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>constraint</em>, for stating validity assumptions.
013 <p>
014 * The {@link Constraint} object class was introduced in SBML Level&nbsp;2
015 * Version&nbsp;2 as a mechanism for stating the assumptions under which a
016 * model is designed to operate.  The <em>constraints</em> are statements
017 * about permissible values of different quantities in a model.
018 * Constraints are not used to compute dynamical values for simulation or
019 * analysis, but rather, they serve an advisory role for
020 * simulation/analysis tools.
021 <p>
022 * SBML's {@link Constraint} object class has one required attribute, 'id', to
023 * give the parameter a unique identifier by which other parts of an SBML
024 * model definition can refer to it.  A {@link Constraint} object can also have an
025 * optional 'name' attribute of type <code>string.</code>  Identifiers and names must
026 * be used according to the guidelines described in the SBML specification
027 * (e.g., Section 3.3 in the Level&nbsp;2 Version 4 specification).  
028 <p>
029 * {@link Constraint} has one subelement, 'math', containing a MathML
030 * formula defining the condition of the constraint.  This formula will
031 * return a Boolean value of <code>true</code> when the model is a <em>valid</em>
032 * state.  The formula can be an arbitrary expression referencing the
033 * variables and other entities in an SBML model.  The evaluation of 'math'
034 * and behavior of constraints are described in more detail below.
035 <p>
036 * In SBML Level&nbsp;2 and SBML Level&nbsp;3 Version&nbsp;1, the 'math'
037 * subelement is required, and its formula must be a Boolean value.  In
038 * SBML Level&nbsp;3 Version&nbsp;2, these restrictions were relaxed:
039 * the 'math' subelement is optional, and numeric values are allowed
040 * in Boolean contexts (a '0' is interpreted as <code>false</code>, and all other
041 * values are interpreted as <code>true</code>).  If a {@link Constraint} with no 'math'
042 * is present in a {@link Model}, no restriction on the {@link Model}'s behavior is
043 * implied or enforced.
044 <p>
045 * A {@link Constraint} structure also has an optional subelement called 'message'.
046 * This can contain a message in XHTML format that may be displayed to the
047 * user when the condition of the formula in the 'math' subelement
048 * evaluates to a value of <code>false.</code>  Software tools are not required to
049 * display the message, but it is recommended that they do so as a matter
050 * of best practice.  The XHTML content within a 'message' subelement must
051 * follow the same restrictions as for the 'notes' element on {@link SBase}
052 * described in in the SBML Level&nbsp;2 specification; please consult the
053 * <a target='_blank' href='http://sbml.org/Documents/Specifications'>SBML
054 * specification document</a> corresponding to the SBML Level and Version
055 * of your model for more information about the requirements for 'notes'
056 * content.
057 <p>
058 * {@link Constraint} was introduced in SBML Level&nbsp;2 Version&nbsp;2.  It is
059 * not available in earlier versions of Level&nbsp;2 nor in any version of
060 * Level&nbsp;1.
061 <p>
062 * <h2>Semantics of Constraints</h2>
063 <p>
064 * In the context of a simulation, a {@link Constraint} has effect at all times
065 * <em>t &#8805; 0</em>.  Each {@link Constraint}'s 'math' subelement is first
066 * evaluated after any {@link InitialAssignment} definitions in a model at <em>t =
067 * 0</em> and can conceivably trigger at that point.  (In other words, a
068 * simulation could fail a constraint immediately.)
069 <p>
070 * {@link Constraint} structures <em>cannot and should not</em> be used to compute
071 * the dynamical behavior of a model as part of, for example, simulation.
072 * Constraints may be used as input to non-dynamical analysis, for instance
073 * by expressing flux constraints for flux balance analysis.
074 <p>
075 * The results of a simulation of a model containing a constraint are
076 * invalid from any simulation time at and after a point when the function
077 * given by the 'math' subelement returns a value of <code>false.</code>  Invalid
078 * simulation results do not make a prediction of the behavior of the
079 * biochemical reaction network represented by the model.  The precise
080 * behavior of simulation tools is left undefined with respect to
081 * constraints.  If invalid results are detected with respect to a given
082 * constraint, the 'message' subelement may optionally be displayed to the
083 * user.  The simulation tool may also halt the simulation or clearly
084 * delimit in output data the simulation time point at which the simulation
085 * results become invalid.
086 <p>
087 * SBML does not impose restrictions on duplicate {@link Constraint} definitions or
088 * the order of evaluation of {@link Constraint} objects in a model.  It is
089 * possible for a model to define multiple constraints all with the same
090 * mathematical expression.  Since the failure of any constraint indicates
091 * that the model simulation has entered an invalid state, a system is not
092 * required to attempt to detect whether other constraints in the model
093 * have failed once any one constraint has failed.
094 */
095
096public class Constraint extends SBase {
097   private long swigCPtr;
098
099   protected Constraint(long cPtr, boolean cMemoryOwn)
100   {
101     super(libsbmlJNI.Constraint_SWIGUpcast(cPtr), cMemoryOwn);
102     swigCPtr = cPtr;
103   }
104
105   protected static long getCPtr(Constraint obj)
106   {
107     return (obj == null) ? 0 : obj.swigCPtr;
108   }
109
110   protected static long getCPtrAndDisown (Constraint obj)
111   {
112     long ptr = 0;
113
114     if (obj != null)
115     {
116       ptr             = obj.swigCPtr;
117       obj.swigCMemOwn = false;
118     }
119
120     return ptr;
121   }
122
123  protected void finalize() {
124    delete();
125  }
126
127  public synchronized void delete() {
128    if (swigCPtr != 0) {
129      if (swigCMemOwn) {
130        swigCMemOwn = false;
131        libsbmlJNI.delete_Constraint(swigCPtr);
132      }
133      swigCPtr = 0;
134    }
135    super.delete();
136  }
137
138  
139/**
140   * Creates a new {@link Constraint} using the given SBML <code>level</code> and <code>version</code>
141   * values.
142   <p>
143   * @param level a long integer, the SBML Level to assign to this {@link Constraint}.
144   <p>
145   * @param version a long integer, the SBML Version to assign to this
146   * {@link Constraint}.
147   <p>
148   * <p>
149 * @throws SBMLConstructorException
150 * Thrown if the given <code>level</code> and <code>version</code> combination are invalid
151 * or if this object is incompatible with the given level and version.
152   <p>
153   * <p>
154 * @note Attempting to add an object to an {@link SBMLDocument} having a different
155 * combination of SBML Level, Version and XML namespaces than the object
156 * itself will result in an error at the time a caller attempts to make the
157 * addition.  A parent object must have compatible Level, Version and XML
158 * namespaces.  (Strictly speaking, a parent may also have more XML
159 * namespaces than a child, but the reverse is not permitted.)  The
160 * restriction is necessary to ensure that an SBML model has a consistent
161 * overall structure.  This requires callers to manage their objects
162 * carefully, but the benefit is increased flexibility in how models can be
163 * created by permitting callers to create objects bottom-up if desired.  In
164 * situations where objects are not yet attached to parents (e.g.,
165 * {@link SBMLDocument}), knowledge of the intented SBML Level and Version help
166 * libSBML determine such things as whether it is valid to assign a
167 * particular value to an attribute.
168   */ public
169 Constraint(long level, long version) throws org.sbml.libsbml.SBMLConstructorException {
170    this(libsbmlJNI.new_Constraint__SWIG_0(level, version), true);
171  }
172
173  
174/**
175   * Creates a new {@link Constraint} using the given {@link SBMLNamespaces} object
176   * <code>sbmlns</code>.
177   <p>
178   * <p>
179 * The {@link SBMLNamespaces} object encapsulates SBML Level/Version/namespaces
180 * information.  It is used to communicate the SBML Level, Version, and (in
181 * Level&nbsp;3) packages used in addition to SBML Level&nbsp;3 Core.  A
182 * common approach to using libSBML's {@link SBMLNamespaces} facilities is to create an
183 * {@link SBMLNamespaces} object somewhere in a program once, then hand that object
184 * as needed to object constructors that accept {@link SBMLNamespaces} as arguments.
185   <p>
186   * @param sbmlns an {@link SBMLNamespaces} object.
187   <p>
188   * <p>
189 * @throws SBMLConstructorException
190 * Thrown if the given <code>sbmlns</code> is inconsistent or incompatible
191 * with this object.
192   <p>
193   * <p>
194 * @note Attempting to add an object to an {@link SBMLDocument} having a different
195 * combination of SBML Level, Version and XML namespaces than the object
196 * itself will result in an error at the time a caller attempts to make the
197 * addition.  A parent object must have compatible Level, Version and XML
198 * namespaces.  (Strictly speaking, a parent may also have more XML
199 * namespaces than a child, but the reverse is not permitted.)  The
200 * restriction is necessary to ensure that an SBML model has a consistent
201 * overall structure.  This requires callers to manage their objects
202 * carefully, but the benefit is increased flexibility in how models can be
203 * created by permitting callers to create objects bottom-up if desired.  In
204 * situations where objects are not yet attached to parents (e.g.,
205 * {@link SBMLDocument}), knowledge of the intented SBML Level and Version help
206 * libSBML determine such things as whether it is valid to assign a
207 * particular value to an attribute.
208   */ public
209 Constraint(SBMLNamespaces sbmlns) throws org.sbml.libsbml.SBMLConstructorException {
210    this(libsbmlJNI.new_Constraint__SWIG_1(SBMLNamespaces.getCPtr(sbmlns), sbmlns), true);
211  }
212
213  
214/**
215   * Copy constructor; creates a copy of this {@link Constraint}.
216   <p>
217   * @param orig the object to copy.
218   */ public
219 Constraint(Constraint orig) throws org.sbml.libsbml.SBMLConstructorException {
220    this(libsbmlJNI.new_Constraint__SWIG_2(Constraint.getCPtr(orig), orig), true);
221  }
222
223  
224/**
225   * Creates and returns a deep copy of this {@link Constraint} object.
226   <p>
227   * @return the (deep) copy of this {@link Constraint} object.
228   */ public
229 Constraint cloneObject() {
230    long cPtr = libsbmlJNI.Constraint_cloneObject(swigCPtr, this);
231    return (cPtr == 0) ? null : new Constraint(cPtr, true);
232  }
233
234  
235/**
236   * Get the message, if any, associated with this {@link Constraint}
237   <p>
238   * @return the message for this {@link Constraint}, as an {@link XMLNode}.
239   */ public
240 XMLNode getMessage() {
241    long cPtr = libsbmlJNI.Constraint_getMessage(swigCPtr, this);
242    return (cPtr == 0) ? null : new XMLNode(cPtr, false);
243  }
244
245  
246/**
247   * Get the message string, if any, associated with this {@link Constraint}
248   <p>
249   * @return the message for this {@link Constraint}, as a string.
250   */ public
251 String getMessageString() {
252    return libsbmlJNI.Constraint_getMessageString(swigCPtr, this);
253  }
254
255  
256/**
257   * Get the mathematical expression of this {@link Constraint}
258   <p>
259   * @return the math for this {@link Constraint}, as an {@link ASTNode}, or <code>null</code> if the math is not set.
260   */ public
261 ASTNode getMath() {
262    long cPtr = libsbmlJNI.Constraint_getMath(swigCPtr, this);
263    return (cPtr == 0) ? null : new ASTNode(cPtr, false);
264  }
265
266  
267/**
268   * Predicate returning <code>true</code> if a
269   * message is defined for this {@link Constraint}.
270   <p>
271   * @return <code>true</code> if the message of this {@link Constraint} is set,
272   * <code>false</code> otherwise.
273   */ public
274 boolean isSetMessage() {
275    return libsbmlJNI.Constraint_isSetMessage(swigCPtr, this);
276  }
277
278  
279/**
280   * Predicate returning <code>true</code> if a
281   * mathematical formula is defined for this {@link Constraint}.
282   <p>
283   * @return <code>true</code> if the 'math' subelement for this {@link Constraint} is
284   * set, <code>false</code> otherwise.
285   */ public
286 boolean isSetMath() {
287    return libsbmlJNI.Constraint_isSetMath(swigCPtr, this);
288  }
289
290  
291/**
292   * Sets the message of this {@link Constraint}.
293   <p>
294   * The {@link XMLNode} tree passed in <code>xhtml</code> is copied.
295   <p>
296   * @param xhtml an XML tree containing XHTML content.
297   <p>
298   * <p>
299 * @return integer value indicating success/failure of the
300 * function.   The possible values
301 * returned by this function are:
302   * <ul>
303   * <li> {@link libsbmlConstants#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS}
304   * <li> {@link libsbmlConstants#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT}
305   * </ul>
306   */ public
307 int setMessage(XMLNode xhtml) {
308    return libsbmlJNI.Constraint_setMessage__SWIG_0(swigCPtr, this, XMLNode.getCPtr(xhtml), xhtml);
309  }
310
311  
312/**
313   * Sets the message of this {@link Constraint}.
314   <p>
315   * @param message an XML string that is to be used as the content of the
316   * 'message' subelement of this object.
317   <p>
318   * @param addXHTMLMarkup a boolean indicating whether to wrap the contents
319   * of the <code>message</code> argument with XHTML paragraph (<code>&lt;p&gt;</code>)
320   * tags.  This is appropriate when the string in <code>message</code> does not already
321   * containg the appropriate XHTML markup.
322   <p>
323   * <p>
324 * @return integer value indicating success/failure of the
325 * function.   The possible values
326 * returned by this function are:
327   * <ul>
328   * <li> {@link libsbmlConstants#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS}
329   * <li> {@link libsbmlConstants#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT}
330   * </ul>
331   */ public
332 int setMessage(String message, boolean addXHTMLMarkup) {
333    return libsbmlJNI.Constraint_setMessage__SWIG_1(swigCPtr, this, message, addXHTMLMarkup);
334  }
335
336  
337/**
338   * Sets the message of this {@link Constraint}.
339   <p>
340   * @param message an XML string that is to be used as the content of the
341   * 'message' subelement of this object.
342   <p>
343   * @param addXHTMLMarkup a boolean indicating whether to wrap the contents
344   * of the <code>message</code> argument with XHTML paragraph (<code>&lt;p&gt;</code>)
345   * tags.  This is appropriate when the string in <code>message</code> does not already
346   * containg the appropriate XHTML markup.
347   <p>
348   * <p>
349 * @return integer value indicating success/failure of the
350 * function.   The possible values
351 * returned by this function are:
352   * <ul>
353   * <li> {@link libsbmlConstants#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS}
354   * <li> {@link libsbmlConstants#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT}
355   * </ul>
356   */ public
357 int setMessage(String message) {
358    return libsbmlJNI.Constraint_setMessage__SWIG_2(swigCPtr, this, message);
359  }
360
361  
362/**
363   * Sets the mathematical expression of this {@link Constraint} to a copy of the
364   * AST given as <code>math</code>.
365   <p>
366   * @param math an {@link ASTNode} expression to be assigned as the 'math'
367   * subelement of this {@link Constraint}.
368   <p>
369   * <p>
370 * @return integer value indicating success/failure of the
371 * function.   The possible values
372 * returned by this function are:
373   * <ul>
374   * <li> {@link libsbmlConstants#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS}
375   * <li> {@link libsbmlConstants#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT}
376   * </ul>
377   */ public
378 int setMath(ASTNode math) {
379    return libsbmlJNI.Constraint_setMath(swigCPtr, this, ASTNode.getCPtr(math), math);
380  }
381
382  
383/**
384   * Unsets the 'message' subelement of this {@link Constraint}.
385   <p>
386   * <p>
387 * @return integer value indicating success/failure of the
388 * function.   The possible values
389 * returned by this function are:
390   * <ul>
391   * <li> {@link libsbmlConstants#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS}
392   * <li> {@link libsbmlConstants#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED}
393   * </ul>
394   */ public
395 int unsetMessage() {
396    return libsbmlJNI.Constraint_unsetMessage(swigCPtr, this);
397  }
398
399  
400/**
401   * <p>
402 * Replaces all uses of a given <code>SIdRef</code> type attribute value with another
403 * value.
404 <p>
405 * <p>
406 * In SBML, object identifiers are of a data type called <code>SId</code>.
407 * In SBML Level&nbsp;3, an explicit data type called <code>SIdRef</code> was
408 * introduced for attribute values that refer to <code>SId</code> values; in
409 * previous Levels of SBML, this data type did not exist and attributes were
410 * simply described to as 'referring to an identifier', but the effective
411 * data type was the same as <code>SIdRef</code> in Level&nbsp;3.  These and
412 * other methods of libSBML refer to the type <code>SIdRef</code> for all
413 * Levels of SBML, even if the corresponding SBML specification did not
414 * explicitly name the data type.
415 <p>
416 * This method works by looking at all attributes and (if appropriate)
417 * mathematical formulas in MathML content, comparing the referenced
418 * identifiers to the value of <code>oldid</code>.  If any matches are found, the
419 * matching values are replaced with <code>newid</code>.  The method does <em>not</em>
420 * 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.Constraint_renameSIdRefs(swigCPtr, this, oldid, newid);
427  }
428
429  
430/**
431   * <p>
432 * Replaces all uses of a given <code>UnitSIdRef</code> type attribute value with
433 * another value.
434 <p>
435 * <p>
436 * In SBML, unit definitions have identifiers of type <code>UnitSId</code>.  In
437 * SBML Level&nbsp;3, an explicit data type called <code>UnitSIdRef</code> was
438 * introduced for attribute values that refer to <code>UnitSId</code> values; in
439 * previous Levels of SBML, this data type did not exist and attributes were
440 * simply described to as 'referring to a unit identifier', but the effective
441 * data type was the same as <code>UnitSIdRef</code> in Level&nbsp;3.  These and
442 * other methods of libSBML refer to the type <code>UnitSIdRef</code> for all
443 * Levels of SBML, even if the corresponding SBML specification did not
444 * explicitly name the data type.
445 <p>
446 * This method works by looking at all unit identifier attribute values
447 * (including, if appropriate, inside mathematical formulas), comparing the
448 * referenced unit identifiers to the value of <code>oldid</code>.  If any matches
449 * are found, the matching values are replaced with <code>newid</code>.  The method
450 * does <em>not</em> descend into child elements.
451 <p>
452 * @param oldid the old identifier.
453 * @param newid the new identifier.
454   */ public
455 void renameUnitSIdRefs(String oldid, String newid) {
456    libsbmlJNI.Constraint_renameUnitSIdRefs(swigCPtr, this, oldid, newid);
457  }
458
459  
460/** * @internal */ public
461 void replaceSIDWithFunction(String id, ASTNode function) {
462    libsbmlJNI.Constraint_replaceSIDWithFunction(swigCPtr, this, id, ASTNode.getCPtr(function), function);
463  }
464
465  
466/**
467   * Returns the libSBML type code for this SBML object.
468   <p>
469   * <p>
470 * LibSBML attaches an identifying code to every kind of SBML object.  These
471 * are integer constants known as <em>SBML type codes</em>.  The names of all
472 * the codes begin with the characters <code>SBML_</code>.
473 * In the Java language interface for libSBML, the
474 * type codes are defined as static integer constants in the interface class
475 * {@link libsbmlConstants}.    Note that different Level&nbsp;3
476 * package plug-ins may use overlapping type codes; to identify the package
477 * to which a given object belongs, call the <code>getPackageName()</code>
478 * method on the object.
479   <p>
480   * @return the SBML type code for this object:
481   * {@link libsbmlConstants#SBML_CONSTRAINT SBML_CONSTRAINT} (default).
482   <p>
483   * <p>
484 * @warning <span class='warning'>The specific integer values of the possible
485 * type codes may be reused by different libSBML plug-ins for SBML Level&nbsp;3.
486 * packages,  To fully identify the correct code, <strong>it is necessary to
487 * invoke both getTypeCode() and getPackageName()</strong>.</span>
488   <p>
489   * @see #getElementName()
490   * @see #getPackageName()
491   */ public
492 int getTypeCode() {
493    return libsbmlJNI.Constraint_getTypeCode(swigCPtr, this);
494  }
495
496  
497/**
498   * Returns the XML element name of this object, which for {@link Constraint}, is
499   * always <code>'constraint'.</code>
500   <p>
501   * @return the name of this element, i.e., <code>'constraint'.</code>
502   */ public
503 String getElementName() {
504    return libsbmlJNI.Constraint_getElementName(swigCPtr, this);
505  }
506
507  
508/**
509   * Predicate returning <code>true</code> if
510   * all the required elements for this {@link Constraint} object
511   * have been set.
512   <p>
513   * @note The required elements for a {@link Constraint} object are:
514   * <ul>
515   * <li> 'math' (through SBML Level&nbsp;3 Version&nbsp;1 only; not 
516   *     required in Level&nbsp;3 Version&nbsp;2+.)
517   *
518   * </ul> <p>
519   * @return a boolean value indicating whether all the required
520   * elements for this object have been defined.
521   */ public
522 boolean hasRequiredElements() {
523    return libsbmlJNI.Constraint_hasRequiredElements(swigCPtr, this);
524  }
525
526}