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 The output from a {@link QualitativeSpecies}. 015 <p> 016 * Each {@link Output} refers to a {@link QualitativeSpecies} that participates in (is 017 * affected by) the corresponding {@link Transition}. In Petri net models these are 018 * the output places of the transition. 019 <p> 020 * In a logical model, a {@link QualitativeSpecies} should be referenced in at most 021 * one {@link ListOfOutputs}, (that of the {@link Transition} defining the evolution of this 022 * species). When a {@link Transition} has several outputs, it is because the 023 * referenced species share the same regulators and the same logical rules. 024 */ 025 026public class Output extends SBase { 027 private long swigCPtr; 028 029 protected Output(long cPtr, boolean cMemoryOwn) 030 { 031 super(libsbmlJNI.Output_SWIGUpcast(cPtr), cMemoryOwn); 032 swigCPtr = cPtr; 033 } 034 035 protected static long getCPtr(Output obj) 036 { 037 return (obj == null) ? 0 : obj.swigCPtr; 038 } 039 040 protected static long getCPtrAndDisown (Output obj) 041 { 042 long ptr = 0; 043 044 if (obj != null) 045 { 046 ptr = obj.swigCPtr; 047 obj.swigCMemOwn = false; 048 } 049 050 return ptr; 051 } 052 053 protected void finalize() { 054 delete(); 055 } 056 057 public synchronized void delete() { 058 if (swigCPtr != 0) { 059 if (swigCMemOwn) { 060 swigCMemOwn = false; 061 libsbmlJNI.delete_Output(swigCPtr); 062 } 063 swigCPtr = 0; 064 } 065 super.delete(); 066 } 067 068 069/** 070 * Creates a new {@link Output} with the given level, version, and package version. 071 <p> 072 * @param level a long integer, the SBML Level to assign to this {@link Output} 073 <p> 074 * @param version a long integer, the SBML Version to assign to this {@link Output} 075 <p> 076 * @param pkgVersion a long integer, the SBML Qual Version to assign to this {@link Output} 077 */ public 078 Output(long level, long version, long pkgVersion) throws org.sbml.libsbml.SBMLConstructorException { 079 this(libsbmlJNI.new_Output__SWIG_0(level, version, pkgVersion), true); 080 } 081 082 083/** 084 * Creates a new {@link Output} with the given level, version, and package version. 085 <p> 086 * @param level a long integer, the SBML Level to assign to this {@link Output} 087 <p> 088 * @param version a long integer, the SBML Version to assign to this {@link Output} 089 <p> 090 * @param pkgVersion a long integer, the SBML Qual Version to assign to this {@link Output} 091 */ public 092 Output(long level, long version) throws org.sbml.libsbml.SBMLConstructorException { 093 this(libsbmlJNI.new_Output__SWIG_1(level, version), true); 094 } 095 096 097/** 098 * Creates a new {@link Output} with the given level, version, and package version. 099 <p> 100 * @param level a long integer, the SBML Level to assign to this {@link Output} 101 <p> 102 * @param version a long integer, the SBML Version to assign to this {@link Output} 103 <p> 104 * @param pkgVersion a long integer, the SBML Qual Version to assign to this {@link Output} 105 */ public 106 Output(long level) throws org.sbml.libsbml.SBMLConstructorException { 107 this(libsbmlJNI.new_Output__SWIG_2(level), true); 108 } 109 110 111/** 112 * Creates a new {@link Output} with the given level, version, and package version. 113 <p> 114 * @param level a long integer, the SBML Level to assign to this {@link Output} 115 <p> 116 * @param version a long integer, the SBML Version to assign to this {@link Output} 117 <p> 118 * @param pkgVersion a long integer, the SBML Qual Version to assign to this {@link Output} 119 */ public 120 Output() throws org.sbml.libsbml.SBMLConstructorException { 121 this(libsbmlJNI.new_Output__SWIG_3(), true); 122 } 123 124 125/** 126 * Creates a new {@link Output} with the given {@link QualPkgNamespaces} object. 127 <p> 128 * @param qualns the {@link QualPkgNamespaces} object 129 */ public 130 Output(QualPkgNamespaces qualns) throws org.sbml.libsbml.SBMLConstructorException { 131 this(libsbmlJNI.new_Output__SWIG_4(QualPkgNamespaces.getCPtr(qualns), qualns), true); 132 } 133 134 135/** 136 * Copy constructor for {@link Output}. 137 <p> 138 * @param orig the {@link Output} instance to copy. 139 */ public 140 Output(Output orig) throws org.sbml.libsbml.SBMLConstructorException { 141 this(libsbmlJNI.new_Output__SWIG_5(Output.getCPtr(orig), orig), true); 142 } 143 144 145/** 146 * Creates and returns a deep copy of this {@link Output} object. 147 <p> 148 * @return a (deep) copy of this {@link Output} object. 149 */ public 150 Output cloneObject() { 151 long cPtr = libsbmlJNI.Output_cloneObject(swigCPtr, this); 152 return (cPtr == 0) ? null : new Output(cPtr, true); 153 } 154 155 156/** 157 * Returns the value of the 'id' attribute of this {@link Output}. 158 <p> 159 * @return the value of the 'id' attribute of this {@link Output} as a string. 160 */ public 161 String getId() { 162 return libsbmlJNI.Output_getId(swigCPtr, this); 163 } 164 165 166/** 167 * Returns the value of the 'qualitativeSpecies' attribute of this {@link Output}. 168 <p> 169 * @return the value of the 'qualitativeSpecies' attribute of this {@link Output} as a string. 170 */ public 171 String getQualitativeSpecies() { 172 return libsbmlJNI.Output_getQualitativeSpecies(swigCPtr, this); 173 } 174 175 176/** 177 * Returns the value of the 'transitionEffect' attribute of this {@link Output}. 178 <p> 179 * @return the value of the 'transitionEffect' attribute of this {@link Output} as a string. 180 */ public 181 int getTransitionEffect() { 182 return libsbmlJNI.Output_getTransitionEffect(swigCPtr, this); 183 } 184 185 186/** 187 * Returns the value of the 'name' attribute of this {@link Output}. 188 <p> 189 * @return the value of the 'name' attribute of this {@link Output} as a string. 190 */ public 191 String getName() { 192 return libsbmlJNI.Output_getName(swigCPtr, this); 193 } 194 195 196/** 197 * Returns the value of the 'outputLevel' attribute of this {@link Output}. 198 <p> 199 * @return the value of the 'outputLevel' attribute of this {@link Output} as a integer. 200 */ public 201 int getOutputLevel() { 202 return libsbmlJNI.Output_getOutputLevel(swigCPtr, this); 203 } 204 205 206/** 207 * Predicate returning <code>true</code> or <code>false</code> depending on whether this 208 * {@link Output}'s 'id' attribute has been set. 209 <p> 210 * @return <code>true</code> if this {@link Output}'s 'id' attribute has been set, 211 * otherwise <code>false</code> is returned. 212 */ public 213 boolean isSetId() { 214 return libsbmlJNI.Output_isSetId(swigCPtr, this); 215 } 216 217 218/** 219 * Predicate returning <code>true</code> or <code>false</code> depending on whether this 220 * {@link Output}'s 'qualitativeSpecies' attribute has been set. 221 <p> 222 * @return <code>true</code> if this {@link Output}'s 'qualitativeSpecies' attribute has been set, 223 * otherwise <code>false</code> is returned. 224 */ public 225 boolean isSetQualitativeSpecies() { 226 return libsbmlJNI.Output_isSetQualitativeSpecies(swigCPtr, this); 227 } 228 229 230/** 231 * Predicate returning <code>true</code> or <code>false</code> depending on whether this 232 * {@link Output}'s 'transitionEffect' attribute has been set. 233 <p> 234 * @return <code>true</code> if this {@link Output}'s 'transitionEffect' attribute has been set, 235 * otherwise <code>false</code> is returned. 236 */ public 237 boolean isSetTransitionEffect() { 238 return libsbmlJNI.Output_isSetTransitionEffect(swigCPtr, this); 239 } 240 241 242/** 243 * Predicate returning <code>true</code> or <code>false</code> depending on whether this 244 * {@link Output}'s 'name' attribute has been set. 245 <p> 246 * @return <code>true</code> if this {@link Output}'s 'name' attribute has been set, 247 * otherwise <code>false</code> is returned. 248 */ public 249 boolean isSetName() { 250 return libsbmlJNI.Output_isSetName(swigCPtr, this); 251 } 252 253 254/** 255 * Predicate returning <code>true</code> or <code>false</code> depending on whether this 256 * {@link Output}'s 'outputLevel' attribute has been set. 257 <p> 258 * @return <code>true</code> if this {@link Output}'s 'outputLevel' attribute has been set, 259 * otherwise <code>false</code> is returned. 260 */ public 261 boolean isSetOutputLevel() { 262 return libsbmlJNI.Output_isSetOutputLevel(swigCPtr, this); 263 } 264 265 266/** 267 * Sets the value of the 'id' attribute of this {@link Output}. 268 <p> 269 * @param id String value of the 'id' attribute to be set 270 <p> 271 * <p> 272 * @return integer value indicating success/failure of the 273 * function. The possible values 274 * returned by this function are: 275 * <ul> 276 * <li> {@link libsbmlConstants#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS} 277 * <li> {@link libsbmlConstants#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE} 278 * </ul> 279 */ public 280 int setId(String id) { 281 return libsbmlJNI.Output_setId(swigCPtr, this, id); 282 } 283 284 285/** 286 * Sets the value of the 'qualitativeSpecies' attribute of this {@link Output}. 287 <p> 288 * @param qualitativeSpecies String value of the 'qualitativeSpecies' attribute to be set 289 <p> 290 * <p> 291 * @return integer value indicating success/failure of the 292 * function. The possible values 293 * returned by this function are: 294 * <ul> 295 * <li> {@link libsbmlConstants#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS} 296 * <li> {@link libsbmlConstants#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE} 297 * </ul> 298 */ public 299 int setQualitativeSpecies(String qualitativeSpecies) { 300 return libsbmlJNI.Output_setQualitativeSpecies(swigCPtr, this, qualitativeSpecies); 301 } 302 303 304/** 305 * Sets the value of the 'transitionEffect' attribute of this {@link Output}. 306 <p> 307 * @param transitionEffect String value of the 'transitionEffect' attribute to be set 308 <p> 309 * <p> 310 * @return integer value indicating success/failure of the 311 * function. The possible values 312 * returned by this function are: 313 * <ul> 314 * <li> {@link libsbmlConstants#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS} 315 * <li> {@link libsbmlConstants#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE} 316 * </ul> 317 */ public 318 int setTransitionEffect(int transitionEffect) { 319 return libsbmlJNI.Output_setTransitionEffect(swigCPtr, this, transitionEffect); 320 } 321 322 323/** 324 * Sets the value of the 'name' attribute of this {@link Output}. 325 <p> 326 * @param name String value of the 'name' attribute to be set 327 <p> 328 * <p> 329 * @return integer value indicating success/failure of the 330 * function. The possible values 331 * returned by this function are: 332 * <ul> 333 * <li> {@link libsbmlConstants#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS} 334 * <li> {@link libsbmlConstants#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE} 335 * </ul> 336 */ public 337 int setName(String name) { 338 return libsbmlJNI.Output_setName(swigCPtr, this, name); 339 } 340 341 342/** 343 * Sets the value of the 'outputLevel' attribute of this {@link Output}. 344 <p> 345 * @param outputLevel int value of the 'outputLevel' attribute to be set 346 <p> 347 * <p> 348 * @return integer value indicating success/failure of the 349 * function. The possible values 350 * returned by this function are: 351 * <ul> 352 * <li> {@link libsbmlConstants#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS} 353 * <li> {@link libsbmlConstants#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE} 354 * </ul> 355 */ public 356 int setOutputLevel(int outputLevel) { 357 return libsbmlJNI.Output_setOutputLevel(swigCPtr, this, outputLevel); 358 } 359 360 361/** 362 * Unsets the value of the 'id' attribute of this {@link Output}. 363 <p> 364 * <p> 365 * @return integer value indicating success/failure of the 366 * function. The possible values 367 * returned by this function are: 368 * <ul> 369 * <li> {@link libsbmlConstants#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS} 370 * <li> {@link libsbmlConstants#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED} 371 * </ul> 372 */ public 373 int unsetId() { 374 return libsbmlJNI.Output_unsetId(swigCPtr, this); 375 } 376 377 378/** 379 * Unsets the value of the 'qualitativeSpecies' attribute of this {@link Output}. 380 <p> 381 * <p> 382 * @return integer value indicating success/failure of the 383 * function. The possible values 384 * returned by this function are: 385 * <ul> 386 * <li> {@link libsbmlConstants#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS} 387 * <li> {@link libsbmlConstants#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED} 388 * </ul> 389 */ public 390 int unsetQualitativeSpecies() { 391 return libsbmlJNI.Output_unsetQualitativeSpecies(swigCPtr, this); 392 } 393 394 395/** 396 * Unsets the value of the 'transitionEffect' attribute of this {@link Output}. 397 <p> 398 * <p> 399 * @return integer value indicating success/failure of the 400 * function. The possible values 401 * returned by this function are: 402 * <ul> 403 * <li> {@link libsbmlConstants#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS} 404 * <li> {@link libsbmlConstants#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED} 405 * </ul> 406 */ public 407 int unsetTransitionEffect() { 408 return libsbmlJNI.Output_unsetTransitionEffect(swigCPtr, this); 409 } 410 411 412/** 413 * Unsets the value of the 'name' attribute of this {@link Output}. 414 <p> 415 * <p> 416 * @return integer value indicating success/failure of the 417 * function. The possible values 418 * returned by this function are: 419 * <ul> 420 * <li> {@link libsbmlConstants#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS} 421 * <li> {@link libsbmlConstants#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED} 422 * </ul> 423 */ public 424 int unsetName() { 425 return libsbmlJNI.Output_unsetName(swigCPtr, this); 426 } 427 428 429/** 430 * Unsets the value of the 'outputLevel' attribute of this {@link Output}. 431 <p> 432 * <p> 433 * @return integer value indicating success/failure of the 434 * function. The possible values 435 * returned by this function are: 436 * <ul> 437 * <li> {@link libsbmlConstants#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS} 438 * <li> {@link libsbmlConstants#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED} 439 * </ul> 440 */ public 441 int unsetOutputLevel() { 442 return libsbmlJNI.Output_unsetOutputLevel(swigCPtr, this); 443 } 444 445 446/** 447 * <p> 448 * Replaces all uses of a given <code>SIdRef</code> type attribute value with another 449 * value. 450 <p> 451 * <p> 452 * In SBML, object identifiers are of a data type called <code>SId</code>. 453 * In SBML Level 3, an explicit data type called <code>SIdRef</code> was 454 * introduced for attribute values that refer to <code>SId</code> values; in 455 * previous Levels of SBML, this data type did not exist and attributes were 456 * simply described to as 'referring to an identifier', but the effective 457 * data type was the same as <code>SIdRef</code>in Level 3. These and 458 * other methods of libSBML refer to the type <code>SIdRef</code> for all 459 * Levels of SBML, even if the corresponding SBML specification did not 460 * explicitly name the data type. 461 <p> 462 * This method works by looking at all attributes and (if appropriate) 463 * mathematical formulas in MathML content, comparing the referenced 464 * identifiers to the value of <code>oldid</code>. If any matches are found, the 465 * matching values are replaced with <code>newid</code>. The method does <em>not</em> 466 * descend into child elements. 467 <p> 468 * @param oldid the old identifier 469 * @param newid the new identifier 470 */ public 471 void renameSIdRefs(String oldid, String newid) { 472 libsbmlJNI.Output_renameSIdRefs(swigCPtr, this, oldid, newid); 473 } 474 475 476/** 477 * Returns the XML name of this object. 478 <p> 479 * @return the name of this element. 480 */ public 481 String getElementName() { 482 return libsbmlJNI.Output_getElementName(swigCPtr, this); 483 } 484 485 486/** 487 * Returns the libSBML type code of this object instance. 488 <p> 489 * <p> 490 * LibSBML attaches an identifying code to every kind of SBML object. These 491 * are integer constants known as <em>SBML type codes</em>. The names of all 492 * the codes begin with the characters <code>SBML_</code>. 493 * In the Java language interface for libSBML, the 494 * type codes are defined as static integer constants in the interface class 495 * {@link libsbmlConstants}. Note that different Level 3 496 * package plug-ins may use overlapping type codes; to identify the package 497 * to which a given object belongs, call the <code>getPackageName()</code> 498 * method on the object. 499 <p> 500 * @return the SBML type code for this object: 501 * {@link libsbmlConstants#SBML_QUAL_OUTPUT SBML_QUAL_OUTPUT} 502 <p> 503 * <p> 504 * @warning <span class='warning'>The specific integer values of the possible 505 * type codes may be reused by different libSBML plug-ins for SBML Level 3. 506 * packages, To fully identify the correct code, <strong>it is necessary to 507 * invoke both getTypeCode() and getPackageName()</strong>.</span> 508 <p> 509 * @see #getElementName() 510 * @see #getPackageName() 511 */ public 512 int getTypeCode() { 513 return libsbmlJNI.Output_getTypeCode(swigCPtr, this); 514 } 515 516 517/** 518 * Predicate returning <code>true</code> if all the required attributes 519 * for this {@link Output} object have been set. 520 <p> 521 * @note The required attributes for a {@link Output} object are: 522 * <ul> 523 * <li> 'qualitativeSpecies' 524 * <li> 'transitionEffect' 525 * 526 * </ul> <p> 527 * @return a boolean value indicating whether all the required 528 * attributes for this object have been defined. 529 */ public 530 boolean hasRequiredAttributes() { 531 return libsbmlJNI.Output_hasRequiredAttributes(swigCPtr, this); 532 } 533 534 535/** * @internal */ public 536 void enablePackageInternal(String pkgURI, String pkgPrefix, boolean flag) { 537 libsbmlJNI.Output_enablePackageInternal(swigCPtr, this, pkgURI, pkgPrefix, flag); 538 } 539 540}