001/* ----------------------------------------------------------------------------
002 * This file was automatically generated by SWIG (http://www.swig.org).
003 * Version 3.0.10
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 *  An SBML <em>initial assignment</em>, evaluated once only.
013 <p>
014 * SBML Level 2 Versions 2&ndash;4 and SBML Level&nbsp;3 provide two ways of assigning initial
015 * values to entities in a model.  The simplest and most basic is to set
016 * the values of the appropriate attributes in the relevant components; for
017 * example, the initial value of a model parameter (whether it is a
018 * constant or a variable) can be assigned by setting its 'value' attribute
019 * directly in the model definition.  However, this approach is not
020 * suitable when the value must be calculated, because the initial value
021 * attributes on different components such as species, compartments, and
022 * parameters are single values and not mathematical expressions.  In those
023 * situations, the {@link InitialAssignment} construct can be used; it permits the
024 * calculation of the value of a constant or the initial value of a
025 * variable from the values of <em>other</em> quantities in a model.
026 <p>
027 * As explained below, the provision of {@link InitialAssignment} does not mean
028 * that models necessarily must use this construct when defining initial
029 * values of quantities in a model.  If a value can be set directly using
030 * the relevant attribute of a component in a model, then that
031 * approach may be more efficient and more portable to other software
032 * tools.  {@link InitialAssignment} should be used when the other mechanism is
033 * insufficient for the needs of a particular model.
034 <p>
035 * The {@link InitialAssignment} construct has some similarities to {@link AssignmentRule}.
036 * The main differences are: (a) an {@link InitialAssignment} can set the value of
037 * a constant whereas an {@link AssignmentRule} cannot, and (b) unlike
038 * {@link AssignmentRule}, an {@link InitialAssignment} definition only applies up to and
039 * including the beginning of simulation time, i.e., <em>t &#8804; 0</em>,
040 * while an {@link AssignmentRule} applies at all times.
041 <p>
042 * {@link InitialAssignment} has a required attribute, 'symbol', whose value must
043 * follow the guidelines for identifiers described in the SBML
044 * specification (e.g., Section 3.3 in the Level 2 Version 4
045 * specification).  The value of this attribute in an {@link InitialAssignment}
046 * object can be the identifier of a {@link Compartment}, {@link Species} or global
047 * {@link Parameter} elsewhere in the model.  The {@link InitialAssignment} defines the
048 * initial value of the constant or variable referred to by the 'symbol'
049 * attribute.  (The attribute's name is 'symbol' rather than 'variable'
050 * because it may assign values to constants as well as variables in a
051 * model.)  Note that an initial assignment cannot be made to reaction
052 * identifiers, that is, the 'symbol' attribute value of an
053 * {@link InitialAssignment} cannot be an identifier that is the 'id' attribute
054 * value of a {@link Reaction} object in the model.  This is identical to a
055 * restriction placed on rules.
056 <p>
057 * {@link InitialAssignment} also has a required 'math' subelement that contains a
058 * MathML expression used to calculate the value of the constant or the
059 * initial value of the variable.  The units of the value computed by the
060 * formula in the 'math' subelement should (in SBML Level&nbsp;2
061 * Version&nbsp;4 and in SBML Level&nbsp;3) or must (in previous Versions) be identical to be the
062 * units associated with the identifier given in the 'symbol' attribute.
063 * (That is, the units are the units of the species, compartment, or
064 * parameter, as appropriate for the kind of object identified by the value
065 * of 'symbol'.)
066 <p>
067 * {@link InitialAssignment} was introduced in SBML Level 2 Version 2.  It is not
068 * available in SBML Level&nbsp;2 Version&nbsp;1 nor in any version of Level 1.
069 <p>
070 * <h2>Semantics of Initial Assignments</h2>
071 <p>
072 * The value calculated by an {@link InitialAssignment} object overrides the value
073 * assigned to the given symbol by the object defining that symbol.  For
074 * example, if a compartment's 'size' attribute is set in its definition,
075 * and the model also contains an {@link InitialAssignment} having that
076 * compartment's identifier as its 'symbol' attribute value, then the
077 * interpretation is that the 'size' assigned in the {@link Compartment} object
078 * should be ignored and the value assigned based on the computation
079 * defined in the {@link InitialAssignment}.  Initial assignments can take place
080 * for {@link Compartment}, {@link Species} and global {@link Parameter} objects regardless of the
081 * value of their 'constant' attribute.
082 <p>
083 * The actions of all {@link InitialAssignment} objects are in general terms
084 * the same, but differ in the precise details depending on the type
085 * of variable being set:
086 * <ul>
087 * <li> <em>In the case of a species</em>, an {@link InitialAssignment} sets the
088 * referenced species' initial quantity (concentration or amount of
089 * substance) to the value determined by the formula in the 'math'
090 * subelement.    The overall units of the formula should (in SBML
091 * Level&nbsp;2 Version&nbsp;4 and in SBML Level&nbsp;3) or must (in previous Versions) be the same
092 * as the units specified for the species.
093 <p>
094 * <li> <em>In the case of a compartment</em>, an {@link InitialAssignment} sets
095 * the referenced compartment's initial size to the size determined by the
096 * formula in 'math'.  The overall units of the formula should (in SBML
097 * Level&nbsp;2 Version&nbsp;4 and in SBML Level&nbsp;3) or must (in previous Versions) be the same
098 * as the units specified for the size of the compartment.
099 <p>
100 * <li> <em>In the case of a parameter</em>, an {@link InitialAssignment} sets the
101 * referenced parameter's initial value to that determined by the formula
102 * in 'math'.  The overall units of the formula should (in SBML
103 * Level&nbsp;2 Version&nbsp;4 and SBML Level&nbsp;3) or must (in previous Versions) be the same
104 * as the units defined for the parameter.  </ul>
105 <p>
106 * In the context of a simulation, initial assignments establish values
107 * that are in effect prior to and including the start of simulation time,
108 * i.e., <em>t &#8804; 0</em>.  Section 3.4.8 in the SBML Level 2
109 * Version 4  and SBML Level&nbsp;3 Version&nbsp;1 Core specifications provides information about the interpretation of
110 * assignments, rules, and entity values for simulation time up to and
111 * including the start time <em>t = 0</em>; this is important for
112 * establishing the initial conditions of a simulation if the model
113 * involves expressions containing the <em>delay</em> 'csymbol'.
114 <p>
115 * There cannot be two initial assignments for the same symbol in a model;
116 * that is, a model must not contain two or more {@link InitialAssignment} objects
117 * that both have the same identifier as their 'symbol' attribute value.  A
118 * model must also not define initial assignments <em>and</em> assignment
119 * rules for the same entity.  That is, there cannot be <em>both</em> an
120 * {@link InitialAssignment} and an {@link AssignmentRule} for the same symbol in a model,
121 * because both kinds of constructs apply prior to and at the start of
122 * simulated time&mdash;allowing both to exist for a given symbol would
123 * result in indeterminism).
124 <p>
125 * The ordering of {@link InitialAssignment} objects is not significant.  The
126 * combined set of {@link InitialAssignment}, {@link AssignmentRule} and {@link KineticLaw}
127 * objects form a set of assignment statements that must be considered as a
128 * whole.  The combined set of assignment statements should not contain
129 * algebraic loops: a chain of dependency between these statements should
130 * terminate.  (More formally, consider the directed graph of assignment
131 * statements where nodes are a model's assignment statements and directed
132 * arcs exist for each occurrence of a symbol in an assignment statement
133 * 'math' attribute.  The directed arcs in this graph start from the
134 * statement assigning the symbol and end at the statement that contains
135 * the symbol in their math elements.  Such a graph must be acyclic.)
136 <p>
137 * Finally, it is worth being explicit about the expected behavior in the
138 * following situation.  Suppose (1) a given symbol has a value <em>x</em>
139 * assigned to it in its definition, and (2) there is an initial assignment
140 * having the identifier as its 'symbol' value and reassigning the value to
141 * <em>y</em>, <em>and</em> (3) the identifier is also used in the
142 * mathematical formula of a second initial assignment.  What value should
143 * the second initial assignment use?  It is <em>y</em>, the value assigned
144 * to the symbol by the first initial assignment, not whatever value was
145 * given in the symbol's definition.  This follows directly from the
146 * behavior described above: if an {@link InitialAssignment} object exists for a
147 * given symbol, then the symbol's value is overridden by that initial
148 * assignment.
149 */
150
151public class InitialAssignment extends SBase {
152   private long swigCPtr;
153
154   protected InitialAssignment(long cPtr, boolean cMemoryOwn)
155   {
156     super(libsbmlJNI.InitialAssignment_SWIGUpcast(cPtr), cMemoryOwn);
157     swigCPtr = cPtr;
158   }
159
160   protected static long getCPtr(InitialAssignment obj)
161   {
162     return (obj == null) ? 0 : obj.swigCPtr;
163   }
164
165   protected static long getCPtrAndDisown (InitialAssignment obj)
166   {
167     long ptr = 0;
168
169     if (obj != null)
170     {
171       ptr             = obj.swigCPtr;
172       obj.swigCMemOwn = false;
173     }
174
175     return ptr;
176   }
177
178  protected void finalize() {
179    delete();
180  }
181
182  public synchronized void delete() {
183    if (swigCPtr != 0) {
184      if (swigCMemOwn) {
185        swigCMemOwn = false;
186        libsbmlJNI.delete_InitialAssignment(swigCPtr);
187      }
188      swigCPtr = 0;
189    }
190    super.delete();
191  }
192
193  
194/**
195   * Creates a new {@link InitialAssignment} using the given SBML <code>level</code> and <code>version</code>
196   * values.
197   <p>
198   * @param level a long integer, the SBML Level to assign to this {@link InitialAssignment}
199   <p>
200   * @param version a long integer, the SBML Version to assign to this
201   * {@link InitialAssignment}
202   <p>
203   * <p>
204 * @throws SBMLConstructorException
205 * Thrown if the given <code>level</code> and <code>version</code> combination are invalid
206 * or if this object is incompatible with the given level and version.
207   <p>
208   * <p>
209 * @note Attempting to add an object to an {@link SBMLDocument} having a different
210 * combination of SBML Level, Version and XML namespaces than the object
211 * itself will result in an error at the time a caller attempts to make the
212 * addition.  A parent object must have compatible Level, Version and XML
213 * namespaces.  (Strictly speaking, a parent may also have more XML
214 * namespaces than a child, but the reverse is not permitted.)  The
215 * restriction is necessary to ensure that an SBML model has a consistent
216 * overall structure.  This requires callers to manage their objects
217 * carefully, but the benefit is increased flexibility in how models can be
218 * created by permitting callers to create objects bottom-up if desired.  In
219 * situations where objects are not yet attached to parents (e.g.,
220 * {@link SBMLDocument}), knowledge of the intented SBML Level and Version help
221 * libSBML determine such things as whether it is valid to assign a
222 * particular value to an attribute.
223   */ public
224 InitialAssignment(long level, long version) throws org.sbml.libsbml.SBMLConstructorException {
225    this(libsbmlJNI.new_InitialAssignment__SWIG_0(level, version), true);
226  }
227
228  
229/**
230   * Creates a new {@link InitialAssignment} using the given {@link SBMLNamespaces} object
231   * <code>sbmlns</code>.
232   <p>
233   * <p>
234 * The {@link SBMLNamespaces} object encapsulates SBML Level/Version/namespaces
235 * information.  It is used to communicate the SBML Level, Version, and (in
236 * Level&nbsp;3) packages used in addition to SBML Level&nbsp;3 Core.  A
237 * common approach to using libSBML's {@link SBMLNamespaces} facilities is to create an
238 * {@link SBMLNamespaces} object somewhere in a program once, then hand that object
239 * as needed to object constructors that accept {@link SBMLNamespaces} as arguments. 
240   <p>
241   * @param sbmlns an {@link SBMLNamespaces} object.
242   <p>
243   * <p>
244 * @throws SBMLConstructorException
245 * Thrown if the given <code>sbmlns</code> is inconsistent or incompatible
246 * with this object.
247   <p>
248   * <p>
249 * @note Attempting to add an object to an {@link SBMLDocument} having a different
250 * combination of SBML Level, Version and XML namespaces than the object
251 * itself will result in an error at the time a caller attempts to make the
252 * addition.  A parent object must have compatible Level, Version and XML
253 * namespaces.  (Strictly speaking, a parent may also have more XML
254 * namespaces than a child, but the reverse is not permitted.)  The
255 * restriction is necessary to ensure that an SBML model has a consistent
256 * overall structure.  This requires callers to manage their objects
257 * carefully, but the benefit is increased flexibility in how models can be
258 * created by permitting callers to create objects bottom-up if desired.  In
259 * situations where objects are not yet attached to parents (e.g.,
260 * {@link SBMLDocument}), knowledge of the intented SBML Level and Version help
261 * libSBML determine such things as whether it is valid to assign a
262 * particular value to an attribute.
263   */ public
264 InitialAssignment(SBMLNamespaces sbmlns) throws org.sbml.libsbml.SBMLConstructorException {
265    this(libsbmlJNI.new_InitialAssignment__SWIG_1(SBMLNamespaces.getCPtr(sbmlns), sbmlns), true);
266  }
267
268  
269/**
270   * Copy constructor; creates a copy of this {@link InitialAssignment}.
271   <p>
272   * @param orig the object to copy.
273   */ public
274 InitialAssignment(InitialAssignment orig) throws org.sbml.libsbml.SBMLConstructorException {
275    this(libsbmlJNI.new_InitialAssignment__SWIG_2(InitialAssignment.getCPtr(orig), orig), true);
276  }
277
278  
279/**
280   * Creates and returns a deep copy of this {@link InitialAssignment} object.
281   <p>
282   * @return the (deep) copy of this {@link InitialAssignment} object.
283   */ public
284 InitialAssignment cloneObject() {
285    long cPtr = libsbmlJNI.InitialAssignment_cloneObject(swigCPtr, this);
286    return (cPtr == 0) ? null : new InitialAssignment(cPtr, true);
287  }
288
289  
290/**
291   * Get the value of the 'symbol' attribute of this {@link InitialAssignment}.
292   <p>
293   * @return the identifier string stored as the 'symbol' attribute value
294   * in this {@link InitialAssignment}.
295   */ public
296 String getSymbol() {
297    return libsbmlJNI.InitialAssignment_getSymbol(swigCPtr, this);
298  }
299
300  
301/**
302   * Get the mathematical formula of this {@link InitialAssignment}.
303   <p>
304   * @return an {@link ASTNode}, the value of the 'math' subelement of this
305   * {@link InitialAssignment}
306   */ public
307 ASTNode getMath() {
308    long cPtr = libsbmlJNI.InitialAssignment_getMath(swigCPtr, this);
309    return (cPtr == 0) ? null : new ASTNode(cPtr, false);
310  }
311
312  
313/**
314   * Predicate returning <code>true</code> if this
315   * {@link InitialAssignment}'s 'symbol' attribute is set.
316   <p>
317   * @return <code>true</code> if the 'symbol' attribute of this {@link InitialAssignment}
318   * is set, <code>false</code> otherwise.
319   */ public
320 boolean isSetSymbol() {
321    return libsbmlJNI.InitialAssignment_isSetSymbol(swigCPtr, this);
322  }
323
324  
325/**
326   * Predicate returning <code>true</code> if this
327   * {@link InitialAssignment}'s 'math' subelement contains a value.
328   <p>
329   * @return <code>true</code> if the 'math' for this {@link InitialAssignment} is set,
330   * <code>false</code> otherwise.
331   */ public
332 boolean isSetMath() {
333    return libsbmlJNI.InitialAssignment_isSetMath(swigCPtr, this);
334  }
335
336  
337/**
338   * Sets the 'symbol' attribute value of this {@link InitialAssignment}.
339   <p>
340   * @param sid the identifier of a {@link Species}, {@link Compartment} or {@link Parameter}
341   * object defined elsewhere in this {@link Model}.
342   <p>
343   * <p>
344 * @return integer value indicating success/failure of the
345 * function.   The possible values
346 * returned by this function are:
347   * <ul>
348   * <li> {@link libsbmlConstants#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS}
349   * <li> {@link libsbmlConstants#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE}
350   * </ul>
351   */ public
352 int setSymbol(String sid) {
353    return libsbmlJNI.InitialAssignment_setSymbol(swigCPtr, this, sid);
354  }
355
356  
357/**
358   * Unsets the 'symbol' attribute value of this {@link InitialAssignment}.
359   <p>
360   * <p>
361 * @return integer value indicating success/failure of the
362 * function.   The possible values
363 * returned by this function are:
364   * <ul>
365   * <li> {@link libsbmlConstants#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS}
366   * <li> {@link libsbmlConstants#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE}
367   * </ul>
368   */ public
369 int unsetSymbol() {
370    return libsbmlJNI.InitialAssignment_unsetSymbol(swigCPtr, this);
371  }
372
373  
374/**
375   * Sets the 'math' subelement of this {@link InitialAssignment}.
376   <p>
377   * The AST passed in <code>math</code> is copied.
378   <p>
379   * @param math an AST containing the mathematical expression to
380   * be used as the formula for this {@link InitialAssignment}.
381   <p>
382   * <p>
383 * @return integer value indicating success/failure of the
384 * function.   The possible values
385 * returned by this function are:
386   * <ul>
387   * <li> {@link libsbmlConstants#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS}
388   * <li> {@link libsbmlConstants#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT}
389   * </ul>
390   */ public
391 int setMath(ASTNode math) {
392    return libsbmlJNI.InitialAssignment_setMath(swigCPtr, this, ASTNode.getCPtr(math), math);
393  }
394
395  
396/**
397   * Calculates and returns a {@link UnitDefinition} that expresses the units
398   * of measurement assumed for the 'math' expression of this
399   * {@link InitialAssignment}.
400   <p>
401   * <p>
402 * The units are calculated based on the mathematical expression in the
403 * {@link InitialAssignment} and the model quantities referenced by
404 * <code>&lt;ci&gt;</code> elements used within that expression.  The method
405 * {@link InitialAssignment#getDerivedUnitDefinition()} returns the calculated
406 * units, to the extent that libSBML can compute them.
407   <p>
408   * <p>
409 * @note The functionality that facilitates unit analysis depends on the
410 * model as a whole.  Thus, in cases where the object has not been added to
411 * a model or the model itself is incomplete, unit analysis is not possible
412 * and this method will return <code>null.</code> 
413   <p>
414   * <p>
415 * @warning <span class='warning'>Note that it is possible the 'math'
416 * expression in the {@link InitialAssignment} contains literal numbers or parameters
417 * with undeclared units.  In those cases, it is not possible to calculate
418 * the units of the overall expression without making assumptions.  LibSBML
419 * does not make assumptions about the units, and
420 * {@link InitialAssignment#getDerivedUnitDefinition()} only returns the units as
421 * far as it is able to determine them.  For example, in an expression <em>X
422 * + Y</em>, if <em>X</em> has unambiguously-defined units and <em>Y</em>
423 * does not, it will return the units of <em>X</em>.  When using this method,
424 * <strong>it is critical that callers also invoke the method</strong>
425 * {@link InitialAssignment#containsUndeclaredUnits()} <strong>to determine whether
426 * this situation holds</strong>.  Callers should take suitable action in
427 * those situations.</span>
428   <p>
429   * @return a {@link UnitDefinition} that expresses the units of the math 
430   * expression of this {@link InitialAssignment}, or <code>null</code> if one cannot be constructed.
431   <p>
432   * @see #containsUndeclaredUnits()
433   */ public
434 UnitDefinition getDerivedUnitDefinition() {
435    long cPtr = libsbmlJNI.InitialAssignment_getDerivedUnitDefinition__SWIG_0(swigCPtr, this);
436    return (cPtr == 0) ? null : new UnitDefinition(cPtr, false);
437  }
438
439  
440/**
441   * Predicate returning <code>true</code> if the math expression of this
442   * {@link InitialAssignment} contains parameters/numbers with undeclared units.
443   <p>
444   * @return <code>true</code> if the math expression of this {@link InitialAssignment}
445   * includes parameters/numbers 
446   * with undeclared units, <code>false</code> otherwise.
447   <p>
448   * @note A return value of <code>true</code> indicates that the {@link UnitDefinition}
449   * returned by InitialAssignment.getDerivedUnitDefinition may not
450   * accurately represent the units of the expression.
451   <p>
452   * @see #getDerivedUnitDefinition()
453   */ public
454 boolean containsUndeclaredUnits() {
455    return libsbmlJNI.InitialAssignment_containsUndeclaredUnits__SWIG_0(swigCPtr, this);
456  }
457
458  
459/**
460   * Returns the libSBML type code for this SBML object.
461   <p>
462   * <p>
463 * LibSBML attaches an identifying code to every kind of SBML object.  These
464 * are integer constants known as <em>SBML type codes</em>.  The names of all
465 * the codes begin with the characters <code>SBML_</code>.
466 * In the Java language interface for libSBML, the
467 * type codes are defined as static integer constants in the interface class
468 * {@link libsbmlConstants}.    Note that different Level&nbsp;3
469 * package plug-ins may use overlapping type codes; to identify the package
470 * to which a given object belongs, call the <code>getPackageName()</code>
471 * method on the object.
472   <p>
473   * @return the SBML type code for this object:
474   * {@link libsbmlConstants#SBML_INITIAL_ASSIGNMENT SBML_INITIAL_ASSIGNMENT} (default).
475   <p>
476   * <p>
477 * @warning <span class='warning'>The specific integer values of the possible
478 * type codes may be reused by different libSBML plug-ins for SBML Level&nbsp;3.
479 * packages,  To fully identify the correct code, <strong>it is necessary to
480 * invoke both getTypeCode() and getPackageName()</strong>.</span>
481   <p>
482   * @see #getElementName()
483   * @see #getPackageName()
484   */ public
485 int getTypeCode() {
486    return libsbmlJNI.InitialAssignment_getTypeCode(swigCPtr, this);
487  }
488
489  
490/**
491   * Returns the XML element name of this object, which for
492   * {@link InitialAssignment}, is always <code>'initialAssignment'.</code>
493   <p>
494   * @return the name of this element, i.e., <code>'initialAssignment'.</code>
495   */ public
496 String getElementName() {
497    return libsbmlJNI.InitialAssignment_getElementName(swigCPtr, this);
498  }
499
500  
501/**
502   * Predicate returning <code>true</code> if all the required attributes for this
503   * {@link InitialAssignment} object have been set.
504   <p>
505   * The required attributes for an {@link InitialAssignment} object are:
506   * <ul>
507   * <li> 'symbol'
508   *
509   * </ul> <p>
510   * @return <code>true</code> if the required attributes have been set, <code>false</code>
511   * otherwise.
512   */ public
513 boolean hasRequiredAttributes() {
514    return libsbmlJNI.InitialAssignment_hasRequiredAttributes(swigCPtr, this);
515  }
516
517  
518/**
519   * Predicate returning <code>true</code> if all the required elements for this
520   * {@link InitialAssignment} object have been set.
521   <p>
522   * @note The required elements for a {@link InitialAssignment} object are:
523   * <ul>
524   * <li> 'math'
525   *
526   * </ul> <p>
527   * @return a boolean value indicating whether all the required
528   * elements for this object have been defined.
529   */ public
530 boolean hasRequiredElements() {
531    return libsbmlJNI.InitialAssignment_hasRequiredElements(swigCPtr, this);
532  }
533
534  
535/** * @internal */ public
536 String getId() {
537    return libsbmlJNI.InitialAssignment_getId(swigCPtr, this);
538  }
539
540  
541/**
542   * <p>
543 * Replaces all uses of a given <code>SIdRef</code> type attribute value with another
544 * value.
545 <p>
546 * <p>
547 * In SBML, object identifiers are of a data type called <code>SId</code>.
548 * In SBML Level&nbsp;3, an explicit data type called <code>SIdRef</code> was
549 * introduced for attribute values that refer to <code>SId</code> values; in
550 * previous Levels of SBML, this data type did not exist and attributes were
551 * simply described to as 'referring to an identifier', but the effective
552 * data type was the same as <code>SIdRef</code>in Level&nbsp;3.  These and
553 * other methods of libSBML refer to the type <code>SIdRef</code> for all
554 * Levels of SBML, even if the corresponding SBML specification did not
555 * explicitly name the data type.
556 <p>
557 * This method works by looking at all attributes and (if appropriate)
558 * mathematical formulas in MathML content, comparing the referenced
559 * identifiers to the value of <code>oldid</code>.  If any matches are found, the
560 * matching values are replaced with <code>newid</code>.  The method does <em>not</em>
561 * descend into child elements.
562 <p>
563 * @param oldid the old identifier
564 * @param newid the new identifier
565   */ public
566 void renameSIdRefs(String oldid, String newid) {
567    libsbmlJNI.InitialAssignment_renameSIdRefs(swigCPtr, this, oldid, newid);
568  }
569
570  
571/**
572   * <p>
573 * Replaces all uses of a given <code>UnitSIdRef</code> type attribute value with
574 * another value.
575 <p>
576 * <p>
577 * In SBML, unit definitions have identifiers of type <code>UnitSId</code>.  In
578 * SBML Level&nbsp;3, an explicit data type called <code>UnitSIdRef</code> was
579 * introduced for attribute values that refer to <code>UnitSId</code> values; in
580 * previous Levels of SBML, this data type did not exist and attributes were
581 * simply described to as 'referring to a unit identifier', but the effective
582 * data type was the same as <code>UnitSIdRef</code> in Level&nbsp;3.  These and
583 * other methods of libSBML refer to the type <code>UnitSIdRef</code> for all
584 * Levels of SBML, even if the corresponding SBML specification did not
585 * explicitly name the data type.
586 <p>
587 * This method works by looking at all unit identifier attribute values
588 * (including, if appropriate, inside mathematical formulas), comparing the
589 * referenced unit identifiers to the value of <code>oldid</code>.  If any matches
590 * are found, the matching values are replaced with <code>newid</code>.  The method
591 * does <em>not</em> descend into child elements.
592 <p>
593 * @param oldid the old identifier
594 * @param newid the new identifier
595   */ public
596 void renameUnitSIdRefs(String oldid, String newid) {
597    libsbmlJNI.InitialAssignment_renameUnitSIdRefs(swigCPtr, this, oldid, newid);
598  }
599
600  
601/** * @internal */ public
602 void replaceSIDWithFunction(String id, ASTNode function) {
603    libsbmlJNI.InitialAssignment_replaceSIDWithFunction(swigCPtr, this, id, ASTNode.getCPtr(function), function);
604  }
605
606  
607/** * @internal */ public
608 void divideAssignmentsToSIdByFunction(String id, ASTNode function) {
609    libsbmlJNI.InitialAssignment_divideAssignmentsToSIdByFunction(swigCPtr, this, id, ASTNode.getCPtr(function), function);
610  }
611
612  
613/** * @internal */ public
614 void multiplyAssignmentsToSIdByFunction(String id, ASTNode function) {
615    libsbmlJNI.InitialAssignment_multiplyAssignmentsToSIdByFunction(swigCPtr, this, id, ASTNode.getCPtr(function), function);
616  }
617
618}