001/* ----------------------------------------------------------------------------
002 * This file was automatically generated by SWIG (http://www.swig.org).
003 * Version 2.0.12
004 *
005 * Do not make changes to this file unless you know what you are doing--modify
006 * the SWIG interface file instead.
007 * ----------------------------------------------------------------------------- */
008
009package org.sbml.libsbml;
010
011/** 
012 *  Implementation of SBML Level 3's Priority construct for
013 * {@link Event}.
014 <p>
015 * The {@link Priority} object class (which was introduced in SBML Level&nbsp;3
016 * Version&nbsp;1), like {@link Delay}, is derived from {@link SBase} and contains a MathML
017 * formula stored in the element 'math'.  This formula is used to compute a
018 * dimensionless numerical value that influences the order in which a
019 * simulator is to perform the assignments of two or more events that
020 * happen to be executed simultaneously.  The formula may evaluate to any
021 * <code>double</code> value (and thus may be a positive or negative number, or
022 * zero), with positive numbers taken to signifying a higher priority than
023 * zero or negative numbers.  If no {@link Priority} object is present on a given
024 * {@link Event} object, no priority is defined for that event.
025 <p>
026 * <h2>The interpretation of priorities on events in a model</h2>
027 <p>
028 * For the purposes of SBML, <em>simultaneous event execution</em> is
029 * defined as the situation in which multiple events have identical
030 * times of execution.  The time of execution is calculated as the
031 * sum of the time at which a given event's {@link Trigger} is <em>triggered</em>
032 * plus its {@link Delay} duration, if any.  Here, <em>identical times</em> means
033 * <em>mathematically equal</em> instants in time.  (In practice,
034 * simulation software adhering to this specification may have to
035 * rely on numerical equality instead of strict mathematical
036 * equality; robust models will ensure that this difference will not
037 * cause significant discrepancies from expected behavior.)
038 <p>
039 * If no {@link Priority} subobjects are defined for two or more {@link Event} objects,
040 * then those events are still executed simultaneously but their order of
041 * execution is <em>undefined by the SBML Level&nbsp;3 Version&nbsp;1
042 * specification</em>.  A software implementation may choose to execute
043 * such simultaneous events in any order, as long as each event is executed
044 * only once and the requirements of checking the 'persistent' attribute
045 * (and acting accordingly) are satisfied.
046 <p>
047 * If {@link Priority} subobjects are defined for two or more
048 * simultaneously-triggered events, the order in which those particular
049 * events must be executed is dictated by their {@link Priority} objects,
050 * as follows.  If the values calculated using the two {@link Priority}
051 * objects' 'math' expressions differ, then the event having
052 * the higher priority value must be executed before the event with
053 * the lower value.  If, instead, the two priority values are
054 * mathematically equal, then the two events must be triggered in a
055 * <em>random</em> order.  It is important to note that a <em>random
056 *   order is not the same as an undefined order</em>: given multiple
057 * runs of the same model with identical conditions, an undefined
058 * ordering would permit a system to execute the events in (for
059 * example) the same order every time (according to whatever scheme
060 * may have been implemented by the system), whereas the explicit
061 * requirement for random ordering means that the order of execution
062 * in different simulation runs depends on random chance.  In other
063 * words, given two events <em>A</em> and <em>B</em>, a randomly-determined
064 * order must lead to an equal chance of executing <em>A</em> first or
065 * <em>B</em> first, every time those two events are executed
066 * simultaneously.
067 <p>
068 * A model may contain a mixture of events, some of which have
069 * {@link Priority} subobjects and some do not.  Should a combination of
070 * simultaneous events arise in which some events have priorities
071 * defined and others do not, the set of events with defined
072 * priorities must trigger in the order determined by their {@link Priority}
073 * objects, and the set of events without {@link Priority} objects must be
074 * executed in an <em>undefined</em> order with respect to each other
075 * and with respect to the events with {@link Priority} subobjects.  (Note
076 * that <em>undefined order</em> does not necessarily mean random
077 * order, although a random ordering would be a valid implementation
078 * of this requirement.)
079 <p>
080 * The following example may help further clarify these points.
081 * Suppose a model contains four events that should be executed
082 * simultaneously, with two of the events having {@link Priority} objects
083 * with the same value and the other two events having {@link Priority}
084 * objects with the same, but different, value.  The two events with
085 * the higher priorities must be executed first, in a random order
086 * with respect to each other, and the remaining two events must be
087 * executed after them, again in a random order, for a total of four
088 * possible and equally-likely event executions: A-B-C-D, A-B-D-C,
089 * B-A-C-D, and B-A-D-C.  If, instead, the model contains four events
090 * all having the same {@link Priority} values, there are 4! or 24
091 * possible orderings, each of which must be equally likely to be
092 * chosen.  Finally, if none of the four events has a {@link Priority}
093 * subobject defined, or even if exactly one of the four events has a
094 * defined {@link Priority}, there are again 24 possible orderings, but the
095 * likelihood of choosing any particular ordering is undefined; the
096 * simulator can choose between events as it wishes.  (The SBML
097 * specification only defines the effects of priorities on {@link Event}
098 * objects with respect to <em>other</em> {@link Event} objects with
099 * priorities.  Putting a priority on a <em>single</em> {@link Event} object
100 * in a model does not cause it to fall within that scope.)
101 <p>
102 * <h2>Evaluation of {@link Priority} expressions</h2>
103 <p>
104 * An event's {@link Priority} object 'math' expression must be
105 * evaluated at the time the {@link Event} is to be <em>executed</em>.  During
106 * a simulation, all simultaneous events have their {@link Priority} values
107 * calculated, and the event with the highest priority is selected for
108 * next execution.  Note that it is possible for the execution of one
109 * {@link Event} object to cause the {@link Priority} value of another
110 * simultaneously-executing {@link Event} object to change (as well as to
111 * trigger other events, as already noted).  Thus, after executing
112 * one event, and checking whether any other events in the model have
113 * been triggered, all remaining simultaneous events that
114 * <em>either</em> (i) have {@link Trigger} objects with attributes
115 * 'persistent'=<code>false</code> <em>or</em> (ii) have {@link Trigger}
116 * expressions that did not transition from <code>true</code> to
117 * <code>false</code>, must have their {@link Priority} expression reevaluated.
118 * The highest-priority remaining event must then be selected for 
119 * execution next.
120 <p>
121 * <h2>Units of {@link Priority} object's mathematical expressions</h2>
122 <p>
123 * The unit associated with the value of a {@link Priority} object's
124 * 'math' expression should be <code>dimensionless.</code>  This is
125 * because the priority expression only serves to provide a relative
126 * ordering between different events, and only has meaning with
127 * respect to other {@link Priority} object expressions.  The value of
128 * {@link Priority} objects is not comparable to any other kind of object in
129 * an SBML model.
130 <p>
131 * @note The {@link Priority} construct exists only in SBML Level&nbsp;3; it cannot
132 * be used in SBML Level&nbsp;2 or Level&nbsp;1 models.
133 <p>
134 * @see Event
135 * @see Delay
136 * @see EventAssignment
137 */
138
139public class Priority extends SBase {
140   private long swigCPtr;
141
142   protected Priority(long cPtr, boolean cMemoryOwn)
143   {
144     super(libsbmlJNI.Priority_SWIGUpcast(cPtr), cMemoryOwn);
145     swigCPtr = cPtr;
146   }
147
148   protected static long getCPtr(Priority obj)
149   {
150     return (obj == null) ? 0 : obj.swigCPtr;
151   }
152
153   protected static long getCPtrAndDisown (Priority obj)
154   {
155     long ptr = 0;
156
157     if (obj != null)
158     {
159       ptr             = obj.swigCPtr;
160       obj.swigCMemOwn = false;
161     }
162
163     return ptr;
164   }
165
166  protected void finalize() {
167    delete();
168  }
169
170  public synchronized void delete() {
171    if (swigCPtr != 0) {
172      if (swigCMemOwn) {
173        swigCMemOwn = false;
174        libsbmlJNI.delete_Priority(swigCPtr);
175      }
176      swigCPtr = 0;
177    }
178    super.delete();
179  }
180
181  
182/**
183   * Creates a new {@link Priority} object using the given SBML <code>level</code> and 
184   * <code>version</code> values.
185   <p>
186   * @param level a long integer, the SBML Level to assign to this {@link Priority}
187   <p>
188   * @param version a long integer, the SBML Version to assign to this
189   * {@link Priority}
190   <p>
191   * @throws SBMLConstructorException 
192   * Thrown if the given <code>level</code> and <code>version</code> combination, or this kind
193   * of SBML object, are either invalid or mismatched with respect to the
194   * parent {@link SBMLDocument} object.
195   <p>
196   * <p>
197 * @note Upon the addition of a {@link Priority} object to an {@link Event} (e.g., using
198 * {@link Event#setPriority(Priority d)}), the SBML Level, SBML Version
199 * and XML namespace of the document <em>override</em> the values used when
200 * creating the {@link Priority} object via this constructor.  This is necessary to
201 * ensure that an SBML document is a consistent structure.  Nevertheless,
202 * the ability to supply the values at the time of creation of a {@link Priority} is
203 * an important aid to producing valid SBML.  Knowledge of the intented
204 * SBML Level and Version determine whether it is valid to assign a
205 * particular value to an attribute, or whether it is valid to add a
206 * particular {@link Priority} object to an existing {@link Event}.<br><br>
207   <p>
208   * <p>
209 * @note The {@link Priority} construct exists only in SBML Level&nbsp;3; it
210 * cannot be used in SBML Level&nbsp;2 or Level&nbsp;1 models.
211   */ public
212 Priority(long level, long version) throws org.sbml.libsbml.SBMLConstructorException {
213    this(libsbmlJNI.new_Priority__SWIG_0(level, version), true);
214  }
215
216  
217/**
218   * Creates a new {@link Priority} object using the given {@link SBMLNamespaces} object
219   * <code>sbmlns</code>.
220   <p>
221   * <p>
222 * The {@link SBMLNamespaces} object encapsulates SBML Level/Version/namespaces
223 * information.  It is used to communicate the SBML Level, Version, and (in
224 * Level&nbsp;3) packages used in addition to SBML Level&nbsp;3 Core.  A
225 * common approach to using libSBML's {@link SBMLNamespaces} facilities is to create an
226 * {@link SBMLNamespaces} object somewhere in a program once, then hand that object
227 * as needed to object constructors that accept {@link SBMLNamespaces} as arguments. 
228   <p>
229   * @param sbmlns an {@link SBMLNamespaces} object.
230   <p>
231   * @throws SBMLConstructorException  
232   * Thrown if the given <code>level</code> and <code>version</code> combination, or this kind
233   * of SBML object, are either invalid or mismatched with respect to the
234   * parent {@link SBMLDocument} object.
235   <p>
236   * <p>
237 * @note Upon the addition of a {@link Priority} object to an {@link Event} (e.g., using
238 * {@link Event#setPriority(Priority d)}), the SBML Level, SBML Version
239 * and XML namespace of the document <em>override</em> the values used when
240 * creating the {@link Priority} object via this constructor.  This is necessary to
241 * ensure that an SBML document is a consistent structure.  Nevertheless,
242 * the ability to supply the values at the time of creation of a {@link Priority} is
243 * an important aid to producing valid SBML.  Knowledge of the intented
244 * SBML Level and Version determine whether it is valid to assign a
245 * particular value to an attribute, or whether it is valid to add a
246 * particular {@link Priority} object to an existing {@link Event}.<br><br>
247   <p>
248   * <p>
249 * @note The {@link Priority} construct exists only in SBML Level&nbsp;3; it
250 * cannot be used in SBML Level&nbsp;2 or Level&nbsp;1 models.
251   */ public
252 Priority(SBMLNamespaces sbmlns) throws org.sbml.libsbml.SBMLConstructorException {
253    this(libsbmlJNI.new_Priority__SWIG_1(SBMLNamespaces.getCPtr(sbmlns), sbmlns), true);
254  }
255
256  
257/**
258   * Copy constructor; creates a copy of this {@link Priority}.
259   <p>
260   * @param orig the object to copy.
261   <p>
262   * @throws SBMLConstructorException 
263   * Thrown if the argument <code>orig</code> is <code>null.</code>
264   */ public
265 Priority(Priority orig) throws org.sbml.libsbml.SBMLConstructorException {
266    this(libsbmlJNI.new_Priority__SWIG_2(Priority.getCPtr(orig), orig), true);
267  }
268
269  
270/**
271   * Creates and returns a deep copy of this {@link Priority}.
272   <p>
273   * @return a (deep) copy of this {@link Priority}.
274   */ public
275 Priority cloneObject() {
276    long cPtr = libsbmlJNI.Priority_cloneObject(swigCPtr, this);
277    return (cPtr == 0) ? null : new Priority(cPtr, true);
278  }
279
280  
281/**
282   * Get the mathematical formula for the priority and return it
283   * as an AST.
284   <p>
285   * @return the math of this {@link Priority}.
286   */ public
287 ASTNode getMath() {
288    long cPtr = libsbmlJNI.Priority_getMath(swigCPtr, this);
289    return (cPtr == 0) ? null : new ASTNode(cPtr, false);
290  }
291
292  
293/**
294   * Predicate to test whether the formula for this delay is set.
295   <p>
296   * @return <code>true</code> if the formula (meaning the <code>math</code> subelement) of
297   * this {@link Priority} is set, <code>false</code> otherwise.
298   */ public
299 boolean isSetMath() {
300    return libsbmlJNI.Priority_isSetMath(swigCPtr, this);
301  }
302
303  
304/**
305   * Sets the math expression of this {@link Priority} instance to a copy of the given
306   * {@link ASTNode}.
307   <p>
308   * @param math an {@link ASTNode} representing a formula tree.
309   <p>
310   * @return integer value indicating success/failure of the
311   * function.   The possible values
312   * returned by this function are:
313   * <ul>
314   * <li> {@link  libsbmlConstants#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS }
315   * <li> {@link  libsbmlConstants#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT }
316   * </ul>
317   */ public
318 int setMath(ASTNode math) {
319    return libsbmlJNI.Priority_setMath(swigCPtr, this, ASTNode.getCPtr(math), math);
320  }
321
322  
323/**
324   * Returns the libSBML type code of this object instance.
325   <p>
326   * <p>
327 * LibSBML attaches an identifying code to every kind of SBML object.  These
328 * are integer constants known as <em>SBML type codes</em>.  The names of all
329 * the codes begin with the characters &ldquo;<code>SBML_</code>&rdquo;. 
330 * In the Java language interface for libSBML, the
331 * type codes are defined as static integer constants in the interface class
332 * {@link libsbmlConstants}.    Note that different Level&nbsp;3 
333 * package plug-ins may use overlapping type codes; to identify the package
334 * to which a given object belongs, call the <code>getPackageName()</code>
335 * method on the object.
336   <p>
337   * @return the SBML type code for this object:
338   * {@link  libsbmlConstants#SBML_PRIORITY SBML_PRIORITY} (default).   <p>
339   * <p>
340 * @warning <span class='warning'>The specific integer values of the possible
341 * type codes may be reused by different Level&nbsp;3 package plug-ins.
342 * Thus, to identifiy the correct code, <strong>it is necessary to invoke
343 * both getTypeCode() and getPackageName()</strong>.</span>
344   <p>
345   * @see #getElementName()
346   * @see #getPackageName()
347   */ public
348 int getTypeCode() {
349    return libsbmlJNI.Priority_getTypeCode(swigCPtr, this);
350  }
351
352  
353/**
354   * Returns the XML element name of this object, which for {@link Priority}, is
355   * always <code>'priority'.</code>
356   <p>
357   * @return the name of this element, i.e., <code>'priority'.</code>
358   <p>
359   * @see #getTypeCode()
360   */ public
361 String getElementName() {
362    return libsbmlJNI.Priority_getElementName(swigCPtr, this);
363  }
364
365  
366/**
367   * Predicate returning <code>true</code> if all the required elements for this
368   * {@link Priority} object have been set.
369   <p>
370   * @note The required elements for a {@link Priority} object are:
371   * <ul>
372   * <li> 'math'
373   *
374   * </ul> <p>
375   * @return a boolean value indicating whether all the required
376   * elements for this object have been defined.
377   */ public
378 boolean hasRequiredElements() {
379    return libsbmlJNI.Priority_hasRequiredElements(swigCPtr, this);
380  }
381
382  
383/**
384   * Finds this {@link Priority}'s {@link Event} parent and calls unsetPriority() on it,
385   * indirectly deleting itself.
386   <p>
387   * Overridden from the {@link SBase} function since the parent is not a {@link ListOf}.
388   <p>
389   * @return integer value indicating success/failure of the
390   * function.   The possible values
391   * returned by this function are:
392   * <ul>
393   * <li> {@link  libsbmlConstants#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS }
394   * <li> {@link  libsbmlConstants#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED }
395   * </ul>
396   */ public
397 int removeFromParentAndDelete() {
398    return libsbmlJNI.Priority_removeFromParentAndDelete(swigCPtr, this);
399  }
400
401  
402/**
403   * Renames all the <code>SIdRef</code> attributes on this element, including any
404   * found in MathML.
405   <p>
406   * <p>
407 * In SBML, object identifiers are of a data type called <code>SId</code>.
408 * In SBML Level&nbsp;3, an explicit data type called <code>SIdRef</code> was
409 * introduced for attribute values that refer to <code>SId</code> values; in
410 * previous Levels of SBML, this data type did not exist and attributes were
411 * simply described to as 'referring to an identifier', but the effective
412 * data type was the same as <code>SIdRef</code>in Level&nbsp;3.  These and
413 * other methods of libSBML refer to the type <code>SIdRef</code> for all
414 * Levels of SBML, even if the corresponding SBML specification did not
415 * explicitly name the data type.
416   <p>
417   * This method works by looking at all attributes and (if appropriate)
418   * mathematical formulas, comparing the identifiers to the value of 
419   * <code>oldid</code>.  If any matches are found, the matching identifiers are replaced
420   * with <code>newid</code>.  The method does <em>not</em> descend into child elements.
421   <p>
422   * @param oldid the old identifier
423   * @param newid the new identifier
424   */ public
425 void renameSIdRefs(String oldid, String newid) {
426    libsbmlJNI.Priority_renameSIdRefs(swigCPtr, this, oldid, newid);
427  }
428
429  
430/**
431   * Renames all the <code>UnitSIdRef</code> attributes on this element.
432   <p>
433   * <p>
434 * In SBML, unit definitions have identifiers of type <code>UnitSId</code>.  In
435 * SBML Level&nbsp;3, an explicit data type called <code>UnitSIdRef</code> was
436 * introduced for attribute values that refer to <code>UnitSId</code> values; in
437 * previous Levels of SBML, this data type did not exist and attributes were
438 * simply described to as 'referring to a unit identifier', but the effective
439 * data type was the same as <code>UnitSIdRef</code> in Level&nbsp;3.  These and
440 * other methods of libSBML refer to the type <code>UnitSIdRef</code> for all
441 * Levels of SBML, even if the corresponding SBML specification did not
442 * explicitly name the data type.
443   <p>
444   * This method works by looking at all unit identifier attribute values
445   * (including, if appropriate, inside mathematical formulas), comparing the
446   * unit identifiers to the value of <code>oldid</code>.  If any matches are found,
447   * the matching identifiers are replaced with <code>newid</code>.  The method does
448   * <em>not</em> descend into child elements.
449   <p>
450   * @param oldid the old identifier
451   * @param newid the new identifier
452   */ public
453 void renameUnitSIdRefs(String oldid, String newid) {
454    libsbmlJNI.Priority_renameUnitSIdRefs(swigCPtr, this, oldid, newid);
455  }
456
457  
458/**
459   * Replace all nodes with the name 'id' from the child 'math' object with the provided function. 
460   <p>
461   * @internal
462   */ public
463 void replaceSIDWithFunction(String id, ASTNode function) {
464    libsbmlJNI.Priority_replaceSIDWithFunction(swigCPtr, this, id, ASTNode.getCPtr(function), function);
465  }
466
467}