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 2 015 * Version 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 2 Version 4 specification). 028 <p> 029 * {@link Constraint} has one required subelement, 'math', containing a MathML 030 * formula defining the condition of the constraint. This formula must 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 * A {@link Constraint} structure also has an optional subelement called 'message'. 037 * This can contain a message in XHTML format that may be displayed to the 038 * user when the condition of the formula in the 'math' subelement 039 * evaluates to a value of <code>false.</code> Software tools are not required to 040 * display the message, but it is recommended that they do so as a matter 041 * of best practice. The XHTML content within a 'message' subelement must 042 * follow the same restrictions as for the 'notes' element on {@link SBase} 043 * described in in the SBML Level 2 specification; please consult the 044 * <a target='_blank' href='http://sbml.org/Documents/Specifications'>SBML 045 * specification document</a> corresponding to the SBML Level and Version 046 * of your model for more information about the requirements for 'notes' 047 * content. 048 <p> 049 * {@link Constraint} was introduced in SBML Level 2 Version 2. It is 050 * not available in earlier versions of Level 2 nor in any version of 051 * Level 1. 052 <p> 053 * <h2>Semantics of Constraints</h2> 054 <p> 055 * In the context of a simulation, a {@link Constraint} has effect at all times 056 * <em>t ≥ 0</em>. Each {@link Constraint}'s 'math' subelement is first 057 * evaluated after any {@link InitialAssignment} definitions in a model at <em>t = 058 * 0</em> and can conceivably trigger at that point. (In other words, a 059 * simulation could fail a constraint immediately.) 060 <p> 061 * {@link Constraint} structures <em>cannot and should not</em> be used to compute 062 * the dynamical behavior of a model as part of, for example, simulation. 063 * Constraints may be used as input to non-dynamical analysis, for instance 064 * by expressing flux constraints for flux balance analysis. 065 <p> 066 * The results of a simulation of a model containing a constraint are 067 * invalid from any simulation time at and after a point when the function 068 * given by the 'math' subelement returns a value of <code>false.</code> Invalid 069 * simulation results do not make a prediction of the behavior of the 070 * biochemical reaction network represented by the model. The precise 071 * behavior of simulation tools is left undefined with respect to 072 * constraints. If invalid results are detected with respect to a given 073 * constraint, the 'message' subelement may optionally be displayed to the 074 * user. The simulation tool may also halt the simulation or clearly 075 * delimit in output data the simulation time point at which the simulation 076 * results become invalid. 077 <p> 078 * SBML does not impose restrictions on duplicate {@link Constraint} definitions or 079 * the order of evaluation of {@link Constraint} objects in a model. It is 080 * possible for a model to define multiple constraints all with the same 081 * mathematical expression. Since the failure of any constraint indicates 082 * that the model simulation has entered an invalid state, a system is not 083 * required to attempt to detect whether other constraints in the model 084 * have failed once any one constraint has failed. 085 */ 086 087public class Constraint extends SBase { 088 private long swigCPtr; 089 090 protected Constraint(long cPtr, boolean cMemoryOwn) 091 { 092 super(libsbmlJNI.Constraint_SWIGUpcast(cPtr), cMemoryOwn); 093 swigCPtr = cPtr; 094 } 095 096 protected static long getCPtr(Constraint obj) 097 { 098 return (obj == null) ? 0 : obj.swigCPtr; 099 } 100 101 protected static long getCPtrAndDisown (Constraint obj) 102 { 103 long ptr = 0; 104 105 if (obj != null) 106 { 107 ptr = obj.swigCPtr; 108 obj.swigCMemOwn = false; 109 } 110 111 return ptr; 112 } 113 114 protected void finalize() { 115 delete(); 116 } 117 118 public synchronized void delete() { 119 if (swigCPtr != 0) { 120 if (swigCMemOwn) { 121 swigCMemOwn = false; 122 libsbmlJNI.delete_Constraint(swigCPtr); 123 } 124 swigCPtr = 0; 125 } 126 super.delete(); 127 } 128 129 130/** 131 * Creates a new {@link Constraint} using the given SBML <code>level</code> and <code>version</code> 132 * values. 133 <p> 134 * @param level a long integer, the SBML Level to assign to this {@link Constraint} 135 <p> 136 * @param version a long integer, the SBML Version to assign to this 137 * {@link Constraint} 138 <p> 139 * <p> 140 * @throws SBMLConstructorException 141 * Thrown if the given <code>level</code> and <code>version</code> combination are invalid 142 * or if this object is incompatible with the given level and version. 143 <p> 144 * <p> 145 * @note Attempting to add an object to an {@link SBMLDocument} having a different 146 * combination of SBML Level, Version and XML namespaces than the object 147 * itself will result in an error at the time a caller attempts to make the 148 * addition. A parent object must have compatible Level, Version and XML 149 * namespaces. (Strictly speaking, a parent may also have more XML 150 * namespaces than a child, but the reverse is not permitted.) The 151 * restriction is necessary to ensure that an SBML model has a consistent 152 * overall structure. This requires callers to manage their objects 153 * carefully, but the benefit is increased flexibility in how models can be 154 * created by permitting callers to create objects bottom-up if desired. In 155 * situations where objects are not yet attached to parents (e.g., 156 * {@link SBMLDocument}), knowledge of the intented SBML Level and Version help 157 * libSBML determine such things as whether it is valid to assign a 158 * particular value to an attribute. 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 * <p> 170 * The {@link SBMLNamespaces} object encapsulates SBML Level/Version/namespaces 171 * information. It is used to communicate the SBML Level, Version, and (in 172 * Level 3) packages used in addition to SBML Level 3 Core. A 173 * common approach to using libSBML's {@link SBMLNamespaces} facilities is to create an 174 * {@link SBMLNamespaces} object somewhere in a program once, then hand that object 175 * as needed to object constructors that accept {@link SBMLNamespaces} as arguments. 176 <p> 177 * @param sbmlns an {@link SBMLNamespaces} object. 178 <p> 179 * <p> 180 * @throws SBMLConstructorException 181 * Thrown if the given <code>sbmlns</code> is inconsistent or incompatible 182 * with this object. 183 <p> 184 * <p> 185 * @note Attempting to add an object to an {@link SBMLDocument} having a different 186 * combination of SBML Level, Version and XML namespaces than the object 187 * itself will result in an error at the time a caller attempts to make the 188 * addition. A parent object must have compatible Level, Version and XML 189 * namespaces. (Strictly speaking, a parent may also have more XML 190 * namespaces than a child, but the reverse is not permitted.) The 191 * restriction is necessary to ensure that an SBML model has a consistent 192 * overall structure. This requires callers to manage their objects 193 * carefully, but the benefit is increased flexibility in how models can be 194 * created by permitting callers to create objects bottom-up if desired. In 195 * situations where objects are not yet attached to parents (e.g., 196 * {@link SBMLDocument}), knowledge of the intented SBML Level and Version help 197 * libSBML determine such things as whether it is valid to assign a 198 * particular value to an attribute. 199 */ public 200 Constraint(SBMLNamespaces sbmlns) throws org.sbml.libsbml.SBMLConstructorException { 201 this(libsbmlJNI.new_Constraint__SWIG_1(SBMLNamespaces.getCPtr(sbmlns), sbmlns), true); 202 } 203 204 205/** 206 * Copy constructor; creates a copy of this {@link Constraint}. 207 <p> 208 * @param orig the object to copy. 209 */ public 210 Constraint(Constraint orig) throws org.sbml.libsbml.SBMLConstructorException { 211 this(libsbmlJNI.new_Constraint__SWIG_2(Constraint.getCPtr(orig), orig), true); 212 } 213 214 215/** 216 * Creates and returns a deep copy of this {@link Constraint} object. 217 <p> 218 * @return the (deep) copy of this {@link Constraint} object. 219 */ public 220 Constraint cloneObject() { 221 long cPtr = libsbmlJNI.Constraint_cloneObject(swigCPtr, this); 222 return (cPtr == 0) ? null : new Constraint(cPtr, true); 223 } 224 225 226/** 227 * Get the message, if any, associated with this {@link Constraint} 228 <p> 229 * @return the message for this {@link Constraint}, as an {@link XMLNode}. 230 */ public 231 XMLNode getMessage() { 232 long cPtr = libsbmlJNI.Constraint_getMessage(swigCPtr, this); 233 return (cPtr == 0) ? null : new XMLNode(cPtr, false); 234 } 235 236 237/** 238 * Get the message string, if any, associated with this {@link Constraint} 239 <p> 240 * @return the message for this {@link Constraint}, as a string. 241 */ public 242 String getMessageString() { 243 return libsbmlJNI.Constraint_getMessageString(swigCPtr, this); 244 } 245 246 247/** 248 * Get the mathematical expression of this {@link Constraint} 249 <p> 250 * @return the math for this {@link Constraint}, as an {@link ASTNode}. 251 */ public 252 ASTNode getMath() { 253 long cPtr = libsbmlJNI.Constraint_getMath(swigCPtr, this); 254 return (cPtr == 0) ? null : new ASTNode(cPtr, false); 255 } 256 257 258/** 259 * Predicate returning <code>true</code> if a 260 * message is defined for this {@link Constraint}. 261 <p> 262 * @return <code>true</code> if the message of this {@link Constraint} is set, 263 * <code>false</code> otherwise. 264 */ public 265 boolean isSetMessage() { 266 return libsbmlJNI.Constraint_isSetMessage(swigCPtr, this); 267 } 268 269 270/** 271 * Predicate returning <code>true</code> if a 272 * mathematical formula is defined for this {@link Constraint}. 273 <p> 274 * @return <code>true</code> if the 'math' subelement for this {@link Constraint} is 275 * set, <code>false</code> otherwise. 276 */ public 277 boolean isSetMath() { 278 return libsbmlJNI.Constraint_isSetMath(swigCPtr, this); 279 } 280 281 282/** 283 * Sets the message of this {@link Constraint}. 284 <p> 285 * The {@link XMLNode} tree passed in <code>xhtml</code> is copied. 286 <p> 287 * @param xhtml an XML tree containing XHTML content. 288 <p> 289 * <p> 290 * @return integer value indicating success/failure of the 291 * function. The possible values 292 * returned by this function are: 293 * <ul> 294 * <li> {@link libsbmlConstants#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS} 295 * <li> {@link libsbmlConstants#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT} 296 * </ul> 297 */ public 298 int setMessage(XMLNode xhtml) { 299 return libsbmlJNI.Constraint_setMessage__SWIG_0(swigCPtr, this, XMLNode.getCPtr(xhtml), xhtml); 300 } 301 302 303/** 304 * Sets the message of this {@link Constraint}. 305 <p> 306 * @param message an XML string that is to be used as the content of the 307 * 'message' subelement of this object 308 <p> 309 * @param addXHTMLMarkup a boolean indicating whether to wrap the contents 310 * of the <code>message</code> argument with XHTML paragraph (<code><p></code>) 311 * tags. This is appropriate when the string in <code>message</code> does not already 312 * containg the appropriate XHTML markup. 313 <p> 314 * <p> 315 * @return integer value indicating success/failure of the 316 * function. The possible values 317 * returned by this function are: 318 * <ul> 319 * <li> {@link libsbmlConstants#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS} 320 * <li> {@link libsbmlConstants#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT} 321 * </ul> 322 */ public 323 int setMessage(String message, boolean addXHTMLMarkup) { 324 return libsbmlJNI.Constraint_setMessage__SWIG_1(swigCPtr, this, message, addXHTMLMarkup); 325 } 326 327 328/** 329 * Sets the message of this {@link Constraint}. 330 <p> 331 * @param message an XML string that is to be used as the content of the 332 * 'message' subelement of this object 333 <p> 334 * @param addXHTMLMarkup a boolean indicating whether to wrap the contents 335 * of the <code>message</code> argument with XHTML paragraph (<code><p></code>) 336 * tags. This is appropriate when the string in <code>message</code> does not already 337 * containg the appropriate XHTML markup. 338 <p> 339 * <p> 340 * @return integer value indicating success/failure of the 341 * function. The possible values 342 * returned by this function are: 343 * <ul> 344 * <li> {@link libsbmlConstants#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS} 345 * <li> {@link libsbmlConstants#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT} 346 * </ul> 347 */ public 348 int setMessage(String message) { 349 return libsbmlJNI.Constraint_setMessage__SWIG_2(swigCPtr, this, message); 350 } 351 352 353/** 354 * Sets the mathematical expression of this {@link Constraint} to a copy of the 355 * AST given as <code>math</code>. 356 <p> 357 * @param math an {@link ASTNode} expression to be assigned as the 'math' 358 * subelement of this {@link Constraint} 359 <p> 360 * <p> 361 * @return integer value indicating success/failure of the 362 * function. The possible values 363 * returned by this function are: 364 * <ul> 365 * <li> {@link libsbmlConstants#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS} 366 * <li> {@link libsbmlConstants#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT} 367 * </ul> 368 */ public 369 int setMath(ASTNode math) { 370 return libsbmlJNI.Constraint_setMath(swigCPtr, this, ASTNode.getCPtr(math), math); 371 } 372 373 374/** 375 * Unsets the 'message' subelement of this {@link Constraint}. 376 <p> 377 * <p> 378 * @return integer value indicating success/failure of the 379 * function. The possible values 380 * returned by this function are: 381 * <ul> 382 * <li> {@link libsbmlConstants#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS} 383 * <li> {@link libsbmlConstants#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED} 384 * </ul> 385 */ public 386 int unsetMessage() { 387 return libsbmlJNI.Constraint_unsetMessage(swigCPtr, this); 388 } 389 390 391/** 392 * <p> 393 * Replaces all uses of a given <code>SIdRef</code> type attribute value with another 394 * value. 395 <p> 396 * <p> 397 * In SBML, object identifiers are of a data type called <code>SId</code>. 398 * In SBML Level 3, an explicit data type called <code>SIdRef</code> was 399 * introduced for attribute values that refer to <code>SId</code> values; in 400 * previous Levels of SBML, this data type did not exist and attributes were 401 * simply described to as 'referring to an identifier', but the effective 402 * data type was the same as <code>SIdRef</code>in Level 3. These and 403 * other methods of libSBML refer to the type <code>SIdRef</code> for all 404 * Levels of SBML, even if the corresponding SBML specification did not 405 * explicitly name the data type. 406 <p> 407 * This method works by looking at all attributes and (if appropriate) 408 * mathematical formulas in MathML content, comparing the referenced 409 * identifiers to the value of <code>oldid</code>. If any matches are found, the 410 * matching values are replaced with <code>newid</code>. The method does <em>not</em> 411 * descend into child elements. 412 <p> 413 * @param oldid the old identifier 414 * @param newid the new identifier 415 */ public 416 void renameSIdRefs(String oldid, String newid) { 417 libsbmlJNI.Constraint_renameSIdRefs(swigCPtr, this, oldid, newid); 418 } 419 420 421/** 422 * <p> 423 * Replaces all uses of a given <code>UnitSIdRef</code> type attribute value with 424 * another value. 425 <p> 426 * <p> 427 * In SBML, unit definitions have identifiers of type <code>UnitSId</code>. In 428 * SBML Level 3, an explicit data type called <code>UnitSIdRef</code> was 429 * introduced for attribute values that refer to <code>UnitSId</code> values; in 430 * previous Levels of SBML, this data type did not exist and attributes were 431 * simply described to as 'referring to a unit identifier', but the effective 432 * data type was the same as <code>UnitSIdRef</code> in Level 3. These and 433 * other methods of libSBML refer to the type <code>UnitSIdRef</code> for all 434 * Levels of SBML, even if the corresponding SBML specification did not 435 * explicitly name the data type. 436 <p> 437 * This method works by looking at all unit identifier attribute values 438 * (including, if appropriate, inside mathematical formulas), comparing the 439 * referenced unit identifiers to the value of <code>oldid</code>. If any matches 440 * are found, the matching values are replaced with <code>newid</code>. The method 441 * does <em>not</em> descend into child elements. 442 <p> 443 * @param oldid the old identifier 444 * @param newid the new identifier 445 */ public 446 void renameUnitSIdRefs(String oldid, String newid) { 447 libsbmlJNI.Constraint_renameUnitSIdRefs(swigCPtr, this, oldid, newid); 448 } 449 450 451/** * @internal */ public 452 void replaceSIDWithFunction(String id, ASTNode function) { 453 libsbmlJNI.Constraint_replaceSIDWithFunction(swigCPtr, this, id, ASTNode.getCPtr(function), function); 454 } 455 456 457/** 458 * Returns the libSBML type code for this SBML object. 459 <p> 460 * <p> 461 * LibSBML attaches an identifying code to every kind of SBML object. These 462 * are integer constants known as <em>SBML type codes</em>. The names of all 463 * the codes begin with the characters <code>SBML_</code>. 464 * In the Java language interface for libSBML, the 465 * type codes are defined as static integer constants in the interface class 466 * {@link libsbmlConstants}. Note that different Level 3 467 * package plug-ins may use overlapping type codes; to identify the package 468 * to which a given object belongs, call the <code>getPackageName()</code> 469 * method on the object. 470 <p> 471 * @return the SBML type code for this object: 472 * {@link libsbmlConstants#SBML_CONSTRAINT SBML_CONSTRAINT} (default). 473 <p> 474 * <p> 475 * @warning <span class='warning'>The specific integer values of the possible 476 * type codes may be reused by different libSBML plug-ins for SBML Level 3. 477 * packages, To fully identify the correct code, <strong>it is necessary to 478 * invoke both getTypeCode() and getPackageName()</strong>.</span> 479 <p> 480 * @see #getElementName() 481 * @see #getPackageName() 482 */ public 483 int getTypeCode() { 484 return libsbmlJNI.Constraint_getTypeCode(swigCPtr, this); 485 } 486 487 488/** 489 * Returns the XML element name of this object, which for {@link Constraint}, is 490 * always <code>'constraint'.</code> 491 <p> 492 * @return the name of this element, i.e., <code>'constraint'.</code> 493 */ public 494 String getElementName() { 495 return libsbmlJNI.Constraint_getElementName(swigCPtr, this); 496 } 497 498 499/** 500 * Predicate returning <code>true</code> if 501 * all the required elements for this {@link Constraint} object 502 * have been set. 503 <p> 504 * @note The required elements for a {@link Constraint} object are: 505 * <ul> 506 * <li> 'math' 507 * 508 * </ul> <p> 509 * @return a boolean value indicating whether all the required 510 * elements for this object have been defined. 511 */ public 512 boolean hasRequiredElements() { 513 return libsbmlJNI.Constraint_hasRequiredElements(swigCPtr, this); 514 } 515 516}