@Override
  public VPackage parse() {

    logger.debug("Starting parsing package: " + xmlFile.getAbsolutePath());

    long startParsing = System.currentTimeMillis();

    try {
      Document document = getDocument();
      Element root = document.getDocumentElement();

      _package = new VPackage(xmlFile);

      Node name = root.getElementsByTagName(EL_NAME).item(0);
      _package.setName(name.getTextContent());
      Node descr = root.getElementsByTagName(EL_DESCRIPTION).item(0);
      _package.setDescription(descr.getTextContent());

      NodeList list = root.getElementsByTagName(EL_CLASS);

      boolean initPainters = false;
      for (int i = 0; i < list.getLength(); i++) {
        PackageClass pc = parseClass((Element) list.item(i));
        if (pc.getPainterName() != null) {
          initPainters = true;
        }
      }

      if (initPainters) {
        _package.initPainters();
      }

      logger.info(
          "Parsing the package '{}' finished in {}ms.\n",
          _package.getName(),
          (System.currentTimeMillis() - startParsing));
    } catch (Exception e) {
      collector.collectDiagnostic(e.getMessage(), true);
      if (RuntimeProperties.isLogDebugEnabled()) {
        e.printStackTrace();
      }
    }

    try {
      checkProblems("Error parsing package file " + xmlFile.getName());
    } catch (Exception e) {
      return null;
    }

    return _package;
  }
  public void addPackageClass(PackageClass pClass) {

    Document doc;
    try {
      doc = getDocument();
    } catch (Exception e) {
      e.printStackTrace();
      return;
    }

    String name = pClass.getName();

    // check if such class exists and remove duplicates
    Element rootEl = doc.getDocumentElement();
    NodeList classEls = rootEl.getElementsByTagName(EL_CLASS);
    for (int i = 0; i < classEls.getLength(); i++) {
      Element nameEl = getElementByName((Element) classEls.item(i), EL_NAME);
      if (name.equals(nameEl.getTextContent())) {
        rootEl.removeChild(classEls.item(i));
      }
    }

    Element classNode = doc.createElement(EL_CLASS);
    doc.getDocumentElement().appendChild(classNode);
    classNode.setAttribute(ATR_TYPE, PackageClass.ComponentType.SCHEME.getXmlName());
    classNode.setAttribute(ATR_STATIC, "false");

    Element className = doc.createElement(EL_NAME);
    className.setTextContent(name);
    classNode.appendChild(className);

    Element desrc = doc.createElement(EL_DESCRIPTION);
    desrc.setTextContent(pClass.getDescription());
    classNode.appendChild(desrc);

    Element icon = doc.createElement(EL_ICON);
    icon.setTextContent(pClass.getIcon());
    classNode.appendChild(icon);

    // graphics
    classNode.appendChild(generateGraphicsNode(doc, pClass.getGraphics()));

    // ports
    List<Port> ports = pClass.getPorts();
    if (!ports.isEmpty()) {
      Element portsEl = doc.createElement(EL_PORTS);
      classNode.appendChild(portsEl);

      for (Port port : ports) {
        portsEl.appendChild(generatePortNode(doc, port));
      }
    }

    // fields
    Collection<ClassField> fields = pClass.getFields();
    if (!fields.isEmpty()) {
      Element fieldsEl = doc.createElement(EL_FIELDS);
      classNode.appendChild(fieldsEl);

      for (ClassField cf : fields) {
        fieldsEl.appendChild(generateFieldNode(doc, cf));
      }
    }

    // write
    try {
      writeDocument(doc, new FileOutputStream(xmlFile));
    } catch (FileNotFoundException e) {
      e.printStackTrace();
    }
  }
  private void parsePort(PackageClass newClass, Element portNode) {
    String name = portNode.getAttribute(ATR_NAME);
    String type = portNode.getAttribute(ATR_TYPE);
    String x = portNode.getAttribute(ATR_X);
    String y = portNode.getAttribute(ATR_Y);
    String portConnection = portNode.getAttribute(ATR_PORT_CONNECTION);
    String strict = portNode.getAttribute(ATR_STRICT);
    String multi = portNode.getAttribute(ATR_MULTI);

    ClassField cf = newClass.getSpecField(name);

    if (newClass.getComponentType().hasSpec()) {

      if (name.indexOf(".") > -1) {
        // TODO - temporarily do not dig into hierarchy
        int idx = name.indexOf(".");
        String root = name.substring(0, idx);

        if (newClass.getSpecField(root) == null) {
          collector.collectDiagnostic(
              "Field "
                  + root
                  + " in class "
                  + newClass.getName()
                  + " is not declared in the specification, variable "
                  + type
                  + " "
                  + name
                  + " ignored ");
          return;
        }

        newClass.addSpecField(new ClassField(name, type));
      } else if (!TypeUtil.TYPE_THIS.equalsIgnoreCase(name)) {
        if (cf == null) {

          collector.collectDiagnostic(
              "Port "
                  + type
                  + " "
                  + name
                  + " in class "
                  + newClass.getName()
                  + " does not have the corresponding field in the specification");
        } else if (!cf.getType().equals(type)
            // type may be declared as "alias", however cf.getType() returns e.g. "double[]", ignore
            // it
            && !(cf.isAlias() && TypeUtil.TYPE_ALIAS.equals(type))) {

          collector.collectDiagnostic(
              "Port "
                  + type
                  + " "
                  + name
                  + " in class "
                  + newClass.getName()
                  + " does not match the field declared in the specification: "
                  + cf.getType()
                  + " "
                  + cf.getName());
        }
      }
    }

    Port newPort =
        new Port(
            name,
            type,
            Integer.parseInt(x),
            Integer.parseInt(y),
            portConnection,
            Boolean.parseBoolean(strict),
            Boolean.parseBoolean(multi));

    if (portNode.hasAttribute(ATR_ID)) newPort.setId(portNode.getAttribute(ATR_ID));

    Element gr;
    // open
    if ((gr = getElementByName(portNode, EL_OPEN)) != null
        && (gr = getElementByName(gr, EL_GRAPHICS)) != null) {
      newPort.setOpenGraphics(getGraphicsParser().parse(gr));
    }

    // closed
    if ((gr = getElementByName(portNode, EL_CLOSED)) != null
        && (gr = getElementByName(gr, EL_GRAPHICS)) != null) {
      newPort.setClosedGraphics(getGraphicsParser().parse(gr));
    }

    newClass.addPort(newPort);
  }
  private void parseField(PackageClass newClass, Element fieldNode) {
    String name = fieldNode.getAttribute(ATR_NAME);
    String type = fieldNode.getAttribute(ATR_TYPE);

    ClassField newField;

    if (newClass.getComponentType().hasSpec()) {
      if (name.indexOf(".") > -1) {
        // TODO - temporarily do not dig into hierarchy
        int idx = name.indexOf(".");
        String root = name.substring(0, idx);

        if (newClass.getSpecField(root) == null) {
          collector.collectDiagnostic(
              "Field "
                  + root
                  + " in class "
                  + newClass.getName()
                  + " is not declared in the specification, variable "
                  + type
                  + " "
                  + name
                  + " ignored ");
          return;
        }

        newField = new ClassField(name, type);
        newClass.addSpecField(newField);
      } else {
        newField = newClass.getSpecField(name);

        if (newField == null) {

          collector.collectDiagnostic(
              "Field "
                  + type
                  + " "
                  + name
                  + " in class "
                  + newClass.getName()
                  + " is not declared in the specification");
          return;
        } else if (!newField.getType().equals(type)) {

          collector.collectDiagnostic(
              "Field "
                  + type
                  + " "
                  + name
                  + " in class "
                  + newClass.getName()
                  + " does not match the field declared in the specification: "
                  + newField.getType()
                  + " "
                  + newField.getName());
          return;
        }
      }
    } else {
      newField = new ClassField(name, type);
      newClass.addSpecField(newField);
    }

    newField.setValue(fieldNode.hasAttribute(ATR_VALUE) ? fieldNode.getAttribute(ATR_VALUE) : null);
    newField.setDescription(fieldNode.getAttribute(ATR_DESCRIPTION));
    newField.setHidden(Boolean.parseBoolean(fieldNode.getAttribute(ATR_HIDDEN)));

    String nature = fieldNode.getAttribute(ATR_NATURE);
    if ("input".equals(nature)) newField.setInput(true);
    else if ("goal".equals(nature)) newField.setGoal(true);

    newClass.addField(newField);

    Element gr;
    // known
    if ((gr = getElementByName(fieldNode, EL_KNOWN)) != null
        && (gr = getElementByName(gr, EL_GRAPHICS)) != null) {
      newField.setKnownGraphics(getGraphicsParser().parse(gr));
    }
    // default
    if ((gr = getElementByName(fieldNode, EL_DEFAULT)) != null
        && (gr = getElementByName(gr, EL_GRAPHICS)) != null) {
      newField.setDefaultGraphics(getGraphicsParser().parse(gr));
    }
  }
  private PackageClass parseClass(Element classNode) {
    PackageClass newClass = new PackageClass();
    _package.getClasses().add(newClass);

    newClass.setComponentType(PackageClass.ComponentType.getType(classNode.getAttribute(ATR_TYPE)));
    newClass.setStatic(Boolean.parseBoolean(classNode.getAttribute(ATR_STATIC)));
    newClass.setName(getElementByName(classNode, EL_NAME).getTextContent());
    final String source = getElementStringByName(classNode, EL_FILE);
    if (source != null) {
      newClass.setSource(source);
    }
    newClass.setTarget(getElementStringByName(classNode, EL_EXTENDS));
    newClass.setDescription(getElementByName(classNode, EL_DESCRIPTION).getTextContent());
    newClass.setIcon(getElementByName(classNode, EL_ICON).getTextContent());

    // parse all variables declared in the corresponding specification
    if (newClass.getComponentType().hasSpec()) {
      final String newClassName = newClass.getName();
      try {
        switch (RuntimeProperties.getSpecParserKind()) {
          case REGEXP:
            {
              ClassList classList = new ClassList();
              SpecParser.parseSpecClass(newClassName, getWorkingDir(), classList);
              newClass.setSpecFields(classList.getType(newClassName).getFields());
              break;
            }
          case ANTLR:
            {
              if (specificationLoader == null) {
                specificationLoader =
                    new SpecificationLoader(new PackageSpecSourceProvider(_package), null);
              }
              final AnnotatedClass annotatedClass =
                  specificationLoader.getSpecification(newClassName);
              newClass.setSpecFields(annotatedClass.getFields());
              break;
            }
          default:
            throw new IllegalStateException("Undefined specification language parser");
        }
      } catch (SpecParseException e) {
        final String msg = "Unable to parse the specification of class " + newClassName;
        logger.error(msg, e);
        collector.collectDiagnostic(msg + "\nReason: " + e.getMessage() + "\nLine: " + e.getLine());
      }
    }

    // Graphics
    Element grNode = getElementByName(classNode, EL_GRAPHICS);
    newClass.addGraphics(
        getGraphicsParser().parse(grNode/*, newClass.getComponentType() == ComponentType.REL*/ ));

    Element painter;
    if ((painter = getElementByName(grNode, EL_PAINTER)) != null) {
      newClass.setPainterName(painter.getTextContent());
    }

    // Ports
    NodeList ports = classNode.getElementsByTagName(EL_PORT);
    for (int i = 0; i < ports.getLength(); i++) {
      parsePort(newClass, (Element) ports.item(i));
    }

    // Fields
    NodeList fields = classNode.getElementsByTagName(EL_FIELD);
    for (int i = 0; i < fields.getLength(); i++) {
      parseField(newClass, (Element) fields.item(i));
    }

    return newClass;
  }