001/* ----------------------------------------------------------------------------
002 * This file was automatically generated by SWIG (http://www.swig.org).
003 * Version 2.0.11
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 * 
013 * Implementation of SBML Level 2's StoichiometryMath construct.
014 * <p>
015 * <h2>Stoichiometries in SBML Level 2</h2>
016 * <p>
017 * In SBML Level 2, product and reactant stoichiometries can be specified
018 * using <em>either</em> the 'stoichiometry' attribute or a 'stoichiometryMath'
019 * element in a {@link SpeciesReference} object.  The 'stoichiometry' attribute is
020 * of type <code>double</code> and should contain values greater than zero (0).  The
021 * 'stoichiometryMath' element is implemented as an element containing a
022 * MathML expression.  These two are mutually exclusive; only one of
023 * 'stoichiometry' or 'stoichiometryMath' should be defined in a given
024 * {@link SpeciesReference} instance.  When neither the attribute nor the element
025 * is present, the value of 'stoichiometry' in the enclosing
026 * {@link SpeciesReference} instance defaults to <code>1.</code>
027 * <p>
028 * For maximum interoperability, {@link SpeciesReference}'s 'stoichiometry'
029 * attribute should be used in preference to 'stoichiometryMath' when a
030 * species' stoichiometry is a simple scalar number (integer or decimal).
031 * When the stoichiometry is a rational number, or when it is a more
032 * complicated formula, 'stoichiometryMath' must be used.  The MathML
033 * expression in 'stoichiometryMath' may also refer to identifiers of
034 * entities in a model (except reaction identifiers).  However, the only
035 * species identifiers that can be used in 'stoichiometryMath' are those
036 * referenced in the enclosing {@link Reaction}'s list of reactants, products and
037 * modifiers.
038 * <p>
039 * The 'stoichiometry' attribute and the 'stoichiometryMath' element, when
040 * either is used, is each interpreted as a factor applied to the reaction
041 * rate to produce the rate of change of the species identified by the
042 * 'species' attribute in the enclosing {@link SpeciesReference}.  This is the
043 * normal interpretation of a stoichiometry, but in SBML, one additional
044 * consideration has to be taken into account.  The reaction rate, which is
045 * the result of the {@link KineticLaw}'s 'math' element, is always in the model's
046 * <em>substance</em> per <em>time</em> units.  However, the rate of change of the
047 * species will involve the species' <em>substance</em> units (i.e., the units
048 * identified by the {@link Species} object's 'substanceUnits' attribute), and
049 * these units may be different from the model's default <em>substance</em>
050 * units.  If the units <em>are</em> different, the stoichiometry must
051 * incorporate a conversion factor for converting the model's <em>substance</em>
052 * units to the species' <em>substance</em> units.  The conversion factor is
053 * assumed to be included in the scalar value of the 'stoichiometry'
054 * attribute if 'stoichiometry' is used.  If instead 'stoichiometryMath' is
055 * used, then the product of the model's 'substance' units times the
056 * 'stoichiometryMath' units must match the <em>substance</em> units of the
057 * species.  Note that in either case, if the species' units and the
058 * model's default <em>substance</em> units are the same, the stoichiometry ends
059 * up being a dimensionless number and equivalent to the standard chemical
060 * stoichiometry found in textbooks.  Examples and more explanations of
061 * this are given in the SBML specification.
062 * <p>
063 * The following is a simple example of a species reference for species 
064 * <code>'X0'</code>, with stoichiometry <code>2</code>, in a list of reactants within a reaction
065 * having the identifier <code>'J1':</code>
066 * <div class='fragment'><pre>
067 &lt;model&gt;
068     ...
069     &lt;listOfReactions&gt;
070         &lt;reaction id='J1'&gt;
071             &lt;listOfReactants&gt;
072                 &lt;speciesReference species='X0' stoichiometry='2'&gt;
073             &lt;/listOfReactants&gt;
074             ...
075         &lt;/reaction&gt;
076         ...
077     &lt;/listOfReactions&gt;
078     ...
079 &lt;/model&gt;
080 </pre></div>
081 * <p>
082 * The following is a more complex example of a species reference for
083 * species <code>'X0'</code>, with a stoichiometry formula consisting of
084 * a rational number:
085 * <div class='fragment'><pre>
086 &lt;model&gt;
087     ...
088     &lt;listOfReactions&gt;
089         &lt;reaction id='J1'&gt;
090             &lt;listOfReactants&gt;
091                 &lt;speciesReference species='X0'&gt;
092                     &lt;stoichiometryMath&gt;
093                         &lt;math xmlns='http://www.w3.org/1998/Math/MathML'&gt; 
094                             &lt;cn type='rational'&gt; 3 &lt;sep/&gt; 2 &lt;/cn&gt;
095                         &lt;/math&gt;
096                     &lt;/stoichiometryMath&gt;
097                 &lt;/speciesReference&gt;
098             &lt;/listOfReactants&gt;
099             ...
100         &lt;/reaction&gt;
101         ...
102     &lt;/listOfReactions&gt;
103     ...
104 &lt;/model&gt;
105 </pre></div>
106 * <p>
107 * Additional discussions of stoichiometries and implications for species
108 * and reactions are included in the documentation of {@link SpeciesReference}
109 * class.
110 * <p>
111 * <h2>Stoichiometries in SBML Level 3</h2>
112 * <p>
113 * The {@link StoichiometryMath} construct is not defined in SBML Level&nbsp;3
114 * Version&nbsp;1 Core.  Instead, Level&nbsp;3 defines the identifier of
115 * {@link SpeciesReference} objects as a stand-in for the stoichiometry of the
116 * reactant or product being referenced, and allows that identifier to be
117 * used elsewhere in SBML models, including (for example) {@link InitialAssignment}
118 * objects.  This makes it possible to achieve the same effect as
119 * {@link StoichiometryMath}, but with other SBML objects.  For instance, to
120 * produce a stoichiometry value that is a rational number, a model can use
121 * {@link InitialAssignment} to assign the identifier of a {@link SpeciesReference} object
122 * to a MathML expression evaluating to a rational number.  This is
123 * analogous to the same way that, in Level&nbsp;2, the model would use
124 * {@link StoichiometryMath} with a MathML expression evaluating to a rational
125 * number.
126 * <p>
127 * In SBML Level 2, the stoichiometry of a reactant or product is a
128 * combination of both a <em>biochemical stoichiometry</em> (meaning, the
129 * standard stoichiometry of a species in a reaction) and any necessary
130 * unit conversion factors. The introduction of an explicit attribute on
131 * the {@link Species} object for a conversion factor allows Level&nbsp;3 to avoid
132 * having to overload the meaning of stoichiometry.  In Level&nbsp;3, the
133 * stoichiometry given by a {@link SpeciesReference} object in a reaction is a
134 * 'proper' biochemical stoichiometry, meaning a dimensionless number free
135 * of unit conversions.
136 * <p>
137 * @see SpeciesReference
138 * @see Reaction
139 */
140
141public class StoichiometryMath extends SBase {
142   private long swigCPtr;
143
144   protected StoichiometryMath(long cPtr, boolean cMemoryOwn)
145   {
146     super(libsbmlJNI.StoichiometryMath_SWIGUpcast(cPtr), cMemoryOwn);
147     swigCPtr = cPtr;
148   }
149
150   protected static long getCPtr(StoichiometryMath obj)
151   {
152     return (obj == null) ? 0 : obj.swigCPtr;
153   }
154
155   protected static long getCPtrAndDisown (StoichiometryMath obj)
156   {
157     long ptr = 0;
158
159     if (obj != null)
160     {
161       ptr             = obj.swigCPtr;
162       obj.swigCMemOwn = false;
163     }
164
165     return ptr;
166   }
167
168  protected void finalize() {
169    delete();
170  }
171
172  public synchronized void delete() {
173    if (swigCPtr != 0) {
174      if (swigCMemOwn) {
175        swigCMemOwn = false;
176        libsbmlJNI.delete_StoichiometryMath(swigCPtr);
177      }
178      swigCPtr = 0;
179    }
180    super.delete();
181  }
182
183  
184/**
185   * Creates a new {@link StoichiometryMath} object using the given SBML <code>level</code>
186   * values.
187   * <p>
188   * @param level a long integer, the SBML Level to assign to this {@link StoichiometryMath}
189   * <p>
190   * @param version a long integer, the SBML Version to assign to this
191   * {@link StoichiometryMath}
192   * <p>
193   * The {@link StoichiometryMath} construct exists only in SBML Level&nbsp;2.  It
194   * is an optional construct available for defining the stoichiometries of
195   * reactants and products in {@link Reaction} objects.  Note that a different
196   * mechanism is used in SBML Level&nbsp;3, where {@link StoichiometryMath} is not
197   * available.  Please consult the top of this libSBML {@link StoichiometryMath}
198   * documentation for more information about the differences between SBML
199   * Level&nbsp;2 and&nbsp;3 with respect to stoichiometries.
200   * <p>
201   * @throws SBMLConstructorException 
202   * Thrown if the given <code>level</code> and <code>version</code> combination, or this kind
203   * of SBML object, are either invalid or mismatched with respect to the
204   * parent {@link SBMLDocument} object.
205   * <p>
206   * @note Upon the addition of a {@link StoichiometryMath} object to an
207   * {@link SBMLDocument} (e.g., using
208   * {@link SpeciesReference#createStoichiometryMath()}), the SBML Level, SBML
209   * Version and XML namespace of the document <em>override</em> the values used
210   * when creating the {@link StoichiometryMath} object via this constructor.  This
211   * is necessary to ensure that an SBML document is a consistent
212   * structure.  Nevertheless, the ability to supply the values at the time
213   * of creation of a {@link StoichiometryMath} is an important aid to producing
214   * valid SBML.  Knowledge of the intented SBML Level and Version
215   * determine whether it is valid to assign a particular value to an
216   * attribute, or whether it is valid to add an object to an existing
217   * {@link SBMLDocument}.
218   */ public
219 StoichiometryMath(long level, long version) throws org.sbml.libsbml.SBMLConstructorException {
220    this(libsbmlJNI.new_StoichiometryMath__SWIG_0(level, version), true);
221  }
222
223  
224/**
225   * Creates a new {@link StoichiometryMath} object using the given {@link SBMLNamespaces} object
226   * <code>sbmlns</code>.
227   * <p>
228   * The {@link SBMLNamespaces} object encapsulates SBML Level/Version/namespaces
229   * information.  It is used to communicate the SBML Level, Version, and
230   * (in Level&nbsp;3) packages used in addition to SBML Level&nbsp;3 Core.
231   * A common approach to using this class constructor is to create an
232   * {@link SBMLNamespaces} object somewhere in a program, once, then pass it to
233   * object constructors such as this one when needed.
234   * <p>
235   * @param sbmlns an {@link SBMLNamespaces} object.
236   * <p>
237   * The {@link StoichiometryMath} construct exists only in SBML Level&nbsp;2.  It
238   * is an optional construct available for defining the stoichiometries of
239   * reactants and products in {@link Reaction} objects.  Note that a different
240   * mechanism is used in SBML Level&nbsp;3, where {@link StoichiometryMath} is not
241   * available.  Please consult the top of this libSBML {@link StoichiometryMath}
242   * documentation for more information about the differences between SBML
243   * Level&nbsp;2 and&nbsp;3 with respect to stoichiometries.
244   * <p>
245   * @throws SBMLConstructorException 
246   * Thrown if the given <code>level</code> and <code>version</code> combination, or this kind
247   * of SBML object, are either invalid or mismatched with respect to the
248   * parent {@link SBMLDocument} object.
249   * <p>
250   * @note Upon the addition of a {@link StoichiometryMath} object to an
251   * {@link SBMLDocument} (e.g., using
252   * {@link SpeciesReference#createStoichiometryMath()}), the SBML XML namespace
253   * of the document <em>overrides</em> the value used when creating the
254   * {@link StoichiometryMath} object via this constructor.  This is necessary to
255   * ensure that an SBML document is a consistent structure.  Nevertheless,
256   * the ability to supply the values at the time of creation of a
257   * {@link StoichiometryMath} is an important aid to producing valid SBML.
258   * Knowledge of the intented SBML Level and Version determine whether it
259   * is valid to assign a particular value to an attribute, or whether it
260   * is valid to add an object to an existing {@link SBMLDocument}.
261   */ public
262 StoichiometryMath(SBMLNamespaces sbmlns) throws org.sbml.libsbml.SBMLConstructorException {
263    this(libsbmlJNI.new_StoichiometryMath__SWIG_1(SBMLNamespaces.getCPtr(sbmlns), sbmlns), true);
264  }
265
266  
267/**
268   * Copy constructor; creates a copy of this {@link StoichiometryMath}.
269   * <p>
270   * @param orig the object to copy.
271   * <p>
272   * @throws SBMLConstructorException 
273   * Thrown if the argument <code>orig</code> is <code>null.</code>
274   */ public
275 StoichiometryMath(StoichiometryMath orig) throws org.sbml.libsbml.SBMLConstructorException {
276    this(libsbmlJNI.new_StoichiometryMath__SWIG_2(StoichiometryMath.getCPtr(orig), orig), true);
277  }
278
279  
280/**
281   * Creates and returns a deep copy of this {@link StoichiometryMath} object.
282   * <p>
283   * @return a (deep) copy of this {@link StoichiometryMath}.
284   */ public
285 StoichiometryMath cloneObject() {
286    long cPtr = libsbmlJNI.StoichiometryMath_cloneObject(swigCPtr, this);
287    return (cPtr == 0) ? null : new StoichiometryMath(cPtr, true);
288  }
289
290  
291/**
292   * Retrieves the mathematical formula within this {@link StoichiometryMath} and
293   * return it as an AST.
294   * <p>
295   * @return the math of this {@link StoichiometryMath}.
296   * <p>
297   * The {@link StoichiometryMath} construct exists only in SBML Level&nbsp;2.  It
298   * is an optional construct available for defining the stoichiometries of
299   * reactants and products in {@link Reaction} objects.  Note that a different
300   * mechanism is used in SBML Level&nbsp;3, where {@link StoichiometryMath} is not
301   * available.  Please consult the top of this libSBML {@link StoichiometryMath}
302   * documentation for more information about the differences between SBML
303   * Level&nbsp;2 and&nbsp;3 with respect to stoichiometries.
304   */ public
305 ASTNode getMath() {
306    long cPtr = libsbmlJNI.StoichiometryMath_getMath(swigCPtr, this);
307    return (cPtr == 0) ? null : new ASTNode(cPtr, false);
308  }
309
310  
311/**
312   * Predicate to test whether the math for this {@link StoichiometryMath} object
313   * is set.
314   * <p>
315   * @return <code>true</code> if the formula (meaning the <code>math</code> subelement) of
316   * this {@link StoichiometryMath} is set, <code>false</code> otherwise.
317   * <p>
318   * The {@link StoichiometryMath} construct exists only in SBML Level&nbsp;2.  It
319   * is an optional construct available for defining the stoichiometries of
320   * reactants and products in {@link Reaction} objects.  Note that a different
321   * mechanism is used in SBML Level&nbsp;3, where {@link StoichiometryMath} is not
322   * available.  Please consult the top of this libSBML {@link StoichiometryMath}
323   * documentation for more information about the differences between SBML
324   * Level&nbsp;2 and&nbsp;3 with respect to stoichiometries.
325   */ public
326 boolean isSetMath() {
327    return libsbmlJNI.StoichiometryMath_isSetMath(swigCPtr, this);
328  }
329
330  
331/**
332   * Sets the 'math' expression of this {@link StoichiometryMath} instance to a
333   * copy of the given {@link ASTNode}.
334   * <p>
335   * @param math an {@link ASTNode} representing a formula tree.
336   * <p>
337   * @return integer value indicating success/failure of the
338   * function.  The possible values
339   * returned by this function are:
340   * <ul>
341   * <li> {@link  libsbmlConstants#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS }
342   * <li> {@link  libsbmlConstants#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT }
343   * </ul>
344   * <p>
345   * The {@link StoichiometryMath} construct exists only in SBML Level&nbsp;2.  It
346   * is an optional construct available for defining the stoichiometries of
347   * reactants and products in {@link Reaction} objects.  Note that a different
348   * mechanism is used in SBML Level&nbsp;3, where {@link StoichiometryMath} is not
349   * available.  Please consult the top of this libSBML {@link StoichiometryMath}
350   * documentation for more information about the differences between SBML
351   * Level&nbsp;2 and&nbsp;3 with respect to stoichiometries.
352   */ public
353 int setMath(ASTNode math) {
354    return libsbmlJNI.StoichiometryMath_setMath(swigCPtr, this, ASTNode.getCPtr(math), math);
355  }
356
357  
358/**
359   * Calculates and returns a {@link UnitDefinition} object that expresses the
360   * units returned by the math expression in this {@link StoichiometryMath}
361   * object.
362   * <p>
363   * The units are calculated based on the mathematical expression in the
364   * {@link StoichiometryMath} and the model quantities referenced by
365   * <code>&lt;ci&gt;</code> elements used within that expression.  The
366   * {@link StoichiometryMath#getDerivedUnitDefinition()} method returns the
367   * calculated units.
368   * <p>
369   * Note that the functionality that facilitates unit analysis depends 
370   * on the model as a whole.  Thus, in cases where the object has not 
371   * been added to a model or the model itself is incomplete,
372   * unit analysis is not possible and this method will return <code>null.</code>
373   * <p>
374   * @warning Note that it is possible the 'math' expression in the
375   * {@link StoichiometryMath} instance contains literal numbers or parameters with
376   * undeclared units.  In those cases, it is not possible to calculate the
377   * units of the overall expression without making assumptions.  LibSBML
378   * does not make assumptions about the units, and
379   * {@link StoichiometryMath#getDerivedUnitDefinition()} only returns the units
380   * as far as it is able to determine them.  For example, in an expression
381   * <em>X + Y</em>, if <em>X</em> has unambiguously-defined units and
382   * <em>Y</em> does not, it will return the units of <em>X</em>.  When
383   * using this method, <strong>it is critical that callers also invoke the
384   * method</strong> {@link StoichiometryMath#containsUndeclaredUnits()}
385   * <strong>to determine whether this situation holds</strong>.  Callers
386   * should take suitable action in those situations.
387   * <p>
388   * @return a {@link UnitDefinition} that expresses the units of the math, 
389   * or <code>null</code> if one cannot be constructed.
390   * <p>
391   * @see #containsUndeclaredUnits()
392   */ public
393 UnitDefinition getDerivedUnitDefinition() {
394    long cPtr = libsbmlJNI.StoichiometryMath_getDerivedUnitDefinition__SWIG_0(swigCPtr, this);
395    return (cPtr == 0) ? null : new UnitDefinition(cPtr, false);
396  }
397
398  
399/**
400   * Predicate returning <code>true</code> if the math
401   * expression of this {@link StoichiometryMath} object contains literal numbers
402   * or parameters with undeclared units.
403   * <p>
404   * The {@link StoichiometryMath#getDerivedUnitDefinition()} method returns what
405   * libSBML computes the units of the Stoichiometry to be, to the extent
406   * that libSBML can compute them.  However, if the expression contains
407   * literal numbers or parameters with undeclared units, libSBML may not
408   * be able to compute the full units of the expression and will only
409   * return what it can compute.  Callers should always use
410   * {@link StoichiometryMath#containsUndeclaredUnits()} when using
411   * {@link StoichiometryMath#getDerivedUnitDefinition()} to decide whether the
412   * returned units may be incomplete.
413   * <p>
414   * @return <code>true</code> if the math expression of this {@link StoichiometryMath}
415   * includes numbers/parameters with undeclared units, <code>false</code> otherwise.
416   * <p>
417   * @note A return value of <code>true</code> indicates that the {@link UnitDefinition}
418   * returned by {@link StoichiometryMath#getDerivedUnitDefinition()} may not
419   * accurately represent the units of the expression.
420   * <p>
421   * @see #getDerivedUnitDefinition()
422   */ public
423 boolean containsUndeclaredUnits() {
424    return libsbmlJNI.StoichiometryMath_containsUndeclaredUnits__SWIG_0(swigCPtr, this);
425  }
426
427  
428/**
429   * Returns the libSBML type code of this object instance.
430   * <p>
431   * LibSBML attaches an identifying code to every
432   * kind of SBML object.  These are known as <em>SBML type codes</em>.  In
433   * other languages, the set of type codes is stored in an enumeration; in
434   * the Java language interface for libSBML, the type codes are defined as
435   * static integer constants in the interface class {@link
436   * libsbmlConstants}.  The names of the type codes all begin with the
437   * characters <code>SBML_.</code> 
438   * <p>
439   * @return the SBML type code for this object, or {@link  libsbmlConstants#SBML_UNKNOWN SBML_UNKNOWN} (default).
440   * <p>
441   * @see #getElementName()
442   */ public
443 int getTypeCode() {
444    return libsbmlJNI.StoichiometryMath_getTypeCode(swigCPtr, this);
445  }
446
447  
448/**
449   * Returns the XML element name of this object, which for {@link StoichiometryMath}, is
450   * always <code>'stoichiometryMath'.</code>
451   * <p>
452   * @return the name of this element, i.e., <code>'stoichiometryMath'.</code> 
453   */ public
454 String getElementName() {
455    return libsbmlJNI.StoichiometryMath_getElementName(swigCPtr, this);
456  }
457
458  
459/**
460   * Predicate returning <code>true</code> if
461   * all the required elements for this {@link StoichiometryMath} object
462   * have been set.
463   * <p>
464   * @note The required elements for a {@link StoichiometryMath} object are:
465   * <ul>
466   * <li> 'math'
467   * </ul>
468   * <p>
469   * @return a boolean value indicating whether all the required
470   * elements for this object have been defined.
471   */ public
472 boolean hasRequiredElements() {
473    return libsbmlJNI.StoichiometryMath_hasRequiredElements(swigCPtr, this);
474  }
475
476  
477/**
478   * Finds this {@link StoichiometryMath}'s {@link SpeciesReference} parent and calls unsetStoichiometryMath() on it, indirectly deleting itself.  Overridden from the {@link SBase} function since the parent is not a {@link ListOf}.
479   * <p>
480   * @return integer value indicating success/failure of the
481   * function.   The possible values
482   * returned by this function are:
483   * <ul>
484   * <li> {@link  libsbmlConstants#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS }
485   * <li> {@link  libsbmlConstants#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED }
486   * </ul>
487   */ public
488 int removeFromParentAndDelete() {
489    return libsbmlJNI.StoichiometryMath_removeFromParentAndDelete(swigCPtr, this);
490  }
491
492  
493/**
494   * Renames all the SIdRef attributes on this element, including any found in MathML
495   */ public
496 void renameSIdRefs(String oldid, String newid) {
497    libsbmlJNI.StoichiometryMath_renameSIdRefs(swigCPtr, this, oldid, newid);
498  }
499
500  
501/**
502   * Renames all the UnitSIdRef attributes on this element
503   */ public
504 void renameUnitSIdRefs(String oldid, String newid) {
505    libsbmlJNI.StoichiometryMath_renameUnitSIdRefs(swigCPtr, this, oldid, newid);
506  }
507
508  
509/**
510   * Replace all nodes with the name 'id' from the child 'math' object with the provided function. 
511   * <p>
512   * @internal
513   */ public
514 void replaceSIDWithFunction(String id, ASTNode function) {
515    libsbmlJNI.StoichiometryMath_replaceSIDWithFunction(swigCPtr, this, id, ASTNode.getCPtr(function), function);
516  }
517
518}