments + ", ";
arguments = arguments + value;
comma = true;
}
return arguments;
}
/**
* Helper method to generate the signatures for binding the factory. Must account for the
* inheritance relationships for any arguments that are classes. Ths, each argument can
* potentially result in a range of values for type, and we have to handle the cross product of
* all of these.
*/
private static Vector makeFactoryNames(IXMLElement constructor) {
String factoryName = XMLUtil.nameOf(constructor.getParent());
Vector allPermutations = new Vector();
for (Enumeration e = constructor.enumerateChildren(); e.hasMoreElements(); ) {
IXMLElement element = (IXMLElement) e.nextElement();
if (!element.getName().equals("arg")) {
break;
}
String argType = XMLUtil.typeOf(element);
Vector argTypeAlternates = new Vector();
argTypeAlternates.add(argType);
if (ModelAccessor.isClass(argType)) {
List ancestors = ModelAccessor.getAncestors(argType);
if (ancestors != null) argTypeAlternates.addAll(ancestors);
}
allPermutations.add(argTypeAlternates);
}
// Generate all the signatures
Vector factoryNames = new Vector();
makeFactoryNames(factoryName, allPermutations, 0, factoryNames);
return factoryNames;
}
/** @brief Generates the signature for the class constructors */
private static void generateSignature(IndentWriter writer, IXMLElement constructor)
throws IOException {
assert (DebugMsg.debugMsg("ClassWriter", "Begin ClassWriter::generateSignature"));
writer.write("constructor(");
boolean comma = false;
for (Enumeration e = constructor.enumerateChildren(); e.hasMoreElements(); ) {
IXMLElement element = (IXMLElement) e.nextElement();
if (!element.getName().equals("arg")) {
break;
}
String argType = XMLUtil.typeOf(element);
String argName = XMLUtil.getAttribute(element, "name");
if (comma) {
writer.write(", ");
}
// Argument are structured as: <arg name="argName" type="argType"/>
if (argType.equals(NddlXmlStrings.x_int)) writer.write("int " + argName);
else if (argType.equals(NddlXmlStrings.x_float)) writer.write("double " + argName);
else if (argType.equals(NddlXmlStrings.x_boolean)) writer.write("bool " + argName);
else if (argType.equals(NddlXmlStrings.x_string)
|| argType.equals(NddlXmlStrings.x_symbol)
|| ModelAccessor.isEnumeration(argType)) writer.write("const LabelStr& " + argName);
else writer.write("const " + argType + "Id& " + argName);
comma = true;
}
writer.write(")");
assert (DebugMsg.debugMsg("ClassWriter", "End ClassWriter::generateSignature"));
}
public static void generateImplementation(IndentWriter writer, IXMLElement klass)
throws IOException {
String superClass = ModelAccessor.getSuperClass(klass);
String name = XMLUtil.getAttribute(klass, "name");
if (ModelAccessor.isPredefinedClass(name)) {
writer.write("// SKIPPING IMPLEMENTATION FOR BUILT-IN CLASS " + name + "\n\n");
return;
}
ModelAccessor.setCurrentObjectType(name);
String longname = XMLUtil.qualifiedName(klass);
boolean extendsBuiltIn = ModelAccessor.isPredefinedClass(superClass);
String superCppClass = ModelAccessor.getCppClass(superClass);
writer.write("\n");
SharedWriter.generateFileLocation(writer, klass);
writer.write(
longname + "::" + name + "(const PlanDatabaseId& planDatabase, const LabelStr& name)\n");
if (extendsBuiltIn)
writer.write(" : " + superCppClass + "(planDatabase, \"" + name + "\", name, true)");
else writer.write(" : " + superCppClass + "(planDatabase, \"" + name + "\", name)");
writer.write(" {\n");
writer.write("}\n");
writer.write(
longname
+ "::"
+ name
+ "(const PlanDatabaseId& planDatabase, const LabelStr& type, const LabelStr& name)\n");
if (extendsBuiltIn) writer.write(" : " + superCppClass + "(planDatabase, type, name, true)");
else writer.write(" : " + superCppClass + "(planDatabase, type, name)");
writer.write(" {\n");
writer.write("}\n");
writer.write(longname + "::" + name + "(const ObjectId& parent, const LabelStr& name)\n");
if (extendsBuiltIn)
writer.write(" : " + superCppClass + "(parent, \"" + name + "\", name, true)");
else writer.write(" : " + superCppClass + "(parent, \"" + name + "\", name)");
writer.write(" {}\n");
writer.write(
longname
+ "::"
+ name
+ "(const ObjectId& parent, const LabelStr& type, const LabelStr& name)\n");
if (extendsBuiltIn) writer.write(" : " + superCppClass + "(parent, type, name, true)");
else writer.write(" : " + superCppClass + "(parent, type, name)");
writer.write(" {}\n");
Vector classVariables = klass.getChildrenNamed("var");
SharedWriter.defineHandleDefaults(writer, klass, classVariables);
generateChildren(writer, klass);
ModelAccessor.resetCurrentObjectType();
}
private static String getVariableType(Vector classVariables, String name) {
String type = "!ERROR";
for (int i = 0; i < classVariables.size(); i++) {
IXMLElement variable = (IXMLElement) classVariables.elementAt(i);
if (XMLUtil.nameOf(variable).equals(name)) {
type = XMLUtil.getAttribute(variable, "type");
String _class = XMLUtil.getAttribute(variable.getParent(), "name");
if (ModelAccessor.isEnumeration(_class + "::" + type)) type = _class + "::" + type;
break;
}
}
return type;
}
public void readFileAndGenerate(boolean onlyUniquePeptides, ISpectrumDataFilter... filters) {
@SuppressWarnings("UnusedDeclaration")
int numberProcessed = 0;
@SuppressWarnings("UnusedDeclaration")
double lastRetentionTime = 0;
@SuppressWarnings("UnusedDeclaration")
int numberUnProcessed = 0;
try {
LineNumberReader rdr = new LineNumberReader(new FileReader(m_File));
String line = rdr.readLine();
while (line != null) {
if (line.contains("<spectrum_query")) {
String retention_time_sec = XMLUtil.extractAttribute(line, "retention_time_sec");
scan_id = XMLUtil.extractAttribute(line, "start_scan");
if (retention_time_sec == null) {
lastRetentionTime = 0;
} else {
try {
lastRetentionTime = Double.parseDouble(retention_time_sec.trim());
} catch (NumberFormatException e) {
lastRetentionTime = 0;
}
}
}
//noinspection StatementWithEmptyBody,StatementWithEmptyBody
if (line.contains("<search_result")) {
String[] searchHitLines = readSearchHitLines(line, rdr);
// System.out.println(line);
boolean processed =
handleSearchHit(searchHitLines, lastRetentionTime, onlyUniquePeptides, filters);
if (processed) {
for (int i = 0; i < searchHitLines.length; i++) {
@SuppressWarnings("UnusedDeclaration")
String searchHitLine = searchHitLines[i];
}
numberProcessed++;
} else numberUnProcessed++;
}
line = rdr.readLine();
}
//noinspection UnnecessaryReturnStatement
return;
} catch (IOException e) {
throw new RuntimeException(e);
}
}
/** Test if the given variable name is listed in the vector of variable xml elements */
private static boolean isMember(Vector classVariables, String name) {
for (int i = 0; i < classVariables.size(); i++) {
IXMLElement variable = (IXMLElement) classVariables.elementAt(i);
if (XMLUtil.nameOf(variable).equals(name)) return true;
}
return false;
}
public static void generateDefaultFactory(IndentWriter writer, IXMLElement klass)
throws IOException {
SharedWriter.generateFileLocation(writer, klass);
if (klass == null) {
throw new RuntimeException("missing class for factory");
}
String longname = XMLUtil.nameOf(klass) + "Factory" + s_factoryCounter++;
String klassName = XMLUtil.nameOf(klass);
writer.write("DECLARE_DEFAULT_OBJECT_FACTORY(" + longname + ", " + klassName + ");\n");
// Generate all appropriate registration information
SchemaWriter.addFactory("REGISTER_OBJECT_FACTORY(id," + longname + ", " + klassName + ");\n");
}
/**
* This method returns a Document from the contents of the XML file as contained in the String
* xmlFile, with no restriction as to the root element.
*/
public Document loadXMLFile(String xmlFile) {
if (!StringUtil.blank(xmlFile)) {
Document CipresDoc = XMLUtil.getDocumentFromString(xmlFile);
return CipresDoc;
}
return null;
}
public static IdentifiedPSM processPeptide(final String line, double retentionTime, String id) {
String peptide = XMLUtil.extractAttribute(line, "peptide");
if (peptide == null) throw new IllegalArgumentException("bad line " + line);
Polypeptide polypeptide = Polypeptide.fromString(peptide);
polypeptide.setRetentionTime(retentionTime);
return new IdentifiedPSM(id, polypeptide);
}
/**
* Sets the {@linkplain #rootTag} property.
*
* @param rootTag to be used as XML root tag
* @throws IllegalArgumentException if tag is null or empty
* @throws IllegalStateException if write isn't in initial state
*/
public void setRootTag(String rootTag) {
if (!XMLUtil.isLegalXMLTag(rootTag)) {
throw new IllegalArgumentException("rootTag: illegal: " + rootTag);
}
if (!this.isInitialState()) {
throw new IllegalStateException("writer write in progress");
}
this.checkNotSharedConfiguration();
this.rootTag = rootTag;
}
public static void declareConstructor(IndentWriter writer, IXMLElement constructor)
throws IOException {
IXMLElement klass = constructor.getParent();
SharedWriter.generateFileLocation(writer, klass);
if (klass == null) {
throw new RuntimeException("constructor not contained in a class");
}
String name = XMLUtil.getAttribute(klass, "name");
writer.write("virtual void ");
generateSignature(writer, constructor);
writer.write(";\n");
}
private static void generateChildren(IndentWriter writer, IXMLElement parent) throws IOException {
for (Enumeration e = parent.enumerateChildren(); e.hasMoreElements(); ) {
IXMLElement element = (IXMLElement) e.nextElement();
if (element.getName().equals("enum")) {
EnumerationWriter.generateImplementation(writer, element);
} else if (element.getName().equals("predicate")) {
PredicateWriter.generateImplementation(writer, element);
} else if (element.getName().equals("var")) {
} else if (element.getName().equals("constructor")) {
defineConstructor(writer, element);
generateFactory(writer, element);
} else {
System.err.println("generateImplementation:");
XMLUtil.dump(element);
}
}
}
protected void init(Element root) {
NodeList children = root.getChildNodes();
for (int i = 0; i < children.getLength(); i++) {
Node child = children.item(i);
if (child.getNodeName().equals("meta")) {
Element meta = (Element) child;
String value = XMLUtil.getText(meta);
this.metaAttributes.put(meta.getAttribute("name"), value);
}
}
// handle registers - OPTIONAL
Element r = XMLUtil.getChildElement(root, "registers");
if (r != null) {
List registers = XMLUtil.getChildElements(r, "register");
for (int i = 0; i < registers.size(); i++) {
Element register = (Element) registers.get(i);
RegisterDescriptor registerDescriptor =
DescriptorFactory.getFactory().createRegisterDescriptor(register);
registerDescriptor.setParent(this);
this.registers.add(registerDescriptor);
}
}
// handle global-conditions - OPTIONAL
Element globalConditionsElement = XMLUtil.getChildElement(root, "global-conditions");
if (globalConditionsElement != null) {
Element globalConditions = XMLUtil.getChildElement(globalConditionsElement, "conditions");
ConditionsDescriptor conditionsDescriptor =
DescriptorFactory.getFactory().createConditionsDescriptor(globalConditions);
conditionsDescriptor.setParent(this);
this.globalConditions = conditionsDescriptor;
}
// handle initial-steps - REQUIRED
Element intialActionsElement = XMLUtil.getChildElement(root, "initial-actions");
List initialActions = XMLUtil.getChildElements(intialActionsElement, "action");
for (int i = 0; i < initialActions.size(); i++) {
Element initialAction = (Element) initialActions.get(i);
ActionDescriptor actionDescriptor =
DescriptorFactory.getFactory().createActionDescriptor(initialAction);
actionDescriptor.setParent(this);
this.initialActions.add(actionDescriptor);
}
// handle global-actions - OPTIONAL
Element globalActionsElement = XMLUtil.getChildElement(root, "global-actions");
if (globalActionsElement != null) {
List globalActions = XMLUtil.getChildElements(globalActionsElement, "action");
for (int i = 0; i < globalActions.size(); i++) {
Element globalAction = (Element) globalActions.get(i);
ActionDescriptor actionDescriptor =
DescriptorFactory.getFactory().createActionDescriptor(globalAction);
actionDescriptor.setParent(this);
this.globalActions.add(actionDescriptor);
}
}
// handle common-actions - OPTIONAL
// - Store actions in HashMap for now. When parsing Steps, we'll resolve
// any common actions into local references.
Element commonActionsElement = XMLUtil.getChildElement(root, "common-actions");
if (commonActionsElement != null) {
List commonActions = XMLUtil.getChildElements(commonActionsElement, "action");
for (int i = 0; i < commonActions.size(); i++) {
Element commonAction = (Element) commonActions.get(i);
ActionDescriptor actionDescriptor =
DescriptorFactory.getFactory().createActionDescriptor(commonAction);
actionDescriptor.setParent(this);
addCommonAction(actionDescriptor);
}
}
// handle timer-functions - OPTIONAL
Element timerFunctionsElement = XMLUtil.getChildElement(root, "trigger-functions");
if (timerFunctionsElement != null) {
List timerFunctions = XMLUtil.getChildElements(timerFunctionsElement, "trigger-function");
for (int i = 0; i < timerFunctions.size(); i++) {
Element timerFunction = (Element) timerFunctions.get(i);
Integer id = new Integer(timerFunction.getAttribute("id"));
FunctionDescriptor function =
DescriptorFactory.getFactory()
.createFunctionDescriptor(XMLUtil.getChildElement(timerFunction, "function"));
function.setParent(this);
this.timerFunctions.put(id, function);
}
}
// handle steps - REQUIRED
Element stepsElement = XMLUtil.getChildElement(root, "steps");
List steps = XMLUtil.getChildElements(stepsElement, "step");
for (int i = 0; i < steps.size(); i++) {
Element step = (Element) steps.get(i);
StepDescriptor stepDescriptor =
DescriptorFactory.getFactory().createStepDescriptor(step, this);
this.steps.add(stepDescriptor);
}
// handle splits - OPTIONAL
Element splitsElement = XMLUtil.getChildElement(root, "splits");
if (splitsElement != null) {
List split = XMLUtil.getChildElements(splitsElement, "split");
for (int i = 0; i < split.size(); i++) {
Element s = (Element) split.get(i);
SplitDescriptor splitDescriptor = DescriptorFactory.getFactory().createSplitDescriptor(s);
splitDescriptor.setParent(this);
this.splits.add(splitDescriptor);
}
}
// handle joins - OPTIONAL:
Element joinsElement = XMLUtil.getChildElement(root, "joins");
if (joinsElement != null) {
List join = XMLUtil.getChildElements(joinsElement, "join");
for (int i = 0; i < join.size(); i++) {
Element s = (Element) join.get(i);
JoinDescriptor joinDescriptor = DescriptorFactory.getFactory().createJoinDescriptor(s);
joinDescriptor.setParent(this);
this.joins.add(joinDescriptor);
}
}
}
public void writeXML(PrintWriter out, int indent) {
XMLUtil.printIndent(out, indent++);
out.println("<workflow>");
Iterator iter = metaAttributes.entrySet().iterator();
while (iter.hasNext()) {
Map.Entry entry = (Map.Entry) iter.next();
XMLUtil.printIndent(out, indent);
out.print("<meta name=\"");
out.print(XMLUtil.encode(entry.getKey()));
out.print("\">");
out.print(XMLUtil.encode(entry.getValue()));
out.println("</meta>");
}
if (registers.size() > 0) {
XMLUtil.printIndent(out, indent++);
out.println("<registers>");
for (int i = 0; i < registers.size(); i++) {
RegisterDescriptor register = (RegisterDescriptor) registers.get(i);
register.writeXML(out, indent);
}
XMLUtil.printIndent(out, --indent);
out.println("</registers>");
}
if (timerFunctions.size() > 0) {
XMLUtil.printIndent(out, indent++);
out.println("<trigger-functions>");
Iterator iterator = timerFunctions.entrySet().iterator();
while (iterator.hasNext()) {
Map.Entry entry = (Map.Entry) iterator.next();
XMLUtil.printIndent(out, indent++);
out.println("<trigger-function id=\"" + entry.getKey() + "\">");
FunctionDescriptor trigger = (FunctionDescriptor) entry.getValue();
trigger.writeXML(out, indent);
XMLUtil.printIndent(out, --indent);
out.println("</trigger-function>");
}
while (iterator.hasNext()) {}
XMLUtil.printIndent(out, --indent);
out.println("</trigger-functions>");
}
if (getGlobalConditions() != null) {
XMLUtil.printIndent(out, indent++);
out.println("<global-conditions>");
getGlobalConditions().writeXML(out, indent);
out.println("</global-conditions>");
}
XMLUtil.printIndent(out, indent++);
out.println("<initial-actions>");
for (int i = 0; i < initialActions.size(); i++) {
ActionDescriptor action = (ActionDescriptor) initialActions.get(i);
action.writeXML(out, indent);
}
XMLUtil.printIndent(out, --indent);
out.println("</initial-actions>");
if (globalActions.size() > 0) {
XMLUtil.printIndent(out, indent++);
out.println("<global-actions>");
for (int i = 0; i < globalActions.size(); i++) {
ActionDescriptor action = (ActionDescriptor) globalActions.get(i);
action.writeXML(out, indent);
}
XMLUtil.printIndent(out, --indent);
out.println("</global-actions>");
}
if (commonActions.size() > 0) {
XMLUtil.printIndent(out, indent++);
out.println("<common-actions>");
Iterator iterator = getCommonActions().values().iterator();
while (iterator.hasNext()) {
ActionDescriptor action = (ActionDescriptor) iterator.next();
action.writeXML(out, indent);
}
XMLUtil.printIndent(out, --indent);
out.println("</common-actions>");
}
XMLUtil.printIndent(out, indent++);
out.println("<steps>");
for (int i = 0; i < steps.size(); i++) {
StepDescriptor step = (StepDescriptor) steps.get(i);
step.writeXML(out, indent);
}
XMLUtil.printIndent(out, --indent);
out.println("</steps>");
if (splits.size() > 0) {
XMLUtil.printIndent(out, indent++);
out.println("<splits>");
for (int i = 0; i < splits.size(); i++) {
SplitDescriptor split = (SplitDescriptor) splits.get(i);
split.writeXML(out, indent);
}
XMLUtil.printIndent(out, --indent);
out.println("</splits>");
}
if (joins.size() > 0) {
XMLUtil.printIndent(out, indent++);
out.println("<joins>");
for (int i = 0; i < joins.size(); i++) {
JoinDescriptor join = (JoinDescriptor) joins.get(i);
join.writeXML(out, indent);
}
XMLUtil.printIndent(out, --indent);
out.println("</joins>");
}
XMLUtil.printIndent(out, --indent);
out.println("</workflow>");
}
/**
* Aliases the given field's name with the given <code>alias</code>. The given alias must not be
* non-null, not-empty and must not contain illegal characters w.r.t. the XML format.
*
* @param f to alias
* @param alias the alias to set
* @return the previous alias, if any, or null
* @throws IllegalArgumentException if alias contains invalid XML chars
* @throws IllegalStateException if shared configuration
*/
public String alias(Field f, String alias) {
XMLUtil.validateAlias(alias);
this.checkNotSharedConfiguration();
return this.aliasing.put(f, alias);
}
public static void defineConstructor(IndentWriter writer, IXMLElement constructor)
throws IOException {
assert (DebugMsg.debugMsg("ClassWriter", "Begin ClassWriter::defineConstructor"));
IXMLElement klass = constructor.getParent();
SharedWriter.generateFileLocation(writer, klass);
if (klass == null) {
throw new RuntimeException("missing class for constructor");
}
String longname = XMLUtil.nameOf(klass);
writer.write("void " + longname + "::");
generateSignature(writer, constructor);
writer.write(" {\n");
writer.indent();
// If the constructor has a call to the super class, invoke it.
assert (DebugMsg.debugMsg(
"ClassWriter", "ClassWriter::defineConstructor - getting children named 'super'"));
Vector superCalls = constructor.getChildrenNamed("super");
assert (DebugMsg.debugMsg(
"ClassWriter",
"ClassWriter::defineConstructor - " + superCalls.size() + " children named retrieved"));
if (!superCalls.isEmpty()) {
assert (DebugMsg.debugMsg("ClassWriter", "ClassWriter::defineConstructor - calling super"));
if (superCalls.size() > 1) writer.write("!ERROR: AT MOST ONE CALL TO SUPER ALLOWED\n");
IXMLElement superCall = (IXMLElement) superCalls.elementAt(0);
String superClass = ModelAccessor.getParentClassName(klass);
String superCppClass = ModelAccessor.getCppClass(superClass);
writer.write(superCppClass + "::constructor(");
String comma = "";
Enumeration arguments = superCall.enumerateChildren();
while (arguments.hasMoreElements()) {
IXMLElement argument = (IXMLElement) arguments.nextElement();
String value = ModelAccessor.getValue(argument);
if (argument.getName().equals("value")
&& XMLUtil.getAttribute(argument, "type").equals("string"))
writer.write(comma + "\"" + value + "\"");
else writer.write(comma + value);
comma = ", ";
}
writer.write(");\n");
}
Set allocatedMemberVariables = new HashSet(); // Store names as we go for reference
/* Now capture names of constructor arguments */
Set constructorArguments = new HashSet(); // Store for names of constructor arguments
{
Vector args = constructor.getChildrenNamed("arg");
assert (DebugMsg.debugMsg(
"ClassWriter",
"ClassWriter::defineConstructor - getting " + args.size() + " arguments"));
for (int i = 0; i < args.size(); i++) {
IXMLElement arg = (IXMLElement) args.elementAt(i);
String argName = XMLUtil.getAttribute(arg, "name");
constructorArguments.add(argName);
}
}
Vector constructorAssignments = constructor.getChildrenNamed("assign");
Vector classVariables = klass.getChildrenNamed("var");
// Use the set below to track when an assignment is being made more than once for same variable
Set assignmentsMade = new HashSet();
for (int i = 0; i < constructorAssignments.size(); i++) {
IXMLElement element = (IXMLElement) constructorAssignments.elementAt(i);
String target = XMLUtil.getAttribute(element, "name");
if (assignmentsMade.contains(target)) {
writer.write("!ERROR: Duplicate assignment for " + target + "\n");
} else {
assignmentsMade.add(target);
// String type = getVariableType(classVariables, target);
// trust in the parser, for it will assign the correct types
String type = XMLUtil.getAttribute(element, "type");
IXMLElement sourceElement = element.getChildAtIndex(0);
if (sourceElement.getName().equals("new")) { // Handle object allocation
assert (DebugMsg.debugMsg(
"ClassWriter", "ClassWriter::defineConstructor - allocating object for " + target));
String sourceType = XMLUtil.typeOf(sourceElement);
writer.write(target + " = addVariable(");
writer.write(
sourceType
+ "Domain((new "
+ sourceType
+ "(m_id, \""
+ target
+ "\"))->getId(), \""
+ sourceType
+ "\")");
writer.write(", " + makeObjectVariableNameString(target) + ");\n");
writer.write(
"Id<"
+ type
+ ">(singleton("
+ target
+ "))->constructor("
+ buildArguments(
classVariables, constructorArguments, allocatedMemberVariables, sourceElement)
+ ");\n"); // Invoke initialization
writer.write(
"Id<"
+ type
+ ">(singleton("
+ target
+ "))->handleDefaults();\n"); // Default variable setup
} else { // Handle variable allocation
String value = ModelAccessor.getValue(sourceElement);
if (sourceElement.getName().equals("id") && type.equals(NddlXmlStrings.x_string))
value = XMLUtil.escapeQuotes(value);
else if (sourceElement.getName().equals(NddlXmlStrings.x_symbol)
|| XMLUtil.getAttribute(sourceElement, "type").equals(NddlXmlStrings.x_string))
value = "LabelStr(\"" + XMLUtil.escapeQuotes(value) + "\")";
else if (ModelAccessor.isNumericPrimitive(type)
&& !type.equals(NddlXmlStrings.x_boolean)) {
// Set both bounds to singleton value
value = value + ", " + value;
}
writer.write(target + " = addVariable(");
if (allocatedMemberVariables.contains(
value)) // If we are assigning one member to another, we obtain the base domain for it
writer.write(value + "->baseDomain()");
else writer.write(ModelAccessor.getDomain(type) + "(" + value + ", \"" + type + "\")");
writer.write(", " + makeObjectVariableNameString(target) + ");\n");
}
// Add member to the set
allocatedMemberVariables.add(target);
}
}
writer.unindent();
writer.write("}\n");
assert (DebugMsg.debugMsg("ClassWriter", "End ClassWriter::defineConstructor"));
}
public static IProtein processProtein(final String line) {
String peptide = XMLUtil.extractAttribute(line, "protein_descr");
if (peptide == null) throw new IllegalArgumentException("bad line " + line);
return Protein.getProtein(peptide, "", "", null);
}
public CIPResCommunicator(MesquiteModule mb, String xmlPrefsString, String[] outputFilePaths) {
if (xmlPrefsString != null) XMLUtil.readXMLPreferences(mb, this, xmlPrefsString);
this.outputFilePaths = outputFilePaths;
ownerModule = mb;
}
public static void generateFactory(IndentWriter writer, IXMLElement constructor)
throws IOException {
IXMLElement klass = constructor.getParent();
SharedWriter.generateFileLocation(writer, klass);
if (klass == null) throw new RuntimeException("missing class for factory");
String longname = XMLUtil.nameOf(klass) + "Factory" + s_factoryCounter++;
writer.write("class " + longname + ": public ObjectFactory {\n");
writer.write("public:\n");
writer.indent();
writer.write(longname + "(const LabelStr& name): ObjectFactory(name){}\n");
writer.unindent();
writer.write("private:\n");
writer.indent();
writer.write("ObjectId createInstance(const PlanDatabaseId& planDb,\n");
writer.write(" const LabelStr& objectType, \n");
writer.write(" const LabelStr& objectName,\n");
writer.write(
" const std::vector<const AbstractDomain*>& arguments) const {\n");
writer.indent();
Vector constructorAssignments = constructor.getChildrenNamed("arg");
String klassName = XMLUtil.nameOf(klass);
String constructorArguments = "";
String comma = "";
// Do some type checking - at least the size must match!
writer.write("check_error(arguments.size() == " + constructorAssignments.size() + ");\n");
// Process arguments, defining local variables and giving them initial values
for (int i = 0; i < constructorAssignments.size(); i++) {
IXMLElement element = (IXMLElement) constructorAssignments.elementAt(i);
String target = XMLUtil.getAttribute(element, "name");
String type = XMLUtil.getAttribute(element, "type");
writer.write("check_error(AbstractDomain::canBeCompared(*arguments[" + i + "], \n");
writer.write(
" planDb->getConstraintEngine()->getCESchema()->baseDomain(\""
+ type
+ "\")), \n");
writer.write(
" \"Cannot convert \" + arguments["
+ i
+ "]->getTypeName().toString() + \" to "
+ type
+ "\");\n");
writer.write("check_error(arguments[" + i + "]->isSingleton());\n");
String localVarType =
makeArgumentType(
type); // Some conversion may be required for Id's or strings or enumerations
// Declare local variable for current argument
writer.write(
localVarType
+ " "
+ target
+ "(("
+ localVarType
+ ")arguments["
+ i
+ "]->getSingletonValue());\n\n");
constructorArguments = constructorArguments + comma + target;
comma = ", ";
}
// Now do the declaration and allocation of the instance
writer.write(
klassName
+ "Id instance = (new "
+ klassName
+ "(planDb, objectType, objectName))->getId();\n");
writer.write("instance->constructor(" + constructorArguments + ");\n");
writer.write("instance->handleDefaults();\n");
writer.write("return instance;\n");
writer.unindent();
writer.write("}\n");
writer.unindent();
writer.write("};\n");
// Generate all appropriate registration informationLabelStr
Vector factoryNames = makeFactoryNames(constructor);
for (int i = 0; i < factoryNames.size(); i++) {
String factoryName = (String) factoryNames.elementAt(i);
SchemaWriter.addFactory(
"REGISTER_OBJECT_FACTORY(id," + longname + ", " + factoryName + ");\n");
}
}