001/* ---------------------------------------------------------------------------- 002 * This file was automatically generated by SWIG (http://www.swig.org). 003 * Version 2.0.12 004 * 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 Implementation of the ListOfTransitions construct from 015 * the 'qual' package. 016 <p> 017 * The {@link ListOfTransitions} is a container for the {@link Transition} elements of a {@link Model}. 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 Transition 063 */ 064 065public class ListOfTransitions extends ListOf { 066 private long swigCPtr; 067 068 protected ListOfTransitions(long cPtr, boolean cMemoryOwn) 069 { 070 super(libsbmlJNI.ListOfTransitions_SWIGUpcast(cPtr), cMemoryOwn); 071 swigCPtr = cPtr; 072 } 073 074 protected static long getCPtr(ListOfTransitions obj) 075 { 076 return (obj == null) ? 0 : obj.swigCPtr; 077 } 078 079 protected static long getCPtrAndDisown (ListOfTransitions obj) 080 { 081 long ptr = 0; 082 083 if (obj != null) 084 { 085 ptr = obj.swigCPtr; 086 obj.swigCMemOwn = false; 087 } 088 089 return ptr; 090 } 091 092 protected void finalize() { 093 delete(); 094 } 095 096 public synchronized void delete() { 097 if (swigCPtr != 0) { 098 if (swigCMemOwn) { 099 swigCMemOwn = false; 100 libsbmlJNI.delete_ListOfTransitions(swigCPtr); 101 } 102 swigCPtr = 0; 103 } 104 super.delete(); 105 } 106 107 108/** 109 * Creates a new {@link ListOfTransitions} with the given level, version, and package version. 110 <p> 111 * @param level a long integer, the SBML Level to assign to this {@link ListOfTransitions} 112 <p> 113 * @param version a long integer, the SBML Version to assign to this {@link ListOfTransitions} 114 <p> 115 * @param pkgVersion a long integer, the SBML Qual Version to assign to this {@link ListOfTransitions} 116 */ public 117 ListOfTransitions(long level, long version, long pkgVersion) throws org.sbml.libsbml.SBMLConstructorException { 118 this(libsbmlJNI.new_ListOfTransitions__SWIG_0(level, version, pkgVersion), true); 119 } 120 121 122/** 123 * Creates a new {@link ListOfTransitions} with the given level, version, and package version. 124 <p> 125 * @param level a long integer, the SBML Level to assign to this {@link ListOfTransitions} 126 <p> 127 * @param version a long integer, the SBML Version to assign to this {@link ListOfTransitions} 128 <p> 129 * @param pkgVersion a long integer, the SBML Qual Version to assign to this {@link ListOfTransitions} 130 */ public 131 ListOfTransitions(long level, long version) throws org.sbml.libsbml.SBMLConstructorException { 132 this(libsbmlJNI.new_ListOfTransitions__SWIG_1(level, version), true); 133 } 134 135 136/** 137 * Creates a new {@link ListOfTransitions} with the given level, version, and package version. 138 <p> 139 * @param level a long integer, the SBML Level to assign to this {@link ListOfTransitions} 140 <p> 141 * @param version a long integer, the SBML Version to assign to this {@link ListOfTransitions} 142 <p> 143 * @param pkgVersion a long integer, the SBML Qual Version to assign to this {@link ListOfTransitions} 144 */ public 145 ListOfTransitions(long level) throws org.sbml.libsbml.SBMLConstructorException { 146 this(libsbmlJNI.new_ListOfTransitions__SWIG_2(level), true); 147 } 148 149 150/** 151 * Creates a new {@link ListOfTransitions} with the given level, version, and package version. 152 <p> 153 * @param level a long integer, the SBML Level to assign to this {@link ListOfTransitions} 154 <p> 155 * @param version a long integer, the SBML Version to assign to this {@link ListOfTransitions} 156 <p> 157 * @param pkgVersion a long integer, the SBML Qual Version to assign to this {@link ListOfTransitions} 158 */ public 159 ListOfTransitions() throws org.sbml.libsbml.SBMLConstructorException { 160 this(libsbmlJNI.new_ListOfTransitions__SWIG_3(), true); 161 } 162 163 164/** 165 * Creates a new {@link ListOfTransitions} with the given {@link QualPkgNamespaces} object. 166 <p> 167 * @param qualns the {@link QualPkgNamespaces} object 168 */ public 169 ListOfTransitions(QualPkgNamespaces qualns) throws org.sbml.libsbml.SBMLConstructorException { 170 this(libsbmlJNI.new_ListOfTransitions__SWIG_4(QualPkgNamespaces.getCPtr(qualns), qualns), true); 171 } 172 173 174/** 175 * Creates and returns a deep copy of this {@link ListOfTransitions} object. 176 <p> 177 * @return a (deep) copy of this {@link ListOfTransitions} object. 178 */ public 179 ListOfTransitions cloneObject() { 180 long cPtr = libsbmlJNI.ListOfTransitions_cloneObject(swigCPtr, this); 181 return (cPtr == 0) ? null : new ListOfTransitions(cPtr, true); 182 } 183 184 185/** 186 * Get a {@link Transition} from the {@link ListOfTransitions}. 187 <p> 188 * @param n the index number of the {@link Transition} to get. 189 <p> 190 * @return the nth {@link Transition} in this {@link ListOfTransitions}. 191 <p> 192 * @see #size() 193 */ public 194 Transition get(long n) { 195 long cPtr = libsbmlJNI.ListOfTransitions_get__SWIG_0(swigCPtr, this, n); 196 return (cPtr == 0) ? null : new Transition(cPtr, false); 197 } 198 199 200/** 201 * Get a {@link Transition} from the {@link ListOfTransitions} 202 * based on its identifier. 203 <p> 204 * @param sid a string representing the identifier 205 * of the {@link Transition} to get. 206 <p> 207 * @return {@link Transition} in this {@link ListOfTransitions} 208 * with the given id or null if no such 209 * {@link Transition} exists. 210 <p> 211 * @see #get(long n) * 212 * @see #size() 213 */ public 214 Transition get(String sid) { 215 long cPtr = libsbmlJNI.ListOfTransitions_get__SWIG_2(swigCPtr, this, sid); 216 return (cPtr == 0) ? null : new Transition(cPtr, false); 217 } 218 219 220/** 221 * Removes the nth {@link Transition} from this {@link ListOfTransitions} 222 * and returns a pointer to it. 223 <p> 224 * The caller owns the returned item and is responsible for deleting it. 225 <p> 226 * @param n the index of the {@link Transition} to remove. 227 <p> 228 * @see #size() 229 */ public 230 Transition remove(long n) { 231 long cPtr = libsbmlJNI.ListOfTransitions_remove__SWIG_0(swigCPtr, this, n); 232 return (cPtr == 0) ? null : new Transition(cPtr, true); 233 } 234 235 236/** 237 * Removes the {@link Transition} from this {@link ListOfTransitions} with the given identifier 238 * and returns a pointer to it. 239 <p> 240 * The caller owns the returned item and is responsible for deleting it. 241 * If none of the items in this list have the identifier <code>sid</code>, then 242 * <code>null</code> is returned. 243 <p> 244 * @param sid the identifier of the {@link Transition} to remove. 245 <p> 246 * @return the {@link Transition} removed. As mentioned above, the caller owns the 247 * returned item. 248 */ public 249 Transition remove(String sid) { 250 long cPtr = libsbmlJNI.ListOfTransitions_remove__SWIG_1(swigCPtr, this, sid); 251 return (cPtr == 0) ? null : new Transition(cPtr, true); 252 } 253 254 255/** 256 * Returns the XML element name of this object, which for {@link ListOfTransitions}, is 257 * always <code>'listOfTransitions'.</code> 258 <p> 259 * @return the name of this element, i.e. <code>'listOfTransitions'.</code> 260 */ public 261 String getElementName() { 262 return libsbmlJNI.ListOfTransitions_getElementName(swigCPtr, this); 263 } 264 265 266/** 267 * Returns the libSBML type code for the SBML objects 268 * contained in this {@link ListOf} object. 269 <p> 270 * <p> 271 * LibSBML attaches an identifying code to every kind of SBML object. These 272 * are integer constants known as <em>SBML type codes</em>. The names of all 273 * the codes begin with the characters “<code>SBML_</code>”. 274 * In the Java language interface for libSBML, the 275 * type codes are defined as static integer constants in the interface class 276 * {@link libsbmlConstants}. Note that different Level 3 277 * package plug-ins may use overlapping type codes; to identify the package 278 * to which a given object belongs, call the <code>getPackageName()</code> 279 * method on the object. 280 <p> 281 * @return the SBML type code for objects contained in this list: 282 * {@link libsbmlConstants#SBML_QUAL_TRANSITION SBML_QUAL_TRANSITION} (default). 283 <p> 284 * @see #getElementName() 285 * @see #getPackageName() 286 */ public 287 int getItemTypeCode() { 288 return libsbmlJNI.ListOfTransitions_getItemTypeCode(swigCPtr, this); 289 } 290 291}