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 A list of {@link FluxObjective} objects. 014 <p> 015 * The {@link ListOfFluxObjectives} is a container for the “fbc” 016 * {@link Objective} that indicate which fluxes (and what ratios for those fluxes) 017 * are to be used in maximizing or minimizing the {@link Objective}. 018 <p> 019 * <p> 020 * The various ListOf___ classes in SBML 021 * are merely containers used for organizing the main components of an SBML 022 * model. In libSBML's implementation, ListOf___ 023 * classes are derived from the 024 * intermediate utility class {@link ListOf}, which 025 * is not defined by the SBML specifications but serves as a useful 026 * programmatic construct. {@link ListOf} is itself is in turn derived from {@link SBase}, 027 * which provides all of the various ListOf___ 028 * classes with common features 029 * defined by the SBML specification, such as 'metaid' attributes and 030 * annotations. 031 <p> 032 * The relationship between the lists and the rest of an SBML model is 033 * illustrated by the following (for SBML Level 2 Version 4): 034 <p> 035 * <figure> 036 <object type="image/svg+xml" data="listof-illustration.svg" class="centered"></object> 037</figure> 038 039 <p> 040 * Readers may wonder about the motivations for using the ListOf___ 041 * containers in SBML. A simpler approach in XML might be to place the 042 * components all directly at the top level of the model definition. The 043 * choice made in SBML is to group them within XML elements named after 044 * ListOf<em>Classname</em>, in part because it helps organize the 045 * components. More importantly, the fact that the container classes are 046 * derived from {@link SBase} means that software tools can add information <em>about</em> 047 * the lists themselves into each list container's 'annotation'. 048 <p> 049 * @see ListOfFunctionDefinitions 050 * @see ListOfUnitDefinitions 051 * @see ListOfCompartmentTypes 052 * @see ListOfSpeciesTypes 053 * @see ListOfCompartments 054 * @see ListOfSpecies 055 * @see ListOfParameters 056 * @see ListOfInitialAssignments 057 * @see ListOfRules 058 * @see ListOfConstraints 059 * @see ListOfReactions 060 * @see ListOfEvents 061 <p> 062 * @see Objective 063 * @see FluxObjective 064 */ 065 066public class ListOfFluxObjectives extends ListOf { 067 private long swigCPtr; 068 069 protected ListOfFluxObjectives(long cPtr, boolean cMemoryOwn) 070 { 071 super(libsbmlJNI.ListOfFluxObjectives_SWIGUpcast(cPtr), cMemoryOwn); 072 swigCPtr = cPtr; 073 } 074 075 protected static long getCPtr(ListOfFluxObjectives obj) 076 { 077 return (obj == null) ? 0 : obj.swigCPtr; 078 } 079 080 protected static long getCPtrAndDisown (ListOfFluxObjectives obj) 081 { 082 long ptr = 0; 083 084 if (obj != null) 085 { 086 ptr = obj.swigCPtr; 087 obj.swigCMemOwn = false; 088 } 089 090 return ptr; 091 } 092 093 protected void finalize() { 094 delete(); 095 } 096 097 public synchronized void delete() { 098 if (swigCPtr != 0) { 099 if (swigCMemOwn) { 100 swigCMemOwn = false; 101 libsbmlJNI.delete_ListOfFluxObjectives(swigCPtr); 102 } 103 swigCPtr = 0; 104 } 105 super.delete(); 106 } 107 108 109/** 110 * Creates a new {@link ListOfFluxObjectives} with the given level, version, and package version. 111 <p> 112 * @param level a long integer, the SBML Level to assign to this {@link ListOfFluxObjectives} 113 <p> 114 * @param version a long integer, the SBML Version to assign to this {@link ListOfFluxObjectives} 115 <p> 116 * @param pkgVersion a long integer, the SBML Fbc Version to assign to this {@link ListOfFluxObjectives} 117 */ public 118 ListOfFluxObjectives(long level, long version, long pkgVersion) throws org.sbml.libsbml.SBMLConstructorException { 119 this(libsbmlJNI.new_ListOfFluxObjectives__SWIG_0(level, version, pkgVersion), true); 120 } 121 122 123/** 124 * Creates a new {@link ListOfFluxObjectives} with the given level, version, and package version. 125 <p> 126 * @param level a long integer, the SBML Level to assign to this {@link ListOfFluxObjectives} 127 <p> 128 * @param version a long integer, the SBML Version to assign to this {@link ListOfFluxObjectives} 129 <p> 130 * @param pkgVersion a long integer, the SBML Fbc Version to assign to this {@link ListOfFluxObjectives} 131 */ public 132 ListOfFluxObjectives(long level, long version) throws org.sbml.libsbml.SBMLConstructorException { 133 this(libsbmlJNI.new_ListOfFluxObjectives__SWIG_1(level, version), true); 134 } 135 136 137/** 138 * Creates a new {@link ListOfFluxObjectives} with the given level, version, and package version. 139 <p> 140 * @param level a long integer, the SBML Level to assign to this {@link ListOfFluxObjectives} 141 <p> 142 * @param version a long integer, the SBML Version to assign to this {@link ListOfFluxObjectives} 143 <p> 144 * @param pkgVersion a long integer, the SBML Fbc Version to assign to this {@link ListOfFluxObjectives} 145 */ public 146 ListOfFluxObjectives(long level) throws org.sbml.libsbml.SBMLConstructorException { 147 this(libsbmlJNI.new_ListOfFluxObjectives__SWIG_2(level), true); 148 } 149 150 151/** 152 * Creates a new {@link ListOfFluxObjectives} with the given level, version, and package version. 153 <p> 154 * @param level a long integer, the SBML Level to assign to this {@link ListOfFluxObjectives} 155 <p> 156 * @param version a long integer, the SBML Version to assign to this {@link ListOfFluxObjectives} 157 <p> 158 * @param pkgVersion a long integer, the SBML Fbc Version to assign to this {@link ListOfFluxObjectives} 159 */ public 160 ListOfFluxObjectives() throws org.sbml.libsbml.SBMLConstructorException { 161 this(libsbmlJNI.new_ListOfFluxObjectives__SWIG_3(), true); 162 } 163 164 165/** 166 * Creates a new {@link ListOfFluxObjectives} with the given {@link FbcPkgNamespaces} object. 167 <p> 168 * @param fbcns the {@link FbcPkgNamespaces} object 169 */ public 170 ListOfFluxObjectives(FbcPkgNamespaces fbcns) throws org.sbml.libsbml.SBMLConstructorException { 171 this(libsbmlJNI.new_ListOfFluxObjectives__SWIG_4(FbcPkgNamespaces.getCPtr(fbcns), fbcns), true); 172 } 173 174 175/** 176 * Creates and returns a deep copy of this {@link ListOfFluxObjectives} object. 177 <p> 178 * @return a (deep) copy of this {@link ListOfFluxObjectives} object. 179 */ public 180 ListOfFluxObjectives cloneObject() { 181 long cPtr = libsbmlJNI.ListOfFluxObjectives_cloneObject(swigCPtr, this); 182 return (cPtr == 0) ? null : new ListOfFluxObjectives(cPtr, true); 183 } 184 185 186/** 187 * Get a {@link FluxObjective} from the {@link ListOfFluxObjectives}. 188 <p> 189 * @param n the index number of the {@link FluxObjective} to get. 190 <p> 191 * @return the nth {@link FluxObjective} in this {@link ListOfFluxObjectives}. 192 <p> 193 * @see #size() 194 */ public 195 FluxObjective get(long n) { 196 long cPtr = libsbmlJNI.ListOfFluxObjectives_get__SWIG_0(swigCPtr, this, n); 197 return (cPtr == 0) ? null : new FluxObjective(cPtr, false); 198 } 199 200 201/** 202 * Get a {@link FluxObjective} from the {@link ListOfFluxObjectives} 203 * based on its identifier. 204 <p> 205 * @param sid a string representing the identifier 206 * of the {@link FluxObjective} to get. 207 <p> 208 * @return {@link FluxObjective} in this {@link ListOfFluxObjectives} 209 * with the given id or null if no such 210 * {@link FluxObjective} exists. 211 <p> 212 * @see #get(long n) * 213 * @see #size() 214 */ public 215 FluxObjective get(String sid) { 216 long cPtr = libsbmlJNI.ListOfFluxObjectives_get__SWIG_2(swigCPtr, this, sid); 217 return (cPtr == 0) ? null : new FluxObjective(cPtr, false); 218 } 219 220 221/** 222 * Adds a copy the given 'FluxObjective' to this {@link ListOfFluxObjectives}. 223 <p> 224 * @param fo; the {@link FluxObjective} object to add 225 <p> 226 * @return integer value indicating success/failure of the 227 * function. The possible values 228 * returned by this function are: 229 * <ul> 230 * <li> {@link libsbmlConstants#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS} 231 * <li> {@link libsbmlConstants#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE} 232 * </ul> 233 */ public 234 int addFluxObjective(FluxObjective fo) { 235 return libsbmlJNI.ListOfFluxObjectives_addFluxObjective(swigCPtr, this, FluxObjective.getCPtr(fo), fo); 236 } 237 238 239/** 240 * Get the number of {@link FluxObjective} objects in this {@link ListOfFluxObjectives}. 241 <p> 242 * @return the number of {@link FluxObjective} objects in this {@link ListOfFluxObjectives} 243 */ public 244 long getNumFluxObjectives() { 245 return libsbmlJNI.ListOfFluxObjectives_getNumFluxObjectives(swigCPtr, this); 246 } 247 248 249/** 250 * Creates a new {@link FluxObjective} object, adds it to the 251 * {@link ListOfFluxObjectives} and returns the {@link FluxObjective} object created. 252 <p> 253 * @return a new {@link FluxObjective} object instance 254 <p> 255 * @see #addFluxObjective(FluxObjective fo) 256 */ public 257 FluxObjective createFluxObjective() { 258 long cPtr = libsbmlJNI.ListOfFluxObjectives_createFluxObjective(swigCPtr, this); 259 return (cPtr == 0) ? null : new FluxObjective(cPtr, false); 260 } 261 262 263/** 264 * Removes the nth {@link FluxObjective} from this {@link ListOfFluxObjectives} 265 * and returns a pointer to it. 266 <p> 267 * The caller owns the returned item and is responsible for deleting it. 268 <p> 269 * @param n the index of the {@link FluxObjective} to remove. 270 <p> 271 * @see #size() 272 */ public 273 FluxObjective remove(long n) { 274 long cPtr = libsbmlJNI.ListOfFluxObjectives_remove__SWIG_0(swigCPtr, this, n); 275 return (cPtr == 0) ? null : new FluxObjective(cPtr, true); 276 } 277 278 279/** 280 * Removes the {@link FluxObjective} from this {@link ListOfFluxObjectives} with the given identifier 281 * and returns a pointer to it. 282 <p> 283 * The caller owns the returned item and is responsible for deleting it. 284 * If none of the items in this list have the identifier <code>sid</code>, then 285 * <code>null</code> is returned. 286 <p> 287 * @param sid the identifier of the {@link FluxObjective} to remove. 288 <p> 289 * @return the {@link FluxObjective} removed. As mentioned above, the caller owns the 290 * returned item. 291 */ public 292 FluxObjective remove(String sid) { 293 long cPtr = libsbmlJNI.ListOfFluxObjectives_remove__SWIG_1(swigCPtr, this, sid); 294 return (cPtr == 0) ? null : new FluxObjective(cPtr, true); 295 } 296 297 298/** 299 * Returns the XML element name of this object. 300 <p> 301 * For {@link ListOfFluxObjectives}, the XML element name is always <code>'listOfFluxObjectives'.</code> 302 <p> 303 * @return the name of this element, i.e. <code>'listOfFluxObjectives'.</code> 304 */ public 305 String getElementName() { 306 return libsbmlJNI.ListOfFluxObjectives_getElementName(swigCPtr, this); 307 } 308 309 310/** 311 * Returns the libSBML type code for this SBML object. 312 <p> 313 * <p> 314 * LibSBML attaches an identifying code to every kind of SBML object. These 315 * are integer constants known as <em>SBML type codes</em>. The names of all 316 * the codes begin with the characters <code>SBML_</code>. 317 * In the Java language interface for libSBML, the 318 * type codes are defined as static integer constants in the interface class 319 * {@link libsbmlConstants}. Note that different Level 3 320 * package plug-ins may use overlapping type codes; to identify the package 321 * to which a given object belongs, call the <code>getPackageName()</code> 322 * method on the object. 323 <p> 324 * @return the SBML type code for this object: 325 * {@link libsbmlConstants#SBML_LIST_OF SBML_LIST_OF} (default). 326 <p> 327 * <p> 328 * @warning <span class='warning'>The specific integer values of the possible 329 * type codes may be reused by different Level 3 package plug-ins. 330 * Thus, to identifiy the correct code, <strong>it is necessary to invoke 331 * both getTypeCode() and getPackageName()</strong>.</span> 332 <p> 333 * @see #getElementName() 334 * @see #getPackageName() 335 */ public 336 int getTypeCode() { 337 return libsbmlJNI.ListOfFluxObjectives_getTypeCode(swigCPtr, this); 338 } 339 340 341/** 342 * Returns the libSBML type code for the objects contained in this {@link ListOf}. 343 <p> 344 * <p> 345 * LibSBML attaches an identifying code to every kind of SBML object. These 346 * are integer constants known as <em>SBML type codes</em>. The names of all 347 * the codes begin with the characters <code>SBML_</code>. 348 * In the Java language interface for libSBML, the 349 * type codes are defined as static integer constants in the interface class 350 * {@link libsbmlConstants}. Note that different Level 3 351 * package plug-ins may use overlapping type codes; to identify the package 352 * to which a given object belongs, call the <code>getPackageName()</code> 353 * method on the object. 354 <p> 355 * @return the SBML type code for the objects contained in this {@link ListOf} 356 * instance: {@link libsbmlConstants#SBML_FBC_FLUXOBJECTIVE SBML_FBC_FLUXOBJECTIVE} (default). 357 <p> 358 * @see #getElementName() 359 * @see #getPackageName() 360 */ public 361 int getItemTypeCode() { 362 return libsbmlJNI.ListOfFluxObjectives_getItemTypeCode(swigCPtr, this); 363 } 364 365}