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's Constraint construct. 014 * <p> 015 * The {@link Constraint} object class was introduced in SBML Level 2 016 * Version 2 as a mechanism for stating the assumptions under which a 017 * model is designed to operate. The <em>constraints</em> are statements 018 * about permissible values of different quantities in a model. 019 * Constraints are not used to compute dynamical values for simulation or 020 * analysis, but rather, they serve an advisory role for 021 * simulation/analysis tools. 022 * <p> 023 * SBML's {@link Constraint} object class has one required attribute, 'id', to 024 * give the parameter a unique identifier by which other parts of an SBML 025 * model definition can refer to it. A {@link Constraint} object can also have an 026 * optional 'name' attribute of type <code>string.</code> Identifiers and names must 027 * be used according to the guidelines described in the SBML specification 028 * (e.g., Section 3.3 in the Level 2 Version 4 specification). 029 * <p> 030 * {@link Constraint} has one required subelement, 'math', containing a MathML 031 * formula defining the condition of the constraint. This formula must 032 * return a boolean value of <code>true</code> when the model is a <em>valid</em> 033 * state. The formula can be an arbitrary expression referencing the 034 * variables and other entities in an SBML model. The evaluation of 'math' 035 * and behavior of constraints are described in more detail below. 036 * <p> 037 * A {@link Constraint} structure also has an optional subelement called 'message'. 038 * This can contain a message in XHTML format that may be displayed to the 039 * user when the condition of the formula in the 'math' subelement 040 * evaluates to a value of <code>false.</code> Software tools are not required to 041 * display the message, but it is recommended that they do so as a matter 042 * of best practice. The XHTML content within a 'message' subelement must 043 * follow the same restrictions as for the 'notes' element on {@link SBase} 044 * described in in the SBML Level 2 specification; please consult the 045 * <a target='_blank' href='http://sbml.org/Documents/Specifications'>SBML 046 * specification document</a> corresponding to the SBML Level and Version 047 * of your model for more information about the requirements for 'notes' 048 * content. 049 * <p> 050 * {@link Constraint} was introduced in SBML Level 2 Version 2. It is 051 * not available in earlier versions of Level 2 nor in any version of 052 * Level 1. 053 * <p> 054 * <h2>Semantics of Constraints</h2> 055 * <p> 056 * In the context of a simulation, a {@link Constraint} has effect at all times 057 * <em>t ≥ 0</em>. Each {@link Constraint}'s 'math' subelement is first 058 * evaluated after any {@link InitialAssignment} definitions in a model at <em>t = 059 * 0</em> and can conceivably trigger at that point. (In other words, a 060 * simulation could fail a constraint immediately.) 061 * <p> 062 * {@link Constraint} structures <em>cannot and should not</em> be used to compute 063 * the dynamical behavior of a model as part of, for example, simulation. 064 * Constraints may be used as input to non-dynamical analysis, for instance 065 * by expressing flux constraints for flux balance analysis. 066 * <p> 067 * The results of a simulation of a model containing a constraint are 068 * invalid from any simulation time at and after a point when the function 069 * given by the 'math' subelement returns a value of <code>false.</code> Invalid 070 * simulation results do not make a prediction of the behavior of the 071 * biochemical reaction network represented by the model. The precise 072 * behavior of simulation tools is left undefined with respect to 073 * constraints. If invalid results are detected with respect to a given 074 * constraint, the 'message' subelement may optionally be displayed to the 075 * user. The simulation tool may also halt the simulation or clearly 076 * delimit in output data the simulation time point at which the simulation 077 * results become invalid. 078 * <p> 079 * SBML does not impose restrictions on duplicate {@link Constraint} definitions or 080 * the order of evaluation of {@link Constraint} objects in a model. It is 081 * possible for a model to define multiple constraints all with the same 082 * mathematical expression. Since the failure of any constraint indicates 083 * that the model simulation has entered an invalid state, a system is not 084 * required to attempt to detect whether other constraints in the model 085 * have failed once any one constraint has failed. 086 * <p> 087 * <!---------------------------------------------------------------------- --> 088 * <p> 089 */ 090 091public class Constraint extends SBase { 092 private long swigCPtr; 093 094 protected Constraint(long cPtr, boolean cMemoryOwn) 095 { 096 super(libsbmlJNI.Constraint_SWIGUpcast(cPtr), cMemoryOwn); 097 swigCPtr = cPtr; 098 } 099 100 protected static long getCPtr(Constraint obj) 101 { 102 return (obj == null) ? 0 : obj.swigCPtr; 103 } 104 105 protected static long getCPtrAndDisown (Constraint obj) 106 { 107 long ptr = 0; 108 109 if (obj != null) 110 { 111 ptr = obj.swigCPtr; 112 obj.swigCMemOwn = false; 113 } 114 115 return ptr; 116 } 117 118 protected void finalize() { 119 delete(); 120 } 121 122 public synchronized void delete() { 123 if (swigCPtr != 0) { 124 if (swigCMemOwn) { 125 swigCMemOwn = false; 126 libsbmlJNI.delete_Constraint(swigCPtr); 127 } 128 swigCPtr = 0; 129 } 130 super.delete(); 131 } 132 133 134/** 135 * Creates a new {@link Constraint} using the given SBML <code>level</code> and <code>version</code> 136 * values. 137 * <p> 138 * @param level a long integer, the SBML Level to assign to this {@link Constraint} 139 * <p> 140 * @param version a long integer, the SBML Version to assign to this 141 * {@link Constraint} 142 * <p> 143 * @throws SBMLConstructorException 144 * Thrown if the given <code>level</code> and <code>version</code> combination, or this kind 145 * of SBML object, are either invalid or mismatched with respect to the 146 * parent {@link SBMLDocument} object. 147 * <p> 148 * @note Upon the addition of a {@link Constraint} object to an {@link SBMLDocument} 149 * (e.g., using {@link Model#addConstraint(Constraint c)}), the 150 * SBML Level, SBML Version and XML namespace of the document 151 * <em>override</em> the values used when creating the {@link Constraint} object via this 152 * constructor. This is necessary to ensure that an SBML document is a 153 * consistent structure. Nevertheless, the ability to supply the values 154 * at the time of creation of a {@link Constraint} is an important aid to 155 * producing valid SBML. Knowledge of the intented SBML Level and 156 * Version determine whether it is valid to assign a particular value to 157 * an attribute, or whether it is valid to add an object to an existing 158 * {@link SBMLDocument}. 159 */ public 160 Constraint(long level, long version) throws org.sbml.libsbml.SBMLConstructorException { 161 this(libsbmlJNI.new_Constraint__SWIG_0(level, version), true); 162 } 163 164 165/** 166 * Creates a new {@link Constraint} using the given {@link SBMLNamespaces} object 167 * <code>sbmlns</code>. 168 * <p> 169 * The {@link SBMLNamespaces} object encapsulates SBML Level/Version/namespaces 170 * information. It is used to communicate the SBML Level, Version, and 171 * (in Level 3) packages used in addition to SBML Level 3 Core. 172 * A common approach to using this class constructor is to create an 173 * {@link SBMLNamespaces} object somewhere in a program, once, then pass it to 174 * object constructors such as this one when needed. 175 * <p> 176 * @param sbmlns an {@link SBMLNamespaces} object. 177 * <p> 178 * @throws SBMLConstructorException 179 * Thrown if the given <code>level</code> and <code>version</code> combination, or this kind 180 * of SBML object, are either invalid or mismatched with respect to the 181 * parent {@link SBMLDocument} object. 182 * <p> 183 * @note Upon the addition of a {@link Constraint} object to an {@link SBMLDocument} 184 * (e.g., using {@link Model#addConstraint(Constraint c)}), the 185 * SBML XML namespace of the document <em>overrides</em> the value used when 186 * creating the {@link Constraint} object via this constructor. This is 187 * necessary to ensure that an SBML document is a consistent structure. 188 * Nevertheless, the ability to supply the values at the time of creation 189 * of a {@link Constraint} is an important aid to producing valid SBML. 190 * Knowledge of the intented SBML Level and Version determine whether it 191 * is valid to assign a particular value to an attribute, or whether it 192 * is valid to add an object to an existing {@link SBMLDocument}. 193 */ public 194 Constraint(SBMLNamespaces sbmlns) throws org.sbml.libsbml.SBMLConstructorException { 195 this(libsbmlJNI.new_Constraint__SWIG_1(SBMLNamespaces.getCPtr(sbmlns), sbmlns), true); 196 } 197 198 199/** 200 * Copy constructor; creates a copy of this {@link Constraint}. 201 * <p> 202 * @param orig the object to copy. 203 * <p> 204 * @throws SBMLConstructorException 205 * Thrown if the argument <code>orig</code> is <code>null.</code> 206 */ public 207 Constraint(Constraint orig) throws org.sbml.libsbml.SBMLConstructorException { 208 this(libsbmlJNI.new_Constraint__SWIG_2(Constraint.getCPtr(orig), orig), true); 209 } 210 211 212/** 213 * Creates and returns a deep copy of this {@link Constraint}. 214 * <p> 215 * @return a (deep) copy of this {@link Constraint}. 216 */ public 217 Constraint cloneObject() { 218 long cPtr = libsbmlJNI.Constraint_cloneObject(swigCPtr, this); 219 return (cPtr == 0) ? null : new Constraint(cPtr, true); 220 } 221 222 223/** 224 * Get the message, if any, associated with this {@link Constraint} 225 * <p> 226 * @return the message for this {@link Constraint}, as an {@link XMLNode}. 227 */ public 228 XMLNode getMessage() { 229 long cPtr = libsbmlJNI.Constraint_getMessage(swigCPtr, this); 230 return (cPtr == 0) ? null : new XMLNode(cPtr, false); 231 } 232 233 234/** 235 * Get the message string, if any, associated with this {@link Constraint} 236 * <p> 237 * @return the message for this {@link Constraint}, as a string. 238 */ public 239 String getMessageString() { 240 return libsbmlJNI.Constraint_getMessageString(swigCPtr, this); 241 } 242 243 244/** 245 * Get the mathematical expression of this {@link Constraint} 246 * <p> 247 * @return the math for this {@link Constraint}, as an {@link ASTNode}. 248 */ public 249 ASTNode getMath() { 250 long cPtr = libsbmlJNI.Constraint_getMath(swigCPtr, this); 251 return (cPtr == 0) ? null : new ASTNode(cPtr, false); 252 } 253 254 255/** 256 * Predicate returning <code>true</code> if a 257 * message is defined for this {@link Constraint}. 258 * <p> 259 * @return <code>true</code> if the message of this {@link Constraint} is set, 260 * <code>false</code> otherwise. 261 */ public 262 boolean isSetMessage() { 263 return libsbmlJNI.Constraint_isSetMessage(swigCPtr, this); 264 } 265 266 267/** 268 * Predicate returning <code>true</code> if a 269 * mathematical formula is defined for this {@link Constraint}. 270 * <p> 271 * @return <code>true</code> if the 'math' subelement for this {@link Constraint} is 272 * set, <code>false</code> otherwise. 273 */ public 274 boolean isSetMath() { 275 return libsbmlJNI.Constraint_isSetMath(swigCPtr, this); 276 } 277 278 279/** 280 * Sets the message of this {@link Constraint}. 281 * <p> 282 * The {@link XMLNode} tree passed in <code>xhtml</code> is copied. 283 * <p> 284 * @param xhtml an XML tree containing XHTML content. 285 * <p> 286 * @return integer value indicating success/failure of the 287 * function. The possible values 288 * returned by this function are: 289 * <ul> 290 * <li> {@link libsbmlConstants#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS } 291 * <li> {@link libsbmlConstants#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT } 292 * </ul> 293 */ public 294 int setMessage(XMLNode xhtml) { 295 return libsbmlJNI.Constraint_setMessage(swigCPtr, this, XMLNode.getCPtr(xhtml), xhtml); 296 } 297 298 299/** 300 * Sets the mathematical expression of this {@link Constraint} to a copy of the 301 * AST given as <code>math</code>. 302 * <p> 303 * @param math an {@link ASTNode} expression to be assigned as the 'math' 304 * subelement of this {@link Constraint} 305 * <p> 306 * @return integer value indicating success/failure of the 307 * function. The possible values 308 * returned by this function are: 309 * <ul> 310 * <li> {@link libsbmlConstants#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS } 311 * <li> {@link libsbmlConstants#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT } 312 * </ul> 313 */ public 314 int setMath(ASTNode math) { 315 return libsbmlJNI.Constraint_setMath(swigCPtr, this, ASTNode.getCPtr(math), math); 316 } 317 318 319/** 320 * Unsets the 'message' subelement of this {@link Constraint}. 321 * <p> 322 * @return integer value indicating success/failure of the 323 * function. The possible values 324 * returned by this function are: 325 * <ul> 326 * <li> {@link libsbmlConstants#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS } 327 * <li> {@link libsbmlConstants#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED } 328 * </ul> 329 */ public 330 int unsetMessage() { 331 return libsbmlJNI.Constraint_unsetMessage(swigCPtr, this); 332 } 333 334 335/** 336 * Renames all the SIdRef attributes on this element, including any found in MathML 337 */ public 338 void renameSIdRefs(String oldid, String newid) { 339 libsbmlJNI.Constraint_renameSIdRefs(swigCPtr, this, oldid, newid); 340 } 341 342 343/** 344 * Renames all the UnitSIdRef attributes on this element 345 */ public 346 void renameUnitSIdRefs(String oldid, String newid) { 347 libsbmlJNI.Constraint_renameUnitSIdRefs(swigCPtr, this, oldid, newid); 348 } 349 350 351/** 352 * Replace all nodes with the name 'id' from the child 'math' object with the provided function. 353 * <p> 354 * @internal 355 */ public 356 void replaceSIDWithFunction(String id, ASTNode function) { 357 libsbmlJNI.Constraint_replaceSIDWithFunction(swigCPtr, this, id, ASTNode.getCPtr(function), function); 358 } 359 360 361/** 362 * Returns the libSBML type code for this SBML object. 363 * <p> 364 * LibSBML attaches an identifying code to every 365 * kind of SBML object. These are known as <em>SBML type codes</em>. In 366 * other languages, the set of type codes is stored in an enumeration; in 367 * the Java language interface for libSBML, the type codes are defined as 368 * static integer constants in the interface class {@link 369 * libsbmlConstants}. The names of the type codes all begin with the 370 * characters <code>SBML_.</code> 371 * <p> 372 * @return the SBML type code for this object, or {@link libsbmlConstants#SBML_UNKNOWN SBML_UNKNOWN} (default). 373 * <p> 374 * @see #getElementName() 375 */ public 376 int getTypeCode() { 377 return libsbmlJNI.Constraint_getTypeCode(swigCPtr, this); 378 } 379 380 381/** 382 * Returns the XML element name of this object, which for {@link Constraint}, is 383 * always <code>'constraint'.</code> 384 * <p> 385 * @return the name of this element, i.e., <code>'constraint'.</code> 386 */ public 387 String getElementName() { 388 return libsbmlJNI.Constraint_getElementName(swigCPtr, this); 389 } 390 391 392/** 393 * Predicate returning <code>true</code> if 394 * all the required elements for this {@link Constraint} object 395 * have been set. 396 * <p> 397 * @note The required elements for a {@link Constraint} object are: 398 * <ul> 399 * <li> 'math' 400 * </ul> 401 * <p> 402 * @return a boolean value indicating whether all the required 403 * elements for this object have been defined. 404 */ public 405 boolean hasRequiredElements() { 406 return libsbmlJNI.Constraint_hasRequiredElements(swigCPtr, this); 407 } 408 409}