libsbml5-dev 5.13.0+dfsg-1 / usr / include / sbml / extension / ASTBasePlugin.h

/**
 * @cond doxygenLibsbmlInternal
 *
 * @file    ASTBasePlugin.h
 * @brief   Definition of ASTBasePlugin, the base class of extension entities
 *          plugged in AST derived classes in the SBML Core package.
 * @author  Sarah Keating
 *
 *
 * <!--------------------------------------------------------------------------
 * This file is part of libSBML.  Please visit http://sbml.org for more
 * information about SBML, and the latest version of libSBML.
 *
 * Copyright (C) 2013-2016 jointly by the following organizations:
 *     1. California Institute of Technology, Pasadena, CA, USA
 *     2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
 *     3. University of Heidelberg, Heidelberg, Germany
 *
 * Copyright (C) 2009-2012 jointly by the following organizations: 
 *     1. California Institute of Technology, Pasadena, CA, USA
 *     2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
 *  
 * Copyright (C) 2006-2008 by the California Institute of Technology,
 *     Pasadena, CA, USA 
 *  
 * Copyright (C) 2002-2005 jointly by the following organizations: 
 *     1. California Institute of Technology, Pasadena, CA, USA
 *     2. Japan Science and Technology Agency, Japan
 * 
 * This library is free software; you can redistribute it and/or modify it
 * under the terms of the GNU Lesser General Public License as published by
 * the Free Software Foundation.  A copy of the license agreement is provided
 * in the file named "LICENSE.txt" included with this software distribution
 * and also available online as http://sbml.org/software/libsbml/license.html
 * ------------------------------------------------------------------------ -->
 *
 * @class ASTBasePlugin
 * @sbmlbrief{core} Base class for extensions that plug into AST classes.
 *
 * @htmlinclude not-sbml-warning.html
 */

#ifndef ASTBasePlugin_h
#define ASTBasePlugin_h

#include <sbml/common/libsbml-config-common.h>

#ifndef LIBSBML_USE_LEGACY_MATH

#include <sbml/common/sbmlfwd.h>
#include <sbml/SBMLTypeCodes.h>
#include <sbml/SBMLErrorLog.h>
#include <sbml/math/ASTBase.h>
#include <sbml/SBMLDocument.h>
#include <sbml/util/StringBuffer.h>

#include <sbml/math/L3ParserSettings.h>

#ifdef __cplusplus

LIBSBML_CPP_NAMESPACE_BEGIN

class ASTBase;

class LIBSBML_EXTERN ASTBasePlugin
{
public:

  /**
   * Destroy this object.
   */
  virtual ~ASTBasePlugin ();


  /**
   * Assignment operator for ASTBasePlugin.
   */
  ASTBasePlugin& operator=(const ASTBasePlugin& orig);


  /**
   * Creates and returns a deep copy of this ASTBasePlugin object.
   *
   * @return the (deep) copy of this ASTBasePlugin object.
   */
  virtual ASTBasePlugin* clone () const;


  /**
   * Returns the XML namespace (URI) of the package extension
   * of this plugin object.
   *
   * @return the URI of the package extension of this plugin object.
   */
  const std::string& getElementNamespace() const;


  /**
   * Returns the prefix of the package extension of this plugin object.
   *
   * @return the prefix of the package extension of this plugin object.
   */
  virtual const std::string& getPrefix() const;


  /**
   * Returns the package name of this plugin object.
   *
   * @return the package name of this plugin object.
   */
  virtual const std::string& getPackageName() const;




  /* open doxygen comment */

  // ---------------------------------------------------------
  //
  // virtual functions (internal implementation) which should 
  // be overridden by subclasses.
  //
  // ---------------------------------------------------------

  virtual int setSBMLExtension (const SBMLExtension* ext);

  virtual int setPrefix (const std::string& prefix);
  /**
   * Sets the parent SBML object of this plugin object to
   * this object and child elements (if any).
   * (Creates a child-parent relationship by this plugin object)
   *
   * This function is called when this object is created by
   * the parent element.
   * Subclasses must override this this function if they have one
   * or more child elements. Also, ASTBasePlugin::connectToParent(@if java SBase@endif)
   * must be called in the overridden function.
   *
   * @param sbase the SBase object to use
   *
   * @see setSBMLDocument
   * @see enablePackageInternal
   */
  virtual void connectToParent (ASTBase *astbase);


  /**
   * Enables/Disables the given package with child elements in this plugin 
   * object (if any).
   * (This is an internal implementation invoked from 
   *  SBase::enablePackageInternal() function)
   *
   * Subclasses which contain one or more SBase derived elements should 
   * override this function if elements defined in them can be extended by
   * some other package extension.
   *
   * @see setSBMLDocument
   * @see connectToParent
   */
  virtual void enablePackageInternal(const std::string& pkgURI,
                                     const std::string& pkgPrefix, bool flag);


  virtual bool stripPackage(const std::string& pkgPrefix, bool flag);


  /* end doxygen comment */

  // ----------------------------------------------------------


  /**
   * Gets the URI to which this element belongs to.
   * For example, all elements that belong to SBML Level 3 Version 1 Core
   * must would have the URI "http://www.sbml.org/sbml/level3/version1/core"; 
   * all elements that belong to Layout Extension Version 1 for SBML Level 3
   * Version 1 Core must would have the URI
   * "http://www.sbml.org/sbml/level3/version1/layout/version1/"
   *
   * Unlike getElementNamespace, this function first returns the URI for this 
   * element by looking into the SBMLNamespaces object of the document with 
   * the its package name. if not found it will return the result of 
   * getElementNamespace
   *
   * @return the URI this elements  
   *
   * @see getPackageName
   * @see getElementNamespace
   * @see SBMLDocument::getSBMLNamespaces
   * @see getSBMLDocument
   */
  std::string getURI() const;

  /* open doxygen comment */

  /**
   * Returns the parent ASTNode object to which this plugin 
   * object connected.
   *
   * @return the parent ASTNode object to which this plugin 
   * object connected.
   */
  ASTBase* getParentASTObject ();

  /* end doxygen comment */

  /* open doxygen comment */

  /**
   * Returns the parent ASTNode object to which this plugin 
   * object connected.
   *
   * @return the parent ASTNode object to which this plugin 
   * object connected.
   */
  const ASTBase* getParentASTObject () const;

  
  /* end doxygen comment */

  /**
   * Sets the XML namespace to which this element belongs to.
   * For example, all elements that belong to SBML Level 3 Version 1 Core
   * must set the namespace to "http://www.sbml.org/sbml/level3/version1/core"; 
   * all elements that belong to Layout Extension Version 1 for SBML Level 3
   * Version 1 Core must set the namespace to 
   * "http://www.sbml.org/sbml/level3/version1/layout/version1/"
   *
   * @copydetails doc_returns_success_code
   * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
   * @li @sbmlconstant{LIBSBML_INVALID_ATTRIBUTE_VALUE, OperationReturnValues_t}
   */
  int setElementNamespace(const std::string &uri);

  /**
   * Returns the SBML level of the package extension of 
   * this plugin object.
   *
   * @return the SBML level of the package extension of
   * this plugin object.
   */
  unsigned int getLevel() const;


  /**
   * Returns the SBML version of the package extension of
   * this plugin object.
   *
   * @return the SBML version of the package extension of
   * this plugin object.
   */
  unsigned int getVersion() const;


  /**
   * Returns the package version of the package extension of
   * this plugin object.
   *
   * @return the package version of the package extension of
   * this plugin object.
   */
  unsigned int getPackageVersion() const;


  
  /* open doxygen comment */
  virtual SBMLNamespaces * getSBMLNamespaces() const;


  virtual bool isSetMath() const;

  virtual const ASTBase * getMath() const;

  virtual void createMath(int type);

  virtual int addChild(ASTBase * child);

  virtual ASTBase* getChild (unsigned int n) const;

  virtual unsigned int getNumChildren() const;

  virtual int insertChild(unsigned int n, ASTBase* newChild);

  virtual int prependChild(ASTBase* newChild);

  virtual int removeChild(unsigned int n);

  virtual int replaceChild(unsigned int n, ASTBase* newChild, bool delreplaced);

  virtual int swapChildren(ASTFunction* that);


  virtual bool read(XMLInputStream& stream, const std::string& reqd_prefix,
                                            const XMLToken& currentElement);
  virtual void addExpectedAttributes(ExpectedAttributes& attributes, 
                                     XMLInputStream& stream, int type);

  virtual bool readAttributes (const XMLAttributes& attributes,
                               const ExpectedAttributes& expectedAttributes,
                               XMLInputStream& stream, const XMLToken& element,
                               int type);

  virtual void writeAttributes(XMLOutputStream& stream, int type) const;

  virtual void writeXMLNS(XMLOutputStream& stream) const;

  virtual bool isNumberNode(int type) const;
  virtual bool isFunctionNode(int type) const;

  virtual bool isLogical(int type) const;
  virtual bool isConstantNumber(int type) const;
  virtual bool isCSymbolFunction(int type) const;
  virtual bool isCSymbolNumber(int type) const;
  virtual bool isName(int type) const;
  virtual bool isNumber(int type) const;
  virtual bool isOperator(int type) const;
  virtual bool isRelational(int type) const;
  virtual bool representsQualifier(int type) const;

  virtual bool isFunction(int type) const;
  virtual bool representsUnaryFunction(int type) const;
  virtual bool representsBinaryFunction(int type) const;
  virtual bool representsNaryFunction(int type) const;

  virtual bool hasCorrectNumberArguments(int type) const;
  virtual bool isWellFormedNode(int type) const;
  
  virtual bool isTopLevelMathMLFunctionNodeTag(const std::string& name) const;

  virtual bool isTopLevelMathMLNumberNodeTag(const std::string& name) const;
  
  virtual int getTypeFromName(const std::string& name) const;

  virtual const char * getNameFromType(int type) const;

  /* end doxygen comment */
  friend class L3ParserSettings;
  friend class ASTBase;

  //The following functions don't do anything on their own, and are meant to be overridden by relevant plugins.
  /**
   * Renames all the SIdRef attributes on this node and its child nodes.
   *
   * @param oldid the old identifier.
   * @param newid the new identifier.
   */
  virtual void renameSIdRefs(const std::string& oldid, const std::string& newid);


  /**
   * Renames all the UnitSIdRef attributes on this node and its child nodes.
   *
   * The only place UnitSIDRefs appear in MathML <code>&lt;cn&gt;</code>
   * elements, so the effects of this method are limited to that.
   *
   * @param oldid the old identifier.
   * @param newid the new identifier.
   */
  virtual void renameUnitSIdRefs(const std::string& oldid, const std::string& newid);


  /** @cond doxygenLibsbmlInternal */
  /**
   * Replace any nodes of type AST_NAME with the name 'id' from the child
   * 'math' object with the provided ASTNode.
   *
   */
  virtual void replaceIDWithFunction(const std::string& id, const ASTNode* function);

protected:
  /* open doxygen comment */
  /**
   * Constructor. Creates an ASTBasePlugin object with the URI and 
   * prefix of an package extension.
   */
  ASTBasePlugin (const std::string &uri);

  ASTBasePlugin ();

  /**
   * Copy constructor. Creates a copy of this SBase object.
   */
  ASTBasePlugin(const ASTBasePlugin& orig);


  /**
   * Returns true if this is a package function which should be written as
   * "functionname(argumentlist)", false otherwise.
   */
  virtual bool isPackageInfixFunction() const;

  /**
   * Returns true if this is a package function which should be written
   * special syntax that the package knows about, false otherwise.
   */
  virtual bool hasPackageOnlyInfixSyntax() const;

  /**
   * Get the precedence of this package function, or -1 if unknown
   */
  virtual int getL3PackageInfixPrecedence() const;

  /**
   * Returns true if this is a package function which should be written
   * special syntax that the package knows about, false otherwise.
   */
  virtual bool hasUnambiguousPackageInfixGrammar(const ASTNode *child) const;

  /**
   * Visits the given ASTNode_t and continues the inorder traversal for nodes whose syntax are determined by packages.
   */
  virtual void visitPackageInfixSyntax ( const ASTNode *parent,
                                         const ASTNode *node,
                                         StringBuffer_t  *sb,
                                         const L3ParserSettings* settings) const;

  /**
   * This function checks the provided ASTNode function to see if it is a 
   * known function with the wrong number of arguments.  If so, 'error' is
   * set and '-1' is returned.  If it has the correct number of arguments,
   * '1' is returned.  If the plugin knows nothing about the function, '0' 
   * is returned.
   */
  virtual int checkNumArguments(const ASTNode* function, std::stringstream& error) const;

  /**
   * The generic parsing function for grammar lines that packages recognize, but not core.
   * When a package recognizes the 'type', it will parse and return the correct ASTNode.
   * If it does not recognize the 'type', or if the arguments are incorrect, NULL is returend.
   */
  virtual ASTNode* parsePackageInfix(L3ParserGrammarLineType_t type, 
    std::vector<ASTNode*> *nodeList = NULL, std::vector<std::string*> *stringList = NULL,
    std::vector<double> *doubleList = NULL) const;


  /**
   * The user input a string of the form "name(...)", and we want to know if
   * 'name' is recognized by a package as being a particular function.  We already
   * know that it is not used in the Model as a FunctionDefinition.  Should do
   * caseless string comparison.  Return the type of the function, or AST_UNKNOWN
   * if nothing found.
   */
  virtual int getPackageFunctionFor(const std::string& name) const;

  /*-- data members --*/

  //
  // An SBMLExtension derived object of corresponding package extension
  // The owner of this object is SBMLExtensionRegistry class.
  //
  const SBMLExtension  *mSBMLExt;

  //
  // Parent ASTNode object to which this plugin object
  // connected.
  //
  ASTBase                *mParentASTNode;

  //
  // XML namespace of corresponding package extension
  //
  std::string          mURI;

  //
  // SBMLNamespaces derived object of this plugin object.
  //
  SBMLNamespaces      *mSBMLNS;

  //
  // Prefix of corresponding package extension
  //
  std::string          mPrefix;

  /* end doxygen comment */
};

LIBSBML_CPP_NAMESPACE_END

#endif  /* __cplusplus */

#ifndef SWIG

LIBSBML_CPP_NAMESPACE_BEGIN
BEGIN_C_DECLS


END_C_DECLS
LIBSBML_CPP_NAMESPACE_END

#endif  /* !SWIG */

#endif /* LIBSBML_USE_LEGACY_MATH */

#endif  /* ASTBasePlugin_h */
/** @endcond */