001/* ----------------------------------------------------------------------------
002 * This file was automatically generated by SWIG (http://www.swig.org).
003 * Version 2.0.12
004 *
005 * Do not make changes to this file unless you know what you are doing--modify
006 * the SWIG interface file instead.
007 * ----------------------------------------------------------------------------- */
008
009package org.sbml.libsbml;
010
011/** 
012 *  Implementation of SBML Level 2's StoichiometryMath
013 * construct.
014 <p>
015 * <h2>Stoichiometries in SBML Level 2</h2>
016 <p>
017 * In SBML Level 2, product and reactant stoichiometries can be specified
018 * using <em>either</em> the 'stoichiometry' attribute or a 'stoichiometryMath'
019 * element in a {@link SpeciesReference} object.  The 'stoichiometry' attribute is
020 * of type <code>double</code> and should contain values greater than zero (0).  The
021 * 'stoichiometryMath' element is implemented as an element containing a
022 * MathML expression.  These two are mutually exclusive; only one of
023 * 'stoichiometry' or 'stoichiometryMath' should be defined in a given
024 * {@link SpeciesReference} instance.  When neither the attribute nor the element
025 * is present, the value of 'stoichiometry' in the enclosing
026 * {@link SpeciesReference} instance defaults to <code>1.</code>
027 <p>
028 * For maximum interoperability, {@link SpeciesReference}'s 'stoichiometry'
029 * attribute should be used in preference to 'stoichiometryMath' when a
030 * species' stoichiometry is a simple scalar number (integer or decimal).
031 * When the stoichiometry is a rational number, or when it is a more
032 * complicated formula, 'stoichiometryMath' must be used.  The MathML
033 * expression in 'stoichiometryMath' may also refer to identifiers of
034 * entities in a model (except reaction identifiers).  However, the only
035 * species identifiers that can be used in 'stoichiometryMath' are those
036 * referenced in the enclosing {@link Reaction}'s list of reactants, products and
037 * modifiers.
038 <p>
039 * The 'stoichiometry' attribute and the 'stoichiometryMath' element, when
040 * either is used, is each interpreted as a factor applied to the reaction
041 * rate to produce the rate of change of the species identified by the
042 * 'species' attribute in the enclosing {@link SpeciesReference}.  This is the
043 * normal interpretation of a stoichiometry, but in SBML, one additional
044 * consideration has to be taken into account.  The reaction rate, which is
045 * the result of the {@link KineticLaw}'s 'math' element, is always in the model's
046 * <em>substance</em> per <em>time</em> units.  However, the rate of change of the
047 * species will involve the species' <em>substance</em> units (i.e., the units
048 * identified by the {@link Species} object's 'substanceUnits' attribute), and
049 * these units may be different from the model's default <em>substance</em>
050 * units.  If the units <em>are</em> different, the stoichiometry must
051 * incorporate a conversion factor for converting the model's <em>substance</em>
052 * units to the species' <em>substance</em> units.  The conversion factor is
053 * assumed to be included in the scalar value of the 'stoichiometry'
054 * attribute if 'stoichiometry' is used.  If instead 'stoichiometryMath' is
055 * used, then the product of the model's 'substance' units times the
056 * 'stoichiometryMath' units must match the <em>substance</em> units of the
057 * species.  Note that in either case, if the species' units and the
058 * model's default <em>substance</em> units are the same, the stoichiometry ends
059 * up being a dimensionless number and equivalent to the standard chemical
060 * stoichiometry found in textbooks.  Examples and more explanations of
061 * this are given in the SBML specification.
062 <p>
063 * The following is a simple example of a species reference for species 
064 * <code>'X0'</code>, with stoichiometry <code>2</code>, in a list of reactants within a reaction
065 * having the identifier <code>'J1':</code>
066 * <div class='fragment'><pre class='fragment'>
067 &lt;model&gt;
068     ...
069     &lt;listOfReactions&gt;
070         &lt;reaction id='J1'&gt;
071             &lt;listOfReactants&gt;
072                 &lt;speciesReference species='X0' stoichiometry='2'&gt;
073             &lt;/listOfReactants&gt;
074             ...
075         &lt;/reaction&gt;
076         ...
077     &lt;/listOfReactions&gt;
078     ...
079 &lt;/model&gt;
080 </pre></div>
081 <p>
082 * The following is a more complex example of a species reference for
083 * species <code>'X0'</code>, with a stoichiometry formula consisting of
084 * a rational number:
085 * <div class='fragment'><pre class='fragment'>
086 &lt;model&gt;
087     ...
088     &lt;listOfReactions&gt;
089         &lt;reaction id='J1'&gt;
090             &lt;listOfReactants&gt;
091                 &lt;speciesReference species='X0'&gt;
092                     &lt;stoichiometryMath&gt;
093                         &lt;math xmlns='http://www.w3.org/1998/Math/MathML'&gt; 
094                             &lt;cn type='rational'&gt; 3 &lt;sep/&gt; 2 &lt;/cn&gt;
095                         &lt;/math&gt;
096                     &lt;/stoichiometryMath&gt;
097                 &lt;/speciesReference&gt;
098             &lt;/listOfReactants&gt;
099             ...
100         &lt;/reaction&gt;
101         ...
102     &lt;/listOfReactions&gt;
103     ...
104 &lt;/model&gt;
105 </pre></div>
106 <p>
107 * Additional discussions of stoichiometries and implications for species
108 * and reactions are included in the documentation of {@link SpeciesReference}
109 * class.
110 <p>
111 * <h2>Stoichiometries in SBML Level 3</h2>
112 <p>
113 * The {@link StoichiometryMath} construct is not defined in SBML Level&nbsp;3
114 * Version&nbsp;1 Core.  Instead, Level&nbsp;3 defines the identifier of
115 * {@link SpeciesReference} objects as a stand-in for the stoichiometry of the
116 * reactant or product being referenced, and allows that identifier to be
117 * used elsewhere in SBML models, including (for example) {@link InitialAssignment}
118 * objects.  This makes it possible to achieve the same effect as
119 * {@link StoichiometryMath}, but with other SBML objects.  For instance, to
120 * produce a stoichiometry value that is a rational number, a model can use
121 * {@link InitialAssignment} to assign the identifier of a {@link SpeciesReference} object
122 * to a MathML expression evaluating to a rational number.  This is
123 * analogous to the same way that, in Level&nbsp;2, the model would use
124 * {@link StoichiometryMath} with a MathML expression evaluating to a rational
125 * number.
126 <p>
127 * In SBML Level 2, the stoichiometry of a reactant or product is a
128 * combination of both a <em>biochemical stoichiometry</em> (meaning, the
129 * standard stoichiometry of a species in a reaction) and any necessary
130 * unit conversion factors. The introduction of an explicit attribute on
131 * the {@link Species} object for a conversion factor allows Level&nbsp;3 to avoid
132 * having to overload the meaning of stoichiometry.  In Level&nbsp;3, the
133 * stoichiometry given by a {@link SpeciesReference} object in a reaction is a
134 * 'proper' biochemical stoichiometry, meaning a dimensionless number free
135 * of unit conversions.
136 <p>
137 * @see SpeciesReference
138 * @see Reaction
139 */
140
141public class StoichiometryMath extends SBase {
142   private long swigCPtr;
143
144   protected StoichiometryMath(long cPtr, boolean cMemoryOwn)
145   {
146     super(libsbmlJNI.StoichiometryMath_SWIGUpcast(cPtr), cMemoryOwn);
147     swigCPtr = cPtr;
148   }
149
150   protected static long getCPtr(StoichiometryMath obj)
151   {
152     return (obj == null) ? 0 : obj.swigCPtr;
153   }
154
155   protected static long getCPtrAndDisown (StoichiometryMath obj)
156   {
157     long ptr = 0;
158
159     if (obj != null)
160     {
161       ptr             = obj.swigCPtr;
162       obj.swigCMemOwn = false;
163     }
164
165     return ptr;
166   }
167
168  protected void finalize() {
169    delete();
170  }
171
172  public synchronized void delete() {
173    if (swigCPtr != 0) {
174      if (swigCMemOwn) {
175        swigCMemOwn = false;
176        libsbmlJNI.delete_StoichiometryMath(swigCPtr);
177      }
178      swigCPtr = 0;
179    }
180    super.delete();
181  }
182
183  
184/**
185   * Creates a new {@link StoichiometryMath} object using the given SBML <code>level</code>
186   * values.
187   <p>
188   * @param level a long integer, the SBML Level to assign to this {@link StoichiometryMath}
189   <p>
190   * @param version a long integer, the SBML Version to assign to this
191   * {@link StoichiometryMath}
192   <p>
193   * @throws SBMLConstructorException 
194   * Thrown if the given <code>level</code> and <code>version</code> combination, or this kind
195   * of SBML object, are either invalid or mismatched with respect to the
196   * parent {@link SBMLDocument} object.
197   <p>
198   * <p>
199 * @note The {@link StoichiometryMath} construct exists only in SBML Level&nbsp;2.
200 * It is an optional construct available for defining the stoichiometries of
201 * reactants and products in {@link Reaction} objects.  Note that a different
202 * mechanism is used in SBML Level&nbsp;3, where {@link StoichiometryMath} is not
203 * available.  Please consult the top of this libSBML {@link StoichiometryMath}
204 * documentation for more information about the differences between SBML
205 * Level&nbsp;2 and&nbsp;3 with respect to stoichiometries.
206   <p>
207   * <p>
208 * @note Upon the addition of a {@link StoichiometryMath} object to an
209 * {@link SBMLDocument} (e.g., using
210 * {@link SpeciesReference#createStoichiometryMath()}), the SBML Level, SBML
211 * Version and XML namespace of the document <em>override</em> the values used
212 * when creating the {@link StoichiometryMath} object via this constructor.  This
213 * is necessary to ensure that an SBML document is a consistent
214 * structure.  Nevertheless, the ability to supply the values at the time
215 * of creation of a {@link StoichiometryMath} is an important aid to producing
216 * valid SBML.  Knowledge of the intented SBML Level and Version
217 * determine whether it is valid to assign a particular value to an
218 * attribute, or whether it is valid to add an object to an existing
219 * {@link SBMLDocument}.
220   */ public
221 StoichiometryMath(long level, long version) throws org.sbml.libsbml.SBMLConstructorException {
222    this(libsbmlJNI.new_StoichiometryMath__SWIG_0(level, version), true);
223  }
224
225  
226/**
227   * Creates a new {@link StoichiometryMath} object using the given {@link SBMLNamespaces} object
228   * <code>sbmlns</code>.
229   <p>
230   * <p>
231 * The {@link SBMLNamespaces} object encapsulates SBML Level/Version/namespaces
232 * information.  It is used to communicate the SBML Level, Version, and (in
233 * Level&nbsp;3) packages used in addition to SBML Level&nbsp;3 Core.  A
234 * common approach to using libSBML's {@link SBMLNamespaces} facilities is to create an
235 * {@link SBMLNamespaces} object somewhere in a program once, then hand that object
236 * as needed to object constructors that accept {@link SBMLNamespaces} as arguments. 
237   <p>
238   * @param sbmlns an {@link SBMLNamespaces} object.
239   <p>
240   * @throws SBMLConstructorException 
241   * Thrown if the given <code>level</code> and <code>version</code> combination, or this kind
242   * of SBML object, are either invalid or mismatched with respect to the
243   * parent {@link SBMLDocument} object.
244   <p>
245   * <p>
246 * @note The {@link StoichiometryMath} construct exists only in SBML Level&nbsp;2.
247 * It is an optional construct available for defining the stoichiometries of
248 * reactants and products in {@link Reaction} objects.  Note that a different
249 * mechanism is used in SBML Level&nbsp;3, where {@link StoichiometryMath} is not
250 * available.  Please consult the top of this libSBML {@link StoichiometryMath}
251 * documentation for more information about the differences between SBML
252 * Level&nbsp;2 and&nbsp;3 with respect to stoichiometries.
253   <p>
254   * <p>
255 * @note Upon the addition of a {@link StoichiometryMath} object to an
256 * {@link SBMLDocument} (e.g., using
257 * {@link SpeciesReference#createStoichiometryMath()}), the SBML Level, SBML
258 * Version and XML namespace of the document <em>override</em> the values used
259 * when creating the {@link StoichiometryMath} object via this constructor.  This
260 * is necessary to ensure that an SBML document is a consistent
261 * structure.  Nevertheless, the ability to supply the values at the time
262 * of creation of a {@link StoichiometryMath} is an important aid to producing
263 * valid SBML.  Knowledge of the intented SBML Level and Version
264 * determine whether it is valid to assign a particular value to an
265 * attribute, or whether it is valid to add an object to an existing
266 * {@link SBMLDocument}.
267   */ public
268 StoichiometryMath(SBMLNamespaces sbmlns) throws org.sbml.libsbml.SBMLConstructorException {
269    this(libsbmlJNI.new_StoichiometryMath__SWIG_1(SBMLNamespaces.getCPtr(sbmlns), sbmlns), true);
270  }
271
272  
273/**
274   * Copy constructor; creates a copy of this {@link StoichiometryMath}.
275   <p>
276   * @param orig the object to copy.
277   <p>
278   * @throws SBMLConstructorException 
279   * Thrown if the argument <code>orig</code> is <code>null.</code>
280   */ public
281 StoichiometryMath(StoichiometryMath orig) throws org.sbml.libsbml.SBMLConstructorException {
282    this(libsbmlJNI.new_StoichiometryMath__SWIG_2(StoichiometryMath.getCPtr(orig), orig), true);
283  }
284
285  
286/**
287   * Creates and returns a deep copy of this {@link StoichiometryMath} object.
288   <p>
289   * @return a (deep) copy of this {@link StoichiometryMath}.
290   */ public
291 StoichiometryMath cloneObject() {
292    long cPtr = libsbmlJNI.StoichiometryMath_cloneObject(swigCPtr, this);
293    return (cPtr == 0) ? null : new StoichiometryMath(cPtr, true);
294  }
295
296  
297/**
298   * Retrieves the mathematical formula within this {@link StoichiometryMath} and
299   * return it as an AST.
300   <p>
301   * @return the math of this {@link StoichiometryMath}.
302   <p>
303   * <p>
304 * @note The {@link StoichiometryMath} construct exists only in SBML Level&nbsp;2.
305 * It is an optional construct available for defining the stoichiometries of
306 * reactants and products in {@link Reaction} objects.  Note that a different
307 * mechanism is used in SBML Level&nbsp;3, where {@link StoichiometryMath} is not
308 * available.  Please consult the top of this libSBML {@link StoichiometryMath}
309 * documentation for more information about the differences between SBML
310 * Level&nbsp;2 and&nbsp;3 with respect to stoichiometries.
311   */ public
312 ASTNode getMath() {
313    long cPtr = libsbmlJNI.StoichiometryMath_getMath(swigCPtr, this);
314    return (cPtr == 0) ? null : new ASTNode(cPtr, false);
315  }
316
317  
318/**
319   * Predicate to test whether the math for this {@link StoichiometryMath} object
320   * is set.
321   <p>
322   * @return <code>true</code> if the formula (meaning the <code>math</code> subelement) of
323   * this {@link StoichiometryMath} is set, <code>false</code> otherwise.
324   <p>
325   * <p>
326 * @note The {@link StoichiometryMath} construct exists only in SBML Level&nbsp;2.
327 * It is an optional construct available for defining the stoichiometries of
328 * reactants and products in {@link Reaction} objects.  Note that a different
329 * mechanism is used in SBML Level&nbsp;3, where {@link StoichiometryMath} is not
330 * available.  Please consult the top of this libSBML {@link StoichiometryMath}
331 * documentation for more information about the differences between SBML
332 * Level&nbsp;2 and&nbsp;3 with respect to stoichiometries.
333   */ public
334 boolean isSetMath() {
335    return libsbmlJNI.StoichiometryMath_isSetMath(swigCPtr, this);
336  }
337
338  
339/**
340   * Sets the 'math' expression of this {@link StoichiometryMath} instance to a
341   * copy of the given {@link ASTNode}.
342   <p>
343   * @param math an {@link ASTNode} representing a formula tree.
344   <p>
345   * @return integer value indicating success/failure of the
346   * function.  The possible values
347   * returned by this function are:
348   * <ul>
349   * <li> {@link  libsbmlConstants#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS }
350   * <li> {@link  libsbmlConstants#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT }
351   *
352   * </ul> <p>
353   * <p>
354 * @note The {@link StoichiometryMath} construct exists only in SBML Level&nbsp;2.
355 * It is an optional construct available for defining the stoichiometries of
356 * reactants and products in {@link Reaction} objects.  Note that a different
357 * mechanism is used in SBML Level&nbsp;3, where {@link StoichiometryMath} is not
358 * available.  Please consult the top of this libSBML {@link StoichiometryMath}
359 * documentation for more information about the differences between SBML
360 * Level&nbsp;2 and&nbsp;3 with respect to stoichiometries.
361   */ public
362 int setMath(ASTNode math) {
363    return libsbmlJNI.StoichiometryMath_setMath(swigCPtr, this, ASTNode.getCPtr(math), math);
364  }
365
366  
367/**
368   * Calculates and returns a {@link UnitDefinition} object that expresses the
369   * units returned by the math expression in this {@link StoichiometryMath}
370   * object.
371   <p>
372   * The units are calculated based on the mathematical expression in the
373   * {@link StoichiometryMath} and the model quantities referenced by
374   * <code>&lt;ci&gt;</code> elements used within that expression.  The
375   * {@link StoichiometryMath#getDerivedUnitDefinition()} method returns the
376   * calculated units.
377   <p>
378   * Note that the functionality that facilitates unit analysis depends 
379   * on the model as a whole.  Thus, in cases where the object has not 
380   * been added to a model or the model itself is incomplete,
381   * unit analysis is not possible and this method will return <code>null.</code>
382   <p>
383   * @return a {@link UnitDefinition} that expresses the units of the math, 
384   * or <code>null</code> if one cannot be constructed.
385   <p>
386   * @warning <span class='warning'>Note that it is possible the 'math'
387   * expression in the {@link StoichiometryMath} instance contains literal numbers or
388   * parameters with undeclared units.  In those cases, it is not possible to
389   * calculate the units of the overall expression without making
390   * assumptions.  LibSBML does not make assumptions about the units, and
391   * {@link StoichiometryMath#getDerivedUnitDefinition()} only returns the units as
392   * far as it is able to determine them.  For example, in an expression
393   * <em>X + Y</em>, if <em>X</em> has unambiguously-defined units and
394   * <em>Y</em> does not, it will return the units of <em>X</em>.  When using
395   * this method, <strong>it is critical that callers also invoke the
396   * method</strong> {@link StoichiometryMath#containsUndeclaredUnits()} <strong>to
397   * determine whether this situation holds</strong>.  Callers should take
398   * suitable action in those situations.</span>
399   <p>
400   * @see #containsUndeclaredUnits()
401   */ public
402 UnitDefinition getDerivedUnitDefinition() {
403    long cPtr = libsbmlJNI.StoichiometryMath_getDerivedUnitDefinition__SWIG_0(swigCPtr, this);
404    return (cPtr == 0) ? null : new UnitDefinition(cPtr, false);
405  }
406
407  
408/**
409   * Predicate returning <code>true</code> if the math
410   * expression of this {@link StoichiometryMath} object contains literal numbers
411   * or parameters with undeclared units.
412   <p>
413   * The {@link StoichiometryMath#getDerivedUnitDefinition()} method returns what
414   * libSBML computes the units of the Stoichiometry to be, to the extent
415   * that libSBML can compute them.  However, if the expression contains
416   * literal numbers or parameters with undeclared units, libSBML may not
417   * be able to compute the full units of the expression and will only
418   * return what it can compute.  Callers should always use
419   * {@link StoichiometryMath#containsUndeclaredUnits()} when using
420   * {@link StoichiometryMath#getDerivedUnitDefinition()} to decide whether the
421   * returned units may be incomplete.
422   <p>
423   * @return <code>true</code> if the math expression of this {@link StoichiometryMath}
424   * includes numbers/parameters with undeclared units, <code>false</code> otherwise.
425   <p>
426   * @note A return value of <code>true</code> indicates that the {@link UnitDefinition}
427   * returned by {@link StoichiometryMath#getDerivedUnitDefinition()} may not
428   * accurately represent the units of the expression.
429   <p>
430   * @see #getDerivedUnitDefinition()
431   */ public
432 boolean containsUndeclaredUnits() {
433    return libsbmlJNI.StoichiometryMath_containsUndeclaredUnits__SWIG_0(swigCPtr, this);
434  }
435
436  
437/**
438   * Returns the libSBML type code of this object instance.
439   <p>
440   * <p>
441 * LibSBML attaches an identifying code to every kind of SBML object.  These
442 * are integer constants known as <em>SBML type codes</em>.  The names of all
443 * the codes begin with the characters &ldquo;<code>SBML_</code>&rdquo;. 
444 * In the Java language interface for libSBML, the
445 * type codes are defined as static integer constants in the interface class
446 * {@link libsbmlConstants}.    Note that different Level&nbsp;3 
447 * package plug-ins may use overlapping type codes; to identify the package
448 * to which a given object belongs, call the <code>getPackageName()</code>
449 * method on the object.
450   <p>
451   * @return the SBML type code for this object:
452   * {@link  libsbmlConstants#SBML_STOICHIOMETRY_MATH SBML_STOICHIOMETRY_MATH} (default).
453   <p>
454   * <p>
455 * @warning <span class='warning'>The specific integer values of the possible
456 * type codes may be reused by different Level&nbsp;3 package plug-ins.
457 * Thus, to identifiy the correct code, <strong>it is necessary to invoke
458 * both getTypeCode() and getPackageName()</strong>.</span>
459   <p>
460   * @see #getElementName()
461   * @see #getPackageName()
462   */ public
463 int getTypeCode() {
464    return libsbmlJNI.StoichiometryMath_getTypeCode(swigCPtr, this);
465  }
466
467  
468/**
469   * Returns the XML element name of this object, which for {@link StoichiometryMath}, is
470   * always <code>'stoichiometryMath'.</code>
471   <p>
472   * @return the name of this element, i.e., <code>'stoichiometryMath'.</code> 
473   */ public
474 String getElementName() {
475    return libsbmlJNI.StoichiometryMath_getElementName(swigCPtr, this);
476  }
477
478  
479/**
480   * Predicate returning <code>true</code> if
481   * all the required elements for this {@link StoichiometryMath} object
482   * have been set.
483   <p>
484   * @note The required elements for a {@link StoichiometryMath} object are:
485   * <ul>
486   * <li> 'math'
487   *
488   * </ul> <p>
489   * @return a boolean value indicating whether all the required
490   * elements for this object have been defined.
491   */ public
492 boolean hasRequiredElements() {
493    return libsbmlJNI.StoichiometryMath_hasRequiredElements(swigCPtr, this);
494  }
495
496  
497/**
498   * Finds this {@link StoichiometryMath}'s {@link SpeciesReference} parent and calls
499   * unsetStoichiometryMath() on it, indirectly deleting itself.
500   <p>
501   * Overridden from the {@link SBase} function since the parent is not a {@link ListOf}.
502   <p>
503   * @return integer value indicating success/failure of the
504   * function.   The possible values
505   * returned by this function are:
506   * <ul>
507   * <li> {@link  libsbmlConstants#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS }
508   * <li> {@link  libsbmlConstants#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED }
509   * </ul>
510   */ public
511 int removeFromParentAndDelete() {
512    return libsbmlJNI.StoichiometryMath_removeFromParentAndDelete(swigCPtr, this);
513  }
514
515  
516/**
517   * Renames all the <code>SIdRef</code> attributes on this element, including any
518   * found in MathML.
519   <p>
520   * <p>
521 * In SBML, object identifiers are of a data type called <code>SId</code>.
522 * In SBML Level&nbsp;3, an explicit data type called <code>SIdRef</code> was
523 * introduced for attribute values that refer to <code>SId</code> values; in
524 * previous Levels of SBML, this data type did not exist and attributes were
525 * simply described to as 'referring to an identifier', but the effective
526 * data type was the same as <code>SIdRef</code>in Level&nbsp;3.  These and
527 * other methods of libSBML refer to the type <code>SIdRef</code> for all
528 * Levels of SBML, even if the corresponding SBML specification did not
529 * explicitly name the data type.
530   <p>
531   * This method works by looking at all attributes and (if appropriate)
532   * mathematical formulas, comparing the identifiers to the value of 
533   * <code>oldid</code>.  If any matches are found, the matching identifiers are replaced
534   * with <code>newid</code>.  The method does <em>not</em> descend into child elements.
535   <p>
536   * @param oldid the old identifier
537   * @param newid the new identifier
538   */ public
539 void renameSIdRefs(String oldid, String newid) {
540    libsbmlJNI.StoichiometryMath_renameSIdRefs(swigCPtr, this, oldid, newid);
541  }
542
543  
544/**
545   * Renames all the <code>UnitSIdRef</code> attributes on this element.
546   <p>
547   * <p>
548 * In SBML, unit definitions have identifiers of type <code>UnitSId</code>.  In
549 * SBML Level&nbsp;3, an explicit data type called <code>UnitSIdRef</code> was
550 * introduced for attribute values that refer to <code>UnitSId</code> values; in
551 * previous Levels of SBML, this data type did not exist and attributes were
552 * simply described to as 'referring to a unit identifier', but the effective
553 * data type was the same as <code>UnitSIdRef</code> in Level&nbsp;3.  These and
554 * other methods of libSBML refer to the type <code>UnitSIdRef</code> for all
555 * Levels of SBML, even if the corresponding SBML specification did not
556 * explicitly name the data type.
557   <p>
558   * This method works by looking at all unit identifier attribute values
559   * (including, if appropriate, inside mathematical formulas), comparing the
560   * unit identifiers to the value of <code>oldid</code>.  If any matches are found,
561   * the matching identifiers are replaced with <code>newid</code>.  The method does
562   * <em>not</em> descend into child elements.
563   <p>
564   * @param oldid the old identifier
565   * @param newid the new identifier
566   */ public
567 void renameUnitSIdRefs(String oldid, String newid) {
568    libsbmlJNI.StoichiometryMath_renameUnitSIdRefs(swigCPtr, this, oldid, newid);
569  }
570
571  
572/**
573   * Replace all nodes with the name 'id' from the child 'math' object with the provided function. 
574   <p>
575   * @internal
576   */ public
577 void replaceSIDWithFunction(String id, ASTNode function) {
578    libsbmlJNI.StoichiometryMath_replaceSIDWithFunction(swigCPtr, this, id, ASTNode.getCPtr(function), function);
579  }
580
581}