001/* ----------------------------------------------------------------------------
002 * This file was automatically generated by SWIG (http://www.swig.org).
003 * Version 3.0.8
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 *  Parent class for SBML <em>rules</em> in libSBML.
013 <p>
014 * In SBML, <em>rules</em> provide additional ways to define the values of
015 * variables in a model, their relationships, and the dynamical behaviors
016 * of those variables.  They enable encoding relationships that cannot be
017 * expressed using {@link Reaction} nor {@link InitialAssignment} objects alone.
018 <p>
019 * The libSBML implementation of rules mirrors the SBML Level&nbsp;3
020 * Version&nbsp;1 Core definition (which is in turn is very similar to the
021 * Level&nbsp;2 Version&nbsp;4 definition), with {@link Rule} being the parent
022 * class of three subclasses as explained below.  The {@link Rule} class itself
023 * cannot be instantiated by user programs and has no constructor; only the
024 * subclasses {@link AssignmentRule}, {@link AlgebraicRule} and {@link RateRule} can be
025 * instantiated directly.
026 <p>
027 * <p>
028 * <h2>General summary of SBML rules</h2>
029 <p>
030 * In SBML Level&nbsp;3 as well as Level&nbsp;2, rules are separated into three
031 * subclasses for the benefit of model analysis software.  The three
032 * subclasses are based on the following three different possible functional
033 * forms (where <em>x</em> is a variable, <em>f</em> is some arbitrary
034 * function returning a numerical result, <b><em>V</em></b> is a vector of
035 * variables that does not include <em>x</em>, and <b><em>W</em></b> is a
036 * vector of variables that may include <em>x</em>):
037 <p>
038 * <table border='0' cellpadding='0' class='centered' style='font-size: small'>
039 * <tr><td width='120px'><em>Algebraic:</em></td><td width='250px'>left-hand side is zero</td><td><em>0 = f(<b>W</b>)</em></td></tr>
040 * <tr><td><em>Assignment:</em></td><td>left-hand side is a scalar:</td><td><em>x = f(<b>V</b>)</em></td></tr>
041 * <tr><td><em>Rate:</em></td><td>left-hand side is a rate-of-change:</td><td><em>dx/dt = f(<b>W</b>)</em></td></tr>
042 * </table>
043 <p>
044 * In their general form given above, there is little to distinguish
045 * between <em>assignment</em> and <em>algebraic</em> rules.  They are treated as
046 * separate cases for the following reasons:
047 <p>
048 * <ul>
049 * <li> <em>Assignment</em> rules can simply be evaluated to calculate
050 * intermediate values for use in numerical methods.  They are statements
051 * of equality that hold at all times.  (For assignments that are only
052 * performed once, see {@link InitialAssignment}.)
053<p>
054 * <li> SBML needs to place restrictions on assignment rules, for example
055 * the restriction that assignment rules cannot contain algebraic loops.
056 <p>
057 * <li> Some simulators do not contain numerical solvers capable of solving
058 * unconstrained algebraic equations, and providing more direct forms such
059 * as assignment rules may enable those simulators to process models they
060 * could not process if the same assignments were put in the form of
061 * general algebraic equations;
062 <p>
063 * <li> Those simulators that <em>can</em> solve these algebraic equations make a
064 * distinction between the different categories listed above; and
065 <p>
066 * <li> Some specialized numerical analyses of models may only be applicable
067 * to models that do not contain <em>algebraic</em> rules.
068 *
069 * </ul> <p>
070 * The approach taken to covering these cases in SBML is to define an
071 * abstract {@link Rule} structure containing a subelement, 'math', to hold the
072 * right-hand side expression, then to derive subtypes of {@link Rule} that add
073 * attributes to distinguish the cases of algebraic, assignment and rate
074 * rules.  The 'math' subelement must contain a MathML expression defining the
075 * mathematical formula of the rule.  This MathML formula must return a
076 * numerical value.  The formula can be an arbitrary expression referencing
077 * the variables and other entities in an SBML model.
078 <p>
079 * Each of the three subclasses of {@link Rule} (AssignmentRule, {@link AlgebraicRule},
080 * {@link RateRule}) inherit the the 'math' subelement and other fields from {@link SBase}.
081 * The {@link AssignmentRule} and {@link RateRule} classes add an additional attribute,
082 * 'variable'.  See the definitions of {@link AssignmentRule}, {@link AlgebraicRule} and
083 * {@link RateRule} for details about the structure and interpretation of each one.
084 <p>
085 * <h2>Additional restrictions on SBML rules</h2>
086 <p>
087 * An important design goal of SBML rule semantics is to ensure that a
088 * model's simulation and analysis results will not be dependent on when or
089 * how often rules are evaluated.  To achieve this, SBML needs to place two
090 * restrictions on rule use.  The first concerns algebraic loops in the system
091 * of assignments in a model, and the second concerns overdetermined systems.
092 <p>
093 * <h3>A model must not contain algebraic loops</h3>
094 <p>
095 * The combined set of {@link InitialAssignment}, {@link AssignmentRule} and {@link KineticLaw}
096 * objects in a model constitute a set of assignment statements that should be
097 * considered as a whole.  (A {@link KineticLaw} object is counted as an assignment
098 * because it assigns a value to the symbol contained in the 'id' attribute of
099 * the {@link Reaction} object in which it is defined.)  This combined set of
100 * assignment statements must not contain algebraic loops&mdash;dependency
101 * chains between these statements must terminate.  To put this more formally,
102 * consider a directed graph in which nodes are assignment statements and
103 * directed arcs exist for each occurrence of an SBML species, compartment or
104 * parameter symbol in an assignment statement's 'math' subelement.  Let the
105 * directed arcs point from the statement assigning the symbol to the
106 * statements that contain the symbol in their 'math' subelement expressions.
107 * This graph must be acyclic.
108 <p>
109 * SBML does not specify when or how often rules should be evaluated.
110 * Eliminating algebraic loops ensures that assignment statements can be
111 * evaluated any number of times without the result of those evaluations
112 * changing.  As an example, consider the set of equations <em>x = x + 1</em>,
113 * <em>y = z + 200</em> and <em>z = y + 100</em>.  If this set of equations
114 * were interpreted as a set of assignment statements, it would be invalid
115 * because the rule for <em>x</em> refers to <em>x</em> (exhibiting one type
116 * of loop), and the rule for <em>y</em> refers to <em>z</em> while the rule
117 * for <em>z</em> refers back to <em>y</em> (exhibiting another type of loop).
118 * Conversely, the following set of equations would constitute a valid set of
119 * assignment statements: <em>x = 10</em>, <em>y = z + 200</em>, and <em>z = x
120 * + 100</em>.
121 <p>
122 * <h3>A model must not be overdetermined</h3>
123 <p>
124 * An SBML model must not be overdetermined; that is, a model must not
125 * define more equations than there are unknowns in a model.  An SBML model
126 * that does not contain {@link AlgebraicRule} structures cannot be overdetermined.
127 <p>
128 * LibSBML implements the static analysis procedure described in
129 * Appendix&nbsp;B of the SBML Level&nbsp;3 Version&nbsp;1 Core
130 * specification for assessing whether a model is overdetermined.
131 <p>
132 * (In summary, assessing whether a given continuous, deterministic,
133 * mathematical model is overdetermined does not require dynamic analysis; it
134 * can be done by analyzing the system of equations created from the model.
135 * One approach is to construct a bipartite graph in which one set of vertices
136 * represents the variables and the other the set of vertices represents the
137 * equations.  Place edges between vertices such that variables in the system
138 * are linked to the equations that determine them.  For algebraic equations,
139 * there will be edges between the equation and each variable occurring in the
140 * equation.  For ordinary differential equations (such as those defined by
141 * rate rules or implied by the reaction rate definitions), there will be a
142 * single edge between the equation and the variable determined by that
143 * differential equation.  A mathematical model is overdetermined if the
144 * maximal matchings of the bipartite graph contain disconnected vertexes
145 * representing equations.  If one maximal matching has this property, then
146 * all the maximal matchings will have this property; i.e., it is only
147 * necessary to find one maximal matching.)
148 <p>
149 * <h2>Rule types for SBML Level 1</h2>
150 <p>
151 * SBML Level 1 uses a different scheme than SBML Level 2 and Level 3 for
152 * distinguishing rules; specifically, it uses an attribute whose value is
153 * drawn from an enumeration of 3 values.  LibSBML supports this using methods
154 * that work with the enumeration values  listed below.
155 <p>
156 * <ul>
157 * <li> {@link libsbmlConstants#RULE_TYPE_RATE RULE_TYPE_RATE}: Indicates
158 * the rule is a 'rate' rule.
159 * <li> {@link libsbmlConstants#RULE_TYPE_SCALAR RULE_TYPE_SCALAR}:
160 * Indicates the rule is a 'scalar' rule.
161 * <li> {@link libsbmlConstants#RULE_TYPE_INVALID RULE_TYPE_INVALID}:
162 * Indicates the rule type is unknown or not yet set.
163 *
164 * </ul>
165 */
166
167public class Rule extends SBase {
168   private long swigCPtr;
169
170   protected Rule(long cPtr, boolean cMemoryOwn)
171   {
172     super(libsbmlJNI.Rule_SWIGUpcast(cPtr), cMemoryOwn);
173     swigCPtr = cPtr;
174   }
175
176   protected static long getCPtr(Rule obj)
177   {
178     return (obj == null) ? 0 : obj.swigCPtr;
179   }
180
181   protected static long getCPtrAndDisown (Rule obj)
182   {
183     long ptr = 0;
184
185     if (obj != null)
186     {
187       ptr             = obj.swigCPtr;
188       obj.swigCMemOwn = false;
189     }
190
191     return ptr;
192   }
193
194  protected void finalize() {
195    delete();
196  }
197
198  public synchronized void delete() {
199    if (swigCPtr != 0) {
200      if (swigCMemOwn) {
201        swigCMemOwn = false;
202        libsbmlJNI.delete_Rule(swigCPtr);
203      }
204      swigCPtr = 0;
205    }
206    super.delete();
207  }
208
209  
210/**
211   * Copy constructor; creates a copy of this {@link Rule}.
212   <p>
213   * @param orig the object to copy.
214   */ public
215 Rule(Rule orig) {
216    this(libsbmlJNI.new_Rule(Rule.getCPtr(orig), orig), true);
217  }
218
219  
220/**
221   * Creates and returns a deep copy of this {@link Rule} object.
222   <p>
223   * @return the (deep) copy of this {@link Rule} object.
224   */ public
225 Rule cloneObject() {
226  return (Rule) libsbml.DowncastSBase(libsbmlJNI.Rule_cloneObject(swigCPtr, this), true);
227}
228
229  
230/**
231   * Returns the mathematical expression of this {@link Rule} in text-string form.
232   <p>
233   * The text string is produced by
234   * <code><a href='libsbml.html#formulaToString(org.sbml.libsbml.ASTNode)'>libsbml.formulaToString()</a></code>; please consult
235   * the documentation for that function to find out more about the format
236   * of the text-string formula.
237   <p>
238   * @return the formula text string for this {@link Rule}.
239   <p>
240   * @note The attribute 'formula' is specific to SBML Level&nbsp;1; in
241   * higher Levels of SBML, it has been replaced with a subelement named
242   * 'math'.  However, libSBML provides a unified interface to the
243   * underlying math expression and this method can be used for models
244   * of all Levels of SBML.
245   <p>
246   * @see #getMath()
247   */ public
248 String getFormula() {
249    return libsbmlJNI.Rule_getFormula(swigCPtr, this);
250  }
251
252  
253/**
254   * Get the mathematical formula of this {@link Rule} as an {@link ASTNode} tree.
255   <p>
256   * @return an {@link ASTNode}, the value of the 'math' subelement of this {@link Rule}.
257   <p>
258   * @note The subelement 'math' is present in SBML Levels&nbsp;2
259   * and&nbsp;3.  In SBML Level&nbsp;1, the equivalent construct is the
260   * attribute named 'formula'.  LibSBML provides a unified interface to
261   * the underlying math expression and this method can be used for models
262   * of all Levels of SBML.
263   <p>
264   * @see #getFormula()
265   */ public
266 ASTNode getMath() {
267    long cPtr = libsbmlJNI.Rule_getMath(swigCPtr, this);
268    return (cPtr == 0) ? null : new ASTNode(cPtr, false);
269  }
270
271  
272/**
273   * Get the value of the 'variable' attribute of this {@link Rule} object.
274   <p>
275   * <p>
276 * In SBML Level&nbsp;1, the different rule types each have a different
277 * name for the attribute holding the reference to the object constituting
278 * the left-hand side of the rule.  (E.g., for SBML Level&nbsp;1's
279 * SpeciesConcentrationRule the attribute is 'species', for
280 * CompartmentVolumeRule it is 'compartment', etc.)  In SBML Levels&nbsp;2
281 * and&nbsp;3, the only two types of {@link Rule} objects with a left-hand side
282 * object reference are {@link AssignmentRule} and {@link RateRule}, and both of them use the
283 * same name for attribute: 'variable'.  In order to make it easier for
284 * application developers to work with all Levels of SBML, libSBML uses a
285 * uniform name for all such attributes, and it is 'variable', regardless of
286 * whether Level&nbsp;1 rules or Level&nbsp;2&ndash;3 rules are being used.
287   <p>
288   * @return the identifier string stored as the 'variable' attribute value
289   * in this {@link Rule}, or <code>null</code> if this object is an {@link AlgebraicRule} object.
290   */ public
291 String getVariable() {
292    return libsbmlJNI.Rule_getVariable(swigCPtr, this);
293  }
294
295  
296/**
297   * Returns the units for the
298   * mathematical formula of this {@link Rule}.
299   <p>
300   * @return the identifier of the units for the expression of this {@link Rule}.
301   <p>
302   * @note The attribute 'units' exists on SBML Level&nbsp;1 ParameterRule
303   * objects only.  It is not present in SBML Levels&nbsp;2 and&nbsp;3.
304   */ public
305 String getUnits() {
306    return libsbmlJNI.Rule_getUnits(swigCPtr, this);
307  }
308
309  
310/**
311   * Predicate returning <code>true</code> if this {@link Rule}'s mathematical expression is
312   * set.
313   <p>
314   * This method is equivalent to isSetMath().  This version is present for
315   * easier compatibility with SBML Level&nbsp;1, in which mathematical
316   * formulas were written in text-string form.
317   <p>
318   * @return <code>true</code> if the mathematical formula for this {@link Rule} is
319   * set, <code>false</code> otherwise.
320   <p>
321   * @note The attribute 'formula' is specific to SBML Level&nbsp;1; in
322   * higher Levels of SBML, it has been replaced with a subelement named
323   * 'math'.  However, libSBML provides a unified interface to the
324   * underlying math expression and this method can be used for models
325   * of all Levels of SBML.
326   <p>
327   * @see #isSetMath()
328   */ public
329 boolean isSetFormula() {
330    return libsbmlJNI.Rule_isSetFormula(swigCPtr, this);
331  }
332
333  
334/**
335   * Predicate returning <code>true</code> if this {@link Rule}'s mathematical expression is
336   * set.
337   <p>
338   * This method is equivalent to isSetFormula().
339   <p>
340   * @return <code>true</code> if the formula (or equivalently the math) for this
341   * {@link Rule} is set, <code>false</code> otherwise.
342   <p>
343   * @note The subelement 'math' is present in SBML Levels&nbsp;2
344   * and&nbsp;3.  In SBML Level&nbsp;1, the equivalent construct is the
345   * attribute named 'formula'.  LibSBML provides a unified interface to
346   * the underlying math expression and this method can be used for models
347   * of all Levels of SBML.
348   <p>
349   * @see #isSetFormula()
350   */ public
351 boolean isSetMath() {
352    return libsbmlJNI.Rule_isSetMath(swigCPtr, this);
353  }
354
355  
356/**
357   * Predicate returning <code>true</code> if this {@link Rule}'s 'variable' attribute is set.
358   <p>
359   * <p>
360 * In SBML Level&nbsp;1, the different rule types each have a different
361 * name for the attribute holding the reference to the object constituting
362 * the left-hand side of the rule.  (E.g., for SBML Level&nbsp;1's
363 * SpeciesConcentrationRule the attribute is 'species', for
364 * CompartmentVolumeRule it is 'compartment', etc.)  In SBML Levels&nbsp;2
365 * and&nbsp;3, the only two types of {@link Rule} objects with a left-hand side
366 * object reference are {@link AssignmentRule} and {@link RateRule}, and both of them use the
367 * same name for attribute: 'variable'.  In order to make it easier for
368 * application developers to work with all Levels of SBML, libSBML uses a
369 * uniform name for all such attributes, and it is 'variable', regardless of
370 * whether Level&nbsp;1 rules or Level&nbsp;2&ndash;3 rules are being used.
371   <p>
372   * @return <code>true</code> if the 'variable' attribute value of this {@link Rule} is
373   * set, <code>false</code> otherwise.
374   */ public
375 boolean isSetVariable() {
376    return libsbmlJNI.Rule_isSetVariable(swigCPtr, this);
377  }
378
379  
380/**
381   * Predicate returning <code>true</code> if this {@link Rule}'s 'units' attribute is set.
382   <p>
383   * @return <code>true</code> if the units for this {@link Rule} is set, <code>false</code>
384   * otherwise
385   <p>
386   * @note The attribute 'units' exists on SBML Level&nbsp;1 ParameterRule
387   * objects only.  It is not present in SBML Levels&nbsp;2 and&nbsp;3.
388   */ public
389 boolean isSetUnits() {
390    return libsbmlJNI.Rule_isSetUnits(swigCPtr, this);
391  }
392
393  
394/**
395   * Sets the 'math' subelement of this {@link Rule} to an expression in text-string
396   * form.
397   <p>
398   * This is equivalent to setMath(ASTNode math).  The provision of
399   * using text-string formulas is retained for easier SBML Level&nbsp;1
400   * compatibility.  The formula is converted to an {@link ASTNode} internally.
401   <p>
402   * @param formula a mathematical formula in text-string form.
403   <p>
404   * <p>
405 * @return integer value indicating success/failure of the
406 * function.   The possible values
407 * returned by this function are:
408   * <ul>
409   * <li> {@link libsbmlConstants#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS}
410   * <li> {@link libsbmlConstants#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT}
411   *
412   * </ul> <p>
413   * @note The attribute 'formula' is specific to SBML Level&nbsp;1; in
414   * higher Levels of SBML, it has been replaced with a subelement named
415   * 'math'.  However, libSBML provides a unified interface to the
416   * underlying math expression and this method can be used for models
417   * of all Levels of SBML.
418   <p>
419   * @see #setMath(ASTNode math)
420   */ public
421 int setFormula(String formula) {
422    return libsbmlJNI.Rule_setFormula(swigCPtr, this, formula);
423  }
424
425  
426/**
427   * Sets the 'math' subelement of this {@link Rule} to a copy of the given
428   * {@link ASTNode}.
429   <p>
430   * @param math the AST structure of the mathematical formula.
431   <p>
432   * <p>
433 * @return integer value indicating success/failure of the
434 * function.   The possible values
435 * returned by this function are:
436   * <ul>
437   * <li> {@link libsbmlConstants#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS}
438   * <li> {@link libsbmlConstants#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT}
439   *
440   * </ul> <p>
441   * @note The subelement 'math' is present in SBML Levels&nbsp;2
442   * and&nbsp;3.  In SBML Level&nbsp;1, the equivalent construct is the
443   * attribute named 'formula'.  LibSBML provides a unified interface to
444   * the underlying math expression and this method can be used for models
445   * of all Levels of SBML.
446   <p>
447   * @see #setFormula(String formula)
448   */ public
449 int setMath(ASTNode math) {
450    return libsbmlJNI.Rule_setMath(swigCPtr, this, ASTNode.getCPtr(math), math);
451  }
452
453  
454/**
455   * Sets the 'variable' attribute value of this {@link Rule} object.
456   <p>
457   * <p>
458 * In SBML Level&nbsp;1, the different rule types each have a different
459 * name for the attribute holding the reference to the object constituting
460 * the left-hand side of the rule.  (E.g., for SBML Level&nbsp;1's
461 * SpeciesConcentrationRule the attribute is 'species', for
462 * CompartmentVolumeRule it is 'compartment', etc.)  In SBML Levels&nbsp;2
463 * and&nbsp;3, the only two types of {@link Rule} objects with a left-hand side
464 * object reference are {@link AssignmentRule} and {@link RateRule}, and both of them use the
465 * same name for attribute: 'variable'.  In order to make it easier for
466 * application developers to work with all Levels of SBML, libSBML uses a
467 * uniform name for all such attributes, and it is 'variable', regardless of
468 * whether Level&nbsp;1 rules or Level&nbsp;2&ndash;3 rules are being used.
469   <p>
470   * @param sid the identifier of a {@link Compartment}, {@link Species} or {@link Parameter}
471   * elsewhere in the enclosing {@link Model} object.
472   <p>
473   * <p>
474 * @return integer value indicating success/failure of the
475 * function.   The possible values
476 * returned by this function are:
477   * <ul>
478   * <li> {@link libsbmlConstants#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS}
479   * <li> {@link libsbmlConstants#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE}
480   * <li> {@link libsbmlConstants#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE}
481   * </ul>
482   */ public
483 int setVariable(String sid) {
484    return libsbmlJNI.Rule_setVariable(swigCPtr, this, sid);
485  }
486
487  
488/**
489   * Sets the units for this {@link Rule}.
490   <p>
491   * @param sname the identifier of the units
492   <p>
493   * <p>
494 * @return integer value indicating success/failure of the
495 * function.   The possible values
496 * returned by this function are:
497   * <ul>
498   * <li> {@link libsbmlConstants#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS}
499   * <li> {@link libsbmlConstants#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE}
500   * <li> {@link libsbmlConstants#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE}
501   *
502   * </ul> <p>
503   * @note The attribute 'units' exists on SBML Level&nbsp;1 ParameterRule
504   * objects only.  It is not present in SBML Levels&nbsp;2 and&nbsp;3.
505   */ public
506 int setUnits(String sname) {
507    return libsbmlJNI.Rule_setUnits(swigCPtr, this, sname);
508  }
509
510  
511/**
512   * Unsets the value of the 'variable' attribute of this {@link Rule} object.
513   <p>
514   * <p>
515 * @return integer value indicating success/failure of the
516 * function.   The possible values
517 * returned by this function are:
518   * <ul>
519   * <li> {@link libsbmlConstants#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS}
520   * <li> {@link libsbmlConstants#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED}
521   * <li> {@link libsbmlConstants#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE}
522   *
523   * </ul> <p>
524   * @see #setVariable(String sid)
525   * @see #isSetVariable()
526   * @see #getVariable()
527   */ public
528 int unsetVariable() {
529    return libsbmlJNI.Rule_unsetVariable(swigCPtr, this);
530  }
531
532  
533/**
534   * Unsets the 'units' for this {@link Rule}.
535   <p>
536   * <p>
537 * @return integer value indicating success/failure of the
538 * function.   The possible values
539 * returned by this function are:
540   * <ul>
541   * <li> {@link libsbmlConstants#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS}
542   * <li> {@link libsbmlConstants#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED}
543   * <li> {@link libsbmlConstants#LIBSBML_UNEXPECTED_ATTRIBUTE LIBSBML_UNEXPECTED_ATTRIBUTE}
544   *
545   * </ul> <p>
546   * @note The attribute 'units' exists on SBML Level&nbsp;1 ParameterRule
547   * objects only.  It is not present in SBML Levels&nbsp;2 and&nbsp;3.
548   */ public
549 int unsetUnits() {
550    return libsbmlJNI.Rule_unsetUnits(swigCPtr, this);
551  }
552
553  
554/**
555   * Calculates and returns a {@link UnitDefinition} that expresses the units of
556   * measurement assumed for the 'math' expression of this {@link Rule}.
557   <p>
558   * <p>
559 * The units are calculated based on the mathematical expression in the
560 * {@link Rule} and the model quantities referenced by <code>&lt;ci&gt;</code>
561 * elements used within that expression.  The method
562 * {@link Rule#getDerivedUnitDefinition()} returns the calculated units, to the
563 * extent that libSBML can compute them. 
564   <p>
565   * <p>
566 * @note The functionality that facilitates unit analysis depends on the
567 * model as a whole.  Thus, in cases where the object has not been added to
568 * a model or the model itself is incomplete, unit analysis is not possible
569 * and this method will return <code>null.</code> 
570   <p>
571   * <p>
572 * @warning <span class='warning'>Note that it is possible the 'math'
573 * expression in the {@link Rule} contains pure numbers or parameters with undeclared
574 * units.  In those cases, it is not possible to calculate the units of the
575 * overall expression without making assumptions.  LibSBML does not make
576 * assumptions about the units, and {@link Rule#getDerivedUnitDefinition()} only
577 * returns the units as far as it is able to determine them.  For example, in
578 * an expression <em>X + Y</em>, if <em>X</em> has unambiguously-defined
579 * units and <em>Y</em> does not, it will return the units of <em>X</em>.
580 * <strong>It is important that callers also invoke the method</strong>
581 * {@link Rule#containsUndeclaredUnits()} <strong>to determine whether this
582 * situation holds</strong>.  Callers may wish to take suitable actions in
583 * those scenarios.</span>
584   <p>
585   * @return a {@link UnitDefinition} that expresses the units of the math 
586   * expression of this {@link Rule}, or <code>null</code> if one cannot be constructed.
587   <p>
588   * @see #containsUndeclaredUnits()
589   */ public
590 UnitDefinition getDerivedUnitDefinition() {
591    long cPtr = libsbmlJNI.Rule_getDerivedUnitDefinition__SWIG_0(swigCPtr, this);
592    return (cPtr == 0) ? null : new UnitDefinition(cPtr, false);
593  }
594
595  
596/**
597   * Predicate returning <code>true</code> if the math expression of this {@link Rule} contains
598   * parameters/numbers with undeclared units.
599   <p>
600   * @return <code>true</code> if the math expression of this {@link Rule} includes
601   * parameters/numbers with undeclared units, <code>false</code> otherwise.
602   <p>
603   * @note A return value of <code>true</code> indicates that the {@link UnitDefinition}
604   * returned by getDerivedUnitDefinition() may not accurately represent
605   * the units of the expression.
606   <p>
607   * @see #getDerivedUnitDefinition()
608   */ public
609 boolean containsUndeclaredUnits() {
610    return libsbmlJNI.Rule_containsUndeclaredUnits__SWIG_0(swigCPtr, this);
611  }
612
613  
614/**
615   * Returns a code representing the type of rule this is.
616   <p>
617   * @return the rule type, which will be one of the following three possible
618   * values:
619   * <ul>
620   * <li> {@link libsbmlConstants#RULE_TYPE_RATE RULE_TYPE_RATE}
621   * <li> {@link libsbmlConstants#RULE_TYPE_SCALAR RULE_TYPE_SCALAR}
622   * <li> {@link libsbmlConstants#RULE_TYPE_INVALID RULE_TYPE_INVALID}
623   *
624   * </ul> <p>
625   * @note The attribute 'type' on {@link Rule} objects is present only in SBML
626   * Level&nbsp;1.  In SBML Level&nbsp;2 and later, the type has been
627   * replaced by subclassing the {@link Rule} object.
628   */ public
629 int getType() {
630    return libsbmlJNI.Rule_getType(swigCPtr, this);
631  }
632
633  
634/**
635   * Predicate returning <code>true</code> if this {@link Rule} is an {@link AlgebraicRule}.
636   <p>
637   * @return <code>true</code> if this {@link Rule} is an {@link AlgebraicRule}, <code>false</code> otherwise.
638   */ public
639 boolean isAlgebraic() {
640    return libsbmlJNI.Rule_isAlgebraic(swigCPtr, this);
641  }
642
643  
644/**
645   * Predicate returning <code>true</code> if this {@link Rule} is an {@link AssignmentRule}.
646   <p>
647   * @return <code>true</code> if this {@link Rule} is an {@link AssignmentRule}, <code>false</code> otherwise.
648   */ public
649 boolean isAssignment() {
650    return libsbmlJNI.Rule_isAssignment(swigCPtr, this);
651  }
652
653  
654/**
655   * Predicate returning <code>true</code> if this {@link Rule} is an CompartmentVolumeRule
656   * or equivalent.
657   <p>
658   * This libSBML method works for SBML Level&nbsp;1 models (where there is
659   * such a thing as an explicit CompartmentVolumeRule), as well as other Levels of
660   * SBML.  For Levels above Level&nbsp;1, this method checks the symbol
661   * being affected by the rule, and returns <code>true</code> if the symbol is the
662   * identifier of a {@link Compartment} object defined in the model.
663   <p>
664   * @return <code>true</code> if this {@link Rule} is a CompartmentVolumeRule, <code>false</code>
665   * otherwise.
666   */ public
667 boolean isCompartmentVolume() {
668    return libsbmlJNI.Rule_isCompartmentVolume(swigCPtr, this);
669  }
670
671  
672/**
673   * Predicate returning <code>true</code> if this {@link Rule} is an ParameterRule or
674   * equivalent.
675   <p>
676   * This libSBML method works for SBML Level&nbsp;1 models (where there is
677   * such a thing as an explicit ParameterRule), as well as other Levels of
678   * SBML.  For Levels above Level&nbsp;1, this method checks the symbol
679   * being affected by the rule, and returns <code>true</code> if the symbol is the
680   * identifier of a {@link Parameter} object defined in the model.
681   <p>
682   * @return <code>true</code> if this {@link Rule} is a ParameterRule, <code>false</code>
683   * otherwise.
684   */ public
685 boolean isParameter() {
686    return libsbmlJNI.Rule_isParameter(swigCPtr, this);
687  }
688
689  
690/**
691   * Predicate returning <code>true</code> if this {@link Rule} is a {@link RateRule} (SBML
692   * Levels&nbsp;2&ndash;3) or has a 'type' attribute value of <code>'rate'</code>
693   * (SBML Level&nbsp;1).
694   <p>
695   * @return <code>true</code> if this {@link Rule} is a {@link RateRule} (Level&nbsp;2) or has
696   * type 'rate' (Level&nbsp;1), <code>false</code> otherwise.
697   */ public
698 boolean isRate() {
699    return libsbmlJNI.Rule_isRate(swigCPtr, this);
700  }
701
702  
703/**
704   * Predicate returning <code>true</code> if this {@link Rule} is an {@link AssignmentRule} (SBML
705   * Levels&nbsp;2&ndash;3) or has a 'type' attribute value of <code>'scalar'</code>
706   * (SBML Level&nbsp;1).
707   <p>
708   * @return <code>true</code> if this {@link Rule} is an {@link AssignmentRule} (Level&nbsp;2) or has
709   * type 'scalar' (Level&nbsp;1), <code>false</code> otherwise.
710   */ public
711 boolean isScalar() {
712    return libsbmlJNI.Rule_isScalar(swigCPtr, this);
713  }
714
715  
716/**
717   * Predicate returning <code>true</code> if this {@link Rule} is a SpeciesConcentrationRule
718   * or equivalent.
719   <p>
720   * This libSBML method works for SBML Level&nbsp;1 models (where there is
721   * such a thing as an explicit SpeciesConcentrationRule), as well as
722   * other Levels of SBML.  For Levels above Level&nbsp;1, this method
723   * checks the symbol being affected by the rule, and returns <code>true</code> if
724   * the symbol is the identifier of a {@link Species} object defined in the model.
725   <p>
726   * @return <code>true</code> if this {@link Rule} is a SpeciesConcentrationRule, <code>false</code>
727   * otherwise.
728   */ public
729 boolean isSpeciesConcentration() {
730    return libsbmlJNI.Rule_isSpeciesConcentration(swigCPtr, this);
731  }
732
733  
734/**
735   * Returns the libSBML type code for this SBML object.
736   <p>
737   * <p>
738 * LibSBML attaches an identifying code to every kind of SBML object.  These
739 * are integer constants known as <em>SBML type codes</em>.  The names of all
740 * the codes begin with the characters <code>SBML_</code>.
741 * In the Java language interface for libSBML, the
742 * type codes are defined as static integer constants in the interface class
743 * {@link libsbmlConstants}.    Note that different Level&nbsp;3
744 * package plug-ins may use overlapping type codes; to identify the package
745 * to which a given object belongs, call the <code>getPackageName()</code>
746 * method on the object.
747   <p>
748   * @return the SBML type code for this object, either
749   * {@link libsbmlConstants#SBML_ASSIGNMENT_RULE SBML_ASSIGNMENT_RULE},
750   * {@link libsbmlConstants#SBML_RATE_RULE SBML_RATE_RULE}, or
751   * {@link libsbmlConstants#SBML_ALGEBRAIC_RULE SBML_ALGEBRAIC_RULE} 
752   * for SBML Core.
753   <p>
754   * <p>
755 * @warning <span class='warning'>The specific integer values of the possible
756 * type codes may be reused by different Level&nbsp;3 package plug-ins.
757 * Thus, to identifiy the correct code, <strong>it is necessary to invoke
758 * both getTypeCode() and getPackageName()</strong>.</span>
759   <p>
760   * @see #getElementName()
761   * @see #getPackageName()
762   */ public
763 int getTypeCode() {
764    return libsbmlJNI.Rule_getTypeCode(swigCPtr, this);
765  }
766
767  
768/**
769   * Returns the SBML Level&nbsp;1 type code for this {@link Rule} object.
770   <p>
771   * This method only applies to SBML Level&nbsp;1 model objects.  If this is
772   * not an SBML Level&nbsp;1 rule object, this method will return
773   * {@link libsbmlConstants#SBML_UNKNOWN SBML_UNKNOWN}.
774   <p>
775   * @return the SBML Level&nbsp;1 type code for this {@link Rule} (namely,
776   * {@link libsbmlConstants#SBML_COMPARTMENT_VOLUME_RULE SBML_COMPARTMENT_VOLUME_RULE},
777   * {@link libsbmlConstants#SBML_PARAMETER_RULE SBML_PARAMETER_RULE},
778   * {@link libsbmlConstants#SBML_SPECIES_CONCENTRATION_RULE SBML_SPECIES_CONCENTRATION_RULE}, or
779   * {@link libsbmlConstants#SBML_UNKNOWN SBML_UNKNOWN}).
780   */ public
781 int getL1TypeCode() {
782    return libsbmlJNI.Rule_getL1TypeCode(swigCPtr, this);
783  }
784
785  
786/**
787   * Returns the XML element name of this object.
788   <p>
789   * The returned value can be any of a number of different strings,
790   * depending on the SBML Level in use and the kind of {@link Rule} object this
791   * is.  The rules as of libSBML version 5.12.0
792
793   * are the following:
794   * <ul>
795   * <li> (Level&nbsp;2 and&nbsp;3) RateRule: returns <code>'rateRule'</code>
796   * <li> (Level&nbsp;2 and&nbsp;3) AssignmentRule: returns <code>'assignmentRule'</code> 
797   * <li> (Level&nbsp;2 and&nbsp;3) AlgebraicRule: returns <code>'algebraicRule'</code>
798   * <li> (Level&nbsp;1 Version&nbsp;1) SpecieConcentrationRule: returns <code>'specieConcentrationRule'</code>
799   * <li> (Level&nbsp;1 Version&nbsp;2) SpeciesConcentrationRule: returns <code>'speciesConcentrationRule'</code>
800   * <li> (Level&nbsp;1) CompartmentVolumeRule: returns <code>'compartmentVolumeRule'</code>
801   * <li> (Level&nbsp;1) ParameterRule: returns <code>'parameterRule'</code>
802   * <li> Unknown rule type: returns <code>'unknownRule'</code>
803   * </ul>
804   <p>
805   * Beware that the last (<code>'unknownRule'</code>) is not a valid SBML element
806   * name.
807   <p>
808   * @return the name of this element
809   */ public
810 String getElementName() {
811    return libsbmlJNI.Rule_getElementName(swigCPtr, this);
812  }
813
814  
815/**
816   * Sets the SBML Level&nbsp;1 type code for this {@link Rule}.
817   <p>
818   * @param type the SBML Level&nbsp;1 type code for this {@link Rule}. The allowable
819   * values are {@link libsbmlConstants#SBML_COMPARTMENT_VOLUME_RULE SBML_COMPARTMENT_VOLUME_RULE},
820   * {@link libsbmlConstants#SBML_PARAMETER_RULE SBML_PARAMETER_RULE}, and
821   * {@link libsbmlConstants#SBML_SPECIES_CONCENTRATION_RULE SBML_SPECIES_CONCENTRATION_RULE}.
822   <p>
823   * <p>
824 * @return integer value indicating success/failure of the
825 * function.   The possible values
826 * returned by this function are:
827   * <ul>
828   * <li> {@link libsbmlConstants#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS}
829   * <li> {@link libsbmlConstants#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE}
830   * if given <code>type</code> value is not one of the above.
831   * </ul>
832   */ public
833 int setL1TypeCode(int type) {
834    return libsbmlJNI.Rule_setL1TypeCode(swigCPtr, this, type);
835  }
836
837  
838/**
839   * Predicate returning <code>true</code> if all the required elements for this {@link Rule}
840   * object have been set.
841   <p>
842   * The only required element for a {@link Rule} object is the 'math' subelement.
843   <p>
844   * @return a boolean value indicating whether all the required
845   * elements for this object have been defined.
846   */ public
847 boolean hasRequiredElements() {
848    return libsbmlJNI.Rule_hasRequiredElements(swigCPtr, this);
849  }
850
851  
852/**
853   * Predicate returning <code>true</code> if all the required attributes for this {@link Rule}
854   * object have been set.
855   <p>
856   * The required attributes for a {@link Rule} object depend on the type of {@link Rule}
857   * it is.  For {@link AssignmentRule} and {@link RateRule} objects (and SBML
858   * Level&nbsp1's SpeciesConcentrationRule, CompartmentVolumeRule, and
859   * ParameterRule objects), the required attribute is 'variable'; for
860   * {@link AlgebraicRule} objects, there is no required attribute.
861   <p>
862   * @return <code>true</code> if the required attributes have been set, <code>false</code>
863   * otherwise.
864   */ public
865 boolean hasRequiredAttributes() {
866    return libsbmlJNI.Rule_hasRequiredAttributes(swigCPtr, this);
867  }
868
869  
870/**
871   * <p>
872 * Replaces all uses of a given <code>SIdRef</code> type attribute value with another
873 * value.
874 <p>
875 * <p>
876 * In SBML, object identifiers are of a data type called <code>SId</code>.
877 * In SBML Level&nbsp;3, an explicit data type called <code>SIdRef</code> was
878 * introduced for attribute values that refer to <code>SId</code> values; in
879 * previous Levels of SBML, this data type did not exist and attributes were
880 * simply described to as 'referring to an identifier', but the effective
881 * data type was the same as <code>SIdRef</code>in Level&nbsp;3.  These and
882 * other methods of libSBML refer to the type <code>SIdRef</code> for all
883 * Levels of SBML, even if the corresponding SBML specification did not
884 * explicitly name the data type.
885 <p>
886 * This method works by looking at all attributes and (if appropriate)
887 * mathematical formulas in MathML content, comparing the referenced
888 * identifiers to the value of <code>oldid</code>.  If any matches are found, the
889 * matching values are replaced with <code>newid</code>.  The method does <em>not</em>
890 * descend into child elements.
891 <p>
892 * @param oldid the old identifier
893 * @param newid the new identifier
894   */ public
895 void renameSIdRefs(String oldid, String newid) {
896    libsbmlJNI.Rule_renameSIdRefs(swigCPtr, this, oldid, newid);
897  }
898
899  
900/**
901   * <p>
902 * Replaces all uses of a given <code>UnitSIdRef</code> type attribute value with
903 * another value.
904 <p>
905 * <p>
906 * In SBML, unit definitions have identifiers of type <code>UnitSId</code>.  In
907 * SBML Level&nbsp;3, an explicit data type called <code>UnitSIdRef</code> was
908 * introduced for attribute values that refer to <code>UnitSId</code> values; in
909 * previous Levels of SBML, this data type did not exist and attributes were
910 * simply described to as 'referring to a unit identifier', but the effective
911 * data type was the same as <code>UnitSIdRef</code> in Level&nbsp;3.  These and
912 * other methods of libSBML refer to the type <code>UnitSIdRef</code> for all
913 * Levels of SBML, even if the corresponding SBML specification did not
914 * explicitly name the data type.
915 <p>
916 * This method works by looking at all unit identifier attribute values
917 * (including, if appropriate, inside mathematical formulas), comparing the
918 * referenced unit identifiers to the value of <code>oldid</code>.  If any matches
919 * are found, the matching values are replaced with <code>newid</code>.  The method
920 * does <em>not</em> descend into child elements.
921 <p>
922 * @param oldid the old identifier
923 * @param newid the new identifier
924   */ public
925 void renameUnitSIdRefs(String oldid, String newid) {
926    libsbmlJNI.Rule_renameUnitSIdRefs(swigCPtr, this, oldid, newid);
927  }
928
929  
930/** * @internal */ public
931 String getId() {
932    return libsbmlJNI.Rule_getId(swigCPtr, this);
933  }
934
935  
936/** * @internal */ public
937 void replaceSIDWithFunction(String id, ASTNode function) {
938    libsbmlJNI.Rule_replaceSIDWithFunction(swigCPtr, this, id, ASTNode.getCPtr(function), function);
939  }
940
941  
942/** * @internal */ public
943 void divideAssignmentsToSIdByFunction(String id, ASTNode function) {
944    libsbmlJNI.Rule_divideAssignmentsToSIdByFunction(swigCPtr, this, id, ASTNode.getCPtr(function), function);
945  }
946
947  
948/** * @internal */ public
949 void multiplyAssignmentsToSIdByFunction(String id, ASTNode function) {
950    libsbmlJNI.Rule_multiplyAssignmentsToSIdByFunction(swigCPtr, this, id, ASTNode.getCPtr(function), function);
951  }
952
953}