001/* ---------------------------------------------------------------------------- 002 * This file was automatically generated by SWIG (http://www.swig.org). 003 * Version 3.0.12 004 * 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 Input} objects. 015 <p> 016 * The {@link ListOfInputs} is a container for the Inputs of a {@link Transition}. 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 Input 073 */ 074 075public class ListOfInputs extends ListOf { 076 private long swigCPtr; 077 078 protected ListOfInputs(long cPtr, boolean cMemoryOwn) 079 { 080 super(libsbmlJNI.ListOfInputs_SWIGUpcast(cPtr), cMemoryOwn); 081 swigCPtr = cPtr; 082 } 083 084 protected static long getCPtr(ListOfInputs obj) 085 { 086 return (obj == null) ? 0 : obj.swigCPtr; 087 } 088 089 protected static long getCPtrAndDisown (ListOfInputs 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_ListOfInputs(swigCPtr); 111 } 112 swigCPtr = 0; 113 } 114 super.delete(); 115 } 116 117 118/** 119 * Creates a new {@link ListOfInputs} with the given level, version, and package version. 120 <p> 121 * @param level a long integer, the SBML Level to assign to this {@link ListOfInputs}. 122 <p> 123 * @param version a long integer, the SBML Version to assign to this {@link ListOfInputs}. 124 <p> 125 * @param pkgVersion a long integer, the SBML Qual Version to assign to this {@link ListOfInputs}. 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 ListOfInputs(long level, long version, long pkgVersion) throws org.sbml.libsbml.SBMLConstructorException { 147 this(libsbmlJNI.new_ListOfInputs__SWIG_0(level, version, pkgVersion), true); 148 } 149 150 151/** 152 * Creates a new {@link ListOfInputs} with the given level, version, and package version. 153 <p> 154 * @param level a long integer, the SBML Level to assign to this {@link ListOfInputs}. 155 <p> 156 * @param version a long integer, the SBML Version to assign to this {@link ListOfInputs}. 157 <p> 158 * @param pkgVersion a long integer, the SBML Qual Version to assign to this {@link ListOfInputs}. 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 ListOfInputs(long level, long version) throws org.sbml.libsbml.SBMLConstructorException { 180 this(libsbmlJNI.new_ListOfInputs__SWIG_1(level, version), true); 181 } 182 183 184/** 185 * Creates a new {@link ListOfInputs} with the given level, version, and package version. 186 <p> 187 * @param level a long integer, the SBML Level to assign to this {@link ListOfInputs}. 188 <p> 189 * @param version a long integer, the SBML Version to assign to this {@link ListOfInputs}. 190 <p> 191 * @param pkgVersion a long integer, the SBML Qual Version to assign to this {@link ListOfInputs}. 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 ListOfInputs(long level) throws org.sbml.libsbml.SBMLConstructorException { 213 this(libsbmlJNI.new_ListOfInputs__SWIG_2(level), true); 214 } 215 216 217/** 218 * Creates a new {@link ListOfInputs} with the given level, version, and package version. 219 <p> 220 * @param level a long integer, the SBML Level to assign to this {@link ListOfInputs}. 221 <p> 222 * @param version a long integer, the SBML Version to assign to this {@link ListOfInputs}. 223 <p> 224 * @param pkgVersion a long integer, the SBML Qual Version to assign to this {@link ListOfInputs}. 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 ListOfInputs() throws org.sbml.libsbml.SBMLConstructorException { 246 this(libsbmlJNI.new_ListOfInputs__SWIG_3(), true); 247 } 248 249 250/** 251 * Creates a new {@link ListOfInputs} 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 ListOfInputs(QualPkgNamespaces qualns) throws org.sbml.libsbml.SBMLConstructorException { 285 this(libsbmlJNI.new_ListOfInputs__SWIG_4(QualPkgNamespaces.getCPtr(qualns), qualns), true); 286 } 287 288 289/** 290 * Creates and returns a deep copy of this {@link ListOfInputs} object. 291 <p> 292 * @return a (deep) copy of this {@link ListOfInputs} object. 293 */ public 294 ListOfInputs cloneObject() { 295 long cPtr = libsbmlJNI.ListOfInputs_cloneObject(swigCPtr, this); 296 return (cPtr == 0) ? null : new ListOfInputs(cPtr, true); 297 } 298 299 300/** 301 * Get a {@link Input} from the {@link ListOfInputs}. 302 <p> 303 * @param n the index number of the {@link Input} to get. 304 <p> 305 * @return the nth {@link Input} in this {@link ListOfInputs}. 306 <p> 307 * @see #size() 308 */ public 309 Input get(long n) { 310 long cPtr = libsbmlJNI.ListOfInputs_get__SWIG_0(swigCPtr, this, n); 311 return (cPtr == 0) ? null : new Input(cPtr, false); 312 } 313 314 315/** 316 * Get a {@link Input} from the {@link ListOfInputs} 317 * based on its identifier. 318 <p> 319 * @param sid a string representing the identifier 320 * of the {@link Input} to get. 321 <p> 322 * @return {@link Input} in this {@link ListOfInputs} 323 * with the given id or <code>null</code> if no such 324 * {@link Input} exists. 325 <p> 326 * @see #get(long n) * 327 * @see #size() 328 */ public 329 Input get(String sid) { 330 long cPtr = libsbmlJNI.ListOfInputs_get__SWIG_2(swigCPtr, this, sid); 331 return (cPtr == 0) ? null : new Input(cPtr, false); 332 } 333 334 335/** 336 * Get a {@link Input} from the {@link ListOfInputs} 337 * based on the qualitativeSpecies to which it refers. 338 <p> 339 * @param sid a string representing the qualitativeSpecies attribute 340 * of the {@link Input} to get. 341 <p> 342 * @return the first {@link Input} in this {@link ListOfInputs} 343 * with the given qualitativeSpecies or <code>null</code> if no such 344 * {@link Input} exists. 345 <p> 346 * @see #get(long n) * 347 * @see #size() 348 */ public 349 Input getBySpecies(String sid) { 350 long cPtr = libsbmlJNI.ListOfInputs_getBySpecies__SWIG_0(swigCPtr, this, sid); 351 return (cPtr == 0) ? null : new Input(cPtr, false); 352 } 353 354 355/** 356 * Removes the nth {@link Input} from this {@link ListOfInputs} 357 * and returns a pointer to it. 358 <p> 359 * The caller owns the returned item and is responsible for deleting it. 360 <p> 361 * @param n the index of the {@link Input} to remove. 362 <p> 363 * @see #size() 364 */ public 365 Input remove(long n) { 366 long cPtr = libsbmlJNI.ListOfInputs_remove__SWIG_0(swigCPtr, this, n); 367 return (cPtr == 0) ? null : new Input(cPtr, true); 368 } 369 370 371/** 372 * Removes the {@link Input} from this {@link ListOfInputs} with the given identifier 373 * and returns a pointer to it. 374 <p> 375 * The caller owns the returned item and is responsible for deleting it. 376 * If none of the items in this list have the identifier <code>sid</code>, then 377 * <code>null</code> is returned. 378 <p> 379 * @param sid the identifier of the {@link Input} to remove. 380 <p> 381 * @return the {@link Input} removed. As mentioned above, the caller owns the 382 * returned item. 383 */ public 384 Input remove(String sid) { 385 long cPtr = libsbmlJNI.ListOfInputs_remove__SWIG_1(swigCPtr, this, sid); 386 return (cPtr == 0) ? null : new Input(cPtr, true); 387 } 388 389 390/** 391 * Returns the XML name of this object. 392 <p> 393 * @return the name of this element. 394 */ public 395 String getElementName() { 396 return libsbmlJNI.ListOfInputs_getElementName(swigCPtr, this); 397 } 398 399 400/** 401 * Returns the libSBML type code for the SBML objects 402 * contained in this {@link ListOf} object. 403 <p> 404 * <p> 405 * LibSBML attaches an identifying code to every kind of SBML object. These 406 * are integer constants known as <em>SBML type codes</em>. The names of all 407 * the codes begin with the characters <code>SBML_</code>. 408 * In the Java language interface for libSBML, the 409 * type codes are defined as static integer constants in the interface class 410 * {@link libsbmlConstants}. Note that different Level 3 411 * package plug-ins may use overlapping type codes; to identify the package 412 * to which a given object belongs, call the 413 * <code>{@link SBase#getPackageName()} 414 * </code> 415 * method on the object. 416 <p> 417 * @return the SBML type code for objects contained in this list: 418 * {@link libsbmlConstants#SBML_QUAL_INPUT SBML_QUAL_INPUT} (default). 419 <p> 420 * @see #getElementName() 421 * @see #getPackageName() 422 */ public 423 int getItemTypeCode() { 424 return libsbmlJNI.ListOfInputs_getItemTypeCode(swigCPtr, this); 425 } 426 427}