001/* ---------------------------------------------------------------------------- 002 * This file was automatically generated by SWIG (http://www.swig.org). 003 * Version 3.0.8 004 * 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-fbc"><a href="group__fbc.html">fbc</a></span> 013 Extension of {@link Model}. 014 */ 015 016public class FbcModelPlugin extends SBasePlugin { 017 private long swigCPtr; 018 019 protected FbcModelPlugin(long cPtr, boolean cMemoryOwn) 020 { 021 super(libsbmlJNI.FbcModelPlugin_SWIGUpcast(cPtr), cMemoryOwn); 022 swigCPtr = cPtr; 023 } 024 025 protected static long getCPtr(FbcModelPlugin obj) 026 { 027 return (obj == null) ? 0 : obj.swigCPtr; 028 } 029 030 protected static long getCPtrAndDisown (FbcModelPlugin obj) 031 { 032 long ptr = 0; 033 034 if (obj != null) 035 { 036 ptr = obj.swigCPtr; 037 obj.swigCMemOwn = false; 038 } 039 040 return ptr; 041 } 042 043 protected void finalize() { 044 delete(); 045 } 046 047 public synchronized void delete() { 048 if (swigCPtr != 0) { 049 if (swigCMemOwn) { 050 swigCMemOwn = false; 051 libsbmlJNI.delete_FbcModelPlugin(swigCPtr); 052 } 053 swigCPtr = 0; 054 } 055 super.delete(); 056 } 057 058 059/** 060 * Creates a new {@link FbcModelPlugin} 061 */ public 062 FbcModelPlugin(String uri, String prefix, FbcPkgNamespaces fbcns) { 063 this(libsbmlJNI.new_FbcModelPlugin__SWIG_0(uri, prefix, FbcPkgNamespaces.getCPtr(fbcns), fbcns), true); 064 } 065 066 067/** 068 * Copy constructor for {@link FbcModelPlugin}. 069 <p> 070 * @param orig; the {@link FbcModelPlugin} instance to copy. 071 */ public 072 FbcModelPlugin(FbcModelPlugin orig) { 073 this(libsbmlJNI.new_FbcModelPlugin__SWIG_1(FbcModelPlugin.getCPtr(orig), orig), true); 074 } 075 076 077/** 078 * Creates and returns a deep copy of this {@link FbcModelPlugin} object. 079 <p> 080 * @return a (deep) copy of this {@link FbcModelPlugin} object. 081 */ public 082 SBasePlugin cloneObject() { 083 long cPtr = libsbmlJNI.FbcModelPlugin_cloneObject(swigCPtr, this); 084 return (cPtr == 0) ? null : new FbcModelPlugin(cPtr, true); 085 } 086 087 088/** * @internal */ public 089 SBase createObject(XMLInputStream stream) { 090 return libsbml.DowncastSBase(libsbmlJNI.FbcModelPlugin_createObject(swigCPtr, this, XMLInputStream.getCPtr(stream), stream), false); 091} 092 093 094/** * @internal */ public 095 int appendFrom(Model model) { 096 return libsbmlJNI.FbcModelPlugin_appendFrom(swigCPtr, this, Model.getCPtr(model), model); 097 } 098 099 100/** 101 * Checks if this plugin object has all the required elements. 102 <p> 103 * Subclasses must override this method 104 * if they have their specific elements. 105 <p> 106 * @return true if this plugin object has all the required elements 107 * otherwise false will be returned. 108 */ public 109 boolean hasRequiredElements() { 110 return libsbmlJNI.FbcModelPlugin_hasRequiredElements(swigCPtr, this); 111 } 112 113 114/** * @internal */ public 115 boolean readOtherXML(SBase parentObject, XMLInputStream stream) { 116 return libsbmlJNI.FbcModelPlugin_readOtherXML(swigCPtr, this, SBase.getCPtr(parentObject), parentObject, XMLInputStream.getCPtr(stream), stream); 117 } 118 119 120/** * @internal */ public 121 void addExpectedAttributes(SWIGTYPE_p_ExpectedAttributes attributes) { 122 libsbmlJNI.FbcModelPlugin_addExpectedAttributes(swigCPtr, this, SWIGTYPE_p_ExpectedAttributes.getCPtr(attributes)); 123 } 124 125 126/** * @internal */ public 127 void readAttributes(XMLAttributes attributes, SWIGTYPE_p_ExpectedAttributes expectedAttributes) { 128 libsbmlJNI.FbcModelPlugin_readAttributes(swigCPtr, this, XMLAttributes.getCPtr(attributes), attributes, SWIGTYPE_p_ExpectedAttributes.getCPtr(expectedAttributes)); 129 } 130 131 132/** * @internal */ public 133 void writeAttributes(XMLOutputStream stream) { 134 libsbmlJNI.FbcModelPlugin_writeAttributes(swigCPtr, this, XMLOutputStream.getCPtr(stream), stream); 135 } 136 137 138/** 139 * Returns the value of the 'strict' attribute of this {@link FbcModelPlugin}. 140 <p> 141 * @return the value of the 'strict' attribute of this {@link FbcModelPlugin} as a boolean. 142 */ public 143 boolean getStrict() { 144 return libsbmlJNI.FbcModelPlugin_getStrict(swigCPtr, this); 145 } 146 147 148/** 149 * Predicate returning <code>true</code> if this {@link FbcModelPlugin}'s 'strict' attribute 150 * is set. 151 <p> 152 * @return <code>true</code> if this {@link FbcModelPlugin}'s 'strict' attribute has been set, 153 * otherwise <code>false</code> is returned. 154 */ public 155 boolean isSetStrict() { 156 return libsbmlJNI.FbcModelPlugin_isSetStrict(swigCPtr, this); 157 } 158 159 160/** 161 * Sets the value of the 'strict' attribute of this {@link FbcModelPlugin}. 162 <p> 163 * @param strict; boolean value of the 'strict' attribute to be set 164 <p> 165 * @return integer value indicating success/failure of the 166 * function. The possible values 167 * returned by this function are: 168 * <ul> 169 * <li> {@link libsbmlConstants#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS} 170 * <li> {@link libsbmlConstants#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE} 171 * </ul> 172 */ public 173 int setStrict(boolean strict) { 174 return libsbmlJNI.FbcModelPlugin_setStrict(swigCPtr, this, strict); 175 } 176 177 178/** 179 * Unsets the value of the 'strict' attribute of this {@link FbcModelPlugin}. 180 <p> 181 * @return integer value indicating success/failure of the 182 * function. The possible values 183 * returned by this function are: 184 * <ul> 185 * <li> {@link libsbmlConstants#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS} 186 * <li> {@link libsbmlConstants#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED} 187 * </ul> 188 */ public 189 int unsetStrict() { 190 return libsbmlJNI.FbcModelPlugin_unsetStrict(swigCPtr, this); 191 } 192 193 194/** 195 * Returns the {@link ListOfFluxBounds} in this plugin object. 196 <p> 197 * @return {@link ListOfFluxBounds} object in this plugin object. 198 */ public 199 ListOfFluxBounds getListOfFluxBounds() { 200 long cPtr = libsbmlJNI.FbcModelPlugin_getListOfFluxBounds__SWIG_0(swigCPtr, this); 201 return (cPtr == 0) ? null : new ListOfFluxBounds(cPtr, false); 202 } 203 204 205/** 206 * Returns the {@link FluxBound} object that belongs to the given index. If the 207 * index is invalid, <code>null</code> is returned. 208 <p> 209 * @param n the index number of the {@link FluxBound} to get. 210 <p> 211 * @return the nth {@link FluxBound} in the {@link ListOfFluxBounds}. 212 */ public 213 FluxBound getFluxBound(long n) { 214 long cPtr = libsbmlJNI.FbcModelPlugin_getFluxBound__SWIG_0(swigCPtr, this, n); 215 return (cPtr == 0) ? null : new FluxBound(cPtr, false); 216 } 217 218 219/** 220 * Returns the {@link FluxBound} object based on its identifier. 221 <p> 222 * @param sid a string representing the identifier 223 * of the {@link FluxBound} to get. 224 <p> 225 * @return {@link FluxBound} in the {@link ListOfFluxBounds} with the given <code>sid</code> 226 * or null if no such {@link FluxBound} exists. 227 <p> 228 * @see #getFluxBound(long n) 229 * @see #getListOfFluxBounds() 230 */ public 231 FluxBound getFluxBound(String sid) { 232 long cPtr = libsbmlJNI.FbcModelPlugin_getFluxBound__SWIG_2(swigCPtr, this, sid); 233 return (cPtr == 0) ? null : new FluxBound(cPtr, false); 234 } 235 236 237/** 238 <p> 239 * @param reaction the id of an reaction to find fluxBounds for 240 <p> 241 * @return a listOfFluxBounds for the given reaction id 242 */ public 243 ListOfFluxBounds getFluxBoundsForReaction(String reaction) { 244 long cPtr = libsbmlJNI.FbcModelPlugin_getFluxBoundsForReaction(swigCPtr, this, reaction); 245 return (cPtr == 0) ? null : new ListOfFluxBounds(cPtr, false); 246 } 247 248 249/** 250 * Adds a copy of the given {@link FluxBound} object to the list of FluxBounds. 251 <p> 252 * @param bound the {@link FluxBound} object to be added to the list of FluxBounds. 253 <p> 254 * <p> 255 * @return integer value indicating success/failure of the 256 * function. The possible values 257 * returned by this function are: 258 * <ul> 259 * <li> {@link libsbmlConstants#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS} 260 * </ul> 261 */ public 262 int addFluxBound(FluxBound bound) { 263 return libsbmlJNI.FbcModelPlugin_addFluxBound(swigCPtr, this, FluxBound.getCPtr(bound), bound); 264 } 265 266 267/** 268 * Creates a new {@link FluxBound} object and adds it to the list of {@link FluxBound} objects 269 * and returns it. 270 <p> 271 * @return a newly created {@link FluxBound} object 272 */ public 273 FluxBound createFluxBound() { 274 long cPtr = libsbmlJNI.FbcModelPlugin_createFluxBound(swigCPtr, this); 275 return (cPtr == 0) ? null : new FluxBound(cPtr, false); 276 } 277 278 279/** 280 * Removes the nth {@link FluxBound} object from this plugin object and 281 * returns a pointer to it. 282 <p> 283 * The caller owns the returned object and is responsible for 284 * deleting it. 285 <p> 286 * @param n the index of the {@link FluxBound} object to remove 287 <p> 288 * @return the {@link FluxBound} object removed. As mentioned above, the 289 * caller owns the returned object. <code>null</code> is returned if the 290 * given index is out of range. 291 */ public 292 FluxBound removeFluxBound(long n) { 293 long cPtr = libsbmlJNI.FbcModelPlugin_removeFluxBound__SWIG_0(swigCPtr, this, n); 294 return (cPtr == 0) ? null : new FluxBound(cPtr, false); 295 } 296 297 298/** 299 * Removes the {@link FluxBound} object with the given <code>sid</code> attribute from 300 * this plugin object and returns a pointer to it. 301 <p> 302 * The caller owns the returned object and is responsible for 303 * deleting it. 304 <p> 305 * @param sid the id attribute of the {@link FluxBound} object to remove 306 <p> 307 * @return the {@link FluxBound} object removed. As mentioned above, the 308 * caller owns the returned object. <code>null</code> is returned if the 309 * given index is out of range. 310 */ public 311 FluxBound removeFluxBound(String sid) { 312 long cPtr = libsbmlJNI.FbcModelPlugin_removeFluxBound__SWIG_1(swigCPtr, this, sid); 313 return (cPtr == 0) ? null : new FluxBound(cPtr, false); 314 } 315 316 317/** 318 * Returns the number of {@link FluxBound} object in this plugin object. 319 <p> 320 * @return the number of {@link FluxBound} object in this plugin object. 321 */ public 322 long getNumFluxBounds() { 323 return libsbmlJNI.FbcModelPlugin_getNumFluxBounds(swigCPtr, this); 324 } 325 326 327/** 328 * Returns the 'ListOfObjectives' in this {@link FbcModelPlugin} object. 329 <p> 330 * @return the 'ListOfObjectives' attribute of this {@link FbcModelPlugin}. 331 */ public 332 ListOfObjectives getListOfObjectives() { 333 long cPtr = libsbmlJNI.FbcModelPlugin_getListOfObjectives__SWIG_0(swigCPtr, this); 334 return (cPtr == 0) ? null : new ListOfObjectives(cPtr, false); 335 } 336 337 338/** 339 * Get a {@link Objective} from the {@link ListOfObjectives}. 340 <p> 341 * @param n the index number of the {@link Objective} to get. 342 <p> 343 * @return the nth {@link Objective} in the {@link ListOfObjectives} within this {@link FbcModelPlugin}. 344 <p> 345 * @see #getNumObjectives() 346 */ public 347 Objective getObjective(long n) { 348 long cPtr = libsbmlJNI.FbcModelPlugin_getObjective__SWIG_0(swigCPtr, this, n); 349 return (cPtr == 0) ? null : new Objective(cPtr, false); 350 } 351 352 353/** 354 * Get a {@link Objective} from the {@link ListOfObjectives} 355 * based on its identifier. 356 <p> 357 * @param sid a string representing the identifier 358 * of the {@link Objective} to get. 359 <p> 360 * @return the {@link Objective} in the {@link ListOfObjectives} 361 * with the given id or null if no such 362 * {@link Objective} exists. 363 <p> 364 * 365 * @see #getNumObjectives() 366 <p> 367 * @see #getObjective(long n) 368 */ public 369 Objective getObjective(String sid) { 370 long cPtr = libsbmlJNI.FbcModelPlugin_getObjective__SWIG_2(swigCPtr, this, sid); 371 return (cPtr == 0) ? null : new Objective(cPtr, false); 372 } 373 374 375/** 376 * Adds a copy the given 'Objective' to this {@link FbcModelPlugin}. 377 <p> 378 * @param o; the {@link Objective} object to add 379 <p> 380 * @return integer value indicating success/failure of the 381 * function. The possible values 382 * returned by this function are: 383 * <ul> 384 * <li> {@link libsbmlConstants#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS} 385 * <li> {@link libsbmlConstants#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE} 386 * </ul> 387 */ public 388 int addObjective(Objective o) { 389 return libsbmlJNI.FbcModelPlugin_addObjective(swigCPtr, this, Objective.getCPtr(o), o); 390 } 391 392 393/** 394 * Get the number of {@link Objective} objects in this {@link FbcModelPlugin}. 395 <p> 396 * @return the number of {@link Objective} objects in this {@link FbcModelPlugin} 397 */ public 398 long getNumObjectives() { 399 return libsbmlJNI.FbcModelPlugin_getNumObjectives(swigCPtr, this); 400 } 401 402 403/** 404 * Creates a new {@link Objective} object, adds it to this FbcModelPlugins 405 * {@link ListOfObjectives} and returns the {@link Objective} object created. 406 <p> 407 * @return a new {@link Objective} object instance 408 <p> 409 * @see #addObjective(Objective o) 410 */ public 411 Objective createObjective() { 412 long cPtr = libsbmlJNI.FbcModelPlugin_createObjective(swigCPtr, this); 413 return (cPtr == 0) ? null : new Objective(cPtr, false); 414 } 415 416 417/** 418 * Removes the nth {@link Objective} from the {@link ListOfObjectives} within this {@link FbcModelPlugin}. 419 * and returns a pointer to it. 420 <p> 421 * The caller owns the returned item and is responsible for deleting it. 422 <p> 423 * @param n the index of the {@link Objective} to remove. 424 <p> 425 * @see #getNumObjectives() 426 */ public 427 Objective removeObjective(long n) { 428 long cPtr = libsbmlJNI.FbcModelPlugin_removeObjective__SWIG_0(swigCPtr, this, n); 429 return (cPtr == 0) ? null : new Objective(cPtr, true); 430 } 431 432 433/** 434 * Removes the {@link Objective} with the given identifier from the {@link ListOfObjectives} within this {@link FbcModelPlugin} 435 * and returns a pointer to it. 436 <p> 437 * The caller owns the returned item and is responsible for deleting it. 438 * If none of the items in this list have the identifier <code>sid</code>, then 439 * <code>null</code> is returned. 440 <p> 441 * @param sid the identifier of the {@link Objective} to remove. 442 <p> 443 * @return the {@link Objective} removed. As mentioned above, the caller owns the 444 * returned item. 445 */ public 446 Objective removeObjective(String sid) { 447 long cPtr = libsbmlJNI.FbcModelPlugin_removeObjective__SWIG_1(swigCPtr, this, sid); 448 return (cPtr == 0) ? null : new Objective(cPtr, true); 449 } 450 451 452/** 453 * Returns the current active objective. 454 */ public 455 Objective getActiveObjective() { 456 long cPtr = libsbmlJNI.FbcModelPlugin_getActiveObjective__SWIG_0(swigCPtr, this); 457 return (cPtr == 0) ? null : new Objective(cPtr, false); 458 } 459 460 461/** 462 * Sets the id of the active objective. 463 */ public 464 int setActiveObjectiveId(String objectiveId) { 465 return libsbmlJNI.FbcModelPlugin_setActiveObjectiveId(swigCPtr, this, objectiveId); 466 } 467 468 469/** 470 * returns the id of the current active objective. 471 */ public 472 String getActiveObjectiveId() { 473 return libsbmlJNI.FbcModelPlugin_getActiveObjectiveId(swigCPtr, this); 474 } 475 476 477/** 478 * Unsets the active objective. 479 */ public 480 void unsetActiveObjectiveId() { 481 libsbmlJNI.FbcModelPlugin_unsetActiveObjectiveId(swigCPtr, this); 482 } 483 484 485/** 486 * Returns the 'ListOfGeneProducts' in this {@link FbcModelPlugin} object. 487 <p> 488 * @return the 'ListOfGeneProducts' attribute of this {@link FbcModelPlugin}. 489 */ public 490 ListOfGeneProducts getListOfGeneProducts() { 491 long cPtr = libsbmlJNI.FbcModelPlugin_getListOfGeneProducts__SWIG_0(swigCPtr, this); 492 return (cPtr == 0) ? null : new ListOfGeneProducts(cPtr, false); 493 } 494 495 496/** 497 * Get a {@link GeneProduct} from the {@link ListOfGeneProducts}. 498 <p> 499 * @param n the index number of the {@link GeneProduct} to get. 500 <p> 501 * @return the nth {@link GeneProduct} in the {@link ListOfGeneProducts} within this {@link FbcModelPlugin}. 502 <p> 503 * @see #getNumGeneProducts() 504 */ public 505 GeneProduct getGeneProduct(long n) { 506 long cPtr = libsbmlJNI.FbcModelPlugin_getGeneProduct__SWIG_0(swigCPtr, this, n); 507 return (cPtr == 0) ? null : new GeneProduct(cPtr, false); 508 } 509 510 511/** 512 * Get a {@link GeneProduct} from the {@link ListOfGeneProducts} 513 * based on its identifier. 514 <p> 515 * @param sid a string representing the identifier 516 * of the {@link GeneProduct} to get. 517 <p> 518 * @return the {@link GeneProduct} in the {@link ListOfGeneProducts} 519 * with the given id or null if no such 520 * {@link GeneProduct} exists. 521 <p> 522 * 523 * @see #getNumGeneProducts() 524 <p> 525 * @see #getGeneProduct(long n) 526 */ public 527 GeneProduct getGeneProduct(String sid) { 528 long cPtr = libsbmlJNI.FbcModelPlugin_getGeneProduct__SWIG_2(swigCPtr, this, sid); 529 return (cPtr == 0) ? null : new GeneProduct(cPtr, false); 530 } 531 532 533/** 534 * Get a {@link GeneProduct} from the {@link ListOfGeneProducts} 535 * based on its label. 536 <p> 537 * @param label a string representing the label 538 * of the {@link GeneProduct} to get. 539 <p> 540 * @return the {@link GeneProduct} in the {@link ListOfGeneProducts} 541 * with the given label or null if no such 542 * {@link GeneProduct} exists. 543 <p> 544 * 545 * @see #getNumGeneProducts() 546 <p> 547 * @see #getGeneProduct(long n) 548 */ public 549 GeneProduct getGeneProductByLabel(String label) { 550 long cPtr = libsbmlJNI.FbcModelPlugin_getGeneProductByLabel(swigCPtr, this, label); 551 return (cPtr == 0) ? null : new GeneProduct(cPtr, false); 552 } 553 554 555/** 556 * Adds a copy the given 'GeneProduct' to this {@link FbcModelPlugin}. 557 <p> 558 * @param gp; the {@link GeneProduct} object to add 559 <p> 560 * @return integer value indicating success/failure of the 561 * function. The possible values 562 * returned by this function are: 563 * <ul> 564 * <li> {@link libsbmlConstants#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS} 565 * <li> {@link libsbmlConstants#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE} 566 * </ul> 567 */ public 568 int addGeneProduct(GeneProduct gp) { 569 return libsbmlJNI.FbcModelPlugin_addGeneProduct(swigCPtr, this, GeneProduct.getCPtr(gp), gp); 570 } 571 572 573/** 574 * Get the number of {@link GeneProduct} objects in this {@link FbcModelPlugin}. 575 <p> 576 * @return the number of {@link GeneProduct} objects in this {@link FbcModelPlugin} 577 */ public 578 long getNumGeneProducts() { 579 return libsbmlJNI.FbcModelPlugin_getNumGeneProducts(swigCPtr, this); 580 } 581 582 583/** 584 * Creates a new {@link GeneProduct} object, adds it to this FbcModelPlugins 585 * {@link ListOfGeneProducts} and returns the {@link GeneProduct} object created. 586 <p> 587 * @return a new {@link GeneProduct} object instance 588 <p> 589 * @see #addGeneProduct(GeneProduct gp) 590 */ public 591 GeneProduct createGeneProduct() { 592 long cPtr = libsbmlJNI.FbcModelPlugin_createGeneProduct(swigCPtr, this); 593 return (cPtr == 0) ? null : new GeneProduct(cPtr, false); 594 } 595 596 597/** 598 * Removes the nth {@link GeneProduct} from the {@link ListOfGeneProducts} within this {@link FbcModelPlugin}. 599 * and returns a pointer to it. 600 <p> 601 * The caller owns the returned item and is responsible for deleting it. 602 <p> 603 * @param n the index of the {@link GeneProduct} to remove. 604 <p> 605 * @see #getNumGeneProducts() 606 */ public 607 GeneProduct removeGeneProduct(long n) { 608 long cPtr = libsbmlJNI.FbcModelPlugin_removeGeneProduct__SWIG_0(swigCPtr, this, n); 609 return (cPtr == 0) ? null : new GeneProduct(cPtr, true); 610 } 611 612 613/** 614 * Removes the {@link GeneProduct} with the given identifier from the {@link ListOfGeneProducts} within this {@link FbcModelPlugin} 615 * and returns a pointer to it. 616 <p> 617 * The caller owns the returned item and is responsible for deleting it. 618 * If none of the items in this list have the identifier <code>sid</code>, then 619 * <code>null</code> is returned. 620 <p> 621 * @param sid the identifier of the {@link GeneProduct} to remove. 622 <p> 623 * @return the {@link GeneProduct} removed. As mentioned above, the caller owns the 624 * returned item. 625 */ public 626 GeneProduct removeGeneProduct(String sid) { 627 long cPtr = libsbmlJNI.FbcModelPlugin_removeGeneProduct__SWIG_1(swigCPtr, this, sid); 628 return (cPtr == 0) ? null : new GeneProduct(cPtr, true); 629 } 630 631 632/** 633 * Returns the {@link ListOfGeneAssociations} annotation object for level 1 in this plugin object. 634 <p> 635 * @return {@link ListOfGeneAssociations} annotation object for level 1 in this plugin object. 636 */ public 637 ListOfGeneAssociations getListOfGeneAssociations() { 638 long cPtr = libsbmlJNI.FbcModelPlugin_getListOfGeneAssociations__SWIG_0(swigCPtr, this); 639 return (cPtr == 0) ? null : new ListOfGeneAssociations(cPtr, false); 640 } 641 642 643/** 644 * Returns the {@link GeneAssociation} annotation object that belongs to the given index. If the 645 * index is invalid, <code>null</code> is returned. 646 <p> 647 * @param n the index number of the {@link GeneAssociation} annotation to get. 648 <p> 649 * @return the nth {@link GeneAssociation} annotation in the {@link ListOfGeneAssociations}. 650 */ public 651 GeneAssociation getGeneAssociation(long n) { 652 long cPtr = libsbmlJNI.FbcModelPlugin_getGeneAssociation__SWIG_0(swigCPtr, this, n); 653 return (cPtr == 0) ? null : new GeneAssociation(cPtr, false); 654 } 655 656 657/** 658 * Returns the {@link GeneAssociation} annotation object based on its identifier. 659 <p> 660 * @param sid a string representing the identifier 661 * of the {@link GeneAssociation} annotation to get. 662 <p> 663 * @return {@link GeneAssociation} annotation in the {@link ListOfGeneAssociations} with the given <code>sid</code> 664 * or null if no such {@link GeneAssociation} annotation exists. 665 <p> 666 * @see #getGeneAssociation(long n) 667 * @see #getListOfGeneAssociations() 668 */ public 669 GeneAssociation getGeneAssociation(String sid) { 670 long cPtr = libsbmlJNI.FbcModelPlugin_getGeneAssociation__SWIG_2(swigCPtr, this, sid); 671 return (cPtr == 0) ? null : new GeneAssociation(cPtr, false); 672 } 673 674 675/** 676 * Adds a copy of the given {@link GeneAssociation} annotation object to the list of GeneAssociations. 677 <p> 678 * @param association the {@link GeneAssociation} annotation object to be added to the list of GeneAssociations. 679 <p> 680 * <p> 681 * @return integer value indicating success/failure of the 682 * function. The possible values 683 * returned by this function are: 684 * <ul> 685 * <li> {@link libsbmlConstants#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS} 686 * </ul> 687 */ public 688 int addGeneAssociation(GeneAssociation association) { 689 return libsbmlJNI.FbcModelPlugin_addGeneAssociation(swigCPtr, this, GeneAssociation.getCPtr(association), association); 690 } 691 692 693/** 694 * Creates a new {@link GeneAssociation} annotation object and adds it to the list of {@link GeneAssociation} objects 695 * and returns it. 696 <p> 697 * @return a newly created {@link GeneAssociation} annotation object 698 */ public 699 GeneAssociation createGeneAssociation() { 700 long cPtr = libsbmlJNI.FbcModelPlugin_createGeneAssociation(swigCPtr, this); 701 return (cPtr == 0) ? null : new GeneAssociation(cPtr, false); 702 } 703 704 705/** 706 * Removes the nth {@link GeneAssociation} annotation object from this plugin object and 707 * returns a pointer to it. 708 <p> 709 * The caller owns the returned object and is responsible for 710 * deleting it. 711 <p> 712 * @param n the index of the {@link GeneAssociation} annotation object to remove 713 <p> 714 * @return the {@link GeneAssociation} annotation object removed. As mentioned above, the 715 * caller owns the returned object. <code>null</code> is returned if the 716 * given index is out of range. 717 */ public 718 GeneAssociation removeGeneAssociation(long n) { 719 long cPtr = libsbmlJNI.FbcModelPlugin_removeGeneAssociation__SWIG_0(swigCPtr, this, n); 720 return (cPtr == 0) ? null : new GeneAssociation(cPtr, false); 721 } 722 723 724/** 725 * Removes the {@link GeneAssociation} annotation object with the given <code>sid</code> attribute from 726 * this plugin object and returns a pointer to it. 727 <p> 728 * The caller owns the returned object and is responsible for 729 * deleting it. 730 <p> 731 * @param sid the id attribute of the {@link GeneAssociation} annotation object to remove 732 <p> 733 * @return the {@link GeneAssociation} annotation object removed. As mentioned above, the 734 * caller owns the returned object. <code>null</code> is returned if the 735 * given index is out of range. 736 */ public 737 GeneAssociation removeGeneAssociation(String sid) { 738 long cPtr = libsbmlJNI.FbcModelPlugin_removeGeneAssociation__SWIG_1(swigCPtr, this, sid); 739 return (cPtr == 0) ? null : new GeneAssociation(cPtr, false); 740 } 741 742 743/** 744 * Returns the number of {@link GeneAssociation} annotation object in this plugin object. 745 <p> 746 * @return the number of {@link GeneAssociation} annotation object in this plugin object. 747 */ public 748 int getNumGeneAssociations() { 749 return libsbmlJNI.FbcModelPlugin_getNumGeneAssociations(swigCPtr, this); 750 } 751 752 753/** * @internal */ public 754 void connectToChild() { 755 libsbmlJNI.FbcModelPlugin_connectToChild(swigCPtr, this); 756 } 757 758 759/** * @internal */ public 760 void connectToParent(SBase sbase) { 761 libsbmlJNI.FbcModelPlugin_connectToParent(swigCPtr, this, SBase.getCPtr(sbase), sbase); 762 } 763 764 765/** * @internal */ public 766 void enablePackageInternal(String pkgURI, String pkgPrefix, boolean flag) { 767 libsbmlJNI.FbcModelPlugin_enablePackageInternal(swigCPtr, this, pkgURI, pkgPrefix, flag); 768 } 769 770}