001/* ----------------------------------------------------------------------------
002 * This file was automatically generated by SWIG (http://www.swig.org).
003 * Version 3.0.7
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 *  Stochiometry expressions in SBML Level 2 reactions.
013 <p>
014 * <h2>Stoichiometries in SBML Level 2</h2>
015 <p>
016 * In SBML Level 2, product and reactant stoichiometries can be specified
017 * using <em>either</em> the 'stoichiometry' attribute or a 'stoichiometryMath'
018 * element in a {@link SpeciesReference} object.  The 'stoichiometry' attribute is
019 * of type <code>double</code> and should contain values greater than zero (0).  The
020 * 'stoichiometryMath' element is implemented as an element containing a
021 * MathML expression.  These two are mutually exclusive; only one of
022 * 'stoichiometry' or 'stoichiometryMath' should be defined in a given
023 * {@link SpeciesReference} instance.  When neither the attribute nor the element
024 * is present, the value of 'stoichiometry' in the enclosing
025 * {@link SpeciesReference} instance defaults to <code>1.</code>
026 <p>
027 * For maximum interoperability, {@link SpeciesReference}'s 'stoichiometry'
028 * attribute should be used in preference to 'stoichiometryMath' when a
029 * species' stoichiometry is a simple scalar number (integer or decimal).
030 * When the stoichiometry is a rational number, or when it is a more
031 * complicated formula, 'stoichiometryMath' must be used.  The MathML
032 * expression in 'stoichiometryMath' may also refer to identifiers of
033 * entities in a model (except reaction identifiers).  However, the only
034 * species identifiers that can be used in 'stoichiometryMath' are those
035 * referenced in the enclosing {@link Reaction}'s list of reactants, products and
036 * modifiers.
037 <p>
038 * The 'stoichiometry' attribute and the 'stoichiometryMath' element, when
039 * either is used, is each interpreted as a factor applied to the reaction
040 * rate to produce the rate of change of the species identified by the
041 * 'species' attribute in the enclosing {@link SpeciesReference}.  This is the
042 * normal interpretation of a stoichiometry, but in SBML, one additional
043 * consideration has to be taken into account.  The reaction rate, which is
044 * the result of the {@link KineticLaw}'s 'math' element, is always in the model's
045 * <em>substance</em> per <em>time</em> units.  However, the rate of change of the
046 * species will involve the species' <em>substance</em> units (i.e., the units
047 * identified by the {@link Species} object's 'substanceUnits' attribute), and
048 * these units may be different from the model's default <em>substance</em>
049 * units.  If the units <em>are</em> different, the stoichiometry must
050 * incorporate a conversion factor for converting the model's <em>substance</em>
051 * units to the species' <em>substance</em> units.  The conversion factor is
052 * assumed to be included in the scalar value of the 'stoichiometry'
053 * attribute if 'stoichiometry' is used.  If instead 'stoichiometryMath' is
054 * used, then the product of the model's 'substance' units times the
055 * 'stoichiometryMath' units must match the <em>substance</em> units of the
056 * species.  Note that in either case, if the species' units and the
057 * model's default <em>substance</em> units are the same, the stoichiometry ends
058 * up being a dimensionless number and equivalent to the standard chemical
059 * stoichiometry found in textbooks.  Examples and more explanations of
060 * this are given in the SBML specification.
061 <p>
062 * The following is a simple example of a species reference for species 
063 * <code>'X0'</code>, with stoichiometry <code>2</code>, in a list of reactants within a reaction
064 * having the identifier <code>'J1':</code>
065 * <pre class='fragment'>
066 &lt;model&gt;
067     ...
068     &lt;listOfReactions&gt;
069         &lt;reaction id='J1'&gt;
070             &lt;listOfReactants&gt;
071                 &lt;speciesReference species='X0' stoichiometry='2'&gt;
072             &lt;/listOfReactants&gt;
073             ...
074         &lt;/reaction&gt;
075         ...
076     &lt;/listOfReactions&gt;
077     ...
078 &lt;/model&gt;
079 </pre>
080 <p>
081 * The following is a more complex example of a species reference for
082 * species <code>'X0'</code>, with a stoichiometry formula consisting of
083 * a rational number:
084 * <pre class='fragment'>
085 &lt;model&gt;
086     ...
087     &lt;listOfReactions&gt;
088         &lt;reaction id='J1'&gt;
089             &lt;listOfReactants&gt;
090                 &lt;speciesReference species='X0'&gt;
091                     &lt;stoichiometryMath&gt;
092                         &lt;math xmlns='http://www.w3.org/1998/Math/MathML'&gt; 
093                             &lt;cn type='rational'&gt; 3 &lt;sep/&gt; 2 &lt;/cn&gt;
094                         &lt;/math&gt;
095                     &lt;/stoichiometryMath&gt;
096                 &lt;/speciesReference&gt;
097             &lt;/listOfReactants&gt;
098             ...
099         &lt;/reaction&gt;
100         ...
101     &lt;/listOfReactions&gt;
102     ...
103 &lt;/model&gt;
104 </pre>
105 <p>
106 * Additional discussions of stoichiometries and implications for species
107 * and reactions are included in the documentation of {@link SpeciesReference}
108 * class.
109 <p>
110 * <h2>Stoichiometries in SBML Level 3</h2>
111 <p>
112 * The {@link StoichiometryMath} construct is not defined in SBML Level&nbsp;3
113 * Version&nbsp;1 Core.  Instead, Level&nbsp;3 defines the identifier of
114 * {@link SpeciesReference} objects as a stand-in for the stoichiometry of the
115 * reactant or product being referenced, and allows that identifier to be
116 * used elsewhere in SBML models, including (for example) {@link InitialAssignment}
117 * objects.  This makes it possible to achieve the same effect as
118 * {@link StoichiometryMath}, but with other SBML objects.  For instance, to
119 * produce a stoichiometry value that is a rational number, a model can use
120 * {@link InitialAssignment} to assign the identifier of a {@link SpeciesReference} object
121 * to a MathML expression evaluating to a rational number.  This is
122 * analogous to the same way that, in Level&nbsp;2, the model would use
123 * {@link StoichiometryMath} with a MathML expression evaluating to a rational
124 * number.
125 <p>
126 * In SBML Level 2, the stoichiometry of a reactant or product is a
127 * combination of both a <em>biochemical stoichiometry</em> (meaning, the
128 * standard stoichiometry of a species in a reaction) and any necessary
129 * unit conversion factors. The introduction of an explicit attribute on
130 * the {@link Species} object for a conversion factor allows Level&nbsp;3 to avoid
131 * having to overload the meaning of stoichiometry.  In Level&nbsp;3, the
132 * stoichiometry given by a {@link SpeciesReference} object in a reaction is a
133 * 'proper' biochemical stoichiometry, meaning a dimensionless number free
134 * of unit conversions.
135 <p>
136 * @see SpeciesReference
137 * @see Reaction
138 */
139
140public class StoichiometryMath extends SBase {
141   private long swigCPtr;
142
143   protected StoichiometryMath(long cPtr, boolean cMemoryOwn)
144   {
145     super(libsbmlJNI.StoichiometryMath_SWIGUpcast(cPtr), cMemoryOwn);
146     swigCPtr = cPtr;
147   }
148
149   protected static long getCPtr(StoichiometryMath obj)
150   {
151     return (obj == null) ? 0 : obj.swigCPtr;
152   }
153
154   protected static long getCPtrAndDisown (StoichiometryMath obj)
155   {
156     long ptr = 0;
157
158     if (obj != null)
159     {
160       ptr             = obj.swigCPtr;
161       obj.swigCMemOwn = false;
162     }
163
164     return ptr;
165   }
166
167  protected void finalize() {
168    delete();
169  }
170
171  public synchronized void delete() {
172    if (swigCPtr != 0) {
173      if (swigCMemOwn) {
174        swigCMemOwn = false;
175        libsbmlJNI.delete_StoichiometryMath(swigCPtr);
176      }
177      swigCPtr = 0;
178    }
179    super.delete();
180  }
181
182  
183/**
184   * Creates a new {@link StoichiometryMath} object using the given SBML <code>level</code>
185   * values.
186   <p>
187   * @param level a long integer, the SBML Level to assign to this {@link StoichiometryMath}
188   <p>
189   * @param version a long integer, the SBML Version to assign to this
190   * {@link StoichiometryMath}
191   <p>
192   * <p>
193 * @throws SBMLConstructorException
194 * Thrown if the given <code>level</code> and <code>version</code> combination are invalid
195 * or if this object is incompatible with the given level and version.
196   <p>
197   * <p>
198 * @note The {@link StoichiometryMath} construct exists only in SBML Level&nbsp;2.
199 * It is an optional construct available for defining the stoichiometries of
200 * reactants and products in {@link Reaction} objects.  Note that a different
201 * mechanism is used in SBML Level&nbsp;3, where {@link StoichiometryMath} is not
202 * available.  Please consult the top of this libSBML {@link StoichiometryMath}
203 * documentation for more information about the differences between SBML
204 * Level&nbsp;2 and&nbsp;3 with respect to stoichiometries.
205   <p>
206   * <p>
207 * @note Attempting to add an object to an {@link SBMLDocument} having a different
208 * combination of SBML Level, Version and XML namespaces than the object
209 * itself will result in an error at the time a caller attempts to make the
210 * addition.  A parent object must have compatible Level, Version and XML
211 * namespaces.  (Strictly speaking, a parent may also have more XML
212 * namespaces than a child, but the reverse is not permitted.)  The
213 * restriction is necessary to ensure that an SBML model has a consistent
214 * overall structure.  This requires callers to manage their objects
215 * carefully, but the benefit is increased flexibility in how models can be
216 * created by permitting callers to create objects bottom-up if desired.  In
217 * situations where objects are not yet attached to parents (e.g.,
218 * {@link SBMLDocument}), knowledge of the intented SBML Level and Version help
219 * libSBML determine such things as whether it is valid to assign a
220 * particular value to an attribute.
221   */ public
222 StoichiometryMath(long level, long version) throws org.sbml.libsbml.SBMLConstructorException {
223    this(libsbmlJNI.new_StoichiometryMath__SWIG_0(level, version), true);
224  }
225
226  
227/**
228   * Creates a new {@link StoichiometryMath} object using the given {@link SBMLNamespaces} object
229   * <code>sbmlns</code>.
230   <p>
231   * <p>
232 * The {@link SBMLNamespaces} object encapsulates SBML Level/Version/namespaces
233 * information.  It is used to communicate the SBML Level, Version, and (in
234 * Level&nbsp;3) packages used in addition to SBML Level&nbsp;3 Core.  A
235 * common approach to using libSBML's {@link SBMLNamespaces} facilities is to create an
236 * {@link SBMLNamespaces} object somewhere in a program once, then hand that object
237 * as needed to object constructors that accept {@link SBMLNamespaces} as arguments. 
238   <p>
239   * @param sbmlns an {@link SBMLNamespaces} object.
240   <p>
241   * <p>
242 * @throws SBMLConstructorException
243 * Thrown if the given <code>sbmlns</code> is inconsistent or incompatible
244 * with this object.
245   <p>
246   * <p>
247 * @note The {@link StoichiometryMath} construct exists only in SBML Level&nbsp;2.
248 * It is an optional construct available for defining the stoichiometries of
249 * reactants and products in {@link Reaction} objects.  Note that a different
250 * mechanism is used in SBML Level&nbsp;3, where {@link StoichiometryMath} is not
251 * available.  Please consult the top of this libSBML {@link StoichiometryMath}
252 * documentation for more information about the differences between SBML
253 * Level&nbsp;2 and&nbsp;3 with respect to stoichiometries.
254   <p>
255   * <p>
256 * @note Attempting to add an object to an {@link SBMLDocument} having a different
257 * combination of SBML Level, Version and XML namespaces than the object
258 * itself will result in an error at the time a caller attempts to make the
259 * addition.  A parent object must have compatible Level, Version and XML
260 * namespaces.  (Strictly speaking, a parent may also have more XML
261 * namespaces than a child, but the reverse is not permitted.)  The
262 * restriction is necessary to ensure that an SBML model has a consistent
263 * overall structure.  This requires callers to manage their objects
264 * carefully, but the benefit is increased flexibility in how models can be
265 * created by permitting callers to create objects bottom-up if desired.  In
266 * situations where objects are not yet attached to parents (e.g.,
267 * {@link SBMLDocument}), knowledge of the intented SBML Level and Version help
268 * libSBML determine such things as whether it is valid to assign a
269 * particular value to an attribute.
270   */ public
271 StoichiometryMath(SBMLNamespaces sbmlns) throws org.sbml.libsbml.SBMLConstructorException {
272    this(libsbmlJNI.new_StoichiometryMath__SWIG_1(SBMLNamespaces.getCPtr(sbmlns), sbmlns), true);
273  }
274
275  
276/**
277   * Copy constructor; creates a copy of this {@link StoichiometryMath}.
278   <p>
279   * @param orig the object to copy.
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 the (deep) copy of this {@link StoichiometryMath} object.
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   * <p>
346 * @return integer value indicating success/failure of the
347 * function.   The possible values
348 * returned by this function are:
349   * <ul>
350   * <li> {@link libsbmlConstants#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS}
351   * <li> {@link libsbmlConstants#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT}
352   *
353   * </ul> <p>
354   * <p>
355 * @note The {@link StoichiometryMath} construct exists only in SBML Level&nbsp;2.
356 * It is an optional construct available for defining the stoichiometries of
357 * reactants and products in {@link Reaction} objects.  Note that a different
358 * mechanism is used in SBML Level&nbsp;3, where {@link StoichiometryMath} is not
359 * available.  Please consult the top of this libSBML {@link StoichiometryMath}
360 * documentation for more information about the differences between SBML
361 * Level&nbsp;2 and&nbsp;3 with respect to stoichiometries.
362   */ public
363 int setMath(ASTNode math) {
364    return libsbmlJNI.StoichiometryMath_setMath(swigCPtr, this, ASTNode.getCPtr(math), math);
365  }
366
367  
368/**
369   * Calculates and returns a {@link UnitDefinition} object that expresses the
370   * units returned by the math expression in this {@link StoichiometryMath}
371   * object.
372   <p>
373   * The units are calculated based on the mathematical expression in the
374   * {@link StoichiometryMath} and the model quantities referenced by
375   * <code>&lt;ci&gt;</code> elements used within that expression.  The
376   * {@link StoichiometryMath#getDerivedUnitDefinition()} method returns the
377   * calculated units.
378   <p>
379   * Note that the functionality that facilitates unit analysis depends 
380   * on the model as a whole.  Thus, in cases where the object has not 
381   * been added to a model or the model itself is incomplete,
382   * unit analysis is not possible and this method will return <code>null.</code>
383   <p>
384   * @return a {@link UnitDefinition} that expresses the units of the math, 
385   * or <code>null</code> if one cannot be constructed.
386   <p>
387   * @warning <span class='warning'>Note that it is possible the 'math'
388   * expression in the {@link StoichiometryMath} instance contains literal numbers or
389   * parameters with undeclared units.  In those cases, it is not possible to
390   * calculate the units of the overall expression without making
391   * assumptions.  LibSBML does not make assumptions about the units, and
392   * {@link StoichiometryMath#getDerivedUnitDefinition()} only returns the units as
393   * far as it is able to determine them.  For example, in an expression
394   * <em>X + Y</em>, if <em>X</em> has unambiguously-defined units and
395   * <em>Y</em> does not, it will return the units of <em>X</em>.  When using
396   * this method, <strong>it is critical that callers also invoke the
397   * method</strong> {@link StoichiometryMath#containsUndeclaredUnits()} <strong>to
398   * determine whether this situation holds</strong>.  Callers should take
399   * suitable action in those situations.</span>
400   <p>
401   * @see #containsUndeclaredUnits()
402   */ public
403 UnitDefinition getDerivedUnitDefinition() {
404    long cPtr = libsbmlJNI.StoichiometryMath_getDerivedUnitDefinition__SWIG_0(swigCPtr, this);
405    return (cPtr == 0) ? null : new UnitDefinition(cPtr, false);
406  }
407
408  
409/**
410   * Predicate returning <code>true</code> if the math
411   * expression of this {@link StoichiometryMath} object contains literal numbers
412   * or parameters with undeclared units.
413   <p>
414   * The {@link StoichiometryMath#getDerivedUnitDefinition()} method returns what
415   * libSBML computes the units of the Stoichiometry to be, to the extent
416   * that libSBML can compute them.  However, if the expression contains
417   * literal numbers or parameters with undeclared units, libSBML may not
418   * be able to compute the full units of the expression and will only
419   * return what it can compute.  Callers should always use
420   * {@link StoichiometryMath#containsUndeclaredUnits()} when using
421   * {@link StoichiometryMath#getDerivedUnitDefinition()} to decide whether the
422   * returned units may be incomplete.
423   <p>
424   * @return <code>true</code> if the math expression of this {@link StoichiometryMath}
425   * includes numbers/parameters with undeclared units, <code>false</code> otherwise.
426   <p>
427   * @note A return value of <code>true</code> indicates that the {@link UnitDefinition}
428   * returned by {@link StoichiometryMath#getDerivedUnitDefinition()} may not
429   * accurately represent the units of the expression.
430   <p>
431   * @see #getDerivedUnitDefinition()
432   */ public
433 boolean containsUndeclaredUnits() {
434    return libsbmlJNI.StoichiometryMath_containsUndeclaredUnits__SWIG_0(swigCPtr, this);
435  }
436
437  
438/**
439   * Returns the libSBML type code of this object instance.
440   <p>
441   * <p>
442 * LibSBML attaches an identifying code to every kind of SBML object.  These
443 * are integer constants known as <em>SBML type codes</em>.  The names of all
444 * the codes begin with the characters <code>SBML_</code>.
445 * In the Java language interface for libSBML, the
446 * type codes are defined as static integer constants in the interface class
447 * {@link libsbmlConstants}.    Note that different Level&nbsp;3
448 * package plug-ins may use overlapping type codes; to identify the package
449 * to which a given object belongs, call the <code>getPackageName()</code>
450 * method on the object.
451   <p>
452   * @return the SBML type code for this object:
453   * {@link libsbmlConstants#SBML_STOICHIOMETRY_MATH SBML_STOICHIOMETRY_MATH} (default).
454   <p>
455   * <p>
456 * @warning <span class='warning'>The specific integer values of the possible
457 * type codes may be reused by different Level&nbsp;3 package plug-ins.
458 * Thus, to identifiy the correct code, <strong>it is necessary to invoke
459 * both getTypeCode() and getPackageName()</strong>.</span>
460   <p>
461   * @see #getElementName()
462   * @see #getPackageName()
463   */ public
464 int getTypeCode() {
465    return libsbmlJNI.StoichiometryMath_getTypeCode(swigCPtr, this);
466  }
467
468  
469/**
470   * Returns the XML element name of this object, which for {@link StoichiometryMath}, is
471   * always <code>'stoichiometryMath'.</code>
472   <p>
473   * @return the name of this element, i.e., <code>'stoichiometryMath'.</code> 
474   */ public
475 String getElementName() {
476    return libsbmlJNI.StoichiometryMath_getElementName(swigCPtr, this);
477  }
478
479  
480/**
481   * Predicate returning <code>true</code> if
482   * all the required elements for this {@link StoichiometryMath} object
483   * have been set.
484   <p>
485   * @note The required elements for a {@link StoichiometryMath} object are:
486   * <ul>
487   * <li> 'math'
488   *
489   * </ul> <p>
490   * @return a boolean value indicating whether all the required
491   * elements for this object have been defined.
492   */ public
493 boolean hasRequiredElements() {
494    return libsbmlJNI.StoichiometryMath_hasRequiredElements(swigCPtr, this);
495  }
496
497  
498/**
499   * Finds this {@link StoichiometryMath}'s {@link SpeciesReference} parent and calls
500   * unsetStoichiometryMath() on it, indirectly deleting itself.
501   <p>
502   * Overridden from the {@link SBase} function since the parent is not a {@link ListOf}.
503   <p>
504   * <p>
505 * @return integer value indicating success/failure of the
506 * function.   The possible values
507 * returned by this function are:
508   * <ul>
509   * <li> {@link libsbmlConstants#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS}
510   * <li> {@link libsbmlConstants#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED}
511   * </ul>
512   */ public
513 int removeFromParentAndDelete() {
514    return libsbmlJNI.StoichiometryMath_removeFromParentAndDelete(swigCPtr, this);
515  }
516
517  
518/**
519   * <p>
520 * Replaces all uses of a given <code>SIdRef</code> type attribute value with another
521 * value.
522 <p>
523 * <p>
524 * In SBML, object identifiers are of a data type called <code>SId</code>.
525 * In SBML Level&nbsp;3, an explicit data type called <code>SIdRef</code> was
526 * introduced for attribute values that refer to <code>SId</code> values; in
527 * previous Levels of SBML, this data type did not exist and attributes were
528 * simply described to as 'referring to an identifier', but the effective
529 * data type was the same as <code>SIdRef</code>in Level&nbsp;3.  These and
530 * other methods of libSBML refer to the type <code>SIdRef</code> for all
531 * Levels of SBML, even if the corresponding SBML specification did not
532 * explicitly name the data type.
533 <p>
534 * This method works by looking at all attributes and (if appropriate)
535 * mathematical formulas in MathML content, comparing the referenced
536 * identifiers to the value of <code>oldid</code>.  If any matches are found, the
537 * matching values are replaced with <code>newid</code>.  The method does <em>not</em>
538 * descend into child elements.
539 <p>
540 * @param oldid the old identifier
541 * @param newid the new identifier
542   */ public
543 void renameSIdRefs(String oldid, String newid) {
544    libsbmlJNI.StoichiometryMath_renameSIdRefs(swigCPtr, this, oldid, newid);
545  }
546
547  
548/**
549   * <p>
550 * Replaces all uses of a given <code>UnitSIdRef</code> type attribute value with
551 * another value.
552 <p>
553 * <p>
554 * In SBML, unit definitions have identifiers of type <code>UnitSId</code>.  In
555 * SBML Level&nbsp;3, an explicit data type called <code>UnitSIdRef</code> was
556 * introduced for attribute values that refer to <code>UnitSId</code> values; in
557 * previous Levels of SBML, this data type did not exist and attributes were
558 * simply described to as 'referring to a unit identifier', but the effective
559 * data type was the same as <code>UnitSIdRef</code> in Level&nbsp;3.  These and
560 * other methods of libSBML refer to the type <code>UnitSIdRef</code> for all
561 * Levels of SBML, even if the corresponding SBML specification did not
562 * explicitly name the data type.
563 <p>
564 * This method works by looking at all unit identifier attribute values
565 * (including, if appropriate, inside mathematical formulas), comparing the
566 * referenced unit identifiers to the value of <code>oldid</code>.  If any matches
567 * are found, the matching values are replaced with <code>newid</code>.  The method
568 * does <em>not</em> descend into child elements.
569 <p>
570 * @param oldid the old identifier
571 * @param newid the new identifier
572   */ public
573 void renameUnitSIdRefs(String oldid, String newid) {
574    libsbmlJNI.StoichiometryMath_renameUnitSIdRefs(swigCPtr, this, oldid, newid);
575  }
576
577  
578/** * @internal */ public
579 void replaceSIDWithFunction(String id, ASTNode function) {
580    libsbmlJNI.StoichiometryMath_replaceSIDWithFunction(swigCPtr, this, id, ASTNode.getCPtr(function), function);
581  }
582
583}