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 * <span class="pkg-marker pkg-color-qual"><a href="group__qual.html">qual</a></span> 013 014 Extension of {@link Species}. 015 <p> 016 * Similarly to the {@link Species} in SBML, the components of qualitative models 017 * refer to pools of entities that are considered indistinguishable and are 018 * each located in a specific {@link Compartment}. However, here components are 019 * characterised by their qualitative influences rather than by taking part 020 * in reactions. Therefore, we define the {@link QualitativeSpecies} element to 021 * represent such pools of entities. 022 <p> 023 * In a Petri net, qualitative species refer to the places of the model, 024 * while in a logical model, they refer to the variables of this model 025 * (i.e. nodes of the influence graph). 026 <p> 027 * A {@link QualitativeSpecies} describes a pool of indistinguishable entities in a 028 * {@link Compartment}. It is associated with a level (an integer representing 029 * e.g. an activity state, or a functional level of concentration, etc.) 030 */ 031 032public class QualitativeSpecies extends SBase { 033 private long swigCPtr; 034 035 protected QualitativeSpecies(long cPtr, boolean cMemoryOwn) 036 { 037 super(libsbmlJNI.QualitativeSpecies_SWIGUpcast(cPtr), cMemoryOwn); 038 swigCPtr = cPtr; 039 } 040 041 protected static long getCPtr(QualitativeSpecies obj) 042 { 043 return (obj == null) ? 0 : obj.swigCPtr; 044 } 045 046 protected static long getCPtrAndDisown (QualitativeSpecies obj) 047 { 048 long ptr = 0; 049 050 if (obj != null) 051 { 052 ptr = obj.swigCPtr; 053 obj.swigCMemOwn = false; 054 } 055 056 return ptr; 057 } 058 059 protected void finalize() { 060 delete(); 061 } 062 063 public synchronized void delete() { 064 if (swigCPtr != 0) { 065 if (swigCMemOwn) { 066 swigCMemOwn = false; 067 libsbmlJNI.delete_QualitativeSpecies(swigCPtr); 068 } 069 swigCPtr = 0; 070 } 071 super.delete(); 072 } 073 074 075/** 076 * Creates a new {@link QualitativeSpecies} with the given level, version, and package version. 077 <p> 078 * @param level a long integer, the SBML Level to assign to this {@link QualitativeSpecies} 079 <p> 080 * @param version a long integer, the SBML Version to assign to this {@link QualitativeSpecies} 081 <p> 082 * @param pkgVersion a long integer, the SBML Qual Version to assign to this {@link QualitativeSpecies} 083 */ public 084 QualitativeSpecies(long level, long version, long pkgVersion) throws org.sbml.libsbml.SBMLConstructorException { 085 this(libsbmlJNI.new_QualitativeSpecies__SWIG_0(level, version, pkgVersion), true); 086 } 087 088 089/** 090 * Creates a new {@link QualitativeSpecies} with the given level, version, and package version. 091 <p> 092 * @param level a long integer, the SBML Level to assign to this {@link QualitativeSpecies} 093 <p> 094 * @param version a long integer, the SBML Version to assign to this {@link QualitativeSpecies} 095 <p> 096 * @param pkgVersion a long integer, the SBML Qual Version to assign to this {@link QualitativeSpecies} 097 */ public 098 QualitativeSpecies(long level, long version) throws org.sbml.libsbml.SBMLConstructorException { 099 this(libsbmlJNI.new_QualitativeSpecies__SWIG_1(level, version), true); 100 } 101 102 103/** 104 * Creates a new {@link QualitativeSpecies} with the given level, version, and package version. 105 <p> 106 * @param level a long integer, the SBML Level to assign to this {@link QualitativeSpecies} 107 <p> 108 * @param version a long integer, the SBML Version to assign to this {@link QualitativeSpecies} 109 <p> 110 * @param pkgVersion a long integer, the SBML Qual Version to assign to this {@link QualitativeSpecies} 111 */ public 112 QualitativeSpecies(long level) throws org.sbml.libsbml.SBMLConstructorException { 113 this(libsbmlJNI.new_QualitativeSpecies__SWIG_2(level), true); 114 } 115 116 117/** 118 * Creates a new {@link QualitativeSpecies} with the given level, version, and package version. 119 <p> 120 * @param level a long integer, the SBML Level to assign to this {@link QualitativeSpecies} 121 <p> 122 * @param version a long integer, the SBML Version to assign to this {@link QualitativeSpecies} 123 <p> 124 * @param pkgVersion a long integer, the SBML Qual Version to assign to this {@link QualitativeSpecies} 125 */ public 126 QualitativeSpecies() throws org.sbml.libsbml.SBMLConstructorException { 127 this(libsbmlJNI.new_QualitativeSpecies__SWIG_3(), true); 128 } 129 130 131/** 132 * Creates a new {@link QualitativeSpecies} with the given {@link QualPkgNamespaces} object. 133 <p> 134 * @param qualns the {@link QualPkgNamespaces} object 135 */ public 136 QualitativeSpecies(QualPkgNamespaces qualns) throws org.sbml.libsbml.SBMLConstructorException { 137 this(libsbmlJNI.new_QualitativeSpecies__SWIG_4(QualPkgNamespaces.getCPtr(qualns), qualns), true); 138 } 139 140 141/** 142 * Copy constructor for {@link QualitativeSpecies}. 143 <p> 144 * @param orig the {@link QualitativeSpecies} instance to copy. 145 */ public 146 QualitativeSpecies(QualitativeSpecies orig) throws org.sbml.libsbml.SBMLConstructorException { 147 this(libsbmlJNI.new_QualitativeSpecies__SWIG_5(QualitativeSpecies.getCPtr(orig), orig), true); 148 } 149 150 151/** 152 * Creates and returns a deep copy of this {@link QualitativeSpecies} object. 153 <p> 154 * @return a (deep) copy of this {@link QualitativeSpecies} object. 155 */ public 156 QualitativeSpecies cloneObject() { 157 long cPtr = libsbmlJNI.QualitativeSpecies_cloneObject(swigCPtr, this); 158 return (cPtr == 0) ? null : new QualitativeSpecies(cPtr, true); 159 } 160 161 162/** 163 * Returns the value of the 'id' attribute of this {@link QualitativeSpecies}. 164 <p> 165 * @return the value of the 'id' attribute of this {@link QualitativeSpecies} as a string. 166 */ public 167 String getId() { 168 return libsbmlJNI.QualitativeSpecies_getId(swigCPtr, this); 169 } 170 171 172/** 173 * Returns the value of the 'compartment' attribute of this {@link QualitativeSpecies}. 174 <p> 175 * @return the value of the 'compartment' attribute of this {@link QualitativeSpecies} as a string. 176 */ public 177 String getCompartment() { 178 return libsbmlJNI.QualitativeSpecies_getCompartment(swigCPtr, this); 179 } 180 181 182/** 183 * Returns the value of the 'constant' attribute of this {@link QualitativeSpecies}. 184 <p> 185 * @return the value of the 'constant' attribute of this {@link QualitativeSpecies} as a boolean. 186 */ public 187 boolean getConstant() { 188 return libsbmlJNI.QualitativeSpecies_getConstant(swigCPtr, this); 189 } 190 191 192/** 193 * Returns the value of the 'name' attribute of this {@link QualitativeSpecies}. 194 <p> 195 * @return the value of the 'name' attribute of this {@link QualitativeSpecies} as a string. 196 */ public 197 String getName() { 198 return libsbmlJNI.QualitativeSpecies_getName(swigCPtr, this); 199 } 200 201 202/** 203 * Returns the value of the 'initialLevel' attribute of this {@link QualitativeSpecies}. 204 <p> 205 * @return the value of the 'initialLevel' attribute of this {@link QualitativeSpecies} as a integer. 206 */ public 207 int getInitialLevel() { 208 return libsbmlJNI.QualitativeSpecies_getInitialLevel(swigCPtr, this); 209 } 210 211 212/** 213 * Returns the value of the 'maxLevel' attribute of this {@link QualitativeSpecies}. 214 <p> 215 * @return the value of the 'maxLevel' attribute of this {@link QualitativeSpecies} as a integer. 216 */ public 217 int getMaxLevel() { 218 return libsbmlJNI.QualitativeSpecies_getMaxLevel(swigCPtr, this); 219 } 220 221 222/** 223 * Predicate returning <code>true</code> or <code>false</code> depending on whether this 224 * {@link QualitativeSpecies}'s 'id' attribute has been set. 225 <p> 226 * @return <code>true</code> if this {@link QualitativeSpecies}'s 'id' attribute has been set, 227 * otherwise <code>false</code> is returned. 228 */ public 229 boolean isSetId() { 230 return libsbmlJNI.QualitativeSpecies_isSetId(swigCPtr, this); 231 } 232 233 234/** 235 * Predicate returning <code>true</code> or <code>false</code> depending on whether this 236 * {@link QualitativeSpecies}'s 'compartment' attribute has been set. 237 <p> 238 * @return <code>true</code> if this {@link QualitativeSpecies}'s 'compartment' attribute has been set, 239 * otherwise <code>false</code> is returned. 240 */ public 241 boolean isSetCompartment() { 242 return libsbmlJNI.QualitativeSpecies_isSetCompartment(swigCPtr, this); 243 } 244 245 246/** 247 * Predicate returning <code>true</code> or <code>false</code> depending on whether this 248 * {@link QualitativeSpecies}'s 'constant' attribute has been set. 249 <p> 250 * @return <code>true</code> if this {@link QualitativeSpecies}'s 'constant' attribute has been set, 251 * otherwise <code>false</code> is returned. 252 */ public 253 boolean isSetConstant() { 254 return libsbmlJNI.QualitativeSpecies_isSetConstant(swigCPtr, this); 255 } 256 257 258/** 259 * Predicate returning <code>true</code> or <code>false</code> depending on whether this 260 * {@link QualitativeSpecies}'s 'name' attribute has been set. 261 <p> 262 * @return <code>true</code> if this {@link QualitativeSpecies}'s 'name' attribute has been set, 263 * otherwise <code>false</code> is returned. 264 */ public 265 boolean isSetName() { 266 return libsbmlJNI.QualitativeSpecies_isSetName(swigCPtr, this); 267 } 268 269 270/** 271 * Predicate returning <code>true</code> or <code>false</code> depending on whether this 272 * {@link QualitativeSpecies}'s 'initialLevel' attribute has been set. 273 <p> 274 * @return <code>true</code> if this {@link QualitativeSpecies}'s 'initialLevel' attribute has been set, 275 * otherwise <code>false</code> is returned. 276 */ public 277 boolean isSetInitialLevel() { 278 return libsbmlJNI.QualitativeSpecies_isSetInitialLevel(swigCPtr, this); 279 } 280 281 282/** 283 * Predicate returning <code>true</code> or <code>false</code> depending on whether this 284 * {@link QualitativeSpecies}'s 'maxLevel' attribute has been set. 285 <p> 286 * @return <code>true</code> if this {@link QualitativeSpecies}'s 'maxLevel' attribute has been set, 287 * otherwise <code>false</code> is returned. 288 */ public 289 boolean isSetMaxLevel() { 290 return libsbmlJNI.QualitativeSpecies_isSetMaxLevel(swigCPtr, this); 291 } 292 293 294/** 295 * Sets the value of the 'id' attribute of this {@link QualitativeSpecies}. 296 <p> 297 * @param id String value of the 'id' attribute to be set 298 <p> 299 * <p> 300 * @return integer value indicating success/failure of the 301 * function. The possible values 302 * returned by this function are: 303 * <ul> 304 * <li> {@link libsbmlConstants#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS} 305 * <li> {@link libsbmlConstants#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE} 306 * </ul> 307 */ public 308 int setId(String id) { 309 return libsbmlJNI.QualitativeSpecies_setId(swigCPtr, this, id); 310 } 311 312 313/** 314 * Sets the value of the 'compartment' attribute of this {@link QualitativeSpecies}. 315 <p> 316 * @param compartment String value of the 'compartment' attribute to be set 317 <p> 318 * <p> 319 * @return integer value indicating success/failure of the 320 * function. The possible values 321 * returned by this function are: 322 * <ul> 323 * <li> {@link libsbmlConstants#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS} 324 * <li> {@link libsbmlConstants#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE} 325 * </ul> 326 */ public 327 int setCompartment(String compartment) { 328 return libsbmlJNI.QualitativeSpecies_setCompartment(swigCPtr, this, compartment); 329 } 330 331 332/** 333 * Sets the value of the 'constant' attribute of this {@link QualitativeSpecies}. 334 <p> 335 * @param constant boolean value of the 'constant' attribute to be set 336 <p> 337 * <p> 338 * @return integer value indicating success/failure of the 339 * function. The possible values 340 * returned by this function are: 341 * <ul> 342 * <li> {@link libsbmlConstants#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS} 343 * <li> {@link libsbmlConstants#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE} 344 * </ul> 345 */ public 346 int setConstant(boolean constant) { 347 return libsbmlJNI.QualitativeSpecies_setConstant(swigCPtr, this, constant); 348 } 349 350 351/** 352 * Sets the value of the 'name' attribute of this {@link QualitativeSpecies}. 353 <p> 354 * @param name String value of the 'name' attribute to be set 355 <p> 356 * <p> 357 * @return integer value indicating success/failure of the 358 * function. The possible values 359 * returned by this function are: 360 * <ul> 361 * <li> {@link libsbmlConstants#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS} 362 * <li> {@link libsbmlConstants#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE} 363 * </ul> 364 */ public 365 int setName(String name) { 366 return libsbmlJNI.QualitativeSpecies_setName(swigCPtr, this, name); 367 } 368 369 370/** 371 * Sets the value of the 'initialLevel' attribute of this {@link QualitativeSpecies}. 372 <p> 373 * @param initialLevel int value of the 'initialLevel' attribute to be set 374 <p> 375 * <p> 376 * @return integer value indicating success/failure of the 377 * function. The possible values 378 * returned by this function are: 379 * <ul> 380 * <li> {@link libsbmlConstants#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS} 381 * <li> {@link libsbmlConstants#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE} 382 * </ul> 383 */ public 384 int setInitialLevel(int initialLevel) { 385 return libsbmlJNI.QualitativeSpecies_setInitialLevel(swigCPtr, this, initialLevel); 386 } 387 388 389/** 390 * Sets the value of the 'maxLevel' attribute of this {@link QualitativeSpecies}. 391 <p> 392 * @param maxLevel int value of the 'maxLevel' attribute to be set 393 <p> 394 * <p> 395 * @return integer value indicating success/failure of the 396 * function. The possible values 397 * returned by this function are: 398 * <ul> 399 * <li> {@link libsbmlConstants#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS} 400 * <li> {@link libsbmlConstants#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE} 401 * </ul> 402 */ public 403 int setMaxLevel(int maxLevel) { 404 return libsbmlJNI.QualitativeSpecies_setMaxLevel(swigCPtr, this, maxLevel); 405 } 406 407 408/** 409 * Unsets the value of the 'id' attribute of this {@link QualitativeSpecies}. 410 <p> 411 * <p> 412 * @return integer value indicating success/failure of the 413 * function. The possible values 414 * returned by this function are: 415 * <ul> 416 * <li> {@link libsbmlConstants#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS} 417 * <li> {@link libsbmlConstants#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED} 418 * </ul> 419 */ public 420 int unsetId() { 421 return libsbmlJNI.QualitativeSpecies_unsetId(swigCPtr, this); 422 } 423 424 425/** 426 * Unsets the value of the 'compartment' attribute of this {@link QualitativeSpecies}. 427 <p> 428 * <p> 429 * @return integer value indicating success/failure of the 430 * function. The possible values 431 * returned by this function are: 432 * <ul> 433 * <li> {@link libsbmlConstants#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS} 434 * <li> {@link libsbmlConstants#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED} 435 * </ul> 436 */ public 437 int unsetCompartment() { 438 return libsbmlJNI.QualitativeSpecies_unsetCompartment(swigCPtr, this); 439 } 440 441 442/** 443 * Unsets the value of the 'constant' attribute of this {@link QualitativeSpecies}. 444 <p> 445 * <p> 446 * @return integer value indicating success/failure of the 447 * function. The possible values 448 * returned by this function are: 449 * <ul> 450 * <li> {@link libsbmlConstants#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS} 451 * <li> {@link libsbmlConstants#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED} 452 * </ul> 453 */ public 454 int unsetConstant() { 455 return libsbmlJNI.QualitativeSpecies_unsetConstant(swigCPtr, this); 456 } 457 458 459/** 460 * Unsets the value of the 'name' attribute of this {@link QualitativeSpecies}. 461 <p> 462 * <p> 463 * @return integer value indicating success/failure of the 464 * function. The possible values 465 * returned by this function are: 466 * <ul> 467 * <li> {@link libsbmlConstants#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS} 468 * <li> {@link libsbmlConstants#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED} 469 * </ul> 470 */ public 471 int unsetName() { 472 return libsbmlJNI.QualitativeSpecies_unsetName(swigCPtr, this); 473 } 474 475 476/** 477 * Unsets the value of the 'initialLevel' attribute of this {@link QualitativeSpecies}. 478 <p> 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 unsetInitialLevel() { 489 return libsbmlJNI.QualitativeSpecies_unsetInitialLevel(swigCPtr, this); 490 } 491 492 493/** 494 * Unsets the value of the 'maxLevel' attribute of this {@link QualitativeSpecies}. 495 <p> 496 * <p> 497 * @return integer value indicating success/failure of the 498 * function. The possible values 499 * returned by this function are: 500 * <ul> 501 * <li> {@link libsbmlConstants#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS} 502 * <li> {@link libsbmlConstants#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED} 503 * </ul> 504 */ public 505 int unsetMaxLevel() { 506 return libsbmlJNI.QualitativeSpecies_unsetMaxLevel(swigCPtr, this); 507 } 508 509 510/** 511 * <p> 512 * Replaces all uses of a given <code>SIdRef</code> type attribute value with another 513 * value. 514 <p> 515 * <p> 516 * In SBML, object identifiers are of a data type called <code>SId</code>. 517 * In SBML Level 3, an explicit data type called <code>SIdRef</code> was 518 * introduced for attribute values that refer to <code>SId</code> values; in 519 * previous Levels of SBML, this data type did not exist and attributes were 520 * simply described to as 'referring to an identifier', but the effective 521 * data type was the same as <code>SIdRef</code>in Level 3. These and 522 * other methods of libSBML refer to the type <code>SIdRef</code> for all 523 * Levels of SBML, even if the corresponding SBML specification did not 524 * explicitly name the data type. 525 <p> 526 * This method works by looking at all attributes and (if appropriate) 527 * mathematical formulas in MathML content, comparing the referenced 528 * identifiers to the value of <code>oldid</code>. If any matches are found, the 529 * matching values are replaced with <code>newid</code>. The method does <em>not</em> 530 * descend into child elements. 531 <p> 532 * @param oldid the old identifier 533 * @param newid the new identifier 534 */ public 535 void renameSIdRefs(String oldid, String newid) { 536 libsbmlJNI.QualitativeSpecies_renameSIdRefs(swigCPtr, this, oldid, newid); 537 } 538 539 540/** 541 * Returns the XML name of this object. 542 <p> 543 * @return the name of this element. 544 */ public 545 String getElementName() { 546 return libsbmlJNI.QualitativeSpecies_getElementName(swigCPtr, this); 547 } 548 549 550/** 551 * Returns the libSBML type code of this object instance. 552 <p> 553 * <p> 554 * LibSBML attaches an identifying code to every kind of SBML object. These 555 * are integer constants known as <em>SBML type codes</em>. The names of all 556 * the codes begin with the characters <code>SBML_</code>. 557 * In the Java language interface for libSBML, the 558 * type codes are defined as static integer constants in the interface class 559 * {@link libsbmlConstants}. Note that different Level 3 560 * package plug-ins may use overlapping type codes; to identify the package 561 * to which a given object belongs, call the <code>getPackageName()</code> 562 * method on the object. 563 <p> 564 * @return the SBML type code for this object: 565 * {@link libsbmlConstants#SBML_QUAL_QUALITATIVE_SPECIES SBML_QUAL_QUALITATIVE_SPECIES} 566 <p> 567 * <p> 568 * @warning <span class='warning'>The specific integer values of the possible 569 * type codes may be reused by different libSBML plug-ins for SBML Level 3. 570 * packages, To fully identify the correct code, <strong>it is necessary to 571 * invoke both getTypeCode() and getPackageName()</strong>.</span> 572 <p> 573 * @see #getElementName() 574 * @see #getPackageName() 575 */ public 576 int getTypeCode() { 577 return libsbmlJNI.QualitativeSpecies_getTypeCode(swigCPtr, this); 578 } 579 580 581/** 582 * Predicate returning <code>true</code> if all the required attributes 583 * for this {@link QualitativeSpecies} object have been set. 584 <p> 585 * @note The required attributes for a {@link QualitativeSpecies} object are: 586 * <ul> 587 * <li> 'id' 588 * <li> 'compartment' 589 * <li> 'constant' 590 * 591 * </ul> <p> 592 * @return a boolean value indicating whether all the required 593 * attributes for this object have been defined. 594 */ public 595 boolean hasRequiredAttributes() { 596 return libsbmlJNI.QualitativeSpecies_hasRequiredAttributes(swigCPtr, this); 597 } 598 599 600/** * @internal */ public 601 void enablePackageInternal(String pkgURI, String pkgPrefix, boolean flag) { 602 libsbmlJNI.QualitativeSpecies_enablePackageInternal(swigCPtr, this, pkgURI, pkgPrefix, flag); 603 } 604 605}