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 A list of {@link Transition} objects. 015 <p> 016 * The {@link ListOfTransitions} is a container for the {@link Transition} elements of a {@link Model}. 017 <p> 018 * <p> 019 * The various ListOf___ classes in SBML 020 * are merely containers used for organizing the main components of an SBML 021 * model. In libSBML's implementation, ListOf___ 022 * classes are derived from the 023 * intermediate utility class {@link ListOf}, which 024 * is not defined by the SBML specifications but serves as a useful 025 * programmatic construct. {@link ListOf} is itself is in turn derived from {@link SBase}, 026 * which provides all of the various ListOf___ 027 * classes with common features 028 * defined by the SBML specification, such as 'metaid' attributes and 029 * annotations. 030 <p> 031 * The relationship between the lists and the rest of an SBML model is 032 * illustrated by the following (for SBML Level 2 Version 4): 033 <p> 034 * <figure> 035 <object type="image/svg+xml" data="listof-illustration.svg" class="centered"></object> 036</figure> 037 038 <p> 039 * SBML Level 3 Version 1 has essentially the same structure as 040 * Level 2 Version 4, depicted above, but SBML Level 3 041 * Version 2 allows 042 * containers to contain zero or more of the relevant object, instead of 043 * requiring at least one. As such, libsbml will write out an 044 * otherwise-empty ListOf___ element that has any optional attribute set 045 * (such as 'id' or 'metaid'), that has an optional child (such 046 * as a 'notes' or 'annotation'), or that has attributes or children set 047 * from any SBML Level 3 package, whether or not the ListOf___ has 048 * any other children. 049 <p> 050 * Readers may wonder about the motivations for using the ListOf___ 051 * containers in SBML. A simpler approach in XML might be to place the 052 * components all directly at the top level of the model definition. The 053 * choice made in SBML is to group them within XML elements named after 054 * ListOf<em>Classname</em>, in part because it helps organize the 055 * components. More importantly, the fact that the container classes are 056 * derived from {@link SBase} means that software tools can add information <em>about</em> 057 * the lists themselves into each list container's 'annotation'. 058 <p> 059 * @see ListOfFunctionDefinitions 060 * @see ListOfUnitDefinitions 061 * @see ListOfCompartmentTypes 062 * @see ListOfSpeciesTypes 063 * @see ListOfCompartments 064 * @see ListOfSpecies 065 * @see ListOfParameters 066 * @see ListOfInitialAssignments 067 * @see ListOfRules 068 * @see ListOfConstraints 069 * @see ListOfReactions 070 * @see ListOfEvents 071 <p> 072 * @see Transition 073 */ 074 075public class ListOfTransitions extends ListOf { 076 private long swigCPtr; 077 078 protected ListOfTransitions(long cPtr, boolean cMemoryOwn) 079 { 080 super(libsbmlJNI.ListOfTransitions_SWIGUpcast(cPtr), cMemoryOwn); 081 swigCPtr = cPtr; 082 } 083 084 protected static long getCPtr(ListOfTransitions obj) 085 { 086 return (obj == null) ? 0 : obj.swigCPtr; 087 } 088 089 protected static long getCPtrAndDisown (ListOfTransitions obj) 090 { 091 long ptr = 0; 092 093 if (obj != null) 094 { 095 ptr = obj.swigCPtr; 096 obj.swigCMemOwn = false; 097 } 098 099 return ptr; 100 } 101 102 protected void finalize() { 103 delete(); 104 } 105 106 public synchronized void delete() { 107 if (swigCPtr != 0) { 108 if (swigCMemOwn) { 109 swigCMemOwn = false; 110 libsbmlJNI.delete_ListOfTransitions(swigCPtr); 111 } 112 swigCPtr = 0; 113 } 114 super.delete(); 115 } 116 117 118/** 119 * Creates a new {@link ListOfTransitions} with the given level, version, and package version. 120 <p> 121 * @param level a long integer, the SBML Level to assign to this {@link ListOfTransitions}. 122 <p> 123 * @param version a long integer, the SBML Version to assign to this {@link ListOfTransitions}. 124 <p> 125 * @param pkgVersion a long integer, the SBML Qual Version to assign to this {@link ListOfTransitions}. 126 <p> 127 * <p> 128 * @note Attempting to add an object to an {@link SBMLDocument} having a different 129 * combination of SBML Level, Version and XML namespaces than the object 130 * itself will result in an error at the time a caller attempts to make the 131 * addition. A parent object must have compatible Level, Version and XML 132 * namespaces. (Strictly speaking, a parent may also have more XML 133 * namespaces than a child, but the reverse is not permitted.) The 134 * restriction is necessary to ensure that an SBML model has a consistent 135 * overall structure. This requires callers to manage their objects 136 * carefully, but the benefit is increased flexibility in how models can be 137 * created by permitting callers to create objects bottom-up if desired. In 138 * situations where objects are not yet attached to parents (e.g., 139 * {@link SBMLDocument}), knowledge of the intented SBML Level and Version help 140 * libSBML determine such things as whether it is valid to assign a 141 * particular value to an attribute. For packages, this means that the 142 * parent object to which this package element is being added must have 143 * been created with the package namespace, or that the package namespace 144 * was added to it, even if that parent is not a package object itself. 145 */ public 146 ListOfTransitions(long level, long version, long pkgVersion) throws org.sbml.libsbml.SBMLConstructorException { 147 this(libsbmlJNI.new_ListOfTransitions__SWIG_0(level, version, pkgVersion), true); 148 } 149 150 151/** 152 * Creates a new {@link ListOfTransitions} with the given level, version, and package version. 153 <p> 154 * @param level a long integer, the SBML Level to assign to this {@link ListOfTransitions}. 155 <p> 156 * @param version a long integer, the SBML Version to assign to this {@link ListOfTransitions}. 157 <p> 158 * @param pkgVersion a long integer, the SBML Qual Version to assign to this {@link ListOfTransitions}. 159 <p> 160 * <p> 161 * @note Attempting to add an object to an {@link SBMLDocument} having a different 162 * combination of SBML Level, Version and XML namespaces than the object 163 * itself will result in an error at the time a caller attempts to make the 164 * addition. A parent object must have compatible Level, Version and XML 165 * namespaces. (Strictly speaking, a parent may also have more XML 166 * namespaces than a child, but the reverse is not permitted.) The 167 * restriction is necessary to ensure that an SBML model has a consistent 168 * overall structure. This requires callers to manage their objects 169 * carefully, but the benefit is increased flexibility in how models can be 170 * created by permitting callers to create objects bottom-up if desired. In 171 * situations where objects are not yet attached to parents (e.g., 172 * {@link SBMLDocument}), knowledge of the intented SBML Level and Version help 173 * libSBML determine such things as whether it is valid to assign a 174 * particular value to an attribute. For packages, this means that the 175 * parent object to which this package element is being added must have 176 * been created with the package namespace, or that the package namespace 177 * was added to it, even if that parent is not a package object itself. 178 */ public 179 ListOfTransitions(long level, long version) throws org.sbml.libsbml.SBMLConstructorException { 180 this(libsbmlJNI.new_ListOfTransitions__SWIG_1(level, version), true); 181 } 182 183 184/** 185 * Creates a new {@link ListOfTransitions} with the given level, version, and package version. 186 <p> 187 * @param level a long integer, the SBML Level to assign to this {@link ListOfTransitions}. 188 <p> 189 * @param version a long integer, the SBML Version to assign to this {@link ListOfTransitions}. 190 <p> 191 * @param pkgVersion a long integer, the SBML Qual Version to assign to this {@link ListOfTransitions}. 192 <p> 193 * <p> 194 * @note Attempting to add an object to an {@link SBMLDocument} having a different 195 * combination of SBML Level, Version and XML namespaces than the object 196 * itself will result in an error at the time a caller attempts to make the 197 * addition. A parent object must have compatible Level, Version and XML 198 * namespaces. (Strictly speaking, a parent may also have more XML 199 * namespaces than a child, but the reverse is not permitted.) The 200 * restriction is necessary to ensure that an SBML model has a consistent 201 * overall structure. This requires callers to manage their objects 202 * carefully, but the benefit is increased flexibility in how models can be 203 * created by permitting callers to create objects bottom-up if desired. In 204 * situations where objects are not yet attached to parents (e.g., 205 * {@link SBMLDocument}), knowledge of the intented SBML Level and Version help 206 * libSBML determine such things as whether it is valid to assign a 207 * particular value to an attribute. For packages, this means that the 208 * parent object to which this package element is being added must have 209 * been created with the package namespace, or that the package namespace 210 * was added to it, even if that parent is not a package object itself. 211 */ public 212 ListOfTransitions(long level) throws org.sbml.libsbml.SBMLConstructorException { 213 this(libsbmlJNI.new_ListOfTransitions__SWIG_2(level), true); 214 } 215 216 217/** 218 * Creates a new {@link ListOfTransitions} with the given level, version, and package version. 219 <p> 220 * @param level a long integer, the SBML Level to assign to this {@link ListOfTransitions}. 221 <p> 222 * @param version a long integer, the SBML Version to assign to this {@link ListOfTransitions}. 223 <p> 224 * @param pkgVersion a long integer, the SBML Qual Version to assign to this {@link ListOfTransitions}. 225 <p> 226 * <p> 227 * @note Attempting to add an object to an {@link SBMLDocument} having a different 228 * combination of SBML Level, Version and XML namespaces than the object 229 * itself will result in an error at the time a caller attempts to make the 230 * addition. A parent object must have compatible Level, Version and XML 231 * namespaces. (Strictly speaking, a parent may also have more XML 232 * namespaces than a child, but the reverse is not permitted.) The 233 * restriction is necessary to ensure that an SBML model has a consistent 234 * overall structure. This requires callers to manage their objects 235 * carefully, but the benefit is increased flexibility in how models can be 236 * created by permitting callers to create objects bottom-up if desired. In 237 * situations where objects are not yet attached to parents (e.g., 238 * {@link SBMLDocument}), knowledge of the intented SBML Level and Version help 239 * libSBML determine such things as whether it is valid to assign a 240 * particular value to an attribute. For packages, this means that the 241 * parent object to which this package element is being added must have 242 * been created with the package namespace, or that the package namespace 243 * was added to it, even if that parent is not a package object itself. 244 */ public 245 ListOfTransitions() throws org.sbml.libsbml.SBMLConstructorException { 246 this(libsbmlJNI.new_ListOfTransitions__SWIG_3(), true); 247 } 248 249 250/** 251 * Creates a new {@link ListOfTransitions} with the given {@link QualPkgNamespaces} object. 252 <p> 253 * <p> 254 * The package namespaces object used in this constructor is derived from a 255 * {@link SBMLNamespaces} object, which encapsulates SBML Level/Version/namespaces 256 * information. It is used to communicate the SBML Level, Version, and 257 * package version and name information used in addition to SBML Level 3 Core. A 258 * common approach to using libSBML's {@link SBMLNamespaces} facilities is to create an 259 * package namespace object somewhere in a program once, then hand that object 260 * as needed to object constructors of that package that accept it as and 261 * argument, such as this one. 262 <p> 263 * @param qualns the {@link QualPkgNamespaces} object. 264 <p> 265 * <p> 266 * @note Attempting to add an object to an {@link SBMLDocument} having a different 267 * combination of SBML Level, Version and XML namespaces than the object 268 * itself will result in an error at the time a caller attempts to make the 269 * addition. A parent object must have compatible Level, Version and XML 270 * namespaces. (Strictly speaking, a parent may also have more XML 271 * namespaces than a child, but the reverse is not permitted.) The 272 * restriction is necessary to ensure that an SBML model has a consistent 273 * overall structure. This requires callers to manage their objects 274 * carefully, but the benefit is increased flexibility in how models can be 275 * created by permitting callers to create objects bottom-up if desired. In 276 * situations where objects are not yet attached to parents (e.g., 277 * {@link SBMLDocument}), knowledge of the intented SBML Level and Version help 278 * libSBML determine such things as whether it is valid to assign a 279 * particular value to an attribute. For packages, this means that the 280 * parent object to which this package element is being added must have 281 * been created with the package namespace, or that the package namespace 282 * was added to it, even if that parent is not a package object itself. 283 */ public 284 ListOfTransitions(QualPkgNamespaces qualns) throws org.sbml.libsbml.SBMLConstructorException { 285 this(libsbmlJNI.new_ListOfTransitions__SWIG_4(QualPkgNamespaces.getCPtr(qualns), qualns), true); 286 } 287 288 289/** 290 * Creates and returns a deep copy of this {@link ListOfTransitions} object. 291 <p> 292 * @return a (deep) copy of this {@link ListOfTransitions} object. 293 */ public 294 ListOfTransitions cloneObject() { 295 long cPtr = libsbmlJNI.ListOfTransitions_cloneObject(swigCPtr, this); 296 return (cPtr == 0) ? null : new ListOfTransitions(cPtr, true); 297 } 298 299 300/** 301 * Get a {@link Transition} from the {@link ListOfTransitions}. 302 <p> 303 * @param n the index number of the {@link Transition} to get. 304 <p> 305 * @return the nth {@link Transition} in this {@link ListOfTransitions}. 306 <p> 307 * @see #size() 308 */ public 309 Transition get(long n) { 310 long cPtr = libsbmlJNI.ListOfTransitions_get__SWIG_0(swigCPtr, this, n); 311 return (cPtr == 0) ? null : new Transition(cPtr, false); 312 } 313 314 315/** 316 * Get a {@link Transition} from the {@link ListOfTransitions} 317 * based on its identifier. 318 <p> 319 * @param sid a string representing the identifier 320 * of the {@link Transition} to get. 321 <p> 322 * @return {@link Transition} in this {@link ListOfTransitions} 323 * with the given id or null if no such 324 * {@link Transition} exists. 325 <p> 326 * @see #get(long n) * 327 * @see #size() 328 */ public 329 Transition get(String sid) { 330 long cPtr = libsbmlJNI.ListOfTransitions_get__SWIG_2(swigCPtr, this, sid); 331 return (cPtr == 0) ? null : new Transition(cPtr, false); 332 } 333 334 335/** 336 * Removes the nth {@link Transition} from this {@link ListOfTransitions} 337 * and returns a pointer to it. 338 <p> 339 * The caller owns the returned item and is responsible for deleting it. 340 <p> 341 * @param n the index of the {@link Transition} to remove. 342 <p> 343 * @see #size() 344 */ public 345 Transition remove(long n) { 346 long cPtr = libsbmlJNI.ListOfTransitions_remove__SWIG_0(swigCPtr, this, n); 347 return (cPtr == 0) ? null : new Transition(cPtr, true); 348 } 349 350 351/** 352 * Removes the {@link Transition} from this {@link ListOfTransitions} with the given identifier 353 * and returns a pointer to it. 354 <p> 355 * The caller owns the returned item and is responsible for deleting it. 356 * If none of the items in this list have the identifier <code>sid</code>, then 357 * <code>null</code> is returned. 358 <p> 359 * @param sid the identifier of the {@link Transition} to remove. 360 <p> 361 * @return the {@link Transition} removed. As mentioned above, the caller owns the 362 * returned item. 363 */ public 364 Transition remove(String sid) { 365 long cPtr = libsbmlJNI.ListOfTransitions_remove__SWIG_1(swigCPtr, this, sid); 366 return (cPtr == 0) ? null : new Transition(cPtr, true); 367 } 368 369 370/** 371 * Returns the XML name of this object. 372 <p> 373 * @return the name of this element. 374 */ public 375 String getElementName() { 376 return libsbmlJNI.ListOfTransitions_getElementName(swigCPtr, this); 377 } 378 379 380/** 381 * Returns the libSBML type code for the SBML objects 382 * contained in this {@link ListOf} object. 383 <p> 384 * <p> 385 * LibSBML attaches an identifying code to every kind of SBML object. These 386 * are integer constants known as <em>SBML type codes</em>. The names of all 387 * the codes begin with the characters <code>SBML_</code>. 388 * In the Java language interface for libSBML, the 389 * type codes are defined as static integer constants in the interface class 390 * {@link libsbmlConstants}. Note that different Level 3 391 * package plug-ins may use overlapping type codes; to identify the package 392 * to which a given object belongs, call the <code>getPackageName()</code> 393 * method on the object. 394 <p> 395 * @return the SBML type code for objects contained in this list: 396 * {@link libsbmlConstants#SBML_QUAL_TRANSITION SBML_QUAL_TRANSITION} (default). 397 <p> 398 * @see #getElementName() 399 * @see #getPackageName() 400 */ public 401 int getItemTypeCode() { 402 return libsbmlJNI.ListOfTransitions_getItemTypeCode(swigCPtr, this); 403 } 404 405}