/**
 * @file    Delay.h
 * @brief   Definition of Delay.
 * @author  Sarah Keating
 *
 * $Id: Delay.h 9063 2009-02-12 17:23:05Z sarahkeating $
 * $HeadURL: https://sbml.svn.sourceforge.net/svnroot/sbml/trunk/libsbml/src/sbml/Delay.h $
 *
 *<!---------------------------------------------------------------------------
 * This file is part of libSBML.  Please visit http://sbml.org for more
 * information about SBML, and the latest version of libSBML.
 *
 * Copyright 2005-2009 California Institute of Technology.
 * Copyright 2002-2005 California Institute of Technology and
 *                     Japan Science and Technology Corporation.
 * 
 * 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 Delay
 * @brief LibSBML implementation of %SBML's %Delay construct for %Event.
 *
 * An Event object defines when the event can occur, the variables that
 * are affected by the event, and how the variables are affected.  The
 * effect of the event can optionally be delayed after the occurrence of
 * the condition which invokes it.  An event delay is defined using an
 * object of class Delay.
 *
 * The object class Delay is derived from SBase and adds a single
 * subelement called "math".  This subelement is used to hold MathML
 * content.  The mathematical formula represented by "math" must evaluate
 * to a numerical value.  It is used as the length of time between when the
 * event has @em fired and when the event's assignments are actually @em
 * executed.  If no delay is present on a given Event, a time delay of zero
 * is assumed.
 *
 * The expression in "math" must be evaluated at the time the rule is @em
 * fired.  The expression must always evaluate to a positive number
 * (otherwise, a nonsensical situation could arise where an event is
 * defined to fire before it is triggered!).
 *
 * @section delay-units The units of the mathematical expression in a Delay
 *
 * In SBML Level&nbsp;2 versions before Version&nbsp;4, the units of the
 * numerical value computed by the Delay's "math" expression were @em
 * required to be in units of time or the model is considered to have a
 * unit consistency error.  In Version&nbsp;4, this requirement is relaxed.
 * The Version&nbsp;4 specification only stipulates that the units of the
 * numerical value computed by a Delay instance's "math" expression @em
 * should match the model's units of time (meaning the definition of the @c
 * time units in the model).  Depending on which Version of SBML
 * Level&nbsp;2 is in use, libSBML may or may not flag unit inconsistencies
 * as errors or just warnings. 
 *
 * Note that <em>units are not predefined or assumed</em> for the contents
 * of "math" in a Delay object; rather, they must be defined explicitly for
 * each instance of a Delay object in a model.  This is an important point
 * to bear in mind when literal numbers are used in delay expressions.  For
 * example, the following Event instance would result in a warning logged
 * by SBMLDocument::checkConsistency() about the fact that libSBML cannot
 * verify the consistency of the units of the expression.  The reason is
 * that the formula inside the "math" element does not have any declared
 * units, whereas what is expected in this context is units of time:
 * @code
 * <model>
 *     ...
 *     <listOfEvents>
 *         <event>
 *             ...
 *             <delay>
 *                 <math xmlns="http://www.w3.org/1998/Math/MathML">
 *                     <cn> 1 </cn>
 *                 </math>
 *             </delay>
 *             ...
 *         </event>
 *     </listOfEvents>
 *     ...
 * </model>
 * @endcode
 * 
 * The <code>&lt;cn&gt; 1 &lt;/cn&gt;</code> within the mathematical formula
 * of the @c delay above has <em>no units declared</em>.  To make the
 * expression have the needed units of time, literal numbers should be
 * avoided in favor of defining Parameter objects for each quantity, and
 * declaring units for the Parameter values.  The following fragment of
 * SBML illustrates this approach:
 * @code
 * <model>
 *     ...
 *     <listOfParameters>
 *         <parameter id="transcriptionDelay" value="10" units="time"/>
 *     </listOfParameters>
 *     ...
 *     <listOfEvents>
 *         <event>
 *             ...
 *             <delay>
 *                 <math xmlns="http://www.w3.org/1998/Math/MathML">
 *                     <ci> transcriptionDelay </ci>
 *                 </math>
 *             </delay>
 *             ...
 *         </event>
 *     </listOfEvents>
 *     ...
 * </model>
 * @endcode
 */

#ifndef Delay_h
#define Delay_h


#include <sbml/common/extern.h>
#include <sbml/common/sbmlfwd.h>


#ifdef __cplusplus


#include <string>

#include <sbml/SBase.h>


class ASTNode;
class SBMLVisitor;


class LIBSBML_EXTERN Delay : public SBase
{
public:

  /**
   * Creates a new Delay, optionally with the given math. 
   *
   * @param math an ASTNode representing the mathematical formula for
   * the delay expression.
   *
   * @docnote The native C++ implementation of this method defines a
   * default argument value.  In the documentation generated for different
   * libSBML language bindings, you may or may not see corresponding
   * arguments in the method declarations.  For example, in Java, a default
   * argument is handled by declaring two separate methods, with one of
   * them having the argument and the other one lacking the argument.
   * However, the libSBML documentation will be @em identical for both
   * methods.  Consequently, if you are reading this and do not see an
   * argument even though one is described, please look for descriptions of
   * other variants of this method near where this one appears in the
   * documentation.
   */
  Delay (const ASTNode* math = NULL);


  /** @cond doxygen-libsbml-internal until after the 3.3.0 release */
  /**
   * Creates a new Delay using the given SBML @p level and @p version
   * values and optionally a set of XMLNamespaces.
   *
   * @param level an unsigned int, the SBML Level to assign to this Delay
   *
   * @param version an unsigned int, the SBML Version to assign to this
   * Delay
   * 
   * @param xmlns XMLNamespaces, a pointer to an array of XMLNamespaces to
   * assign to this Delay
   *
   * @note Once a Delay has been added to an SBMLDocument, the @p level,
   * @p version and @p xmlns namespaces for the document @em override those used
   * to create the Delay.  Despite this, the ability to supply the values
   * at creation time is an important aid to creating valid SBML.  Knowledge of
   * the intented SBML Level and Version determine whether it is valid to
   * assign a particular value to an attribute, or whether it is valid to add
   * an object to an existing SBMLDocument.
   *
   * @docnote The native C++ implementation of this method defines a
   * default argument value.  In the documentation generated for different
   * libSBML language bindings, you may or may not see corresponding
   * arguments in the method declarations.  For example, in Java, a default
   * argument is handled by declaring two separate methods, with one of
   * them having the argument and the other one lacking the argument.
   * However, the libSBML documentation will be @em identical for both
   * methods.  Consequently, if you are reading this and do not see an
   * argument even though one is described, please look for descriptions of
   * other variants of this method near where this one appears in the
   * documentation.
   */
  Delay (unsigned int level, unsigned int version, 
               XMLNamespaces* xmlns = 0);
  /** @endcond doxygen-libsbml-internal */


  /**
   * Destroys this Delay.
   */
  virtual ~Delay ();


  /**
   * Copy constructor; creates a copy of this Delay.
   */
  Delay (const Delay& orig);


  /**
   * Assignment operator
   */
  Delay& operator=(const Delay& rhs);


  /**
   * Accepts the given SBMLVisitor for this instance of Delay.
   *
   * @param v the SBMLVisitor instance to be used.
   *
   * @return the result of calling <code>v.visit()</code>.
   */
  virtual bool accept (SBMLVisitor& v) const;


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


  /**
   * Get the mathematical formula for the delay and return it
   * as an AST.
   * 
   * @return the math of this Delay.
   */
  const ASTNode* getMath () const;


  /**
   * Predicate to test whether the formula for this delay has been set.
   *
   * @htmlinclude libsbml-comment-set-methods.html
   *
   * @return @c true if the formula (meaning the @c math subelement) of
   * this Delay has been set, @c false otherwise.
   */
  bool isSetMath () const;


  /**
   * Sets the delay expression of this Delay instance to a copy of the given
   * ASTNode.
   *
   * @htmlinclude libsbml-comment-set-methods.html
   *
   * @param math an ASTNode representing a formula tree.
   */
  void setMath (const ASTNode* math);


  /**
   * Calculates and returns a UnitDefinition that expresses the units
   * of measurement assumed for the "math" expression of this Delay.
   *
   * Delay elements in SBML express a time delay for an Event.  Beginning
   * with SBML Level&nbsp;2 Version&nbsp;2, the units of that time are
   * calculated based on the mathematical expression and the model
   * quantities referenced by <code>&lt;ci&gt;</code> elements used within
   * that expression.  The Delay::getDerivedUnitDefinition() method returns
   * what libSBML computes the units to be, to the extent that libSBML can
   * compute them.
   *
   * (Prior to SBML Level&nbsp;2 Version&nbsp;2, there existed an attribute
   * on Event called "timeUnits".  This attribute could be used to set the
   * intended units of the delay expression.  For such models, this will
   * return a UnitDefinition object that corresponds to the declared
   * "timeUnits" units.)
   *
   * @warning Note that it is possible the "math" expression in the Delay
   * contains literal numbers or parameters with undeclared units.  In
   * those cases, it is not possible to calculate the units of the overall
   * expression without making assumptions.  LibSBML does not make
   * assumptions about the units, and Delay::getDerivedUnitDefinition()
   * only returns the units as far as it is able to determine them.  For
   * example, in an expression <em>X + Y</em>, if <em>X</em> has
   * unambiguously-defined units and <em>Y</em> does not, it will return
   * the units of <em>X</em>.  When using this method, <strong>it is
   * critical that callers also invoke the method</strong>
   * Delay::containsUndeclaredUnits() <strong>to determine whether this
   * situation holds</strong>.  Callers should take suitable action in
   * those situations.
   * 
   * @return a UnitDefinition that expresses the units of the math 
   * expression of this Delay.
   *
   * @see containsUndeclaredUnits()
   */
  UnitDefinition * getDerivedUnitDefinition();


  /**
   * Predicate returning @c true or @c false depending on whether 
   * the "math" expression in this Delay instance contains
   * parameters with undeclared units or literal numbers.
   * 
   * Delay elements in SBML express a time delay for an Event.  Beginning
   * with SBML Level&nbsp;2 Version&nbsp;2, the units of that time are
   * calculated based on the mathematical expression and the model
   * quantities referenced by <code>&lt;ci&gt;</code> elements used within
   * that expression.  The Delay::getDerivedUnitDefinition() method returns
   * what libSBML computes the units to be, to the extent that libSBML can
   * compute them.  However, if the expression contains literal numbers or
   * parameters with undeclared units, libSBML may not be able to compute
   * the full units of the expression and will only return what it can
   * compute.  Callers should always use Delay::containsUndeclaredUnits()
   * when using Delay::getDerivedUnitDefinition() to decide whether the
   * returned units may be incomplete.
   * 
   * @return @c true if the math expression of this Delay includes
   * numbers/parameters with undeclared units, @c false otherwise.
   *
   * @note A return value of @c true indicates that the UnitDefinition
   * returned by Delay::getDerivedUnitDefinition() may not accurately
   * represent the units of the expression.
   *
   * @see getDerivedUnitDefinition()
   */
  bool containsUndeclaredUnits();


  /** @cond doxygen-libsbml-internal */

  /**
   * Sets the parent SBMLDocument of this SBML object.
   *
   * @param d the SBMLDocument to use.
   */
  virtual void setSBMLDocument (SBMLDocument* d);


  /**
   * Sets the parent SBML object of this SBML object.
   *
   * @param sb the SBML object to use
   */
  virtual void setParentSBMLObject (SBase* sb);

  /** @endcond doxygen-libsbml-internal */


  /**
   * Returns the libSBML type code of this object instance.
   *
   * @if clike LibSBML attaches an identifying code to every
   * kind of SBML object.  These are known as <em>SBML type codes</em>.
   * The set of possible type codes is defined in the enumeration
   * #SBMLTypeCode_t.  The names of the type codes all begin with the
   * characters @c SBML_. @endif@if java LibSBML attaches an
   * identifying code to every kind of SBML object.  These are known as
   * <em>SBML type codes</em>.  In other languages, the set of type codes
   * is stored in an enumeration; in the Java language interface for
   * libSBML, the type codes are defined as static integer constants in
   * interface class {@link libsbmlConstants}.  The names of the type codes
   * all begin with the characters @c SBML_. @endif
   *
   * @return the SBML type code for this object, or @c SBML_UNKNOWN (default).
   *
   * @see getElementName()
   */
  virtual SBMLTypeCode_t getTypeCode () const;


  /**
   * Returns the XML element name of this object, which for Delay, is
   * always @c "delay".
   * 
   * @return the name of this element, i.e., @c "delay".
   *
   * @see getTypeCode()
   */
  virtual const std::string& getElementName () const;


  /** @cond doxygen-libsbml-internal */

  /**
   * Returns the position of this element.
   * 
   * @return the ordinal position of the element with respect to its
   * siblings or -1 (default) to indicate the position is not significant.
   */
  virtual int getElementPosition () const;


  /**
   * Subclasses should override this method to write out their contained
   * SBML objects as XML elements.  Be sure to call your parents
   * implementation of this method as well.
   */
  virtual void writeElements (XMLOutputStream& stream) const;

  /** @endcond doxygen-libsbml-internal */


protected:
  /** @cond doxygen-libsbml-internal */

  /**
   * Subclasses should override this method to read (and store) XHTML,
   * MathML, etc. directly from the XMLInputStream.
   *
   * @return true if the subclass read from the stream, false otherwise.
   */
  virtual bool readOtherXML (XMLInputStream& stream);

  /**
   * @return the SBML object corresponding to next XMLToken in the
   * XMLInputStream or @c NULL if the token was not recognized.
   */
//  virtual SBase* createObject (XMLInputStream& stream);

  /**
   * Subclasses should override this method to read values from the given
   * XMLAttributes set into their specific fields.  Be sure to call your
   * parents implementation of this method as well.
   */
  virtual void readAttributes (const XMLAttributes& attributes);

  /**
   * Subclasses should override this method to write their XML attributes
   * to the XMLOutputStream.  Be sure to call your parents implementation
   * of this method as well.
   */
  virtual void writeAttributes (XMLOutputStream& stream) const;


  ASTNode*     mMath;

  /** @endcond doxygen-libsbml-internal */
};


#endif  /* __cplusplus */


#ifndef SWIG


BEGIN_C_DECLS

/*-----------------------------------------------------------------------------
 * See the .cpp file for the documentation of the following functions.
 *---------------------------------------------------------------------------*/


LIBSBML_EXTERN
Delay_t *
Delay_create (void);


LIBSBML_EXTERN
Delay_t *
Delay_createWithMath ( const ASTNode_t *math);


/** @cond doxygen-libsbml-internal */
LIBSBML_EXTERN
Delay_t *
Delay_createWithLevelVersionAndNamespaces (unsigned int level,
              unsigned int version, XMLNamespaces_t *xmlns);
/** @endcond doxygen-libsbml-internal */


LIBSBML_EXTERN
void
Delay_free (Delay_t *d);


LIBSBML_EXTERN
Delay_t *
Delay_clone (const Delay_t *d);


LIBSBML_EXTERN
const XMLNamespaces_t *
Delay_getNamespaces(Delay_t *c);


LIBSBML_EXTERN
const ASTNode_t *
Delay_getMath (const Delay_t *d);


LIBSBML_EXTERN
int
Delay_isSetMath (const Delay_t *d);


LIBSBML_EXTERN
void
Delay_setMath (Delay_t *d, const ASTNode_t *math);


LIBSBML_EXTERN
UnitDefinition_t * 
Delay_getDerivedUnitDefinition(Delay_t *d);


LIBSBML_EXTERN
int 
Delay_containsUndeclaredUnits(Delay_t *d);

END_C_DECLS


#endif  /* !SWIG */
#endif  /* Delay_h */
